RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7164
(2307 letters)
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 842 bits (2176), Expect = 0.0
Identities = 334/654 (51%), Positives = 415/654 (63%), Gaps = 116/654 (17%)
Query: 30 MSVEKIYQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFD 89
+VE+ YQKK+Q+EHILLRPDTYIGS+E TE MW+ + E N M + ITYVPGLYKIFD
Sbjct: 4 KTVEERYQKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLYKIFD 63
Query: 90 EILVNACDNKQRDP---KMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFG 146
EILVNA DNK RD +M IK+T+++E ISV+N+G+GIPV HK+ K++VP MIFG
Sbjct: 64 EILVNAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFG 123
Query: 147 HLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFV 206
HLLTSSNY+D E +VTG GRNG+GAKL NIFS+KF
Sbjct: 124 HLLTSSNYDDTEKRVTG-------------------------GRNGFGAKLTNIFSTKFT 158
Query: 207 VETSCSEYKKSFKQVWKDNMSKVTSPEIKS-GSKDDFTKITFTPDLTKFKMTSLDKDMVD 265
VE S+ K FK W DNMSK + P I S K D+TK+TF PD KF MT D DM+
Sbjct: 159 VECVDSKSGKKFKMTWTDNMSKKSEPRITSYDGKKDYTKVTFYPDYAKFGMTEFDDDMLR 218
Query: 266 LITRRAYDAAASTKDVKVFLNGEKLPVKNFQDYVKLY-TDRQDEDGDPVKIIYENVNPRW 324
L+ +R YD A +KV+LNGE++ +K+F+DYV LY D ++ P +Y +VN RW
Sbjct: 219 LLKKRVYDLAGCFGKLKVYLNGERIAIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNGRW 278
Query: 325 EVAIAPSDRGFQQVSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFG 384
EV ++ SD FQQVSFVNSI TTKGG HV+ ++D ++ ++ E KKK K
Sbjct: 279 EVVVSLSDGQFQQVSFVNSICTTKGGTHVNYILDQLISKLQEKAKKKKK----------- 327
Query: 385 NKFNNVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMT 444
G +KP Q+KNH+W+F+NCLIVNP+FDSQTKE +T
Sbjct: 328 ------------------------KGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLT 363
Query: 445 LQKGSFGSTCV---------------------------------------------PKLE 459
+ FGSTC PKL+
Sbjct: 364 TKPSKFGSTCELSEKLIKYVLKSPILENIVEWAQAKLAAELNKKMKAGKKSRILGIPKLD 423
Query: 460 DANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQIL 519
DANDAG KNS +CTLILTEGDSAK+LA++GL VVGRD YGVFPLRGKLLNVR+A+ KQ++
Sbjct: 424 DANDAGGKNSEECTLILTEGDSAKALALAGLSVVGRDYYGVFPLRGKLLNVRDASLKQLM 483
Query: 520 ENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWP 579
N EI NL KILGL KKY ED K LRYG LMIMTDQD DGSHIKGL+IN IHH WP
Sbjct: 484 NNKEIQNLFKILGLDIGKKY---EDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWP 540
Query: 580 TLLRLP-FLEEFITPIIKATK-AREELSFYSLPEFEEWKEETTNWHTYKIKYYK 631
+LL+ P FL+EFITPI+KATK + +SF+++P+FE+WK +T +KIKYYK
Sbjct: 541 SLLKNPGFLKEFITPIVKATKKGNQVISFFTIPDFEKWK-QTVGLKGWKIKYYK 593
Score = 166 bits (423), Expect = 5e-41
Identities = 59/116 (50%), Positives = 82/116 (70%), Gaps = 1/116 (0%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EP +Y+PIIPMVLVNGAEGIGTG+ T IPN+NP +I+DN++R + GE+ P+ PWY+ F
Sbjct: 803 VEPFYYVPIIPMVLVNGAEGIGTGFSTSIPNYNPLDIIDNLRRRLNGEEVRPLVPWYRGF 862
Query: 720 KGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTLDTLLHGAEKDEV 775
KG I+ +F+ G + D +EITEL +GKWT DYK+ L++ EKD +
Sbjct: 863 KGTIERNPKGKFISKGIYEKVPDGTVEITELPIGKWTEDYKEFLESETL-KEKDVI 917
Score = 97.8 bits (244), Expect = 5e-20
Identities = 67/354 (18%), Positives = 115/354 (32%), Gaps = 37/354 (10%)
Query: 812 ELAKPQKTGPQLERQERQAAEGEDDEAGSQTQEEEDPDKDYDYLLGMTFWSLTMERKNEL 871
++ K + E +E + E D+ + EE YDYLL M WSLT E+ +L
Sbjct: 1050 DIIKKKSEKITAEEEEGAEEDDEADDEDDE--EELGAAVSYDYLLSMPIWSLTKEKVEKL 1107
Query: 872 LKKRDDKMTELNILKKKAPTDLWSDDLDALREKDKIHPCPGGNRTRGLALKRQTRYQPSN 931
+ + K EL LK P D+W +DLD E + + + S
Sbjct: 1108 NAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQ------EEVEEKEIAKEQRLKSK 1161
Query: 932 RVLTSRDEPMVVSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKK 991
+ + + K S K K A+ K SD D +
Sbjct: 1162 TKGKAS--KLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSN 1219
Query: 992 KTAAAKKAKPAKKESEYSSTVCLFKRFGRRNCNDGGLIPKSQREGAQDSDLENNCRLDEV 1051
+ + ++ +K S+V K + + ++D+D E +
Sbjct: 1220 SSGSDQEDDEEQKTKPKKSSVKRLKS-----------KKNNSSKSSEDND-EFSSDDLSK 1267
Query: 1052 ERKEKEEENSNITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAA 1111
E K K S KR S + PS+ ++ K E + A K
Sbjct: 1268 EGKPKNAPKRVSAVQYSPPP---PSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKK 1324
Query: 1112 APKKPNEVLPGWESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEES 1165
+ +A K +S+ R + + ++S R+ +
Sbjct: 1325 KKSEKK------------TARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSE 1366
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 803 bits (2076), Expect = 0.0
Identities = 354/652 (54%), Positives = 425/652 (65%), Gaps = 118/652 (18%)
Query: 31 SVEKIYQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDE 90
++E+ YQKK+QLEHILLRPDTYIGS E T+T+W+ M RE+TYVPGLYKIFDE
Sbjct: 2 TIEETYQKKTQLEHILLRPDTYIGSTEKHTQTLWVYEGGE--MVNREVTYVPGLYKIFDE 59
Query: 91 ILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLT 150
ILVNA DNKQRDP M+ +K+ ++ E NTISV+NNGKGIPV HK+E ++VP +IFGHLLT
Sbjct: 60 ILVNAADNKQRDPSMDSLKVDIDVEQNTISVYNNGKGIPVEIHKEEGVYVPELIFGHLLT 119
Query: 151 SSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETS 210
SSN++D E K TG GRNGYGAKL NIFS++F VET+
Sbjct: 120 SSNFDDNEKKTTG-------------------------GRNGYGAKLANIFSTEFTVETA 154
Query: 211 CSEYKKSFKQVWKDNMSKVTSPEIKS-GSKDDFTKITFTPDLTKFKMTSLDKDMVDLITR 269
K +KQV+ +NMS + P+I S + +++TKITF PDL KF MT LD+D+V L+++
Sbjct: 155 DGNRGKKYKQVFTNNMSVKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVVALMSK 214
Query: 270 RAYDAAA-STKDVKVFLNGEKLPVKNFQDYVKLYTDRQDEDGDPVKIIYENVNPRWEVAI 328
R YD A K +KV LNG+KLPVK+FQDYV LY + DP+ IYE VN RWEV +
Sbjct: 215 RVYDIAGCLGKKLKVELNGKKLPVKSFQDYVGLY-LGPNSREDPLPRIYEKVNDRWEVCV 273
Query: 329 APSDRGFQQVSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFGNKFN 388
+ SD FQQVSFVNSIAT KGG HVD V D IVK I E VKKKNK
Sbjct: 274 SLSDGSFQQVSFVNSIATIKGGTHVDYVADQIVKHIQEKVKKKNK--------------- 318
Query: 389 NVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMTLQKG 448
+KPFQ+KNH+W+F+NCLI NPTFDSQTKE +T +
Sbjct: 319 --------------------NATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPS 358
Query: 449 SFGSTC--------------------------------------------VPKLEDANDA 464
SFGS C +PKL+DANDA
Sbjct: 359 SFGSKCELSEEFLKKVEKCGVVENILSWAQFKQQKELKKKDGAKRQRLTGIPKLDDANDA 418
Query: 465 GTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEI 524
G K S DCTLILTEGDSAK+LA+SGL VVGRD YGVFPLRGKLLNVREA+HKQI++NAEI
Sbjct: 419 GGKKSKDCTLILTEGDSAKALAMSGLSVVGRDHYGVFPLRGKLLNVREASHKQIMKNAEI 478
Query: 525 NNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRL 584
N+ +ILGLQ+ K Y E+ K+LRYG LMIMTDQD DGSHIKGLIINF H WP+LL++
Sbjct: 479 TNIKQILGLQFGKTY-DEENTKSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKI 537
Query: 585 P-FLEEFITPIIKATKAREELSFYSLPEFEEWKE----ETTNWHTYKIKYYK 631
P FL EFITPI+KATK + LSFY++PE+E WKE ET W IKYYK
Sbjct: 538 PGFLVEFITPIVKATKGGKSLSFYTMPEYEAWKESLEGETKGW---TIKYYK 586
Score = 173 bits (441), Expect = 3e-43
Identities = 67/119 (56%), Positives = 82/119 (68%), Gaps = 3/119 (2%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKN 718
IEPEWY PIIPMVLVNG+EGIGTGW T IPN+NPR+I+ NI+R++RGE+ PM PWY+
Sbjct: 795 SIEPEWYCPIIPMVLVNGSEGIGTGWSTFIPNYNPRDIIANIRRLLRGEELEPMHPWYRG 854
Query: 719 FKGEI---DYCGDSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTLDTLLHGAEKDE 774
FKG I + V G I + D + ITEL V KWT DYK+ L+ LL G +K E
Sbjct: 855 FKGTITEVSTSRSGSYTVTGIIEQIGDTTIRITELPVRKWTQDYKEFLEALLTGTKKKE 913
Score = 71.3 bits (175), Expect = 5e-12
Identities = 38/103 (36%), Positives = 47/103 (45%), Gaps = 2/103 (1%)
Query: 802 EEIEEVFHDNELAKPQKTGPQLERQERQAAEGEDDEAGSQTQEEEDPDKDYDYLLGMTFW 861
E+ + K KT E +GE E + E YDYLLGM
Sbjct: 1033 AELLAELEEKGFDKFPKTAKISETNVVGDRDGEASEEEEASDNELAKS--YDYLLGMPIS 1090
Query: 862 SLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDALREK 904
SLT+E+ +EL +R K TE+ LKK P DLW DLDA E
Sbjct: 1091 SLTLEKVDELRAERAKKETEVEELKKTTPEDLWRKDLDAFEEA 1133
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 725 bits (1874), Expect = 0.0
Identities = 338/671 (50%), Positives = 433/671 (64%), Gaps = 117/671 (17%)
Query: 12 VQQNGNGPSPKKKTPANK-MSVEKIYQKKSQLEHILLRPDTYIGSVEPITETMWLMNRET 70
+Q++ + ++ ++E++YQKKSQLEHILLRPDTYIGS+E T+T+W+ ET
Sbjct: 7 LQESNSANVAAAPAASSGGKTIEEMYQKKSQLEHILLRPDTYIGSIEKHTQTLWVY--ET 64
Query: 71 NHMERREITYVPGLYKIFDEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPV 130
+ M +R +TYVPGLYKIFDEILVNA DNKQRDPKM+ +++ ++ E N ISV+NNG G+PV
Sbjct: 65 DKMVQRSVTYVPGLYKIFDEILVNAADNKQRDPKMDSLRVVIDVEQNLISVYNNGDGVPV 124
Query: 131 VEHKDEKMFVPTMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGR 190
H++E ++ VP MIFGHLLTSSNY+D E K TGGR
Sbjct: 125 EIHQEEGVY-------------------------VPEMIFGHLLTSSNYDDNEKKTTGGR 159
Query: 191 NGYGAKLCNIFSSKFVVETSCSEYKKSFKQVWKDNMSKVTSPEI-KSGSKDDFTKITFTP 249
NGYGAKL NIFS++FV+ET+ + +K +KQV+ +NM K + P I K +++TK+TF P
Sbjct: 160 NGYGAKLTNIFSTEFVIETADGKRQKKYKQVFSNNMGKKSEPVITKCKKSENWTKVTFKP 219
Query: 250 DLTKFKMTSLDKDMVDLITRRAYDAAAST-KDVKVFLNGEKLPVKNFQDYVKLYTDRQDE 308
DL KF MT L+ D+V L+ +R D A K VKV LNG+++PVK+F DYV LY + ++
Sbjct: 220 DLAKFNMTHLEDDVVALMKKRVVDIAGCLGKTVKVELNGKRIPVKSFSDYVDLYLESANK 279
Query: 309 DG-DPVKIIYENVNPRWEVAIAPSDRGFQQVSFVNSIATTKGGRHVDAVVDAIVKQIIEV 367
+ + IYE VN RWEV ++ S+ FQQVSFVNSIAT KGG HVD V + I ++E
Sbjct: 280 SRPENLPRIYEKVNDRWEVCVSLSEGQFQQVSFVNSIATIKGGTHVDYVTNQIANHVMEA 339
Query: 368 VKKKNKDLGCTIIMLFGNKFNNVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFIN 427
V KKNK+ N +K VKNH+W+F+N
Sbjct: 340 VNKKNKN---------AN---------------------------IKAHNVKNHLWVFVN 363
Query: 428 CLIVNPTFDSQTKENMTLQKGSFGSTC--------------------------------- 454
LI NP FDSQTKE +TL++ SFGS C
Sbjct: 364 ALIDNPAFDSQTKETLTLRQSSFGSKCELSEDFLKKVMKSGIVENLLSWADFKQSKELKK 423
Query: 455 -----------VPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPL 503
+PKLEDAN+AG KNS CTLILTEGDSAK+LAV+GL VVGR+ YGVFPL
Sbjct: 424 TDGAKTTRVTGIPKLEDANEAGGKNSEKCTLILTEGDSAKALAVAGLSVVGRNYYGVFPL 483
Query: 504 RGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDG 563
RGKLLNVREA+HKQI+ NAEI N+ +ILGLQ+ K+Y E +K+LRYG LMIMTDQD DG
Sbjct: 484 RGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQY---ESVKSLRYGHLMIMTDQDHDG 540
Query: 564 SHIKGLIINFIHHNWPTLLRLP-FLEEFITPIIKATKA-REELSFYSLPEFEEWKEETT- 620
SHIKGL+INFIH WP+LL++P FL EFITPI+KAT+ ++ LSFYS+PE+EEWKE
Sbjct: 541 SHIKGLLINFIHSFWPSLLKVPSFLVEFITPIVKATRRGKKVLSFYSMPEYEEWKESLGG 600
Query: 621 NWHTYKIKYYK 631
N + IKYYK
Sbjct: 601 NATGWSIKYYK 611
Score = 160 bits (407), Expect = 3e-39
Identities = 61/119 (51%), Positives = 79/119 (66%), Gaps = 4/119 (3%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKN 718
IEP WY+PIIP VLVNGAEGIGTGW T IPN+NPR+IV NI+R++ GE PM PWY+
Sbjct: 820 SIEPTWYMPIIPTVLVNGAEGIGTGWSTFIPNYNPRDIVANIRRLLNGESMEPMHPWYRG 879
Query: 719 FKGEID----YCGDSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTLDTLLHGAEKD 773
FKG I+ G + + G +D+ L ITEL + +WT DYK+ L++L K+
Sbjct: 880 FKGTIEKTASKEGGCTYTITGLYEEVDETTLRITELPIRRWTDDYKEFLESLKTDNNKN 938
Score = 73.0 bits (179), Expect = 2e-12
Identities = 83/386 (21%), Positives = 136/386 (35%), Gaps = 38/386 (9%)
Query: 824 ERQERQAAEGEDDEAGSQTQEEEDPD---------KDYDYLLGMTFWSLTMERKNELLKK 874
+ E A DD A +EEE+ D DYDYLL M +LT+E+ EL
Sbjct: 1079 KSVEAAVAGATDDAA----EEEEEIDVSSSSGVRGSDYDYLLSMAIGTLTLEKVQELCAD 1134
Query: 875 RDDKMTELNILKKKAPTDLWSDDLDAL-REKDKIHPCPGGNRTRGLALKRQTRYQPSNRV 933
RD E+ LKK P LW DLDAL +E DK+ + A ++ R
Sbjct: 1135 RDKLNIEVEDLKKTTPKSLWLKDLDALEKELDKLDK---EDAKAEEAREKLQRAAARGE- 1190
Query: 934 LTSRDEPMVVSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKT 993
S V P P K KK + ++ S +++ ++ K +
Sbjct: 1191 --SGAAKKVSRQAPKKPAPKKT----TKKASESETTEETYGSSAMETENVAEVVKPKGRA 1244
Query: 994 AAAKKAKPAKKE-SEYSSTVCLFKRFGRRNCN----DGGLIPKSQREGAQDSDLENNCRL 1048
A KKA A KE E + L R N + + ++ + L
Sbjct: 1245 GAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEETVKAVPARRAAARKKPL 1304
Query: 1049 DEVERKEKEEENSNITKIKSKLKEKGSKK--RNPLSSLDDTMPSAAGRRVEPKYEELLIK 1106
V +++ + ++ L E+ KK R P ++ A +
Sbjct: 1305 ASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKAAKPPAAAKKRG-------P 1357
Query: 1107 AEKAAAPKKPNEVLPGWESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEEST 1166
A + K E+L E+ K + + ++ + S + + E +
Sbjct: 1358 ATVQSGQKLLTEMLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAATNKETESSENVS 1417
Query: 1167 QTVQVELREGVNISAPKPQASSTKNA 1192
+ E E + P+PQ ++ K
Sbjct: 1418 GSSSSEKDEIDVSAKPRPQRANRKQT 1443
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 618 bits (1595), Expect = 0.0
Identities = 200/612 (32%), Positives = 283/612 (46%), Gaps = 138/612 (22%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPT 142
GL+ + DEI+ NA D M+ IK+T++++ N+ISV +NG+GIPV H EK + P
Sbjct: 1 GLHHLVDEIVDNAADEALAGY-MDTIKVTIDKD-NSISVEDNGRGIPVEIHPKEKKYAPE 58
Query: 143 MIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFS 202
+IF L ++D+ KV+G G +G GA + N S
Sbjct: 59 VIFTVLHAGGKFDDDAYKVSG-------------------------GLHGVGASVVNALS 93
Query: 203 SKFVVETSCSEYKKSFKQVWKDNMSKVTSPEIKSGSKDDFTKITFTPDLTKFKMTSLDKD 262
++F VE + K +KQ + +N ++ P+I +K D TK+TF PDL F MT+ D
Sbjct: 94 TEFEVEVARD--GKEYKQSFSNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTT--DD 149
Query: 263 MVDLITRRAYDAAASTKDVKVFLNGEK-------LPVKNFQDYVKLYT-DRQDEDGDPVK 314
+L+ RR + A K VK+ LN E+ L +DYV+L +++ +P
Sbjct: 150 DFELLKRRLRELAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTY 209
Query: 315 IIYENVNPRWEVAIAPSDRG-FQQVSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNK 373
I E N R EVA +D VSFVN+IATT+GG H + DA+ + I E KKK K
Sbjct: 210 IEGEKDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKK 269
Query: 374 DLGCTIIMLFGNKFNNVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNP 433
L +K V+ + FI+ I P
Sbjct: 270 ----------------------------------LKEKNIKGEDVREGLTAFISVKIPEP 295
Query: 434 TFDSQTKENMTLQKGSFG------------------------------------------ 451
F+ QTKE + + FG
Sbjct: 296 QFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARE 355
Query: 452 ---------STCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFP 502
+ KL DA+ AG K C L L EGDSA A SG RD + P
Sbjct: 356 LTRKKKLSSISLPGKLADASSAGPKK---CELFLVEGDSAGGSAKSGR---DRDFQAILP 409
Query: 503 LRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQD 562
LRGK+LNV +A+ +IL+N EI L+ LGL K + D++ LRYG+++IMTD D D
Sbjct: 410 LRGKILNVEKASLDKILKNEEIQALITALGLGIGKDF----DIEKLRYGKIIIMTDADVD 465
Query: 563 GSHIKGLIINFIHHNWPTLLRLPFLEEFITPIIKATKAR--EELSFYSLPEFEEWKEET- 619
GSHIKGL++ F + P L+ F+ I P+ K TK + SFYSL E+E+W E+T
Sbjct: 466 GSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDEYEKWLEKTE 525
Query: 620 TNWHTYKIKYYK 631
N Y+I+ YK
Sbjct: 526 GNKSKYEIQRYK 537
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 377 bits (971), Expect = e-114
Identities = 157/658 (23%), Positives = 252/658 (38%), Gaps = 159/658 (24%)
Query: 36 YQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNA 95
Q LE + RP YIGS GL+ + E++ N+
Sbjct: 11 IQVLEGLEAVRKRPGMYIGSTGDGR----------------------GLHHLVWEVVDNS 48
Query: 96 CDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYN 155
D + I +T++++ +ISV +NG+GIPV H EK+ +IF L ++
Sbjct: 49 IDEALAG-YADRIDVTLHED-GSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFD 106
Query: 156 DEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCSEYK 215
+ +Y KV+GG +G G + N S+ VE
Sbjct: 107 N--------------------DSY-----KVSGGLHGVGVSVVNALSTWLEVEVK--RDG 139
Query: 216 KSFKQVWKDNMSKVTSPEI-KSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDA 274
K ++Q ++ + I + +K TK+ F PD F T + +++ RR +
Sbjct: 140 KIYRQRFERGVPVTPLEVIGSTDTKKTGTKVRFKPDPEIFGET---EFDYEILKRRLREL 196
Query: 275 AASTKDVKVFLNGEKLPVKN----FQDYVKLYTDRQDEDGDPV--KIIY---ENVNPRWE 325
A K VK+ L E+ + ++ +K Y + ++ P+ +I Y E E
Sbjct: 197 AFLNKGVKITLTDERTGEEKKEFHYEGGLKDYVEYLNKGKTPLHEEIFYFNGEKDGIAVE 256
Query: 326 VAIAPSD-RGFQQVSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFG 384
VA+ +D +SFVN+I T +GG H A+ + I E KKKN
Sbjct: 257 VALQWNDGYSENILSFVNNIPTREGGTHEAGFRSALTRAINEYAKKKNL----------- 305
Query: 385 NKFNNVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMT 444
L L ++ + I+ I +P F+ QTKE +
Sbjct: 306 -----------------------LKEGDLTGDDIREGLTAVISVKIPDPQFEGQTKEKLG 342
Query: 445 LQKGSFGSTCV------------------------------------------------P 456
+ + P
Sbjct: 343 NSEVRSIVEKLVSEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIP 402
Query: 457 KLEDAN-DAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATH 515
L D +K+ L L EGDSA A G R+ + PLRGK+LNV +A
Sbjct: 403 GLPGKLADCTSKDPEKSELFLVEGDSAGGSAKQGR---DREFQAILPLRGKILNVEKARL 459
Query: 516 KQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIH 575
+IL+N EI ++ LG K + D++ LRY +++IMTD D DG+HI+ L++ F +
Sbjct: 460 DKILKNEEIQTIITALGTGIGKDF----DLEKLRYHKIIIMTDADVDGAHIRTLLLTFFY 515
Query: 576 HNWPTLLRLPFLEEFITPIIKATKAREELSFYSLPEFEEWK--EETTNWHTYKIKYYK 631
P L+ + P+ K K ++ FY+ + E K E Y+I+ YK
Sbjct: 516 RYMPPLIENGHVYIAQPPLYKVKKGKKT--FYAYDDEELEKLLERLGKKKGYEIQRYK 571
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1. Rev1 is a translesion
synthesis (TLS) polymerase found in eukaryotes.
