RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780229|ref|YP_003064642.1| hypothetical protein
CLIBASIA_00570 [Candidatus Liberibacter asiaticus str. psy62]
(1775 letters)
>gnl|CDD|161845 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT). A
number of related proteins are characterized as
helicases.
Length = 637
Score = 66.4 bits (162), Expect = 6e-11
Identities = 65/297 (21%), Positives = 116/297 (39%), Gaps = 69/297 (23%)
Query: 1358 KDVKFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVA 1417
K +FD+ ++DE+SQ L + + +++++ GD KQLPPT HD ++
Sbjct: 358 KGWEFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPPT-ILSHDAEE-------- 408
Query: 1418 AVSQTESILDALLPLFSMRR--LQWHYRSLNENLIACSNYYFYDNSLIVFPS-------- 1467
++ + L+ + R L YR +N+ ++ + FY+ L S
Sbjct: 409 ---LELTLFERLIKEYPERSRTLNVQYR-MNQKIMEFPSREFYNGKLTAHESVANILLRD 464
Query: 1468 -----------------PYTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDHALRY 1510
P +D G +K + NP EA +++ ++ ++
Sbjct: 465 LPKVEATDSEDDLETEIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQA-LVKM 523
Query: 1511 --PEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDE 1568
P +GVI Q DL+ + + ++E + +++ QG E
Sbjct: 524 GVPANDIGVITPYDAQVDLLRQLLEH---RHIDIE--------------VSSVDGFQGRE 566
Query: 1569 RDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625
++ I ISF R G + RRLNV TR+RR++ V R L
Sbjct: 567 KEVIIISFVRS---------NRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSN 614
Score = 60.6 bits (147), Expect = 4e-09
Identities = 67/296 (22%), Positives = 119/296 (40%), Gaps = 43/296 (14%)
Query: 316 IEESKSHWAVRRYGVLGLLNFSKMLMYLDLDHLRWPEGEDNIL-NHDIIQRLFIAQSCDH 374
+EES W+++R + N D+ R E + NH + + +
Sbjct: 92 LEESVPQWSLKRVRIDLYAN--------DVTFKRMKEALRALTENHSRLLEFILGREAPS 143
Query: 375 DKDNASSNQNIEYKIDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNL-IIEGPPGTGKS 433
Q + ++E SQ AV ++ K+L +I GPPGTGK+
Sbjct: 144 KASEIHDFQFFDPNLNE----------------SQKEAVSFALSSKDLFLIHGPPGTGKT 187
Query: 434 QTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLEL-HSHKVHKRAILDD 492
+T+ +I + G ++L A A++ + RL A + + L H ++ K
Sbjct: 188 RTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERL--ALCDQKIVRLGHPARLLKSNKQHS 245
Query: 493 LRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTELSIHQILMGAAR-- 550
L I+N + +I +I +EL + N+ + Q + LS +IL A +
Sbjct: 246 LDYLIENHPKYQIVADIREKI---DELIEERNKKLKPSPQKRRG--LSDIKILRKALKKR 300
Query: 551 -YRHNLPLDPVQLHVEGLSGENADRLLRS------RLEDQIKAFKDVIVEFHKQAG 599
R L + + ++ DRLL+ R+E++I A DV+ + AG
Sbjct: 301 EARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVVQSTNSSAG 356
>gnl|CDD|162366 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD.
