RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780799|ref|YP_003065212.1| DNA translocase FtsK
[Candidatus Liberibacter asiaticus str. psy62]
(806 letters)
>gnl|CDD|182344 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 492 bits (1267), Expect = e-139
Identities = 247/496 (49%), Positives = 329/496 (66%), Gaps = 19/496 (3%)
Query: 309 LPSKEILSTSQSPVNQM-TFSPKVMQNNACTLKSVLSDFGIQGEIVNVRPGPVITLYELE 367
LPS ++L+ S V + TF+ + M A +++ L+DF I+ ++VN PGPVIT +EL
Sbjct: 866 LPSLDLLTPPPSEVEPVDTFALEQM---ARLVEARLADFRIKADVVNYSPGPVITRFELN 922
Query: 368 PAPGIKSSRIIGLSDDIARSMSAISARVA-VIPRRNAIGIELPNDIRETVMLRDLIVSRV 426
APG+K++RI LS D+ARS+S ++ RV VIP + +G+ELPN R+TV LR+++ +
Sbjct: 923 LAPGVKAARISNLSRDLARSLSTVAVRVVEVIPGKPYVGLELPNKKRQTVYLREVLDNAK 982
Query: 427 FEKNQCDLAINLGKSIEGKPIIADLARMPHLLIAGTTGSGKSVAINTMILSLLYRMTPAQ 486
F N L + LGK I G+P++ADLA+MPHLL+AGTTGSGKSV +N MILS+LY+ P
Sbjct: 983 FRDNPSPLTVVLGKDIAGEPVVADLAKMPHLLVAGTTGSGKSVGVNAMILSMLYKAQPED 1042
Query: 487 CRLIMIDPKMLELSVYDGIPNLLTPVVTNPQKAVTVLKWLVCEMEERYQKMSKIGVRNID 546
R IMIDPKMLELSVY+GIP+LLT VVT+ + A L+W V EME RY+ MS +GVRN+
Sbjct: 1043 VRFIMIDPKMLELSVYEGIPHLLTEVVTDMKDAANALRWCVNEMERRYKLMSALGVRNLA 1102
Query: 547 GFNLKVAQYHNTGKKFNRTVQTGFDRKTGEAIYETEHFDFQHMPYIVVVIDEMADLMMVA 606
G+N K+A+ R + + K G+++ + +H + PYIVV++DE ADLMM
Sbjct: 1103 GYNEKIAEADRMM----RPIPDPY-WKPGDSM-DAQHPVLKKEPYIVVLVDEFADLMMTV 1156
Query: 607 RKDIESAVQRLAQMARASGIHVIMATQRPSVDVITGTIKANFPTRISFQVSSKIDSRTIL 666
K +E + RLAQ ARA+GIH+++ATQRPSVDVITG IKAN PTRI+F VSSKIDSRTIL
Sbjct: 1157 GKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKANIPTRIAFTVSSKIDSRTIL 1216
Query: 667 GEQGAEQLLGQGDMLYMTGGGRVQ-RIHGPFVSDIEVEKVVSHLKTQGEAKYIDIKDKIL 725
+ GAE LLG GDMLY + R+HG FV D EV VV K +G +Y+ D I
Sbjct: 1217 DQAGAESLLGMGDMLYSGPNSTLPVRVHGAFVRDQEVHAVVQDWKARGRPQYV---DGIT 1273
Query: 726 LNEEMRFS----ENSSVADDLYKQAVDIVLRDNKASISYIQRRLGIGYNRAASIIENMEE 781
+ E + + D L+ QAV V KASIS +QR+ IGYNRAA IIE ME
Sbjct: 1274 SDSESEGGAGGFDGAEELDPLFDQAVQFVTEKRKASISGVQRQFRIGYNRAARIIEQMEA 1333
Query: 782 KGVIGPASSTGKREIL 797
+G++ G RE+L
Sbjct: 1334 QGIVSEQGHNGNREVL 1349
>gnl|CDD|150161 pfam09397, Ftsk_gamma, Ftsk gamma domain. This domain directs
oriented DNA translocation and forms a winged helix
structure. Mutated proteins with substitutions in the
FtsK gamma DNA-recognition helix are impaired in DNA
binding.
