RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|255764496|ref|YP_003065012.2| excinuclease ABC subunit C
[Candidatus Liberibacter asiaticus str. psy62]
(616 letters)
>gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 723 bits (1869), Expect = 0.0
Identities = 260/610 (42%), Positives = 373/610 (61%), Gaps = 29/610 (4%)
Query: 7 PECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTE 66
P+ PGVY+M D G V+YVGKA NL+ R++SY ++ + + M+S+I +I + VT +E
Sbjct: 12 PDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSE 71
Query: 67 VEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFA 126
EALLLE N+IK+ KPR+N+LLRDDKS+PYI IT + P L R + +G YFGP+
Sbjct: 72 TEALLLENNLIKKYKPRYNVLLRDDKSYPYIKITTNEEFPRLAITRGVAKDKGRYFGPYP 131
Query: 127 SVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHE 186
S AV +T++ LQ+ F LR+C DSVF++R RPCLL+QI RC PC G IS E+Y E V E
Sbjct: 132 SAGAVRETLDLLQKLFPLRTCEDSVFKNRKRPCLLYQIGRCLAPCVGLISKEEYAELVDE 191
Query: 187 AKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNH----NDSIYNRM 242
AK FLSG + +++ M +A+ ++E A +RD++ AL +Q +
Sbjct: 192 AKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQKVSLKDGEDA- 250
Query: 243 DCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPEN 302
D ++ + AC+Q F G+ G ++F K E+ +IL FL QFY K P+
Sbjct: 251 DVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVS-ETELEEILEAFLGQFYLQKSIPKE 309
Query: 303 ILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISH 362
IL+ E ++ L E G KVKI VP++G+K++++E A NA + +KLS + +
Sbjct: 310 ILVPHELDDEELAEA---LLAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQ 366
Query: 363 QMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDV 422
Q L++ + LP P RIE +D SHI G + V MVV + G K++YR++N+ V
Sbjct: 367 QQALEELAELLGLPEPPYRIECFDISHIQGTATVASMVVFEDGGPDKSEYRRYNIK--GV 424
Query: 423 KTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGV 482
DD A MR VL RR+S+L+K F PD++++DGGKGQL+AA+ V
Sbjct: 425 TGGDDYAAMREVLTRRYSRLLK--------------EFGPLPDLILIDGGKGQLNAAKEV 470
Query: 483 LKKLNVENRITIISIAKGPKRSAGMEKFFVK-KGEALVLNMRDPILYFIQRLRDEAHRFA 541
L++L ++ I ++ +AKG KR AG E+ F + E ++L P LY +QR+RDEAHRFA
Sbjct: 471 LEELGLD--IPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFA 528
Query: 542 ITTHRKRRKKAAY-SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIA 600
IT HRK+R KA S LD+I GIGP R++ LL+ FG++K I +S E LA + GISKK+A
Sbjct: 529 ITFHRKKRSKARLTSALDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLA 588
Query: 601 CKIYNHFHKN 610
IY HK
Sbjct: 589 EAIYEALHKK 598
>gnl|CDD|161756 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments.
Length = 574
Score = 449 bits (1156), Expect = e-126
Identities = 224/592 (37%), Positives = 337/592 (56%), Gaps = 32/592 (5%)
Query: 4 EQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVT 63
+ +P+ PG Y M D G+VLYVGKA NL+KR+ SY NN + + ++ QI +I + +T
Sbjct: 6 KNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFRENN-SAKTQALVKQIADIEYILT 64
Query: 64 CTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFG 123
E EAL+LEAN+IK+ +PR+N+LL+DDK +PYI IT + P L R +G YFG
Sbjct: 65 KNENEALILEANLIKQYQPRYNVLLKDDKGYPYIYITHEKY-PRLLITRKLKQDKGKYFG 123
Query: 124 PFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEF 183
PF + A+ +T++ L + F LR CA +R RPCL +QI RC GPC EI+ E+Y +
Sbjct: 124 PFTNAFALRETLDLLLKLFPLRKCAK---HNRNRPCLYYQIGRCLGPCVKEITEEEYQQI 180
Query: 184 VHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHI-QNHNDSIYNR- 241
V + + F +G + +++ + M +A+ ++E A RD++AA+ + + + S+ +
Sbjct: 181 VEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSLTDLI 240
Query: 242 -MDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYT----D 296
+D ++ + N+A IQ F G+ G F + + + FL QFY +
Sbjct: 241 DLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPGTDLDELVET-FLIQFYQQGYQN 299
Query: 297 KPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKL 356
+ P IL+S E+ LLE +Q G K+ + PK+G+K+K++E A+ NA + QK
Sbjct: 300 RLIPSEILVSLSLEDLKLLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKW 359
Query: 357 STEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFN 416
+ L+D LP I KRIEI+D SHI G VG MVV + +K YR++N
Sbjct: 360 TQFERKTQALEDLASLLNLPKI-KRIEIFDISHIDGSQTVGSMVVFEDGKPLKASYRRYN 418
Query: 417 LHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQL 476
+ N + DD A MR VL RR+S + K K PD++++DGGKGQL
Sbjct: 419 I--NSITGGDDYAAMREVLRRRYSSIQK---------KNNL----PLPDLILIDGGKGQL 463
Query: 477 SAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDE 536
+AA VLK L V N+ +I +AK + + K+G + LN P L +Q +RDE
Sbjct: 464 NAALEVLKSLGVVNKPIVIGLAKAKRHETDIFLIGDKQGINIDLN--SPALQLLQHIRDE 521
Query: 537 AHRFAITTHRKRRKKAAY-SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPE 587
AHRFAI+ HRK+R KA+ SPL +I G+G R + LL+ FG++K I ++S E
Sbjct: 522 AHRFAISFHRKKRLKASLQSPLLKIPGVGEKRVQKLLKYFGSLKGIKKASVE 573
>gnl|CDD|183423 PRK12306, uvrC, excinuclease ABC subunit C; Reviewed.
