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= 036141
(220 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|P69732|GAG_EIAVY Gag polyprotein OS=Equine infectious anemia virus (strain Wyoming)
GN=gag PE=1 SV=1
Length = 486
Score = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 10/166 (6%)
Query: 54 GNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARS 113
G QN G + + E+VD + Q I+S QE+ SK + ++ E R+
Sbjct: 270 GKPKAQNIRQGAKEPYPEFVDRLLSQ--IKSEGHPQEI---SKFLTDTLTIQNANEECRN 324
Query: 114 NLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQ- 172
+ R L P + K + Q ++ K +A KG ++ Q
Sbjct: 325 AM--RHLRPEDTLEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQT 382
Query: 173 CFSCKEYRHIVVKC-AKKFCNYCKKPGHIIKECPTRPQNC-QASQA 216
C++C + H+ +C A K C CK+PGH K+C + P+N Q +Q
Sbjct: 383 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRSVPKNGKQGAQG 428
>sp|P69731|GAG_EIAVC Gag polyprotein OS=Equine infectious anemia virus (isolate CL22)
GN=gag PE=3 SV=1
Length = 486
Score = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 10/166 (6%)
Query: 54 GNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARS 113
G QN G + + E+VD + Q I+S QE+ SK + ++ E R+
Sbjct: 270 GKPKAQNIRQGAKEPYPEFVDRLLSQ--IKSEGHPQEI---SKFLTDTLTIQNANEECRN 324
Query: 114 NLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQ- 172
+ R L P + K + Q ++ K +A KG ++ Q
Sbjct: 325 AM--RHLRPEDTLEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQT 382
Query: 173 CFSCKEYRHIVVKC-AKKFCNYCKKPGHIIKECPTRPQNC-QASQA 216
C++C + H+ +C A K C CK+PGH K+C + P+N Q +Q
Sbjct: 383 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRSVPKNGKQGAQG 428
>sp|P69730|GAG_EIAV9 Gag polyprotein OS=Equine infectious anemia virus (isolate 1369)
GN=gag PE=1 SV=1
Length = 486
Score = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 10/166 (6%)
Query: 54 GNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARS 113
G QN G + + E+VD + Q I+S QE+ SK + ++ E R+
Sbjct: 270 GKPKAQNIRQGAKEPYPEFVDRLLSQ--IKSEGHPQEI---SKFLTDTLTIQNANEECRN 324
Query: 114 NLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQ- 172
+ R L P + K + Q ++ K +A KG ++ Q
Sbjct: 325 AM--RHLRPEDTLEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQT 382
Query: 173 CFSCKEYRHIVVKC-AKKFCNYCKKPGHIIKECPTRPQNC-QASQA 216
C++C + H+ +C A K C CK+PGH K+C + P+N Q +Q
Sbjct: 383 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRSVPKNGKQGAQG 428
>sp|P24106|GAG_HV2CA Gag polyprotein OS=Human immunodeficiency virus type 2 subtype A
(isolate CAM2) GN=gag PE=3 SV=3
Length = 521
Score = 39.7 bits (91), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 149 MHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECP 205
M I +AAA + R ++C++C + H +C ++ C C KPGHI+ CP
Sbjct: 373 MGPPPIPFAAAQQR------RTIKCWNCGKEGHSARQCRAPRRQGCWKCGKPGHIMTNCP 426
Query: 206 TR 207
R
Sbjct: 427 DR 428
>sp|Q82851|POL_JEMBR Gag-Pol polyprotein OS=Jembrana disease virus GN=gag-pol PE=3 SV=1
Length = 1432
Score = 39.3 bits (90), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 146 QNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECP 205
+ KM A A+AA + K G R C+ C + HI C + C C KPGH+ + C
Sbjct: 346 KQKMQFLAEAFAAINVKGDGEVQR---CYGCGKPGHIRRDCKNQKCFKCGKPGHLQRNCK 402
Query: 206 TR 207
++
Sbjct: 403 SK 404
>sp|Q82850|GAG_JEMBR Gag polyprotein OS=Jembrana disease virus GN=gag PE=3 SV=1
Length = 436
Score = 39.3 bits (90), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 146 QNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECP 205