Length = 67
Score = 106 bits (267), Expect = 3e-23
Identities = 33/61 (54%), Positives = 46/61 (75%)
Query: 740 DDLYKQAVDIVLRDNKASISYIQRRLGIGYNRAASIIENMEEKGVIGPASSTGKREILIS 799
D+LY +AV+ V+ KAS S +QRRL IGYNRAA +IE MEE+G++GPA+ + RE+L+
Sbjct: 6 DELYDEAVEFVIETQKASTSLLQRRLRIGYNRAARLIEQMEEEGIVGPANGSKPREVLVP 65
Query: 800 S 800
Sbjct: 66 K 66
>gnl|CDD|129076 smart00843, Ftsk_gamma, This domain directs oriented DNA
translocation and forms a winged helix structure.
Mutated proteins with substitutions in the FtsK gamma
DNA-recognition helix are impaired in DNA binding.
Length = 63
Score = 105 bits (264), Expect = 7e-23
Identities = 31/60 (51%), Positives = 48/60 (80%)
Query: 740 DDLYKQAVDIVLRDNKASISYIQRRLGIGYNRAASIIENMEEKGVIGPASSTGKREILIS 799
D+LY +AV++V+ KAS S +QRRL IGYNRAA +I+ +EE+G++GPA+ + RE+L++
Sbjct: 4 DELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPANGSKPREVLVT 63
>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 = 40.6 bits (96), Expect = 0.001
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 442 IEGKPIIADLARMPHLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMIDPK 495
I G P+ H+LI GTTG+GK+ A+ ++ + R R I+ DP
Sbjct: 4 IAGVPLPRRSETQ-HILIVGTTGTGKTQALRELLDQIRAR----GDRAIIYDPT 52
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 36.2 bits (84), Expect = 0.031
Identities = 18/31 (58%), Positives = 21/31 (67%)
Query: 441 SIEGKPIIADLARMPHLLIAGTTGSGKSVAI 471
I G P+I + H+LI GTTGSGKSVAI
Sbjct: 163 KIGGLPLIKFGSETQHILIHGTTGSGKSVAI 193
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 35.9 bits (83), Expect = 0.041
Identities = 27/174 (15%), Positives = 59/174 (33%), Gaps = 34/174 (19%)
Query: 451 LARMPHLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMIDPKMLELSVYDGIPNLLT 510
L+ + +++A TGSGK++A L L R + L+++ + L +
Sbjct: 21 LSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRV-LVLVPTRELAEQWAE------- 72
Query: 511 PVVTNPQKAVTVLKWLVCEMEERYQKMSKIGVRNIDGFNLKVAQYHNTGKKFNRTVQTGF 570
E+++ + V G + + K + V T
Sbjct: 73 ------------------ELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTT-- 112
Query: 571 DRKTGEAIYETEHFDFQHMPYIVVVIDEMADLM--MVARKDIESAVQRLAQMAR 622
G + E+ + +V++DE A + +E ++ L + +
Sbjct: 113 ---PGRLLDLLENDLLELSNVDLVILDE-AHRLLDGGFGDQLEKLLKLLPKNVQ 162
>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 = 35.7 bits (83), Expect = 0.048
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 445 KPIIADLARMP-HLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMIDPK 495
+ + L H L+ GTTG GK+ +I + R +I+IDPK
Sbjct: 166 EDVYLPLGHRVGHTLVLGTTGVGKTRLAELLITQDIRRGDV----VIVIDPK 213
>gnl|CDD|180487 PRK06247, PRK06247, pyruvate kinase; Provisional.
Length = 476
Score = 35.3 bits (82), Expect = 0.064
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 14/65 (21%)
Query: 596 IDEMADLMMVARKDI------ES--AVQ-RLAQMARASGIHVIMATQRPSVDVITGTIKA 646
I E +D +MVAR D+ E +Q R+ + AR +G V++ATQ ++ I+
Sbjct: 230 IVEASDAIMVARGDLGVEVPLEQVPLIQKRIIRAARRAGKPVVVATQ-----MLESMIEN 284
Query: 647 NFPTR 651
PTR
Sbjct: 285 PVPTR 289
>gnl|CDD|163456 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves.