Length = 519
Score = 349 bits (898), Expect = 1e-96
Identities = 193/570 (33%), Positives = 294/570 (51%), Gaps = 81/570 (14%)
Query: 4 EQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVT 63
+P PG Y D G ++YVGKA NL+KR+ SY +H + ++ I +I F VT
Sbjct: 5 STIPTNPGCYLYKDEEGTIIYVGKAKNLKKRVSSYFQKKDHDPKTQSLVKAIRDIEFIVT 64
Query: 64 CTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFG 123
EVEALLLE +IK+ P++NI L+D K + YI I+++ K P + R+ S +G +FG
Sbjct: 65 DNEVEALLLENTLIKKHWPKYNIDLKDSKRYAYIYISEE-KFPRIGIARNKSG-KGKFFG 122
Query: 124 PFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEF 183
PF S + ++ L++TF LRSC RPCL + I C+ PCTG ISS++Y+E
Sbjct: 123 PFVSAKERDYVLDVLKKTFQLRSCK----NMPKRPCLRYHIGNCTAPCTGNISSDEYLEQ 178
Query: 184 VHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQ---------NH 234
V +A++ L G L EK+ M + + +E A++ RD + A+ ++Q +
Sbjct: 179 VKKAEEVLKGKIDELIEKLEEEMAEKAKNQQFERALVIRDEINAIENLQERQNVERQKKY 238
Query: 235 NDSIYN--------RMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQIL 286
++ + N + F++Y L + F +G+N L
Sbjct: 239 DEDVINYLVKDGTVYLMVFNVY-KGTLFDKKEFVFDYGEN------------------FL 279
Query: 287 SYFLRQFYTDKPCPENILLSEEAEETSLLEISFF-KQYGYKVKITVPKQGEKRKIIEQAL 345
FL Q+Y++ P+ I++SE E + + G KVK+TVPKQGEK+++++ AL
Sbjct: 280 EEFLVQYYSENEPPKEIIVSELPENLDEALAEYLSHKKGSKVKVTVPKQGEKKQLLDLAL 339
Query: 346 INAHRSHTQKLSTEISH---QMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVV 402
N EI ++ L++ K LP P IE +D SH+ G S VG MV
Sbjct: 340 KN----------LEIYFFGDEIKLEELKNKLHLPKPPNVIECFDISHLSGTSTVGSMVQF 389
Query: 403 GENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPS 462
K YR+F + V+ DD A + V+ RR+S+L+ EEN
Sbjct: 390 RNGKPDKKNYRRFKI--KTVEGIDDFASIAEVVRRRYSRLL--EENSEL----------- 434
Query: 463 WPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGE-ALVLN 521
PD++++DGGKGQLS+A L+KL + +I +ISIAK E+ +V + L +
Sbjct: 435 -PDLIVIDGGKGQLSSAFKELRKLGL--KIPLISIAKRE------EEIYVPGIKNPLPIK 485
Query: 522 MRDPILYFIQRLRDEAHRFAITTHRKRRKK 551
+ F+Q +RDEAHRFAIT +R RKK
Sbjct: 486 KNEKASLFLQEIRDEAHRFAITYNRLLRKK 515
>gnl|CDD|184786 PRK14671, uvrC, excinuclease ABC subunit C; Provisional.
Length = 621
Score = 339 bits (871), Expect = 1e-93
Identities = 209/636 (32%), Positives = 325/636 (51%), Gaps = 65/636 (10%)
Query: 6 MPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYM-HSNNHTHRITHMISQINNIRFTVTC 64
+P PGVYQ + AGRV+YVGKA NL+ R++SY +S + + ++ I ++ +T
Sbjct: 19 LPTSPGVYQFKNAAGRVIYVGKAKNLRNRVRSYFRNSRQLSGKTLVLVGHIADLEVIITS 78
Query: 65 TEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHR----DSSTIQGS 120
+EVEAL+LE N+IK LKPR+N+ L+DDK++PY++IT++ P ++ R D ST
Sbjct: 79 SEVEALILENNLIKELKPRYNVNLKDDKTYPYLVITNE-PFPRIFITRQVRRDGST---- 133
Query: 121 YFGPFASVDAVEKTINSLQRTFFLRSC-----ADSVFRHRTRPCLLFQIKRCSGPCTGEI 175
YFGP+ + ++ + F +RSC +++ + + CL + I +C GPC G
Sbjct: 134 YFGPYTEARQLRSILDLIGSIFPVRSCKLKLTPENIAAGKYKVCLDYHIHKCKGPCEGLQ 193
Query: 176 SSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHN 235
S E Y+E + E + L G L + M +A + +E A +D++ +L
Sbjct: 194 SEEDYLEMIEEIVRLLKGKTSALIRSLTEEMQRAAAELKFEEAAELKDQIESLKRYAERQ 253
Query: 236 DSIYNRM---DCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQ 292
+ D F++ ++ AC G+ G+ F+L ++A +L+ FL +
Sbjct: 254 KVVSQDGADRDVFAVAVGEDDACGVVFKIREGKLLGSQHFYLSNTEGESDANLLARFLEK 313
Query: 293 FY--TDKPCPENILLSEE--AEETSLLEISFFKQY-----GYKVKITVPKQGEKRKIIEQ 343
+Y T P+ ILL EE AEET LE ++ +V+ TVP+ GEK +++
Sbjct: 314 YYLETPDLIPDEILLQEELPAEETEALEALLREKQSEETRKKQVRFTVPQIGEKAHLVDM 373
Query: 344 ALINAHRSH-----TQKL----STEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCS 394
NA R H QK + LK + L +P+RIE +DNSH G
Sbjct: 374 CRQNA-RHHLEEYLIQKQKRGEAAREHPA--LKALQEALHLEKLPRRIECFDNSHFQGTD 430
Query: 395 AVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPK 454
V MV + K+ YRKF L + DD A MR V+ RR+S + E
Sbjct: 431 YVSSMVCFVDGKPKKSDYRKFKL--RSFEGSDDYAAMREVVTRRYSGSLAEE-------- 480
Query: 455 KQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKK 514
P PD++++DGGKGQ+++A VL++L + + +I +AK + E F
Sbjct: 481 -----LP-LPDLIVIDGGKGQVNSAWKVLQELGL--SVPVIGLAKRLE-----EIFTPND 527
Query: 515 GEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAY-SPLDEINGIGPLRKRLLLQ 573
+ L P L +Q+LRDEAHRFAIT HRK R K + L +I GIG LL+
Sbjct: 528 SDPFNLPKTSPALKLLQQLRDEAHRFAITYHRKLRSKRTLQTELTDIAGIGEKTAEKLLE 587
Query: 574 SFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609
FG+V+ ++++S E LA++ G K A IY ++H
Sbjct: 588 HFGSVEKVAKASLEELAAVAG--PKTAETIYRYYHP 621
>gnl|CDD|173132 PRK14669, uvrC, excinuclease ABC subunit C; Provisional.
