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= psy5610
(237 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>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 = 39.3 bits (90), Expect = 0.025, Method: Composition-based stats.
Identities = 30/88 (34%), Positives = 44/88 (50%), Gaps = 10/88 (11%)
Query: 10 AILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLILTNKSK 67
A L AI ++ NVN I +DS A+ L Q S +P+ +I L++ K
Sbjct: 1093 AKLTAIKMALEDSGPNVN-----IVTDSQYAMGILTAQPTQSDSPLVEQIIALMI---QK 1144
Query: 68 LNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+ WVP+H GI GNEE D+L + +
Sbjct: 1145 QQIYLQWVPAHKGIGGNEEIDKLVSKGI 1172
>sp|A9W185|RNH_METEP Ribonuclease H OS=Methylobacterium extorquens (strain PA1) GN=rnhA
PE=3 SV=1
Length = 228
Score = 38.9 bits (89), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 14/103 (13%)
Query: 6 LELTAILFAI-HFSISAHLN-NVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILT 63
+ELTA + A+ HF A + + Y+V S++ G ++++ L
Sbjct: 48 MELTAAIRALEHFPEGAAIEMRCDSQYVV---KSVTEWMRGWKARGWRTATGPVKNIDLM 104
Query: 64 NK-----SKLNVRFIWVPSHVGIAGNEEADRLA----KEALTS 97
+ + +VR+ WV H G AGNE ADRLA +EAL+
Sbjct: 105 QRLDALAAARDVRWTWVRGHAGEAGNERADRLATLGRREALSG 147
>sp|P35956|POL_VILVK Pol polyprotein OS=Maedi visna virus (strain KV1772) GN=pol PE=1
SV=1
Length = 1101
Score = 38.9 bits (89), Expect = 0.028, Method: Composition-based stats.
Identities = 21/43 (48%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKE 93
NPI I +L+ NK K+ V WVP H GI NEE DR E
Sbjct: 646 NPIQARIMELV-HNKEKIGVH--WVPGHKGIPQNEEIDRYISE 685
>sp|P23427|POL_VILV2 Pol polyprotein OS=Maedi visna virus (strain 1514 / clone LV1-1KS2)
GN=pol PE=3 SV=1
Length = 1105
Score = 38.9 bits (89), Expect = 0.029, Method: Composition-based stats.
Identities = 21/43 (48%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKE 93
NPI I +L+ NK K+ V WVP H GI NEE DR E
Sbjct: 650 NPIQARIMELV-HNKEKIGVH--WVPGHKGIPQNEEIDRYISE 689
>sp|P03370|POL_VILV Pol polyprotein OS=Maedi visna virus (strain 1514) GN=pol PE=3 SV=1
Length = 1105
Score = 38.9 bits (89), Expect = 0.029, Method: Composition-based stats.
Identities = 21/43 (48%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKE 93
NPI I +L+ NK K+ V WVP H GI NEE DR E
Sbjct: 650 NPIQARIMELV-HNKEKIGVH--WVPGHKGIPQNEEIDRYISE 689
>sp|P23426|POL_VILV1 Pol polyprotein OS=Maedi visna virus (strain 1514 / clone LV1-1KS1)
GN=pol PE=3 SV=1
Length = 1105
Score = 38.9 bits (89), Expect = 0.033, Method: Composition-based stats.
Identities = 21/43 (48%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKE 93
NPI I +L + NK K+ V WVP H GI NEE DR E
Sbjct: 650 NPIQARIMEL-MHNKEKIGVH--WVPGHKGIPQNEEIDRYISE 689
>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 = 38.1 bits (87), Expect = 0.052, Method: Composition-based stats.
Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 14/89 (15%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLILTN 64
EL AIL A+ S + + I +DS AL + Q S +PI +I + LT
Sbjct: 1064 ELMAILLALQDS---------KETVNIVTDSQYALGVISSQPTQSESPIVQQIIEE-LTK 1113
Query: 65 KSKLNVRFIWVPSHVGIAGNEEADRLAKE 93
K + V WVP+H GI GNE+ D+L +
Sbjct: 1114 KEQ--VYLTWVPAHKGIGGNEKIDKLVSK 1140
>sp|O70338|RNH1_MOUSE Ribonuclease H1 OS=Mus musculus GN=Rnaseh1 PE=2 SV=1
Length = 285
Score = 37.7 bits (86), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 68 LNVRFIWVPSHVGIAGNEEADRLAKEALTSTH 99
++++++ +P H G GNEEADRLA+E +
Sbjct: 253 MDIQWMHIPGHSGFVGNEEADRLAREGAKQSE 284
>sp|Q5BK46|RNH1_RAT Ribonuclease H1 OS=Rattus norvegicus GN=Rnaseh1 PE=2 SV=1
Length = 285
Score = 37.7 bits (86), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 21/27 (77%)
Query: 68 LNVRFIWVPSHVGIAGNEEADRLAKEA 94
++++++ +P H G GNEEADRLA+E
Sbjct: 253 MDIQWMHIPGHSGFVGNEEADRLAREG 279
>sp|O60930|RNH1_HUMAN Ribonuclease H1 OS=Homo sapiens GN=RNASEH1 PE=1 SV=2
Length = 286
Score = 37.4 bits (85), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 68 LNVRFIWVPSHVGIAGNEEADRLAKEALTSTH 99
++++++ VP H G GNEEADRLA+E +
Sbjct: 254 MDIQWMHVPGHSGFIGNEEADRLAREGAKQSE 285
>sp|P22382|POL_SIVGB Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate GB1)
GN=gag-pol PE=3 SV=2
Length = 1441
Score = 37.4 bits (85), Expect = 0.093, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+PI EI +L+ K K + W+P+H GI GNE+ D+L +
Sbjct: 1111 HPIVKEIIELM---KGKEKIYLSWLPAHKGIGGNEQIDKLVSSGI 1152
>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 = 37.4 bits (85), Expect = 0.094, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ + VN I +DS AL +Q P E + +I K
Sbjct: 1059 LHAIHLALQDSGSEVN-----IVTDSQYALGIIQ----AQPDRSESEIVNQIIEKLIEKE 1109
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1110 KVYLSWVPAHKGIGGNEQVDKLVSSGI 1136
>sp|Q8AII1|POL_SIVTN Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate TAN1)
GN=gag-pol PE=3 SV=4
Length = 1462
Score = 37.0 bits (84), Expect = 0.11, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 10 AILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI--FSLNPIAGEIRDLILTNKSK 67
A L+A+ ++ VN I +DS + LQ + S +PI + +I K
Sbjct: 1091 AELWAVDLALKDSGAQVN-----IVTDSQYVMGVLQGLPDQSDSPI---VEQIIQKLTQK 1142
Query: 68 LNVRFIWVPSHVGIAGNEEADRLAKE 93
+ WVP+H GI GNEE D+L +
Sbjct: 1143 TAIYLAWVPAHKGIGGNEEVDKLVSK 1168
>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 = 37.0 bits (84), Expect = 0.13, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ + VN I +DS AL +Q P E + +I K
Sbjct: 1061 LQAIHLALQDSGSEVN-----IVTDSQYALGIIQ----AQPDKSESELVNQIIEQLIQKE 1111
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1112 KVYLSWVPAHKGIGGNEQVDKLVSSGI 1138
>sp|A4IYE6|RNH_FRATW Ribonuclease H OS=Francisella tularensis subsp. tularensis (strain
WY96-3418) GN=rnhA PE=3 SV=1
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>sp|Q0BMB7|RNH_FRATO Ribonuclease H OS=Francisella tularensis subsp. holarctica (strain
OSU18) GN=rnhA PE=3 SV=1
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>sp|A0Q6W0|RNH_FRATN Ribonuclease H OS=Francisella tularensis subsp. novicida (strain
U112) GN=rnhA PE=3 SV=1
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>sp|B2SFV9|RNH_FRATM Ribonuclease H OS=Francisella tularensis subsp. mediasiatica
(strain FSC147) GN=rnhA PE=3 SV=1
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>sp|Q2A3X6|RNH_FRATH Ribonuclease H OS=Francisella tularensis subsp. holarctica (strain
LVS) GN=rnhA PE=3 SV=1
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>sp|A7NBM9|RNH_FRATF Ribonuclease H OS=Francisella tularensis subsp. holarctica (strain
FTNF002-00 / FTA) GN=rnhA PE=3 SV=1
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>sp|Q14IN1|RNH_FRAT1 Ribonuclease H OS=Francisella tularensis subsp. tularensis (strain
FSC 198) GN=rnhA PE=3 SV=2
Length = 152
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
LTNK NV + WV H G AGNE+AD LA +A+
Sbjct: 115 LTNKH--NVTWGWVKGHSGNAGNEKADELANKAI 146
>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 = 36.6 bits (83), Expect = 0.15, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ + VN I +DS AL +Q P E + +I K
Sbjct: 1071 LQAIHLALQDSGSEVN-----IVTDSQYALGIIQ----AQPDKSESEIVNQIIEQLIQKD 1121
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1122 KVYLSWVPAHKGIGGNEQVDKLVSSGI 1148
>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 = 36.6 bits (83), Expect = 0.16, Method: Composition-based stats.