Length = 893
Score = 34.2 bits (79), Expect = 0.12
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 456 HLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMID 493
HLLI G TG+GKS + +++ ++ P RL +++
Sbjct: 477 HLLILGPTGAGKSATLTNLLMQVMAVHRP---RLFIVE 511
>gnl|CDD|131585 TIGR02533, type_II_gspE, general secretory pathway protein E. This
family describes GspE, the E protein of the type II
secretion system, also called the main terminal branch
of the general secretion pathway. This model separates
GspE from the PilB protein of type IV pilin
biosynthesis.
Length = 486
Score = 33.9 bits (78), Expect = 0.16
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 19/99 (19%)
Query: 389 SAISARVAVIPRRNAIGIELPNDIRETVML--RDL--------------IVSRVFEKNQC 432
+A+ +RV ++ + N LP D R ++ + RD+ +V R+ +K
Sbjct: 158 AALVSRVKIMAKLNIAEKRLPQDGRISLRVGGRDIDIRVSTVPTSHGERVVMRLLDKTAV 217
Query: 433 DLAI-NLGKSIEGKPIIADLARMPH--LLIAGTTGSGKS 468
L + LG S E L R PH +L+ G TGSGK+
Sbjct: 218 RLDLETLGMSPELLSRFERLIRRPHGIILVTGPTGSGKT 256
>gnl|CDD|184357 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 33.0 bits (76), Expect = 0.34
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 456 HLLIAGTTGSGKSVAINTMIL 476
H L+ G TG+GKSV + M L
Sbjct: 443 HTLVVGPTGAGKSVLLALMAL 463
>gnl|CDD|163531 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 32.7 bits (75), Expect = 0.42
Identities = 26/112 (23%), Positives = 47/112 (41%), Gaps = 36/112 (32%)
Query: 384 IARSMSAISARVAVIPRRNAIGIELPNDIRETVMLRDLIVSRVFEKNQCDLAINLGKSIE 443
+A + +S RV PR T L +L+ S F
Sbjct: 135 VATDGTCLSLRV---PRP------------RTFTLDELVASGTFPP-------------G 166
Query: 444 GKPIIADL--ARMPHLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMID 493
++ + AR+ LI+G TGSGK+ T++ +LL + P + R+++++
Sbjct: 167 VARLLRAIVAARLA-FLISGGTGSGKT----TLLSALLALVAPDE-RIVLVE 212
>gnl|CDD|182509 PRK10513, PRK10513, sugar phosphate phosphatase; Provisional.
Length = 270
Score = 32.4 bits (74), Expect = 0.43
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 589 MPYIVVVIDEMADLMMVARKDIESAVQRLAQMARASGIHVIMATQRPSVDV 639
M ++ ID M +++ I AV++ ARA G++V++ T RP V
Sbjct: 1 MAIKLIAID-MDGTLLLPDHTISPAVKQAIAAARAKGVNVVLTTGRPYAGV 50
>gnl|CDD|183479 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
Length = 400
Score = 31.7 bits (72), Expect = 0.68
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 350 GEIVNVRPGPVITLYELEPAPGIKSSRIIGLSDDIARSMSAISARVAV 397
G+ V+PGP I Y EPA G+ S L+++ ++ S +A
Sbjct: 172 GKGPVVKPGPQIGRYASEPAGGLTS-----LTEEAGKARYNASKALAE 214
>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 = 31.6 bits (71), Expect = 0.82
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 453 RMPHLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMIDPKMLELSVYDGIPNLLT 510
+LI G GSGK+ T+ +L + P +I ID + + V D + ++
Sbjct: 1 PGEVILIVGPPGSGKT----TLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIV 54
>gnl|CDD|180277 PRK05826, PRK05826, pyruvate kinase; Provisional.
