RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11423
(655 letters)
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 763 bits (1974), Expect = 0.0
Identities = 285/660 (43%), Positives = 414/660 (62%), Gaps = 31/660 (4%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
R+ EL++EL+ H AYY+ D P ISD +YD+L EL +E ++PEL+T DS TQ VG
Sbjct: 8 RIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRVGGAP 67
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
+ + V H M+SLDN FS+E++ F+KR+ L + Y+ ELK DG+AV+L YE
Sbjct: 68 LDGFEKVRHLVPMLSLDNAFSEEELRAFDKRVRKRLP-DPPLTYLCELKIDGLAVSLLYE 126
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L +A+TRGDG GE+IT N+ I IPL L+ P E LEVR EV + K DF LN+
Sbjct: 127 NGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHGNEP-ERLEVRGEVFMPKADFEALNE 185
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
R G K F NPRNAAAG LRQL+PKI + L FFA+GVGE+ G +P S SE L +
Sbjct: 186 ERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEGGELPDSQSEALEFL 245
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
+ G + + + + +++ FY++I +R +LPY+IDGVV K++ L+ Q++LGFT++A
Sbjct: 246 KAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKA 305
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
PR+A+AYKF ++EA TK+ I +Q+GRTG +TPVA L+PV + G+T++RATLHN EI R
Sbjct: 306 PRWAIAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIER 365
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
K+I+IGDTVVV R+G+VIP++ +L RP D + +P CP+C S+++ +E + RC
Sbjct: 366 KDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVMPTHCPVCGSELVRVEGEAVLRC 425
Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
+ + C AQ K L HF SR AM+I GLG+K+IE+L ++ DL+K+ ++LL L
Sbjct: 426 TNG-LSCPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGL 484
Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
+ K A N+L AI+KSK T+ +RF+YALGIRHVGE AK LA +F +LE + A+EE+
Sbjct: 485 EGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEE 544
Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
L + +G ++ ++F +R LI +L + G+
Sbjct: 545 LAAVEGVGEVVAQSIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLEQ 604
Query: 602 -------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 648
G KV +SK T+ +V G+ G KL KA +L I++LDE+ F++++
Sbjct: 605 LSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 697 bits (1800), Expect = 0.0
Identities = 283/663 (42%), Positives = 408/663 (61%), Gaps = 37/663 (5%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
+ EL++ L++H+ YY+ D P +SD +YDQL EL+++EEK+PEL+T DS TQ VG
Sbjct: 10 EIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDSPTQRVGAAP 69
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
K V H M+SLDN F +E++ F++RI L ++EY+ E K DG+A++L YE
Sbjct: 70 LNAFKKVRHPVPMLSLDNAFDEEELRAFDRRIRKFLGD--SVEYVVEPKIDGLAISLVYE 127
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L +A+TRGDG GE+IT N+ I IPL + P +LEVR EV + K+DF LN+
Sbjct: 128 NGKLVRAATRGDGTTGEDITANVRTIRSIPL--KLPGAPAVLEVRGEVFMPKEDFEALNE 185
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
R G K F NPRNAAAG LRQL+PKI + L FF + VG+ + + SE L +
Sbjct: 186 EREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEGLLADTQSERLAFL 245
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
+ G + + ++++ FY++ KR +LPY+IDGVV K+N L+ Q++LGFTS+A
Sbjct: 246 KAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKA 305
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
PR+A+AYKF ++EA+TK+ I +Q+GRTG ITPVA L+PV + G+T++RATLHN EI R
Sbjct: 306 PRWAIAYKFPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEIKR 365
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
K+I+IGDTVVV ++G+VIP++ +L RP + K P CP+C S+++ E ++ RC
Sbjct: 366 KDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNEKPIPFPTHCPVCGSELVREEGEVVIRC 425
Query: 437 SGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRL 496
+ + C AQ K L HF SR A++I GLG+K+IE+L ++ DLY + ++LL L
