RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781225|ref|YP_003065638.1| P4 family phage/plasmid
primase [Candidatus Liberibacter asiaticus str. psy62]
(789 letters)
>gnl|CDD|130674 TIGR01613, primase_Cterm, phage/plasmid primase, P4 family,
C-terminal domain. This model represents a clade within
a larger family of proteins from viruses of bacteria and
animals. Members of this family are found in phage and
plasmids of bacteria and archaea only. The model
describes a domain of about 300 residues, found
generally toward the protein C-terminus.
Length = 304
Score = 146 bits (371), Expect = 2e-35
Identities = 82/303 (27%), Positives = 130/303 (42%), Gaps = 13/303 (4%)
Query: 427 RFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESE-EVMDY 485
L +G+ DL TGQ + T+ T + + + F + E+++Y
Sbjct: 1 YKLNVANGVYDLRTGQLEPHDPDEIHTRKITTEYDPKADCPTWNGFLLETFGGDNELIEY 60
Query: 486 FTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPE 545
R +G +L G Q+ + G GG+GKST NL+ G+ Y A AS M E
Sbjct: 61 LQRVIGYSLTGNYTEQKLFFLYGNGGNGKSTFQNLLSNLLGD-YATTAVASLKMN----E 115
Query: 546 AGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFT 605
+ L RL G R VI E + + + K +TGGD +TAR + + +P FT
Sbjct: 116 FQEHRFGLARLEGKRAVIGDEVQKGYRDDESTFKSLTGGDTITARFKNKDPFEFTP-KFT 174
Query: 606 PFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTLEAK---KWFLKG 662
N +R D RR +IPF K + L+ Y E W ++G
Sbjct: 175 LVQSTNHLPRIRGFDGGIKRRLRIIPFTKVFPGEKKNK--ALKEDYINEKDVILYWAVEG 232
Query: 663 VKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESHSLAKSYSEYR 722
++ G D IP+ L+A EE ++ D ++++CCD E + ++Y E+
Sbjct: 233 IRLDQRIG-DFSIPKAVLEATEEYKEENDVVARFLEECCDDSEGEKVPVRFVYEAYKEWC 291
Query: 723 EQE 725
E+
Sbjct: 292 EEG 294
>gnl|CDD|180825 PRK07078, PRK07078, hypothetical protein; Validated.
Length = 759
Score = 138 bits (349), Expect = 6e-33
Identities = 102/363 (28%), Positives = 157/363 (43%), Gaps = 25/363 (6%)
Query: 415 FSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELYITK-STGTPFVEGEPSQEFLDLV 473
+ TS+ D+ L G++DL TG+ +E +TK +T TP + + FL V
Sbjct: 406 HAATSEEWDADPWLLNTPGGVVDLRTGRLRPHRREDRMTKITTATPAGDCPTWRRFLAEV 465
Query: 474 SGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINA 533
+G E+ Y R G AL G + G G +GKS +N + G+ Y NA
Sbjct: 466 TG--GDAELQAYLQRMAGYALTGSTSEHALFFLYGTGANGKSVFVNTLATILGD-YAANA 522
Query: 534 EASDIMQNRPPEAGKANPS-LIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLN 592
M+ R G +P+ L L G+R V ET + +K+K +TGGD ++AR
Sbjct: 523 PMDTFMETR----GDRHPTDLAGLRGARFVSAIETEQGRRWAESKVKNLTGGDKISARFM 578
Query: 593 YGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPF--DKPIANRDASFAQKLETK 650
+ + P F I N +RN D+A RR +IPF P RD QKL +
Sbjct: 579 RQDFFEFFP-QFKLLIAGNHKPAIRNVDEAMKRRLHLIPFTVTVPPERRDKRLQQKLLAE 637
Query: 651 YTLEAKKWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEE 710
W ++G + GLD P+ ++A EE + D WI++ C+ G N E
Sbjct: 638 RD-GILAWAVEGCLDWQRNGLDP--PQSVVEATEEYFEAEDALGQWIEERCERGANAKEL 694
Query: 711 SHSLAKSYSEYREQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRIIKGLK 770
+ L + E+ E+ + S + + L +GF + R +G+
Sbjct: 695 TAELFNDWKEWAERAGEFVG---SQKRFSDLLATRGFEKW-------RLTGGLRGFRGIG 744
Query: 771 LKP 773
LKP
Sbjct: 745 LKP 747
>gnl|CDD|173172 PRK14709, PRK14709, hypothetical protein; Provisional.