Length = 465
Score = 31.7 bits (73), Expect = 0.89
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 12/50 (24%)
Query: 596 IDEM---ADLMMVARKD--IE------SAVQ-RLAQMARASGIHVIMATQ 633
IDE+ +D +MVAR D +E +Q ++ + AR +G VI ATQ
Sbjct: 231 IDEIIEASDGIMVARGDLGVEIPDEEVPGLQKKIIRKAREAGKPVITATQ 280
>gnl|CDD|162184 TIGR01064, pyruv_kin, pyruvate kinase. This enzyme is a
homotetramer. Some forms are active only in the presence
of fructose-1,6-bisphosphate or similar phosphorylated
sugars.
Length = 473
Score = 31.5 bits (72), Expect = 0.92
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 14/65 (21%)
Query: 596 IDEMADLMMVARKD--IE-SAVQ------RLAQMARASGIHVIMATQRPSVDVITGTIKA 646
I E +D +MVAR D +E A + ++ + +G VI ATQ ++ IK
Sbjct: 232 IAEASDGIMVARGDLGVEIPAEEVPIAQKKMIRKCNRAGKPVITATQ-----MLDSMIKN 286
Query: 647 NFPTR 651
PTR
Sbjct: 287 PRPTR 291
>gnl|CDD|162997 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 31.5 bits (72), Expect = 0.95
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 458 LIAGTTGSGKSVAINTMILSLL 479
+ G +G+GKS + +I+ L
Sbjct: 434 AVVGGSGAGKSFFMQELIVDNL 455
>gnl|CDD|150299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 31.4 bits (72), Expect = 0.98
Identities = 27/100 (27%), Positives = 49/100 (49%), Gaps = 7/100 (7%)
Query: 82 FGIASVFFLPPPTMWALSLLFDKKIYCFSKRATAWLINIL--VSATFFASFSPSQSWPIQ 139
GI++V LP L LL +K+ Y + IN L ++ SF+ +Q +
Sbjct: 224 GGISAVVLLPT----VLGLLNNKRAYTEVSILLTFDINPLDLLAKLLIGSFNFTQMGGLP 279
Query: 140 NGFGGIIGDLIIRLPFLFFESYPRKLGILFFQMILFLAMS 179
N + G++ L++ + + F + K +LF ++LFL +S
Sbjct: 280 NIYVGLLP-LLLLILYFFNKLIKLKEKLLFALLLLFLILS 318
>gnl|CDD|183378 PRK11913, phhA, phenylalanine 4-monooxygenase; Reviewed.
Length = 275
Score = 31.4 bits (72), Expect = 1.0
Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 17/73 (23%)
Query: 574 TGEAIYETEH-------FDFQHM---PY-------IVVVIDEMADLMMVARKDIESAVQR 616
GE +Y E FD + + PY VID L +A D + V R
Sbjct: 196 PGETLYALESDSPNRRPFDLERVMRTPYRIDIFQPTYFVIDSFEQLFDIAEPDFMALVAR 255
Query: 617 LAQMARASGIHVI 629
Q+ + V
Sbjct: 256 AKQLGLFAPGFVP 268
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 31.1 bits (71), Expect = 1.3
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 459 IAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMID 493
I G TG+GKS IN LL R+ Q I+ID
Sbjct: 366 IVGPTGAGKSTLIN-----LLQRVFDPQSGRILID 395
>gnl|CDD|118392 pfam09862, DUF2089, Protein of unknown function(DUF2089). This
domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 113
Score = 30.7 bits (70), Expect = 1.6
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 747 VDIVLRDNKASISYIQRRLGIGY----NRAASIIENMEEKGVIGPASSTGKREIL 797
V++ ++ + +I +++ LGI Y NR II + + P K+EIL
Sbjct: 42 VELFIK-CRGNIKEVEKELGISYPTVRNRLDEIIAALGYEEEPEPEKRVDKKEIL 95
>gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 30.5 bits (70), Expect = 1.8
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 452 ARMPHLLIAGTTGSGKSVAINTM 474
A M +++ G +G+GKSVA+ +
Sbjct: 4 APMRLVIVTGLSGAGKSVALRAL 26
>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 30.0 bits (68), Expect = 2.4
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 448 IADLARMPHLLIAGTTGSGKSVAI 471
D +PHLL+ G GSGK+ A+
Sbjct: 30 AVDSPNLPHLLVQGPPGSGKTAAV 53
>gnl|CDD|184806 PRK14725, PRK14725, pyruvate kinase; Provisional.