Sbjct: 426 TNG-LNCPAQLKERLIHFVSRNALDIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSL 484
Query: 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQ 556
+ K A N+L AI+KSK +RF+YALGIRHVGETTAK LA +F LE + A+EE+
Sbjct: 485 EGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEE 544
Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTK--------------- 601
L +IP IG ++ I+F +R LI +L G+ W
Sbjct: 545 LASIPGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTG 604
Query: 602 -----------------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVK 644
G KV +SK T+Y+V G+ G KL KA +L +KI+DE+ F+
Sbjct: 605 TLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLA 664
Query: 645 IVK 647
++
Sbjct: 665 LLG 667
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 650 bits (1678), Expect = 0.0
Identities = 278/657 (42%), Positives = 402/657 (61%), Gaps = 40/657 (6%)
Query: 21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENS 80
L+K + H+ YY+ D P ISD +YD+L EL+++EEK+PEL+T DS TQ VG
Sbjct: 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVGAAPLSRF 60
Query: 81 KYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYL 140
V H+ M+SLDN F ++++ F KRI +L L +EY+ E K DG++V+L YE G L
Sbjct: 61 PKVRHSTPMLSLDNAFDEDELAAFIKRIRRQLGLK--VEYVVEPKIDGLSVSLTYENGVL 118
Query: 141 KQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYH 200
+A TRGDG +GE++T N+ I IPL L PPE LEVR EV + K+DF LN+ R
Sbjct: 119 VRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEVRGEVFMPKEDFEALNEERRE 178
Query: 201 LGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIG 260
G K F NPRNAAAG LRQL+P+I + L FFA+G+GE + + E L W +K G
Sbjct: 179 QGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLELPDAT-QYEALAWLKKWG 237
Query: 261 LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFA 320
+ + + +++E+Y++I KR +LPYEIDGVV K++ L+ Q +LGFTS+APR+A
Sbjct: 238 FPVSPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWA 297
Query: 321 LAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQ 380
+AYKF ++EA TK+ + +Q+GRTG ITPVA L+PV + G T++RATLHNE EI +I+
Sbjct: 298 IAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIR 357
Query: 381 IGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSW 440
IGDTVVV ++G+VIPK+ +L R + + P CP C S ++ IE + RC
Sbjct: 358 IGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPSCGSPLVKIEEEAVIRCPNL- 416
Query: 441 IECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS 500
C AQR ++HF+SR AM+I GLG K+IE+L +V + DLY + ++LL L+
Sbjct: 417 -NCPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFG 475
Query: 501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNI 560
K A N+L AI+KSK +R ++ALGIRHVGE TAK LA +F L+ + A+ E+LL++
Sbjct: 476 EKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSV 535
Query: 561 PKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW-------------------------- 594
+G ++ + F + P +R LI +L ++G+
Sbjct: 536 EGVGPKVAESIVNFFHDPNNRQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGT 595
Query: 595 LNNPNTK---------GGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNF 642
L+ + GGKV + +SK T+Y++ G+K G KL KA +L I I++E+
Sbjct: 596 LSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINEEEL 652
>gnl|CDD|214709 smart00532, LIGANc, Ligase N family.
Length = 441
Score = 502 bits (1295), Expect = e-174
Identities = 205/443 (46%), Positives = 291/443 (65%), Gaps = 5/443 (1%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
++EL+K L++H+ YY+ D PIISD +YD+L+ ELK++EEK+PEL T DS TQ VG
Sbjct: 4 EISELRKLLNQHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGGKP 63
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
E V H M+SLDN F ++++ F++RI L Y+ E K DG++V+L YE
Sbjct: 64 LEGFNKVRHPVPMLSLDNAFDEDELRAFDERIEKALGS--PFAYVVEPKIDGLSVSLLYE 121
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L QA+TRGDG +GE++T N+ I IPL L+ P E LEVR EV + K+DF+ LN+
