RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA
[Candidatus Liberibacter asiaticus str. psy62]
(731 letters)
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 762 bits (1971), Expect = 0.0
Identities = 289/712 (40%), Positives = 434/712 (60%), Gaps = 56/712 (7%)
Query: 15 EQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGP 74
E+A+K + L +E+++H YY P I D+EYD L R A+ P+L P+ P
Sbjct: 3 EEAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELIT---PDSP 59
Query: 75 LNKIGGEMNLSLF-KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133
++GG L F KV H +P LSL+ ++ E+LR F R+ + D + + E K
Sbjct: 60 TQRVGGAP-LDGFEKVRHLVPMLSLDNAFSEEELRAFDKRVRKRL---PDPPLTYLCELK 115
Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYI 193
IDG +++ YE G V AA RGDG +GED++A +R I +IP L N PE +EVRGEV++
Sbjct: 116 IDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHGNEPERLEVRGEVFM 175
Query: 194 SKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT--RYLNFFVHGLGKTSEIF- 250
K DF ALN+E G KP+ANPRNAA+G LR+L+P IT R L+FF +G+G+
Sbjct: 176 PKADFEALNEERREEGEKPFANPRNAAAGSLRQLDPK-ITAKRPLSFFAYGVGEVEGGEL 234
Query: 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFS 310
Q E L+ ++ GFPVN + + ++++Y E++ R LPYDIDG+V KVD+ +
Sbjct: 235 PDSQSEALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLA 294
Query: 311 LQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITN 370
LQ++LG A++PRW I++KF ++A+T+LLDI++Q+GRTG +TPVARLEPV + G ++
Sbjct: 295 LQEELGFTAKAPRWAIAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSR 354
Query: 371 ATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSF 430
ATLHN D I+ DIR+GD V+V+RAG+VIP+VV +++ +R D +
Sbjct: 355 ATLHNADEIERK-----------DIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVM 403
Query: 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQ 490
P+ CP+C S +VR G+ A RCT GL+C AQ ERL HFVSR+A +I+GLG++
Sbjct: 404 PTHCPVCGSELVR----VEGE--AVLRCTNGLSCPAQLKERLIHFVSRNAMDIDGLGEKI 457
Query: 491 LDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISL 550
++ F+ I PAD+F L + + + GFG+ S NL D+I K + SL
Sbjct: 458 IEQLFEKGL----IHDPADLFKL------TAEDLLGLEGFGEKSAQNLLDAIEKSKETSL 507
Query: 551 ERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQ 610
RF+++LGIRHVG + A++LA+++ S + L V VG+++AQ
Sbjct: 508 ARFLYALGIRHVGEKAAKALARHFGSLEALRA----------ASEEELAAVEGVGEVVAQ 557
Query: 611 AIVEFYQNPRNICAVEALLKEVSPSIGRH--EKNVSSEIENKKLVFTGTLQKIQRHKAQE 668
+IVEF+ N ++ LL G + K ++ K +V TGTL+++ R +A+E
Sbjct: 558 SIVEFFAVEENRELIDELL-----EAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKE 612
Query: 669 YVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQ 720
+ LGA VS +S+KTD+++ G+ GSKL KAQ+LG+++++EE+FL LL +
Sbjct: 613 KLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664
>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 = 646 bits (1668), Expect = 0.0
Identities = 279/699 (39%), Positives = 424/699 (60%), Gaps = 55/699 (7%)
Query: 24 LEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMN 83
L + I +HD YY +P I D+EYD L R + P+L P+ P ++G
Sbjct: 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELIT---PDSPTQRVGAAPL 57
Query: 84 LSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY 143
KV HS P LSL+ ++ ++L FI RI R K + + +EPKIDG +++ Y
Sbjct: 58 SRFPKVRHSTPMLSLDNAFDEDELAAFIKRIRRQLGLK----VEYVVEPKIDGLSVSLTY 113
Query: 144 EKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSL-NIPEIIEVRGEVYISKNDFLALN 202
E G V A RGDG GEDV+A +R I +IP L+ N PE +EVRGEV++ K DF ALN
Sbjct: 114 ENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEVRGEVFMPKEDFEALN 173
Query: 203 DEMIAVGRKPYANPRNAASGILRRLNPTDIT--RYLNFFVHGLGKTSEIFAKGQYEMLQK 260
+E G KP+ANPRNAA+G LR+L+P IT R L FF +GLG+ E+ QYE L
Sbjct: 174 EERREQGEKPFANPRNAAAGSLRQLDP-RITAKRKLRFFAYGLGEGLELPDATQYEALAW 232
Query: 261 MRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR 320
