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= psy10810
(786 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|P21328|RTJK_DROME RNA-directed DNA polymerase from mobile element jockey
OS=Drosophila melanogaster GN=pol PE=1 SV=1
Length = 916
Score = 67.8 bits (164), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 46/191 (24%), Positives = 94/191 (49%), Gaps = 21/191 (10%)
Query: 167 IVCGIPQGGVVSGTLFAIAINS------ITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVS 220
I G+PQG V+ TL+++ + +T + + + DD A+ T+ K+ S
Sbjct: 638 IAAGVPQGSVLGPTLYSVFASDMPTHTPVTEVDEEDVLIATYADDTAVLTKSKSILAATS 697
Query: 221 IMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLG 280
+QE +D + ++ + + + +K V F+ + + +++ I +K+LG
Sbjct: 698 GLQEYLDAFQQWAENWNVRINAEKCANVTFANR---TGSCPGVSLNGRLIRHHQAYKYLG 754
Query: 281 LTFDKKMTWKVHLKNLKQSCLSRSRILKILSKKAW-AADRKML-----IRIYKSLIRSKL 334
+T D+K+T+ H+ N++Q+ ++ +++ +W A R L + IYKS++ L
Sbjct: 755 ITLDRKLTFSRHITNIQQAFRTK------VARMSWLIAPRNKLSLGCKVNIYKSILAPCL 808
Query: 335 DYGCPVYNSAS 345
YG VY A+
Sbjct: 809 FYGLQVYGIAA 819
Score = 37.0 bits (84), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/100 (22%), Positives = 47/100 (47%), Gaps = 7/100 (7%)
Query: 70 HLPIFLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINS------ITS 123
L + + +++ R+F + ++ S I G+PQG V+ TL+++ + +T
Sbjct: 610 QLYLVVKSFLEERTFHVSVDG-YKSSIKPIAAGVPQGSVLGPTLYSVFASDMPTHTPVTE 668
Query: 124 YIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSE 163
+ + + DD A+ T+ K+ S +QE +D +
Sbjct: 669 VDEEDVLIATYADDTAVLTKSKSILAATSGLQEYLDAFQQ 708
>sp|Q03270|PO12_NASVI Retrovirus-related Pol polyprotein from type-1 retrotransposable
element R1 2 (Fragment) OS=Nasonia vitripennis PE=4 SV=1
Length = 410
Score = 61.6 bits (148), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 37/155 (23%), Positives = 75/155 (48%), Gaps = 6/155 (3%)
Query: 170 GIPQGGVVSGTLFAIAINSITSYIHPS-LSSSLFVDDFAIFTRDKNKEVLVSIMQESIDK 228
G PQG + L+ +++N + + S +S F DD AI ++ + ++ E ++
Sbjct: 1 GCPQGSIGGPILWNLSMNGMLIELAGSGVSVCAFADDVAILAEGNTRKEVERVINEKMEI 60
Query: 229 LENFSNDTGLFFSPQKSQCVLFSRKY----KQLNTSINLNMYDTRIEVVDTFKFLGLTFD 284
+ + G+ S +K+ C+L KY + + S +N+Y RI+ V F++LG+
Sbjct: 61 VYKWGEKMGVSVSEEKTVCMLLKGKYVTSNRAVRVSKTINVYK-RIKYVSCFRYLGVNVT 119
Query: 285 KKMTWKVHLKNLKQSCLSRSRILKILSKKAWAADR 319
+ M + H++ +K + LK + ++ W R
Sbjct: 120 EGMGFGEHVRGMKVKVAKGVQKLKRVLRRDWGLRR 154
>sp|P21329|RTJK_DROFU RNA-directed DNA polymerase from mobile element jockey
OS=Drosophila funebris GN=jockey\pol PE=1 SV=1
Length = 916
Score = 60.1 bits (144), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 46/190 (24%), Positives = 89/190 (46%), Gaps = 19/190 (10%)
Query: 167 IVCGIPQGGVVSGTLFAIAI------NSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVS 220
I G+PQG V+ TL++I N++T + + + DD A+ T+
Sbjct: 638 IEAGVPQGSVLGPTLYSIFTADMPNQNAVTGLAEGEVLIATYADDIAVLTKSTCIVEATD 697
Query: 221 IMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQL-NTSINLNMYDTRIEVVDTFKFL 279
+QE +D + ++ + + K V F+ + +IN ++ E +K+L
Sbjct: 698 ALQEYLDAFQEWAVKWNVSINAGKCANVTFTNAIRDCPGVTINGSLLSHTHE----YKYL 753
Query: 280 GLTFDKKMTWKVHLKNLKQSCLSRSRILK----ILSKKAWAADRKMLIRIYKSLIRSKLD 335
G+ D+ +T++ H+ +L+ S R+RI K + ++ + D K ++IYK ++ L
Sbjct: 754 GVILDRSLTFRRHITSLQHSF--RTRITKMNWLLAARNKLSLDNK--VKIYKCIVAPGLF 809
Query: 336 YGCPVYNSAS 345
Y VY A+
Sbjct: 810 YAIQVYGIAA 819
Score = 37.4 bits (85), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 7/96 (7%)
Query: 74 FLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAI------NSITSYIHP 127
+ + + R F + + S F I G+PQG V+ TL++I N++T
Sbjct: 614 LIKSFWEGRKFSVTADGCRSSVKF-IEAGVPQGSVLGPTLYSIFTADMPNQNAVTGLAEG 672
Query: 128 SLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSE 163
+ + + DD A+ T+ +QE +D E
Sbjct: 673 EVLIATYADDIAVLTKSTCIVEATDALQEYLDAFQE 708
Score = 34.3 bits (77), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 50/105 (47%), Gaps = 12/105 (11%)
Query: 371 PFTMWELESVLKLLKSQSSPGPDEIHNQMLRHLPSN-------IRRKILSSNYIAKTLSI 423
P T+ E++ ++ LK + +PG D + N+ +R LP I IL Y K
Sbjct: 437 PVTLEEVKELVSKLKPKKAPGEDLLDNRTIRLLPDQALLYLVLIFNSILRVGYFPKARPT 496
Query: 424 ENHPNIMR-TLNPLYVRKYENSNMKPTIGIQKKNLETIIPFNNIM 467
+ I++ PL V Y +++ P++G K LE +I N I+
Sbjct: 497 ASIIMILKPGKQPLDVDSYRPTSLLPSLG---KMLERLI-LNRIL 537
>sp|P11204|POL_EIAV9 Pol polyprotein OS=Equine infectious anemia virus (isolate 1369)
GN=pol PE=1 SV=1
Length = 1146
Score = 59.7 bits (143), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 45/147 (30%), Positives = 70/147 (47%), Gaps = 23/147 (15%)
Query: 498 QMFQNEFKNKLAENFQSHIKIYTDGSK-NEQGVGCALTIPEKNIAKRFGLNKNASIFH-- 554