Translesion synthesis is a process that allows the bypass
of a variety of DNA lesions. TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Rev1 has both
structural and enzymatic roles. Structurally, it is
believed to interact with other nonclassical polymerases
and replication machinery to act as a scaffold.
Enzymatically, it catalyzes the specific insertion of
dCMP opposite abasic sites. Rev1 interacts with the Rev7
subunit of the B-family TLS polymerase Pol zeta
(Rev3/Rev7). Rev1 is known to actively promote the
introduction of mutations, potentially making it a
significant target for cancer treatment.
Length = 404
Score = 292 bits (749), Expect = 1e-87
Identities = 125/306 (40%), Positives = 171/306 (55%), Gaps = 45/306 (14%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ AVSCDE +D + LL+E P + A +R I + TGC+ S G G N L ARLAT+K
Sbjct: 142 IEAVSCDEALIDITSLLEETYELPEELAEAIRNEIRETTGCSASVGIGPNILLARLATRK 201
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKR--LQN 2016
AKP+GQ+HL+ + + +F+ + + DLPGVG SL KL L TCG L+ S + LQ
Sbjct: 202 AKPDGQYHLSAEKVEEFLSQLKVGDLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQK 261
Query: 2017 EVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEK 2076
+G K G LY +CRG DD+ +T E +RKSVSAE+NYGIRF N ++E FL++L+ E+ K
Sbjct: 262 VLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYGIRFTNVDDVEQFLQRLSEELSK 321
Query: 2077 RLEEVKMKGKCITLKLMVRSAEAPREASKFLGHGVCDYITKSSSLPIYERPLIITYFLLL 2136
RLEE + G+ ITLKLM R+ AP E K++GHG+CD +KSS+L +
Sbjct: 322 RLEESNVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGV------------- 368
Query: 2137 VRSAEAPREASKFLGHGVCDYITKSSSLPMYISQASQILKEVLFIVNKLKVDPVELRGIG 2196
+ I E + L + P ELRG+G
Sbjct: 369 ----------------------------AT--DDSGVIGTEAKKLFRDLSIPPEELRGVG 398
Query: 2197 IQVSKL 2202
IQV+KL
Sbjct: 399 IQVTKL 404
Score = 176 bits (449), Expect = 1e-47
Identities = 80/225 (35%), Positives = 103/225 (45%), Gaps = 62/225 (27%)
Query: 1543 FLGEFYNKSRLHHLSTMGSMFKQYVNELREKHDGVFRGIEAIRKWKTSLGITEDEDLEET 1602
FL F+ SRLHH+ST + K + EL +E
Sbjct: 1 FLENFFKHSRLHHISTWKARLKDFFRELSNGS-------------------------KEA 35
Query: 1603 FSDNPSPSEPEPVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAE 1662
N + + +IMH+D DCFFVSV IR+ P+L+ +PVAV HGKG +S
Sbjct: 36 DPSNSIHPDLQRIIMHVDFDCFFVSVSIRNRPDLKGKPVAVCHGKGPNS----------- 84
Query: 1663 FDI----YRQRTMNRMGLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYN 1718
+I Y R YG+ NGM+VG A K CP L +PYDFE Y+EVS Y
Sbjct: 85 -EIASCNYE----------ARSYGIKNGMWVGQAKKLCPQLVTLPYDFEAYEEVSLTFYE 133
Query: 1719 LIASLTLNIEAVS----LYTNESFLNALPED-------IRQEVLD 1752
++AS T NIEAVS L S L E IR E+ +
Sbjct: 134 ILASYTDNIEAVSCDEALIDITSLLEETYELPEELAEAIRNEIRE 178
Score = 38.1 bits (89), Expect = 0.047
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 1197 FLGEFYNKSRLHHLSTMGSMFKQYVNQL 1224
FL F+ SRLHH+ST + K + +L
Sbjct: 1 FLENFFKHSRLHHISTWKARLKDFFREL 28
>gnl|CDD|173785 cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in proteins of the type IIA family of DNA
topoisomerases similar to Saccharomyces cerevisiae
Topoisomerase II. TopoIIA enzymes cut both strands of
the duplex DNA to remove (relax) both positive and
negative supercoils in DNA. These enzymes covalently
attach to the 5' ends of the cut DNA, separate the free
ends of the cleaved strands, pass another region of the
duplex through this gap, then rejoin the ends. These
proteins also catenate/ decatenate duplex rings. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in strand joining and as a general acid in
strand cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 120
Score = 245 bits (628), Expect = 2e-75
Identities = 94/122 (77%), Positives = 105/122 (86%), Gaps = 3/122 (2%)
Query: 472 CTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
CTLILTEGDSAK+LAV+GL VVGRD YGVFPLRGKLLNVREA+HKQI+ENAEI N+ KIL
Sbjct: 1 CTLILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKIL 60
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLP-FLEEF 590
GLQ+ K E K+LRYGRLMIMTDQD DGSHIKGL+INFIH WP+LL++P FL EF
Sbjct: 61 GLQHGKS--DYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKIPGFLVEF 118
Query: 591 IT 592
IT
Sbjct: 119 IT 120
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 246 bits (629), Expect = 2e-69
Identities = 187/617 (30%), Positives = 274/617 (44%), Gaps = 99/617 (16%)
Query: 40 SQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNACDNK 99
S EHIL RP YIGSV +L + ++ YVPGL KI DEI+ N+ D
Sbjct: 8 SDREHILKRPGMYIGSVAYEAHERFLFG------KFTQVEYVPGLVKIIDEIIDNSVDEA 61
Query: 100 QRDPKMNCIKITVNQETNTISVWNNGKGIP---VVEHKDEKMFVPTMIFGHLLTSSNYND 156
R KI V + N ++V +NG+GIP V + E++ P + SN+
Sbjct: 62 IRTNFKFANKIDVTIKNNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAAWTRTKAGSNF-- 119
Query: 157 EEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCSEYKK 216
D+ ++VTGG NG G+ L N FS F+ ET + +
Sbjct: 120 ------------------------DDTNRVTGGMNGVGSSLTNFFSVLFIGETCDGKNEV 155
Query: 217 SFKQVWKDNMSKVTSPEIKSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDAAA 276
+ + ++ K T +TF PD + F++ LD+ +D+I R A
Sbjct: 156 TVN--CSNGAENISWSTKPGKGKG--TSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAV 211
Query: 277 STKDVKVFLNGEKLPVKNFQDYVKLYTDRQDEDGDPVKIIYENVNPRWEVAIAPSDRGFQ 336
D+K NG+K+ F+ Y K + D I+ EN N +A+APS GF+
Sbjct: 212 VFPDIKFTFNGKKVS-GKFKKYAKQFGD--------DTIVQENDN--VSIALAPSPDGFR 260
Query: 337 QVSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNK-DLG------CTIIMLFGNKFNN 389
Q+SFVN + T GG HVD V+D I +++I ++KKK+K ++ C I+LF +N
Sbjct: 261 QLSFVNGLHTKNGGHHVDCVMDDICEELIPMIKKKHKIEVTKARVKECLTIVLFVRNMSN 320
Query: 390 VKNNKLQMAKTLIDIGVRLGGMALKPF-QVKNHI---------WIFINCLIVNPTFDS-- 437
+ + Q + L PF +++NHI I I+ P ++
Sbjct: 321 PRFDS-QTKERLTS-----------PFGEIRNHIDLDYKKIAKQILKTEAIIMPIIEAAL 368
Query: 438 -----QTKENMTLQKGSFGSTCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGV 492
K T V K AN G + TL LTEGDSA + V
Sbjct: 369 ARKLAAEKAAETKAAKKAKKAKVAKHIKANLIGK--DAETTLFLTEGDSAIGYLIE---V 423
Query: 493 VGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGR 552
+ +G +PLRGK+LN ++ IL+N E+ ++ I GL +K E+M Y
Sbjct: 424 RDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEK---AENMN---YKN 477
Query: 553 LMIMTDQDQDG-SHIKGLIINFIHHNWPTLLRLPFLEEFITPIIKATKAREELSFYSLPE 611
+ IMTD D DG I L++ F WP L + TP+I A +E FYSL E
Sbjct: 478 IAIMTDADVDGKGSIYPLLLAFF-SRWPELFEQGRIRFVKTPVIIAQVGKETKWFYSLDE 536
Query: 612 FEEWKEETTNWHTYKIK 628
FE+ K+ W IK
Sbjct: 537 FEKAKDSLKKWSIRYIK 553
>gnl|CDD|239563 cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to Saccharomyces
cerevisiae Topo IIA. S. cerevisiae Topo IIA is a
homodimer encoded by a single gene. The type IIA enzymes
are the predominant form of topoisomerase and are found
in some bacteriophages, viruses and archaea, and in all
bacteria and eukaryotes. All type IIA topoisomerases
are related to each other at amino acid sequence level,
though their oligomeric organization sometimes differs.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. TopoIIA enzymes also
catenate/ decatenate duplex rings. This transducer
domain is homologous to the second domain of the DNA
gyrase B subunit, which is known to be important in
nucleotide hydrolysis and the transduction of structural
signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes.
Length = 153
Score = 210 bits (538), Expect = 6e-63
Identities = 92/179 (51%), Positives = 108/179 (60%), Gaps = 37/179 (20%)
Query: 293 KNFQDYVKLY-TDRQDEDGDPVKIIYENVNPRWEVAIAPSDRGFQQVSFVNSIATTKGGR 351
K+F+DYVKLY D EDG P ++YE VN RWEVA+A SD FQQVSFVNSIATTKGG
Sbjct: 1 KSFKDYVKLYLKDANKEDGPPPPVVYEPVNDRWEVAVALSDGQFQQVSFVNSIATTKGGT 60
Query: 352 HVDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFGNKFNNVKNNKLQMAKTLIDIGVRLGGM 411
HVD V D IVK++ EVVKKKNK GG+
Sbjct: 61 HVDYVADQIVKKLDEVVKKKNK-----------------------------------GGI 85
Query: 412 ALKPFQVKNHIWIFINCLIVNPTFDSQTKENMTLQKGSFGSTCVPKLEDANDAGTKNSI 470
+KPFQVKNH+WIF+NCLI NP+FDSQTKE +T + SFGS C + A K+ I
Sbjct: 86 NVKPFQVKNHLWIFVNCLIENPSFDSQTKETLTTKPKSFGSKCELSEKFLKKAV-KSGI 143
>gnl|CDD|173780 cd01030, TOPRIM_TopoIIA_like, TOPRIM_TopoIIA_like:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to Saccharomyces cerevisiae Topoisomerase II.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. These proteins also catenate/
decatenate duplex rings. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). The conserved glutamate may act as a general base
in strand joining and as a general acid in strand
cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 115
Score = 198 bits (506), Expect = 3e-59
Identities = 59/121 (48%), Positives = 75/121 (61%), Gaps = 6/121 (4%)
Query: 472 CTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
C LIL EGDSA A G V VFPLRGK+LNV +A+ K+IL+N EI N++K L
Sbjct: 1 CELILVEGDSAGGSAKQGRDRV---FQAVFPLRGKILNVEKASLKKILKNEEIQNIIKAL 57
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLPFLEEFI 591
GL K D+ LRYG+++IMTD D DGSHI+ L++ F + WP+LL FL
Sbjct: 58 GLGIGKDD---FDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQ 114
Query: 592 T 592
T
Sbjct: 115 T 115
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa. Pol IV, also
known as Pol kappa, DinB, and Dpo4, is a translesion
synthesis (TLS) polymerase. Translesion synthesis is a
process that allows the bypass of a variety of DNA
lesions. TLS polymerases lack proofreading activity and
have low fidelity and low processivity. They use damaged
DNA as templates and insert nucleotides opposite the
lesions. Known primarily as Pol IV in prokaryotes and
Pol kappa in eukaryotes, this polymerase has a propensity
for generating frameshift mutations. The eukaryotic Pol
kappa differs from Pol IV and Dpo4 by an N-terminal
extension of ~75 residues known as the "N-clasp" region.
The structure of Pol kappa shows DNA that is almost
totally encircled by Pol kappa, with the N-clasp region
augmenting the interactions between DNA and the
polymerase. Pol kappa is more resistant than Pol eta and
Pol iota to bulky guanine adducts and is efficient at
catalyzing the incorporation of dCTP. Bacterial pol IV
has a higher error rate than other Y-family polymerases.
Length = 334
Score = 155 bits (395), Expect = 3e-41
Identities = 63/197 (31%), Positives = 111/197 (56%), Gaps = 2/197 (1%)
Query: 1896 SKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLA 1955
+ +V +S DE Y+D + ++ L + + A +R I +ETG T S G NK A++A
Sbjct: 89 TPLVEPLSIDEAYLDVTDYVR-LFGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIA 147
Query: 1956 TKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQ 2015
+ KPNG + P+ + +F+ +P+ +PGVG KL LG +T GDL + ++ L+
Sbjct: 148 SDLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLKELGIKTIGDLAKLDVELLK 207
Query: 2016 NEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVE 2075
+ K+G LY+ RG D++ + + +RKS+ E + + +E+ L +LA E+
Sbjct: 208 K-LFGKSGRRLYELARGIDNRPVEPDRERKSIGVERTFSEDLTDPEELLEELLELAEELA 266
Query: 2076 KRLEEVKMKGKCITLKL 2092
+RL + +KG+ +T+KL
Sbjct: 267 ERLRKRGLKGRTVTVKL 283
Score = 92.2 bits (230), Expect = 1e-19
Identities = 44/155 (28%), Positives = 76/155 (49%), Gaps = 43/155 (27%)
Query: 1617 MHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMGL 1676
+HIDMD F+ SV R +PEL+ +PVAV G+S + GV +
Sbjct: 1 IHIDMDAFYASVEQRDNPELKGKPVAVG---GSSDR---GV------------------V 36
Query: 1677 NT-----REYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVS 1731
+T R++G+ + M + A K CPNL VP F+ Y+EVS + ++ T +E +S
Sbjct: 37 STASYEARKFGVRSAMPIFQAKKLCPNLIFVPPRFDKYREVSRQIMEILREYTPLVEPLS 96
Query: 1732 LYTNESFLN------------ALPEDIRQEVLDDL 1754
+ +E++L+ + ++IR + ++
Sbjct: 97 I--DEAYLDVTDYVRLFGSATEIAKEIRARIREET 129
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 158 bits (401), Expect = 6e-41
Identities = 45/113 (39%), Positives = 62/113 (54%), Gaps = 4/113 (3%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDP----LPMKP 714
IEP PIIP +LVNG+ GI G T IP HN RE++D ++R+I D L M P
Sbjct: 144 EIEPTVLPPIIPNLLVNGSSGIAVGMATNIPPHNLREVIDAVRRLIDNPDASIDELMMIP 203
Query: 715 WYKNFKGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTLDTLL 767
W +F + G ++VV G+I I DD+ + ITEL T D + + L+
Sbjct: 204 WGPDFPTGGEIVGPGKYVVRGKIEIEDDNTIVITELPYQVNTADLIEKIAELV 256
Score = 56.8 bits (138), Expect = 1e-07
Identities = 12/49 (24%), Positives = 21/49 (42%)
Query: 846 EDPDKDYDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLW 894
E + D +L M LT +L K+ + E+ L+K ++ W
Sbjct: 394 ELSEIQADAILDMRLRRLTKLEVEKLEKELKELEKEIEDLEKILASEEW 442
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 144 bits (366), Expect = 2e-36
Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 11/120 (9%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPL---PMKPW 715
EP PIIP +LVNGA GI G T IP HN E++D + ++ G + P
Sbjct: 123 EKEPTVLPPIIPNLLVNGASGIAVGMATNIPPHNLGEVIDALIALLDGPEITLLKIPGPD 182
Query: 716 YKNFKGEIDY--------CGDSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTLDTLL 767
+ G I G + V +I I + + ITEL G WT ++++ L+
Sbjct: 183 FPTGGGIIGSGGIREAYKTGRGKITVRAKIEIEERKTIVITELPYGVWTEKLIESIEELV 242
Score = 50.2 bits (121), Expect = 9e-06
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 849 DKDYDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAP--TDLWSDDLD 899
+ DYLL M LT E +L K+ ++ E+ L+K LW +LD
Sbjct: 375 EIQADYLLDMRLRRLTKEEIEKLEKEIEELEKEIAELEKILASEKKLWIKELD 427
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 148 bits (376), Expect = 2e-36
Identities = 130/613 (21%), Positives = 222/613 (36%), Gaps = 182/613 (29%)
Query: 42 LEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNACD---- 97
LE + RP YIGS GL+ + E++ N+ D
Sbjct: 19 LEPVRKRPGMYIGS-----------TDTR------------GLHHLVQEVIDNSVDEALA 55
Query: 98 ---NKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNY 154
+ I++T++ ++SV +NG+GIPV H +E +I L +
Sbjct: 56 GHGKR--------IEVTLH-ADGSVSVRDNGRGIPVGIHPEEGKSGVEVILTKLHAGGKF 106
Query: 155 NDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVET--SCS 212
+ + Y K +GG +G G + N SS+ VE
Sbjct: 107 S--------------------NKAY-----KFSGGLHGVGVSVVNALSSRLEVEVKRDGK 141
Query: 213 EYKKSFKQVWKDNMSKVTSPEI--KSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRR 270
Y++ F+ V E+ +G + T++ F PD F + + R
Sbjct: 142 VYRQRFE-----GGDPVGPLEVVGTAGKRKTGTRVRFWPDPKIFDSPKFS---PERLKER 193
Query: 271 AYDAAASTKDVKVFLNGEKLPVK-NFQDYVKLYTDRQDEDGDPVKIIY------ENVNPR 323
A + + LN E+ ++++ +K Y +E + + + E
Sbjct: 194 LRSKAFLLPGLTITLNDERERQTFHYENGLKDYLAELNEGKETLPEEFVGSFEGEAEGEA 253
Query: 324 WEVAIA--PSDRGFQQVSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIM 381
E A+ + S+VN I T +GG H + + ++K + E
Sbjct: 254 VEWALQWTDEGGENIE-SYVNLIPTPQGGTHENGFREGLLKAVRE--------------- 297
Query: 382 LFGNKFNNVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTK- 440
F K N + K ++ D+ L + ++ I P F+ QTK
Sbjct: 298 -FAEKRNLLPKGK-KLEGE--DVREGLAAV--------------LSVKIPEPQFEGQTKE 339
Query: 441 ------------------------ENMTL------------------------QKGSFGS 452
+N L +K + G
Sbjct: 340 KLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKVKRKKKTSGP 399
Query: 453 TCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKY--GVFPLRGKLLNV 510
KL D + + L L EGDSA G RD+ + PLRGK+LN
Sbjct: 400 ALPGKLADCTSQDPERT---ELFLVEGDSA-----GGSAKQARDREFQAILPLRGKILNT 451
Query: 511 REATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLI 570
EA+ +L N EI++++ +G+ + D++ LRYG+++IMTD D DG+HI L+
Sbjct: 452 WEASLDDVLANEEIHDIIVAIGIGPGDSF----DLEDLRYGKIIIMTDADVDGAHIATLL 507
Query: 571 INFIHHNWPTLLR 583
+ F + ++P L+
Sbjct: 508 LTFFYRHFPPLVE 520
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in DNA
repair [DNA replication, recombination, and repair].
