RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780766|ref|YP_003065179.1| recombination protein F
[Candidatus Liberibacter asiaticus str. psy62]
(375 letters)
>gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 344 bits (886), Expect = 2e-95
Identities = 124/365 (33%), Positives = 191/365 (52%), Gaps = 13/365 (3%)
Query: 7 IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR 66
+ L++++FRNY L L + VG+NG GKTN+LEAI L+PGR R A ++ R
Sbjct: 3 LTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIR 62
Query: 67 IGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLV 126
G+ + RVE + ++++ + R VR IN R + EL L +
Sbjct: 63 FGAEAAV-IHGRVEKGGRELPLGLEIDKKGGRKVR---INGEPQRKLAELAGLLNVVLFT 118
Query: 127 PSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSI 186
P R+ G ERRRFLDR++F I+P + + +ER ++ RN LL + D +W
Sbjct: 119 PEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQRNALLKQA--DYAWLDVW 176
Query: 187 EAQMAELGVKINIARVEMINALSSLIMEYVQKEN--FPHIKLSLTGFLDGKFDQSFCALK 244
+ Q+AELG I AR+E + L+ L + Q+ + F LS + + ++
Sbjct: 177 DEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSV----EDDAEKIE 232
Query: 245 EEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHA 304
E+ + L R+ D RTL+GPHR DL + GSTG+QK++L+ + LA A
Sbjct: 233 EDLLEALAKNRERDRARGRTLVGPHRDDLRF-RINGLPAADFGSTGQQKLLLLALKLAEA 291
Query: 305 RLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDSLNETAKF 364
L+ TG APILLLD++++ LD+ +R AL + +G+Q+F+T TD L E AK
Sbjct: 292 ELLKEETGEAPILLLDDVASELDDGRRAALLERLKGLGAQVFITTTDLEDLADLLENAKI 351
Query: 365 MRISN 369
+
Sbjct: 352 FHVEQ 356
>gnl|CDD|161957 TIGR00611, recf, recF protein. All proteins in this family for
which functions are known are DNA binding proteins that
assist the filamentation of RecA onto DNA for the
initiation of recombination or recombinational repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University).
Length = 365
Score = 151 bits (384), Expect = 2e-37
Identities = 97/350 (27%), Positives = 165/350 (47%), Gaps = 13/350 (3%)
Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVT 65
+ L +++FRNY ++ L + VG NG GKTN+LEAI +L+ GR R + +
Sbjct: 2 YLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLI 61
Query: 66 RIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWL 125
R G+ +F RV + +++I LE + + ++N + +L L +
Sbjct: 62 RFGAEAFV-IEGRVSKGDR--EVTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLF 118
Query: 126 VPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEG---YFDSSW 182
P + G RRRFLD +F ++P + D++R+++ RN L + Y D +
Sbjct: 119 APEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLKQRNAALKQAQRQYGDRTT 178
Query: 183 CSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCA 242
++Q+AELG K++ R E I L + Q SL+ F G+
Sbjct: 179 LEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQ--LLLPELESLSLFYRGELW----D 232
Query: 243 LKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLA 302
+ +YA+ L + D TL+GPHR DL + S G+ + + + + LA
Sbjct: 233 KETDYAEALARNFERDLERGYTLVGPHRDDLRF-RLNGLPVEDFASQGQLRSLALALRLA 291
Query: 303 HARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDK 352
L+ G PILLLD++++ LD+ +R L ++ +G Q+F+T
Sbjct: 292 EGELLREEGGEYPILLLDDVASELDDQRRRLLAELLQSLGVQVFVTAISL 341
>gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional.