Sbjct: 122 NGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVP-ERLEVRGEVFMPKEDFLALNE 180
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
G K F NPRNAAAG LRQL+P+I + L F +G+G + +P + SE L W
Sbjct: 181 ELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQSEALKWL 240
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
+++G + + +++IE+Y++ KR LPYEIDGVV K++ L+ Q++LGFTS+A
Sbjct: 241 KELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKA 300
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
PR+A+AYKF ++EA TK+ I +Q+GRTG ITPVA L+PV + G T++RATLHNE EI
Sbjct: 301 PRWAIAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEE 360
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARC 436
K+I+IGDTVVV ++G+VIPK+ + RP D + ++P CP C S+++ E + RC
Sbjct: 361 KDIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEMPTHCPSCGSELVREEGEVDIRC 420
Query: 437 SGSWIECIAQRKAGLQHFSSRKA 459
C AQ + HF+SRKA
Sbjct: 421 PN--PLCPAQLIERIIHFASRKA 441
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 689
Score = 458 bits (1181), Expect = e-153
Identities = 222/662 (33%), Positives = 359/662 (54%), Gaps = 54/662 (8%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
+ +L++ + H+ YY+ +P+I+D YD L L+ +E+ + +L T++S T+ VG
Sbjct: 35 QAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTENSPTRRVGGEP 93
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
+ + V H M+S+D +DV F++R+ E+ +EY+ E KFDG++V + YE
Sbjct: 94 LDELETVEHVAPMLSIDQSGEADDVREFDERVRREVG---AVEYVCEPKFDGLSVEVVYE 150
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G ++A+TRGDG G+++T N+ I +P L YP + L VR EV + K F N+
Sbjct: 151 DGEYQRAATRGDGREGDDVTANVRTIRSVPQKLRGDYP-DFLAVRGEVYMPKDAFQAYNR 209
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256
R G + F NPRNAAAG LRQL+P + + L F V L + SH E L +
Sbjct: 210 ERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDV--LDASELFDSHWEELERF 267
Query: 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRA 316
+ GL + + ++ I + ++ R +L YEIDGVV K++ +++LG T+RA
Sbjct: 268 PEWGLRVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARA 327
Query: 317 PRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYR 376
PR+A AYKF ++ T I+ I +Q+GRTG +TPVALL PV + G+T++RA+LHN +EI
Sbjct: 328 PRWAFAYKFPARAEETTIRDIVVQVGRTGRLTPVALLDPVDVGGVTVSRASLHNPAEIEE 387
Query: 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESN-LIAR 435
+ +GD V V R+G+VIP + ++ + F+ P+ CP+C+S +E + +A
Sbjct: 388 LGVNVGDRVRVKRAGDVIPYV-EEVVEKDSEGT--FEFPDTCPVCDSA---VERDGPLAF 441
Query: 436 CSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLR 495
C+G + C AQ + ++H++SR A++I GLG++ +++LV+A +V + DLY + +L
Sbjct: 442 CTGG-LACPAQLERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAE 500
Query: 496 LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEE 555
L+ A N+L ++ S+ + F+ ALGI VG TTA+ LA F E + A EE
Sbjct: 501 LEGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEE 560
Query: 556 QLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN---------------- 599
L + +G T + +F + +R +I L D G+ +P
Sbjct: 561 ALRAVDDVGPTVAEEIREFFDSERNRAVIDDLLDHGV----DPQPAESEGGDALDGLTFV 616
Query: 600 ------------------TKGGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEK 640
GG +S NT+YLV G+ PG+ K + A ++ LDE+
Sbjct: 617 FTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEE 676
Query: 641 NF 642
F
Sbjct: 677 EF 678
>gnl|CDD|238062 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA
ligases catalyze the crucial step of joining the breaks
in duplex DNA during DNA replication, repair and
recombination, utilizing either ATP or NAD(+) as a
cofactor, but using the same basic reaction mechanism.
The enzyme reacts with the cofactor to form a
phosphoamide-linked AMP with the amino group of a
conserved Lysine in the KXDG motif, and subsequently
transfers it to the DNA substrate to yield adenylated
DNA. This alignment contains members of the NAD+
dependent subfamily only.