Length = 469
Score = 132 bits (333), Expect = 4e-31
Identities = 99/366 (27%), Positives = 161/366 (43%), Gaps = 29/366 (7%)
Query: 415 FSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTG-TPFVEGEPSQ--EFLD 471
F++TS+ D+ LG G +DL TG+ E IT+ T P + + FLD
Sbjct: 118 FAVTSEDWDADPWLLGTPGGTVDLRTGKLRAADPEDMITRLTAVAPADTADCPRWLRFLD 177
Query: 472 LVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVI 531
+G +E++ + + G L G + + + G GG+GKS +N++ G+ Y
Sbjct: 178 EATG--GDDELIRFLQQWCGYCLTGDTREHALVFVFGGGGNGKSVFLNVLAGILGD-YAT 234
Query: 532 NAEASDIMQNRPPEAGKANPS-LIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTAR 590
A M +P+ L L G+R+V SET E A+IKQMTGGD +TAR
Sbjct: 235 TAA----MDTFTASKHDRHPTDLAMLRGARLVTASETEEGRAWAEARIKQMTGGDTITAR 290
Query: 591 LNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFAQKLETK 650
+ + P F IV N +RN D+A RR+ ++PF + A D KL +
Sbjct: 291 FMRQDFFEFVP-QFKLTIVGNHKPRLRNVDEAARRRFNIVPFTRKPARPDPDLEAKLRAE 349
Query: 651 YTLEAKKWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDI---GENL 707
+ +W + G + + GL P +A EE DT+ W+++ C +
Sbjct: 350 WP-AILRWMIDGCLDWQANGLVR--PAAVTEATEEYFAEQDTFGQWLEERCIVDPGNPVC 406
Query: 708 WEESHSLAKSYSEYREQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRIIK 767
W+ L S+ E+ E + + +++ GF +K K R +
Sbjct: 407 WDVLQDLYASWCEFARAEG---EPAGTAKEFGERMEKLGF------KKDRK--NRGRGFR 455
Query: 768 GLKLKP 773
G++L+P
Sbjct: 456 GIQLRP 461
>gnl|CDD|150055 pfam09250, Prim-Pol, Bifunctional DNA primase/polymerase,
N-terminal. Members of this family adopt a structure
consisting of a core of antiparallel beta sheets. They
are found in various bacterial hypothetical proteins,
and have been shown to harbour both primase and
polymerase activities.
Length = 161
Score = 61.3 bits (149), Expect = 9e-10
Identities = 39/167 (23%), Positives = 58/167 (34%), Gaps = 22/167 (13%)
Query: 10 AKQAIHNGFKLIPLRLGDKRPQRLGKWEEQLLSSEKIDKL----PACGFGFVCGVGEQPL 65
A + NG+ ++PL G K+P W++ +I + P G G L
Sbjct: 1 ALRYAANGWAVLPLDPGSKKPLDPKGWQDATTDPAEIRRWWARNPGANIGLPTGRSG--L 58
Query: 66 YAFDIDSKDEKTANTFKDTFEILHG----TPIVRIGQKPKILIPFRMNKEGIKKKKTT-- 119
D+D+K A E G T +VR + FR+ K+
Sbjct: 59 VVLDVDTKAGGDA---LAALERAGGPLPPTLVVRTP-SGGRHLYFRVPDGPELKRNLLFA 114
Query: 120 -ESTQGHLDILGCG-QYFVAY-NIHPKTKKEYTWTTPPHRFKVEDTP 163
+ G +DI G Y VA ++HP Y WT P
Sbjct: 115 KDGGGGGIDIRAGGGGYVVAPPSVHPGG--PYEWTGGTPL-PPAPAP 158
>gnl|CDD|149686 pfam08707, PriCT_2, Primase C terminal 2 (PriCT-2). This alpha
helical domain is found at the C terminal of primases.