Length = 349
Score = 107 bits (268), Expect = 6e-24
Identities = 94/339 (27%), Positives = 152/339 (44%), Gaps = 24/339 (7%)
Query: 15 FRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFS 74
+RN A L F T VG+N GKTN+LEAI +L+ AD+ R G +
Sbjct: 11 YRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAI-YLALTGELPNGRLADLVRFGEGEAW- 68
Query: 75 TFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFS 134
A VE GL+ +LE R L+++ V + + EL + + P +
Sbjct: 69 VHAEVETGGGLS----RLEVGLGPGRRELKLDGVRVSL-RELARLPGAVLIRPEDLELVL 123
Query: 135 GLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSI-EAQMAEL 193
G RR +LDR++ + R+ + +ER ++ RN L G W + + ++ +L
Sbjct: 124 GPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQRNAALKSG---GGWGLHVWDDELVKL 180
Query: 194 GVKINIARVEMINALSSLIME-YVQKENFPHIKLSLTGFLDGKFDQSFCALKEEYAKKLF 252
G +I R + LS L E Y + + ++L L+ E Y L
Sbjct: 181 GDEIMALRRRALTRLSELAREAYAELGSRKPLRLELSESTAP----------EGYLAALE 230
Query: 253 DGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTG 312
R + T++GPHR DL++ + + S GE + V + + LA RL+ G
Sbjct: 231 ARRAEELARGATVVGPHRDDLVLTLEGRPAH-RYASRGEARTVALALRLAEHRLLWEHFG 289
Query: 313 FAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTD 351
AP+LL+D+ +A LD +R AL + + Q + GT+
Sbjct: 290 EAPVLLVDDFTAELDPRRRGALLALAASL-PQAIVAGTE 327
>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 41.6 bits (98), Expect = 3e-04
Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 5 IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS---FLSPGRGFRRASY 61
+KI+ L I FR++ S + FD + +G NG GK++ILEAI + G +
Sbjct: 1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWGHGSKPKGLKK 60
Query: 62 ADVTRIGS 69
D TRIG
Sbjct: 61 DDFTRIGG 68
>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 = 35.8 bits (82), Expect = 0.018
Identities = 24/142 (16%), Positives = 42/142 (29%), Gaps = 7/142 (4%)
Query: 28 QHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGMEGLAD 87
+ + VG G GKT + A++ G Y D I + G + +
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPG-GGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 88 ISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSMERRRFLDRM 147
R ++ DV+I +DE+ L + L + + +
Sbjct: 62 SGELRL-RLALALARKLKPDVLI--LDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLT 118
Query: 148 VFAIDPRHRRRMIDFERLMRGR 169
V L+R R
Sbjct: 119 VILT---TNDEKDLGPALLRRR 137
>gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 34.6 bits (80), Expect = 0.039
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 26 DAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57
+ T+ G NG GK+ +LEA++F G+ FR
Sbjct: 26 KVKKTLITGKNGAGKSTMLEALTFALFGKPFR 57
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 34.5 bits (79), Expect = 0.044
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 7 IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF 49
IK + + F ++ + FD I G NG GK++I++AI F
Sbjct: 3 IKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRF 45
Score = 32.6 bits (74), Expect = 0.20
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
S GE+ V + +A A+ ++N L++DE +A LDED+R L I+
Sbjct: 803 SGGEKTAVAFALRVAVAQFLNNDKSL---LIMDEPTAFLDEDRRTNLKDII 850
>gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
Length = 402
Score = 34.4 bits (79), Expect = 0.046
Identities = 29/95 (30%), Positives = 40/95 (42%), Gaps = 34/95 (35%)
Query: 252 FDGRKMDSMSRRTLIGPHRS---------DLIVD----------YCDKAITIAHGSTGEQ 292
FD R++ M R PHRS V+ + D+ +T G GE+
Sbjct: 92 FDVRQVVEMGRT----PHRSRFDTWTETDRAAVERAMERTGVAQFADRPVTSLSG--GER 145
Query: 293 KVVLVGIFLAHARLISNTTGFAPILLLDEISAHLD 327
+ VL+ LA A P+LLLDE +A LD
Sbjct: 146 QRVLLARALAQA---------TPVLLLDEPTASLD 171
Score = 28.3 bits (63), Expect = 3.3
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 33 VGDNGVGKTNILEAIS-FLSPGRG 55
VG NG GKT +L AI+ L+P G
Sbjct: 35 VGPNGAGKTTLLRAINGTLTPTAG 58
>gnl|CDD|161971 TIGR00634, recN, DNA repair protein RecN. All proteins in this
family for which functions are known are ATP binding
proteins involved in the initiation of recombination and
recombinational repair.