Length = 307
Score = 356 bits (915), Expect = e-119
Identities = 144/310 (46%), Positives = 201/310 (64%), Gaps = 7/310 (2%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVG-LV 75
R+ EL++ L++H+ YY+ D P +SD +YD+L EL+ +EE++PEL T DS TQ VG
Sbjct: 2 RIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGGTP 61
Query: 76 GGENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY 135
K V H M+SLDN F +E++ F++RI L + Y+ E K DG++++LRY
Sbjct: 62 LSGFKK-VRHPVPMLSLDNAFDEEELRAFDERIKRFLG--EEPAYVVEPKIDGLSISLRY 118
Query: 136 EYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLN 195
E G L QA+TRGDG GE++T N+ I IPL + PE LEVR EV + K DF LN
Sbjct: 119 ENGVLVQAATRGDGTTGEDVTENVRTIRSIPL--TLAGAPETLEVRGEVFMPKADFEALN 176
Query: 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNW 255
K R G K F NPRNAAAG LRQL+PKI + L FF +G+GE G+ P + SE L +
Sbjct: 177 KEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG-PKTQSEALAF 235
Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
++ G + E + + +++ FY +I KR +LPYEIDGVV K++ L+ Q++LGFTS+
Sbjct: 236 LKEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSK 295
Query: 316 APRFALAYKF 325
APR+A+AYKF
Sbjct: 296 APRWAIAYKF 305
>gnl|CDD|216629 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation
domain. DNA ligases catalyze the crucial step of
joining the breaks in duplex DNA during DNA replication,
repair and recombination, utilising either ATP or NAD(+)
as a cofactor. This domain is the catalytic adenylation
domain. The NAD+ group is covalently attached to this
domain at the lysine in the KXDG motif of this domain.
This enzyme- adenylate intermediate is an important
feature of the proposed catalytic mechanism.
Length = 314
Score = 323 bits (830), Expect = e-106
Identities = 131/310 (42%), Positives = 193/310 (62%), Gaps = 4/310 (1%)
Query: 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVG 76
+ L++ + +++ YY+ DNP + D +YD+L L+ +EEK+PEL+T DS TQ VG
Sbjct: 6 EIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELITPDSPTQRVGAPL 65
Query: 77 GENSKYVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYE 136
+ K V H M+SLDN F ++++ + +RI L Y+ E K DG+AV+L YE
Sbjct: 66 LGDFKKVRHPAPMLSLDNAFDEDELAAWIRRIRRRLGN-SEKAYVVEPKIDGVAVSLTYE 124
Query: 137 YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196
G L +A+TRGDG GE++T N+ I IPL + P LEVR EV + K+DF LN+
Sbjct: 125 DGVLVRAATRGDGTTGEDVTQNVKTIRAIPL--TLPGDPARLEVRGEVFMPKEDFEALNE 182
Query: 197 YRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNW 255
R G K F NPRNAAAG LRQL+P+I + L FF +G+G G+ + P + SE L
Sbjct: 183 EREEEGEKPFANPRNAAAGSLRQLDPEITAKRKLRFFVYGLGLPEGLELGPQTQSEALKQ 242
Query: 256 YQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSR 315
+ +G + + +++++++Y + KR LP+EIDGVV K+N L Q++LGFTS+
Sbjct: 243 LKSLGFPVSPHTRLCKNIDEVLDYYAEWEKKRDELPFEIDGVVVKVNELPLQRELGFTSK 302
Query: 316 APRFALAYKF 325
APR+A+AYKF
Sbjct: 303 APRWAIAYKF 312
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 669
Score = 282 bits (723), Expect = 6e-86
Identities = 206/685 (30%), Positives = 339/685 (49%), Gaps = 71/685 (10%)
Query: 12 SKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQH 71
+ + +LKK + + + YY+ +P + D YD+ L L+++E KYPE T DS T
Sbjct: 3 KDIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLK 62
Query: 72 VGLVGGENSKYVHHTFKMMSLDNGFS-DEDVIIFNKRITNELKLTKNIEYIAELKFDGIA 130
G + K V H+F ++SLD + + K L + E K DG +
Sbjct: 63 FGSDLLNDFKEVEHSFPILSLDKVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCS 122
Query: 131 VNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKD 190
+ L Y+ G L++A TRGDG G ++T N+ I +PL ++ K L +R E+ I K++
Sbjct: 123 IVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDEKVE---LVLRGEIYITKEN 179
Query: 191 FIKLNKYRYHLGLKK-FTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249
F+K+NK L+K +TN RN A+GILR+++ + N L F + + + + ++H
Sbjct: 180 FLKINKT-----LEKPYTNARNLASGILRRIDSREVANFPLDIFVYDILY-SSLELKTNH 233
Query: 250 SELLNWYQKIGLSI---CGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306
+ + +K G + C + + + +++ + K I KR + YEIDGVV K++ +
Sbjct: 234 -DAFDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFAL 292
Query: 307 QKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRA 366