Length = 74
Score = 50.4 bits (121), Expect = 2e-06
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 224 GSHDEWIPVVMAVHHETRGSSKGKEIARRWSKQGSTYDEENFNYKWDTFD 273
+D W+ V MA+ HE +G E+ WS + S YD KWD+F
Sbjct: 13 DDYDSWLRVGMALKHEF--GEEGLELWDEWSAKSSKYDPGECERKWDSFK 60
>gnl|CDD|149685 pfam08706, D5_N, D5 N terminal like. This domain is found in D5
proteins of DNA viruses and bacteriophage P4 DNA
primases phages.
Length = 145
Score = 39.0 bits (91), Expect = 0.005
Identities = 35/170 (20%), Positives = 56/170 (32%), Gaps = 30/170 (17%)
Query: 304 ASRFSDAYNKAMFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMNFLVSMK 363
A R +D Y K Y T WY D W K + + L+ +
Sbjct: 1 AKRLADRYGK---------DLRYVPGTGGWYVWDG---KRWEEDSKKAIRELADKLLRLI 48
Query: 364 EDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQNVEENSKAKSTAQSLEAGSIFSITSDLLD 423
+ + ++E K S+S N EA ++ +T D LD
Sbjct: 49 LEEAEAAKELRKFAKRSRSKSGVKNV------------------LREAKAMLDVTLDELD 90
Query: 424 SSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLV 473
+ L +G+LDL TG+ E +TK T + + +
Sbjct: 91 ADPYLLNFPNGVLDLRTGELRPHDPEDRLTKITPVDYDPDADCPLWKQFL 140
>gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 34.5 bits (80), Expect = 0.11
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 478 ESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMN-LIKYAFGNQYVI 531
E+ E+ K RF+ + G GSGKS L+ + YA +V+
Sbjct: 6 ETLELTKKLKE-----ADASKKVVRFV-LTGERGSGKSVLLAQAMAYALTQGWVV 54
>gnl|CDD|182511 PRK10517, PRK10517, magnesium-transporting ATPase MgtA;
Provisional.
Length = 902
Score = 33.5 bits (77), Expect = 0.20
Identities = 25/67 (37%), Positives = 32/67 (47%), Gaps = 18/67 (26%)
Query: 587 MTARLNYGNTYSESPAS-FTPFI--VPNKHLFVRNPDDAWWRRY----IVIPFDKPIANR 639
MTA N+GN +S AS F PF+ +P HL ++N Y + IPFD N
Sbjct: 705 MTASSNFGNVFSVLVASAFLPFLPMLP-LHLLIQN------LLYDVSQVAIPFD----NV 753
Query: 640 DASFAQK 646
D QK
Sbjct: 754 DDEQIQK 760
>gnl|CDD|178984 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 33.1 bits (77), Expect = 0.29
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 503 FIHIRGVGGSGKSTLMNLIKY 523
F + GV GSGKSTL+N Y
Sbjct: 637 FTCVTGVSGSGKSTLINETLY 657
>gnl|CDD|185336 PRK15439, PRK15439, autoinducer 2 ABC transporter ATP-binding
protein LsrA; Provisional.
Length = 510
Score = 31.6 bits (72), Expect = 0.82
Identities = 17/38 (44%), Positives = 19/38 (50%), Gaps = 14/38 (36%)
Query: 486 FTRCVGM--ALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
FT G ALLGGN G+GKSTLM +I
Sbjct: 32 FTLHAGEVHALLGGN------------GAGKSTLMKII 57
>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 529
Score = 31.6 bits (72), Expect = 0.92
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 461 VEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNL 520
G+P+ E DL GY S V+D V + L G + + I G GSGKSTL+ L
Sbjct: 329 GLGKPTLELRDLSFGYPGSPPVLD----GVSLDLPPGER----VAILGPSGSGKSTLLML 380
Query: 521 I 521
+
Sbjct: 381 L 381
>gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM bacteriocin system ABC
transporter, ATP-binding protein. Members of this
protein family are ABC transporter ATP-binding subunits,
part of a three-gene putative bacteriocin transport
operon. The other subunits include another ATP-binding
subunit (TIGR03796), which has an N-terminal propeptide
cleavage domain, and an HlyD homolog (TIGR03794). In a
number of genomes, a conserved propeptide sequence with
a classic Gly-Gly motif.