Length = 563
Score = 34.3 bits (79), Expect = 0.047
Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 11/98 (11%)
Query: 10 LNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGS 69
L I+ F L + F+ T+ G+ G GK+ I++A+S L R A R G
Sbjct: 5 LRINNFALIRVLTVEFERGLTVLTGETGAGKSMIIDALSLLGGQRA-----GASRVRSGE 59
Query: 70 PS------FFSTFARVEGMEGLADISIKLETRDDRSVR 101
F + L I ++ E D +
Sbjct: 60 NRAVVEGRFTTESLDDADYPALQAIELEEEDEDGEVIL 97
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 33.9 bits (78), Expect = 0.066
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF 49
+ + + F+ YA L + T+ G NG GK+++LEA F
Sbjct: 2 RFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEACFF 45
>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent.
Length = 1164
Score = 33.9 bits (78), Expect = 0.076
Identities = 29/128 (22%), Positives = 45/128 (35%), Gaps = 16/128 (12%)
Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASYA 62
+I+ N F + F T+ G NG GK+NI +AI F LS + R +
Sbjct: 4 RIELENFKSFGKKK--VIPFSKGFTVISGPNGSGKSNIGDAILFALGLSSSKAMRAERLS 61
Query: 63 DVTRIGSPSFFSTFARVE--------GMEGLADISIKLETRDDRSVRCLQINDVVIR--- 111
D+ G A V ++ +L+ DD +N +R
Sbjct: 62 DLISNGKNGQSGNEAYVTVTFKNDDGKFPDELEVVRRLKVTDDGKYSYYYLNGQRVRLSE 121
Query: 112 VVDELNKH 119
+ D L
Sbjct: 122 IHDFLAAA 129
>gnl|CDD|162972 TIGR02680, TIGR02680, conserved hypothetical protein TIGR02680.
Members of this protein family belong to a conserved gene
four-gene neighborhood found sporadically in a
phylogenetically broad range of bacteria: Nocardia
farcinica, Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length.
Length = 1353
Score = 32.9 bits (75), Expect = 0.16
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 288 STGEQKVVL-VGIFLA-HARLISNTTGFAP-ILLLDEISAHLDEDKRNALFRIVTDIGSQ 344
S GE+ + L V +F A + AP ++LLDE A +D++ R LF ++ +
Sbjct: 1249 SGGERALALYVPLFAAASSHYTQEAYPHAPRLILLDEAFAGVDDNARAHLFGLLRALDLD 1308
Query: 345 IFMT 348
MT
Sbjct: 1309 FVMT 1312
>gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
Length = 248
Score = 31.8 bits (73), Expect = 0.27
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 27/87 (31%)
Query: 288 STGE-QKVVLVGIFL-------AHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVT 339
S GE Q+V L + L +L LLLDE LD ++ AL R+++
Sbjct: 128 SGGEWQRVRLAAVVLQVWPDINPAGQL----------LLLDEPMNSLDVAQQAALDRLLS 177
Query: 340 DIGSQ---IFMTGTDKSVFDSLNETAK 363
++ Q + M+ D LN T +
Sbjct: 178 ELCQQGIAVVMSSHD------LNHTLR 198
Score = 28.0 bits (63), Expect = 3.8
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 32 FVGDNGVGKTNILEAISFLSPGRG 55
VG NG GK+ +L ++ L PG G
Sbjct: 27 LVGPNGAGKSTLLARMAGLLPGSG 50
>gnl|CDD|162739 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing
and segregating chromosomes for partition. SMC proteins
are found in bacteria, archaea, and eukaryotes. This
family represents the SMC protein of most bacteria. The
smc gene is often associated with scpB (TIGR00281) and
scpA genes, where scp stands for segregation and
condensation protein. SMC was shown (in Caulobacter
crescentus) to be induced early in S phase but present
and bound to DNA throughout the cell cycle.