Length = 354
Score = 138 bits (350), Expect = 3e-35
Identities = 68/237 (28%), Positives = 110/237 (46%), Gaps = 6/237 (2%)
Query: 1898 IVSAVSCDEMYVDCSQLLQELSLTPL-QFASYLRETIAKETGCTCSTGFGSNKLQARLAT 1956
+V +S DE ++D + L+ L L + A +R I E G T S G NK A++A+
Sbjct: 94 LVEPLSIDEAFLDLTDALRLLGLADAPRIALEIRFGILLELGLTASVGISDNKFLAKIAS 153
Query: 1957 KKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQN 2016
KP+G + P+ + + +P+ + GVG KL LG T GDL L L+
Sbjct: 154 DLNKPDGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKK 213
Query: 2017 EVGNKNGLTLYKHCRGEDDKELTFEHQR-KSVSAEVNYGIRFQNNQEM-ETFLKQLAGEV 2074
G K G LY+ RG D++ + + R KS+ AE + + +E+ E +L EV
Sbjct: 214 RFG-KLGERLYRLARGIDNRPVREQALRAKSIGAESTFEEDLTDAEELIERLRARLGEEV 272
Query: 2075 EKRLEEVKMKGKCITLKLMVRSAEAPREASKFLGHGVCDYIT-KSSSLPIYERPLII 2130
RL + G+ +++KL + S+ L D I +++LP+ L
Sbjct: 273 VSRLRKSGRHGRTVSVKLKT-ADFPTNTRSRKLAQPTSDPIEIYAAALPLLPPLLFR 328
Score = 80.4 bits (199), Expect = 1e-15
Identities = 43/163 (26%), Positives = 69/163 (42%), Gaps = 39/163 (23%)
Query: 1614 PVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGV--DRQAEFDIYRQRTM 1671
I+H+DMD F+ SV R +PEL+ +PV V G GV E
Sbjct: 1 RKILHVDMDAFYASVEERDNPELKGKPVVVGGGA------PRGVVLAASYEA-------- 46
Query: 1672 NRMGLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVS 1731
R +G+ + M + ALK CP + P +F Y+ S + ++ T +E +S
Sbjct: 47 -------RAFGVRSAMPLFEALKLCPRAIVAPPNFAAYRLASAEIRAILERYTPLVEPLS 99
Query: 1732 LYTNESFLNA--------------LPEDIRQEVLDDLSRQQSV 1760
+ +E+FL+ + +IR +L +L SV
Sbjct: 100 I--DEAFLDLTDALRLLGLADAPRIALEIRFGILLELGLTASV 140
>gnl|CDD|233254 TIGR01059, gyrB, DNA gyrase, B subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV. Proteins scoring
above the noise cutoff for this model and below the
trusted cutoff for topoisomerase IV models probably
should be designated GyrB [DNA metabolism, DNA
replication, recombination, and repair].
Length = 654
Score = 141 bits (358), Expect = 3e-34
Identities = 143/605 (23%), Positives = 235/605 (38%), Gaps = 181/605 (29%)
Query: 42 LEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKI----FDEILVNACD 97
LE + RP YIGS +H+ +Y++ DE + CD
Sbjct: 12 LEAVRKRPGMYIGSTGE---------TGLHHL----------VYEVVDNSIDEAMAGYCD 52
Query: 98 NKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYNDE 157
I +T+N + +++V +NG+GIPV H + + +
Sbjct: 53 T---------INVTINDD-GSVTVEDNGRGIPVDIH--PEEGISAV-------------- 86
Query: 158 EDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVET--SCSEYK 215
++ L ++ + KV+GG +G G + N S V Y+
Sbjct: 87 ---------EVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYR 137
Query: 216 KSFKQVWKDNMSKVTSP-EIKSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDA 274
+ F++ P E+ +K T + F PD F+ T D D ++ +R +
Sbjct: 138 QEFER------GIPLGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFD---ILAKRLREL 188
Query: 275 AASTKDVKVFLNGEKL-PVKNFQDY----VKLYTDRQDEDGDPV--KIIY---ENVNPRW 324
A VK+ L E+ K+ + +K + + + +P+ +IIY E
Sbjct: 189 AFLNSGVKISLEDERDGKGKSVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEV 248
Query: 325 EVAIAPSDRGFQQ--VSFVNSIATTKGGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIML 382
EVA+ +D G+ + +SFVN+I T +GG H++ A+ + I K
Sbjct: 249 EVALQWND-GYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKL--------- 298
Query: 383 FGNKFNNVKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTK-- 440
+K +K L +R G A+ I+ + +P F+ QTK
Sbjct: 299 -------LKESK----PNLTGEDIREGLTAV------------ISVKVPDPQFEGQTKTK 335
Query: 441 -----------------------EN--------------------------MTLQKGSFG 451
EN +T +K +
Sbjct: 336 LGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALD 395
Query: 452 STCVP-KLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKY--GVFPLRGKLL 508
S +P KL D + +K+ L + EGDSA G GRD+ + PLRGK+L
Sbjct: 396 SGGLPGKLADCS---SKDPSKSELYIVEGDSA-----GGSAKQGRDRKFQAILPLRGKIL 447
Query: 509 NVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKG 568
NV +A +IL N EI ++ LG K + D++ LRY +++IMTD D DGSHI+
Sbjct: 448 NVEKARLDKILSNQEIGAIITALGCGIGKDF----DLEKLRYHKIIIMTDADVDGSHIRT 503
Query: 569 LIINF 573
L++ F
Sbjct: 504 LLLTF 508
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 137 bits (348), Expect = 5e-34
Identities = 37/127 (29%), Positives = 57/127 (44%), Gaps = 18/127 (14%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDP-------LP 711
+EPE PI P +LVNG+ GI G T IP HN RE++D ++ +I + +
Sbjct: 124 EVEPEVLPPIFPNLLVNGSSGIAVGMATNIPPHNLREVIDALRALIDNPEASIDELMEII 183
Query: 712 MKPWYKNFK--------GEIDYCGDSRFVVNGEIAILDD---DKLEITELQVGKWTTDYK 760
P + E G R+++ G+ I DD + +EITEL K
Sbjct: 184 KGPDFPTGGIIEGRAGIREAYETGRGRYIIRGKYEIEDDEGRNTIEITELPYQVNKAKLK 243
Query: 761 DTLDTLL 767
+ + L+
Sbjct: 244 EKIAELV 250
Score = 58.7 bits (143), Expect = 2e-08
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 849 DKDYDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKK-----APTDLWSDDLDAL 901
+ D +L M LT + +LLK+ + E+ L+K P DLW ++LD
Sbjct: 388 EIQADAILDMRLRRLTKLEREKLLKELKELEAEIEDLEKILASEERPKDLWKEELDEF 445
>gnl|CDD|235035 PRK02406, PRK02406, DNA polymerase IV; Validated.
Length = 343
Score = 134 bits (340), Expect = 8e-34
Identities = 67/193 (34%), Positives = 101/193 (52%), Gaps = 6/193 (3%)
Query: 1903 SCDEMYVDCSQLLQEL-SLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKP 1961
S DE Y+D + + S T A +R+ I +E G T S G NK A++A+ KP
Sbjct: 93 SLDEAYLDVTDNKLCIGSAT--LIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKP 150
Query: 1962 NGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNK 2021
NG F +TP+ + F+ +P+ +PGVG KL++LG TC DLQ L L G K
Sbjct: 151 NGLFVITPEEVDAFLATLPVEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELIRHFG-K 209
Query: 2022 NGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEV 2081
G LY+ RG D++ + + +RKSV E + + + L +LA ++E+RLE
Sbjct: 210 FGRRLYERARGIDERPVKPDRERKSVGVERTFAEDLYDLEACLAELPRLAEKLERRLERA 269
Query: 2082 KM--KGKCITLKL 2092
K + K + +KL
Sbjct: 270 KPDKRIKTVGVKL 282
Score = 72.5 bits (179), Expect = 5e-13
Identities = 48/150 (32%), Positives = 73/150 (48%), Gaps = 40/150 (26%)
Query: 1621 MDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMGLNT-- 1678
MDCF+ +V +R +PEL+ +PVAV G S R GV ++T
Sbjct: 1 MDCFYAAVEMRDNPELRGKPVAV----GGSPGRR-GV------------------ISTCN 37
Query: 1679 ---REYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSL--- 1732
R++G+ + M ALK CP+L VP F+ YKEVS + + T IE +SL
Sbjct: 38 YEARKFGVRSAMPTAQALKLCPDLIFVPGRFDVYKEVSRQIREIFRRYTDLIEPLSLDEA 97
Query: 1733 Y---TNESFLNALP-----EDIRQEVLDDL 1754
Y T ++ L ++IRQ++ ++L
Sbjct: 98 YLDVT-DNKLCIGSATLIAQEIRQDIFEEL 126
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 134 bits (338), Expect = 8e-32
Identities = 151/631 (23%), Positives = 252/631 (39%), Gaps = 116/631 (18%)
Query: 42 LEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNACDNKQR 101
L+ + RP YIGS T GL+ + EI+ N+ D
Sbjct: 16 LDAVRKRPGMYIGS-----------------------TDSKGLHHLVWEIVDNSVDEVLA 52
Query: 102 DPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYNDEEDKV 161
N I +T++ + N+I+V ++G+GIP H+D + T
Sbjct: 53 GYADN-ITVTLH-KDNSITVQDDGRGIPTGIHQDGN--IST------------------- 89
Query: 162 TGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCSEYKKSFKQV 221
+F L ++ K GG +G GA + N SS V + ++Q
Sbjct: 90 ----VETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVK--RDGQIYQQR 143
Query: 222 WKDNMSKVTSPEIKSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDAAASTKDV 281
+++ V S + +K T + F PD T FK T + + +I R ++A K +
Sbjct: 144 FENGGKIVQSLKKIGTTKKTGTLVHFHPDPTIFKTTQFNSN---IIKERLKESAFLLKKL 200
Query: 282 KVFLNGEKLPVK-------NFQDYVKLYTDRQDEDGDPVKIIYENVNPRWEVAIAPSDRG 334
K+ ++ D+V + ++ E EVA +D G
Sbjct: 201 KLTFTDKRTNKTTVFFYENGLVDFVDYINETKETLSQVTYFEGEKNGIEVEVAFQFND-G 259
Query: 335 FQQ--VSFVNSIATTKGGRHVDAVVDAIVKQIIE------VVKKKNKDLGCT-------- 378
+ +SF NS+ T +GG H + AI I ++K+K+K+L +
Sbjct: 260 DSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSA 319
Query: 379 IIMLFGNKFNNVKNNKLQM-AKTLIDIGVRLGGMALKPFQVKNHIWIFIN------CLIV 431
II + + +Q +T + + V++H++ F+ L++
Sbjct: 320 IISV------RIPEELIQFEGQTKSKLFSPEARNVVDEI-VQDHLFFFLEENNNDAKLLI 372
Query: 432 NPTFD-SQTKENMTLQKGSFGSTCVPKLEDA------NDAGTKNSIDCTLILTEGDSAKS 484
+ KE + S PK E A +KN L L EGDSA
Sbjct: 373 DKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSA-- 430
Query: 485 LAVSGLGVVGRDK--YGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTV 542
G GRD+ + PLRGK+LNV +A IL+N EIN ++ +G +
Sbjct: 431 ---GGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGIGADF--- 484
Query: 543 EDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLPFLEEFITPIIKATKARE 602
+K L+Y +++IMTD D DG+HI+ L++ F + L+ L + + P+ K +K
Sbjct: 485 -SIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKKDG 543
Query: 603 ELSFY--SLPEFEEWKEETTNWHTYKIKYYK 631
+ Y S E E K++ N Y ++ YK
Sbjct: 544 KKVKYAWSDLELESVKKKLKN---YTLQRYK 571
>gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases. Y-family DNA polymerases
are a specialized subset of polymerases that facilitate
translesion synthesis (TLS), a process that allows the
bypass of a variety of DNA lesions. Unlike replicative
polymerases, TLS polymerases lack proofreading activity
and have low fidelity and low processivity. They use
damaged DNA as templates and insert nucleotides opposite
the lesions. The active sites of TLS polymerases are
large and flexible to allow the accomodation of distorted
bases. Most TLS polymerases are members of the Y-family,
including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol
V, which is found exclusively in bacteria. In
eukaryotes, the B-family polymerase Pol zeta also
functions as a TLS polymerase. Expression of Y-family
polymerases is often induced by DNA damage and is
believed to be highly regulated. TLS is likely induced by
the monoubiquitination of the replication clamp PCNA,
which provides a scaffold for TLS polymerases to bind in
order to access the lesion. Because of their high error
rates, TLS polymerases are potential targets for cancer
treatment and prevention.
Length = 343
Score = 119 bits (299), Expect = 2e-28
Identities = 65/231 (28%), Positives = 108/231 (46%), Gaps = 8/231 (3%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
+ Y+ + + S ++ + +V S DE+++D + L + A ++ IA
Sbjct: 73 DLYRRLSERLLSELE----EVAPLVEVASIDELFLDLTGS-ARLLGLGSEVALRIKRHIA 127
Query: 1935 KETG-CTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLF 1993
++ G T S G SNKL A+LA K AKP+G L P+ + F+ +PL+DLPG+G
Sbjct: 128 EQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAK 187
Query: 1994 KLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNY 2053
+L ++G GDL S L G +G L+ RG DD+ L+ RKS S E
Sbjct: 188 RLEAVGINPIGDLLAASPDALLALWGGVSGERLWYALRGIDDEPLSPPRPRKSFSHERVL 247
Query: 2054 GIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKLMVRSAEAPREAS 2104
+N ++ L+ L ++ +RL L+L +R+ +
Sbjct: 248 PRDSRNAEDARPLLRLLLEKLARRLRRDGRGATR--LRLWLRTVDGRWSGH 296
Score = 78.6 bits (194), Expect = 5e-15
Identities = 35/113 (30%), Positives = 49/113 (43%), Gaps = 19/113 (16%)
Query: 1618 HIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMGLN 1677
HID D FF SV PEL+ PV V +S+ V +A
Sbjct: 2 HIDFDNFFASVEQLARPELKGRPVVVVPFNSDSTCVI-ACSYEA---------------- 44
Query: 1678 TREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAV 1730
R+YG+ GM V A K CPNL +VP + Y+ +S L + + + + V
Sbjct: 45 -RKYGVKRGMPVREARKMCPNLILVPARLDLYRRLSERLLSELEEV-APLVEV 95
>gnl|CDD|215785 pfam00204, DNA_gyraseB, DNA gyrase B. This family represents the
second domain of DNA gyrase B which has a ribosomal S5
domain 2-like fold. This family is structurally related
to PF01119.
Length = 173
Score = 103 bits (260), Expect = 4e-25
Identities = 38/170 (22%), Positives = 58/170 (34%), Gaps = 39/170 (22%)
Query: 294 NFQDYVKLYTDRQDEDGDPVKIIY--ENVNPRWEVAIAP---SDRGFQQVSFVNSIATTK 348
+DYVK + V E + R EV +A VSFVN+I T
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDSYSENIVSFVNNIPTPD 60
Query: 349 GGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFGNKFNNVKNNKLQMAKTLIDIGVRL 408
GG HVD A+ + + E KKK +K
Sbjct: 61 GGTHVDGFRAALTRALNEYAKKKGL----------------LKKKD-------------- 90
Query: 409 GGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMTL-QKGSFGSTCVPK 457
+ ++ + ++ I NP F+ QTKE + + S + V +
Sbjct: 91 ---KITGDDIREGLTAVVSVKIPNPQFEGQTKEKLGNSEVRSAVESVVSE 137
>gnl|CDD|184529 PRK14133, PRK14133, DNA polymerase IV; Provisional.
Length = 347
Score = 105 bits (264), Expect = 5e-24
Identities = 63/195 (32%), Positives = 110/195 (56%), Gaps = 5/195 (2%)
Query: 1898 IVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATK 1957
IV VS DE Y+D + + +E P++ A Y+++ + KETG T S G NK A+LA+
Sbjct: 96 IVEPVSIDEAYLDITNIKEE----PIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASD 151
Query: 1958 KAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNE 2017
KP+G +T +I D + +P+S + G+G + KLN++G T DL +S + L
Sbjct: 152 WNKPDGIKIITEDMIPDILKPLPISKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEY 211
Query: 2018 VGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKR 2077
G K G+ +Y+ RG D +E+ +RKS+ E ++ +E++ +LK + + +
Sbjct: 212 FG-KFGVEIYERIRGIDYREVEVSRERKSIGKETTLKKDTKDKEELKKYLKDFSNIISEE 270
Query: 2078 LEEVKMKGKCITLKL 2092
L++ + GK +T+K+
Sbjct: 271 LKKRNLYGKTVTVKI 285
Score = 65.1 bits (159), Expect = 1e-10
Identities = 42/139 (30%), Positives = 69/139 (49%), Gaps = 22/139 (15%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
VI+H+DMD FF SV +P+L+ +PV V G S+ GV ++
Sbjct: 4 VIIHVDMDAFFASVEQMDNPKLKGKPVIV----GGISE--RGVVSTCSYE---------- 47
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSL-- 1732
R+YG+ + M V A K+CP+ +P E YKEVS ++ ++ +T +E VS+
Sbjct: 48 ---ARKYGVHSAMPVFMAKKRCPHGIFLPVRHERYKEVSKNIFKILYEVTPIVEPVSIDE 104
Query: 1733 -YTNESFLNALPEDIRQEV 1750
Y + + + P I + +
Sbjct: 105 AYLDITNIKEEPIKIAKYI 123
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional.