++ LG+TS P++++AYKF S +K+ I +Q+GR+G ITPVA ++ V + G IT A
Sbjct: 293 REILGYTSHHPKWSMAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNA 352
Query: 367 TLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKII 426
+LHN+ I + +GD V + R G+VIP + I L FKIP+ CP C + +I
Sbjct: 353 SLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKL---SVGFFKIPDNCPSCKTALI 409
Query: 427 YIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486
++L C + + + +++F S+K MNI+GL K IE L + + +DLY
Sbjct: 410 KEGAHLF--CVNNHCPSVIVER--IKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLY 465
Query: 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKEL----ANY 542
NF L+ L +K NN+ +I+ SK FS+ + ++GI+ +GE T L N
Sbjct: 466 TFNFDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNNLNS 525
Query: 543 FKNLECMFKATE---EQLLNIPKIGSTTVKAFIKFINQPL-------------------- 579
F + + + E +LL I IG I+ N +
Sbjct: 526 FDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSI 585
Query: 580 -----HRLLISQ-----------LRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG 623
+ L + R V I L KG ++K ++L+ G+K G
Sbjct: 586 NIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTK---KGAIFNTCVTKYLDFLLVGEKAG 642
Query: 624 KKLEKAIKLNIKIL---DEKNFVKI 645
KL+KA L IKI+ D K++V +
Sbjct: 643 LKLKKANNLGIKIMSLFDIKSYVDL 667
>gnl|CDD|145978 pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-fold domain.
DNA ligases catalyze the crucial step of joining the
breaks in duplex DNA during DNA replication, repair and
recombination, utilising either ATP or NAD(+) as a
cofactor. This family is a small domain found after the
adenylation domain pfam01653 in NAD dependent ligases.
OB-fold domains generally are involved in nucleic acid
binding.
Length = 82
Score = 123 bits (310), Expect = 1e-33
Identities = 47/81 (58%), Positives = 65/81 (80%)
Query: 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHR 389
A+TK+ I +Q+GRTG+ITPVA+L+PV + G T++RATLHNE EI K+I+IGDTVVV +
Sbjct: 1 AVTKLLDIEVQVGRTGVITPVAILEPVELAGTTVSRATLHNEDEIEEKDIRIGDTVVVRK 60
Query: 390 SGNVIPKITSSILSLRPNDSK 410
+G+VIPKI +L RP D++
Sbjct: 61 AGDVIPKIVGVVLEKRPGDTR 81
>gnl|CDD|236150 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed.
Length = 562
Score = 96.5 bits (241), Expect = 7e-21
Identities = 106/492 (21%), Positives = 192/492 (39%), Gaps = 83/492 (16%)
Query: 125 KFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEV 184
K DG+AV L Y G L QA +RG+G GE+ T +I IP + L ++ E+
Sbjct: 125 KVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQ--QLPGALANLVLQGEL 182
Query: 185 LIYKKDFIKLNKYR-YHLGLKKFTNPRNAAAGILR--QLNPKINKNKILHFFA----HGV 237
F++ + +G N R AG++ +P +N+ + F G
Sbjct: 183 ------FLRREGHIQQQMGGI---NARAKVAGLMMRKDPSPTLNQ---IGVFVWAWPDG- 229
Query: 238 GELRGMNMPSSHSELLNWYQKIGLSICGEYSV----LSGVNKLIEFYKKINIKRFNLPYE 293
P+S E L G + Y+ V + E + R LP+
Sbjct: 230 --------PASMPERLAQLATAGFPLTQRYTHPVKNAEEVARWRERWY-----RAPLPFV 276
Query: 294 IDGVVYKINCLSTQKKLG--FTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVA 351
DGVV + ++ G + +A+A+K+ + + +++A+ +GRTG IT V
Sbjct: 277 TDGVVVR----QAKEPPGRYWQPGQGEWAVAWKYPPVQQVAEVRAVQFAVGRTGKITVVL 332
Query: 352 LLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKI 411
L+PV++D ++R + + + +I GD V+V +G IP++ + R +
Sbjct: 333 ELEPVMLDDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLDKVV--WRGAERTK 390
Query: 412 FKIPNI-------C----PICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAM 460
P+ C P C + +AR W+ S ++ +
Sbjct: 391 PTPPDADRFHSLSCFRASPGC-------QEQFLARL--VWL-------------SGKQGL 428
Query: 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFS 520
+ G+G+ L + + + L + A + ++ FS
Sbjct: 429 GLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFS 488
Query: 521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH 580
R++ ALGI + + L + + + + +E+Q +P IG + I F+ P
Sbjct: 489 RWLKALGIP-LPQAALNALDDR--SWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPEV 545
Query: 581 RLLISQLRDVGI 592
+ L L GI
Sbjct: 546 KALADWLAAQGI 557
>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif. The HhH domain of
DisA, a bacterial checkpoint control protein, is a
DNA-binding domain.