Length = 1179
Score = 32.0 bits (73), Expect = 0.28
Identities = 17/43 (39%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 6 KIKFLNISEFRNYA-SLRLVFDAQHTIFVGDNGVGKTNILEAI 47
++K L ++ F+++A + FD T VG NG GK+NI++AI
Sbjct: 1 RLKKLELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAI 43
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 31.6 bits (72), Expect = 0.33
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 306 LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341
LI N +LLLDEI++ LDE + V +I
Sbjct: 148 LIRNLQFMPKVLLLDEITSALDESNK----HNVNEI 179
>gnl|CDD|129694 TIGR00606, rad50, rad50. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University).
Length = 1311
Score = 31.6 bits (71), Expect = 0.36
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 30 TIFVGDNGVGKTNILEAISFLSPG 53
TI VG NG GKT I+E + ++ G
Sbjct: 31 TILVGPNGAGKTTIIECLKYICTG 54
>gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.
Unfortunately, the gene symbol nomenclature adopted
based on this operon in B. subtilis assigns cydC to the
third gene in the operon where this gene is actually
homologous to the E. coli cydD gene. We have chosen to
name all homologs in this family in accordance with the
precedence of publication of the E. coli name, CydD.
Length = 529
Score = 31.1 bits (71), Expect = 0.44
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 314 APILLLDEISAHLDEDKRNALFRIV 338
AP+LLLDE +AHLD + + +
Sbjct: 477 APLLLLDEPTAHLDAETEALVTEAL 501
>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 = 30.8 bits (70), Expect = 0.53
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 5/37 (13%)
Query: 301 LAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFR 336
LA AR L+++ APILLLDE + HLD + L
Sbjct: 479 LALARALLAD----APILLLDEPTEHLDAGTESELLE 511
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University).
Length = 1042
Score = 29.6 bits (66), Expect = 1.4
Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 5/101 (4%)
Query: 252 FDGRKMDSMSRRTLIGPHRSDLIVD--YCDKAITIAHGSTGEQKVVLVGIFLAHARLISN 309
F GR DS L+V Y A S GE + + + LA A L+S
Sbjct: 916 FHGRYADSHVNAR--KYQGLALLVADAYTGSVRPSATLSGGETFLASLSLALALADLLST 973
Query: 310 TTGFA-PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTG 349
+ G L +DE LDED + I+ I M G
Sbjct: 974 SGGTVLDSLFIDEGFGSLDEDSLDRAIGILDAIREGSKMIG 1014
Score = 28.0 bits (62), Expect = 4.2
Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 13/85 (15%)
Query: 25 FDAQHTIFV--GDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGM 82
F A IF+ G G GKT +L+AI++ G+ R S +
Sbjct: 22 FTALGPIFLICGKTGAGKTTLLDAITYALYGK-LPRRSEVIRSLNS-------LYAAPSE 73
Query: 83 EGLADISIKLET---RDDRSVRCLQ 104
A++ L T R R++RC +
Sbjct: 74 AAFAELEFSLGTKIYRVHRTLRCTR 98
>gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 195
Score = 29.1 bits (65), Expect = 1.8
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 9/51 (17%)
Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
S+G QK+V A ARLI+ + + LLDE+ +L ++ R+ L ++
Sbjct: 125 SSGMQKIV------AIARLIA---CQSDLWLLDEVETNLSKENRDLLNNLI 166
>gnl|CDD|151518 pfam11073, NSs, Rift valley fever virus non structural protein
(NSs) like. This family contains several Phlebovirus
non structural proteins which act as a major determinant
of virulence by antagonising interferon beta gene
expression.
