BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy16693
(196 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|P04588|POL_HV1MA Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype A (isolate MAL) GN=gag-pol PE=1 SV=3
Length = 1440
Score = 43.1 bits (100), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S + + I L+ K+K ++ +WVP+H GI GNE
Sbjct: 1083 SEVNIVTDSQYALGIIQAQPDKSESEIVNQIIEQLIQKDK----VYLSWVPAHKGIGGNE 1138
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1139 QVDKLVSSGI 1148
>sp|Q1A267|POL_SIVMB Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate MB66)
GN=gag-pol PE=3 SV=4
Length = 1438
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 23 EKSECQVYLTPDN--SLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGI 80
+ SE +V + D+ +L +Q + S S + + I L+ K K ++ +WVP+H GI
Sbjct: 1073 QDSEVEVNIVTDSQYALGIIQGQPDTSESEIVNQIIEELIKKEK----VYLSWVPAHKGI 1128
Query: 81 AGNEEADRLAKEAL 94
GNE+ D+L +
Sbjct: 1129 GGNEQIDKLVSSGI 1142
>sp|P24740|POL_HV1U4 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype A (isolate U455) GN=gag-pol PE=1 SV=3
Length = 1428
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S + + I L++K K ++ +WVP+H GI GNE
Sbjct: 1071 SEVNIVTDSQYALGIIQAQPDRSESEIVNQIIEKLIEKEK----VYLSWVPAHKGIGGNE 1126
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1127 QVDKLVSSGI 1136
>sp|Q79666|POL_HV1MV Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O
(isolate MVP5180) GN=gag-pol PE=3 SV=3
Length = 1446
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 23 EKSECQVYLTPDNS-LSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIA 81
+ S+ QV + D+ + + S Q S +PI ++I L K + V+ TWVP+H GI
Sbjct: 1075 QDSKEQVNIVTDSQYVLGIISSQPTQSDSPIVQQIIEELTKKERVY---LTWVPAHKGIG 1131
Query: 82 GNEEADRL 89
GNE+ D+L
Sbjct: 1132 GNEKIDKL 1139
>sp|P05959|POL_HV1RH Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate RF/HAT3) GN=gag-pol PE=1 SV=3
Length = 1436
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1080 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1135
Query: 86 ADRLAKEAL 94
DRL +
Sbjct: 1136 VDRLVSTGI 1144
>sp|P18802|POL_HV1ND Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype D (isolate NDK) GN=gag-pol PE=3 SV=3
Length = 1432
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1076 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1131
Query: 86 ADRLAKEAL 94
D+L + +
Sbjct: 1132 VDKLVSQGI 1140
>sp|P12499|POL_HV1Z2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype D (isolate Z2/CDC-Z34) GN=gag-pol PE=1 SV=3
Length = 1436
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1080 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1135
Query: 86 ADRLAKEAL 94
D+L + +
Sbjct: 1136 VDKLVSQGI 1144
>sp|Q8AII1|POL_SIVTN Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate TAN1)
GN=gag-pol PE=3 SV=4
Length = 1462
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 14 YQVDLTGTAEKSECQVYLTPDNS--LSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHF 71
+ VDL + S QV + D+ + LQ + + S S + + I+ L K +++
Sbjct: 1094 WAVDLA--LKDSGAQVNIVTDSQYVMGVLQGLPDQSDSPIVEQIIQKLTQKT----AIYL 1147
Query: 72 TWVPSHVGIAGNEEADRLA 90
WVP+H GI GNEE D+L
Sbjct: 1148 AWVPAHKGIGGNEEVDKLV 1166
>sp|Q9QBZ5|POL_HV1MP Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype F2 (isolate MP255) GN=gag-pol PE=3 SV=3
Length = 1430
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S + + I L+ K K ++ +WVP+H GI GNE
Sbjct: 1073 SEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIQKEK----VYLSWVPAHKGIGGNE 1128
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1129 QVDKLVSSGI 1138
>sp|Q77373|POL_HV1AN Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O
(isolate ANT70) GN=gag-pol PE=3 SV=3
Length = 1435
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 42 SIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLA 90
S Q S +PI ++I L K + V+ TWVP+H GI GNE+ D+L
Sbjct: 1093 SSQPTQSESPIVQQIIEELTKKEQVY---LTWVPAHKGIGGNEKIDKLV 1138
>sp|P17283|POL_SIVCZ Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate CPZ
GAB1) GN=gag-pol PE=3 SV=2
Length = 1384
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 23 EKSECQVYLTPDNS--LSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGI 80