Length = 624
Score = 333 bits (854), Expect = 1e-91
Identities = 198/619 (31%), Positives = 316/619 (51%), Gaps = 41/619 (6%)
Query: 5 QMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRIT-HMISQINNIRFTVT 63
+P PGVY + G V+YVGKA NL+ R++SY + + T +I + +I + +
Sbjct: 9 TLPTSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFSEDKLGNIKTGSLIREAVDIDYILV 68
Query: 64 CTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFG 123
E EAL LE N+IK+ KPRFNILLRDDK++PY+ +T K P +Y R Y+G
Sbjct: 69 DNEKEALALENNLIKQYKPRFNILLRDDKTYPYVKLTLGEKYPRVYVTRRLRKDGAQYYG 128
Query: 124 PFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCT-GEISSEKYME 182
PF + + ++ + R F + SC + R+ RPCL F I RC GPC G + E Y E
Sbjct: 129 PFFPANLAYRLVDLIHRHFLVPSCKVDLTRYHPRPCLQFYIHRCLGPCVQGLTTDEAYAE 188
Query: 183 FVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHN---DSIY 239
V + + FL G + +L + M A L+ +E A +RD + + ++ +
Sbjct: 189 AVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVEELEEKQRMAAAKG 248
Query: 240 NRMDCFSLYHNKNLACIQTCFFHF--GQNRGTCTFF------LKTDSESTNAQILSYFLR 291
+ D F ++ + + FH G+ FF ++ + E S L+
Sbjct: 249 DDADVFGYHYENPMVAVN--LFHMRGGKIVDRREFFWEDLGEVQVEFEYDEGLFFSSLLK 306
Query: 292 QFYTDKP-CPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHR 350
Q Y D+ P I + E E+ LE +Q +++I VP++G+KR +++ NA +
Sbjct: 307 QIYLDQQYVPREIYVPVEFEDREALEELLTEQRHRRIEIRVPQRGDKRSLLDLVEQNAKQ 366
Query: 351 SHTQKLSTEISHQMILKD-FTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVK 409
S+ Q+ +++ LP +P RIE +D SHI G V MVV + K
Sbjct: 367 SYDQRFRVMKPSSRAIQEALQDALNLPELPSRIECFDISHIQGAETVASMVVWEDGKMKK 426
Query: 410 NQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVIL 469
+ YRKF + V DD A MR V+ RR+S+L + ++ + P +V++
Sbjct: 427 SDYRKFII--KTVVGVDDFASMREVVTRRYSRLQEEKQPM--------------PGLVLI 470
Query: 470 DGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYF 529
DGG GQL AA L+ + + ++ + SIAK + + F ++ E +VL+ P+L+
Sbjct: 471 DGGLGQLHAAAEALEAIGITDQ-PLASIAKREE----IIYVFGQEDEPIVLDRFSPVLHL 525
Query: 530 IQRLRDEAHRFAITTHRKRRK-KAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPET 588
+Q +RDEAHRFAIT HRKRR+ + S L EI G+G + LL+ FG+++ + ++
Sbjct: 526 VQSIRDEAHRFAITFHRKRRETRDRTSELLEIPGVGAKTVQRLLKHFGSLERVRAATETQ 585
Query: 589 LASIEGISKKIACKIYNHF 607
LA++ + + A I HF
Sbjct: 586 LAAV--VGRAAAEAIIAHF 602
>gnl|CDD|184785 PRK14668, uvrC, excinuclease ABC subunit C; Provisional.