Q+ ++++ KL E S I IYTDG K N +G+ +T + KR G + H
Sbjct: 603 QVVHDDWRMKLVEEPTSGITIYTDGGKQNGEGIAAYVTSNGRTKQKRLG-----PVTHQV 657
Query: 555 AELFALLQSLLTIKELGACKALIITDSLSCLQAITNMFHEN-------PLVKRVQEELSS 607
AE A+ +L ++ + I+TDS C + IT P+++ ++E+
Sbjct: 658 AERMAIQMALEDTRDK---QVNIVTDSYYCWKNITEGLGLEGPQSPWWPIIQNIREK--- 711
Query: 608 IEPSIEFLWCPSHVGIAGNEAADEEAK 634
+ F W P H GI GN+ ADE AK
Sbjct: 712 --EIVYFAWVPGHKGICGNQLADEAAK 736
>sp|P32542|POL_EIAVC Pol polyprotein OS=Equine infectious anemia virus (isolate CL22)
GN=pol PE=1 SV=1
Length = 1146
Score = 59.7 bits (143), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 45/147 (30%), Positives = 70/147 (47%), Gaps = 23/147 (15%)
Query: 498 QMFQNEFKNKLAENFQSHIKIYTDGSK-NEQGVGCALTIPEKNIAKRFGLNKNASIFH-- 554
Q+ ++++ KL E S I IYTDG K N +G+ +T + KR G + H
Sbjct: 603 QVVHDDWRMKLVEEPTSGITIYTDGGKQNGEGIAAYVTSNGRTKQKRLG-----PVTHQV 657
Query: 555 AELFALLQSLLTIKELGACKALIITDSLSCLQAITNMFHEN-------PLVKRVQEELSS 607
AE A+ +L ++ + I+TDS C + IT P+++ ++E+
Sbjct: 658 AERMAIQMALEDTRDK---QVNIVTDSYYCWKNITEGLGLEGPQSPWWPIIQNIREK--- 711
Query: 608 IEPSIEFLWCPSHVGIAGNEAADEEAK 634
+ F W P H GI GN+ ADE AK
Sbjct: 712 --EIVYFAWVPGHKGICGNQLADEAAK 736
>sp|P03371|POL_EIAVY Pol polyprotein OS=Equine infectious anemia virus (strain Wyoming)
GN=pol PE=3 SV=1
Length = 1145
Score = 58.9 bits (141), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 46/147 (31%), Positives = 72/147 (48%), Gaps = 23/147 (15%)
Query: 498 QMFQNEFKNKLAENFQSHIKIYTDGSK-NEQGVGCALTIPEKNIAKRFGLNKNASIFH-- 554
Q+ ++++ KL E S I IYTDG K N +G+ +T + KR G + H
Sbjct: 602 QVVHDDWRMKLVEEPTSGITIYTDGGKQNGEGIAAYVTSNGRTKQKRLG-----PVTHQV 656
Query: 555 AELFALLQSLLTIKELGACKALIITDSLSCLQAITNMFH----ENP---LVKRVQEELSS 607
AE A+ +L ++ + I+TDS C + IT +NP +++ ++E+
Sbjct: 657 AERMAIQMALEDTRDK---QVNIVTDSYYCWKNITEGLGLEGPQNPWWPIIQNIREK--- 710
Query: 608 IEPSIEFLWCPSHVGIAGNEAADEEAK 634
+ F W P H GI GN+ ADE AK
Sbjct: 711 --EIVYFAWVPGHKGIYGNQLADEAAK 735
>sp|Q03271|PO13_NASVI Retrovirus-related Pol polyprotein from type-1 retrotransposable
element R1 3 (Fragment) OS=Nasonia vitripennis PE=4 SV=1
Length = 383
Score = 56.6 bits (135), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 32/143 (22%), Positives = 64/143 (44%), Gaps = 3/143 (2%)
Query: 202 FVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSI 261
F DD + + + L E++ + + + G+ S K+ C++ LN +
Sbjct: 4 FADDLLLLVQGNRRNELEQSASEALSVVYRYGTNIGVEVSDSKTVCMMLKGSLNMLNRVV 63
Query: 262 NL---NMYDTRIEVVDTFKFLGLTFDKKMTWKVHLKNLKQSCLSRSRILKILSKKAWAAD 318
++ M D RI VD ++LG+ M + VH+ +K+ + L+ + +K+W
Sbjct: 64 HVSTNGMDDKRIRCVDRVRYLGVNVGIGMDFSVHIDGMKRRLTTAIMRLRGVLRKSWGLK 123
Query: 319 RKMLIRIYKSLIRSKLDYGCPVY 341
R ++ + K L + YG V+
Sbjct: 124 RGVVSMVVKGLFLPAVMYGASVW 146
>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 = 50.8 bits (120), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 40/116 (34%), Positives = 61/116 (52%), Gaps = 9/116 (7%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + E+ K L++ + AEL A+L +L KE I
Sbjct: 1027 YVDGAANRETKLGKAGYVTEQGKQKIIKLDETTN-QKAELMAILLALQDSKET----VNI 1081
Query: 578 ITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L I++ E+P+V+++ EEL+ E + W P+H GI GNE D+
Sbjct: 1082 VTDSQYALGVISSQPTQSESPIVQQIIEELTKKE-QVYLTWVPAHKGIGGNEKIDK 1136
>sp|P16425|Y2R2_DROME Putative 115 kDa protein in type-1 retrotransposable element R1DM
OS=Drosophila melanogaster PE=4 SV=1
Length = 1021
Score = 50.1 bits (118), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 33/172 (19%), Positives = 71/172 (41%), Gaps = 3/172 (1%)
Query: 170 GIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKL 229
G PQG + ++ I ++ + + P S + DD + ++ VL + + +
Sbjct: 631 GCPQGSISGPFIWDILMDVLLQRLQPYCQLSAYADDLLLLVEGNSRAVLEEKGAQLMSIV 690
Query: 230 ENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTFDKKMTW 289
E + + G S K+ +L ++ T + + V + ++LG+T + M +
Sbjct: 691 ETWGAEVGDCLSTSKTVIMLLKGALRRAPT---VRFAGRNLPYVRSCRYLGITVSEGMKF 747
Query: 290 KVHLKNLKQSCLSRSRILKILSKKAWAADRKMLIRIYKSLIRSKLDYGCPVY 341
H+ +L+Q L + + W + IY L+ + +G PV+
Sbjct: 748 LTHIASLRQRMTGVVGALARVLRADWGFSPRARRTIYDGLMAPCVLFGAPVW 799
>sp|P19560|POL_BIV29 Gag-Pol polyprotein OS=Bovine immunodeficiency virus (strain R29)
GN=gag-pol PE=1 SV=2
Length = 1475
Score = 48.5 bits (114), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 58/202 (28%), Positives = 85/202 (42%), Gaps = 31/202 (15%)
Query: 454 KKNLETIIPFNNIMVKTTPKEPWLLKPPICDLSLSSYKKENVPAQMFQNEFK-------- 505
KK L T+ N +V T +E L P + ++ +KE Q+F +F
Sbjct: 934 KKILRTMNELNRTVVIMTGREASFLLPGSSEDWEAALQKEESLTQIFPVKFYRHSCRWTS 993
Query: 506 --NKLAENFQSHIKIYTDGSKNEQGVGCALTIPEKNIAKRF-GLNKNASIFHAELFALLQ 562