++ GFPV+ +R ++ ++ YY E++ R +LPY+IDG+V KVD+ +LQ +LG ++
Sbjct: 233 LKKWGFPVSPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSK 292
Query: 321 SPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIK 380
+PRW I++KF ++A T+LLD+ +Q+GRTG +TPVA+LEPV + G ++ ATLHNED I+
Sbjct: 293 APRWAIAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIE 352
Query: 381 GLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSR 440
L DIR+GD V+V++AG+VIPKVV +++ +R +P FP+ CP C S
Sbjct: 353 EL-----------DIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPSCGSP 401
Query: 441 VVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDP 500
+V+ A RC L C AQ++ER+KHF SR+A +IEGLG + ++ F+ +
Sbjct: 402 LVKIEEE------AVIRCP-NLNCPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKK-- 452
Query: 501 AFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIR 560
+R AD++ L++ ++E GFG+ S NL ++I K + L R +F+LGIR
Sbjct: 453 --LVRSVADLYALKKED---LLELE---GFGEKSAQNLLNAIEKSKEKPLARLLFALGIR 504
Query: 561 HVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPR 620
HVG A++LAK++ + ++ + A + ++ L+ V VG +A++IV F+ +P
Sbjct: 505 HVGEVTAKNLAKHFGT-------LDKLKAASLEE---LLSVEGVGPKVAESIVNFFHDPN 554
Query: 621 NICAVEALLKEVSPSIGRHEKNVSSEIEN-----KKLVFTGTLQKIQRHKAQEYVTQLGA 675
N ++ L+E+ + + V++E+ K V TGTL ++ R +A+E + LG
Sbjct: 555 NRQLIKK-LEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGG 613
Query: 676 VVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQF 714
V++ +S+KTD +I G+ GSKL KAQ+LG+ I+NEE+
Sbjct: 614 KVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINEEEL 652
>gnl|CDD|128805 smart00532, LIGANc, Ligase N family.
Length = 441
Score = 490 bits (1265), Expect = e-139
Identities = 201/466 (43%), Positives = 288/466 (61%), Gaps = 27/466 (5%)
Query: 17 ARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLN 76
A+KE+S L + ++ HD YY PII D+EYD L R + P+L P+ P
Sbjct: 1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELK---TPDSPTQ 57
Query: 77 KIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDG 136
++GG+ KV H +P LSL+ ++ ++LR F RI +K + + +EPKIDG
Sbjct: 58 RVGGKPLEGFNKVRHPVPMLSLDNAFDEDELRAFDERI----EKALGSPFAYVVEPKIDG 113
Query: 137 TMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN 196
+++ YE GK V AA RGDG GEDV+ ++ I +IP LS ++PE +EVRGEV++ K
Sbjct: 114 LSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVPERLEVRGEVFMPKE 173
Query: 197 DFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKTSEIF-AKGQ 254
DFLALN+E+ G KP+ANPRNAA+G LR+L+P R L F +GLG E+F K Q
Sbjct: 174 DFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQ 233
Query: 255 YEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQ 314
E L+ ++ LGFPV+ R ++ YY E + R+ LPY+IDG+V KVD+ +LQ++
Sbjct: 234 SEALKWLKELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRE 293
Query: 315 LGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLH 374
LG +++PRW I++KF ++A T+LLDI +Q+GRTG +TPVA LEPV + G+ ++ ATLH
Sbjct: 294 LGFTSKAPRWAIAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLH 353
Query: 375 NEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFC 434
NED I+ DIR+GD V+V++AG+VIPKVV ++ +R D + P+ C
Sbjct: 354 NEDEIEEK-----------DIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEMPTHC 402
Query: 435 PICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDA 480
P C S +VR+ + RC L C AQ +ER+ HF SR A
Sbjct: 403 PSCGSELVRE------EGEVDIRCPNPL-CPAQLIERIIHFASRKA 441
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 689
Score = 470 bits (1211), Expect = e-133
Identities = 256/721 (35%), Positives = 388/721 (53%), Gaps = 57/721 (7%)
Query: 8 PIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLAR 67
P+E LS ++A ++ L + I HD YY + P+I D YDAL R A+ AF DL
Sbjct: 23 PVEELSEDEAEEQAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDT 81
Query: 68 SEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIF 127