Length = 720
Score = 39.8 bits (93), Expect = 0.006
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 406 DSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIA-AAMLHG-KKILFCA 454
Q A+ I K +I+ G PGTGK+ II A L G + A
Sbjct: 325 SEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAA 375
Score = 30.9 bits (70), Expect = 3.0
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 1350 SVANYLEPKDVKFDLVIMDESSQIKPEDA---LGVIARGKQIVVVGDPKQLPP 1399
N+LE + DL+I+DESS + A L + ++++VGD QLP
Sbjct: 406 FRHNHLEDP-IDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPS 457
>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 = 37.0 bits (85), Expect = 0.042
Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 25/166 (15%)
Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLE 478
G+ ++I GPPG+GK+ + G +++ + EV+ L G+
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKK--- 58
Query: 479 LHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTE 538
L + +D EIT + + + E ++ +
Sbjct: 59 ---ASGSGELRLRLALALARKLKPDVLI--LD-EITSLLDAEQEALLLLLEELRLLLLLK 112
Query: 539 LSIHQILMGAARYRHNLPLDPVQLHVEGLSGENADRLLRSRLEDQI 584
+ ++ +L LLR R + +I
Sbjct: 113 SEKNLTVILTTNDEKDL----------------GPALLRRRFDRRI 142
>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 36.6 bits (85), Expect = 0.065
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 16/62 (25%)
Query: 421 NLIIEGPPGTGKSQTITNIIA----------AAMLHGKKILFCAQKMAAIEVVRHRLEKA 470
+LI+ GPPG GK+ T+ IIA A+L G K L A ++ + RLE+
Sbjct: 54 SLILYGPPGVGKT-TLARIIANHTRAHFSSLNAVLAGVKDL-----RAEVDRAKERLERH 107
Query: 471 GL 472
G
Sbjct: 108 GK 109
>gnl|CDD|184869 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
Length = 659
Score = 34.8 bits (80), Expect = 0.22
Identities = 47/199 (23%), Positives = 90/199 (45%), Gaps = 33/199 (16%)
Query: 979 FKRIQKLHCDELSKKITKVFGRIQELEQFLPKQKELQN-RSALFVGEGNVFDSLIQ-RLS 1036
++ + ELS+ TK RI+ELE+++ + L+N R ++F +D+++ L+
Sbjct: 251 SSKVSSMLNSELSRVTTK---RIKELEEYVLRDLLLENYRDSVF------WDTVVSCYLN 301
Query: 1037 HN----FDPWQNWFKEDEI-----LLQEAQEFSAKLHKIREKNIVLAEESLIKKFFGEEI 1087
+ FD + ++F + EI L+ E +L K +V+ E L K EEI
Sbjct: 302 FDFTKYFDKYGHYFDKKEIEDVKMLINGLPESLGELKTYCLKYLVM--EYLFNKLDEEEI 359
Query: 1088 KLSVFDSNTKESNKSLAVINSTLEFAH-SIRERVLFDELIQGINHIDDHTIYNSFIKDLK 1146
K + N + +E+A + L DE + + +I F+K+LK
Sbjct: 360 K--------EIKNHFKKKPENFMEWAEKNYLNASLLDEFRKKVKNITKSP--EEFVKELK 409
Query: 1147 NLRMIWQQQVKTQEDFIED 1165
+ M+ ++++ I+D
Sbjct: 410 DKAMVSDEELEKYRKEIKD 428
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 33.4 bits (76), Expect = 0.50
Identities = 22/102 (21%), Positives = 48/102 (47%), Gaps = 15/102 (14%)
Query: 1060 SAKLHKIREKNIVLAE---ESLIKKFFGEEI---KLSVFDSNTKESNKSLAVINSTLEFA 1113
S K+ +++E ++ E + L+ + E + K + D T+ L I+
Sbjct: 273 SRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHD----- 327
Query: 1114 HSIRERVLFDELIQGINHIDDHTIYNSFIKDLKNLRMIWQQQ 1155
++E V+ ++L G D +I +SF D ++L+++ Q +
Sbjct: 328 LGVQEFVIINDLALGH----DASIIHSFSADSESLKLLKQTE 365
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 33.2 bits (76), Expect = 0.62
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 20/85 (23%)
Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMA----------AIEVVRHRL 467
N NLI+ GPPGTGK+ T+I+A A ++L K A I+VVR+++
Sbjct: 33 NMPNLILSGPPGTGKT---TSILALA----HELLGPNYKEAVLELNASDDRGIDVVRNKI 85
Query: 468 EKAGLGEFCLELHSHKVHKRAILDD 492
+ + L HK+ ILD+
Sbjct: 86 KMFAQKKVTLPPGRHKI---VILDE 107
>gnl|CDD|148013 pfam06152, Phage_min_cap2, Phage minor capsid protein 2. Family of
related phage minor capsid proteins.