+ EN ++ YTDG K + + +K F G N+ AEL A+
Sbjct: 994 ICGPVRENLTTY---YTDGGKKGKTAAAVYWCEGRTKSKVFPGTNQ-----QAELKAICM 1045
Query: 563 SLLTIKELGACKALIITDSLSCLQAITNMFHENPLVKR--VQEELSSIEPSIEFL---WC 617
+LL G K IITDS A M E R + E++ I P +++ W
Sbjct: 1046 ALLD----GPPKMNIITDSRY---AYEGMREEPETWAREGIWLEIAKILPFKQYVGVGWV 1098
Query: 618 PSHVGIAGNEAADEEAKQAINN 639
P+H GI GN ADE K+A+
Sbjct: 1099 PAHKGIGGNTEADEGVKKALEQ 1120
>sp|Q03277|PO11_SCICO Retrovirus-related Pol polyprotein from type-1 retrotransposable
element R1 (Fragment) OS=Sciara coprophila PE=4 SV=1
Length = 1004
Score = 48.1 bits (113), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/173 (19%), Positives = 68/173 (39%), Gaps = 2/173 (1%)
Query: 170 GIPQGGVVSGTLFAIAINSIT-SYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDK 228
G PQG ++ + +N + + + F DD I ++ L + +
Sbjct: 604 GCPQGSKSGPAMWKLVMNELLLALVAAGFFIVAFADDGTIVIGANSRSALEELGTRCLQL 663
Query: 229 LENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTFDKKMT 288
+ + S K+ C+L + + N + + T I K LG+ ++M
Sbjct: 664 CHEWGKRVCVPVSAGKTTCILM-KGHLSANRPPCIRLNGTSISYKSEVKHLGIFVAERMN 722
Query: 289 WKVHLKNLKQSCLSRSRILKILSKKAWAADRKMLIRIYKSLIRSKLDYGCPVY 341
++ H L+ L L+ + +K+W R+ +YK L + + YG V+
Sbjct: 723 FRPHFVYLRGKILGLVGCLRRVMRKSWGLGRRATCILYKGLFVACMSYGASVW 775
>sp|Q9NBX4|RTXE_DROME Probable RNA-directed DNA polymerase from transposon X-element
OS=Drosophila melanogaster GN=X-element\ORF2 PE=3 SV=1
Length = 908
Score = 47.8 bits (112), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 37/196 (18%), Positives = 86/196 (43%), Gaps = 22/196 (11%)
Query: 160 TLSEDFSIVCGIPQGGVVSGTLFAIAIN-----SITSYIHPSLSSSLFVDDFAIFTRDKN 214
+S + ++ G+PQG V+ L+ + + ++ Y L++ F DD + R +
Sbjct: 629 AISTEHNVAAGVPQGSVLGPLLYCLYSHDMPQPDVSLYGKSMLAT--FADDVCVTYRSRC 686
Query: 215 KEVLVSIMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVD 274
+ +Q+ + ++ + + KS V F+ K + T + + + + +
Sbjct: 687 EHDAADGIQDFAYRFSEWARRWNIGINSSKSNNVCFTLKRR---TPPPVYIEEVPVPQPN 743
Query: 275 TFKFLGLTFDKKMTWKVHLKNLKQSCLSRSRILKILSKKAWAADRKML------IRIYKS 328
K+LG+ D+++T+ H+ ++ R+R+ ++K W + + IYK
Sbjct: 744 AAKYLGVLLDRRLTFSKHVTDI------RTRLRAKVAKHYWLLSSRSKLSLSNKLTIYKQ 797
Query: 329 LIRSKLDYGCPVYNSA 344
++ YGC ++ A
Sbjct: 798 ILAPNWKYGCQIWGLA 813
>sp|Q82851|POL_JEMBR Gag-Pol polyprotein OS=Jembrana disease virus GN=gag-pol PE=3 SV=1
Length = 1432
Score = 46.6 bits (109), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 40/128 (31%), Positives = 55/128 (42%), Gaps = 14/128 (10%)
Query: 519 YTDGSKNEQGVGCALTIPEKNIAKRF-GLNKNASIFHAELFALLQSLLTIKELGACKALI 577
YTDG K A K + F G N+ AEL A+L +L + G K I
Sbjct: 966 YTDGGKKGSKAAAAYWREGKIRREVFPGTNQ-----QAELKAVLMAL----QDGPAKMNI 1016
Query: 578 ITDSLSCLQAITN---MFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
ITDS + + + L K + EEL E + W P H GI GN D+E +
Sbjct: 1017 ITDSRYAFEGMREEPETWGREGLWKEIGEELRRKE-YVGVSWVPGHKGIGGNTEVDQEVQ 1075
Query: 635 QAINNDVT 642
+A+ +T
Sbjct: 1076 KALQGPIT 1083
>sp|Q03269|PO11_NASVI Retrovirus-related Pol polyprotein from type-1 retrotransposable
element R1 (Fragment) OS=Nasonia vitripennis PE=4 SV=1
Length = 337
Score = 43.9 bits (102), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 29/177 (16%), Positives = 78/177 (44%), Gaps = 6/177 (3%)
Query: 170 GIPQGGVVSGTLFAIAINSITSYIHPSLSSSL--FVDDFAIFTRDKNKEVLVSIMQESID 227
G PQG + ++ + +N + + +++ + + DD I ++ + + E +
Sbjct: 1 GCPQGSISGPYMWNLCMNGLLDRL-SAMNERIVAYADDLMIVANGNSRMEMERMADECMR 59
Query: 228 KLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYD---TRIEVVDTFKFLGLTFD 284
+ + + G+ S +K+ C++ K + + + + + I V + ++LG+
Sbjct: 60 IVYEWGREVGVSISEKKTVCIMLKGKLNVDGRRMRVAVAEGTISSIGYVKSARYLGVCMG 119
Query: 285 KKMTWKVHLKNLKQSCLSRSRILKILSKKAWAADRKMLIRIYKSLIRSKLDYGCPVY 341
++M++ ++ L + L+ + +K W +K K L+ + + YG V+
Sbjct: 120 ERMSFADDIRGLITKVMGAIGGLRRVMRKEWGVKKKTAYTWAKGLLLAGVMYGSSVW 176
>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 = 43.9 bits (102), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 37/116 (31%), Positives = 59/116 (50%), Gaps = 9/116 (7%)
Query: 519 YTDGSKNEQG-VGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N +G A + E+ L + + AEL A+L +L KE + I
Sbjct: 1029 YVDGAANRNTKLGKAGYVTEQGKQNIIKLEETTN-QKAELMAVLIALQDSKE----QVNI 1083
Query: 578 ITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L I++ ++P+V+++ EEL+ E + W P+H GI GNE D+
Sbjct: 1084 VTDSQYVLGIISSQPTQSDSPIVQQIIEELTKKE-RVYLTWVPAHKGIGGNEKIDK 1138
>sp|C3LPN8|RNH_VIBCM Ribonuclease H OS=Vibrio cholerae serotype O1 (strain M66-2)
GN=rnhA PE=3 SV=1
Length = 156
Score = 43.1 bits (100), Expect = 0.008, Method: Composition-based stats.