Length = 608
Score = 29.9 bits (68), Expect = 2.5
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 9/39 (23%)
Query: 604 MVARKD--IESAVQRLAQ-------MARASGIHVIMATQ 633
M+AR D +E +RLA+ + A+ + VI ATQ
Sbjct: 505 MIARGDLAVEVGFERLAEVQEEILWLCEAAHVPVIWATQ 543
>gnl|CDD|178776 PLN03238, PLN03238, probable histone acetyltransferase MYST;
Provisional.
Length = 290
Score = 29.8 bits (67), Expect = 2.7
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 594 VVIDEMADLMMVARKDIESAVQRLAQMARASGIHVIMATQR 634
V I +++ + +DI S +Q L + G HVI QR
Sbjct: 224 VSIKDLSLATGIRGEDIVSTLQSLNLIKYWKGQHVIHVDQR 264
>gnl|CDD|182240 PRK10098, PRK10098, putative dehydrogenase; Provisional.
Length = 350
Score = 29.6 bits (67), Expect = 3.0
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 181 LLIYSSSAIFQGKRRVPYNM-----ADCLISDESKTQLE-DVMASSLL 222
LL +++SAI GK RV +N CLI + VM S L
Sbjct: 178 LLDFATSAIAFGKTRVAWNKGVPVPPGCLIDVNGVPTTDPAVMQESPL 225
>gnl|CDD|130947 TIGR01892, AcOrn-deacetyl, acetylornithine deacetylase (ArgE).
This model represents a clade of acetylornithine
deacetylases from proteobacteria. This enzyme is the
final step of the "acetylated" ornithine biosynthesis
pathway. The enzyme is closely related to dapE,
succinyl-diaminopimelate desuccinylase, and outside of
this clade annotation is very inaccurate as to which
function should be ascribed to genes.
Length = 364
Score = 29.4 bits (66), Expect = 3.4
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)
Query: 350 GEIVNVRPGPVITLYELEPAPGIKSSRIIGLSDDIARSMSAIS-ARVAVIPRRNAI-GIE 407
G+ VN+ PG ++E P PG+ ++ L + IA+++ I + G+
Sbjct: 233 GKAVNIIPGACEFVFEWRPIPGMDPEELLQLLETIAQALVRDEPGFEVQIEVVSTDPGVN 292
Query: 408 LPNDIRETVMLRDL 421
D L +L
Sbjct: 293 TEPDAELVAFLEEL 306
>gnl|CDD|162351 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation.
Length = 343
Score = 29.2 bits (66), Expect = 4.4
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 446 PIIADLARMPH--LLIAGTTGSGKSVAINTMI 475
P++ +LA P +L+ G TGSGKS + +MI
Sbjct: 112 PVLRELAERPRGLILVTGPTGSGKSTTLASMI 143
>gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity.
Length = 512
Score = 29.3 bits (66), Expect = 4.4
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 11/85 (12%)
Query: 597 DEMADLMMVARKDIE---SAVQRLAQMARASGIHVIMATQRPSVDVITGTIKANFPTRIS 653
++A+L+ AR + S +++LAQ G + A + +V T R+
Sbjct: 18 AKLAELLKAARDKLSKLKSQLEQLAQPPSTYGTFLQTAIDDETAEVFTAG------RRMR 71
Query: 654 FQVSSKIDSRTILGEQGAEQLLGQG 678
VS +++ ++ G L +
Sbjct: 72 VTVSPNVNAAELV--PGQTVRLNEA 94
>gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. At position
126-127 of the seed alignment, this family lacks the HM
motif of gamma/tau; at 132 it has a near-invariant A vs.
an invariant F in gamma/tau.
Length = 188
Score = 29.1 bits (66), Expect = 4.8
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 9/48 (18%)
Query: 453 RMPH-LLIAGTTGSGKSVAINTMILSLLYRM--------TPAQCRLIM 491
R+ H L AG G GK + + +LL CRLI
Sbjct: 12 RLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIE 59
>gnl|CDD|114590 pfam05872, DUF853, Bacterial protein of unknown function (DUF853).