Length = 577
Score = 320 bits (822), Expect = 7e-88
Identities = 193/611 (31%), Positives = 309/611 (50%), Gaps = 63/611 (10%)
Query: 6 MPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCT 65
+P PGVYQ + G VLYVGKA +L+ R++SY ++ + RI M+ + ++I F VT T
Sbjct: 13 LPREPGVYQFVA-GGTVLYVGKAVDLRDRVRSY--ADPRSERIRRMVERADDIDFAVTDT 69
Query: 66 EVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPF 125
E +ALLLEAN+IKR +PR+N+ L+DDKS+P + +TD H +P + RD + FGP+
Sbjct: 70 ETQALLLEANLIKRHQPRYNVRLKDDKSYPLVQLTD-HPVPRIEVTRDPDE-GATVFGPY 127
Query: 126 ASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVH 185
VE + +L+ T+ LR C+D + +R RPCL +++ C+ PCTGEI E Y E V
Sbjct: 128 TDKGRVETVVKALRETYGLRGCSDHKYSNRDRPCLDYEMGLCTAPCTGEIDEEAYAEDVE 187
Query: 186 EAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALS--H------IQNHNDS 237
A++F G L + + R M A +++E A RDRL A+ H + + D
Sbjct: 188 SAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVEAFHGGGGEAVSSTGD- 246
Query: 238 IYNRMDCFSLYHNKNLACIQTCFFHFGQ--NRGTCTFFLKTDSESTNAQILSYFLRQFYT 295
+D + + A + GQ +R + A +L+ F+ Q+Y
Sbjct: 247 -ERAVDVLGVAIEGDRATVARLHAEGGQLVDRDRHRLEAPDGEDRGAA-VLAAFIVQYYA 304
Query: 296 DKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRS--HT 353
++ P+ +LLSE + + ++ + G V + VP G + +++ AL NA R
Sbjct: 305 ERELPDALLLSERPGDDDV--RAWLEAEG--VDVRVPGAGREATLVDLALKNARRRGGRD 360
Query: 354 QKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYR 413
++ L D + P+RIE +D SH G + VG V + YR
Sbjct: 361 DEVGA-------LAD---ALGIDR-PERIEGFDVSHAQGRAVVGSNVCFVDGSAETADYR 409
Query: 414 KFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGK 473
+ L + DD A MR ++ R + ++ ++ P PD++++DGG
Sbjct: 410 RKKL----TERNDDYANMRELVRWRAERAVEGRDD---RPD---------PDLLLIDGGD 453
Query: 474 GQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRL 533
GQL AA+ L + + + I++AK E+ V P L+ +QR+
Sbjct: 454 GQLGAARDALAETGWD--VPAIALAKA-------EELVVTPDRTYDWPDDAPQLHLLQRV 504
Query: 534 RDEAHRFAITTHRKRRKKAAYSPLDEINGIGP-LRKRLLLQSFGTVKMISRSSPETLASI 592
RDEAHRFA+ H+ R + + LD++ G+GP RKR LL+ FG+V+ + +S E L +
Sbjct: 505 RDEAHRFAVQYHQTLRDDVS-TVLDDVPGVGPETRKR-LLRRFGSVEGVREASVEDLRDV 562
Query: 593 EGISKKIACKI 603
G+ +K A I
Sbjct: 563 PGVGEKTAETI 573
>gnl|CDD|184784 PRK14667, uvrC, excinuclease ABC subunit C; Provisional.
Length = 567
Score = 245 bits (628), Expect = 2e-65
Identities = 168/605 (27%), Positives = 286/605 (47%), Gaps = 59/605 (9%)
Query: 4 EQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVT 63
E+ PE PGVY + R +Y+GKA N++ R+ + + + + S+ +++ + +T
Sbjct: 11 EKAPEEPGVY-LFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIIT 69
Query: 64 CTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFG 123
E EAL+LE ++I++ KP++N+LL+ +P +LITD + P + R + +G YFG
Sbjct: 70 RNEYEALVLEIDLIQQYKPKYNVLLKSGSGYPMLLITDD-EYPTVKIVRGTGE-KGEYFG 127
Query: 124 PFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEF 183
PF K + + F LR+C R PC+ + + CSGPC G+IS E Y
Sbjct: 128 PFLPARKARKVKKLIHKLFKLRTCDP--MPKRKEPCMDYHLGLCSGPCCGKISKEDYELS 185
Query: 184 VHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSI---YN 240
V AK FLSG + ++ + + + K +E A + RD++ AL ++ +
Sbjct: 186 VKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALENLIKGQEVSGLPIE 245
Query: 241 RMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCP 300
D F Y + + F ++ + +SE Q + +Y P
Sbjct: 246 EADIF--YFMGSRLGL----FLVRSSKLVGKEEFRLESEE---QEEEEVILGYYYSNYIP 296
Query: 301 ENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEI 360
+ I+ + E + +S K+ G V+ E K IE+ I +
Sbjct: 297 QKIITNFELSDNLKQWLS--KRKGGDVEFLTLIPKELEKFIEEN-IGIK----------V 343
Query: 361 SHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFV-KNQYRKFNLHP 419
+++ ++F K F P +P+RIE +D SH G VG VV E+G + K +YR++ +
Sbjct: 344 DLEVLKEEFKKTFGFP-LPERIEGFDISHFYGEFTVGSCVV-WEDGSMNKKEYRRYKI-- 399
Query: 420 NDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAA 479
V DD A +R VL RR + + E + PD+ ++DGGKGQLS
Sbjct: 400 KTVDGIDDYASLREVLTRRARRYKEGENPM--------------PDLWLIDGGKGQLSVG 445
Query: 480 QGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHR 539
V +L + I + S+AK E + + G+ + L + +RDEAHR
Sbjct: 446 IEVRDRLGLN--IKVFSLAKKE------EILYTEDGKEIPLKENPILYKVFGLIRDEAHR 497
Query: 540 FAITTHRK-RRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKK 598
FA++ +RK R K+ LD+I GIG ++K ++ ++F T+ ++ E L + GI
Sbjct: 498 FALSYNRKLREKEGLKDILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPS 556
Query: 599 IACKI 603
+ ++
Sbjct: 557 VKQEV 561
>gnl|CDD|173133 PRK14670, uvrC, excinuclease ABC subunit C; Provisional.