Identities = 29/87 (33%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1067 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVSQIIEQLIKKE 1117
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ DRL +
Sbjct: 1118 KVYLAWVPAHKGIGGNEQVDRLVSTGI 1144
>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 = 36.6 bits (83), Expect = 0.17, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ + VN I +DS AL +Q P E + +I K
Sbjct: 1061 LQAIHLALQDSGSEVN-----IVTDSQYALGIIQ----AQPDKSESELVNQIIEQLIKKD 1111
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1112 RVYLSWVPAHKGIGGNEQVDKLVSSGI 1138
>sp|P19028|POL_FIVSD Pol polyprotein OS=Feline immunodeficiency virus (strain San Diego)
GN=pol PE=3 SV=1
Length = 1124
Score = 36.2 bits (82), Expect = 0.20, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 42 QTLQNIFSLNPIAGE-IRDLILTNKSKLNVRFI-WVPSHVGIAGNEEADRLAKEAL 95
Q + NI S P E I +L K FI WVP H GI GNEE D+L + +
Sbjct: 656 QYMINILSQQPDKMEGIWQEVLEELEKKTAIFIDWVPGHKGIPGNEEVDKLCQTMM 711
>sp|P27980|POL_SIVVG Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.vervet
(isolate AGM3) GN=gag-pol PE=3 SV=2
Length = 1465
Score = 36.2 bits (82), Expect = 0.20, Method: Composition-based stats.
Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 10/88 (11%)
Query: 10 AILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLILTNKSK 67
A L AI ++ NVN I +DS A+ L Q S +P+ +I L++ K
Sbjct: 1091 AELMAIKMALEDSGPNVN-----IVTDSQYAMGILTAQPTQSDSPLIEQIIALMV---QK 1142
Query: 68 LNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+ WVP+ GI GNEE D+L + +
Sbjct: 1143 HQIYLQWVPADKGIGGNEEIDKLVSQGM 1170
>sp|P31822|POL_FIVT2 Pol polyprotein OS=Feline immunodeficiency virus (isolate TM2)
GN=pol PE=3 SV=1
Length = 1124
Score = 36.2 bits (82), Expect = 0.21, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 42 QTLQNIFSLNP--IAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
Q + NI + P + G ++++ + K+ + WVP H GI GNEE D+L + +
Sbjct: 655 QYILNILNQQPDLMEGLWQEVLEQMEKKIAIFIDWVPGHKGIPGNEEVDKLCQTMM 710
>sp|P19560|POL_BIV29 Gag-Pol polyprotein OS=Bovine immunodeficiency virus (strain R29)
GN=gag-pol PE=1 SV=2
Length = 1475
Score = 35.8 bits (81), Expect = 0.28, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 74 WVPSHVGIAGNEEADRLAKEALTSTHP 100
WVP+H GI GN EAD K+AL P
Sbjct: 1097 WVPAHKGIGGNTEADEGVKKALEQMAP 1123
>sp|Q0AE34|RNH_NITEC Ribonuclease H OS=Nitrosomonas eutropha (strain C91) GN=rnhA PE=3
SV=1
Length = 162
Score = 35.8 bits (81), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 70 VRFIWVPSHVGIAGNEEADRLAKEALTS 97
V + WV H G AGNE ADRLA + + S
Sbjct: 128 VEWFWVRGHNGHAGNERADRLANQGVES 155
>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 = 35.4 bits (80), Expect = 0.31, Method: Composition-based stats.