Length = 238
Score = 29.2 bits (66), Expect = 2.0
Identities = 30/142 (21%), Positives = 47/142 (33%), Gaps = 34/142 (23%)
Query: 155 HRRRMIDFERLMRGRNRLLTEGYFDSSW---CSSIEAQMAELGVKINIARVEMINALSSL 211
R + DF + G F + W CSS+ + I LS
Sbjct: 48 SRPTLSDF----------YSVGEFPARWGPGCSSVTKPSTKF-------FDGTIEDLSRF 90
Query: 212 IMEYVQKENFPHIKLSL---TGFLDGKF-DQSFCALKEEYAKKLFDGRKMDSMSRRTLIG 267
+E + P+IK +L G+ +F + S + Y K D ++ +G
Sbjct: 91 DIESFLRSCLPNIKKALSWPLGYPSLEFFELSNI---DSY--LFLWETKCDFATQILRMG 145
Query: 268 PHRSDLIVDYCDKAITIAHGST 289
S L D +I AH
Sbjct: 146 LQGSGL-----DDSIVEAHKKI 162
>gnl|CDD|182605 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 28.6 bits (64), Expect = 3.0
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 316 ILLLDEISAHLDEDKRNAL 334
+LLLDE + HLD D R AL
Sbjct: 451 LLLLDEPTNHLDLDMRQAL 469
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 28.1 bits (63), Expect = 3.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 31 IFVGDNGVGKTNILE 45
+ VG+ GVGKT I E
Sbjct: 207 LLVGEPGVGKTAIAE 221
>gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 28.1 bits (63), Expect = 3.5
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 21/71 (29%)
Query: 73 FSTFARVE-GMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDR 131
F F RVE G+EGL IS + + R +++ + V++V DE+ V +D
Sbjct: 307 FGAFVRVEEGIEGLVHIS-------ELAERHVEVPEQVVQVGDEV--------FVKVID- 350
Query: 132 IFSGLSMERRR 142
+ +ERRR
Sbjct: 351 ----IDLERRR 357
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein
which is localized in the photoreceptor outer segment
discs. Mutation/s in its genetic loci is implicated in
the recessive Stargardt's disease.
Length = 2272
Score = 28.1 bits (62), Expect = 3.8
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 25 FDAQHTIFVGDNGVGKTNILEAISFLSP 52
++ Q T F+G NG GKT L ++ L P
Sbjct: 954 YENQITAFLGHNGAGKTTTLSILTGLLP 981
>gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
The Aquifex aeolicus ortholog is split into consecutive
open reading frames. Consequently, this model was build
in fragment mode (-f option).
Length = 245
Score = 28.1 bits (63), Expect = 3.9
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 300 FLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348
FL A PI++L++I DED I +IG Q+ MT
Sbjct: 59 FLVVA----EAQNIEPIIVLNKIDLLDDEDMEKEQLDIYRNIGYQVLMT 103
>gnl|CDD|179591 PRK03545, PRK03545, putative arabinose transporter; Provisional.
Length = 390
Score = 27.9 bits (63), Expect = 4.6
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 299 IFLAHARLISNTTGFAPILLLDEISAHLD 327
+ LA A I NTT F P+ LL +I+
Sbjct: 12 VTLALAAFIFNTTEFVPVGLLSDIAQSFH 40
>gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 27.9 bits (63), Expect = 5.0
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 31 IFVGDNGVGKTNILE 45
I +GD+GVGK+++L
Sbjct: 4 ILIGDSGVGKSSLLS 18
>gnl|CDD|162147 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70).
Length = 615
Score = 27.6 bits (61), Expect = 5.1
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 221 FPHIKLSLTGFLDGKFDQSFCALKEEYAKKLFD 253
F HI+L +T + +G S + KK F
Sbjct: 434 FSHIQLGVTQYKEGSIASSMATFRR--CKKNFP 464
>gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
protein DNA-binding domain. The plasmid conjugative
coupling protein TrwB forms hexamers from six
structurally very similar protomers. This hexamer
contains a central channel running from the cytosolic
pole (made up by the AADs) to the membrane pole ending
at the transmembrane pore shaped by 12 transmembrane
helices, rendering an overall mushroom-like structure.