Length = 574
Score = 225 bits (576), Expect = 2e-59
Identities = 172/608 (28%), Positives = 292/608 (48%), Gaps = 65/608 (10%)
Query: 15 MLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEA 74
M ++LY+GKA NL+ R+K+Y +H+ ++ + NI T +E EALLLE
Sbjct: 1 MYSENNKILYIGKAKNLRSRVKNYF-LEKISHKTKILMKNVKNIEVITTNSEYEALLLEC 59
Query: 75 NMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKT 134
N+IK KP +NI L+DDK +P I IT + K P ++K R YFGP+ +V ++
Sbjct: 60 NLIKTHKPDYNIKLKDDKGYPMIRITCE-KYPRIFKTRKIINDGSEYFGPYVNVKKLDLV 118
Query: 135 INSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGG 194
++ + +TF R C + PCL F + +C G C E ++Y + V + K L+G
Sbjct: 119 LDLINKTFKTRKCK----KKSKNPCLYFHMGQCLGVCYREDLEKEYQKEVDKIKHILNGN 174
Query: 195 NHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLA 254
L +I M +A KED+E+AI ++ +L I+ I +++ S+ +
Sbjct: 175 ISKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSL--IEISQTQIITKINKLSIDY----- 227
Query: 255 CIQTCFFHFGQNRGTCTFFLKTDSESTNAQI------------LSYFLRQFYT--DKPCP 300
+ H +N T D + I + F+ Q+YT + P
Sbjct: 228 ----VYIHPTENLNTIVILKYKDGKLVEKDINFDESIYEEDELILQFITQYYTSINMIVP 283
Query: 301 ENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAH---RSHTQKLS 357
+ I + ++ +T + + K +I + E KI+E A+ NA R + + +
Sbjct: 284 DKIHIFKKI-DTKNITKLINELKNTKTEIIYKETKEIIKIMEMAISNAKLALREYENEKN 342
Query: 358 TEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNL 417
+ I+ + K +PK IE +D +H+ G V +V K+ YR + +
Sbjct: 343 KALESLKIILEMDK------LPKTIEGFDIAHLNGQKTVASLVTFKMGKPFKDGYRVYKI 396
Query: 418 HPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS 477
+ DD ++ V+ RR+S+LI + L P+++++DGGKGQL+
Sbjct: 397 NSLLKGEIDDFKAIKEVISRRYSKLINEQLEL--------------PNLILIDGGKGQLN 442
Query: 478 AAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEA 537
AA +LK L +EN++ + ++AK + F K + + L +P L +Q +RDEA
Sbjct: 443 AAYSILKGLKIENKVKVCALAKKEETI-----FLPNKKQGIKLPKGNPALRILQNVRDEA 497
Query: 538 HRFAITTHRKRRK--KAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGI 595
HR A ++K R+ K Y+ +I GIG + + +L+S GT K I + + +A I
Sbjct: 498 HRKANGFNKKLRENIKLNYT---KIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKI 554
Query: 596 SKKIACKI 603
+ K+A KI
Sbjct: 555 NIKMAKKI 562
>gnl|CDD|173129 PRK14666, uvrC, excinuclease ABC subunit C; Provisional.
Length = 694
Score = 191 bits (486), Expect = 5e-49
Identities = 84/224 (37%), Positives = 124/224 (55%), Gaps = 1/224 (0%)
Query: 6 MPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHS-NNHTHRITHMISQINNIRFTVTC 64
+P PGVY D AGR++YVGKA +L++R+ SY + T + M+ I T
Sbjct: 9 IPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSALTPKTVAMLRHAVTIDTLSTT 68
Query: 65 TEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGP 124
TE EALLLEA++IK+ +PR+NI+LRDDK + + KH P L R + YFGP
Sbjct: 69 TEKEALLLEASLIKKHRPRYNIVLRDDKQYVLFRLGAKHPYPRLEIVRKARRDGARYFGP 128
Query: 125 FASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFV 184
F S A +T ++ R F LR C+D F +R R CL + +C GPC ++ E Y V
Sbjct: 129 FTSASAARETWKTIHRAFPLRRCSDRAFGNRVRACLYHFMGQCLGPCVNDVPRETYAALV 188
Query: 185 HEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAAL 228
+ + LSG + L + + M A+ ++E A + RD++ A+
Sbjct: 189 RKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAV 232
Score = 130 bits (329), Expect = 9e-31
Identities = 89/323 (27%), Positives = 146/323 (45%), Gaps = 44/323 (13%)
Query: 298 PCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLS 357
+ + +LE + G V+I P+ + ++++ A+ NA R ++ +
Sbjct: 396 QAATLAGAAPKGATHLMLEETLADLRGGPVRIVPPRNPAENRLVDMAMSNA-REEARRKA 454
Query: 358 TEISHQMILKD-FTKKFALPHIPKRIEIYDNSHIMGCSA-VGCMVVVGENGF-VKNQYRK 414
+ L+D + L P RIE D SH G + VG +VV E+G ++ YR
Sbjct: 455 -----ETPLQDLLARALHLSGPPHRIEAVDVSHTGGRNTRVG--MVVFEDGKPARDAYRT 507
Query: 415 FNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKG 474
+ + DD + RR S P WPD++++DGG+G
Sbjct: 508 YAFEDGE---GDDYGTLAAWAGRRVE------------------SGPPWPDLLLVDGGRG 546
Query: 475 QLSAAQGVLKKLNVENRITIISIAKG------PKRSAG--MEKFFVKKGEALVLNMRD-- 524
QL+A L++ + + SIAK R AG ++ F+ G A L +R
Sbjct: 547 QLAAVVRALEEAGMGGLFAVASIAKARTEEGRADRRAGNVADRIFL-PGRANPLPLRAGA 605
Query: 525 PILYFIQRLRDEAHRFAITTHRKRRKKAAYS-PLDEINGIGPLRKRLLLQSFGTVKMISR 583
P L F+Q +RD H +AI HR+ R AA + L + GIGP RLL + FG+++ ++
Sbjct: 606 PELLFLQHVRDTVHDYAIGRHRRARAGAALTGELQRVEGIGPATARLLWERFGSLQAMAA 665
Query: 584 SSPETLASIEGISKKIACKIYNH 606
+ E LA++ GI A ++ H
Sbjct: 666 AGEEGLAAVPGIGPARAAALHEH 688
>gnl|CDD|149497 pfam08459, UvrC_HhH_N, UvrC Helix-hairpin-helix N-terminal. This
domain is found in the C subunits of the bacterial and
archaeal UvrABC system which catalyses nucleotide
excision repair in a multi-step process. UvrC catalyses
the first incision on the fourth or fifth phosphodiester
bond 3' and on the eighth phosphodiester bond 5' from
the damage that is to be excised. The domain described
here is found to the N-terminus of a helix hairpin helix
(pfam00633) motif and also co-occurs with the pfam01541
catalytic domain which is found at the N-terminus of the
same proteins.