Length = 686
Score = 31.5 bits (72), Expect = 0.97
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNL 520
+ F+ I G GSGKSTL+ L
Sbjct: 477 EPGEFVAIVGPSGSGKSTLLRL 498
>gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein.
Length = 617
Score = 31.2 bits (71), Expect = 1.00
Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 21/76 (27%)
Query: 446 PTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIH 505
+ F P + L VSG + E++ A++G +
Sbjct: 17 DGSWKQLVSRLRGCFCRERPRKHLLKNVSGVAKPGELL---------AVMGSS------- 60
Query: 506 IRGVGGSGKSTLMNLI 521
G+GK+TLMN +
Sbjct: 61 -----GAGKTTLMNAL 71
>gnl|CDD|161968 TIGR00630, uvra, excinuclease ABC, A subunit. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 924
Score = 31.1 bits (71), Expect = 1.1
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 502 RFIHIRGVGGSGKSTLMNLIKYA 524
F I GV GSGKSTL+N Y
Sbjct: 634 LFTCITGVSGSGKSTLINDTLYP 656
>gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease
protein; Provisional.
Length = 648
Score = 31.2 bits (71), Expect = 1.1
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 500 AQRFIHIRGVGGSGKSTLMNLI 521
A + I G GSGKSTLMN++
Sbjct: 33 AGEMVAIVGASGSGKSTLMNIL 54
>gnl|CDD|130034 TIGR00960, 3a0501s02, Type II (General) Secretory Pathway (IISP)
Family protein.
Length = 216
Score = 30.5 bits (69), Expect = 1.5
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
+ + G G+GKST + LI
Sbjct: 31 MVFLVGHSGAGKSTFLKLI 49
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 29.7 bits (67), Expect = 2.7
Identities = 29/128 (22%), Positives = 52/128 (40%), Gaps = 32/128 (25%)
Query: 392 RRQNVEENSKAKSTAQSLEAGSIFSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELY 451
R + E S + +EAG + ++DL D S E+D ++ E+G+ + + L
Sbjct: 712 RAKKAGETSASNKN--DIEAGEVLG-STDLTDESDDVNDEKD--MEKESGEDIFHWRNL- 765
Query: 452 ITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGG 511
T ++ E L+ V G+ + + AL+G G
Sbjct: 766 ----TYEVKIKKEKRV-ILNNVDGWVKPGTLT---------ALMG------------ASG 799
Query: 512 SGKSTLMN 519
+GK+TL+N
Sbjct: 800 AGKTTLLN 807
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 29.9 bits (68), Expect = 2.9
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 504 IHIRGVGGSGKSTLMNLI 521
+ I G G+GKSTL+NLI
Sbjct: 28 VAILGPSGAGKSTLLNLI 45
>gnl|CDD|162162 TIGR01026, fliI_yscN, ATPase FliI/YscN family. This family of
ATPases demonstrates extensive homology with ATP
synthase F1, beta subunit. It is a mixture of members
with two different protein functions. The first group is
exemplified by Salmonella typhimurium FliI protein. It
is needed for flagellar assembly, its ATPase activity is
required for flagellation, and it may be involved in a
specialized protein export pathway that proceeds without
signal peptide cleavage. The second group of proteins
function in the export of virulence proteins;
exemplified by Yersinia sp. YscN protein an ATPase
involved in the type III secretory pathway for the
antihost Yops proteins.