+ S+ QV + D+ L +QS + S S + + I L+ K K ++ +WVP+H GI
Sbjct: 1023 QDSDQQVNIVTDSQYVLGIIQSQPDHSESELVNQIIEELIKKEK----IYLSWVPAHKGI 1078
Query: 81 AGNEEADRLAKEAL 94
GNE+ D+L +
Sbjct: 1079 GGNEQVDKLVSAGI 1092
>sp|P19028|POL_FIVSD Pol polyprotein OS=Feline immunodeficiency virus (strain San Diego)
GN=pol PE=3 SV=1
Length = 1124
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 46/91 (50%), Gaps = 15/91 (16%)
Query: 16 VDLTGTAEKSECQVYL-----TPD--NSLSALQSIQNVSSSNP-----IAREIRNLLDKN 63
++L G+ +K+E Q L P+ N ++ Q + N+ S P I +E+ L+K
Sbjct: 624 MELEGSNQKAEIQALLLALKAGPEEMNIITDSQYMINILSQQPDKMEGIWQEVLEELEKK 683
Query: 64 KHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+F WVP H GI GNEE D+L + +
Sbjct: 684 TAIF---IDWVPGHKGIPGNEEVDKLCQTMM 711
>sp|Q9QBY3|POL_HV196 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype K (isolate 96CM-MP535) GN=gag-pol PE=3 SV=3
Length = 1430
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S+ + + I L+ K + ++ +WVP+H GI GNE
Sbjct: 1073 SEVNIVTDSQYALGIIQAQPDKSESDLVNQIIEQLIKKER----IYLSWVPAHKGIGGNE 1128
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1129 QVDKLVSAGI 1138
>sp|O89290|POL_HV193 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype F1 (isolate 93BR020) GN=gag-pol PE=3 SV=3
Length = 1430
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S + + I L+ K K ++ +WVP+H GI GNE
Sbjct: 1073 SEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLSWVPAHKGIGGNE 1128
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1129 QVDKLVSAGI 1138
>sp|P03369|POL_HV1A2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate ARV2/SF2) GN=gag-pol PE=1 SV=3
Length = 1437
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 1 MLGIPDTCDEHIYYQ-VDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNL 59
++ I DT ++ Q + L E + +L +Q+ + S S +++ I L
Sbjct: 1055 VVSIADTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQL 1114
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+ K K ++ WVP+H GI GNE+ D+L +
Sbjct: 1115 IKKEK----VYLAWVPAHKGIGGNEQVDKLVSAGI 1145
>sp|O89940|POL_HV1SE Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype G (isolate SE6165) GN=gag-pol PE=3 SV=3
Length = 1433
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 24 KSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGN 83
+SE + +L +Q+ + S + + + I L+ K K ++ +WVP+H GI GN
Sbjct: 1075 RSEVNIVTDSQYALGIIQAQPDRSEAELVNQIIEQLIKKEK----VYLSWVPAHKGIGGN 1130
Query: 84 EEADRLAKEAL 94
E+ D+L +
Sbjct: 1131 EQVDKLVSSGI 1141
>sp|Q9QBZ9|POL_HV197 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype K (isolate 97ZR-EQTB11) GN=gag-pol PE=3 SV=2
Length = 1429
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S + + I L+ K++ ++ +WVP+H GI GNE
Sbjct: 1073 SEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKDR----VYLSWVPAHKGIGGNE 1128
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1129 QVDKLVSSGI 1138
>sp|P16088|POL_FIVPE Pol polyprotein OS=Feline immunodeficiency virus (isolate Petaluma)
GN=pol PE=1 SV=1
Length = 1124
Score = 41.6 bits (96), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 15/91 (16%)
Query: 16 VDLTGTAEKSECQVYLTP-------DNSLSALQSIQNVSSSNP-----IAREIRNLLDKN 63
+DL G+ +K+E Q L N ++ Q + N+ P I +E+ L+K
Sbjct: 624 MDLEGSNQKAEIQALLLALKAGSEEMNIITDSQYVINIILQQPDMMEGIWQEVLEELEKK 683
Query: 64 KHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+F WVP H GI GNEE D+L + +
Sbjct: 684 TAIF---IDWVPGHKGIPGNEEVDKLCQTMM 711
>sp|P20892|POL_HV1OY Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate OYI) GN=gag-pol PE=3 SV=3
Length = 1434
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1078 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1133
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1134 VDKLVSAGI 1142
>sp|P20875|POL_HV1JR Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate JRCSF) GN=gag-pol PE=1 SV=3
Length = 1439
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1083 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1138
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1139 VDKLVSAGI 1147
>sp|O12158|POL_HV192 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype C (isolate 92BR025) GN=gag-pol PE=1 SV=2