Length = 154
Score = 184 bits (471), Expect = 4e-47
Identities = 70/173 (40%), Positives = 100/173 (57%), Gaps = 22/173 (12%)
Query: 371 KKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAM 430
+ LP +P RIE +D SHI G VG MVV + K++YR++N+ DD A
Sbjct: 3 ELLGLPKLPHRIECFDISHIQGTDTVGSMVVFEDGKPDKSEYRRYNIK--GTPG-DDYAS 59
Query: 431 MRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVEN 490
MR VL RRFS+L+K + PD++++DGGKGQL+AA+ VL++L ++
Sbjct: 60 MREVLTRRFSRLLKEKLP--------------LPDLILIDGGKGQLNAAKEVLEELGLD- 104
Query: 491 RITIISIAKGPKRSAGMEKFFV-KKGEALVLNMRDPILYFIQRLRDEAHRFAI 542
I +I +AKG + EK F+ E + L P L+ +QR+RDEAHRFAI
Sbjct: 105 -IPVIGLAKGEEHKT--EKLFLPGGPEPIPLPPDSPALHLLQRIRDEAHRFAI 154
>gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated.
Length = 557
Score = 178 bits (453), Expect = 4e-45
Identities = 70/228 (30%), Positives = 109/228 (47%), Gaps = 3/228 (1%)
Query: 3 SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTV 62
++ +P PGVY +G VLYVG A NL++R++SY + R+ M++ +
Sbjct: 211 ADGLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTAAETRGRMREMVALAERVDHVE 270
Query: 63 TCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYF 122
+EA + E +I KP +N + + ++ +TD P L R +Y
Sbjct: 271 CAHALEAEVRELRLIAAHKPPYNRRSKFPERRWWVRLTD-EAFPRLSVVRAVEDDGAAYL 329
Query: 123 GPFASVDAVEKTINSLQRTFFLRSCADSVFRH--RTRPCLLFQIKRCSGPCTGEISSEKY 180
GPF S A E+ +L R F LR C D + R C L ++ RC PC G S+ +Y
Sbjct: 330 GPFRSRRAAEEAAEALARAFPLRQCTDRLSRRARHGPACALAELGRCPAPCDGRESAAEY 389
Query: 181 MEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAAL 228
E V A+ L+G + + + +++ E +E A RDRLAAL
Sbjct: 390 AEAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDRLAAL 437
>gnl|CDD|173135 PRK14672, uvrC, excinuclease ABC subunit C; Provisional.
Length = 691
Score = 141 bits (355), Expect = 7e-34
Identities = 91/306 (29%), Positives = 148/306 (48%), Gaps = 9/306 (2%)
Query: 7 PECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTE 66
P GVY D+ G V+YVGKA +L+ R+ SY H + ++S+ + + T E
Sbjct: 19 PSTSGVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCR-HDPKTRVLMSRAAALEYLQTQHE 77
Query: 67 VEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFA 126
EALLLE +IK+ PR+NI L+D K++P + +T + P +++ R YFGPF
Sbjct: 78 YEALLLENTLIKKHTPRYNICLKDGKTYPLLKLTCE-PFPRIFRTRQFCQDGARYFGPFP 136
Query: 127 SVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHE 186
V ++ + + RT+ +R+C + R R PCL + +KRC PC G +S Y + +HE
Sbjct: 137 DVQILDSFLKLILRTYKIRTC--TTLRKRKNPCLYYHLKRCDAPCCGWVSPRTYQKDIHE 194
Query: 187 AKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHN---DSIYNRMD 243
L G ++ + M +A +E +E+A RD + A+ I + + D D
Sbjct: 195 ITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITHKSLVQDMDERARD 254
Query: 244 CFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENI 303
+ + G+ G F +T S +ILS FL +Y+D P ++
Sbjct: 255 YIAWSSTGAIVTFAVLRMRGGKLNGRELF--RTRSLKNEEEILSEFLITYYSDHTIPPHL 312
Query: 304 LLSEEA 309
+ A
Sbjct: 313 FVHSSA 318
Score = 118 bits (296), Expect = 5e-27
Identities = 83/255 (32%), Positives = 128/255 (50%), Gaps = 25/255 (9%)
Query: 338 RKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVG 397
R I+ A +NAH T+ L + LK+ K+ L IP IE +D SH+ G V
Sbjct: 414 RAILAMAQLNAHEDITRYLKNRGADDA-LKELQKQLHLARIPTLIEGFDISHLGGKYTVA 472
Query: 398 CMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQE 457
++ YR FNL +D + DD A MR + RR++ +
Sbjct: 473 SLICFKNGAPDTKNYRLFNLRAHDTRI-DDFASMREAIARRYTH------------TPEG 519
Query: 458 YSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEA 517
Y+ P D++++DGG G +SAAQ VL L + I ++ +AK + E F
Sbjct: 520 YTLP---DLILVDGGIGHVSAAQHVLDALGLS--IPLVGLAKRAE-----ELFIPNSPTP 569
Query: 518 LVLNMRDPILYFIQRLRDEAHRFAITTHRK-RRKKAAYSPLDEINGIGPLRKRLLLQSFG 576
LVL+ R+P L+ +QR+RDEAHRFAIT +R R KK + + +G +R LL FG
Sbjct: 570 LVLDRRNPALHMLQRIRDEAHRFAITRNRHLRTKKELVLSFERLPHVGKVRAHRLLAHFG 629
Query: 577 TVKMISRSSPETLAS 591
+ + + ++P+ +A+
Sbjct: 630 SFRSLQSATPQDIAT 644
>gnl|CDD|182535 PRK10545, PRK10545, nucleotide excision repair endonuclease;
Provisional.