Length = 454
Score = 105 bits (264), Expect = 3e-23
Identities = 57/197 (28%), Positives = 100/197 (50%)
Query: 1896 SKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLA 1955
S +V +S DE +V+ ++L + FA LR + +ETG S G GS K A++A
Sbjct: 97 SPVVEQLSFDEAFVEPAELAGASAEEVEAFAERLRARVREETGLPASVGAGSGKQIAKIA 156
Query: 1956 TKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQ 2015
+ AKP+G + P + + +P+ L G+G KL+ LG +T GDL +S +
Sbjct: 157 SGLAKPDGIRVVPPGEERELLAPLPVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVA 216
Query: 2016 NEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVE 2075
N +G G L++ RG DD+ + + K +SAE + + ++ ++++A
Sbjct: 217 NLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFAVDLTTRAQLREAIERIAEHAH 276
Query: 2076 KRLEEVKMKGKCITLKL 2092
+RL + + +T+KL
Sbjct: 277 RRLLKDGRGARTVTVKL 293
Score = 42.6 bits (101), Expect = 0.002
Identities = 35/142 (24%), Positives = 59/142 (41%), Gaps = 32/142 (22%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAV--AHGKGNSSKVREGVDRQAEFDIYRQRTMNR 1673
++H+DMD FF SV P L+ PV V G+G V G +A
Sbjct: 7 VLHLDMDAFFASVEQLTRPTLRGRPVLVGGLGGRG----VVAGASYEA------------ 50
Query: 1674 MGLNTREYGLGNGMFVGHALKKCPNLKIV-PYDFEGYKEVSYCLYNLIASLTLNIEAVSL 1732
R +G + M + A + N +V P F Y+ S +++ + L+ +E +S
Sbjct: 51 -----RVFGARSAMPMHQARRLVGNGAVVLPPRFVVYRAASRRVFDTLRELSPVVEQLSF 105
Query: 1733 YTNESFLN------ALPEDIRQ 1748
+E+F+ A E++
Sbjct: 106 --DEAFVEPAELAGASAEEVEA 125
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated.
Length = 346
Score = 96.2 bits (240), Expect = 6e-21
Identities = 60/178 (33%), Positives = 87/178 (48%), Gaps = 5/178 (2%)
Query: 1922 PLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPL 1981
P A +R + + TG +CS G G NKL+A++AT AKP G F LT M + P
Sbjct: 120 PEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDANWMAVMGDRPT 179
Query: 1982 SDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFE 2041
L GVG +L +LG T DL L G G L RG D E++ E
Sbjct: 180 DALWGVGPKTAKRLAALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAE 239
Query: 2042 -HQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCIT-LKLMVRSA 2097
+S S EV + + E+E+ +++LA V L+EV +G+ +T + + VR+A
Sbjct: 240 PWVPRSRSREVTFPQDLTDRAEVESAVRELARRV---LDEVVAEGRPVTRVAVKVRTA 294
Score = 64.3 bits (157), Expect = 2e-10
Identities = 37/144 (25%), Positives = 63/144 (43%), Gaps = 24/144 (16%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMG 1675
++H+D+D F +V + PEL PV V G G+ ++ R V A ++
Sbjct: 7 VLHVDLDQFIAAVELLRRPELAGLPVIVG-GNGDPTEPR-KVVTCASYE----------- 53
Query: 1676 LNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYTN 1735
R +G+ GM + A ++CP+ +P D Y S + + L + +E +
Sbjct: 54 --ARAFGVRAGMPLRTAARRCPDAVFLPSDPAAYDAASEEVMATLRDLGVPVEV--WGWD 109
Query: 1736 ESFLNALPED-------IRQEVLD 1752
E+FL +D IR VL+
Sbjct: 110 EAFLGVDTDDPEALAEEIRAAVLE 133
>gnl|CDD|173786 cd03366, TOPRIM_TopoIIA_GyrB, TOPRIM_TopoIIA_GyrB:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to the Escherichia coli GyrB subunit. TopoIIA
enzymes cut both strands of the duplex DNA to remove
(relax) both positive and negative supercoils in DNA.
These enzymes covalently attach to the 5' ends of the
cut DNA, separate the free ends of the cleaved strands,
pass another region of the duplex through this gap, then
rejoin the ends. These proteins also catenate/
decatenate duplex rings. DNA gyrase is more effective
at relaxing supercoils than decatentating DNA. DNA
gyrase in addition inserts negative supercoils in the
presence of ATP. The TOPRIM domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD). The
conserved glutamate may act as a general base in strand
joining and as a general acid in strand cleavage by
topisomerases. The DXD motif may co-ordinate Mg2+, a
cofactor required for full catalytic function.
Length = 114
Score = 88.9 bits (221), Expect = 1e-20
Identities = 43/113 (38%), Positives = 63/113 (55%), Gaps = 11/113 (9%)
Query: 472 CTLILTEGDSAKSLAVSGLGVVGRDKY--GVFPLRGKLLNVREATHKQILENAEINNLVK 529
L + EGDSA A G RD+ + PLRGK+LNV +A +IL+N EI L+
Sbjct: 1 SELYIVEGDSAGGSAKQG-----RDRRFQAILPLRGKILNVEKARLDKILKNEEIRALIT 55
Query: 530 ILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLL 582
LG + + D++ LRY +++IMTD D DG+HI+ L++ F L+
Sbjct: 56 ALGTGIGEDF----DLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLI 104
>gnl|CDD|216135 pfam00817, IMS, impB/mucB/samB family. These proteins are involved
in UV protection.
Length = 148
Score = 88.4 bits (220), Expect = 4e-20
Identities = 41/149 (27%), Positives = 67/149 (44%), Gaps = 34/149 (22%)
Query: 1619 IDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMGLNT 1678
IDMD F+ SV PEL+ +PVAV G + +A
Sbjct: 1 IDMDAFYASVERLRDPELRGKPVAVGGGNARGVVI--AASYEA----------------- 41
Query: 1679 REYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASL-TLNIEAVSLYTNES 1737
R+YG+ +GM + A K CP+L +VP DFE Y+ S + ++ +E S+ +E+
Sbjct: 42 RKYGVKSGMPLFEAKKLCPDLIVVPPDFELYRRASRRIAEILRRFSPPKVEVYSI--DEA 99
Query: 1738 FLN------------ALPEDIRQEVLDDL 1754
FL+ AL + +R+ + ++
Sbjct: 100 FLDLTGLERLFGGEEALAKRLRRAIAEET 128
Score = 64.9 bits (159), Expect = 8e-12
Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E Y+ + ++ + V S DE ++D + L L A LR IA
Sbjct: 70 ELYRRASRRIAEILRRFSPPK---VEVYSIDEAFLDLTGLE-RLFGGEEALAKRLRRAIA 125
Query: 1935 KETGCTCSTGFGSNKLQARLATK 1957
+ETG TCS G NKL A+LA+
Sbjct: 126 EETGLTCSIGIAPNKLLAKLASD 148
>gnl|CDD|222896 PHA02592, 52, DNA topisomerase II medium subunit; Provisional.
Length = 439
Score = 90.9 bits (226), Expect = 1e-18
Identities = 38/110 (34%), Positives = 55/110 (50%)
Query: 658 GRIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYK 717
I P +Y+PIIPMVL+NG GI TG+ T I H+P+ ++ + + G+D K +
Sbjct: 143 EHIPPAFYLPIIPMVLLNGVSGIATGYATNILPHSPKSVIKAVLAALNGKDITEPKVQFP 202
Query: 718 NFKGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTLDTLL 767
FKGE+ + + G + KL ITE+ V Y LD L
Sbjct: 203 EFKGEVVEIEPGSYEIRGTYELNGKTKLHITEIPVKYDRETYVAVLDPLE 252
Score = 33.9 bits (78), Expect = 1.1
Identities = 15/65 (23%), Positives = 30/65 (46%)
Query: 837 EAGSQTQEEEDPDKDYDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSD 896
E + + +D + D L+ M +S+T + + +L K+ ++ E KK +
Sbjct: 373 ELTEELSDNKDFGEYADKLVAMNIYSMTSDEREKLQKEAEELEKEHEYWKKTTAKKEYIK 432
Query: 897 DLDAL 901
DL+ L
Sbjct: 433 DLEEL 437
>gnl|CDD|130127 TIGR01055, parE_Gneg, DNA topoisomerase IV, B subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason. This protein is active as an
alpha(2)beta(2) heterotetramer [DNA metabolism, DNA
replication, recombination, and repair].
Length = 625
Score = 91.9 bits (228), Expect = 2e-18
Identities = 111/537 (20%), Positives = 208/537 (38%), Gaps = 77/537 (14%)
Query: 108 IKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYNDEEDKVTGVVPT 167
I + ++Q+ +I V++NG+G+PV H E V+ V
Sbjct: 54 IMVILHQD-QSIEVFDNGRGMPVDIHPKEG-----------------------VSAV--E 87
Query: 168 MIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVET--SCSEYKKSFKQVWKDN 225
+I L ++++ +GG +G G + N S + ++ Y +F +N
Sbjct: 88 VILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAF-----EN 142
Query: 226 MSKVTSPEI--KSGSKDDFTKITFTPDLTKFKMTSLD-KDMVDLITRRAYDAAASTKDVK 282
+KVT G + T + FTPD F + ++ +A + +
Sbjct: 143 GAKVTDLISAGTCGKRLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFE 202
Query: 283 VFLNGEKLPVKNFQDYVKLYTDRQDEDGDPV--------KIIYENVNPRWEVAIAPSDRG 334
+N K + N+ D +K Y + +GD ++ W + P
Sbjct: 203 DEVNNTK-ALWNYPDGLKDYLS-EAVNGDNTLPPKPFSGNFEGDDEAVEWALLWLPEGGE 260
Query: 335 FQQVSFVNSIATTKGGRHVDAVVDAI---VKQIIEVVKKKNKDLGCTI--IMLFGNKFNN 389
S+VN I T +GG HV+ + + +++ E+ + + T I + +
Sbjct: 261 LFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGVKLTAEDIWDRCSYVLS 320
Query: 390 VKNNKLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPT-----------FDSQ 438
+K Q A + +K+ +++N + +
Sbjct: 321 IKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKR 380
Query: 439 TKENMTLQKGSFGSTCVPKLEDANDAGTKNSIDCT-LILTEGDSAKSLAVSGLGVVGRDK 497
+ + +K + G KL D T+ ++ T L L EGDSA S R+
Sbjct: 381 AAKKVVRKKLTSGPALPGKLADC----TRQDLEGTELFLVEGDSAGG---SAKQARDREY 433
Query: 498 YGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMT 557
+ PL GK+LN E + ++L + EI+++ LG+ D+ LRYG++ I+
Sbjct: 434 QAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDS-----NDLSQLRYGKICILA 488
Query: 558 DQDQDGSHIKGLIINFIHHNWPTLLRLPFLEEFITPIIKATKAREELSFYSLPEFEE 614
D D DG HI L+ ++P L+ + P+ + ++E +Y+L E E+
Sbjct: 489 DADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKE--VYYALDEEEK 543
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 92.3 bits (230), Expect = 2e-18
Identities = 32/127 (25%), Positives = 44/127 (34%), Gaps = 19/127 (14%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGED----------P 709
EPE P +LVNG+ GI G T IP HN E++D + +I D
Sbjct: 154 KEPEVLPARFPNLLVNGSSGIAVGMATNIPPHNLGEVIDALIALIDNPDATIDELMEIIK 213
Query: 710 LPMKPWYKNFKG-----EIDYCGDSRFVVNGEIAILDDDK----LEITELQVGKWTTDYK 760
P P G E G V + I D + ITE+
Sbjct: 214 GPDFPTGGIIIGRSGIREAYETGRGSIRVRAKAEIEDTKNGREQIVITEIPYQVNKAKLI 273
Query: 761 DTLDTLL 767
+ + L+
Sbjct: 274 EKIAELV 280
>gnl|CDD|176454 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V. umuC
subunit of Pol V. Pol V is a bacterial translesion
synthesis (TLS) polymerase that consists of the
heterotrimer of one umuC and two umuD subunits.
Translesion synthesis is a process that allows the bypass
of a variety of DNA lesions. TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol V, RecA,
single stranded DNA-binding protein, beta sliding clamp,
and gamma clamp loading complex are responsible for
inducing the SOS response in bacteria to repair
UV-induced DNA damage.
Length = 344
Score = 88.0 bits (219), Expect = 4e-18
Identities = 54/194 (27%), Positives = 88/194 (45%), Gaps = 9/194 (4%)
Query: 1903 SCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLAT----KK 1958
S DE ++D + L+ L + A +R I +ETG + G G K A+LA KK
Sbjct: 97 SIDESFLDLTGSLRFGDLE--ELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKK 154
Query: 1959 AKPNGQFHLTPQIISDFMLNI-PLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNE 2017
G LT + + D +L I P+ D+ G+G KLN++G T GDL L+ +
Sbjct: 155 NPYGGVVDLTDEEVRDKLLKILPVGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLLRKK 214
Query: 2018 VGNKNGLTLYKHCRGEDDKELTFEHQ-RKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEK 2076
G G L + G D L +KS+ + ++G + E++ L + A +
Sbjct: 215 FG-VVGERLVRELNGIDCLPLEEYPPPKKSIGSSRSFGRDVTDLDELKQALAEYAERAAE 273
Query: 2077 RLEEVKMKGKCITL 2090
+L K + I++
Sbjct: 274 KLRRQKSVARTISV 287
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 87.8 bits (219), Expect = 3e-17
Identities = 50/134 (37%), Positives = 76/134 (56%), Gaps = 15/134 (11%)
Query: 443 MTLQKGSFGSTCVP-KLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKY--G 499
+T +K + S+ +P KL D + +K+ + L + EGDSA A G RD+
Sbjct: 394 LTRRKSALESSSLPGKLADCS---SKDPEESELYIVEGDSAGGSAKQG-----RDRRFQA 445
Query: 500 VFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQ 559
+ PLRGK+LNV +A +IL+N EI L+ LG + D+ LRY +++IMTD
Sbjct: 446 ILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDF----DISKLRYHKIIIMTDA 501
Query: 560 DQDGSHIKGLIINF 573
D DG+HI+ L++ F
Sbjct: 502 DVDGAHIRTLLLTF 515
Score = 68.2 bits (168), Expect = 4e-11
Identities = 91/366 (24%), Positives = 143/366 (39%), Gaps = 113/366 (30%)
Query: 42 LEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKI----FDEILVNACD 97
LE + RP YIGS R +H+ +Y+I DE L CD
Sbjct: 19 LEAVRKRPGMYIGSTGE---------RGLHHL----------VYEIVDNSIDEALAGYCD 59
Query: 98 NKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYNDE 157
+ I++T+N++ +I+V +NG+GIPV H P +
Sbjct: 60 H---------IEVTINED-GSITVTDNGRGIPVDIHPKTG--KPAV-------------- 93
Query: 158 EDKVTGVVPTMI-----FGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCS 212
E VV T++ FG Y KV+GG +G G + N S+ VE
Sbjct: 94 E-----VVLTVLHAGGKFG----GGGY-----KVSGGLHGVGVSVVNALSTWLEVE---- 135
Query: 213 EYKKSFKQVWKDN--------MSKVTSP-EIKSGSKDDFTKITFTPDLTKFKMTSLDKDM 263
V +D +P E+ + + T +TF PD F+ T D D
Sbjct: 136 --------VKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFKPDPEIFETTEFDYD- 186
Query: 264 VDLITRRAYDAAASTKDVKVFLN---GEKLPVKNFQ------DYVKLYTDRQDEDGDPV- 313
+ R + A K +K+ L + + F +YV+ Y +R E P+
Sbjct: 187 --TLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVE-YLNRNKE---PLH 240
Query: 314 -KIIY---ENVNPRWEVAIAPSDRGFQQ--VSFVNSIATTKGGRHVDAVVDAIVKQIIEV 367
+ IY E EVA+ +D G+ + +SF N+I T +GG H + A+ + I +
Sbjct: 241 EEPIYFEGEKDGIEVEVAMQYND-GYSENILSFANNINTHEGGTHEEGFKTALTRVINDY 299
Query: 368 VKKKNK 373
+K
Sbjct: 300 ARKNKL 305
>gnl|CDD|176456 cd01702, PolY_Pol_eta, DNA Polymerase eta. Pol eta, also called
Rad30A, is a translesion synthesis (TLS) polymerase.
Translesion synthesis is a process that allows the bypass
of a variety of DNA lesions. TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Unlike other
Y-family members, Pol eta can efficiently and accurately
replicate DNA past UV-induced lesions. Its activity is
initiated by two simultaneous interactions: the PIP box
in pol eta interacting with PCNA, and the UBZ
(ubiquitin-binding zinc finger) in pol eta interacting
with monoubiquitin attached to PCNA. Pol eta is more
efficient in copying damaged DNA than undamaged DNA and
seems to recognize when a lesion has been passed,
facilitating a lesion-dependent dissociation from the
DNA.
Length = 359
Score = 85.4 bits (212), Expect = 3e-17
Identities = 62/218 (28%), Positives = 102/218 (46%), Gaps = 20/218 (9%)
Query: 1893 SSESKIVSAVSCDEMYVDC-SQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQ 1951
+V S DE Y+D S++++E+ R+ + E G TCS G NK+
Sbjct: 106 KRFGDVVEKASIDEAYLDLGSRIVEEI-----------RQQVYDELGYTCSAGIAHNKML 154
Query: 1952 ARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKL-NSLGAQTCGDLQNI- 2009
A+LA+ KPN Q L ++ F+ ++P++ + G+G L ++ + LG T GD+
Sbjct: 155 AKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFR 214
Query: 2010 -SLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNY-GIRFQNNQEMETFL 2067
S LQ G K G LY RG D + + KS+ + N+ G + ++++ +L
Sbjct: 215 SSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPGKTALSTEDVQHWL 274
Query: 2068 KQLAGEVEKRLEEV----KMKGKCITLKLMVRSAEAPR 2101
LA E+ RLE+ + K + L L R R
Sbjct: 275 LVLASELNSRLEDDRYENNRRPKTLVLSLRQRGDGVRR 312
Score = 50.8 bits (122), Expect = 5e-06
Identities = 39/164 (23%), Positives = 63/164 (38%), Gaps = 50/164 (30%)
Query: 1618 HIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMGLN 1677
HIDMD FF V L+++PVAV + V A
Sbjct: 2 HIDMDAFFAQVEQVRLGLLRNDPVAVVQWNSIIA-----VSYAA---------------- 40
Query: 1678 TREYGLGNGMFVGHALKKCPNLKI--VPY---------------------DFEGYKEVSY 1714
R +G+ M + A KKCP+L + V + Y+ S
Sbjct: 41 -RAFGVTRFMTIDEAKKKCPDLILAHVATYKKGEDEADYHENPSPARHKVSLDPYRRASR 99
Query: 1715 CLYNLIASLTLNIEAVSLYTNESFLN---ALPEDIRQEVLDDLS 1755
+ N++ +E S+ +E++L+ + E+IRQ+V D+L
Sbjct: 100 KILNILKRFGDVVEKASI--DEAYLDLGSRIVEEIRQQVYDELG 141
>gnl|CDD|179473 PRK02794, PRK02794, DNA polymerase IV; Provisional.
Length = 419
Score = 82.7 bits (205), Expect = 5e-16
Identities = 61/202 (30%), Positives = 99/202 (49%), Gaps = 17/202 (8%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLT-------P-LQFASYLRETIAKETGCTCSTGFGSNKL 1950
V +S DE ++D LS T P + A + R + +E G T S G NK
Sbjct: 129 VEPLSIDEAFLD-------LSGTERLHGAPPAVVLARFARR-VEREIGITVSVGLSYNKF 180
Query: 1951 QARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNIS 2010
A++A+ KP G + F+ P+ + GVG + +L G +T GDLQ
Sbjct: 181 LAKIASDLDKPRGFSVIGRAEALAFLAPKPVGIIWGVGPATAARLARDGIRTIGDLQRAD 240
Query: 2011 LKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQL 2070
L G GL L++ RG DD++++ + + KSVSAE + + +++E L +L
Sbjct: 241 EADLMRRFG-SMGLRLWRLARGIDDRKVSPDREAKSVSAETTFETDLSDFEDLEPILWRL 299
Query: 2071 AGEVEKRLEEVKMKGKCITLKL 2092
+ +V +RL+ + G+ +TLKL
Sbjct: 300 SEKVSRRLKAAGLAGRTVTLKL 321
Score = 58.8 bits (143), Expect = 2e-08
Identities = 40/124 (32%), Positives = 61/124 (49%), Gaps = 22/124 (17%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMG 1675
I HID D F+ SV R +PEL+D+PV + GK GV A Y R
Sbjct: 38 IAHIDCDAFYASVEKRDNPELRDKPVIIGGGK-------RGVVSTA---CYIARI----- 82
Query: 1676 LNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYTN 1735
+G+ + M + ALK CP+ ++ D E Y V + ++ +LT +E +S+ +
Sbjct: 83 -----HGVRSAMPMFKALKLCPDAVVIKPDMEKYVRVGREVRAMMQALTPLVEPLSI--D 135
Query: 1736 ESFL 1739
E+FL
Sbjct: 136 EAFL 139
>gnl|CDD|235104 PRK03103, PRK03103, DNA polymerase IV; Reviewed.