+ KM A A+AA + K G R C+ C + HI C + C C KPGH+ + C
Sbjct: 346 KQKMQFLAEAFAAINVKGDGEVQR---CYGCGKPGHIRRDCKNQKCFKCGKPGHLQRNCK 402
Query: 206 TR 207
++
Sbjct: 403 SK 404
>sp|P31821|GAG_FIVT2 Gag polyprotein OS=Feline immunodeficiency virus (isolate TM2)
GN=gag PE=3 SV=1
Length = 449
Score = 39.3 bits (90), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 173 CFSCKEYRHIVVKCAK-KFCNYCKKPGHIIKEC 204
CF+CK+ H+ +C + K CN C KPGH+ C
Sbjct: 377 CFNCKKPGHLARQCKEAKRCNNCGKPGHLAANC 409
>sp|P16087|GAG_FIVPE Gag polyprotein OS=Feline immunodeficiency virus (isolate Petaluma)
GN=gag PE=3 SV=1
Length = 450
Score = 39.3 bits (90), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 173 CFSCKEYRHIVVKCAK-KFCNYCKKPGHIIKEC 204
CF+CK+ H+ +C + K CN C KPGH+ +C
Sbjct: 377 CFNCKKPGHLARQCREVKKCNKCGKPGHLAAKC 409
>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 = 0.024, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 164 KGRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKEC 204
+GR V+C++C ++ H+ +C K C C KPGH+ K+C
Sbjct: 395 RGRPRPPVKCYNCGKFGHMQRQCPEPRKMRCLKCGKPGHLAKDC 438
>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 = 38.9 bits (89), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 164 KGRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKEC 204
+GR V+C++C ++ H+ +C K C C KPGH+ K+C
Sbjct: 395 RGRPRPPVKCYNCGKFGHMQRQCPEPRKMRCLKCGKPGHLAKDC 438
>sp|P27978|GAG_SIVVG Gag polyprotein OS=Simian immunodeficiency virus agm.vervet
(isolate AGM3) GN=gag PE=3 SV=1
Length = 521
Score = 38.9 bits (89), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 37/162 (22%), Positives = 65/162 (40%), Gaps = 29/162 (17%)
Query: 56 LSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNL 115
+S+ + G + + +YVD Y + E + EV + + P + L
Sbjct: 293 VSVLDIRQGPKEAFKDYVDRFYKAIRAEQASG--EVKQWMTESLLIQNANPDCKVILKGL 350
Query: 116 -MNRDLSPSLDVC-------FKELLREE--QRLATQTILQQNKMHDNAIAYAAAHWKSKG 165
M+ L L C +K + E Q + +Q ++QQ +G
Sbjct: 351 GMHPTLEEMLTACQGVGGPSYKAKVMAEMMQNMQSQNMMQQGG--------------QRG 396
Query: 166 RDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKEC 204
R V+C++C ++ H+ +C K C C KPGH+ K+C
Sbjct: 397 RPRPPVKCYNCGKFGHMQRQCPEPRKMRCLKCGKPGHLAKDC 438
>sp|P19027|GAG_FIVSD Gag polyprotein OS=Feline immunodeficiency virus (strain San Diego)
GN=gag PE=3 SV=1
Length = 450
Score = 38.5 bits (88), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 173 CFSCKEYRHIVVKCAK-KFCNYCKKPGHIIKEC 204
CF+CK+ H+ +C K CN C KPGH+ +C
Sbjct: 377 CFNCKKPGHLARQCRDVKKCNKCGKPGHLAAKC 409
>sp|P24107|POL_HV2CA Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype
A (isolate CAM2) GN=gag-pol PE=3 SV=3
Length = 1462
Score = 38.5 bits (88), Expect = 0.035, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 134 EEQRLATQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KKF 190
++ RL + + + M I +AAA + R ++C++C + H +C ++
Sbjct: 360 QKARLMAEAL--KEAMGPPPIPFAAAQQR------RTIKCWNCGKEGHSARQCRAPRRQG 411
Query: 191 CNYCKKPGHIIKECPTR 207
C C KPGHI+ CP R
Sbjct: 412 CWKCGKPGHIMTNCPDR 428
>sp|Q9NUD5|ZCHC3_HUMAN Zinc finger CCHC domain-containing protein 3 OS=Homo sapiens
GN=ZCCHC3 PE=1 SV=1
Length = 404
Score = 38.5 bits (88), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 170 QVQCFSCKEYRHIVVKCAKKF-CNYCKKPGHIIKECPTRPQNCQASQ 215
Q +CF C E H+ C K CN C K GH +CP N A+Q
Sbjct: 351 QDRCFRCGEEGHLSPYCRKGIVCNLCGKRGHAFAQCPKAVHNSVAAQ 397
>sp|Q05313|GAG_FIVWO Gag polyprotein OS=Feline immunodeficiency virus (isolate Wo)
GN=gag PE=3 SV=1
Length = 450