Identities = 40/145 (27%), Positives = 61/145 (42%), Gaps = 25/145 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G + EK +A+ + L N + E+ A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGIVMRYKQVEKTLARGYRLTTNNRM---EMLAAVMALQALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFHENPL-------VKRVQE-------ELSSIEPSIEF 614
E C+ ++ TDS Q IT H L K V+ + + +E+
Sbjct: 61 E--PCRVILTTDSQYVRQGITQWIHNWKLRGWKTADKKPVKNADLWQALDKETARHQVEW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQAINN 639
W H G NE DE A+QA N
Sbjct: 119 RWVKGHAGHRENEMCDELARQAAEN 143
>sp|Q9KPX8|RNH_VIBCH Ribonuclease HI OS=Vibrio cholerae serotype O1 (strain ATCC 39315 /
El Tor Inaba N16961) GN=rnhA PE=3 SV=1
Length = 156
Score = 43.1 bits (100), Expect = 0.008, Method: Composition-based stats.
Identities = 40/145 (27%), Positives = 61/145 (42%), Gaps = 25/145 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G + EK +A+ + L N + E+ A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGIVMRYKQVEKTLARGYRLTTNNRM---EMLAAVMALQALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFHENPL-------VKRVQE-------ELSSIEPSIEF 614
E C+ ++ TDS Q IT H L K V+ + + +E+
Sbjct: 61 E--PCRVILTTDSQYVRQGITQWIHNWKLRGWKTADKKPVKNADLWQALDKETARHQVEW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQAINN 639
W H G NE DE A+QA N
Sbjct: 119 RWVKGHAGHRENEMCDELARQAAEN 143
>sp|A5F633|RNH_VIBC3 Ribonuclease H OS=Vibrio cholerae serotype O1 (strain ATCC 39541 /
Ogawa 395 / O395) GN=rnhA PE=3 SV=1
Length = 156
Score = 43.1 bits (100), Expect = 0.008, Method: Composition-based stats.
Identities = 40/145 (27%), Positives = 61/145 (42%), Gaps = 25/145 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G + EK +A+ + L N + E+ A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGIVMRYKQVEKTLARGYRLTTNNRM---EMLAAVMALQALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFHENPL-------VKRVQE-------ELSSIEPSIEF 614
E C+ ++ TDS Q IT H L K V+ + + +E+
Sbjct: 61 E--PCRVILTTDSQYVRQGITQWIHNWKLRGWKTADKKPVKNADLWQALDKETARHQVEW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQAINN 639
W H G NE DE A+QA N
Sbjct: 119 RWVKGHAGHRENEMCDELARQAAEN 143
>sp|A4SPI4|RNH_AERS4 Ribonuclease H OS=Aeromonas salmonicida (strain A449) GN=rnhA PE=3
SV=1
Length = 154
Score = 43.1 bits (100), Expect = 0.009, Method: Composition-based stats.
Identities = 46/142 (32%), Positives = 58/142 (40%), Gaps = 25/142 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIPE--KNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
HI +YTDGS G G L + K I+ F L N + EL A + L T+
Sbjct: 4 HIDLYTDGSCLGNPGPGGYGAVLVYGDHRKEISGGFRLTTNNRM---ELMAAIMGLRTLN 60
Query: 569 ELGACKALIITDSLSCLQAITN----------MFHENPLVKRVQ--EELSS--IEPSIEF 614
AC+ + TDS Q IT M VK V +EL + IE+
Sbjct: 61 --AACQVRLTTDSQYVRQGITQWIIGWKKKGWMTSNRQPVKNVDLWKELDAEVARHQIEW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQA 636
LW H G NE DE A+ A
Sbjct: 119 LWVKGHSGHPENERCDELARDA 140
>sp|A7MY21|RNH_VIBHB Ribonuclease H OS=Vibrio harveyi (strain ATCC BAA-1116 / BB120)
GN=rnhA PE=3 SV=1
Length = 154
Score = 43.1 bits (100), Expect = 0.009, Method: Composition-based stats.
Identities = 42/147 (28%), Positives = 63/147 (42%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
H++I+TDGS G G L EK +AK + L N + E+ A + +L T+K
Sbjct: 4 HVEIFTDGSCLGNPGPGGYGIVLRYKQTEKTLAKGYTLTTNNRM---EMLAAVVALQTLK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ + TDS Q IT H + P L + + +E + +
Sbjct: 61 E--PCQVTLTTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNADLWQALDKE--TARHKV 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 DWHWVKGHAGHRENEICDELARTAAEN 143
>sp|Q95SX7|RTBS_DROME Probable RNA-directed DNA polymerase from transposon BS
OS=Drosophila melanogaster GN=RTase PE=2 SV=1
Length = 906
Score = 42.7 bits (99), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 43/189 (22%), Positives = 79/189 (41%), Gaps = 19/189 (10%)
Query: 169 CGIPQGGVVSGTLFAIAINSI---TSYIHPSLSSSL---FVDDFAIFTRDKNKEVLVSIM 222
G+PQG V+ L+++ + +Y +L + DD A+ +
Sbjct: 639 AGVPQGSVLGPLLYSVFTADLPCPNAYHMADPRKALLATYADDIALLYSSNCCNEAARGL 698
Query: 223 QESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLT 282
QE + L + L +PQK+ F+ K T+ + + ++ K+LG+T
Sbjct: 699 QEYLTTLAAWCKRWILKVNPQKTINPCFTLKTLSPVTA-PIELEGVILDQPSQAKYLGIT 757
Query: 283 FDKKMTWKVHLKNLKQSCLSRSRILKILSKKAWAADRK--MLIR----IYKSLIRSKLDY 336
DK++T+ HLK + C R + L+ W +RK M +R +Y + Y
Sbjct: 758 LDKRLTFGPHLKATTRRCYQRMQQLR------WLLNRKSTMTLRAKRAVYVHCVAPIWLY 811
Query: 337 GCPVYNSAS 345
G ++ A+
Sbjct: 812 GIQIWGIAA 820
>sp|Q87MG2|RNH_VIBPA Ribonuclease HI OS=Vibrio parahaemolyticus serotype O3:K6 (strain
RIMD 2210633) GN=rnhA PE=3 SV=1
Length = 154
Score = 42.0 bits (97), Expect = 0.017, Method: Composition-based stats.