The TrwB_AAD (all-alpha domain) domain appears to be
the DNA-binding domain of the structure. TrwB, a basic
integral inner-membrane nucleoside-triphosphate-binding
protein, is the structural prototype for the type IV
secretion system coupling proteins, a family of
proteins essential for macromolecular transport between
cells and export.
Length = 386
Score = 27.6 bits (62), Expect = 5.2
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 25 FDAQHTIFVGDNGVGKTNILEAI 47
+ QH + VG G GKT L +
Sbjct: 13 SETQHILIVGTTGTGKTQALREL 35
>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 27.5 bits (62), Expect = 5.7
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 9 FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47
L+ E L+ + + T+ G +GVGK+ +L A+
Sbjct: 146 ELSAKEGEGLDELKPLLAGKVTVLAGQSGVGKSTLLNAL 184
>gnl|CDD|149065 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 27.6 bits (62), Expect = 5.8
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 26/95 (27%)
Query: 85 LADISIKLETRDDRSVRCL--QINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSMERRR 142
+A+ I DD L +I ++V R+++E + +F+ L E +
Sbjct: 407 IAEAGIGWGGDDDGLRDSLYAKIEEIVQRILNEFDDDP----------SLFAELLEEFQA 456
Query: 143 FLDRMVFAIDPRHR-----RRMIDFERLMRGRNRL 172
FL++ R R +R + E GR RL
Sbjct: 457 FLEQE------RRRSELVEQRTREAE---EGRARL 482
>gnl|CDD|180838 PRK07102, PRK07102, short chain dehydrogenase; Provisional.
Length = 243
Score = 27.6 bits (62), Expect = 6.3
Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 2/51 (3%)
Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334
IA G+ G+Q A A T PI LL ++ + +
Sbjct: 82 IAVGTLGDQAACEAD--PALALREFRTNFEGPIALLTLLANRFEARGSGTI 130
>gnl|CDD|178142 PLN02527, PLN02527, aspartate carbamoyltransferase.
Length = 306
Score = 27.4 bits (61), Expect = 6.5
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 315 PILLLDEISAHLDEDKRNALFR 336
P+ LDEI+ +D D R A FR
Sbjct: 265 PLPRLDEITTDVDSDPRAAYFR 286
>gnl|CDD|163250 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
protein UrtE. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity.
Length = 230
Score = 27.5 bits (62), Expect = 6.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 34 GDNGVGKTNILEAISFLSPGRG 55
G NGVGKT +L+ + L P +
Sbjct: 33 GRNGVGKTTLLKTLMGLLPVKS 54
>gnl|CDD|183835 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 27.4 bits (62), Expect = 7.1
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 57 RRASYADVTRIGSPSFFSTFARVEGMEGLADISIKLE 93
R Y DV+ + +P+FF G+ +I +++E
Sbjct: 990 HREEYGDVSVLPTPTFF------YGLRPGEEIEVEIE 1020
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 27.1 bits (61), Expect = 7.3
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 314 APILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355
A + LLDE SAHLD ++R A+ + + + + +
Sbjct: 472 ADLYLLDEPSAHLDVEQRLAVAKAI-----RRIAEEREATAL 508
>gnl|CDD|183531 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
Length = 426
Score = 27.2 bits (61), Expect = 7.4
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 13/81 (16%)
Query: 16 RNYASLRLVFDAQHT-IFVGDNGVGKTNIL---EAISF---LSPGRGFRRASYADVTRIG 68
NY +L F + T + GD +G ++L A + L G+ + +Y VT
Sbjct: 336 TNYGAL---FLGERTNVAYGDKVIGTNHVLPTSGAARYTGGLWVGKFLKTVTYQRVTDEA 392
Query: 69 SPSF---FSTFARVEGMEGLA 86
S S R+EG EG A
Sbjct: 393 SAEIGEYCSRLCRLEGFEGHA 413
>gnl|CDD|178337 PLN02736, PLN02736, long-chain acyl-CoA synthetase.