Length = 64
Score = 79.4 bits (197), Expect = 1e-18
Identities = 29/64 (45%), Positives = 42/64 (65%)
Query: 521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH 580
R ++ALGIRHVGE TAK LA +F +L+ + A+ E+LL I IG ++ ++F P +
Sbjct: 1 RLLFALGIRHVGEKTAKLLAKHFGSLDALANASVEELLEIDDIGPIVAQSIVEFFANPAN 60
Query: 581 RLLI 584
R LI
Sbjct: 61 RELI 64
>gnl|CDD|227600 COG5275, COG5275, BRCT domain type II [General function prediction
only].
Length = 276
Score = 44.7 bits (105), Expect = 8e-05
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGFSTE 652
GG+V S T +LV G G K+EK +L IK +DE+ F ++K
Sbjct: 184 GGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDTPAA 235
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 41.4 bits (98), Expect = 0.002
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 512 QKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA 570
+K +T + Y + + VG A+ L +F ++E + A+EE+L+ + IG T K
Sbjct: 703 EKKAMTLKEQQEYIVESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKR 762
Query: 571 FIKFINQP 578
+ +
Sbjct: 763 IREVVTSE 770
>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 = 35.4 bits (82), Expect = 0.007
Identities = 18/39 (46%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDE 639
GGKV + +SK T +++ G+ G KL KAI L I I+ E
Sbjct: 32 GGKVTDSLSKKTTHVIVGENAGTLKLLKAIALGIPIVTE 70
>gnl|CDD|202542 pfam03119, DNA_ligase_ZBD, NAD-dependent DNA ligase C4 zinc finger
domain. DNA ligases catalyze the crucial step of
joining the breaks in duplex DNA during DNA replication,
repair and recombination, utilising either ATP or NAD(+)
as a cofactor. This family is a small zinc binding motif
that is presumably DNA binding. IT is found only in NAD
dependent DNA ligases.
Length = 27
Score = 33.6 bits (78), Expect = 0.011
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 418 CPICNSKIIYIESNLIARCSGSWIECIA 445
CP+C S ++ E + RC+ C A
Sbjct: 2 CPVCGSPLVREEGEVDIRCTNG--SCPA 27
>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 = 33.8 bits (78), Expect = 0.023
Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 602 GGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDE 639
GGKV + +SK T +++ G G KKL KAIKL I I+
Sbjct: 26 GGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTP 64
>gnl|CDD|235735 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 36.7 bits (85), Expect = 0.026
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 14/61 (22%)
Query: 602 GGKVVNFISKNTNYLVKGQKPGKKL---EKAIKL-----------NIKILDEKNFVKIVK 647
GG V + ++K T YLV K + L E + KL NIK L+E+ F++ K
Sbjct: 248 GGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEFLQKCK 307
Query: 648 G 648
Sbjct: 308 E 308
>gnl|CDD|237782 PRK14666, uvrC, excinuclease ABC subunit C; Provisional.