Identities = 41/147 (27%), Positives = 64/147 (43%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
H++I+TDGS G G L EK ++K + L N + E+ A + +L T+K
Sbjct: 4 HVEIFTDGSCLGNPGPGGYGIVLRYKDVEKTLSKGYTLTTNNRM---EMLAAVVALQTLK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ + TDS Q IT H + P L + + +E + + +
Sbjct: 61 E--PCRVTLTTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNADLWQALDKETARHQ--V 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 DWHWVKGHAGHRENEICDELARTAAEN 143
>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 = 42.0 bits (97), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 40/119 (33%), Positives = 58/119 (48%), Gaps = 17/119 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + ++ K + +N + AEL A+L L ++E G +A I
Sbjct: 1038 YVDGAANKETKLGKAGFVTDRGRQKVVSI-ENTTNQKAELQAIL---LALQESGQ-EANI 1092
Query: 578 ITDSLSCLQAITNMFHENP------LVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAAD 630
+TDS Q + H P LV ++ EEL E + W P+H GI GNE D
Sbjct: 1093 VTDS----QYAMGIIHSQPDKSESDLVGQIIEELIKKE-RVYLSWVPAHKGIGGNEQVD 1146
>sp|P05962|POL_HV2NZ Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype A
(isolate NIH-Z) GN=gag-pol PE=3 SV=3
Length = 1461
Score = 42.0 bits (97), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 41/135 (30%), Positives = 57/135 (42%), Gaps = 9/135 (6%)
Query: 506 NKLAENFQSHIKIYTDGSKNEQGV-GCALTIPEKNIAKRFGLNKNASIFHAELFALLQSL 564
N + E YTDGS N Q G A I ++ R + + + AEL A +L
Sbjct: 1036 NLVGEPVPGAETFYTDGSCNRQSKEGKAGYITDRG-RDRVKVLEQTTNQQAELEAFAMAL 1094
Query: 565 LTIKELGACKALIITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVG 622
KA II DS + + EN +V ++ EE+ E +I W P+H G
Sbjct: 1095 TD----SGPKANIIVDSQYVMGIVAGQPTESENRIVNQIIEEMIKKE-AIYVAWVPAHKG 1149
Query: 623 IAGNEAADEEAKQAI 637
I GN+ D Q I
Sbjct: 1150 IGGNQEVDHLVSQGI 1164
>sp|Q5E3G5|RNH_VIBF1 Ribonuclease H OS=Vibrio fischeri (strain ATCC 700601 / ES114)
GN=rnhA PE=3 SV=1
Length = 157
Score = 41.6 bits (96), Expect = 0.022, Method: Composition-based stats.
Identities = 41/143 (28%), Positives = 59/143 (41%), Gaps = 21/143 (14%)
Query: 515 HIKIYTDGS--KNEQGVGCALTIPEKNIAKRF--GLNKNASIFHAELFALLQSLLTIKEL 570
++I+TDGS N G + + K K F G NK + E+ A + +L +KE
Sbjct: 8 QVEIFTDGSCLGNPGPGGYGIVMRYKGTEKTFSEGFNKTTN-NRMEMLAAVVALRKLKE- 65
Query: 571 GACKALIITDSLSCLQAITNMFH-----------ENPLVKR---VQEELSSIEPSIEFLW 616
C ++ TDS Q IT H + P+V Q + S I++ W
Sbjct: 66 -PCSVILTTDSQYVRQGITQWIHGWKKRDWKKADKKPVVNADLWKQLDAESERHKIDWRW 124
Query: 617 CPSHVGIAGNEAADEEAKQAINN 639
H G NE DE A+ A N
Sbjct: 125 VKGHAGHRENEMCDELARTAAEN 147
>sp|Q8AII1|POL_SIVTN Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate TAN1)
GN=gag-pol PE=3 SV=4
Length = 1462
Score = 41.6 bits (96), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 64/117 (54%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N + G A + + + L +N + AEL+A+ L +K+ GA + I
Sbjct: 1055 YVDGAANRDSKKGRAGYVTNRGRYRSKDL-ENTTNQQAELWAVD---LALKDSGA-QVNI 1109
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS + LQ + + ++P+V+++ ++L+ + +I W P+H GI GNE D+
Sbjct: 1110 VTDSQYVMGVLQGLPDQ-SDSPIVEQIIQKLTQ-KTAIYLAWVPAHKGIGGNEEVDK 1164
>sp|Q2Y8K1|RNH_NITMU Ribonuclease H OS=Nitrosospira multiformis (strain ATCC 25196 /
NCIMB 11849) GN=rnhA PE=3 SV=1
Length = 155
Score = 41.6 bits (96), Expect = 0.028, Method: Composition-based stats.
Identities = 44/150 (29%), Positives = 69/150 (46%), Gaps = 23/150 (15%)
Query: 505 KNKLAENFQSHIKIYTDGS-KNEQGVGCALTIPEKNIAKR--FGLNKNASIFHAELFALL 561
K KLAE ++I+TDG+ K GVG + + N +R FG K + EL A++
Sbjct: 2 KAKLAEV----VEIFTDGACKGNPGVGGWGALLQYNGHRRELFGGEKMTTNNRMELLAVI 57
Query: 562 QSLLTIKELGACKALIITDSLSCLQAITNMFH----------ENPLVKR----VQEELSS 607
++L + + C+ + TDSL + I+ H + VK + +L +
Sbjct: 58 RALEALTK--PCEVRLHTDSLYVQKGISEWIHAWKKRDWRTADKKPVKNDDLWRELDLLT 115
Query: 608 IEPSIEFLWCPSHVGIAGNEAADEEAKQAI 637
IE+LW H G GNE AD A + +
Sbjct: 116 QRHKIEWLWVRGHSGHDGNEYADMLANRGV 145
>sp|P12502|POL_SIVS4 Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate
F236/smH4) GN=gag-pol PE=3 SV=2
Length = 1449
Score = 41.2 bits (95), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 44/137 (32%), Positives = 58/137 (42%), Gaps = 13/137 (9%)
Query: 506 NKLAENFQSHIKIYTDGSKNEQ---GVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQ 562
N + E Q Y DGS N Q G +T ++ AK N AEL A
Sbjct: 1024 NLVKEPIQGAETFYVDGSCNRQSREGKAGYVTDRGRDKAKLLEQTTNQ---QAELEAFY- 1079
Query: 563 SLLTIKELGACKALIITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSH 620
L + + G KA II DS + I E+ LV ++ EE+ E +I W P+H
Sbjct: 1080 --LALADSGP-KANIIVDSQYVMGIIAGQPTESESRLVNQIIEEMIKKE-AIYVAWVPAH 1135
Query: 621 VGIAGNEAADEEAKQAI 637
GI GN+ D Q I
Sbjct: 1136 KGIGGNQEVDHLVSQGI 1152
>sp|Q5HSF7|RNH_CAMJR Ribonuclease H OS=Campylobacter jejuni (strain RM1221) GN=rnhA PE=3
SV=1
Length = 146
Score = 40.8 bits (94), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 63/135 (46%), Gaps = 16/135 (11%)
Query: 515 HIKIYTDGS--KNEQGVGCALTIPEKNIAKR-FGLNKNASIFHAELFALLQSLLTIKELG 571