Length = 1431
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 1 MLGIPDTCDEHIYYQ-VDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNL 59
++ I +T ++ Q + L SE + +L +Q+ + S S + + I L
Sbjct: 1049 IVSITETTNQKTELQAIQLALQDSGSEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL 1108
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+ K + ++ +WVP+H GI GNE+ D+L +
Sbjct: 1109 IKKER----VYLSWVPAHKGIGGNEQVDKLVSSGI 1139
>sp|P05961|POL_HV1MN Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate MN) GN=gag-pol PE=1 SV=3
Length = 1441
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1085 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1140
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1141 VDKLVSAGI 1149
>sp|Q73368|POL_HV1B9 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (strain 89.6) GN=gag-pol PE=3 SV=3
Length = 1435
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1135 VDKLVSAGI 1143
>sp|P35963|POL_HV1Y2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate YU-2) GN=gag-pol PE=1 SV=3
Length = 1435
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDRSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1135 VDKLVSAGI 1143
>sp|Q9QSR3|POL_HV1VI Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype F1 (isolate VI850) GN=gag-pol PE=3 SV=3
Length = 1430
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 10 EHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSL 69
+ IY + +G SE + +L +Q+ + S S + + I L+ K + +
Sbjct: 1062 QAIYLALQDSG----SEVNIVTDSQYALGIIQAQPDKSESEIVNQIIEQLIQKER----V 1113
Query: 70 HFTWVPSHVGIAGNEEADRLAKEAL 94
+ +WVP+H GI GNE+ D+L +
Sbjct: 1114 YLSWVPAHKGIGGNEQVDKLVSAGV 1138
>sp|P04589|POL_HV1EL Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype D (isolate ELI) GN=gag-pol PE=3 SV=3
Length = 1435
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D+L + +
Sbjct: 1135 VDKLVSQGI 1143
>sp|O91080|POL_HV1YF Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group N
(isolate YBF30) GN=gag-pol PE=3 SV=3
Length = 1449
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 1 MLGIPDTCDEHIYYQVDLTGTAEKS-ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNL 59
++ I DT ++ Q L E + + ++ + S + S S +++ I L
Sbjct: 1063 VVSIADTTNQKAELQAILMALQESGRDVNIVTDSQYAMGIIHSQPDKSESELVSQIIEEL 1122
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+ K + ++ +WVP+H GI GNE+ D+L +
Sbjct: 1123 IKKER----VYLSWVPAHKGIGGNEQVDKLVSSGI 1153
>sp|O41798|POL_HV19N Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype G (isolate 92NG083) GN=gag-pol PE=3 SV=3
Length = 1435
Score = 40.8 bits (94), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 14 YQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTW 73
+ + L + E + +L +Q+ + S S + + I L+ K K ++ +W
Sbjct: 1067 HAIQLALQDSRPEVNIVTDSQYALGIIQAQPDRSGSELVNQIIEQLIKKEK----VYLSW 1122
Query: 74 VPSHVGIAGNEEADRLAKEAL 94
VP+H GI GNE+ D+L +
Sbjct: 1123 VPAHKGIGGNEQVDKLVSSGI 1143
>sp|Q9QBZ1|POL_HV1M2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype F2 (isolate MP257) GN=gag-pol PE=3 SV=3
Length = 1434
Score = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L +Q+ + S S + + I L+ K + ++ +WVP+H GI GNE
Sbjct: 1077 SEVNIVTDSQYALGIIQAHPDKSESEIVNQIIEQLIQKER----VYLSWVPAHKGIGGNE 1132
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1133 QVDKLVSTGI 1142
>sp|P05895|POL_SIVVT Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.vervet
(isolate AGM TYO-1) GN=gag-pol PE=3 SV=2
Length = 1467
Score = 40.4 bits (93), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 31 LTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLA 90
+T + + Q S +P+ +I L+ + + ++ WVP+H GI GNEE D+L
Sbjct: 1112 VTDSQYAMGILTAQPTQSDSPLVEQIIALMIQKQQIY---LQWVPAHKGIGGNEEIDKLV 1168
Query: 91 KEAL 94
+ +
Sbjct: 1169 SKGI 1172
>sp|Q9WC63|POL_HV1S9 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype J (isolate SE9173) GN=gag-pol PE=3 SV=3
Length = 1432
Score = 40.4 bits (93), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ +WVP+H GI GNE+
Sbjct: 1076 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEELIKKEK----VYLSWVPAHKGIGGNEQ 1131
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1132 VDKLVSSGI 1140