Length = 286
Score = 78.6 bits (194), Expect = 4e-15
Identities = 54/190 (28%), Positives = 85/190 (44%), Gaps = 33/190 (17%)
Query: 4 EQMPECPGVYQML-DIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTV 62
E +P+ PGVY + LY+GK+ N++ R+ S++ T M+ Q I +
Sbjct: 29 EDLPKLPGVYLFHGESDTMPLYIGKSVNIRSRVLSHLR----TPDEAAMLRQSRRISWIC 84
Query: 63 TCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALY-KHRDSSTIQGSY 121
T E+ ALLLEA +IK +P FN LR ++ + + + ++ +Y K D S +
Sbjct: 85 TAGEIGALLLEARLIKEQQPLFNKRLRRNRQLCSLQLNEG-RVDVVYAKEVDFSRAPNLF 143
Query: 122 FGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRT-------------RPCLLFQIKRCS 168
G FA+ A + L+S AD + R C +KRC+
Sbjct: 144 -GLFANRRAALQA---------LQSIAD---EQKLCYGLLGLEPLSRGRACFRSALKRCA 190
Query: 169 GPCTGEISSE 178
G C G+ S E
Sbjct: 191 GACCGKESHE 200
>gnl|CDD|128741 smart00465, GIYc, GIY-YIG type nucleases (URI domain).
Length = 84
Score = 64.0 bits (156), Expect = 1e-10
Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 10 PGVYQMLDIAGRVLYVGKAYNLQKRIKSY-MHSNNHTHRITHMISQINNIRFTVT-CTEV 67
PGVY + + LYVGKA NL+ R+K + S I ++ N F + +
Sbjct: 2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDALLKYGGNFEFIILESFDE 61
Query: 68 EALLLEANMIKRLKPRFNILLRD 90
AL LE +IK KP++N+LL+
Sbjct: 62 SALELEKYLIKEYKPKYNLLLKG 84
>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 44.5 bits (106), Expect = 7e-05
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 560 INGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604
+ +GP+ R LL+ FG+V+ + +S E L +EGI +K A +I
Sbjct: 720 LPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIR 764
>gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent. 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.
Length = 652
Score = 44.2 bits (105), Expect = 1e-04
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 560 INGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610
I +G + + L + FGT+ + +S E L S+EG+ K+A I N FH
Sbjct: 503 IRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDP 553
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 39.0 bits (92), Expect = 0.003
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 563 IGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610
+G + L + FG+++ + +S E LA++EG+ + +A I F
Sbjct: 519 VGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVE 566
>gnl|CDD|166873 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 38.3 bits (89), Expect = 0.006
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHF 607
L + IG R R L + F +++ I + P L +EGI KI I+ H
Sbjct: 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHL 698
>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA.
This family consists exclusively of archaeal RadA
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239), and archaeal RadB
(TIGR02237). This protein is involved in DNA repair and
recombination. The member from Pyrococcus horikoshii
contains an intein.
Length = 310
Score = 33.6 bits (77), Expect = 0.15
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 557 LDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKI 603
L+++ G+GP L ++ + T + I+ +SP+ L+ I GIS+ A KI
Sbjct: 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKI 48
>gnl|CDD|177561 PHA03232, PHA03232, DNA packaging protein UL32; Provisional.
Length = 586
Score = 32.7 bits (75), Expect = 0.26
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 16/60 (26%)
Query: 94 FPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFR 153
F ++ I DKH + R +T+ G+ F T+ +QR FFL C FR
Sbjct: 144 FEFVYIMDKH-----FLRRHGATLVGA-FARRVL------TLVDIQRHFFLHGC----FR 187
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 32.5 bits (74), Expect = 0.31
Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 560 INGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYN 605
I +G +R R L + F TV I+RSSPE + I G S +A I N
Sbjct: 617 IPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVN 663
>gnl|CDD|179814 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 31.4 bits (72), Expect = 0.73
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 557 LDEINGIGP-LRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKI 603
L+++ G+GP ++L + TV+ I+ +SP+ L+ GI + A KI
Sbjct: 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKI 55
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 689
Score = 30.9 bits (70), Expect = 1.1
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 556 PLDE------INGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607
PL + I +GP R L + FGT + I + E L +++ + +A +I F
Sbjct: 523 PLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFF 580
>gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 30.8 bits (70), Expect = 1.2
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 50 HMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPY 96
+ I+F T EAL+L+ RLK +F + L ++++ +
Sbjct: 305 EAFKEAKAIKFNSFITNEEALILQ-----RLKKKFGLKLINEEALKF 346
>gnl|CDD|130293 TIGR01226, phe_am_lyase, phenylalanine ammonia-lyase. Members of
this family are found, so far, in plants and fungi. From
phenylalanine, this enzyme yields cinnaminic acid, a
precursor of many important plant compounds. This
protein shows extensive homology to histidine
ammonia-lyase, the first enzyme of a histidine
degradation pathway.
Length = 680
Score = 29.8 bits (67), Expect = 2.3
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 15/80 (18%)
Query: 393 CSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCA-MMRMVLERRFSQLIKNEENLN- 450
SA+ C V+ G+ F + K HP Q + A +M +L+ S K+ E
Sbjct: 261 LSAMFCEVMNGKPEFTDHLTHKLKHHP----GQIEAAAIMEHILDG--SSYAKHAEKEVE 314
Query: 451 ----FHPKKQEYSF---PSW 463
PK+ Y+ P W
Sbjct: 315 MDPLQKPKQDRYALRTSPQW 334
>gnl|CDD|129193 TIGR00084, ruvA, Holliday junction DNA helicase, RuvA subunit.
RuvA specifically binds Holliday junctions as a sandwich
of two tetramers and maintains the configuration of the
junction. It forms a complex with two hexameric rings of
RuvB, the subunit that contains helicase activity. The
complex drives ATP-dependent branch migration of the
Holliday junction recombination intermediate. The
endonuclease RuvC resolves junctions.
Length = 191
Score = 29.6 bits (67), Expect = 2.5
Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 8/99 (8%)
Query: 510 FFVKKGEALVLNMRDPILYFIQRL-RDEAHR-FAITTHRKRRKKAAYSPLDEINGIGPLR 567
V A LN+ F + R++A F T ++ + L ++NG+GP
Sbjct: 28 LQVPMTCAYELNLEQKAQVFTHLVVREDAELLFGFNT---LEERELFKELIKVNGVGPKL 84
Query: 568 KRLLLQSFGT---VKMISRSSPETLASIEGISKKIACKI 603
+L + V I + L I G+ KK A ++
Sbjct: 85 ALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERL 123
>gnl|CDD|177425 PHA02598, denA, endonuclease II; Provisional.