N P ++GGE L V H P LS+++ +D+R+F R+ +++ ++
Sbjct: 82 ---ENSPTRRVGGEPLDELETVEHVAPMLSIDQSGEADDVREFDERV-----RREVGAVE 133
Query: 128 FTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEV 187
+ EPK DG + + YE G++ AA RGDG G+DV+A +R I ++P+ L + P+ + V
Sbjct: 134 YVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVPQKLRGDYPDFLAV 193
Query: 188 RGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKT 246
RGEVY+ K+ F A N E I G +P+ANPRNAA+G LR+L+P+ + R L+ F +
Sbjct: 194 RGEVYMPKDAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDA 253
Query: 247 SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV 306
SE+F +E L++ G V + + + ++Y + + + R L Y+IDG+V KV
Sbjct: 254 SELFDS-HWEELERFPEWGLRVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKV 312
Query: 307 DEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGA 366
D+ +++LG AR+PRW ++KF + T + DI +Q+GRTG LTPVA L+PV++GG
Sbjct: 313 DDRDAREELGATARAPRWAFAYKFPARAEETTIRDIVVQVGRTGRLTPVALLDPVDVGGV 372
Query: 367 LITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQ 426
++ A+LHN I+ L + VGDRV VKRAG+VIP V +++ E+ +
Sbjct: 373 TVSRASLHNPAEIEEL-----------GVNVGDRVRVKRAGDVIPYVEEVV--EKDSEGT 419
Query: 427 PFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL 486
F FP CP+C S V RD G L CTGGLAC AQ ++H+ SRDA +IEGL
Sbjct: 420 -FEFPDTCPVCDSAVERD-----GPLAF---CTGGLACPAQLERSIEHYASRDALDIEGL 470
Query: 487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR 546
G++++ + + AD++ L ++E G+G+ S NL + R
Sbjct: 471 GEERVQQLVDAG----LVESLADLYDLTV---ADLAELE---GWGETSAENLLAELEASR 520
Query: 547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGD 606
L F+ +LGI VG AR+L A+E A + D +L V VG
Sbjct: 521 EPPLADFLVALGIPEVGPTTARNL----------AREFGTFEAIMDADEEALRAVDDVGP 570
Query: 607 IIAQAIVEFYQNPRNICAVEALLKE-VSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHK 665
+A+ I EF+ + RN ++ LL V P E ++ VFTG+L R +
Sbjct: 571 TVAEEIREFFDSERNRAVIDDLLDHGVDPQ--PAESEGGDALDGLTFVFTGSLSGYTRSE 628
Query: 666 AQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLGVKIMNEEQFLFLLQQYNTT 724
AQE V G + +S TD ++VG+NPG SK + A+ V ++EE+F LL +
Sbjct: 629 AQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAERGVA 688
Query: 725 L 725
L
Sbjct: 689 L 689
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 669
Score = 327 bits (840), Expect = 6e-90
Identities = 206/710 (29%), Positives = 358/710 (50%), Gaps = 63/710 (8%)
Query: 14 IEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNG 73
+ + E+ L++ I D YY S P + D YD R + +P+ + P
Sbjct: 2 SKDIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPT- 60
Query: 74 PLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133
K G ++ +V HS P LSL+K+++++ L+ +I ++ ++EPK
Sbjct: 61 --LKFGSDLLNDFKEVEHSFPILSLDKVYDLKLLKLWIEKM-DLENSNLGFDFGISVEPK 117
Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEV--RGEV 191
IDG I + Y+ G A RGDG G DV+ +R I +P L I E +E+ RGE+
Sbjct: 118 IDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVP----LFIDEKVELVLRGEI 173
Query: 192 YISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRY-LNFFVHGLGKTSEIF 250
YI+K +FL +N + KPY N RN ASGILRR++ ++ + L+ FV+ + S +
Sbjct: 174 YITKENFLKINKTL----EKPYTNARNLASGILRRIDSREVANFPLDIFVYDI-LYSSLE 228
Query: 251 AKGQYEMLQKMRCLGFPVNNGVR---QANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVD 307
K ++ K++ GF VN R N+ I++Y +++ R++ Y+IDG+V KV
Sbjct: 229 LKTNHDAFDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVS 288
Query: 308 EFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGAL 367
+F+L++ LG + P+W +++KF +++ DI +Q+GR+G +TPVA +E V + GA
Sbjct: 289 DFALREILGYTSHHPKWSMAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAF 348
Query: 368 ITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQP 427
ITNA+LHN+DYI + + VGD V + R G+VIP V++++ +
Sbjct: 349 ITNASLHNQDYIDSI-----------GLNVGDVVKISRRGDVIP-AVELVIEKLSVGF-- 394