Identities = 30/92 (32%), Positives = 41/92 (44%), Gaps = 16/92 (17%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILT 63
ELTA+ A+ S NVN I +DS Q + NI + P + +I
Sbjct: 1087 ELTAVKMALEDSGE----NVN-----IVTDS----QYVMNILTACPQESNSPLVEQIIQA 1133
Query: 64 NKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
K V WVP+H GI GN E D+L + +
Sbjct: 1134 LMKKRQVYLQWVPAHKGIGGNTEIDKLVSKGI 1165
>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 = 35.4 bits (80), Expect = 0.31, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 14/89 (15%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLILTN 64
EL A+L A+ S + + I +DS L + Q S +PI +I + LT
Sbjct: 1066 ELMAVLIALQDS---------KEQVNIVTDSQYVLGIISSQPTQSDSPIVQQIIEE-LTK 1115
Query: 65 KSKLNVRFIWVPSHVGIAGNEEADRLAKE 93
K + V WVP+H GI GNE+ D+L +
Sbjct: 1116 KER--VYLTWVPAHKGIGGNEKIDKLVSK 1142
>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 = 35.4 bits (80), Expect = 0.38, Method: Composition-based stats.
Identities = 29/92 (31%), Positives = 40/92 (43%), Gaps = 16/92 (17%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILT 63
EL AI A+ S R+ + I +DS AL +Q P E + +I
Sbjct: 1063 ELQAIQLALQDS---------RSEVNIVTDSQYALGIIQ----AQPDRSEAELVNQIIEQ 1109
Query: 64 NKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
K V WVP+H GI GNE+ D+L +
Sbjct: 1110 LIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGI 1141
>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 = 35.4 bits (80), Expect = 0.39, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1078 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVNQIIEQLIKKE 1128
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1129 KVYLAWVPAHKGIGGNEQVDKLVSAGI 1155
>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 = 35.4 bits (80), Expect = 0.39, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1066 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVSQIIEQLIKKE 1116
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1117 KVYLAWVPAHKGIGGNEQVDKLVSAGI 1143
>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 = 35.4 bits (80), Expect = 0.40, Method: Composition-based stats.
Identities = 32/100 (32%), Positives = 44/100 (44%), Gaps = 15/100 (15%)
Query: 2 ATSVLELT---AILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE-- 56
A S+ E T A L AI ++ + VN I +DS AL +Q P E
Sbjct: 1048 AVSLTETTNQKAELQAIQLALQDSGSEVN-----IVTDSQYALGIIQ----AQPDKSESE 1098
Query: 57 -IRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+ +I K V WVP+H GI GNE+ D+L +
Sbjct: 1099 LVNQIIEQLIKKEKVYLSWVPAHKGIGGNEQVDKLVSAGI 1138
>sp|P27973|POL_SIVV1 Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.vervet
(isolate AGM155) GN=gag-pol PE=3 SV=2
Length = 1470
Score = 35.0 bits (79), Expect = 0.41, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 10/89 (11%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKS 66
ELTAI A+ ++ + +V S + T Q S +P+ + +I
Sbjct: 1091 ELTAIKMALE-------DSGPKVNIVTDSQYAMGILTAQPTQSDSPL---VEQIIAQMVQ 1140
Query: 67 KLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
K + WVP+H GI GNEE D+L + +
Sbjct: 1141 KEAIYLQWVPAHKGIGGNEEIDKLVSKGV 1169
>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 = 35.0 bits (79), Expect = 0.42, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1078 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVNQIIEQLIKKE 1128
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1129 KVYLAWVPAHKGIGGNEQVDKLVSAGI 1155
>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 = 35.0 bits (79), Expect = 0.42, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 66 SKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
SK V WVP+H GI GNE+ D+L +
Sbjct: 1118 SKERVYLSWVPAHKGIGGNEQVDKLVSSGI 1147
>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 = 35.0 bits (79), Expect = 0.43, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1065 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVSQIIEQLIKKE 1115