Length = 138
Score = 29.3 bits (66), Expect = 2.8
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 18 IAGRVLYVGKAYNLQKRIKSYMHSNN 43
+ ++Y+GK NL+KRI Y +S N
Sbjct: 41 VDDELVYIGKTKNLRKRIDYYRNSKN 66
>gnl|CDD|184207 PRK13648, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 269
Score = 29.3 bits (66), Expect = 3.2
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 464 PDVVILDGGKGQLSAAQ-----GVLKKLNVENRITIISI 497
P V+ILD L +++K+ E+ ITIISI
Sbjct: 161 PSVIILDEATSMLDPDARQNLLDLVRKVKSEHNITIISI 199
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed.
Length = 224
Score = 28.9 bits (66), Expect = 3.7
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 569 RLLLQSFGTVKMISRSSPETLASIEGISKKIACKI 603
R LLQ FG+++ + +S E L SI+GI A ++
Sbjct: 48 RELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQL 82
>gnl|CDD|162370 TIGR01453, grpIintron_endo, group I intron endonuclease. This
model represents one subfamily of endonucleases
containing the endo/excinuclease amino terminal domain,
Pfam:PF01541 at its amino end. A distinct subfamily
includes excinuclease abc subunit c (uvrC). Members of
pfam01541 are often termed GIY-YIG endonucleases after
conserved motifs near the amino end. This subfamily in
this model is found in open reading frames of group I
introns in both phage and mitochondria. The closely
related endonucleases of phage T4: segA, segB, segC,
segD and segE, score below the trusted cutoff for the
family.
Length = 214
Score = 28.9 bits (65), Expect = 4.0
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 15/89 (16%)
Query: 11 GVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQ-------INNIRFTV- 62
G+Y++ + +YVG + NL+KR+K ++ + + Q +N F +
Sbjct: 3 GIYKITNNINGKIYVGSSVNLEKRLKEHL---KLLKKGNRIKLQKALNKYGWSNFSFEIL 59
Query: 63 --TCTEVEALLLEANMIKRLKPRF--NIL 87
C + + + E IK L P NIL
Sbjct: 60 EYYCNKDDLIERETYYIKLLNPDAGYNIL 88
>gnl|CDD|151089 pfam10544, T5orf172, T5orf172 domain. This domain was identified
by Iyer and colleagues.
Length = 79
Score = 28.4 bits (64), Expect = 5.7
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 18 IAGRVLY-VGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANM 76
A + LY +G NL++R+K + + +I ++N ++E LL
Sbjct: 1 SANKDLYKIGYTTNLERRLKELNTGSPFPDELVAVIELVDN------ARKLERLLHRELK 54
Query: 77 IKRLKPR 83
KR P
Sbjct: 55 DKRGNPH 61
>gnl|CDD|184454 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 28.2 bits (64), Expect = 6.1
Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 10/52 (19%)
Query: 512 VKKGEALVLNMRDPI-LYFIQRL--------RDEAHRFAITTHRKRRKKAAY 554
VK VLN DP+ +R D + I HR + +A Y
Sbjct: 601 VKPDGYAVLNADDPMVAAMAERCKGKVIFFSMDPDNP-VIAEHRAQGGRAVY 651
>gnl|CDD|180795 PRK07021, fliL, flagellar basal body-associated protein FliL;
Reviewed.
Length = 162
Score = 28.3 bits (64), Expect = 6.3
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 24/63 (38%)
Query: 532 RLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLAS 591
RL DEA R + + L E+ R RLLL ++SR LA+
Sbjct: 88 RLPDEATRERLKDY-----------LPEV------RSRLLL-------LLSRKHAAELAT 123
Query: 592 IEG 594
EG
Sbjct: 124 EEG 126
>gnl|CDD|184079 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 28.2 bits (64), Expect = 6.6
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 571 LLQSFGTVKMISRSSPETLASIEGISKKIACKI 603
L++ FG+++ + +S E L +EGI + A I
Sbjct: 303 LVEHFGSLQGLLAASIEDLDEVEGIGEVRARAI 335
>gnl|CDD|180031 PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional.
Length = 554
Score = 27.8 bits (63), Expect = 8.2
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 520 LNMRDPILYFIQRLRDEAHR 539
+NMRDP+LY I HR
Sbjct: 186 INMRDPVLYRI--RHAHHHR 203
>gnl|CDD|128751 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 27.9 bits (63), Expect = 8.7
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 560 INGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606
+ GIG LL+ FG+++ I L +++ + KK+ K+ H
Sbjct: 191 VPGIGEKTAAKLLKEFGSLENI-------LENLDKLKKKLREKLLAH 230
>gnl|CDD|184762 PRK14606, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 188
Score = 27.7 bits (61), Expect = 9.2
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 548 RRKKAAYSPLDEINGIGPLRKRLLLQSFGT---VKMISRSSPETLASIEGISKKIACKI 603
RKK + L +++ +GP ++ + V MI+ E L+ + GISKK A +I
Sbjct: 66 ERKKELFLSLTKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERI 124
>gnl|CDD|149835 pfam08897, DUF1841, Domain of unknown function (DUF1841). This
family of proteins are functionally uncharacterized.
Length = 137
Score = 27.6 bits (62), Expect = 9.5
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 534 RDEAHRFAITTHRKRRKKAAYSPLDEI 560
RD+ RF RK + +PL+ I
Sbjct: 3 RDQVRRFFCDAWRKYQAGEPLTPLETI 29
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.322 0.135 0.399
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 9,803,007
Number of extensions: 629258
Number of successful extensions: 1327
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1243
Number of HSP's successfully gapped: 53
Length of query: 616
Length of database: 5,994,473
Length adjustment: 99
Effective length of query: 517
Effective length of database: 3,855,281
Effective search space: 1993180277
Effective search space used: 1993180277
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 (21.9 bits)
S2: 60 (26.9 bits)