Score = 38.1 bits (87), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 173 CFSCKEYRHIVVKCAK-KFCNYCKKPGHIIKEC 204
CF+CK H+ +C K CN C KPGH+ +C
Sbjct: 377 CFNCKRPGHLARQCRDVKKCNKCGKPGHLAAKC 409
>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 = 38.1 bits (87), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 166 RDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R R+++CF+C + H+ C KK C C K GH +K+C R N
Sbjct: 379 RGPRRIKCFNCGKEGHLAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 426
>sp|P31634|GAG_SIVMS Gag polyprotein OS=Simian immunodeficiency virus (isolate STM)
GN=gag PE=3 SV=1
Length = 510
Score = 37.7 bits (86), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 149 MHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECP 205
+ +AAA + +GR R V+C++C + H +C ++ C C KPGH + +CP
Sbjct: 373 FQPGPLPFAAA--QQQGR--RTVKCWNCGKEGHTAKQCKAPRRQGCWKCGKPGHQMAKCP 428
Query: 206 TR 207
R
Sbjct: 429 ER 430
>sp|P24736|GAG_HV1U4 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype A (isolate U455) GN=gag PE=1 SV=3
Length = 493
Score = 37.7 bits (86), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 166 RDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R R+++CF+C + H+ C KK C C K GH +K+C R N
Sbjct: 379 RGPRRIKCFNCGKEGHLAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 426
>sp|Q76634|POL_HV2UC Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype
B (isolate UC1) GN=gag-pol PE=3 SV=3
Length = 1471
Score = 37.7 bits (86), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 154 IAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTR 207
I +AAA K+ R V C++C + H +C ++ C C K GHI+ +CP R
Sbjct: 373 IPFAAAQQKAGKRGT--VTCWNCGKVGHTAKQCRAPRRQGCWKCGKQGHIMSKCPER 427
>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 = 37.7 bits (86), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +KEC R N
Sbjct: 388 KNVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKECTERQAN 432
>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 = 37.7 bits (86), Expect = 0.065, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R ++CF+C + H+ C KK C C K GH +KEC R N
Sbjct: 389 RIIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQMKECTERQAN 433
>sp|P20873|GAG_HV1JR Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate JRCSF) GN=gag PE=3 SV=3
Length = 504
Score = 37.4 bits (85), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +KEC R N
Sbjct: 388 KNVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKECTERQAN 432
>sp|P12451|POL_HV2SB Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype
A (isolate SBLISY) GN=gag-pol PE=3 SV=3
Length = 1462
Score = 37.4 bits (85), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 56/138 (40%), Gaps = 30/138 (21%)
Query: 94 QSKRDQFLMKLRP-KYEAARSNLMNRDL----SPSLDVCFKEL----LREEQRLATQTIL 144
QS D+F LR + +AA N M + L +P + K L EE A Q I
Sbjct: 296 QSYVDRFYKSLRAEQTDAAVKNWMTQTLLVQSNPDCKLVLKGLGMNPTLEEMLTACQGIG 355
Query: 145 QQNK------------MHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KK 189
+ M I +AAA K R ++C++C + H +C ++
Sbjct: 356 GPGQKARLMAEALKEAMRPAPIPFAAAQQK------RAIKCWNCGKEGHSARQCRAPRRQ 409
Query: 190 FCNYCKKPGHIIKECPTR 207
C C K GHI+ CP R
Sbjct: 410 GCWKCGKSGHIMANCPDR 427
>sp|A9ACL8|RLME_BURM1 Ribosomal RNA large subunit methyltransferase E OS=Burkholderia
multivorans (strain ATCC 17616 / 249) GN=rlmE PE=3 SV=1
Length = 220
Score = 37.4 bits (85), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 50/111 (45%), Gaps = 13/111 (11%)