Query: 428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLG 487
F P CP C++ ++++ AH C + +ER+K+F S+ NI GL
Sbjct: 395 FKIPDNCPSCKTALIKE---------GAHLFCVNNHCPSVIVERIKYFCSKKCMNIVGLS 445
Query: 488 KQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRN 547
+ ++F F+ + I D++T + ++ N+ GF D + NL SI +
Sbjct: 446 DKTIEFLFEKK----FISSEIDLYTF------NFDRLINLKGFKDKRINNLKRSIEASKK 495
Query: 548 ISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDI 607
+ + S+GI+ +G L + N +I+ + L+++ +G+
Sbjct: 496 RPFSKLLLSMGIKDLGENTILLL---INNNLNSFDKISTLCQDREFALSKLLKIKGIGEK 552
Query: 608 IAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIEN-----KKLVFTGTLQKIQ 662
IA I+E + N + I K + + E +++ ++EN KK TG+
Sbjct: 553 IALNIIEAF-NDKIILDKFNFFKNLGFKM--EEDSINIDVENSFLFGKKFCITGSFNGYS 609
Query: 663 RHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEE 712
R + +T+ GA+ + +++ D ++VG+ G KL+KA LG+KIM+
Sbjct: 610 RSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKLKKANNLGIKIMSLF 659
>gnl|CDD|181228 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed.
Length = 562
Score = 148 bits (377), Expect = 4e-36
Identities = 144/642 (22%), Positives = 245/642 (38%), Gaps = 157/642 (24%)
Query: 13 SIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPN 72
S +A++E+++L+Q+++ DD Y++ K + D YD L+ R F +
Sbjct: 26 SPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPE---PRD 82
Query: 73 GPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEP 132
PL + G KV H + ++K+ + + L +++ W ++P
Sbjct: 83 VPLPPLNG-------KVLHPVAHTGVKKLADKQALARWMAGRSDLW-----------VQP 124
Query: 133 KIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVY 192
K+DG +T+ Y GK V A RG+G GED +A R IP IP+ L + ++ ++GE++
Sbjct: 125 KVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLPGALANLV-LQGELF 183
Query: 193 ISKNDFLALNDEMIAV--GRKPYANPRNAASGILRRLNPTDITRYLNFFV----HGLGKT 246
L + G N R +G++ R +P+ + FV G
Sbjct: 184 ------LRREGHIQQQMGG----INARAKVAGLMMRKDPSPTLNQIGVFVWAWPDG---- 229
Query: 247 SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVS----------YYNEMKSIRSTLP 296
E L ++ GFP+ Q T H + + +Y R+ LP
Sbjct: 230 ----PASMPERLAQLATAGFPLT----QRYT-HPVKNAEEVARWRERWY------RAPLP 274
Query: 297 YDIDGLVYKVDEFSLQKQLGE--RARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTP 354
+ DG+V + ++ G + W ++ K+ Q + + +GRTG +T
Sbjct: 275 FVTDGVVVR----QAKEPPGRYWQPGQGEWAVAWKYPPVQQVAEVRAVQFAVGRTGKITV 330
Query: 355 VARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGR-DIRVGDRVLVKRAGEVIPKV 413
V LEPV + ++ + G V R + DI GD+VLV AG+ IP++
Sbjct: 331 VLELEPVMLDDKRVSRVNI------------GSVRRWQQWDIAPGDQVLVSLAGQGIPRL 378
Query: 414 VDII--VNERH----PDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ 467
++ ER PDA F S C A+ C Q
Sbjct: 379 DKVVWRGAERTKPTPPDADRFHSLS-C-----------------FRASP------GCQEQ 414
Query: 468 QLERLKHFVSRDAFNIEGLGK---QQL---DFFFKSEDPAFSIRIPADIF---TLQRRQQ 518
L RL + ++G+G+ + L F +F L Q
Sbjct: 415 FLARLVWLSGKQGLGLDGIGEGTWRALHQTGLF-------------EHLFSWLALTPEQ- 460
Query: 519 TSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQ 578
+ N G G L+ N R R++ +LGI A + + S+Q
Sbjct: 461 -----LANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDR---SWQ 512
Query: 579 NFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPR 620
+ W L P +G+ A+ ++ F Q+P
Sbjct: 513 QLLS-------RSEQQWQQL---PGIGEGRARQLIAFLQHPE 544
>gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 61.0 bits (148), Expect = 1e-09
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 14/86 (16%)
Query: 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--------- 694
+ + + +VFTG L + R +A V +LG V + +++KT ++
Sbjct: 218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEM 277
Query: 695 GSKLEKAQQL-----GVKIMNEEQFL 715
+KL+KA L +K +NEE+FL
Sbjct: 278 SNKLKKAIDLKKKGQNIKFLNEEEFL 303
>gnl|CDD|128588 smart00292, BRCT, breast cancer carboxy-terminal domain.