This family consists of several bacterial proteins of
unknown function. One member from Brucella melitensis is
thought to be an ATPase.
Length = 504
Score = 28.9 bits (65), Expect = 5.4
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 456 HLLIAGTTGSGKSVAINTMILSL 478
H LIAG TG+GK+V + + S
Sbjct: 23 HGLIAGATGTGKTVTLQVLAESF 45
>gnl|CDD|165253 PHA02943, PHA02943, hypothetical protein; Provisional.
Length = 165
Score = 28.7 bits (64), Expect = 5.7
Identities = 8/35 (22%), Positives = 20/35 (57%)
Query: 751 LRDNKASISYIQRRLGIGYNRAASIIENMEEKGVI 785
L D + S I +LG+ ++ A + + + ++G++
Sbjct: 20 LADGCKTTSRIANKLGVSHSMARNALYQLAKEGMV 54
>gnl|CDD|178040 PLN02420, PLN02420, endoglucanase.
Length = 525
Score = 28.8 bits (64), Expect = 6.0
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 10/50 (20%)
Query: 744 KQAVDIVLRDNKASISYIQRRLGIG-------YNRAASIIENMEEKGVIG 786
K +D +L N SY+ +G G ++R ASI E KG IG
Sbjct: 400 KSQIDYILGSNPMETSYL---VGYGPKYPTRVHHRGASIASFKEHKGFIG 446
>gnl|CDD|162115 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 28.8 bits (65), Expect = 6.1
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 456 HLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMID 493
H LI G TGSGK+ +N +L+ + + + D
Sbjct: 436 HTLIFGPTGSGKTTLLN-FLLAQMQKYGGM--TIFAFD 470
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 28.7 bits (64), Expect = 6.3
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 6/45 (13%)
Query: 457 LLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMIDPKMLELSV 501
+L+ G TGSGK+ T+I ++ P Q RLI I+ LEL +
Sbjct: 165 MLLCGPTGSGKTTMSKTLISAI-----PPQERLITIE-DTLELVI 203
>gnl|CDD|182098 PRK09828, PRK09828, putative fimbrial outer membrane usher protein;
Provisional.
Length = 865
Score = 28.6 bits (64), Expect = 7.3
Identities = 28/93 (30%), Positives = 40/93 (43%), Gaps = 20/93 (21%)
Query: 369 APGIKSSRIIGLSDDIARS----MSAISARVAVIPRRNAIGI---ELPNDI-----RETV 416
APG K +RI + I R SA+S R N + + L ND+
Sbjct: 705 APGAKGARINYGNSTIDRWGYGVTSALSPY-----RENRVALDINTLENDVELKSTSAVA 759
Query: 417 MLRD-LIVSRVFEKNQCDLAI-NLGKSIEGKPI 447
+ R +V FE +Q AI N+ +S +GK I
Sbjct: 760 VPRQGAVVLADFETDQGRSAIMNITRS-DGKNI 791
>gnl|CDD|177721 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 28.5 bits (64), Expect = 7.8
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 593 VVVIDEMADLMMVARKDIESAVQRLAQMARASGIHVIMATQR 634
+ I E++D+ + +DI S +Q L + G HVI A +
Sbjct: 374 NISIKELSDMTAIKAEDIVSTLQSLNLIQYRKGQHVICADPK 415
>gnl|CDD|131777 TIGR02730, carot_isom, carotene isomerase. Members of this family,
including sll0033 (crtH) of Synechocystis sp. PCC 6803,
catalyze a cis-trans isomerization of carotenes to the
all-trans lycopene, a reaction that can also occur
non-enzymatically in light through photoisomerization.