Query: 80 VPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLA 139
+P+E +ADV + + D+ L +L E +L+ D++P+L +A
Sbjct: 94 LPMEPIADVHFIQGDFREDEVLHQLEAVLEGRTVDLVISDMAPNL-----------SGVA 142
Query: 140 TQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKF 190
+ + + D A+ +A H K G + V+CF Y IV K ++F
Sbjct: 143 SADAARIEHVCDLALEFAQNHLKPDGALL--VKCFHGSGYSQIVEKFKQQF 191
>sp|Q76633|GAG_HV2UC Gag polyprotein OS=Human immunodeficiency virus type 2 subtype B
(isolate UC1) GN=gag PE=3 SV=3
Length = 521
Score = 37.4 bits (85), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 154 IAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTR 207
I +AAA K+ R V C++C + H +C ++ C C K GHI+ +CP R
Sbjct: 373 IPFAAAQQKAGKRGT--VTCWNCGKVGHTAKQCRAPRRQGCWKCGKQGHIMSKCPER 427
>sp|P05960|POL_HV1C4 Gag-Pol polyprotein (Fragment) OS=Human immunodeficiency virus type
1 group M subtype B (isolate CDC-451) GN=gag-pol PE=3
SV=3
Length = 550
Score = 37.4 bits (85), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 166 RDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R + V+CF+C + HI C KK C C + GH +K+C R N
Sbjct: 385 RQGKTVKCFNCGKEGHIARNCKAPRKKGCWKCGREGHQMKDCTERQAN 432
>sp|P05890|GAG_HV1RH Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate RF/HAT3) GN=gag PE=3 SV=3
Length = 501
Score = 37.0 bits (84), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 162 KSKGRDMRQ-VQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKEC 204
K RD R+ V+CF+C + HI C KK C C K GH +K+C
Sbjct: 380 KGNFRDQRKIVKCFNCGKVGHIAKNCRAPRKKGCWKCGKEGHQMKDC 426
>sp|Q8AII2|GAG_SIVTN Gag polyprotein OS=Simian immunodeficiency virus (isolate TAN1)
GN=gag PE=3 SV=3
Length = 524
Score = 37.0 bits (84), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 170 QVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTR 207
Q+QCF+C + H C KK C C + GH +K+C TR
Sbjct: 416 QLQCFNCGKVGHTARNCRAPRKKGCWRCGQEGHQMKDCTTR 456
>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 = 37.0 bits (84), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 162 KSKGRDMRQ-VQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKEC 204
K RD R+ V+CF+C + HI C KK C C K GH +K+C
Sbjct: 380 KGNFRDQRKIVKCFNCGKVGHIAKNCRAPRKKGCWKCGKEGHQMKDC 426
>sp|Q0BGJ2|RLME_BURCM Ribosomal RNA large subunit methyltransferase E OS=Burkholderia
ambifaria (strain ATCC BAA-244 / AMMD) GN=rlmE PE=3 SV=1
Length = 220
Score = 37.0 bits (84), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 49/111 (44%), Gaps = 13/111 (11%)
Query: 80 VPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLA 139
+P+E +ADV + + D L +L E +L+ D++P+L +A
Sbjct: 94 LPMEPIADVHFIQGDFREDDVLRQLEDVLEGRAVDLVISDMAPNL-----------SGVA 142
Query: 140 TQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKF 190
+ + + D A+ +A H K G + V+CF Y IV K ++F
Sbjct: 143 SADAARIEHLCDLALEFAQNHLKPDGALL--VKCFHGSGYSQIVEKFKQQF 191
>sp|B1YMW2|RLME_BURA4 Ribosomal RNA large subunit methyltransferase E OS=Burkholderia
ambifaria (strain MC40-6) GN=rlmE PE=3 SV=1
Length = 220
Score = 37.0 bits (84), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 49/111 (44%), Gaps = 13/111 (11%)
Query: 80 VPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLA 139
+P+E +ADV + + D L +L E +L+ D++P+L +A
Sbjct: 94 LPMEPIADVHFIQGDFREDDVLRQLEDVLEGRAVDLVISDMAPNL-----------SGVA 142
Query: 140 TQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKF 190
+ + + D A+ +A H K G + V+CF Y IV K ++F
Sbjct: 143 SADAARIEHLCDLALEFAQNHLKPDGALL--VKCFHGSGYSQIVEKFKQQF 191