Length = 80
Score = 55.1 bits (133), Expect = 7e-08
Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKT-DIIIVGDNPGSKLE--KAQQL 704
+ K V TG K +R + +E + LG V++ LS KT +IVG G KLE A L
Sbjct: 4 KGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIAL 63
Query: 705 GVKIMNEEQFLFLLQ 719
G+ I+ E+ L L+
Sbjct: 64 GIPIVTEDWLLDCLK 78
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon;
Provisional.
Length = 313
Score = 35.4 bits (82), Expect = 0.051
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 668 EYVTQLGAVVSAILSRKTDIIIVGD-NPG-SKLEKAQQLGVKIMNEEQFLFLLQ 719
E + G S + R T +++ D P K A+QLGV +++E FL LL+
Sbjct: 253 ERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELLR 306
>gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases.
Length = 654
Score = 30.8 bits (70), Expect = 1.3
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 357 RLEPVNIGGALITNATLHNEDYIKGLDASGKVMRG---GRDIRVGDRVLVK 404
RL+ I G LI +TLHN+ Y+ D + G G+ R+GDRV VK
Sbjct: 591 RLDDNGIDG-LIHISTLHNDYYV--FDQEKMALIGKGTGKVYRIGDRVTVK 638
>gnl|CDD|179229 PRK01122, PRK01122, potassium-transporting ATPase subunit B;
Provisional.
Length = 679
Score = 30.5 bits (70), Expect = 1.8
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 6/32 (18%)
Query: 394 DIRVGDRVLVKRAGEVIPKVVDII-----VNE 420
++R GD VLV+ AGE+IP ++I V+E
Sbjct: 122 ELRKGDIVLVE-AGEIIPADGEVIEGVASVDE 152
>gnl|CDD|162397 TIGR01512, ATPase-IB2_Cd, heavy
metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase. .
Length = 536
Score = 30.0 bits (68), Expect = 2.1
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 393 RDIRVGDRVLVKRAGEVIP---KVVD--IIVNERH 422
+++VGD V+V + GE +P V+ V+E
Sbjct: 71 EELKVGDVVVV-KPGERVPVDGVVLSGTSTVDESA 104
>gnl|CDD|162399 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase.
This alignment encompasses two equivalog models for the
copper and cadmium-type heavy metal transporting P-type
ATPases (TIGR01511 and TIGR01512) as well as those
species which score ambiguously between both models. For
more comments and references, see the files on TIGR01511
and 01512.
Length = 556
Score = 29.5 bits (67), Expect = 2.9
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 3/26 (11%)
Query: 393 RDIRVGDRVLVKRAGEVIPKVVDIIV 418
+++VGD V+V R GE IP VD +V
Sbjct: 72 EELQVGDIVIV-RPGERIP--VDGVV 94
>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.1 bits (66), Expect = 4.0
Identities = 13/64 (20%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 552 RFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQA 611
+I + VG +AR+L +++ S + ++ + ++ L+ V +G+ A+
Sbjct: 714 EYIVE-SLPDVGPVLARNLLEHFGS-------VEAVMTASEEE---LMEVEGIGEKTAKR 762
Query: 612 IVEF 615
I E
Sbjct: 763 IREV 766
>gnl|CDD|162681 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions.