Length = 694
Score = 35.2 bits (81), Expect = 0.13
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 531 VGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRL 582
+G TA+ L F +L+ M A EE L +P IG A +++ L L
Sbjct: 645 IGPATARLLWERFGSLQAMAAAGEEGLAAVPGIG----PARAAALHEHLKTL 692
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 34.6 bits (80), Expect = 0.17
Identities = 28/119 (23%), Positives = 37/119 (31%), Gaps = 15/119 (12%)
Query: 121 IAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEV 180
A+L LRY YGY +Q+ DG E K E +
Sbjct: 128 AADLGLPLTGYGLRYRYGYFRQSD--VDGWQVELPDEW----LKYGNPWEFLRDAEGVPY 181
Query: 181 RCEVLIYKKDFIKLNKYRYHLG-----LKKFTNPRNA--AAGILRQLNPKINKNKILHF 232
V Y + L ++ +G L F N A I R L P +K L
Sbjct: 182 DVPVPGYDNRVVTLRLWQAQVGRVPLYLLDFNVGENKNDARNITRVLYP--GDSKELRL 238
>gnl|CDD|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication,
recombination, and repair].
Length = 254
Score = 33.5 bits (77), Expect = 0.27
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 498 RVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQ 556
R + ++ +K T +Y L I +G A+ L F ++E + A+EE+
Sbjct: 156 REQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASEEE 215
Query: 557 LLNIPKIGSTTVKAFIKFINQPLHRL 582
L+ + IG + +F+ +
Sbjct: 216 LMKVKGIGEKKAREIYRFLRTEYKLI 241
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 31.2 bits (72), Expect = 2.0
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 531 VGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA 570
+G K L +F +L+ + +A+ E+L +P I +A
Sbjct: 551 IGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEA 590
>gnl|CDD|226865 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 821
Score = 31.4 bits (71), Expect = 2.1
Identities = 26/119 (21%), Positives = 45/119 (37%), Gaps = 11/119 (9%)
Query: 457 RKAMNIIGLGKKMIEKLVNANIVVTA---VDLYKINFKNLLRLDRVSNKLANNILLAIQK 513
+ +G+ K+ E+LV ++TA + L + K+L R + + IL Q
Sbjct: 661 DGLLQALGVTHKLAEELV--AELITASRRLGLEEQLAKDLARNEGSGVERD--ILAERQV 716
Query: 514 SKLTT-FSRFIYALGIRHVGETTAKELANYFKNLECMFKAT-EEQLLNIPKIGSTTVKA 570
TT FI LG + E K A+ ++ +F N+ K+
Sbjct: 717 FLATTRIGDFIAWLGFDGIPE--EKRPASRVEDGIRIFAQRPRSNHTNLTKLAKEPRNF 773
>gnl|CDD|132356 TIGR03313, Se_sel_red_Mo, probable selenate reductase,
molybdenum-binding subunit. Our comparative genomics
suggests this protein family to be a subunit of a
selenium-dependent molybdenum hydroxylase, although the
substrate is not specified. This protein is suggested by
Bebien, et al., to be the molybdenum-binding subunit of
a molydbopterin-containing selenate reductase. Xi, et
al, however, show that mutation of this gene in E. coli
conferred sensitivity to adenine, suggesting a defect in
purine interconversion. This finding, plus homology of
nearby genes in a 23-gene purine catabolism region in E.
coli to xanthine dehydrogase subunits suggests xanthine
dehydrogenase activity.
Length = 951
Score = 31.1 bits (70), Expect = 2.5
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 77 GENSKYVHHTFKMMSLDN-----GFSDEDVIIFNKRITN 110
GEN + + M S+ N GF+ D I+FN + N
Sbjct: 15 GENVQTLLFNMGMHSVRNSDDGFGFAGSDAILFNGVLKN 53
>gnl|CDD|217204 pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase,
carbamoyl-P binding domain.
Length = 140
Score = 29.4 bits (67), Expect = 2.6
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 518 TFSRFIYALGIRHVGETTAKELANY 542
SR++ A+ IRH +ELA Y
Sbjct: 88 VLSRYVDAIVIRHPSHGALEELAKY 112
>gnl|CDD|237784 PRK14669, uvrC, excinuclease ABC subunit C; Provisional.
