1. Alineamiento de dos secuencias.

1.1 Realice el alineamiento de las 2 secuencias de proteínas utilizando el servidor

EMBL-EBI : -ir a Tools
-Elegir opción Sequense Analysis
-Align
#######################################
# Program: needle
# Rundate: Wed 5 May 2010 23:01:04
# Commandline: needle
# [-asequence] /ebi/extserv/old-work/needle-20100505-2301032641.input.1
# [-bsequence] /ebi/extserv/old-work/needle-20100505-2301032641.input.2
# -outfile /ebi/extserv/old-work/needle-20100505-2301032641.output
# -gapopen 10.0
# -gapextend 0.5
# -datafile EBLOSUM62
# -sprotein1
# -sprotein2
# -auto
# Align_format: srspair
# Report_file: /ebi/extserv/old-work/needle-20100505-2301032641.output
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: RPE_YEAST
# 2: RPE_MYCPN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 251
# Identity: 64/251 (25.5%)
# Similarity: 101/251 (40.2%)
# Gaps: 49/251 (19.5%)
# Score: 120.0
#
#
#=======================================

RPE_YEAST 1 ----MVKPIIAPS-I-LASDFANLGCECHKVINAGADWLHIDVMDGHFVP 44
:|...||.| : |...|.....|.... : |...:|.|||| |||.
RPE_MYCPN 1 MLNLVVNREIAFSLLPLLHQFDRKLLEQFFA-D-GLRLIHYDVMD-HFVD 47

RPE_YEAST 45 NITLGQPIVTSLRRSVPRPGDASNTEKKPTAF-FDCHMMVENPEKWVDDF 93
| :|.: |:.. .|.:...| .:.|:||:..|:.:..:
RPE_MYCPN 48 N-------------TVFQ-GEHL-DELQQIGFQVNVHLMVQALEQILPVY 82

RPE_YEAST 94 AKCGA-DQFTFHYEATQDP-L-HLVKLIKSKGIKAACAIKPGTSVDVLFE 140

....| .:.:||.|....| : |.:..||..|.:...|.|..|.:.....
RPE_MYCPN 83 LHHQAVKRISFHVEPFDIPTIKHFIAQIKQAGKQVGLAFKFTTPLVNYER 132

RPE_YEAST 141 LAPHLDMALVMTVEPGFGGQKFMEDMMPKVETLRAKFPHLNIQVDGGLGK 190

|...||...:|:|.||.|||.|...:...:: :|...|.:|::|||:..
RPE_MYCPN 133 LVQQLDFVTLMSVPPGKGGQAFNSAVFNNLK--QAHKYHCSIEIDGGIKL 180

RPE_YEAST 191 ETIPKAAKAGANVIVAGTSVFTAADPHDVISFMKEEVSKELRSRDLLD-- 238

:.|.: .:...|.||.| : .|:|.| ..:.:.||.
RPE_MYCPN 181 DNIHQ-IQDDVNFIVMG------S------GFIKLE---RWQRQQLLKTN 214

RPE_YEAST 238 - 238

RPE_MYCPN 215 Q 215

#---------------------------------------
#---------------------------------------

########################################
# Program: water
# Rundate: Wed 5 May 2010 23:15:53
# Commandline: water
# [-asequence] /ebi/extserv/old-work/water-20100505-2315528998.input.1
# [-bsequence] /ebi/extserv/old-work/water-20100505-2315528998.input.2
# -outfile /ebi/extserv/old-work/water-20100505-2315528998.output
# -gapopen 10.0
# -gapextend 0.5
# -datafile EBLOSUM62
# -sprotein1
# -sprotein2
# -auto
# Align_format: srspair
# Report_file: /ebi/extserv/old-work/water-20100505-2315528998.output
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: RPE_YEAST
# 2: RPE_MYCPN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 185
# Identity: 51/185 (27.6%)
# Similarity: 81/185 (43.8%)
# Gaps: 25/185 (13.5%)
# Score: 133.5
#
#
#=======================================

RPE_YEAST 29 GADWLHIDVMDGHFVPN-ITLGQPIVTSLRRSVPRPGDASNTEKKPTAF- 76
|...:|.|||| |||.| :..|:.: .|.:...|
RPE_MYCPN 33 GLRLIHYDVMD-HFVDNTVFQGEHL----------------DELQQIGFQ 65