HI+IYTDGS N G A + K K FG N + EL A+++SL +KE
Sbjct: 3 HIEIYTDGSCLNNPGFGGWAYILRYKEYQKEGFGAEANTTNNRMELMAIIESLKALKE-- 60
Query: 572 ACKALIITDSLSCLQAITNMFHENPLVKRVQ--------EELSSIEPS--IEFLWCPSHV 621
C+ + TDS +Q+I N + E + K + +E + S I+ W +H
Sbjct: 61 PCEISLFTDSNLMVQSI-NEWLEGWIKKDFKGKKNIDLWKEYIKVAKSHKIKAFWVKAHN 119
Query: 622 GIAGNEAADEEAKQA 636
G NE D A++A
Sbjct: 120 GHLENERCDTLAREA 134
>sp|A1W1N8|RNH_CAMJJ Ribonuclease H OS=Campylobacter jejuni subsp. jejuni serotype
O:23/36 (strain 81-176) GN=rnhA PE=3 SV=1
Length = 146
Score = 40.8 bits (94), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 63/135 (46%), Gaps = 16/135 (11%)
Query: 515 HIKIYTDGS--KNEQGVGCALTIPEKNIAKR-FGLNKNASIFHAELFALLQSLLTIKELG 571
HI+IYTDGS N G A + K K FG N + EL A+++SL +KE
Sbjct: 3 HIEIYTDGSCLNNPGFGGWAYILRYKEYQKEGFGAEANTTNNRMELMAIIESLKALKE-- 60
Query: 572 ACKALIITDSLSCLQAITNMFHENPLVKRVQ--------EELSSIEPS--IEFLWCPSHV 621
C+ + TDS +Q+I N + E + K + +E + S I+ W +H
Sbjct: 61 PCEISLFTDSNLMVQSI-NEWLEGWIKKDFKGKKNIDLWKEYIKVAKSHKIKAFWVKAHN 119
Query: 622 GIAGNEAADEEAKQA 636
G NE D A++A
Sbjct: 120 GHLENERCDTLAREA 134
>sp|Q9PM39|RNH_CAMJE Ribonuclease HI OS=Campylobacter jejuni subsp. jejuni serotype O:2
(strain NCTC 11168) GN=rnhA PE=1 SV=1
Length = 146
Score = 40.8 bits (94), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 63/135 (46%), Gaps = 16/135 (11%)
Query: 515 HIKIYTDGS--KNEQGVGCALTIPEKNIAKR-FGLNKNASIFHAELFALLQSLLTIKELG 571
HI+IYTDGS N G A + K K FG N + EL A+++SL +KE
Sbjct: 3 HIEIYTDGSCLNNPGFGGWAYILRYKEYQKEGFGAEANTTNNRMELMAIIESLKALKE-- 60
Query: 572 ACKALIITDSLSCLQAITNMFHENPLVKRVQ--------EELSSIEPS--IEFLWCPSHV 621
C+ + TDS +Q+I N + E + K + +E + S I+ W +H
Sbjct: 61 PCEISLFTDSNLMVQSI-NEWLEGWIKKDFKGKKNIDLWKEYIKVAKSHKIKAFWVKAHN 119
Query: 622 GIAGNEAADEEAKQA 636
G NE D A++A
Sbjct: 120 GHLENERCDTLAREA 134
>sp|A8FNU8|RNH_CAMJ8 Ribonuclease H OS=Campylobacter jejuni subsp. jejuni serotype O:6
(strain 81116 / NCTC 11828) GN=rnhA PE=3 SV=1
Length = 146
Score = 40.8 bits (94), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 63/135 (46%), Gaps = 16/135 (11%)
Query: 515 HIKIYTDGS--KNEQGVGCALTIPEKNIAKR-FGLNKNASIFHAELFALLQSLLTIKELG 571
HI+IYTDGS N G A + K K FG N + EL A+++SL +KE
Sbjct: 3 HIEIYTDGSCLNNPGFGGWAYILRYKEYQKEGFGAEANTTNNRMELMAIIESLKALKE-- 60
Query: 572 ACKALIITDSLSCLQAITNMFHENPLVKRVQ--------EELSSIEPS--IEFLWCPSHV 621
C+ + TDS +Q+I N + E + K + +E + S I+ W +H
Sbjct: 61 PCEISLFTDSNLMVQSI-NEWLEGWIKKDFKGKKNIDLWKEYIKVAKSHKIKAFWVKAHN 119
Query: 622 GIAGNEAADEEAKQA 636
G NE D A++A
Sbjct: 120 GHLENERCDTLAREA 134
>sp|P19505|POL_SIVSP Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate
PBj14/BCL-3) GN=gag-pol PE=1 SV=2
Length = 1449
Score = 40.8 bits (94), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 43/137 (31%), Positives = 58/137 (42%), Gaps = 13/137 (9%)
Query: 506 NKLAENFQSHIKIYTDGSKNEQ---GVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQ 562
N + E Q Y DGS N Q G +T ++ AK N AEL A
Sbjct: 1024 NLVKEPIQGAETFYVDGSCNRQSREGKAGYVTDRGRDKAKLLEQTTNQ---QAELEAFY- 1079
Query: 563 SLLTIKELGACKALIITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSH 620
L + + G KA II DS + + E+ LV ++ EE+ E +I W P+H
Sbjct: 1080 --LALADSGP-KANIIVDSQYVMGIVAGQPTESESRLVNQIIEEMIKKE-AIYVAWVPAH 1135
Query: 621 VGIAGNEAADEEAKQAI 637
GI GN+ D Q I
Sbjct: 1136 KGIGGNQEVDHLVSQGI 1152
>sp|Q73K21|RNH_TREDE Ribonuclease H OS=Treponema denticola (strain ATCC 35405 / CIP
103919 / DSM 14222) GN=rnhA PE=3 SV=1
Length = 160
Score = 40.4 bits (93), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 47/154 (30%), Positives = 70/154 (45%), Gaps = 32/154 (20%)
Query: 515 HIKIYTDG--SKNEQGVGCALTIPEKN----IAKRFGLNKNASIFHAELFALLQSLLTIK 568
+I+IYTDG SKN G A + K+ I + G K+ + EL A++++L IK
Sbjct: 2 NIEIYTDGACSKNPGPGGWAYIMVNKDSKEEICRENGGEKSTTNNRMELMAVIRALKKIK 61
Query: 569 ELGAC------KAL------IITDSLSCLQAITNMF-----------HENPLVKR-VQEE 604
E A KAL + TDS Q I++ + P+ + + +E
Sbjct: 62 EGAASLADKSGKALDYKSISVHTDSQYVQQGISSWIFNWKKNNWKTASKQPVKNQDLWQE 121
Query: 605 LSSIEPSI--EFLWCPSHVGIAGNEAADEEAKQA 636
L S+ SI E++W H G NEA D A +A
Sbjct: 122 LDSLSASIKPEWIWVKGHAGNPLNEACDRLAVEA 155
>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 = 40.0 bits (92), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 39/120 (32%), Positives = 53/120 (44%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E G A + +K K L + HA AL S L +
Sbjct: 1025 YVDGASNRETKTGKAGYVTDKGRQKVVTLTDTTNQKTELHAIYLALRDSGLEVN------ 1078
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ EEL E + W P+H GI GNE D+
Sbjct: 1079 --IVTDSQYALGIIQAQPDK-SESELVNQIIEELIKKE-KVYLSWVPAHKGIGGNEQVDK 1134
>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 = 40.0 bits (92), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 39/122 (31%), Positives = 54/122 (44%), Gaps = 9/122 (7%)
Query: 519 YTDGSKNEQGV-GCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
YTDGS N Q G A + ++ K L + + AEL A +L KA I
Sbjct: 1050 YTDGSCNRQSKEGKAGYVTDRGRDKVKILEQTTN-QQAELEAFAMALTD----SGPKANI 1104