>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: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 170 QVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTR 207
Q+QCF+C + H C KK C C + GH +K+C TR
Sbjct: 416 QLQCFNCGKVGHTARNCRAPRKKGCWRCGQEGHQMKDCTTR 456
>sp|Q39HN2|RLME_BURS3 Ribosomal RNA large subunit methyltransferase E OS=Burkholderia sp.
(strain 383) GN=rlmE PE=3 SV=1
Length = 220
Score = 37.0 bits (84), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 53/119 (44%), Gaps = 14/119 (11%)
Query: 80 VPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLA 139
+P+E +ADV + + D+ L +L E +L+ D++P+L +A
Sbjct: 94 LPMEPIADVHFLQGDFREDEVLHQLEEVLEGRDVDLVISDMAPNL-----------SGVA 142
Query: 140 TQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYC-KKP 197
+ + + D A+ +A H K G + V+CF Y IV K ++F +KP
Sbjct: 143 SADAARIEHLCDLALEFAQNHLKPDGALL--VKCFHGSGYSQIVEKFKQQFKTVAPRKP 199
>sp|P12450|GAG_HV2SB Gag polyprotein OS=Human immunodeficiency virus type 2 subtype A
(isolate SBLISY) GN=gag PE=3 SV=3
Length = 520
Score = 37.0 bits (84), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 56/138 (40%), Gaps = 30/138 (21%)
Query: 94 QSKRDQFLMKLRP-KYEAARSNLMNRDL----SPSLDVCFKEL----LREEQRLATQTIL 144
QS D+F LR + +AA N M + L +P + K L EE A Q I
Sbjct: 296 QSYVDRFYKSLRAEQTDAAVKNWMTQTLLVQSNPDCKLVLKGLGMNPTLEEMLTACQGIG 355
Query: 145 QQNK------------MHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCA---KK 189
+ M I +AAA K R ++C++C + H +C ++
Sbjct: 356 GPGQKARLMAEALKEAMRPAPIPFAAAQQK------RAIKCWNCGKEGHSARQCRAPRRQ 409
Query: 190 FCNYCKKPGHIIKECPTR 207
C C K GHI+ CP R
Sbjct: 410 GCWKCGKSGHIMANCPDR 427
>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 = 37.0 bits (84), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R ++CF+C + H+ C KK C C K GH +K+C R N
Sbjct: 385 RTIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQVKDCTERQAN 429
>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 = 37.0 bits (84), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 387 RIVKCFNCGKQGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 431
>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 = 36.6 bits (83), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 387 RIVKCFNCGKQGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 431
>sp|O12157|GAG_HV192 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype C (isolate 92BR025) GN=gag PE=3 SV=3
Length = 496
Score = 36.6 bits (83), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R ++CF+C + H+ C KK C C K GH +K+C R N
Sbjct: 385 RTIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQVKDCTERQAN 429
>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 = 36.6 bits (83), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 383 RIVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQAN 427
>sp|Q9WC53|GAG_HV1S2 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype J (isolate SE9280) GN=gag PE=3 SV=3
Length = 497
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 387 RIVKCFNCGKQGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 431
>sp|A6T081|RLME_JANMA Ribosomal RNA large subunit methyltransferase E
OS=Janthinobacterium sp. (strain Marseille) GN=rlmE PE=3
SV=1
Length = 214
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 52/119 (43%), Gaps = 14/119 (11%)
Query: 80 VPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLA 139
+P+E +ADV + + + L +L + + +L+ D++P+L +A
Sbjct: 88 LPMEPIADVHFIQGDFREQEVLEQLEQVLQGRKVDLVISDMAPNL-----------SGIA 136
Query: 140 TQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKFCNYC-KKP 197