Length = 493
Score = 28.2 bits (63), Expect = 7.9
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 12/78 (15%)
Query: 372 IKSSRIIGLSDD-----IARSMSAISARVAVIPRRNAIGIELPNDIRETVMLRDLIVSRV 426
+ +S I G D + R+++A+ ++ IP I LPN + ++ V R
Sbjct: 51 VGASMIFGFGDKGTTNLLTRALAAVGRKLETIPDPVQIHYHLPNGL-------NVKVHRE 103
Query: 427 FEKNQCDLAINLGKSIEG 444
++ +L EG
Sbjct: 104 YDDFIQELVAKFPHEKEG 121
>gnl|CDD|181993 PRK09616, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 552
Score = 28.2 bits (64), Expect = 8.0
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 12/46 (26%)
Query: 753 DNKASISYIQRRLGIGYN------------RAASIIENMEEKGVIG 786
+ K+ + + R LGI Y R A I+ N ++ GVIG
Sbjct: 477 EIKSVVQALLRELGIEYEVEESEHPSFIPGRCADILVNGKKIGVIG 522
>gnl|CDD|115248 pfam06578, YscK, YOP proteins translocation protein K (YscK). This
family consists of several YscK proteins. The function
of this protein is unknown but it belongs to an operon
involved in the secretion of Yop proteins across
bacterial membranes.
Length = 206
Score = 28.1 bits (63), Expect = 8.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 663 RTILGEQGAEQLLGQGDML 681
+LGE+G LL QGD+L
Sbjct: 101 NNLLGEEGHRFLLQQGDLL 119
>gnl|CDD|129495 TIGR00400, mgtE, Mg2+ transporter (mgtE). This family of
prokaryotic proteins models a class of Mg++ transporter
first described in Bacillus firmus. May form a
homodimer.
Length = 449
Score = 28.3 bits (63), Expect = 8.5
Identities = 29/126 (23%), Positives = 49/126 (38%), Gaps = 27/126 (21%)
Query: 102 FDKKIYCFSKRATAWLINILVSATFFASFSPSQS------------WPIQNGFGGIIGD- 148
FD I +K WL+ +LVS+TF A+ + P+ G G
Sbjct: 273 FDTSILVMAKNRIIWLLVLLVSSTFTATIISNYEDLLLSLVALANFIPLLMDTSGNAGSQ 332
Query: 149 ---LIIRLPFL-------FFESYPRKLGILFFQMILFLAMSWLLIYSSSAIFQGKRRVPY 198
++IR L FF+ R++ + IL A+ + + FQGK + +
Sbjct: 333 SSAVVIRGLALETVKVKDFFKVILREICV----SILVGAILASVNFLRIVFFQGKLLIAF 388
Query: 199 NMADCL 204
++ L
Sbjct: 389 VVSSSL 394
>gnl|CDD|130326 TIGR01259, comE, comEA protein. This model describes the ComEA
protein in bacteria. The com E locus is obligatory for
bacterial cell competence - the process of internalizing
the exogenous added DNA. Lesions in the loci has been
variously described for the appearance of
competence-related pheonotypes and impairment of
competence, suggesting their intimate functional role in
bacterial transformation.
Length = 120
Score = 28.3 bits (63), Expect = 8.6
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 722 DKILLNEEMRFSENSS---VADDLYK-QAVDIVLRDNKASISYIQRRLGIGYNRAASIIE 777
D++ + M+ E S K AV+I N AS+ +Q GIG +A +IIE
Sbjct: 31 DEMFVYVPMKGEEAVSQQGTQSSAGKLAAVNI----NAASLEELQALPGIGPAKAKAIIE 86
Query: 778 NMEEKG 783
EE G
Sbjct: 87 YREENG 92
>gnl|CDD|163021 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 28.1 bits (63), Expect = 8.7
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 20/59 (33%)
Query: 434 LAINLGKSIEGKPIIADLARMPHLLIAGTTGSGKSVAINTMILSLLYRMTPAQCRLIMI 492
LAI K+I +I+G TGSGK T L L P R+I I
Sbjct: 139 LAIASRKNI---------------IISGGTGSGK-----TTFLKSLVDEIPKDERIITI 177
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 0.137 0.398
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 13,220,826
Number of extensions: 896323
Number of successful extensions: 2116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2107
Number of HSP's successfully gapped: 76
Length of query: 806
Length of database: 5,994,473
Length adjustment: 101
Effective length of query: 705
Effective length of database: 3,812,065
Effective search space: 2687505825
Effective search space used: 2687505825
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: 61 (27.3 bits)