Query: 578 ITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQ 635
I DS + + EN +V ++ EE+ E +I W P+H GI GN+ D Q
Sbjct: 1105 IVDSQYVMGIVAGQPTESENRIVNQIIEEMIKKE-AIYVAWVPAHKGIGGNQEVDHLVSQ 1163
Query: 636 AI 637
I
Sbjct: 1164 GI 1165
>sp|Q1A249|POL_SIVEK Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate EK505)
GN=gag-pol PE=3 SV=3
Length = 1448
Score = 39.7 bits (91), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 37/120 (30%), Positives = 57/120 (47%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + ++ K +++ + AEL A+L +L + + I
Sbjct: 1037 YVDGAANRETKLGKAGFVTDRGRQKVTSISETTN-QQAELQAVLMAL----QDAGQEVNI 1091
Query: 578 ITDSLSCLQAITNMFHENP------LVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS Q + + H P LV ++ EEL E I W P+H GI GNE D+
Sbjct: 1092 VTDS----QYVLGIIHSQPDKSESELVNQIIEELIKKE-RIYLSWVPAHKGIGGNEQIDK 1146
>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 = 39.7 bits (91), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 9/116 (7%)
Query: 519 YTDGSKNEQGV-GCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N Q G A I ++ +R +N + AEL A+ +L E K I
Sbjct: 1054 YVDGACNRQSKEGKAGYITQQG-KQRVQQLENTTNQQAELTAIKMAL----EDSGPKVNI 1108
Query: 578 ITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS + +T ++PLV+++ ++ E +I W P+H GI GNE D+
Sbjct: 1109 VTDSQYAMGILTAQPTQSDSPLVEQIIAQMVQKE-AIYLQWVPAHKGIGGNEEIDK 1163
>sp|Q7MII6|RNH_VIBVY Ribonuclease H OS=Vibrio vulnificus (strain YJ016) GN=rnhA PE=3
SV=1
Length = 155
Score = 39.7 bits (91), Expect = 0.11, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 62/147 (42%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK +A+ + L N + E+ A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGVVLRYKQVEKTLAQGYRLTTNNRM---EMMATIVALQALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C ++ TDS Q IT H + P L + + +E + +I
Sbjct: 61 E--PCNVILTTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNADLWQALDKE--TTRHTI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 DWRWVKGHAGHRENEMCDELARAAAEN 143
>sp|Q8DBD5|RNH_VIBVU Ribonuclease HI OS=Vibrio vulnificus (strain CMCP6) GN=rnhA PE=3
SV=1
Length = 155
Score = 39.7 bits (91), Expect = 0.11, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 62/147 (42%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK +A+ + L N + E+ A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGVVLRYKQVEKTLAQGYRLTTNNRM---EMMATIVALQALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C ++ TDS Q IT H + P L + + +E + +I
Sbjct: 61 E--PCNVILTTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNADLWQALDKE--TTRHTI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 DWRWVKGHAGHRENEMCDELARAAAEN 143
>sp|Q74120|POL_HV2KR Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype A
(isolate KR) GN=gag-pol PE=3 SV=3
Length = 1463
Score = 39.3 bits (90), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 39/122 (31%), Positives = 54/122 (44%), Gaps = 9/122 (7%)
Query: 519 YTDGSKNEQGV-GCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
YTDGS N Q G A I ++ K L + + AEL A +L KA I
Sbjct: 1051 YTDGSCNRQSKEGKAGYITDRGRDKVRILEQTTN-QQAELEAFAMALTD----SGPKANI 1105
Query: 578 ITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQ 635
I DS + + E+ LV ++ EE+ E ++ W P+H GI GN+ D Q
Sbjct: 1106 IVDSQYVMGIVAGQPTESESKLVNQIIEEMIKKE-TLYVAWVPAHKGIGGNQEVDHLVSQ 1164
Query: 636 AI 637
I
Sbjct: 1165 GI 1166
>sp|A1VMW5|RNH_POLNA Ribonuclease H OS=Polaromonas naphthalenivorans (strain CJ2)
GN=rnhA PE=3 SV=1
Length = 161
Score = 39.3 bits (90), Expect = 0.14, Method: Composition-based stats.
Identities = 40/142 (28%), Positives = 60/142 (42%), Gaps = 21/142 (14%)
Query: 515 HIKIYTDGS-KNEQGVGC--ALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELG 571
H+ IYTDG+ K G G AL + FG + E+ A++++L +K+
Sbjct: 15 HVVIYTDGACKGNPGPGGWGALLASGGTEKEIFGGEMGTTNNRMEMTAVIEALAALKK-- 72
Query: 572 ACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSIEFL 615
C + DS L+ IT H + P L +R+ L S SI++
Sbjct: 73 PCTVTLYLDSQYVLKGITEWIHGWKARGWRTAAKAPVKNVDLWQRLDALLVSSGHSIDWR 132
Query: 616 WCPSHVGIAGNEAADEEAKQAI 637
W H G GNE AD A + +
Sbjct: 133 WVRGHNGDPGNERADALANKGV 154
>sp|A4W6V4|RNH_ENT38 Ribonuclease H OS=Enterobacter sp. (strain 638) GN=rnhA PE=3 SV=1
Length = 155
Score = 38.9 bits (89), Expect = 0.14, Method: Composition-based stats.
Identities = 44/149 (29%), Positives = 61/149 (40%), Gaps = 29/149 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + L N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGHEKTFNEGYHLTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C +I TDS Q IT H + P L KR+ LS +I
Sbjct: 61 E--DCDVVISTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWKRLDAALS--HHTI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINNDV 641
++ W H G NE DE A+ A N +
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMNPI 145
>sp|C5BEV5|RNH_EDWI9 Ribonuclease H OS=Edwardsiella ictaluri (strain 93-146) GN=rnhA
PE=3 SV=1
Length = 154
Score = 38.9 bits (89), Expect = 0.16, Method: Composition-based stats.