Length = 409
Score = 80.8 bits (200), Expect = 2e-15
Identities = 59/208 (28%), Positives = 103/208 (49%), Gaps = 9/208 (4%)
Query: 1896 SKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLA 1955
+ +V S DE ++D + Q+L +PL+ A +++ I +ETG G G NKL A++A
Sbjct: 96 TDLVEPFSIDEQFLDVTGS-QKLFGSPLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMA 154
Query: 1956 T---KKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLK 2012
K P+G F L + + + +P+ L GVG + L +G +T G L N L+
Sbjct: 155 CDNFAKKNPDGLFTLDKEDVPADLWPLPVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLE 214
Query: 2013 RLQNEVGNKNGLTLYKHCRGEDDKELTFE-HQR-KSVSAEVNYGIRFQNNQEMETFLKQL 2070
RL+ G NG L++ G D +T R K++ ++ ++ +E++ L +L
Sbjct: 215 RLKKRWG-INGEVLWRTANGIDYSPVTPHSLDRQKAIGHQMTLPRDYRGFEEIKVVLLEL 273
Query: 2071 AGEVEKRLEEVKMKGKCITLKLMVRSAE 2098
EV +R G+ T+ + +R A+
Sbjct: 274 CEEVCRRARAKGYMGR--TVSVSLRGAD 299
Score = 49.2 bits (118), Expect = 2e-05
Identities = 36/127 (28%), Positives = 58/127 (45%), Gaps = 19/127 (14%)
Query: 1613 EPVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMN 1672
E VI+ +DM F+ SV +PEL+ PV V+ G+ + R GV A
Sbjct: 2 ERVILLVDMQSFYASVEKAANPELKGRPVIVS---GDPER-RSGVVLAACPL-------- 49
Query: 1673 RMGLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSL 1732
+ YG+ + A +KCP+L +V + Y +VS + ++ T +E S+
Sbjct: 50 -----AKAYGVKTAERLWEAQQKCPDLVVVKPRMQRYIDVSLQITRILEDFTDLVEPFSI 104
Query: 1733 YTNESFL 1739
+E FL
Sbjct: 105 --DEQFL 109
>gnl|CDD|221229 pfam11799, IMS_C, impB/mucB/samB family C-terminal. These proteins
are involved in UV protection.
Length = 136
Score = 71.8 bits (176), Expect = 2e-14
Identities = 26/85 (30%), Positives = 41/85 (48%)
Query: 2012 KRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLA 2071
LQ G G LY RG DD + +RKS+S+E + + +E+E L +LA
Sbjct: 1 AELQKRFGGVTGERLYNLARGIDDDPVEPREERKSISSERTFPRDLTDREELEALLLRLA 60
Query: 2072 GEVEKRLEEVKMKGKCITLKLMVRS 2096
E+ +RL + + +T+KL
Sbjct: 61 EELAERLRRRGLAARTVTVKLRYSD 85
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 77.4 bits (191), Expect = 2e-14
Identities = 43/152 (28%), Positives = 75/152 (49%), Gaps = 30/152 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
VI H+DM+ FF SV I + P LQ +P+AVA GN K R+G+ ++
Sbjct: 6 VIFHVDMNSFFASVEIAYDPSLQGKPLAVA---GN-EKERKGIIVTCSYE---------- 51
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R YG+ M + A + CP L + +F+ Y+E S ++ +++ T ++ VS+
Sbjct: 52 ---ARAYGIRTTMPLWEAKRLCPQLIVRRPNFDRYREASRQMFQILSEFTPLVQPVSI-- 106
Query: 1735 NESFLN-----------ALPEDIRQEVLDDLS 1755
+E +L+ + + I+Q +L +L
Sbjct: 107 DEGYLDITDCYALGSPLEIAKMIQQRLLTELQ 138
Score = 76.6 bits (189), Expect = 4e-14
Identities = 55/204 (26%), Positives = 98/204 (48%), Gaps = 7/204 (3%)
Query: 1896 SKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLA 1955
+ +V VS DE Y+D + +PL+ A +++ + E CS G NK A++A
Sbjct: 98 TPLVQPVSIDEGYLDITDCYA--LGSPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMA 155
Query: 1956 TKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQ 2015
+ KP G L + + + + +P+ ++ G+G KL +G QT GDL L+
Sbjct: 156 SDMKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLKDIGIQTIGDLAKADEHILR 215
Query: 2016 NEVGNKNGLTLYKHCRGEDDKELTFE--HQRKSVSAEVNYGIRFQNNQEMETFLKQLAGE 2073
++G NG+ L + G DD+ + E +Q KSV +E+ L++L+
Sbjct: 216 AKLG-INGVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLSHDMDEEKELLDVLRRLSKS 274
Query: 2074 VEKRLEEVKMKGKCITLKLMVRSA 2097
V KRL++ + +++M+R
Sbjct: 275 VSKRLQKKTVVSY--NVQIMIRYH 296
>gnl|CDD|213388 cd12145, Rev1_C, C-terminal domain of the Y-family polymerase Rev1.
Rev1 is a eukaryotic translesion synthesis (TLS)
polymerase; TLS is a process that allows the bypass of a
variety of DNA lesions. TLS polymerases lack proofreading
activity and have low fidelity and low processivity. They
use damaged DNA as templates and insert nucleotides
opposite the lesions. Rev1 has both structural and
enzymatic roles. Structurally, it is believed to interact
with other nonclassical polymerases and replication
machinery to act as a scaffold. The C-terminal domain
modeled here is essential for TLS and has been shown to
mediate interactions with the Rev7 subunit of the
B-family TLS polymerase Pol zeta (Rev3/Rev7), as well as
with the RIRs (Rev1-interacting regions) of polymerases
kappa, iota, and eta. Rev1 is known to actively promote
the introduction of mutations, potentially making it a
significant target for cancer treatment.
Length = 94
Score = 70.0 bits (172), Expect = 3e-14
Identities = 31/85 (36%), Positives = 57/85 (67%), Gaps = 1/85 (1%)
Query: 1808 LSSNVSLQEMRTMLREWMCESQ-PEPSDIEMFSEYLSNLVEERHLNPIVILLRFLRRHVG 1866
LS SL+E++T+L+EW+ + P D+E+F +YLS L++E++L + +LL++L+R V
Sbjct: 3 LSGATSLEEVKTLLKEWITSTPGPNEEDVELFVKYLSRLIDEKNLEKVDLLLKYLKRLVQ 62
Query: 1867 KKESTVWAEAYQEMLSCVQSAMKHK 1891
+ ++ W EAY ++ VQ+ +K
Sbjct: 63 QSGNSTWEEAYDRIIDVVQNRVKQT 87
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated.
Length = 351
Score = 74.4 bits (183), Expect = 1e-13
Identities = 38/159 (23%), Positives = 68/159 (42%), Gaps = 5/159 (3%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ + + + S+ + S DE Y+D S ++ ++ I
Sbjct: 79 EVYQQVSNRIMKLL----REYSEKIEIASIDEAYLDISDKVKNYQ-DAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + F+ + ++D+PG+G K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFINELDIADIPGIGDITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGE 2033
L LG D I L+ +G L+ R E
Sbjct: 194 LKKLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNE 232
Score = 35.9 bits (83), Expect = 0.21
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 17/126 (13%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+I+ +D D FF V +P L+ +PV V G G A ++
Sbjct: 2 IILFVDFDYFFAQVEEVLNPSLKGKPVVVCVYSGRFE--DSGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A K PN +P E Y++VS + L+ + IE S+
Sbjct: 50 ---ARKLGIKAGMPIVEAKKILPNAVYLPMRKEVYQQVSNRIMKLLREYSEKIEIASI-- 104
Query: 1735 NESFLN 1740
+E++L+
Sbjct: 105 DEAYLD 110
>gnl|CDD|179663 PRK03858, PRK03858, DNA polymerase IV; Validated.
Length = 396
Score = 73.5 bits (181), Expect = 3e-13
Identities = 53/195 (27%), Positives = 93/195 (47%), Gaps = 1/195 (0%)
Query: 1898 IVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATK 1957
+V +S DE ++D L + +S TP+Q A+ LR + +E G + G K A++A++
Sbjct: 93 LVEGLSIDEAFLDVGGL-RRISGTPVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQ 151
Query: 1958 KAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNE 2017
AKP+G + P F+ +P+ L GVG KL + G T GD+ + L +
Sbjct: 152 VAKPDGLLVVPPDRELAFLHPLPVRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVSL 211
Query: 2018 VGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKR 2077
+G G L+ D + + +R+SV A+ G + E++ + L V +R
Sbjct: 212 LGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALGRGPNSPAEVDAVVVALVDRVARR 271
Query: 2078 LEEVKMKGKCITLKL 2092
+ G+ + L+L
Sbjct: 272 MRAAGRTGRTVVLRL 286
Score = 52.3 bits (126), Expect = 2e-06
Identities = 36/156 (23%), Positives = 58/156 (37%), Gaps = 41/156 (26%)
Query: 1611 EPEPVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRT 1670
+ I+H D+D F+ SV R P L+ PV V GV A ++
Sbjct: 1 RADASILHADLDSFYASVEQRDDPALRGRPVIVG----------GGVVLAASYE------ 44
Query: 1671 MNRMGLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAV 1730
+ YG+ M A + CP +VP Y S ++ + T +E +
Sbjct: 45 -------AKAYGVRTAMGGRQARRLCPQAVVVPPRMSAYSRASKAVFEVFRDTTPLVEGL 97
Query: 1731 SLYTNESFLN----------------ALPEDIRQEV 1750
S+ +E+FL+ L +R+EV
Sbjct: 98 SI--DEAFLDVGGLRRISGTPVQIAARLRRRVREEV 131
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 69.5 bits (170), Expect = 2e-11
Identities = 72/295 (24%), Positives = 131/295 (44%), Gaps = 59/295 (20%)
Query: 338 VSFVNSIATTKGGRHVDAVVDAIVKQI------IEVVKKKNKDL-------GCTIIM--- 381
SF N+++TT G H+D AI + + K ++ G T I+
Sbjct: 425 KSFANNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVK 483
Query: 382 LFGNKFNNVKNNKL--QMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFD-SQ 438
L G +F+ KL + KT+++ V + F+ + I+ L F+ ++
Sbjct: 484 LNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAK 543
Query: 439 TKENMTLQKGS-FGSTCVP-KLEDANDAGTKNSIDCT-LILTEGDSAKSLAVSGLGVVGR 495
+++ QK + + ST +P KL D + I+ L + EG+SA A + R
Sbjct: 544 AAKDLIRQKNNQYYSTILPGKLVDC----ISDDIERNELFIVEGESA---AGNAKQARNR 596
Query: 496 DKYGVFPLRGKLLNVREAT-HKQILENAEINNLVKILGLQYS----KKYTTVEDMK---- 546
+ V PL+GK+LN+ + +K++ EN+EI L+ +GL + ++Y K
Sbjct: 597 EFQAVLPLKGKILNIEKIKNNKKVFENSEIKLLITSIGLSVNPVTWRQYDLSHGTKASKD 656
Query: 547 --------------------TLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTL 581
LRYG+++++TD D DG H++ L++ ++ P+L
Sbjct: 657 ESVQNNNSTLTKKKNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSL 711
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 69.0 bits (170), Expect = 2e-11
Identities = 49/142 (34%), Positives = 72/142 (50%), Gaps = 30/142 (21%)
Query: 443 MTLQKGSFGSTCVP-KLEDANDAGTKNSIDCTLILTEGDSA----KSLAVSGLGVVGRD- 496
+T +KG+ +P KL D + K+ L L EGDSA K GRD
Sbjct: 392 LTRRKGALDIAGLPGKLADCQE---KDPALSELYLVEGDSAGGSAKQ---------GRDR 439
Query: 497 KY-GVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVE----DMKTLRYG 551
K+ + PL+GK+LNV +A ++L + EI L+ LG + + LRY
Sbjct: 440 KFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALG-------CGIGRDEFNPDKLRYH 492
Query: 552 RLMIMTDQDQDGSHIKGLIINF 573
+++IMTD D DGSHI+ L++ F
Sbjct: 493 KIIIMTDADVDGSHIRTLLLTF 514
Score = 38.9 bits (92), Expect = 0.040
Identities = 39/188 (20%), Positives = 65/188 (34%), Gaps = 66/188 (35%)
Query: 89 DEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHL 148
DE L CD+ I +T++ + ++SV +NG+GIP H +E + +I L
Sbjct: 51 DEALAGHCDD---------ITVTIHAD-GSVSVSDNGRGIPTDIHPEEGVSAAEVIMTVL 100
Query: 149 LTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVE 208
++ ++Y KV+GG +G G + N S +
Sbjct: 101 HAGGKFDQ--------------------NSY-----KVSGGLHGVGVSVVNALSEWLELT 135
Query: 209 TSCSEYKKSFKQVWKDN----MS----------KVTSPEIKSGSKDDFTKITFTPDLTKF 254
+ +D KV K+G T++ F P F
Sbjct: 136 ------------IRRDGKIHEQEFEHGVPVAPLKVVGETDKTG-----TEVRFWPSPEIF 178
Query: 255 KMTSLDKD 262
+ T D D
Sbjct: 179 ENTEFDYD 186
>gnl|CDD|176457 cd01703, PolY_Pol_iota, DNA Polymerase iota. Pol iota, also called
Rad30B, is a translesion synthesis (TLS) polymerase.
Translesion synthesis is a process that allows the bypass
of a variety of DNA lesions. TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol iota is
thought to be one of the least efficient polymerases,
particularly when opposite pyrimidines; it can
incorporate the correct nucleotide opposite a purine much
more efficiently than opposite a pyrimidine, and prefers
to insert guanosine instead of adenosine opposite
thymidine. Pol iota is believed to use Hoogsteen rather
than Watson-Crick base pairing, which may explain the
varying efficiency for different template nucleotides.
Length = 379
Score = 62.1 bits (151), Expect = 1e-09
Identities = 59/246 (23%), Positives = 102/246 (41%), Gaps = 37/246 (15%)
Query: 1905 DEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQ 1964
DE ++D +++ L + A +RE I E G TC G SNKL A+L KPN Q
Sbjct: 98 DENFMDVTEM--RLLVAS-HIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQ 154
Query: 1965 FHLTPQIISDFMLNIPLSDL---PGVGHSLLFKLNSLGAQTCGDLQN------------- 2008
L P +D M + L DL PG+G+ KL + G + DLQ
Sbjct: 155 TTLLPPSCADLMDFMDLHDLRKIPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAP 214
Query: 2009 --ISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQR-KSVSAEVNYG-IRFQNNQEME 2064
+ L + E G G ++K G D + + +S E +Y + +E
Sbjct: 215 SLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYKKCSLEEIREAR 274
Query: 2065 TFLKQLAGEVEKRLEEVKMKGKC------ITLKLMVRSAEAPREASKFLGHGVCDYITKS 2118
+++L + +R+++ + K TL+L +R + ++ + +K
Sbjct: 275 NKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTSTKKHY--------NRESKQ 326
Query: 2119 SSLPIY 2124
+ +P +
Sbjct: 327 APIPSH 332
Score = 46.3 bits (110), Expect = 1e-04
Identities = 29/128 (22%), Positives = 54/128 (42%), Gaps = 31/128 (24%)
Query: 1618 HIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQR----TMNR 1673
H+D+DCF+ V P L+ +P+ + +Q+ T N
Sbjct: 2 HLDLDCFYAQVEEIRDPSLKSKPLGI-----------------------QQKYIVVTCNY 38
Query: 1674 MGLNTREYGLGNGMFVGHALKKCPNLKIVP-YDFEGYKEVSYCLYNLIASLTLNIEAVSL 1732
R G+ M + A + CP+L +V D ++++S +Y L+ S + N L
Sbjct: 39 EA---RRLGVKKLMSIKDAKEICPDLVLVNGEDLTPFRDMSKKVYRLLRSYSWNDRVERL 95
Query: 1733 YTNESFLN 1740
+E+F++
Sbjct: 96 GFDENFMD 103
>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. The GyrB
dimerizes in response to ATP binding, and is homologous
to the N-terminal half of eukaryotic Topo II and the
ATPase fragment of MutL. Type II DNA topoisomerases
catalyze the ATP-dependent transport of one DNA duplex
through another, in the process generating transient
double strand breaks via covalent attachments to both
DNA strands at the 5' positions. Included in this group
are proteins similar to human MLH1 and PMS2. MLH1 forms
a heterodimer with PMS2 which functions in meiosis and
in DNA mismatch repair (MMR). Cells lacking either hMLH1
or hPMS2 have a strong mutator phenotype and display
microsatellite instability (MSI). Mutation in hMLH1
accounts for a large fraction of Lynch syndrome (HNPCC)
families.
Length = 107
Score = 55.0 bits (133), Expect = 9e-09
Identities = 29/157 (18%), Positives = 43/157 (27%), Gaps = 63/157 (40%)
Query: 295 FQDYVKLYTDRQDEDGDPVKIIYENVNP---RWEVAIAPSD----RGFQQVSFVNSIATT 347
+D + + D K+IY R E AI+ D +Q SFVN
Sbjct: 1 LKDRLAEILGDKVAD----KLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVR 56
Query: 348 KGGRHVDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFGNKFNNVKNNKLQMAKTLIDIGVR 407
+GG HV AV +A +
Sbjct: 57 EGGTHVKAVREAYTR--------------------------------------------- 71
Query: 408 LGGMALKPFQVKNHIWIFINCLIVN--PTFD-SQTKE 441
AL V+ + ++ I + TKE
Sbjct: 72 ----ALNGDDVRRYPVAVLSLKIPPSLVDVNVHPTKE 104
>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain. The BRCT domain is
found predominantly in proteins involved in cell cycle
checkpoint functions responsive to DNA damage. The BRCT
domain of XRCC1 forms a homodimer in the crystal
structure. This suggests that pairs of BRCT domains
associate as homo- or heterodimers. BRCT domains are
often found as tandem-repeat pairs. Structures of the
BRCA1 BRCT domains revealed a basis for a widely utilised
head-to-tail BRCT-BRCT oligomerisation mode. This
conserved tandem BRCT architecture facilitates formation
of the canonical BRCT phospho-peptide interaction cleft
at a groove between the BRCT domains. Disease associated
missense and nonsense mutations in the BRCA1 BRCT domains
disrupt peptide binding by directly occluding this
peptide binding groove, or by disrupting key conserved
BRCT core folding determinants.
Length = 77
Score = 53.5 bits (129), Expect = 1e-08
Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 13/87 (14%)
Query: 1342 RGGIFQGVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYHHYESSRTTHIIASN 1401
+ +F+G + G EEL+ L+ GG S +TTH+I
Sbjct: 2 KEKLFKGKTFVITGLDS-----------LEREELEELIEKLGGKVTDSLSKKTTHVIVGE 50
Query: 1402 LPHTK--IKKLKPGDKIIKPEWIVDSI 1426
T +K + G I+ EW++D I
Sbjct: 51 NAGTLKLLKAIALGIPIVTEEWLLDCI 77
>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1),
carboxy-terminal domain. The BRCT domain is found within
many DNA damage repair and cell cycle checkpoint
proteins. The unique diversity of this domain superfamily
allows BRCT modules to interact forming homo/hetero BRCT
multimers, BRCT-non-BRCT interactions, and interactions
within DNA strand breaks.
Length = 72
Score = 50.0 bits (120), Expect = 2e-07
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 12/81 (14%)
Query: 1348 GVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYHHYESSRTTHIIASNL--PHT 1405
G+ + G +ELK L+ GG S +TTH+I + P
Sbjct: 1 GLTFVITGDLPS----------EERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKK 50
Query: 1406 KIKKLKPGDKIIKPEWIVDSI 1426
+K +K G I+ PEW++D +
Sbjct: 51 LLKAIKLGIPIVTPEWLLDCL 71
>gnl|CDD|140232 PTZ00205, PTZ00205, DNA polymerase kappa; Provisional.