Length = 864
Score = 29.0 bits (65), Expect = 4.9
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 15/93 (16%)
Query: 340 LDIDIQIGRTGILTPVA-------RLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGG 392
L + I++ R GI T A R N+GGA + HN I+ + A+ +
Sbjct: 698 LGVPIELIRAGIRTFDADAAQAPGRFNLFNLGGAHVLVDYGHNPAAIEAVGAAIRNWPAR 757
Query: 393 RDIRV----GDRV---LVKRAGEVIPKVVDIIV 418
R I V GDR LV++ GE++ D I+
Sbjct: 758 RRIGVIGGPGDRRDEDLVEQ-GELLGGAFDQII 789
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc.
Length = 708
Score = 28.9 bits (65), Expect = 5.2
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 570 LAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQN 618
YYL + I+ I H L +I + L+ I Q I+ + Q
Sbjct: 174 AGSYYLQ-----KIIDTYIPHKMMGTLGIISIGLIIAYIIQQILSYIQI 217
>gnl|CDD|184554 PRK14179, PRK14179, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 28.6 bits (64), Expect = 7.0
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 14/56 (25%)
Query: 687 IIIVGDNPGS------KLEKAQQLGVK--------IMNEEQFLFLLQQYNTTLRIH 728
+I+VGDNP S K A G K +++E+ L L+++YN H
Sbjct: 37 VILVGDNPASQVYVRNKERSALAAGFKSEVVRLPETISQEELLDLIERYNQDPTWH 92
>gnl|CDD|162406 TIGR01536, asn_synth_AEB, asparagine synthase
(glutamine-hydrolyzing). This model describes the
glutamine-hydrolysing asparagine synthase. A poorly
conserved C-terminal extension was removed from the
model. Bacterial members of the family tend to have a
long, poorly conserved insert lacking from archaeal and
eukaryotic sequences. Multiple isozymes have been
demonstrated, such as in Bacillus subtilis. Long-branch
members of the phylogenetic tree (which typically were
also second or third candidate members from their
genomes) were removed from the seed alignment and score
below trusted cutoff.
Length = 467
Score = 28.1 bits (63), Expect = 7.6
Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 13/99 (13%)
Query: 44 LDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEK--- 100
E +A+ R D IAH PD + E +G N I G L++ ++ +S E
Sbjct: 11 AVEEDEAILRMSDTIAHRGPDASGIEYKDG--NAILGHRRLAIIDLSGGAQPMSNEGKTY 68
Query: 101 -------IWNIEDLRK-FITRIYRFWQKKDDNSIFFTLE 131
I+N E+LR+ + Y F D I E
Sbjct: 69 VIVFNGEIYNHEELREELEAKGYTFQTDSDTEVILHLYE 107
>gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 28.3 bits (64), Expect = 7.9
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 96 LSLEKIWNIEDLRKFITRIYRFWQKKDD 123
+++E+ W+IE+ + R Y + D+
Sbjct: 436 MAIERPWDIEEAYNIVRRAYPYRDLSDE 463
>gnl|CDD|148092 pfam06277, EutA, Ethanolamine utilisation protein EutA. This
family consists of several bacterial EutA ethanolamine
utilisation proteins. The EutA protein is thought to
protect the lyase (EutBC) from inhibition by CNB12.
Length = 473
Score = 28.0 bits (63), Expect = 9.8
Identities = 30/121 (24%), Positives = 46/121 (38%), Gaps = 22/121 (18%)
Query: 333 KQASTRLLDIDIQIGRTGI-LTPVARLEP---VNIGGALITNATLHNEDYIKGLDASGKV 388
K+ T +L+IDI G T + L + ++IGG LI YI S K
Sbjct: 139 KEHHTTVLNIDIGGGTTNLALFENGEVIDTACLDIGGRLIKIDPTGRITYI-----SPKG 193
Query: 389 MR----GGRDIRVGDRVLVKRAGEVIPKVVDIIVN-----ERHPDAQPF----SFPSFCP 435
R G ++ VGDR ++ +V ++ ++ P AQ P
Sbjct: 194 RRLIAELGLELEVGDRATPEQLDQVCREMAQLLEEVLGGQPESPLAQLLMTTKPLPGLDR 253
Query: 436 I 436
I
Sbjct: 254 I 254
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
0.321 0.138 0.400
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 12,288,064
Number of extensions: 835934
Number of successful extensions: 1833
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1780
Number of HSP's successfully gapped: 38
Length of query: 731
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 631
Effective length of database: 3,833,673
Effective search space: 2419047663
Effective search space used: 2419047663
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: 61 (27.1 bits)