Identities = 41/142 (28%), Positives = 61/142 (42%), Gaps = 25/142 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK ++ + L N + EL A + +L T+
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRQHEKALSAGYRLTTNNRM---ELMAAIVALETLT 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH----------ENPLVKRV---QEELSSIEP-SIEF 614
AC+ + +DS Q IT H + VK V Q +I P +E+
Sbjct: 61 S--ACQVALFSDSQYVRQGITQWIHGWKRRDWKTADKKPVKNVDLWQRLDQAIGPHQVEW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQA 636
+W H G NE DE A++A
Sbjct: 119 IWIKGHAGHPENERCDELARRA 140
>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 = 0.17, Method: Compositional matrix adjust.
Identities = 39/124 (31%), Positives = 53/124 (42%), Gaps = 13/124 (10%)
Query: 519 YTDGSKNEQ---GVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKA 575
YTDGS N Q G +T K+ K+ N AEL A +L K
Sbjct: 1052 YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQ---QAELEAFAMALTD----SGPKV 1104
Query: 576 LIITDS--LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEA 633
II DS + + A E+ +V ++ EE+ E +I W P+H GI GN+ D
Sbjct: 1105 NIIVDSQYVMGISASQPTESESKIVNQIIEEMIKKE-AIYVAWVPAHKGIGGNQEVDHLV 1163
Query: 634 KQAI 637
Q I
Sbjct: 1164 SQGI 1167
>sp|Q9I2S9|RNH_PSEAE Ribonuclease HI OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1
/ 1C / PRS 101 / LMG 12228) GN=rnhA PE=3 SV=1
Length = 148
Score = 38.5 bits (88), Expect = 0.19, Method: Composition-based stats.
Identities = 38/145 (26%), Positives = 63/145 (43%), Gaps = 25/145 (17%)
Query: 513 QSHIKIYTDGS-KNEQGVGC--ALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
+ + IYTDG+ K G G AL + + + +G + + EL A +Q+L +K
Sbjct: 4 KEQVVIYTDGACKGNPGRGGWGALLLYKGAERELWGGEPDTTNNRMELMAAIQALAALKR 63
Query: 570 LGACKALIITDSLSCLQAITNMFHENPLVKRVQEELSSIEP-----------------SI 612
+C +ITDS ++ IT P K+ + +S +P +
Sbjct: 64 --SCPIRLITDSEYVMRGITEWL---PNWKKRGWKTASKQPVKNADLWQALDEQVARHQV 118
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAI 637
E+ W H G GNE AD+ A + +
Sbjct: 119 EWQWVRGHTGDPGNERADQLANRGV 143
>sp|Q02KV8|RNH_PSEAB Ribonuclease H OS=Pseudomonas aeruginosa (strain UCBPP-PA14)
GN=rnhA PE=3 SV=1
Length = 148
Score = 38.5 bits (88), Expect = 0.19, Method: Composition-based stats.
Identities = 38/145 (26%), Positives = 63/145 (43%), Gaps = 25/145 (17%)
Query: 513 QSHIKIYTDGS-KNEQGVGC--ALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
+ + IYTDG+ K G G AL + + + +G + + EL A +Q+L +K
Sbjct: 4 KEQVVIYTDGACKGNPGRGGWGALLLYKGAERELWGGEPDTTNNRMELMAAIQALAALKR 63
Query: 570 LGACKALIITDSLSCLQAITNMFHENPLVKRVQEELSSIEP-----------------SI 612
+C +ITDS ++ IT P K+ + +S +P +
Sbjct: 64 --SCPIRLITDSEYVMRGITEWL---PNWKKRGWKTASKQPVKNADLWQALDEQVARHQV 118
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAI 637
E+ W H G GNE AD+ A + +
Sbjct: 119 EWQWVRGHTGDPGNERADQLANRGV 143
>sp|B7VB62|RNH_PSEA8 Ribonuclease H OS=Pseudomonas aeruginosa (strain LESB58) GN=rnhA
PE=3 SV=1
Length = 148
Score = 38.5 bits (88), Expect = 0.19, Method: Composition-based stats.
Identities = 38/145 (26%), Positives = 63/145 (43%), Gaps = 25/145 (17%)
Query: 513 QSHIKIYTDGS-KNEQGVGC--ALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
+ + IYTDG+ K G G AL + + + +G + + EL A +Q+L +K
Sbjct: 4 KEQVVIYTDGACKGNPGRGGWGALLLYKGAERELWGGEPDTTNNRMELMAAIQALAALKR 63
Query: 570 LGACKALIITDSLSCLQAITNMFHENPLVKRVQEELSSIEP-----------------SI 612
+C +ITDS ++ IT P K+ + +S +P +
Sbjct: 64 --SCPIRLITDSEYVMRGITEWL---PNWKKRGWKTASKQPVKNADLWQALDEQVARHQV 118
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAI 637
E+ W H G GNE AD+ A + +
Sbjct: 119 EWQWVRGHTGDPGNERADQLANRGV 143
>sp|P0A2B9|RNH_SALTY Ribonuclease HI OS=Salmonella typhimurium (strain LT2 / SGSC1412 /
ATCC 700720) GN=rnhA PE=3 SV=1
Length = 155
Score = 38.5 bits (88), Expect = 0.19, Method: Composition-based stats.
Identities = 42/147 (28%), Positives = 61/147 (41%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK ++ + L N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGHEKTFSEGYTLTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ + TDS Q IT H + P L KR+ L + I
Sbjct: 61 E--HCEVTLSTDSQYVRQGITQWIHNWKKRGWKTAEKKPVKNVDLWKRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
+++W H G NE DE A+ A N
Sbjct: 117 KWVWVKGHAGHPENERCDELARAAAMN 143
>sp|P0A2C0|RNH_SALTI Ribonuclease HI OS=Salmonella typhi GN=rnhA PE=3 SV=1
Length = 155
Score = 38.5 bits (88), Expect = 0.19, Method: Composition-based stats.
Identities = 42/147 (28%), Positives = 61/147 (41%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK ++ + L N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGHEKTFSEGYTLTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ + TDS Q IT H + P L KR+ L + I
Sbjct: 61 E--HCEVTLSTDSQYVRQGITQWIHNWKKRGWKTAEKKPVKNVDLWKRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
+++W H G NE DE A+ A N
Sbjct: 117 KWVWVKGHAGHPENERCDELARAAAMN 143
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
0.319 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 284,429,507
Number of Sequences: 539616
Number of extensions: 11858728
Number of successful extensions: 31424
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 228
Number of HSP's that attempted gapping in prelim test: 31286
Number of HSP's gapped (non-prelim): 341
length of query: 786
length of database: 191,569,459
effective HSP length: 126
effective length of query: 660
effective length of database: 123,577,843
effective search space: 81561376380
effective search space used: 81561376380
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: 65 (29.6 bits)