RPE_YEAST 77 FDCHMMVENPEKWVDDFAKCGA-DQFTFHYEATQDPL--HLVKLIKSKGI 123

.:.|:||:..|:.:..:....| .:.:||.|....|. |.:..||..|.
RPE_MYCPN 66 VNVHLMVQALEQILPVYLHHQAVKRISFHVEPFDIPTIKHFIAQIKQAGK 115

RPE_YEAST 124 KAACAIKPGTSVDVLFELAPHLDMALVMTVEPGFGGQKFMEDMMPKVETL 173

:...|.|..|.:.....|...||...:|:|.||.|||.|...:...::
RPE_MYCPN 116 QVGLAFKFTTPLVNYERLVQQLDFVTLMSVPPGKGGQAFNSAVFNNLK-- 163

RPE_YEAST 174 RAKFPHLNIQVDGGLGKETIPKAAKAGANVIVAGT 208

:|...|.:|::|||:..:.|.: .:...|.||.|:
RPE_MYCPN 164 QAHKYHCSIEIDGGIKLDNIHQ-IQDDVNFIVMGS 197

#---------------------------------------
#---------------------------------------

########################################
# Program: needle
# Rundate: Wed 5 May 2010 23:19:34
# Commandline: needle
# [-asequence] /ebi/extserv/old-work/needle-20100505-2319336494.input.1
# [-bsequence] /ebi/extserv/old-work/needle-20100505-2319336494.input.2
# -outfile /ebi/extserv/old-work/needle-20100505-2319336494.output
# -gapopen 10.0
# -gapextend 0.5
# -datafile EBLOSUM40
# -sprotein1
# -sprotein2
# -auto
# Align_format: srspair
# Report_file: /ebi/extserv/old-work/needle-20100505-2319336494.output
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: RPE_YEAST
# 2: RPE_MYCPN
# Matrix: EBLOSUM40
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 251
# Identity: 65/251 (25.9%)
# Similarity: 110/251 (43.8%)
# Gaps: 49/251 (19.5%)
# Score: 294.0
#
#
#=======================================

RPE_YEAST 1 ----MVKPIIAPS-I-LASDFANLGCECHKVINAGADWLHIDVMDGHFVP 44
:|...||.| : |...|..... .:.:..|...:|.|||| |||.
RPE_MYCPN 1 MLNLVVNREIAFSLLPLLHQFDRKLL--EQFFADGLRLIHYDVMD-HFVD 47

RPE_YEAST 45 NITLGQPIVTSLRRSVPRPGDASNTEKKPTAFFDCHMMVENPEKWVDDFA 94
|.::....:..| : :.|...| : |:||:..|:.:..:.
RPE_MYCPN 48 NTVFQGEHLDEL-Q---QIGFQVN-----V-----HLMVQALEQILPVYL 83

RPE_YEAST 95 KCGA-DQFTFHYEATQDP-L-HLVKLIKSKGIKAACAIKPGTSVDVLFE- 140

...| .:::||.|....| : |::..||:.|.:.:.|:|..|.: |.:|
RPE_MYCPN 84 HHQAVKRISFHVEPFDIPTIKHFIAQIKQAGKQVGLAFKFTTPL-VNYER 132

RPE_YEAST 141 LAPHLDMALVMTVEPGFGGQKFMEDMMPKVETLRAKFPHLNIQVDGGLGK 190

|...||...:|:|.||.|||.|...:...:: :|...|.:|::|||:..
RPE_MYCPN 133 LVQQLDFVTLMSVPPGKGGQAFNSAVFNNLK--QAHKYHCSIEIDGGIKL 180

RPE_YEAST 191 ETIPKAAKAGANVIVAGTSVFTAADPHDVISFMKEEVSKELRSRDLLD-- 238

:.|.:.... .|.||.| : .|:|.| :..|:: ||.
RPE_MYCPN 181 DNIHQIQDD-VNFIVMG----S--------GFIKLE--RWQRQQ-LLKTN 214

RPE_YEAST 238 - 238

RPE_MYCPN 215 Q 215

#---------------------------------------
#---------------------------------------