Length = 571
Score = 54.3 bits (130), Expect = 7e-07
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 22/116 (18%)
Query: 1617 MHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMGL 1676
+H+DMD F+ +V I+ HPE P+A+ + +T N +
Sbjct: 136 IHLDMDMFYAAVEIKKHPEYAAIPLAIG-------------------TMTMLQTANYVA- 175
Query: 1677 NTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSL 1732
R G+ GM ALK CPNL I+P DF+ Y E S + ++A N + L
Sbjct: 176 --RGRGIRQGMPGFLALKICPNLLILPPDFDAYNEESNTVRRIVAEYDPNYISFGL 229
Score = 48.9 bits (116), Expect = 3e-05
Identities = 47/208 (22%), Positives = 89/208 (42%), Gaps = 17/208 (8%)
Query: 1901 AVSCDEMYVDCSQLLQ--ELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ DE+ ++ S ++ E + T AS LR + ET T S G G A++A+
Sbjct: 226 SFGLDELTLEVSAYIERFEGTKTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNI 285
Query: 1959 AKPNGQFHLTPQIISDFML---NIPLSDLPGVGHSLLFKLNSLGAQTCGDLQN--ISLKR 2013
KPNGQ L D M ++ L +PGVG L LG T D+ N + L
Sbjct: 286 NKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLKGLGITTLSDIYNRRVELCY 345
Query: 2014 LQNE------VGNKNGLTLYK---HCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEME 2064
+ + +G G+ + ++ E QRK++S+E ++ + + ++
Sbjct: 346 ILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISSERSFTT-PRTKEGLQ 404
Query: 2065 TFLKQLAGEVEKRLEEVKMKGKCITLKL 2092
+ + + + + ++ + I+L +
Sbjct: 405 EMVDTVFNGAYEEMRKSELMCRQISLTI 432
>gnl|CDD|176458 cd03468, PolY_like, DNA Polymerase Y-family. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active sites
of TLS polymerases are large and flexible to allow the
accomodation of distorted bases. Expression of Y-family
polymerases is often induced by DNA damage and is
believed to be highly regulated. TLS is likely induced by
the monoubiquitination of the replication clamp PCNA,
which provides a scaffold for TLS polymerases to bind in
order to access the lesion. Because of their high error
rates, TLS polymerases are potential targets for cancer
treatment and prevention.
Length = 335
Score = 50.8 bits (122), Expect = 4e-06
Identities = 26/157 (16%), Positives = 47/157 (29%), Gaps = 5/157 (3%)
Query: 1938 GCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNS 1997
G + G A L + G + +L + + L
Sbjct: 129 GLSARAGIADTPGAAWLLARAGGGRGVLRREALAAALVLLAPLPVAALRLPPETVELLAR 188
Query: 1998 LGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKS--VSAEVNYGI 2055
LG +T GDL + L G L G D + L F + E+
Sbjct: 189 LGLRTLGDLAALPRAELARRFGL-ALLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLEE 247
Query: 2056 RFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKL 2092
+ + L++L ++ L + + ++L L
Sbjct: 248 --PIARGLLFPLRRLLEQLCAFLALRGLGARRLSLTL 282
>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain.
Length = 78
Score = 46.2 bits (110), Expect = 4e-06
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 14/87 (16%)
Query: 1344 GIFQGVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYHHYESS-RTTHIIASNL 1402
+F+G ++ G +ELK L+ GG SS TTH+I +
Sbjct: 2 KLFKGKTFYITGSFDK----------EERDELKELIEALGGKVTSSLSSKTTTHVIVGSP 51
Query: 1403 P---HTKIKKLKPGDKIIKPEWIVDSI 1426
+K + G I+K EW++D +
Sbjct: 52 EGGKLELLKAIALGIPIVKEEWLLDCL 78
>gnl|CDD|179607 PRK03609, umuC, DNA polymerase V subunit UmuC; Reviewed.
Length = 422
Score = 48.6 bits (116), Expect = 3e-05
Identities = 35/123 (28%), Positives = 52/123 (42%), Gaps = 10/123 (8%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
V S DE + D + + LT F +R T+ + T T G K A+LA
Sbjct: 95 VEIYSIDEAFCDLTGVRNCRDLT--DFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHA 152
Query: 1959 AKP-NGQFH----LT-PQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDL--QNIS 2010
AK Q L+ + + P+ ++ GVG + KLN++G +T DL NI
Sbjct: 153 AKKWQRQTGGVVDLSNLERQRKLLSLQPVEEVWGVGRRISKKLNAMGIKTALDLADTNIR 212
Query: 2011 LKR 2013
R
Sbjct: 213 FIR 215
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 42.4 bits (100), Expect = 1e-04
Identities = 25/116 (21%), Positives = 38/116 (32%), Gaps = 34/116 (29%)
Query: 472 CTLILTEGDS-AKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKI 530
LI+ EG S A +LA +G V L G LN L ++
Sbjct: 1 KKLIIVEGPSDALALAQAG-----GYGGAVVALGGHALN------------KTRELLKRL 43
Query: 531 LGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLPF 586
LG ++I TD D++G I ++ + + RL
Sbjct: 44 LG----------------EAKEVIIATDADREGEAIALRLLELLKSLGKKVRRLLL 83
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine kinase,
DNA gyrase B and HSP90.
Length = 111
Score = 42.3 bits (100), Expect = 2e-04
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVP 141
L ++ +L NA + ++ + + + I+V +NG GIP K+F P
Sbjct: 5 RLRQVLSNLLDNAIKHAPAGGEIE-VTLERDGGRLRITVEDNGIGIP--PEDLPKIFEP 60
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesises the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyze the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 86
Score = 41.5 bits (98), Expect = 2e-04
Identities = 21/103 (20%), Positives = 34/103 (33%), Gaps = 32/103 (31%)
Query: 473 TLILTEGDS-AKSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
LI+ EG S A +L +G G V G L++ I L K L
Sbjct: 1 ELIIVEGPSDAIALEKAG----GVLGGAVVATSGHALDL-----------EHIKELKKAL 45
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFI 574
+++ TD D++G I ++ +
Sbjct: 46 K----------------GAKEVILATDPDREGEAIALKLLELL 72
>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
Length = 805
Score = 45.8 bits (110), Expect = 3e-04
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 669 IPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDP 709
P +LVNG+ GI G T IP HN E++D +I ++P
Sbjct: 160 FPNLLVNGSSGIAVGMATNIPPHNLGEVIDACLALI--DNP 198
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 45.5 bits (107), Expect = 4e-04
Identities = 80/394 (20%), Positives = 161/394 (40%), Gaps = 36/394 (9%)
Query: 954 KASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKKESEYSSTVC 1013
KA KK AAK A + +D +++ + A+ KKK A KKA AKK++E
Sbjct: 1337 KAEEAKKAAEAAKAEAEAA--ADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394
Query: 1014 LFKRFGRRNCNDGGLIPKSQREGAQDSDL----ENNCRLDEVERKEKEEENSNITKIKSK 1069
K+ + + K+ + + E + DE ++K +E + ++ K K++
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAE 1454
Query: 1070 LKEKG---SKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKPNEVLPGWESN 1126
+K KK D+ A + K +E KAE+A KK +E E+
Sbjct: 1455 EAKKAEEAKKKAEEAKKADEAKKKAEEAK---KADEAKKKAEEAK--KKADEAKKAAEAK 1509
Query: 1127 LRP-SADKAESRKRTQTSQGTESEERKGHLRRW--RRKEEESTQTVQVELREGVNISAPK 1183
+ A KAE K+ ++ E ++ ++ ++K +E + +++ E +
Sbjct: 1510 KKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEA 1569
Query: 1184 PQASSTKN-ASNEDFLGEFYNKSRLHHLSTMGSMFKQYVNQLISLQQDKQLPAIQVISIR 1242
+A KN A + + ++R+ + + K+ + ++ ++ A ++
Sbjct: 1570 KKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEEL---- 1625
Query: 1243 SPRARPPRRSSTMGSMFKQYVNELREKHDGVFRGIEAIRKWKTSLGITEDEDLEETFSDN 1302
+++ K+ V +L++K + E ++K + I E+ ++ D
Sbjct: 1626 -------KKAEEE----KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDK 1674
Query: 1303 PSPSEPKTTAPKKKKKGGYMEAKKRKLEEQFELE 1336
E K +KK EA K++ EE + E
Sbjct: 1675 KKAEEAKKAEEDEKKAA---EALKKEAEEAKKAE 1705
Score = 40.9 bits (95), Expect = 0.010
Identities = 59/261 (22%), Positives = 98/261 (37%), Gaps = 27/261 (10%)
Query: 954 KASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKKESEYSSTVC 1013
KA KKK AK+ A +D + ++ A KK AKKA AKK E
Sbjct: 1491 KAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADE 1550
Query: 1014 LFKRFGRRNCNDGGLIPKSQRE---------------GAQDSDLENNCRLDEVERKEKEE 1058
L K + + ++++ A+++ +E +L E E+K K E
Sbjct: 1551 LKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAE 1610
Query: 1059 E--NSNITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKP 1116
E + KIK++ +K +++ + L + E K E K + A KK
Sbjct: 1611 EAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKA 1670
Query: 1117 NEVLPGWESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTV-QVELRE 1175
E + A KAE ++ + E ++KE E + +++ E
Sbjct: 1671 EE-----DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAE 1725
Query: 1176 GVNISAPKPQASSTKNASNED 1196
N K +A K + ED
Sbjct: 1726 EEN----KIKAEEAKKEAEED 1742
Score = 40.1 bits (93), Expect = 0.017
Identities = 76/387 (19%), Positives = 140/387 (36%), Gaps = 49/387 (12%)
Query: 954 KASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASR-KKKTAAAKKAKPAKKESEYSSTV 1012
KA KK A K+ + + ++ A KKK AKKA AKK++E +
Sbjct: 1426 KAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKA 1485
Query: 1013 CLFKRFGRRNCNDGGLIPKSQREGAQDSDL---ENNCRLDEVERKEKEEENSNITKIKSK 1069
K+ K+ + + E + DE ++ E+ ++ K + K
Sbjct: 1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEK 1545
Query: 1070 LKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAE--KAAAPKKPNEVLPGWESNL 1127
K KK L ++ + ++ E L KAE K A + EV+ +E
Sbjct: 1546 KKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEK 1605
Query: 1128 RPSAD---KAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTVQVELREGVNISAPKP 1184
+ A+ KAE K EE+K + +++ EE + +++ E N K
Sbjct: 1606 KMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEN----KI 1661
Query: 1185 QASSTKNASNEDFLGEFYNKSRLHHLSTMGSMFKQYVNQLISLQQDKQLPAIQVISIRSP 1244
+A+ + ED K+ + ++D++ A +
Sbjct: 1662 KAAEEAKKAEED---------------------KKKAEEAKKAEEDEKKAAEAL------ 1694
Query: 1245 RARPPRRSSTMGSMFKQYVNELREKHDGVFRGIEAIRKWKTSLGITEDEDLEETFSDNPS 1304
+ + + EL++K + E ++K + I +E +E D
Sbjct: 1695 ----KKEAEE-----AKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKK 1745
Query: 1305 PSEPKTTAPKKKKKGGYMEAKKRKLEE 1331
E K +KKK + +++K EE
Sbjct: 1746 AEEAKKDEEEKKKIAHLKKEEEKKAEE 1772
Score = 34.3 bits (78), Expect = 1.0
Identities = 49/240 (20%), Positives = 93/240 (38%), Gaps = 18/240 (7%)
Query: 959 KKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKKESEYSSTVCLFKRF 1018
+K K+ K + + ++ KKK AKKA AKK++E +
Sbjct: 1277 ARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEA--------- 1327
Query: 1019 GRRNCNDGGLIPKSQREGAQDSDLENNCRLDEVERKEKEEENSNITKIKSKLKEKGSKKR 1078
++ + + ++ A+ + E DE E E++ E + K ++K K +KK+
Sbjct: 1328 -KKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKK 1386
Query: 1079 NPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKPNEVLPGWESNLRPSAD---KAE 1135
D A + K +EL +KAAA KK + + + + KAE
Sbjct: 1387 AEEKKKADEAKKKA-EEDKKKADEL----KKAAAAKKKADEAKKKAEEKKKADEAKKKAE 1441
Query: 1136 SRKRTQTSQGTESEERKGHLRRWRRKEEESTQTVQVELREGVNISAPKPQASSTKNASNE 1195
K+ ++ E +K + + +E + + + E K +A K ++E
Sbjct: 1442 EAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADE 1501
Score = 33.2 bits (75), Expect = 2.6
Identities = 37/182 (20%), Positives = 71/182 (39%), Gaps = 13/182 (7%)
Query: 987 ASRKKKTAAAKKAKPAKKESEYSSTVCLFKRFGRRNCNDGGLIPKSQREGAQDSDLENNC 1046
A +K A+KA+ AKK + K R D +++ E
Sbjct: 1160 AEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARK-------AEEER 1212
Query: 1047 RLDEVERKEKEEENSNITKIK-SKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLI 1105
+ +E + E ++ + K + +K + +KK + ++ R + I
Sbjct: 1213 KAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAI 1272
Query: 1106 KAEKAAAPKKPNEVLPGWESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEES 1165
KAE+A +K +E+ E A KAE +K+ ++ E +K ++K EE+
Sbjct: 1273 KAEEA---RKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKAD--EAKKKAEEA 1327
Query: 1166 TQ 1167
+
Sbjct: 1328 KK 1329
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 45.1 bits (108), Expect = 4e-04
Identities = 17/37 (45%), Positives = 22/37 (59%)
Query: 669 IPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIR 705
P +L+NGA GI G T IP HN RE++D +I
Sbjct: 165 FPNLLLNGATGIAVGMATDIPPHNLREVIDAAIHLID 201
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 41.5 bits (98), Expect = 5e-04
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVNQETN--TISVWNNGKGIPVVEHKDEKMFV 140
L ++ +L NA + I +T+ ++ + I+V +NG GIP EK+F
Sbjct: 5 RLRQVLSNLLDNAIKYTPEGGR---ITVTLERDGDHVEITVEDNGPGIP--PEDLEKIFE 59
Query: 141 P 141
P
Sbjct: 60 P 60
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 44.2 bits (105), Expect = 9e-04
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 645 LHKVTSDSISMFIGRI-EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRM 703
+ K T D + + G EP P +LVNG+ GI G T IP HN EI+D +
Sbjct: 131 IDKETVDFVPNYDGSEQEPTVLPSRFPNLLVNGSSGIAVGMATNIPPHNLGEIIDALLAY 190
Query: 704 IRGED 708
I D
Sbjct: 191 IDNPD 195
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 40.3 bits (95), Expect = 0.001
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 84 LYKIFDEILVNACDNKQRDPKMNCIKITVNQETN--TISVWNNGKGIPVVEHKDEKMFVP 141
L ++ +L NA + I I+V ++ + I V +NG GIP E E++F
Sbjct: 1 LQQVLLNLLSNAIKHTPEGGG--RITISVERDGDHLEIRVEDNGPGIP--EEDLERIFER 56
>gnl|CDD|238419 cd00822, TopoII_Trans_DNA_gyrase, TopoIIA_Trans_DNA_gyrase:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to the B subunits
of E. coli DNA gyrase and E. coli Topoisomerase IV which
are heterodimers composed of two subunits. The type
IIA enzymes are the predominant form of topoisomerase
and are found in some bacteriophages, viruses and
archaea, and in all bacteria and eukaryotes. All type
IIA topoisomerases are related to each other at amino
acid sequence level, though their oligomeric
organization sometimes differs. TopoIIA enzymes cut
both strands of the duplex DNA to remove (relax) both
positive and negative supercoils in DNA. These enzymes
covalently attach to the 5' ends of the cut DNA,
separate the free ends of the cleaved strands, pass
another region of the duplex through this gap, then
rejoin the ends. TopoIIA enzymes also catenate/
decatenate duplex rings. E.coli DNA gyrase is a
heterodimer composed of two subunits. E. coli DNA gyrase
B subunit is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes.
Length = 172
Score = 41.8 bits (99), Expect = 0.001
Identities = 35/149 (23%), Positives = 57/149 (38%), Gaps = 38/149 (25%)
Query: 297 DYVKLYTDRQDEDG--DPVKIIYENVNPRWEVAIAPSDRGFQQV--SFVNSIATTKGGRH 352
D+V+ ++ E +P+ I E EVA+ +D + + SFVN+I T +GG H
Sbjct: 5 DFVE-ELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTD-SYSENILSFVNNIPTPEGGTH 62
Query: 353 VDAVVDAIVKQIIEVVKKKNKDLGCTIIMLFGNKFNNVKNNKLQMAKTLIDIGVRLGGMA 412
A+ + I + KK N L K + + DI L +
Sbjct: 63 ETGFRAALTRAINDYAKKNN---------LLKKKDVKLTGD---------DIREGLTAV- 103
Query: 413 LKPFQVKNHIWIFINCLIVNPTFDSQTKE 441
I+ + P F+ QTK+
Sbjct: 104 -------------ISVKVPEPQFEGQTKD 119
>gnl|CDD|233255 TIGR01061, parC_Gpos, DNA topoisomerase IV, A subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 738
Score = 43.3 bits (102), Expect = 0.002
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 661 EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMI 704
EP + P +L+NGA GI G+ T IP HN E++D + I
Sbjct: 148 EPTVLPALFPNLLINGATGIAAGYATNIPPHNLNEVIDALIYRI 191
>gnl|CDD|236598 PRK09631, PRK09631, DNA topoisomerase IV subunit A; Provisional.
Length = 635
Score = 42.8 bits (101), Expect = 0.002
Identities = 32/100 (32%), Positives = 48/100 (48%), Gaps = 6/100 (6%)
Query: 661 EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNFK 720
EP IP++L+ GAEGI G TKI HN EI+ +K + GE + P +
Sbjct: 137 EPLCLPAKIPVILIQGAEGIAVGMATKILPHNFNEILQAVKSELLGE-SFALYPDFPT-G 194
Query: 721 GEIDYC----GDSRFVVNGEIAILDDDKLEITELQVGKWT 756
G +D G+ + +V +I D+ + I E+ G T
Sbjct: 195 GIVDVSEYADGNGKVLVRAKIETKDEKTIVIREIPFGTTT 234
>gnl|CDD|222719 pfam14377, DUF4414, Domain of unknown function (DUF4414). This
family is frequently found on DNA binding proteins of the
URE-B1 type and on ligases.
Length = 105
Score = 38.1 bits (89), Expect = 0.007
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 1735 NESFLNALPEDIRQEVLDDLSRQQSVLSREQNTTEPLA 1772
N FL ALP +IR+EVL +++ +RE
Sbjct: 41 NPEFLAALPPEIREEVLQQERQERQRRAREIAAAGAAT 78
Score = 36.6 bits (85), Expect = 0.020
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 1737 SFLNALPEDIRQEVLDD----LSRQQSVLSREQNTT 1768
+FL ALPED+R+EV+ RQ + S E+ T
Sbjct: 4 TFLAALPEDLREEVIAQQLRASVRQSTSASGEEPTE 39
>gnl|CDD|130134 TIGR01062, parC_Gneg, DNA topoisomerase IV, A subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 735
Score = 41.0 bits (96), Expect = 0.007
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 644 NLHKVTSDSISMFIGRIEPEWYIPI-IPMVLVNGAEGIGTGWMTKIPNHNPREIVD 698
L + T D F G + +P +P +L+NG GI G T IP HN E+ D
Sbjct: 131 ELGQGTVDFRPNFDGTLLEPVILPARLPNILLNGTTGIAVGMATDIPPHNLHELAD 186
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 39.6 bits (93), Expect = 0.022
Identities = 33/102 (32%), Positives = 47/102 (46%), Gaps = 12/102 (11%)
Query: 670 PMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNFK--GEIDYCG 727
P++L GAEGI G TKI HN E++D ++G++ Y +F G ID
Sbjct: 165 PLLLAQGAEGIAVGLSTKILPHNFNELIDASIAYLKGKEF----KLYPDFPTGGIIDVSN 220
Query: 728 ------DSRFVVNGEIAILDDDKLEITELQVGKWTTDYKDTL 763
R V +I LD L ITE+ G T+ D++
Sbjct: 221 YNDGERGGRVRVRAKIEKLDKKTLVITEIPYGTTTSSLIDSI 262
>gnl|CDD|204747 pfam11798, IMS_HHH, IMS family HHH motif. These proteins are
involved in UV protection, eg.
Length = 32
Score = 34.3 bits (80), Expect = 0.023
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 1972 ISDFMLNIPLSDLPGVGHSLLFKLNSLG 1999
+ +F+ +P+S +PG+G KL +LG
Sbjct: 4 VPEFLWPLPISKIPGIGRKTAEKLEALG 31
>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated.