+ + D AI + H K G + V+CF+ Y +IV K +F KKP
Sbjct: 137 VADAARMIDLIDLAIDFTQHHMKPSGSLL--VKCFNGSGYSYIVEKFRDEFKTVVQKKP 193
>sp|Q9WC62|GAG_HV1S9 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype J (isolate SE9173) GN=gag PE=1 SV=3
Length = 497
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 387 RIVKCFNCGKQGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 431
>sp|P05887|GAG_HV1C4 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate CDC-451) GN=gag PE=3 SV=3
Length = 500
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 166 RDMRQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R + V+CF+C + HI C KK C C + GH +K+C R N
Sbjct: 385 RQGKTVKCFNCGKEGHIARNCKAPRKKGCWKCGREGHQMKDCTERQAN 432
>sp|Q9QBZ6|GAG_HV1MP Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype F2 (isolate MP255) GN=gag PE=3 SV=2
Length = 492
Score = 36.6 bits (83), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
R V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 383 RIVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQAN 427
>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 = 36.6 bits (83), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 388 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 432
>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 = 36.2 bits (82), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 388 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 432
>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 = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 388 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 432
>sp|A4JDA6|RLME_BURVG Ribosomal RNA large subunit methyltransferase E OS=Burkholderia
vietnamiensis (strain G4 / LMG 22486) GN=rlmE PE=3 SV=1
Length = 220
Score = 36.2 bits (82), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 50/111 (45%), Gaps = 13/111 (11%)
Query: 80 VPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQRLA 139
+P+E +ADV + + D L +L E +L+ D++P+L +A
Sbjct: 94 LPMEPIADVHFLQGDFREDDVLHQLEGVLEGRPVDLVISDMAPNL-----------SGVA 142
Query: 140 TQTILQQNKMHDNAIAYAAAHWKSKGRDMRQVQCFSCKEYRHIVVKCAKKF 190
+ + + D A+ +A H K +G + V+CF Y IV K ++F
Sbjct: 143 SADAARIEHICDLALEFAQNHLKPEGALL--VKCFHGSGYSQIVEKFKQQF 191
>sp|P35962|GAG_HV1Y2 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (isolate YU-2) GN=gag PE=1 SV=2
Length = 500
Score = 36.2 bits (82), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 388 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 432
>sp|Q73367|GAG_HV1B9 Gag polyprotein OS=Human immunodeficiency virus type 1 group M
subtype B (strain 89.6) GN=gag PE=3 SV=3
Length = 500
Score = 36.2 bits (82), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI C KK C C K GH +K+C R N
Sbjct: 388 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 432
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
0.321 0.131 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 78,311,552
Number of Sequences: 539616
Number of extensions: 2970656
Number of successful extensions: 8713
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 184
Number of HSP's that attempted gapping in prelim test: 8333
Number of HSP's gapped (non-prelim): 356
length of query: 220
length of database: 191,569,459
effective HSP length: 113
effective length of query: 107
effective length of database: 130,592,851
effective search space: 13973435057
effective search space used: 13973435057
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (27.3 bits)