1.2 Repita el alineamiento de las 2 secuencias de proteínas utilizando el servidor:

 NCBI: -ir a BLAST
-buscar Specialized BLAST
-ir a Align
-Elegir BLASTP

>lcl|59497 RPE_MYCPN
Length=215

Score = 51.2 bits (121), Expect = 2e-11, Method: Compositional matrix

adjust.
Identities = 49/183 (26%), Positives = 79/183 (43%), Gaps = 21/183 (11%)

Query 29 GADWLHIDVMDGHFVPNITLGQPIVTSLRRSVPRPGDASNTEKKPTAFFDCHMMVENPEK 88
G +H DVMD HFV N G+ + ++ + H+MV+ E+
Sbjct 33 GLRLIHYDVMD-HFVDNTVF--------------QGEHLDELQQIGFQVNVHLMVQALEQ 77

Query 89 WVDDFAKCGA-DQFTFHYEATQDPL--HLVKLIKSKGIKAACAIKPGTSVDVLFELAPHL 145

+ + A + +FH E P H + IK G + A K T + L L
Sbjct 78 ILPVYLHHQAVKRISFHVEPFDIPTIKHFIAQIKQAGKQVGLAFKFTTPLVNYERLVQQL 137

Query 146 DMALVMTVEPGFGGQKFMEDMMPKVETLRAKFPHLNIQVDGGLGKETIPKAAKAGANVIV 205

D +M+V PG GGQ F + ++ +A H +I++DGG+ + I + + N IV
Sbjct 138 DFVTLMSVPPGKGGQAFNSAVFNNLK--QAHKYHCSIEIDGGIKLDNIHQ-IQDDVNFIV 194

Query 206 AGT 208

G+
Sbjct 195 MGS 197

Score = 12.3 bits (20), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 4/9 (44%), Positives = 6/9 (66%), Gaps = 0/9 (0%)

Query 2 VKPIIAPSI 10
V+P P+I
Sbjct 95 VEPFDIPTI 103

>lcl|10927 RPE_MYCPN
Length=215

Score = 48.5 bits (150), Expect = 9e-11, Method: Compositional matrix

adjust.
Identities = 49/184 (26%), Positives = 79/184 (42%), Gaps = 21/184 (11%)

Query 29 GADWLHIDVMDGHFVPNITLGQPIVTSLRRSVPRPGDASNTEKKPTAFFDCHMMVENPEK 88
G +H DVMD HFV N G+ + ++ + H+MV+ E+
Sbjct 33 GLRLIHYDVMD-HFVDNTVF--------------QGEHLDELQQIGFQVNVHLMVQALEQ 77

Query 89 WVDDFAKCGA-DQFTFHYEATQDPL--HLVKLIKSKGIKAACAIKPGTSVDVLFELAPHL 145

+ + A + +FH E P H + IK G + A K T + L L
Sbjct 78 ILPVYLHHQAVKRISFHVEPFDIPTIKHFIAQIKQAGKQVGLAFKFTTPLVNYERLVQQL 137

Query 146 DMALVMTVEPGFGGQKFMEDMMPKVETLRAKFPHLNIQVDGGLGKETIPKAAKAGANVIV 205

D +M+V PG GGQ F + ++ +A H +I++DGG+ + I + + N IV
Sbjct 138 DFVTLMSVPPGKGGQAFNSAVFNNLK--QAHKYHCSIEIDGGIKLDNIHQ-IQDDVNFIV 194

Query 206 AGTS 209

G+
Sbjct 195 MGSG 198
Score = 12.8 bits (28), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 4/9 (44%), Positives = 6/9 (66%), Gaps = 0/9 (0%)

Query 2 VKPIIAPSI 10
V+P P+I
Sbjct 95 VEPFDIPTI 103

Score = 12.5 bits (27), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 4/10 (40%), Positives = 6/10 (60%), Gaps = 0/10 (0%)

Query 136 DVLFELAPHL 145

++ F L P L
Sbjct 9 EIAFSLLPLL 18

2. Realice el alineamiento de 2 secuencias de nucleótidos descritas a

continuación siguiendo las indicaciones de 1.1 y 1.2.