Length = 651
Score = 27.0 bits (60), Expect = 7.8
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 14/68 (20%)
Query: 247 YAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARL 306
Y+K L GR S + P D+ I G+TG K G+ L H L
Sbjct: 201 YSKLLAQGR----SSPQPFRPPKPEDV------ATICYTSGTTGTPK----GVVLTHGNL 246
Query: 307 ISNTTGFA 314
I+N G +
Sbjct: 247 IANVAGSS 254
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 27.2 bits (60), Expect = 7.9
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 31 IFVGDNGVGKTNIL 44
+ +GD+GVGK+NIL
Sbjct: 16 VLIGDSGVGKSNIL 29
>gnl|CDD|131499 TIGR02446, FadI, fatty oxidation complex, beta subunit FadI. This
subunit of the FadJI complex has acetyl-CoA
C-acyltransferase (EC 2.3.1.16) activity, and is also
known as beta-ketothiolase and fatty oxidation complex,
beta subunit, and YfcY. This protein is almost always
located adjacent to FadJ (TIGR02440). The FadJI complex
is needed for anaerobic beta-oxidation of short-chain
fatty acids in E. coli.
Length = 430
Score = 26.9 bits (59), Expect = 8.6
Identities = 13/42 (30%), Positives = 17/42 (40%)
Query: 13 SEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGR 54
S YA LR FD +H N T+ A+ + GR
Sbjct: 242 STLAGYAKLRPAFDRKHGSVTAANSTPLTDGAAAVILMREGR 283
>gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein;
Provisional.
Length = 258
Score = 27.0 bits (60), Expect = 8.6
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 1 MTNRIKIKFLNISEFRNYASLRLVFDAQHTI-------FVGDNGVGKTNIL 44
M RI +K LNI Y S V D I F+G +G GK+ +L
Sbjct: 1 MAKRIDVKDLNIY----YGSFHAVEDVNLNIEPRSVTAFIGPSGCGKSTVL 47
>gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or lesions
in the genetic loci have been linked to the aetiology of
asthma, bronchiectasis, chronic obstructive pulmonary
disease etc. Disease-causing mutations have been studied
by 36Cl efflux assays in vitro cell cultures and
electrophysiology, all of which point to the impairment
of chloride channel stability and not the biosynthetic
processing per se.
Length = 1490
Score = 26.8 bits (59), Expect = 8.6
Identities = 12/14 (85%), Positives = 12/14 (85%)
Query: 314 APILLLDEISAHLD 327
A ILLLDE SAHLD
Sbjct: 1372 AKILLLDEPSAHLD 1385
>gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 26.7 bits (59), Expect = 8.9
Identities = 13/19 (68%), Positives = 13/19 (68%)
Query: 316 ILLLDEISAHLDEDKRNAL 334
ILLLDE S HLD D AL
Sbjct: 648 ILLLDEPSNHLDLDAVEAL 666
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 26.9 bits (60), Expect = 9.5
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 315 PILLLDEISAHLDEDKRNALFRIVTDI 341
PILLLDE + LD R + +V+ +
Sbjct: 149 PILLLDEPFSALDPALRQEMLTLVSQV 175
>gnl|CDD|163455 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL
subfamily. Members of this protein family are the
putative conjugative coupling factor, TraD (or TraG),
rather distantly related to the well-characterized TraD
of the F plasmid. Members are associated with
conjugative-transposon-like mobile genetic elements of
the class that includes SXT, an antibiotic resistance
transfer element in some Vibrio cholerae strains.
Length = 634
Score = 26.9 bits (60), Expect = 9.5
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 29 HTIFVGDNGVGKTNILEAISF 49
HT+ +G GVGKT + E +
Sbjct: 178 HTLVLGTTGVGKTRLAELLIT 198
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
0.326 0.139 0.402
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,245,335
Number of extensions: 421075
Number of successful extensions: 1383
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1369
Number of HSP's successfully gapped: 75
Length of query: 375
Length of database: 5,994,473
Length adjustment: 95
Effective length of query: 280
Effective length of database: 3,941,713
Effective search space: 1103679640
Effective search space used: 1103679640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.1 bits)