Length = 624
Score = 30.6 bits (69), Expect = 2.9
Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 11/88 (12%)
Query: 494 LRLDRVSNKL---------ANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK 544
+ LDR S L A+ + + + T R L I VG T + L +F
Sbjct: 514 IVLDRFSPVLHLVQSIRDEAHRFAITFHRKRRETRDRTSELLEIPGVGAKTVQRLLKHFG 573
Query: 545 NLECMFKATEEQLLNIPKIGSTTVKAFI 572
+LE + ATE QL + +G +A I
Sbjct: 574 SLERVRAATETQLAAV--VGRAAAEAII 599
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 30.3 bits (69), Expect = 3.3
Identities = 29/120 (24%), Positives = 48/120 (40%), Gaps = 20/120 (16%)
Query: 440 WIECIAQRKAGLQHFSSRKAMNIIGLGK--KMIEKLVNANIVVTAVDLYKINFKNLLRLD 497
WI+ + ++ A Q R ++ +GL + M +++ + V T V+L K N L L
Sbjct: 58 WIDQLGKKPAHKQPPDLRWLLH-LGLYQLRYM-DRIPASAAVNTTVELAKQN--GLGGLA 113
Query: 498 RVSNKLANNILLAIQKSK-LTTFSRFIYALGIRH-------------VGETTAKELANYF 543
V N + L A + L I L I H +G A++L +F
Sbjct: 114 GVVNGILRQYLRAREAGDPLPLPEDPIERLAILHSFPDWLVKLWLEWLGLEEAEQLCKWF 173
>gnl|CDD|214744 smart00611, SEC63, Domain of unknown function in Sec63p, Brr2p and
other proteins.
Length = 312
Score = 30.3 bits (69), Expect = 3.4
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 553 TEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGI-YWLNNPNTKGGKVVNFISK 611
T+ LL +P + +K K L LL +L D L + +G +V +S+
Sbjct: 149 TDSPLLQLPHLPEEILKRLEKKKVLSLEDLL--ELEDEERGELLGLLDAEGERVYKVLSR 206
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 29.2 bits (66), Expect = 3.4
Identities = 18/108 (16%), Positives = 33/108 (30%), Gaps = 28/108 (25%)
Query: 467 KKMIEKLVNANIVVTAVDLYKIN---FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFI 523
K+ ++L T DL + + + L++ + A I
Sbjct: 15 NKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIK--------------- 59
Query: 524 YALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAF 571
A+ L + L + E LL +P +G T +A
Sbjct: 60 ----------ELARILVEGYLGLVPLDLEELEALLALPGVGRWTAEAV 97
>gnl|CDD|181402 PRK08363, PRK08363, alanine aminotransferase; Validated.
Length = 398
Score = 30.2 bits (68), Expect = 3.6
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 35 YDNPIISDNKYDQLLFELKKIEEKYPELLTKDS 67
+D P+ISD YD + +E K + P LTKD
Sbjct: 198 HDLPVISDEIYDLMTYEGKHVS---PGSLTKDV 227
>gnl|CDD|182084 PRK09800, PRK09800, putative hypoxanthine oxidase; Provisional.
Length = 956
Score = 29.8 bits (67), Expect = 5.1
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 77 GENSKYVHHTFKMMSLDN-----GFSDEDVIIFNKRITN 110
GEN + + M S+ N GF+ D IIFN I N
Sbjct: 19 GENVQKLLFNMGMHSVRNSDDGFGFAGSDAIIFNGNIVN 57
>gnl|CDD|223399 COG0322, UvrC, Nuclease subunit of the excinuclease complex [DNA
replication, recombination, and repair].
Length = 581
Score = 29.2 bits (66), Expect = 9.1
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 526 LGIRHVGETTAKELANYFKNLECMFKATEEQL 557
I +G K L +F +L+ + A+ E+L
Sbjct: 533 DDIPGIGPKRRKALLKHFGSLKGIKSASVEEL 564
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
0.321 0.139 0.397
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,542,136
Number of extensions: 3406191
Number of successful extensions: 3419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3369
Number of HSP's successfully gapped: 67
Length of query: 655
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 552
Effective length of database: 6,369,140
Effective search space: 3515765280
Effective search space used: 3515765280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.6 bits)