Length = 430
Score = 39.2 bits (91), Expect = 0.025
Identities = 36/205 (17%), Positives = 66/205 (32%), Gaps = 32/205 (15%)
Query: 798 DSEEEEIEEVFHDNELAKPQKTGPQLERQERQAAEGEDDEAGSQTQEEEDPDKDYDYLLG 857
D E+ + E E A+ + + E + E ++ +
Sbjct: 6 DLEDLKKEAARRAKEEARKRLVAKHGAEISKLEEENREKEKALPKNDDMTIE-------- 57
Query: 858 MTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDALREKDKIHPCPGGNRTR 917
E K K L K++ ++ ++ + K + +
Sbjct: 58 --------EAKRRAAAAAKAKAAALAKQKREGTEEVTEEEKAKAKAK-----AAAAAKAK 104
Query: 918 GLALKRQTRYQPSNRVLTSRDEPMVVSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDL 977
AL +Q R V+ E A KA+ K K AA + + ++
Sbjct: 105 AAALAKQKREGTEE-----------VTEEEKAAAKAKAAAAAKAKAAALAKQKREGTEEV 153
Query: 978 SDSDGDSDFASRKKKTAAAKKAKPA 1002
++ + ++D K K AAA KAK A
Sbjct: 154 TEEEEETDKEKAKAKAAAAAKAKAA 178
Score = 33.0 bits (75), Expect = 2.0
Identities = 20/56 (35%), Positives = 22/56 (39%)
Query: 947 EDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPA 1002
E+ KA K AAK A S +GDS K K AA KAK A
Sbjct: 193 EEVTEEEKAKAKAKAAAAAKAKAAALAKQKASQGNGDSGDEDAKAKAIAAAKAKAA 248
Score = 31.5 bits (71), Expect = 5.4
Identities = 39/207 (18%), Positives = 76/207 (36%), Gaps = 27/207 (13%)
Query: 800 EEEEIEEVFHDNELAKPQKTGPQLERQERQAAEGEDDEAGSQTQEEEDPDKDYDYLLGMT 859
E ++EE + E A P+ +E +R+AA +A + +++ + ++
Sbjct: 33 EISKLEEENREKEKALPKNDDMTIEEAKRRAAAAAKAKAAALAKQKREGTEE-------- 84
Query: 860 FWSLTMERKNELLKKRDD----KMTELNILKKKAPTDLWSDDLDALREKDKIHPCPGGNR 915
+T E K + K K L K++ ++ ++ A + K +
Sbjct: 85 ---VTEEEKAKAKAKAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAA-----AAAK 136
Query: 916 TRGLALKRQTRYQPSNRVLTSRDEPMVVSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSS 975
+ AL +Q R + + + A A+ K A ++ A + +
Sbjct: 137 AKAAALAKQKREGTEEVTEEEEETDKEKAKAKAA----AAAKAKAAALAKQKAAEAGEGT 192
Query: 976 DLSDSDGDSDFASRKKKTAAAKKAKPA 1002
+ + A K K AAA KAK A
Sbjct: 193 EEVTEEEK---AKAKAKAAAAAKAKAA 216
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 39.3 bits (92), Expect = 0.028
Identities = 19/38 (50%), Positives = 23/38 (60%)
Query: 661 EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVD 698
EPE P +LVNGA GI G T IP HN +E++D
Sbjct: 160 EPEVLPARYPNLLVNGAFGIAVGLATNIPPHNLKEVID 197
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 35.9 bits (82), Expect = 0.23
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 77 EITYVPGLYKIFDEILVNACDN--KQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHK 134
E+ YV G + ++LVN N K I + + E TISV + G GIP E +
Sbjct: 218 ELPYVLGDPERLRQVLVNLLSNAIKYTPGGEITISVRQDDEQVTISVEDTGPGIP--EEE 275
Query: 135 DEKMFVP 141
E++F P
Sbjct: 276 LERIFEP 282
>gnl|CDD|193214 pfam12738, PTCB-BRCT, twin BRCT domain. This is a BRCT domain that
appears in duplicate in most member sequences. BRCT
domains are peptide- and phosphopeptide-binding modules.
BRCT domains are present in a number of proteins involved
in DNA checkpoint controls and DNA repair.
Length = 63
Score = 32.2 bits (74), Expect = 0.24
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 2/63 (3%)
Query: 1360 CMMLDAYYIVPSAEELKALMMLHGGIYHHYESSRTTHIIASNLPHTKIKK-LKPGDKIIK 1418
+ + Y + L+ L+ G Y + + TH+I K +K K G ++
Sbjct: 2 VICVSGYS-GDDRKYLQKLIEALGAEYSKDLTKKVTHLICKRGEGEKYEKAKKWGIPVVS 60
Query: 1419 PEW 1421
W
Sbjct: 61 HLW 63
>gnl|CDD|235494 PRK05482, PRK05482, potassium-transporting ATPase subunit A;
Provisional.
Length = 559
Score = 35.9 bits (84), Expect = 0.31
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 18/53 (33%)
Query: 649 TSDSISMFIGRIEPEWYIPIIPMVLVNG--------AEGIGTGWMTKIPNHNP 693
+ I+M +GR ++PIIP++ + G E GT +P P
Sbjct: 482 LTLGIAMLLGR-----FLPIIPVLAIAGSLAAKKRVPESAGT-----LPTDGP 524
>gnl|CDD|148139 pfam06346, Drf_FH1, Formin Homology Region 1. This region is found
in some of the Diaphanous related formins (Drfs). It
consists of low complexity repeats of around 12 residues.
Length = 160
Score = 33.8 bits (77), Expect = 0.51
Identities = 18/57 (31%), Positives = 21/57 (36%), Gaps = 10/57 (17%)
Query: 2220 GKPPDQLNNPRPGPSNSTITPGPSNSTLPPGPSNSTLPPGPSNSTLLPGPSFGLSLP 2276
PP P P P + P P PP P +PP P P P FG +P
Sbjct: 108 AVPP-----PPPLPGGPGVPPPP-----PPFPGAPGIPPPPPGMGSPPPPPFGFGVP 154
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 35.2 bits (82), Expect = 0.52
Identities = 19/73 (26%), Positives = 34/73 (46%)
Query: 1470 VETSSHTSTVSDSVDNTEESKSEAVNSEESKSEAANPIESKQTVKTKESKLETVNISAPK 1529
+E SH+STV + EE+K EA ++++E A E+++ K + + +A
Sbjct: 29 IEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEA 88
Query: 1530 PQASSTKNASNED 1542
A+ ED
Sbjct: 89 AAAAEAAARPAED 101
Score = 34.8 bits (81), Expect = 0.63
Identities = 19/151 (12%), Positives = 45/151 (29%)
Query: 1056 KEEENSNITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKK 1115
+E + ++ KLKE G + ++ S++++ + E + E E AAA +
Sbjct: 10 AKELGVSSKELLEKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAE 69
Query: 1116 PNEVLPGWESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTVQVELRE 1175
+ A +A + + R R K +++ + + +
Sbjct: 70 EEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPK 129
Query: 1176 GVNISAPKPQASSTKNASNEDFLGEFYNKSR 1206
+ + R
Sbjct: 130 KKKPKRKAARGGKRGKGGKGRRRRRGRRRRR 160
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 34.5 bits (79), Expect = 0.60
Identities = 17/60 (28%), Positives = 20/60 (33%), Gaps = 1/60 (1%)
Query: 946 GEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKT-AAAKKAKPAKK 1004
G +P K KS + +S S KK AAK AK AKK
Sbjct: 195 GAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKK 254
Score = 32.9 bits (75), Expect = 1.7
Identities = 13/62 (20%), Positives = 17/62 (27%)
Query: 943 VSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPA 1002
KKK A K+ + + A + K AA K A
Sbjct: 212 AKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAA 271
Query: 1003 KK 1004
KK
Sbjct: 272 KK 273
>gnl|CDD|191251 pfam05283, MGC-24, Multi-glycosylated core protein 24 (MGC-24). This
family consists of several MGC-24 (or Cd164 antigen)
proteins from eukaryotic organisms. MGC-24/CD164 is a
sialomucin expressed in many normal and cancerous
tissues. In humans, soluble and transmembrane forms of
MGC-24 are produced by alternative splicing.
Length = 187
Score = 33.8 bits (77), Expect = 0.68
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 2225 QLNNPRPGPSNSTITPGPSNSTLPPGPSNSTLPPGPSNSTLLPGPS 2270
Q+ N S +T TP P+NST P + S + T P +
Sbjct: 100 QIYNTTDSCSVATTTPVPTNSTAKPTITPSP-TTSHHHVTSEPKTN 144
Score = 33.4 bits (76), Expect = 0.87
Identities = 18/76 (23%), Positives = 26/76 (34%), Gaps = 10/76 (13%)
Query: 2206 SKTLATIDTFFTNKGKPPDQLNNPRPGPSNSTITPGPSNSTLPPGPSNSTLPPGPSNSTL 2265
S ++AT TN P +P + T P + + P P +
Sbjct: 107 SCSVATTTPVPTNSTAKPTITPSPTTSHHHVTSEPKTNTTVTPTSQ--------PDRKST 158
Query: 2266 LPGPSF--GLSLPLGL 2279
SF G+ L LGL
Sbjct: 159 FDAASFIGGIVLVLGL 174
>gnl|CDD|219715 pfam08070, DTHCT, DTHCT (NUC029) region. The DTCHT region is the
C-terminal part of DNA gyrases B / topoisomerase IV /
HATPase proteins. This region is composed of quite low
complexity sequence.
Length = 95
Score = 31.8 bits (72), Expect = 0.73
Identities = 14/54 (25%), Positives = 23/54 (42%)
Query: 947 EDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAK 1000
E + + KKPA + S + DS+F + K+A +KK+K
Sbjct: 10 ETVNSDSDSEAGVPKKPAPPKGKGSKKRKPSSSDESDSNFGKKVSKSATSKKSK 63
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is a
positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting pathway
to dissociate the endosomal sorting complex required for
transport (ESCRT). Vta1 promotes correct assembly of Vps4
and stimulates its ATPase activity through its conserved
Vta1/SBP1/LIP5 region.
Length = 315
Score = 33.9 bits (78), Expect = 1.0
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 2213 DTFFTNKGKPPDQLNNPRPGPSNSTITPGPSNSTLPPGPSN------STLPPGPSNSTLL 2266
D + PP PS PS+S+LPP PS+ P P+N +
Sbjct: 178 DPASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPP 237
Query: 2267 PGP 2269
PGP
Sbjct: 238 PGP 240
>gnl|CDD|187756 cd09299, TDT, The Tellurite-resistance/Dicarboxylate Transporter
(TDT) family. The Tellurite-resistance/Dicarboxylate
Transporter (TDT) family includes members from all three
kingdoms, but only three members of the family have been
functionally characterized: the TehA protein of E. coli
functioning as a tellurite-resistance uptake permease,
the Mae1 protein of S. pombe functioning in the uptake
of malate and other dicarboxylates, and the sulfite
efflux pump (SSU1) of Saccharomyces cerevisiae. In
plants, the plasma membrane protein SLAC1 (Slow Anion
Channel-Associated 1), which is preferentially expressed
in guard cells, encodes a distant homolog of fungal and
bacterial dicarboxylate/malic acid transport proteins.
SLAC1 is essential in mediating stomatal responses to
physiological and stress stimuli. Members of the TDT
family exhibit 10 putative transmembrane alpha-helical
spanners (TMSs).
Length = 326
Score = 33.5 bits (77), Expect = 1.1
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 7/45 (15%)
Query: 630 YKVVYVTGVLLFKMNLHKVTSDSISMFIGRIEPEWYIPIIPMVLV 674
+V GV H + IS P W +PI+P +
Sbjct: 112 LSLVSAVGVPYLLFTNHVYEIEHIS-------PAWLLPIVPPMTS 149
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1, of
polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 33.7 bits (77), Expect = 1.3
Identities = 36/219 (16%), Positives = 66/219 (30%), Gaps = 40/219 (18%)
Query: 951 PPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKKESEYSS 1010
+K + +K + A + S+ S F +K K KK E S
Sbjct: 186 DTSKETTTEKTEGKTSVKAASLKRNPPKKSNIMSSFFKKKTKEKKEKKEASESTVKEESE 245
Query: 1011 TVCLFKRFGRRNCNDGGLIPKSQREGAQDSDLENNCRLDEVERKEKEEENSNITKIKSKL 1070
+R+ + + LDE E +++ + + + + +
Sbjct: 246 E------------------ESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEET 287
Query: 1071 KEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKPNEVLPGWESNLRPS 1130
+EK +KR L +++ +E E P+ P E E P
Sbjct: 288 EEKEKEKRKRL------------KKMMEDEDE---DEEMEIVPESPVEEEESEEPEPPPL 332
Query: 1131 ADKAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTV 1169
K E ++ S RR RR+ +
Sbjct: 333 PKKEEEKEEVTVSPDGGR-------RRGRRRVMKKKTFK 364
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This protein,
which interacts with both microtubules and TRAF3 (tumour
necrosis factor receptor-associated factor 3), is
conserved from worms to humans. The N-terminal region is
the microtubule binding domain and is well-conserved; the
C-terminal 100 residues, also well-conserved, constitute
the coiled-coil region which binds to TRAF3. The central
region of the protein is rich in lysine and glutamic acid
and carries KKE motifs which may also be necessary for
tubulin-binding, but this region is the least
well-conserved.
Length = 506
Score = 33.7 bits (77), Expect = 1.4
Identities = 44/250 (17%), Positives = 85/250 (34%), Gaps = 34/250 (13%)
Query: 943 VSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPA 1002
V G P K P K+ K + + K + + K+ +K K
Sbjct: 80 VEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEE---KKKKKEKPKEEPKDRKPKEE 136
Query: 1003 KKESEYSSTVCLFKRFGRRNCNDGGLIPKSQREGAQDSDLENNCRLDEVERKEKEEENSN 1062
KE + +E ++ + + D E K++E +
Sbjct: 137 AKE------------------------KRPPKEKEKEKEKKVEEPRDREEEKKRERVRAK 172
Query: 1063 ITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKPNEVLPG 1122
K K+ +KK+ P ++ AA V+ K EE + E+ +
Sbjct: 173 SRPKKPPKKKPPNKKKEP--PEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDR--- 227
Query: 1123 WESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTVQVELREGVNISAP 1182
E+ P ++ ESR+ ++ S+ + S +K E + + E R ++ P
Sbjct: 228 -ETTTSPM-EEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTSLRPP 285
Query: 1183 KPQASSTKNA 1192
+ +S + A
Sbjct: 286 SARPASARPA 295
Score = 31.0 bits (70), Expect = 8.0
Identities = 36/234 (15%), Positives = 75/234 (32%), Gaps = 27/234 (11%)
Query: 945 SGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKK 1004
+ + VK++K K PK + D + + K+K +K +
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEK-PKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPR 158
Query: 1005 ESEYSSTVCLFKRFGRRNCNDGGLIPKSQR-----EGAQDSDLENNCRLDEVERKEKEEE 1059
+ E +R PK ++ E R E + + E
Sbjct: 159 DRE---------EEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPE 209
Query: 1060 NSNITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKPNEV 1119
++ + + K ++ G + S +++ + + I +++ KKP+
Sbjct: 210 EPDVNEEREKEEDDGKDRETTTSPMEE----------DESRQSSEISRRSSSSLKKPDPS 259
Query: 1120 LPGWESNLRPSADKAESRKRTQTSQGT--ESEERKGHLRRWRRKEEESTQTVQV 1171
R S+ + E+R RT + + R R R++ Q Q
Sbjct: 260 PSMASPETRESSKRTETRPRTSLRPPSARPASARPAPPRVKRKEIVTVLQDAQG 313
>gnl|CDD|223033 PHA03291, PHA03291, envelope glycoprotein I; Provisional.
Length = 401
Score = 33.4 bits (76), Expect = 1.4
Identities = 22/87 (25%), Positives = 31/87 (35%), Gaps = 5/87 (5%)
Query: 927 YQPSNRVLTSRDEPMVVSSGEDAPPP-TKASPVKKKKPAAKRPAPKSDSSDLSDSDGDSD 985
+ P+ T R P +S E P P T SP PA + +++G
Sbjct: 203 FVPA----TPRPTPRTTASPETTPTPSTTTSPPSTTIPAPSTTIAAPQAGTTPEAEGTPA 258
Query: 986 FASRKKKTAAAKKAKPAKKESEYSSTV 1012
+ A A PA + S Y TV
Sbjct: 259 PPTPGGGEAPPANATPAPEASRYELTV 285
>gnl|CDD|224971 COG2060, KdpA, K+-transporting ATPase, A chain [Inorganic ion
transport and metabolism].
Length = 560
Score = 33.4 bits (77), Expect = 1.8
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 18/53 (33%)
Query: 649 TSDSISMFIGRIEPEWYIPIIPMVLVNG--------AEGIGTGWMTKIPNHNP 693
+ ++M +GR ++PIIP++ + G GT +P P
Sbjct: 485 LTLGVAMLLGR-----FLPIIPVLAIAGSLAAKKTVPATSGT-----LPTDGP 527
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part of
a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 33.5 bits (77), Expect = 1.8
Identities = 64/369 (17%), Positives = 118/369 (31%), Gaps = 55/369 (14%)
Query: 794 KIDDDSEEEEIEEVFHDNELAKPQKTGPQLERQERQAAEGEDDEAGSQTQEEEDPDKDYD 853
D DSEEE+ ++ D++ P L ++ + EGEDDE S
Sbjct: 329 DEDSDSEEEDEDDDEDDDDGENPWM----LRKKLGKLKEGEDDEENSG------------ 372
Query: 854 YLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDALREKDKIHPCPG- 912
LL M F RK E E+ L+++ + + E++ P
Sbjct: 373 -LLSMKFMQRAEARKKEENDA------EIEELRRE------LEGEEESDEEENEEPSKKN 419
Query: 913 -GNR--TRGLALKRQTRYQPSNRVLTSRDEPMVVSSGEDAPPPTKASPVKKKKPAAKRPA 969
G R K + E E+ +A K KR
Sbjct: 420 VGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSE 479
Query: 970 PKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKKESEYSSTVCLFKRFGRRNCNDGGLI 1029
+ + D + + + + K K+ S + +
Sbjct: 480 KAQKEEEEEELD-EENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKK 538
Query: 1030 PKSQREGAQDSDLENNCRLDEVERKEKEEENSNITKIKSKLKEKGSKKRNPLSSLDDTMP 1089
K + D ++ + E++E++ + + K+K D +
Sbjct: 539 KKEKSIDLDDDLIDEEDSIKLDVDDEEDEDDEELPFL---FKQK------------DLIK 583
Query: 1090 SA-AGRRVEPKYEELLIKAEKAAAPKKPNEVLPGWES----NLRPSA-DKAESRKRTQTS 1143
A AG V ++E+ + + PK+ + LPGW S ++ + R+
Sbjct: 584 EAFAGDDVVAEFEKEKKEVIEEEDPKEIDLTLPGWGSWAGDGIKKRKKKRKRKRRFLTKI 643
Query: 1144 QGTESEERK 1152
+G + E+RK
Sbjct: 644 EGVKKEKRK 652
>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 33.2 bits (76), Expect = 2.0
Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 3/76 (3%)
Query: 769 GAEKDEVHPGPGRKSHPRPIAPKSYKIDDDSEEEEIEEVFHDNELAKPQKTGPQLE--RQ 826
+ P P P P P DD ++++ E++ D + ++ R
Sbjct: 405 ADGGGGLAPPPEPPRPPPPPFPDDDDEGDDEDDDDWEDLGFDLDEDDVYD-LKDVDEWRL 463
Query: 827 ERQAAEGEDDEAGSQT 842
ER+ A E E G +
Sbjct: 464 ERRIATAERWELGQRL 479
Score = 31.3 bits (71), Expect = 7.1
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 6/64 (9%)
Query: 923 RQTRYQPSNRVLTSRDEPMVVSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDLSDSDG 982
R R + + R R + E A P + +P P P D D D +
Sbjct: 383 RVLRGEFAERR---RPRGPPENEDEADGGGGLAPPPEPPRPP---PPPFPDDDDEGDDED 436
Query: 983 DSDF 986
D D+
Sbjct: 437 DDDW 440
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 33.1 bits (75), Expect = 2.0
Identities = 28/122 (22%), Positives = 47/122 (38%), Gaps = 3/122 (2%)
Query: 938 DEPMVVSSGEDAPPPTKASPVKKKKPAAKRPAPKSDSSDL-SDSDGDSDFASRKKKTAAA 996
DE + PT++ KK + P + S+L + D D S+K
Sbjct: 59 DEEPDENGAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTR 118
Query: 997 KKAKPAKKESEYSSTVCLFKRFGRRNCNDGGLIPKSQREGAQDSDLENNCRLDEVERKEK 1056
+KA A + E T K RR + Q ++ SD+E + + +E + +
Sbjct: 119 RKAAAASSDVEEEKTEK--KVRKRRKVKKMDEDVEDQGSESEVSDVEESEFVTSLENESE 176
Query: 1057 EE 1058
EE
Sbjct: 177 EE 178
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 33.0 bits (76), Expect = 2.2
Identities = 12/43 (27%), Positives = 18/43 (41%)
Query: 955 ASPVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAK 997
+ AAK + KS ++D D A+R KK A +
Sbjct: 31 EAKAAAAAAAAKGRSRKSAAADDETMDPTQYRANRLKKVEALR 73
>gnl|CDD|187832 cd09701, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Multidomain protein with
permuted HD nuclease domain, inactivated palm domain and
Zn-ribbon; signature gene for type III.