Length = 440
Score = 29.6 bits (67), Expect = 2.9
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 480 EEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
E++ R + LL K QR I I G GKSTL+ +I
Sbjct: 144 REILSTGVRSID-GLLTVGKGQR-IGIFAGSGVGKSTLLGMI 183
>gnl|CDD|163011 TIGR02774, rexB_recomb, ATP-dependent nuclease subunit B. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RecAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
The partner may be designated AddB, as in Bacillus and
in alphaproteobacteria, or RexB as in Streptococcus and
Lactococcus. Note, however, that RexB proteins lack an
N-terminal GxxGxGK[ST] ATP-binding motif found in
Bacillus subtilis and related species, and this
difference may be important; this model represents
specifically RexB proteins as found in Streptococcus and
Lactococcus.
Length = 1076
Score = 29.4 bits (66), Expect = 3.3
Identities = 24/93 (25%), Positives = 44/93 (47%), Gaps = 8/93 (8%)
Query: 392 RRQNVEENSKAKSTAQSLEAG---SIFSITSDLLDSSSRFLGEQDGILDLETGQKVKPTK 448
+ + SK +++E+G S T ++D +RF E++ ++ L G+ V+
Sbjct: 158 NQGQYAQQSKLAHFIEAIESGKLDSDLKNTVLVIDGFTRFSAEEEALVSLLHGKGVEIII 217
Query: 449 ELYIT-KSTGTPFVEG---EPSQEFL-DLVSGY 476
Y + K+ + F EG + S +FL DL Y
Sbjct: 218 GAYASQKAYKSSFSEGNLYQASVKFLHDLAQKY 250
>gnl|CDD|181578 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 29.6 bits (67), Expect = 3.5
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 493 ALLGGNKAQRFIHIRGVGGSGKSTLM 518
L G A RF ++ G GSG+S L+
Sbjct: 34 ELAAGPVADRFFYLWGEAGSGRSHLL 59
>gnl|CDD|130587 TIGR01524, ATPase-IIIB_Mg, magnesium-translocating P-type ATPase.
The magnesium ATPases have been classified as type IIIB
by a phylogenetic analysis.
Length = 867
Score = 29.4 bits (66), Expect = 3.8
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 16/83 (19%)
Query: 587 MTARLNYGNTYSESPAS-FTPFI-VPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFA 644
MTA N+GN +S AS F PF+ + + HL ++N + + +P+DK D F
Sbjct: 670 MTASSNFGNVFSVLVASAFIPFLPMLSLHLLIQNL--LYDFSQLTLPWDK----MDREFL 723
Query: 645 QKLETKYTLEAKKWFLKGVKAYI 667
+K +W KG+ ++
Sbjct: 724 KK--------PHQWEQKGMGRFM 738
>gnl|CDD|179089 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 29.0 bits (66), Expect = 4.4
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 502 RFIHIRGVGGSGKSTLMNLIK 522
FI I G+ G+GKST + L+K
Sbjct: 4 MFITIEGIDGAGKSTQIELLK 24
>gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This
model describes FtsE, a member of the ABC transporter
ATP-binding protein family. This protein, and its
permease partner FtsX, localize to the division site. In
a number of species, the ftsEX gene pair is located next
to FtsY, the signal recognition particle-docking
protein.
Length = 214
Score = 29.1 bits (66), Expect = 4.7
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 503 FIHIRGVGGSGKSTLMNLI-KYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMG 558
F+ + G G+GK+TL+ L+ ++ + D+ + R G+ P L R +G
Sbjct: 30 FLFLTGPSGAGKTTLLKLLYGALTPSRGQVRIAGEDVNRLR----GRQLPLLRRRIG 82
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo and
salvage pathways of DTTP synthesis. Catalytic activity:
ATP + thymidine 5'-phosphate = ADP + thymidine
5'-diphosphate.
Length = 195
Score = 28.9 bits (65), Expect = 5.2
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 503 FIHIRGVGGSGKSTLMNLIK 522
FI I G+ G+GK+T NL+K
Sbjct: 5 FIVIEGIDGAGKTTQANLLK 24
>gnl|CDD|162558 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion.