>sp|Q9WC54|POL_HV1S2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype J (isolate SE9280) GN=gag-pol PE=3 SV=3
Length = 1432
Score = 40.4 bits (93), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ +WVP+H GI GNE+
Sbjct: 1076 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEELIKKEK----VYLSWVPAHKGIGGNEQ 1131
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1132 VDKLVSSGI 1140
>sp|Q9Q720|POL_HV1V9 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype H (isolate VI991) GN=gag-pol PE=3 SV=3
Length = 1436
Score = 40.4 bits (93), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K + +WVP+H GI GNE+
Sbjct: 1080 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEELIKKEK----FYLSWVPAHKGIGGNEQ 1135
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1136 VDKLVSSGI 1144
>sp|O93215|POL_HV190 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype H (isolate 90CF056) GN=gag-pol PE=3 SV=4
Length = 1435
Score = 40.0 bits (92), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ +WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEELIKKEK----VYLSWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1135 VDKLVSSGV 1143
>sp|P04585|POL_HV1H2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate HXB2) GN=gag-pol PE=1 SV=4
Length = 1435
Score = 40.0 bits (92), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1135 VDKLVSAGI 1143
>sp|P0C6F2|POL_HV1LW Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate LW123) GN=gag-pol PE=1 SV=1
Length = 1435
Score = 40.0 bits (92), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1135 VDKLVSAGI 1143
>sp|P04587|POL_HV1B5 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate BH5) GN=gag-pol PE=1 SV=3
Length = 1447
Score = 40.0 bits (92), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ WVP+H GI GNE+
Sbjct: 1091 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1146
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1147 VDKLVSAGI 1155
>sp|P03367|POL_HV1BR Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate BRU/LAI) GN=gag-pol PE=1 SV=3
Length = 1447
Score = 40.0 bits (92), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ WVP+H GI GNE+
Sbjct: 1091 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1146
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1147 VDKLVSAGI 1155
>sp|P03366|POL_HV1B1 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate BH10) GN=gag-pol PE=1 SV=3
Length = 1447
Score = 40.0 bits (92), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S + + I L+ K K ++ WVP+H GI GNE+
Sbjct: 1091 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1146
Query: 86 ADRLAKEAL 94
D+L +
Sbjct: 1147 VDKLVSAGI 1155
>sp|P31822|POL_FIVT2 Pol polyprotein OS=Feline immunodeficiency virus (isolate TM2)
GN=pol PE=3 SV=1
Length = 1124
Score = 40.0 bits (92), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 16 VDLTGTAEKSECQVYLTP-------DNSLSALQSIQNVSSSNPIARE--IRNLLDKNKHV 66
+++ G+ +K+E Q L N ++ Q I N+ + P E + +L++ +
Sbjct: 623 MEIEGSNQKAEVQALLLALKAGSEEMNIITDSQYILNILNQQPDLMEGLWQEVLEQMEKK 682
Query: 67 FSLHFTWVPSHVGIAGNEEADRLAKEAL 94
++ WVP H GI GNEE D+L + +
Sbjct: 683 IAIFIDWVPGHKGIPGNEEVDKLCQTMM 710
>sp|P12497|POL_HV1N5 Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate NY5) GN=gag-pol PE=1 SV=4
Length = 1435
Score = 39.7 bits (91), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26 ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
E + +L +Q+ + S S +++ I L+ K K ++ WVP+H GI GNE+
Sbjct: 1079 EVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 1134
Query: 86 ADRLAKEAL 94
D L +
Sbjct: 1135 VDGLVSAGI 1143
>sp|Q9IDV9|POL_HV1YB Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group N
(isolate YBF106) GN=gag-pol PE=3 SV=3
Length = 1449
Score = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 44/95 (46%), Gaps = 5/95 (5%)
Query: 1 MLGIPDTCDEHIYYQVDLTGTAEKS-ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNL 59
++ I +T ++ Q L E E + ++ + S + S S+ + + I L
Sbjct: 1063 VVSIENTTNQKAELQAILLALQESGQEANIVTDSQYAMGIIHSQPDKSESDLVGQIIEEL 1122
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+ K + ++ +WVP+H GI GNE+ D L +
Sbjct: 1123 IKKER----VYLSWVPAHKGIGGNEQVDXLVSSGI 1153