Length = 909
Score = 32.8 bits (75), Expect = 2.5
Identities = 32/143 (22%), Positives = 44/143 (30%), Gaps = 24/143 (16%)
Query: 1041 DLENNCRL-DEVERKEKEEENSNITKIKSKLKEKG-------SKKRNPLSSLDDTMPSAA 1092
DLE E +++ I K ++ E SK L+SL A
Sbjct: 289 DLERLLDETLECAVGDEKLIEEEILKTFNEELENEGELVITLSKASRLLTSLAPEREKAL 348
Query: 1093 GRRVEPKYEELLIKAEKAAAPKKPNEVLPGWESN--------LRPSAD--KAESRKRTQT 1142
+ P LL A PN + N LRP KAE ++R
Sbjct: 349 ENELPPIISPLLFDISPATQADIPNF--WENKENKGICPVCGLRPQGPTSKAEEKERCDI 406
Query: 1143 SQGTESEERKGHLRRWRRKEEES 1165
E R + W EE+
Sbjct: 407 CD----ERRTDRAKEWLHSLEET 425
>gnl|CDD|220047 pfam08866, DUF1831, Putative amino acid metabolism. Solution of
the structure of the Lactobacillus plantarum protein
from this family has indicated a potential new fold with
remote similarities to TBP-like (TATA-binding protein)
structures. This similarity, in combination with genomic
context analysis, leads us to propose an involvement in
amino-acid metabolism. The potentially novel fold is an
alpha + beta fold comprising two beta sheets packed
against a single helix. The enzyme is present in the
cytosol.
Length = 111
Score = 30.7 bits (70), Expect = 2.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 244 KITFTPDLTKFKMTSLDKD 262
KIT DLT FKM++ D +
Sbjct: 58 KITINKDLTGFKMSTTDAN 76
>gnl|CDD|184621 PRK14324, glmM, phosphoglucosamine mutase; Provisional.
Length = 446
Score = 32.7 bits (75), Expect = 2.9
Identities = 16/33 (48%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 797 DDSEEEEIEEVFHDNEL-AKPQKTGPQLERQER 828
D+ EE+EIEE+F D EL QKTG ++ +R
Sbjct: 119 DEEEEKEIEEIFFDEELIQSSQKTGEEIGSAKR 151
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 32.5 bits (74), Expect = 3.0
Identities = 28/111 (25%), Positives = 43/111 (38%), Gaps = 6/111 (5%)
Query: 2170 QASQILKEVLFIVNKLKVDPVELRGIGIQVSKLEHQSKTLATIDTFFTNKGKPPDQLNNP 2229
Q +I +E+ + + D + +G + L Q K L T G+P Q+
Sbjct: 84 QYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGA--NPVTATGEPVPQMPAS 141
Query: 2230 RPGPSNSTITPGPSNSTLPPGPSNSTLPPG---PSNSTLLPGPSFGLSLPL 2277
PGP PG + + PP S + PP P N P S+P+
Sbjct: 142 PPGP-EGEPQPGNTPVSFPPQGSVAVPPPTAFYPGNGVTPPPQVTYQSVPV 191
>gnl|CDD|165563 PHA03308, PHA03308, transcriptional regulator ICP4; Provisional.
Length = 1463
Score = 32.9 bits (74), Expect = 3.1
Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 7/106 (6%)
Query: 909 PCPGGNRTRGLALKRQTRYQPSNRVLTSRDEPM---VVSSGEDAPPPTKAS----PVKKK 961
PCP + A++RQ + S RV SR + S+ P P + S P + K
Sbjct: 167 PCPLPAVEKTTAVRRQEVVRKSERVARSRSRRPWRDLWSNRRPVPSPQRTSKDRLPKRGK 226
Query: 962 KPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKKESE 1007
+ +K+ P +S S S + R+ + A ++ ++K +E
Sbjct: 227 REFSKKMGPSHLTSSSSSSSSSFSLSGRRGRLARRLESAGSEKSTE 272
>gnl|CDD|115336 pfam06673, L_lactis_ph-MCP, Lactococcus lactis bacteriophage major
capsid protein. This family consists of several
Lactococcus lactis bacteriophage major capsid proteins.
Length = 347
Score = 32.4 bits (73), Expect = 3.1
Identities = 28/131 (21%), Positives = 57/131 (43%), Gaps = 18/131 (13%)
Query: 1483 VDNTEESKSEAVNSEESKSEAANPIESKQTVKTKESKLETVNISAPKPQASSTK------ 1536
+ T+E +A+ + E +E + + K NI + KP+ + K
Sbjct: 3 ANETQEIMKQAIEAGVKVRELEAKVEELNKEREELKKEREANIPSEKPEDAERKFMRELG 62
Query: 1537 ----NASNEDFLGEFYNKSRLHHLSTMGSMFKQYVNELREKHDGVFRGIEAIRKWKTSLG 1592
+ FL EF N + L+ ++++GS+ +Y + G++ G A++ L
Sbjct: 63 DKMAEMPEQGFLREFANAAALNVVNSLGSITSKYA-----RKSGIYDG--AMKARFQGLT 115
Query: 1593 ITEDEDLEETF 1603
+ ED +++TF
Sbjct: 116 LAED-GVDDTF 125
>gnl|CDD|224256 COG1337, COG1337, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 249
Score = 32.0 bits (73), Expect = 3.1
Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 3/78 (3%)
Query: 1016 KRFGRRNCNDGGLIPKSQREGAQDSDLENNCRLDEVERKEKEEENSNITKIK-SKLKEKG 1074
R IP S +G S LE R + + + + ++ S LKE G
Sbjct: 37 NPVIRDPVTGLPYIPGSSLKGKFRSLLERLLRKNPIGYHSCGLDECVVCRLFGSALKEGG 96
Query: 1075 SKKRNPLSSL--DDTMPS 1090
K+R S L D +
Sbjct: 97 EKERCIPSRLFGRDAFLT 114
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 32.3 bits (73), Expect = 3.6
Identities = 39/180 (21%), Positives = 68/180 (37%), Gaps = 7/180 (3%)
Query: 1032 SQREGAQDSDLENNCRLDEVERKEKEEENSNITKIKSKLKEKGSKKRNPLSSLDDTMPSA 1091
++ E D C+ +E E + +EEE ++ E + K + + A
Sbjct: 133 TKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKLKHTEN-TFSRGGA 191
Query: 1092 AGRRVEPKYEELLIKAEKAAAPKKPNEVLPGWESNLRPSADKAESRKRTQTSQGTESEER 1151
G +VE E +K ++ A + E+ E + ++ + RK+ + + + EE
Sbjct: 192 EGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEE 251
Query: 1152 KGHLR---RWRRKEE-ESTQTVQ--VELREGVNISAPKPQASSTKNASNEDFLGEFYNKS 1205
K L+ RR E E Q V + P+ SS K +FL KS
Sbjct: 252 KRRLKEEIERRRAEAAEKRQKVPEDGLSEDKKPFKCFTPKGSSLKITERAEFLNRSIQKS 311
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 32.5 bits (74), Expect = 4.0
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 2/51 (3%)
Query: 2222 PPDQLNNPRPGPSNSTITPGPSNSTLPPGPSNST--LPPGPSNSTLLPGPS 2270
P + P S ST+ P P P + PP P+ P PS
Sbjct: 79 APANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPS 129
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 32.2 bits (73), Expect = 4.2
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 2/83 (2%)
Query: 769 GAEKDEVHPGPGRKSHPRPIAPKSYKIDDDSEEEEIEEVFHDNELAKPQKTGPQLERQER 828
+ K P A + D+DSEE E E+ + L+K K +L + +
Sbjct: 290 SSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKL--KGK 347
Query: 829 QAAEGEDDEAGSQTQEEEDPDKD 851
+ +DD ++ D D +
Sbjct: 348 KNGLDKDDSDSGDDSDDSDIDGE 370
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 32.3 bits (74), Expect = 4.5
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 86 KIFDEILVNACDNKQR-DPKMNCIKITVNQETN--TISVWNNGKGIPVVEHKDEKMF 139
+ +++L+N +N + P + I+I E SV + G GIP E + E++F
Sbjct: 774 PLIEQVLINLLENALKYAPPGSEIRINAGVERENVVFSVIDEGPGIP--EGELERIF 828
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 31.5 bits (71), Expect = 4.6
Identities = 19/76 (25%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 947 EDAPPPTKAS----PVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKA--K 1000
TK + K K AAK KS + + KK + AKK K
Sbjct: 26 SKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVTVKFEKTESVKKESVAKKTVKK 85
Query: 1001 PAKKESEYSSTVCLFK 1016
A + ++ LFK
Sbjct: 86 EAVSAEVFEASNKLFK 101
>gnl|CDD|148314 pfam06632, XRCC4, DNA double-strand break repair and V(D)J
recombination protein XRCC4. This family consists of
several eukaryotic DNA double-strand break repair and
V(D)J recombination protein XRCC4 sequences. In the
non-homologous end joining pathway of DNA double-strand
break repair, the ligation step is catalyzed by a complex
of XRCC4 and DNA ligase IV. It is thought that XRCC4 and
ligase IV are essential for alignment-based gap filling,
as well as for final ligation of the breaks.
Length = 331
Score = 31.4 bits (71), Expect = 5.2
Identities = 33/145 (22%), Positives = 57/145 (39%), Gaps = 8/145 (5%)
Query: 1058 EENSNITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAAAPKKPN 1117
E+ + I + L E +++ + + S + KY+ E+ AP KP+
Sbjct: 186 EKKAKIRSLHKLLSEAQELEKSIKQKKETSACSDKTPDEDSKYDG--STDEEQEAPPKPS 243
Query: 1118 EVLPGWES-----NLRPSA-DKAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTVQV 1171
E +P S P D A SRKR Q Q E K + + +E+E
Sbjct: 244 ESMPAAVSKDDSLISSPDITDIAPSRKRRQRMQKNLGTEPKMATQEQQLQEKEKPDPSPP 303
Query: 1172 ELREGVNISAPKPQASSTKNASNED 1196
+ + + SA + +N+S +D
Sbjct: 304 QTTKKTHSSAENMSLETLRNSSPDD 328
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This family
consists of several bovine specific leukaemia virus
receptors which are thought to function as transmembrane
proteins, although their exact function is unknown.
Length = 561
Score = 32.0 bits (72), Expect = 5.3
Identities = 25/119 (21%), Positives = 47/119 (39%), Gaps = 6/119 (5%)
Query: 1052 ERKEKEEENSNITKIKSKLKEKGSKKRNPLSSLDDTMPSAAGRRVEPKYEELLIKAEKAA 1111
++KEK+E+ K K K E ++ L +LDD+ SAA + + A
Sbjct: 203 KKKEKKEKEKERDKDKKKEVEGF---KSLLLALDDSPASAASVAEADEASLANTVSGTAP 259
Query: 1112 APKKPNEVLPGWESNLRPSADKAESRKRTQTSQGTESEERKGHLRRWRRKEEESTQTVQ 1170
+ E + K +K+ + + + +++K H R + + Q VQ
Sbjct: 260 DSEPDEPKDAEAEETKKSPKHK---KKKQRKEKEEKKKKKKHHHHRCHHSDGGAEQPVQ 315
>gnl|CDD|130146 TIGR01074, rep, ATP-dependent DNA helicase Rep. Designed to identify
rep members of the uvrD/rep subfamily [DNA metabolism,
DNA replication, recombination, and repair].
Length = 664
Score = 31.6 bits (72), Expect = 5.4
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 18/80 (22%)
Query: 1393 RTTHIIASNLPHTKIKKL----KPGDKII---------KPEWIVDSISAGKLLDHKKY-- 1437
+ +I+ +N PH KKL G+KI + E I I A KL++ +Y
Sbjct: 284 KAANILIANNPHVFEKKLFSELGYGEKIKVIECNNEEHEAERIAGEIIAHKLVNKTQYKD 343
Query: 1438 --LLYTGT-DAKPLTKLLQK 1454
+LY G ++ L K L +
Sbjct: 344 YAILYRGNHQSRLLEKALMQ 363
>gnl|CDD|170022 PRK09630, PRK09630, DNA topoisomerase IV subunit A; Provisional.
Length = 479
Score = 31.8 bits (72), Expect = 5.4
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 661 EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVD 698
EP+ +P++L++G +GI G TKI HN E+++
Sbjct: 137 EPDILPAKLPLLLLHGVDGIAVGMTTKIFPHNFCELLE 174
>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421). This
family represents a conserved region approximately 350
residues long within a number of plant proteins of
unknown function.
Length = 357
Score = 31.4 bits (71), Expect = 5.8
Identities = 17/83 (20%), Positives = 26/83 (31%), Gaps = 9/83 (10%)
Query: 2216 FTNKGKPPDQLNN------PRPGPSNSTITPGPSNSTLPPGPSNSTLPPGPSNSTLLPGP 2269
+ G PP + N+ G S S T PS P + P + P
Sbjct: 253 YGYSGPPPSKGNHGSVASYAPQGSSQSYSTAYPSLPAATVLPQALPMSSAPMSGGGSGSP 312
Query: 2270 SFGLSLPLGLSNLMVHKAVRFKF 2292
G +P+ ++ K F
Sbjct: 313 QSGNRVPID---DVIEKVATMGF 332
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 31.6 bits (72), Expect = 6.2
Identities = 9/48 (18%), Positives = 16/48 (33%)
Query: 957 PVKKKKPAAKRPAPKSDSSDLSDSDGDSDFASRKKKTAAAKKAKPAKK 1004
++ K AA + ++ + + K AAKK K
Sbjct: 814 EPREPKAAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAKKTAARKT 861
>gnl|CDD|215397 PLN02744, PLN02744, dihydrolipoyllysine-residue acetyltransferase
component of pyruvate dehydrogenase complex.
Length = 539
Score = 31.4 bits (71), Expect = 6.8
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 945 SGEDAPPPTKASP------VKKKKPAAKRPAPKSDSSDLSDSDGDSDFAS 988
S AP KA P ++ + A P PK+ S GD FAS
Sbjct: 203 SSSAAPAAPKAKPSPPPPKEEEVEKPASSPEPKASKPSAPPSSGDRIFAS 252
>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional.
Length = 196
Score = 30.3 bits (68), Expect = 8.0
Identities = 10/56 (17%), Positives = 27/56 (48%)
Query: 797 DDSEEEEIEEVFHDNELAKPQKTGPQLERQERQAAEGEDDEAGSQTQEEEDPDKDY 852
+ EE+++ + + ++ P + + Q +Q E +E + Q++E ++Y
Sbjct: 9 NKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVEAQEY 64
>gnl|CDD|222977 PHA03089, PHA03089, late transcription factor VLTF-4; Provisional.
Length = 191
Score = 30.2 bits (68), Expect = 8.2
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 1274 FRGIEAIRKWKTSLGITEDEDLEETFSDN---PSPSEPKTTAPKKKKKGGYMEAKKRKLE 1330
F+ ++ IR S + D+ ++ F ++ PS K +KK + KK+K E
Sbjct: 14 FKTLDEIRAHVKSTTESVDKVNDDIFPEDVEIPSKKTSKKKKTTPRKKKTTKKTKKKKKE 73
Query: 1331 EQFELEANS 1339
++ E +
Sbjct: 74 KEEVPELAA 82
>gnl|CDD|147381 pfam05167, DUF711, Uncharacterized ACR (DUF711). The proteins in
this family are functionally uncharacterized. The
proteins are around 450 amino acids long. It is likely
that this family represents a group of
glycerol-3-phosphate dehydrogenases.
Length = 390
Score = 30.7 bits (70), Expect = 8.8
Identities = 31/122 (25%), Positives = 50/122 (40%), Gaps = 28/122 (22%)
Query: 245 ITFTPDLTKFKMTSLDKDMVDLITRRAYDAAASTKDVKVFLNGEKLPVKNFQDYVKLYTD 304
I+ TP + D D V L +A D AA V F+ G F V
Sbjct: 53 ISVTP--ISLVAEASDDDYVSLA--KALDKAAKDVGVD-FIGG-------FSALVHKGFT 100
Query: 305 RQDEDGDPVKIIYENVNPRWEVAIAPSDRGFQQVSFVNSIATTKGGRHVDAVVDA--IVK 362
R D + I + A+A ++R V ++A+TK G ++DAV + ++K
Sbjct: 101 RGDRA--LIDSIPD--------ALASTER----VCSSVNVASTKAGINMDAVKEMGKLIK 146
Query: 363 QI 364
++
Sbjct: 147 RL 148
>gnl|CDD|233088 TIGR00679, hpr-ser, Hpr(Ser) kinase/phosphatase. Members of this
family are the bifunctional enzyme, HPr
kinase/phosphatase. All members of the seed alignment
(n=57) have a gene tightly clustered with a gene for the
phospocarrier protein HPr, its target [Regulatory
functions, Protein interactions, Signal transduction,
PTS].
Length = 300
Score = 30.5 bits (70), Expect = 9.6
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 12/80 (15%)
Query: 1737 SFLNALPEDIRQEVLDDLSRQQS---VLSREQNTTEPLAQDIICADSHT-LVRTP-SPSP 1791
S+L +L E+ R+E L+ L + + +++R E L + + + + L+RT S S
Sbjct: 58 SYLESLDEEERKERLEKLLKLKPPCIIVTRGLEPPEELLE--LAEEYNVPLLRTSLSTSE 115
Query: 1792 ILDMSTSILD-----TTTSH 1806
++ T+ LD TT H
Sbjct: 116 LITTLTTYLDEQLAPRTTVH 135
>gnl|CDD|218787 pfam05871, ESCRT-II, ESCRT-II complex subunit. This family of
conserved eukaryotic proteins are subunits of the
endosome associated complex ESCRT-II which recruits
transport machinery for protein sorting at the
multivesicular body (MVB). This protein complex
transiently associates with the endosomal membrane and
thereby initiates the formation of ESCRT-III, a
membrane-associated protein complex that functions
immediately downstream of ESCRT-II during sorting of MVB
cargo. ESCRT-II in turn functions downstream of ESCRT-I,
a protein complex that binds to ubiquitinated endosomal
cargo.
Length = 139
Score = 29.5 bits (67), Expect = 9.6
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 1713 SYCLYNLIASLTLNIEAV--SLYTNESFLNALPEDIRQEVLDDLSRQQSVLSREQNTTE 1769
YC ++ I SL++ EA L+ N+ L + +E+LD L ++ + ++ T
Sbjct: 31 DYCRHHKIFSLSVL-EAQDSPLFNNKKIQRRLSPEFIKEILDQLVKKGNAEWIDKGKTR 88
>gnl|CDD|225401 COG2845, COG2845, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 354
Score = 30.5 bits (69), Expect = 9.7
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 923 RQTRYQPSNRVLTSRDEPMVVSSGEDAPPPT----KASPVKKKKPAAKR 967
RQ P +V S D P ++ E AP P A+ + K A +
Sbjct: 70 RQGFPPPIAKVGPSLDMPRASAASEVAPRPGATAEPATTIAAKSRDADK 118
>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein.
Length = 198
Score = 30.1 bits (68), Expect = 9.7
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 1274 FRGIEAIRKWKTSLGITEDEDLEETFSDN---PSPSEPKTTAPKKKKKGGYMEAKKRKLE 1330
F+ +E IR S + D+ ++ F ++ PSP +PK P +K + K+K +
Sbjct: 14 FKTLEEIRAHVRSTTESVDKVRDDIFPEDIEIPSPKQPKKKRPTTPRKPATTKKSKKKDK 73
Query: 1331 EQFELEA 1337
E+ E
Sbjct: 74 EKLTEEE 80
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.313 0.131 0.377
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 115,543,864
Number of extensions: 11506826
Number of successful extensions: 10120
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9778
Number of HSP's successfully gapped: 239
Length of query: 2307
Length of database: 10,937,602
Length adjustment: 112
Effective length of query: 2195
Effective length of database: 5,969,954
Effective search space: 13104049030
Effective search space used: 13104049030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 67 (29.7 bits)