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1116 KVYLAWVPAHKGIGGNEQVDKLVSAGI 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 = 35.0 bits (79), Expect = 0.43, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1070 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVSQIIEQLIKKE 1120
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1121 KVYLAWVPAHKGIGGNEQVDKLVSAGI 1147
>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 = 35.0 bits (79), Expect = 0.43, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1068 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVSQIIEQLIKKE 1118
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1119 KVYLAWVPAHKGIGGNEQVDKLVSAGI 1145
>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 = 35.0 bits (79), Expect = 0.44, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 12 LFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKL 68
L AIH ++ VN I +DS AL +Q P E + +I K
Sbjct: 1072 LQAIHLALQDSGLEVN-----IVTDSQYALGIIQ----AQPDKSESELVSQIIEQLIKKE 1122
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEAL 95
V WVP+H GI GNE+ D+L +
Sbjct: 1123 KVYLAWVPAHKGIGGNEQVDKLVSAGI 1149
>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 = 35.0 bits (79), Expect = 0.46, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 67 KLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
K V WVP+H GI GNE+ D+L + +
Sbjct: 1112 KEKVYLAWVPAHKGIGGNEQVDKLVSQGI 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 = 35.0 bits (79), Expect = 0.49, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 67 KLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
K V WVP+H GI GNE+ D+L + +
Sbjct: 1116 KEKVYLAWVPAHKGIGGNEQVDKLVSQGI 1144
>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 = 35.0 bits (79), Expect = 0.50, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 67 KLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
K V WVP+H GI GNE+ D+L + +
Sbjct: 1115 KEKVYLAWVPAHKGIGGNEQVDKLVSQGI 1143
>sp|B3Q6U1|RNH_RHOPT Ribonuclease H OS=Rhodopseudomonas palustris (strain TIE-1) GN=rnhA
PE=3 SV=1
Length = 155
Score = 34.7 bits (78), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEALT 96
++R+ WV H G A NE AD+LA++ LT
Sbjct: 119 SIRWHWVKGHAGHAENERADQLARDGLT 146
>sp|Q6N1Y3|RNH_RHOPA Ribonuclease H OS=Rhodopseudomonas palustris (strain ATCC BAA-98 /
CGA009) GN=rnhA PE=3 SV=1
Length = 155
Score = 34.7 bits (78), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEALT 96
++R+ WV H G A NE AD+LA++ LT
Sbjct: 119 SIRWHWVKGHAGHAENERADQLARDGLT 146
>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 = 34.7 bits (78), Expect = 0.61, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 42 QTLQNIFSLNPIAGE---IRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
Q + I + P E +R++I K + WVP+H G+ GN+E D L + +
Sbjct: 1108 QYVMGIVAAQPTETESPIVREIIEEMIKKEKIYVGWVPAHKGLGGNQEVDHLVSQGI 1164
>sp|B0TZ91|RNH_FRAP2 Ribonuclease H OS=Francisella philomiragia subsp. philomiragia
(strain ATCC 25017) GN=rnhA PE=3 SV=1
Length = 152
Score = 34.3 bits (77), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 66 SKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+K NV + WV H G GNE+AD LA +A+
Sbjct: 117 TKHNVTWSWVKGHSGNQGNEKADELANKAI 146
>sp|A1URX4|RNH_BARBK Ribonuclease H OS=Bartonella bacilliformis (strain ATCC 35685 /
KC583) GN=rnhA PE=3 SV=1
Length = 155
Score = 34.3 bits (77), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 66 SKLNVRFIWVPSHVGIAGNEEADRLAKEALT 96
++ NVR+ WV H G NE AD LA++A+T
Sbjct: 115 ARHNVRWHWVKGHAGHPDNERADALARKAIT 145
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
0.320 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 84,317,655
Number of Sequences: 539616
Number of extensions: 3336148
Number of successful extensions: 9795
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 109
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 9686
Number of HSP's gapped (non-prelim): 124
length of query: 237
length of database: 191,569,459
effective HSP length: 114
effective length of query: 123
effective length of database: 130,053,235
effective search space: 15996547905
effective search space used: 15996547905
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)