>sp|Q89928|POL_HV2EH Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype B
(isolate EHO) GN=gag-pol PE=3 SV=3
Length = 1464
Score = 39.7 bits (91), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 28 QVYLTPDNS-LSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEA 86
QV + D+ + + + Q + +PI REI + K + ++ WVP+H G+ GN+E
Sbjct: 1100 QVNIIVDSQYVMGIVAAQPTETESPIVREIIEEMIKKEKIY---VGWVPAHKGLGGNQEV 1156
Query: 87 DRLAKEAL 94
D L + +
Sbjct: 1157 DHLVSQGI 1164
>sp|P22382|POL_SIVGB Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate GB1)
GN=gag-pol PE=3 SV=2
Length = 1441
Score = 38.9 bits (89), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 48 SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+ +PI +EI L+ + ++ +W+P+H GI GNE+ D+L +
Sbjct: 1109 TDHPIVKEIIELMKGKEKIY---LSWLPAHKGIGGNEQIDKLVSSGI 1152
>sp|P04584|POL_HV2RO Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype A
(isolate ROD) GN=gag-pol PE=1 SV=3
Length = 1464
Score = 38.9 bits (89), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 41 QSIQNVSSSNPIARE---IRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
Q + +S+S P E + ++++ +++ WVP+H GI GN+E D L + +
Sbjct: 1111 QYVMGISASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 1167
>sp|A9W185|RNH_METEP Ribonuclease H OS=Methylobacterium extorquens (strain PA1) GN=rnhA
PE=3 SV=1
Length = 228
Score = 38.5 bits (88), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLA----KEALSSNS 98
LD + +TWV H G AGNE ADRLA +EALS +
Sbjct: 107 LDALAAARDVRWTWVRGHAGEAGNERADRLATLGRREALSGKT 149
>sp|Q02836|POL_SIVG1 Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.grivet
(isolate AGM gr-1) GN=gag-pol PE=3 SV=2
Length = 1472
Score = 38.1 bits (87), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 48 SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
S++P+ +I L K + V+ WVP+H GI GN E D+L + +
Sbjct: 1122 SNSPLVEQIIQALMKKRQVY---LQWVPAHKGIGGNTEIDKLVSKGI 1165
>sp|Q75002|POL_HV1ET Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M
subtype C (isolate ETH2220) GN=gag-pol PE=3 SV=3
Length = 1439
Score = 38.1 bits (87), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 25 SECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE 84
SE + +L + + + S S + + I L+ K + ++ +WVP+H GI GNE
Sbjct: 1082 SEVNIVTDSQYALGIILAQPDKSESEIVNQIIEQLISKER----VYLSWVPAHKGIGGNE 1137
Query: 85 EADRLAKEAL 94
+ D+L +
Sbjct: 1138 QVDKLVSSGI 1147
>sp|Q1A249|POL_SIVEK Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate EK505)
GN=gag-pol PE=3 SV=3
Length = 1448
Score = 37.4 bits (85), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 7/93 (7%)
Query: 4 IPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNS--LSALQSIQNVSSSNPIAREIRNLLD 61
I +T ++ Q L + + +V + D+ L + S + S S + + I L+
Sbjct: 1065 ISETTNQQAELQAVLMALQDAGQ-EVNIVTDSQYVLGIIHSQPDKSESELVNQIIEELIK 1123
Query: 62 KNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
K + ++ +WVP+H GI GNE+ D+L +
Sbjct: 1124 KER----IYLSWVPAHKGIGGNEQIDKLVSTGI 1152
>sp|P15833|POL_HV2D2 Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype B
(isolate D205) GN=gag-pol PE=3 SV=3
Length = 1465
Score = 37.0 bits (84), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 25 SECQVYLTPDNS-LSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGN 83
SE QV + D+ + + + Q + +PI +I + K + V+ WVP+H G+ GN
Sbjct: 1098 SEPQVNIIVDSQYVMGIIAAQPTETESPIVAKIIEEMIKKEAVY---VGWVPAHKGLGGN 1154
Query: 84 EEADRLAKEAL 94
+E D L + +
Sbjct: 1155 QEVDHLVSQGI 1165
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.316 0.131 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 74,911,255
Number of Sequences: 539616
Number of extensions: 2861323
Number of successful extensions: 7094
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 129
Number of HSP's successfully gapped in prelim test: 40
Number of HSP's that attempted gapping in prelim test: 6962
Number of HSP's gapped (non-prelim): 172
length of query: 196
length of database: 191,569,459
effective HSP length: 111
effective length of query: 85
effective length of database: 131,672,083
effective search space: 11192127055
effective search space used: 11192127055
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)