Length = 694
Score = 28.9 bits (65), Expect = 5.3
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLIK 522
K FI I G GSGKSTL L++
Sbjct: 481 KPGEFIGIVGPSGSGKSTLTKLLQ 504
>gnl|CDD|163254 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP.
Length = 226
Score = 28.7 bits (65), Expect = 5.6
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 495 LGGNKAQRFIHIRGVGGSGKSTLM 518
L K RF+++ G GSGKS L+
Sbjct: 32 LAAGKGDRFLYLWGESGSGKSHLL 55
>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
Provisional.
Length = 258
Score = 28.7 bits (65), Expect = 5.9
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 506 IRGVGGSGKSTLMNLI 521
I G GSGK+TL+N +
Sbjct: 37 IVGESGSGKTTLLNAL 52
>gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria.
Length = 650
Score = 28.9 bits (65), Expect = 6.0
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 504 IHIRGVGGSGKSTLMNLIKYA-FGNQ-YVINAEASDIMQ------NRPPEAGKANPSLIR 555
I I G+ G+GK+TL++ I+ A +G + Q NR AGK NP+ I
Sbjct: 31 ILIGGLNGAGKTTLLDAIQLALYGKRALCSGRGNKSYEQYLRGLINRQ--AGKTNPASIT 88
Query: 556 L 556
L
Sbjct: 89 L 89
>gnl|CDD|179463 PRK02714, PRK02714, O-succinylbenzoate synthase; Provisional.
Length = 320
Score = 28.4 bits (64), Expect = 6.4
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 40 LLSSEKI----DKLPACGFGFVC 58
++ E+I D LPAC FGF
Sbjct: 71 EITPEQIFSIPDALPACQFGFES 93
>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.5 bits (63), Expect = 6.8
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 502 RFIHIRGVGGSGKSTLMNLI----KYAFGNQYVINAEAS 536
I I G GSGK+TL + G I+ E
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDI 41
>gnl|CDD|130252 TIGR01184, ntrCD, nitrate transport ATP-binding subunits C and D.
This model describes the ATP binding subunits of nitrate
transport in bacteria and archaea. This protein belongs
to the ATP-binding cassette (ABC) superfamily. It is
thought that the two subunits encoded by ntrC and ntrD
form the binding surface for interaction with ATP. This
model is restricted in identifying ATP binding subunit
associated with the nitrate transport. Nitrate
assimilation is aided by other proteins derived from the
operon which among others include products of ntrA - a
regulatory protein; ntrB - a hydropbobic transmembrane
permease and narB - a reductase.
Length = 230
Score = 28.6 bits (64), Expect = 7.1
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
FI + G G GKSTL+NLI
Sbjct: 13 FISLIGHSGCGKSTLLNLI 31
>gnl|CDD|184127 PRK13540, PRK13540, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 200
Score = 28.4 bits (63), Expect = 7.1
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
+H++G G+GK+TL+ LI
Sbjct: 29 LLHLKGSNGAGKTTLLKLI 47
>gnl|CDD|183250 PRK11638, PRK11638, lipopolysaccharide biosynthesis protein WzzE;
Provisional.
Length = 342
Score = 28.1 bits (63), Expect = 9.3
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 385 FWFNTDYRRQNVEENSKA 402
FW TDY +Q +E N+KA
Sbjct: 111 FWLQTDYYKQRMEGNAKA 128
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 28.0 bits (63), Expect = 9.3
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLIKYAF 525
K + + I G G+GKSTL+NL++ F
Sbjct: 359 KPGQTVAIVGPTGAGKSTLINLLQRVF 385
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
0.316 0.134 0.401
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 12,969,936
Number of extensions: 845506
Number of successful extensions: 1860
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1845
Number of HSP's successfully gapped: 51
Length of query: 789
Length of database: 5,994,473
Length adjustment: 101
Effective length of query: 688
Effective length of database: 3,812,065
Effective search space: 2622700720
Effective search space used: 2622700720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.2 bits)