>lcl|1351 SVP-10
Length=1260

Score = 1709 bits (925), Expect = 0.0

Identities = 1148/1240 (92%), Gaps = 77/1240 (6%)
Strand=Plus/Plus

Query 27 GTAGCACAGAGAGCTTGCTCTCGGGTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAA 86
|||||| | ||||||| | ||| ||| |||||| || ||| |||| |||| ||| || |
Sbjct 50 GTAGCA-A-AGAGCTT-C-CTC-GGT-ACGAGT-GC-GAC-GGTG-GTAA-GTC--GG-A 95

Query 87 ACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAA 146

|||| ||||| || |||||| |||||||| ||| ||||||||| |||||||||| ||||
Sbjct 96 ACTG-CTGAT-GA-GGGGAT-ACTACTGG-AAC-GTAGCTAAT--CGCATAACGT-GCAA 146

Query 147 GACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTA 206

| | |||| ||||| |||| || |||||| ||||||||||| |||||| ||| ||||||
Sbjct 147 G--C-AAGA-GGGGA-CTTC-GG-CTCTTG-CATCAGATGTG-CCAGAT-GGA-TAGCTA 195

Query 207 GTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAG 266

||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||||
Sbjct 196 GTAGGTGGGGT-AC-GCTCA-CTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAG 252

Query 267 CCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGC 326

|||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct 253 CCACACTGGAACTGAGACACGGTCCAGACT-CTACGGGAGGCAGCAGTGGGGAATATTGC 311

Query 327 ACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTC-GGGTTGT 385

|||||||||||||| |||||||||||||||||||||||||||||||| |||| | |||||
Sbjct 312 ACAATGGGCGCAAG-CTGATGCAGCCATGCCGCGTGTATGAAGAAGG-CTTCTGCGTTGT 369

Query 386 AAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACC 445

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 370 AAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACC 429

Query 446 CGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGC 505

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 430 CGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGC 489

Query 506 GTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAA 565

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 490 GTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAA 549
Query 566 TCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGG 625
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 550 TCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGG 609

Query 626 GGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAA 685

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 610 GGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAA 669

Query 686 GGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATT 745

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 670 GGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATT 729

Query 746 AGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCG 805

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 730 AGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCG 789

Query 806 TGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAA 865

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 790 TGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAA 849

Query 866 CTCAAATGAATT-GACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCA 924

|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 850 CTCAAATGAATTTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCA 909

Query 925 ACGCGAAGAACCTTACCTACTCTTGACATCCAGAGAACTTAGCAGAGATGCTTTGGTGCC 984

||||| ||||||||||||||||||||||||||||||||||| ||||||||| ||||||||
Sbjct 910 ACGCGGAGAACCTTACCTACTCTTGACATCCAGAGAACTTA-CAGAGATGCATTGGTGCC 968

Query 985 TTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGG

1044
|||||||||||||| |||| ||||||||||||||||||||||||||||| ||| ||||||
Sbjct 969 TTCGGGAACTCTGAAACAG-TGCTGCATGGCTGTCGTCAGCTCGTGTTG-GAA-TGTTGG
1025

Query 1045 GTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACT

1104
|||| ||||| |||||||||||||||||||| |||||||| ||||||| |||||||||||
Sbjct 1026 GTTA-GTCCC-CAACGAGCGCAACCCTTATC-TTTGTTGC-AGCGGTC-GGCCGGGAACT
1080

Query 1105 CAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGC

1164
||| ||| ||||||| |||||| ||| || ||| || |||| |||||||| | |||||
Sbjct 1081 CAA-GGAAACTGCCA-TGATAA-CTGAAG-AAG-TG---ATGA-GTCAAGTCTTTATGGC
1131

Query 1165 CCTTACGAGTAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGAACTCGCG

1224
|||||| | |||| |||||| |||| || |||| || | ||||| ||||||||||| |
Sbjct 1132 CCTTACAA-TAGG-CTACAC---TGCTCCA-TGGC-CAAA-AAAGA-AAGCGAACTCG-G
1181

Query 1225 AGAGCAAGCGGA-CCTCATAAAGTGCGTCGTAGTCCGGAT 1263

||| || | ||| ||| |||| || | || | |||||||
Sbjct 1182 AGA-CACG-GGAACCTT-TAAATTG-GCCG-A-TCCGGAT 1215