Length = 361
Score = 32.0 bits (73), Expect = 1.3
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 140 IREIEKKIEISLQKLTSIIQNYGYADIEDLERAIKE--NKPLKPPHFQNNLSDNQIQTAY 197
I+ I K ++ + +T +I+N G I+D+++ + E NK L N +
Sbjct: 65 IKLIAKYTGVAEEAITRVIKNAGLKIIKDIDKQLSEALNKGLGADPESNFQTIVDKVLNA 124
Query: 198 FQDKLESILRLIN 210
+Q + S L L+N
Sbjct: 125 YQRQAWSDLNLVN 137
>gnl|CDD|163008 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA. This
protein contains domains distinctive of a single strand
exonuclease (N-terminus, MobA/MobL, pfam03389) as well as
a helicase domain (central region, homologous to the
corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 31.7 bits (72), Expect = 1.5
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 1363 DLVIMDESSQIKPEDALGVIA----RGKQIVVVGDPKQLPP 1399
D++++DE+ + V+ G ++V+VGDP+QL P
Sbjct: 441 DVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQP 481
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 31.8 bits (72), Expect = 1.6
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
G NL++ GPPG GKS I A + +G ++LF
Sbjct: 105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLF 139
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 31.8 bits (72), Expect = 1.7
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 406 DSSQHSAVIDVINGK-NLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
D+ H +D + GK N++ GPPGTGK+ + A G ++LF
Sbjct: 84 DTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF 131
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 31.6 bits (73), Expect = 1.9
Identities = 13/24 (54%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 421 NLIIEGPPGTGKSQTITNIIAAAM 444
++I+ GPPGTGK+ T+ IIA A
Sbjct: 38 SMILWGPPGTGKT-TLARIIAGAT 60
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 31.5 bits (72), Expect = 2.0
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 9/55 (16%)
Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRHRLEK 469
I G+ ++I GPPGTGK+ +A A+ G+ FC ++ EV ++K
Sbjct: 48 IAGRAVLIAGPPGTGKTA-----LAIAISKELGEDTPFCP--ISGSEVYSLEMKK 95
>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli.
Length = 850
Score = 31.3 bits (71), Expect = 2.1
Identities = 53/246 (21%), Positives = 86/246 (34%), Gaps = 46/246 (18%)
Query: 977 QLFKRIQKLHCDELSKKI----TKVFGRIQELEQFLPKQKELQNRSALFVGEGNVFDSLI 1032
QL KRIQ+L E+ +K+ TK + + K LQ S L D L
Sbjct: 483 QLLKRIQQLEKQEILEKLFDFETKDILKDLQAIL-DKLNKLLQIFSELSH---KTVDQLR 538
Query: 1033 ---QRLSHNFDPWQNWFKEDEILLQEAQEFSAKLHKIREKNIVLAEESLIKKFFGEEIKL 1089
L +F + KE + K + L K+
Sbjct: 539 KFDLALKDDFKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLL------ 592
Query: 1090 SVFDSNTKESNKSLAVINSTLEFAHSIRERVLFDELIQGINHIDDH--TIYNSFIKDLKN 1147
KSL ++TL+F+HS F+ Q + D H TI + + +N
Sbjct: 593 --------PKFKSLIFTSATLKFSHS------FESFPQLLGLTDVHFNTIEPTPLNYAEN 638
Query: 1148 LRMIWQQQVKTQEDFIEDTQLDMAQWAARCNDELVKLISRNSEAIKKPRWLNGWVN--LM 1205
Q+V D + ++A ++++ AI P+ L + + ++
Sbjct: 639 ------QRVLIPTDAPAIQNKSLEEYAQEIASYIIEI-----TAITSPKILVLFTSYEML 687
Query: 1206 HMVQDM 1211
HMV DM
Sbjct: 688 HMVYDM 693
>gnl|CDD|180288 PRK05850, PRK05850, acyl-CoA synthetase; Validated.
Length = 578
Score = 31.5 bits (72), Expect = 2.3
Identities = 34/112 (30%), Positives = 47/112 (41%), Gaps = 29/112 (25%)
Query: 1463 IVFPSPYTSVD---RYG-VGFTH---------VKNGVVVDQGN--PE--EA--------R 1497
+V PSP T R G +GF +K+ ++VD N P+ EA R
Sbjct: 426 LVDPSPGTPEGPWLRTGDLGFISEGELFIVGRIKDLLIVDGRNHYPDDIEATIQEITGGR 485
Query: 1498 VIALAVKDHALRYPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKL 1549
V A++V D E L I K+ D E +++L EV AISK
Sbjct: 486 VAAISVPDDG----TEKLVAIIELKKRGDSDEEAMDRLRTVKREVTSAISKS 533
>gnl|CDD|128765 smart00489, DEXDc3, DEAD-like helicases superfamily.
Length = 289
Score = 31.2 bits (71), Expect = 2.4
Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 31/119 (26%)
Query: 418 NGKNLIIEGPPGTGKSQT-ITNIIAAAMLHGKKILFCAQKMAAIEVVR--HRLEKAGLGE 474
GK I+E P GTGK+ + + + ++I QK+ I + R +EK
Sbjct: 26 RGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI----QKIKLIYLSRTVSEIEKR---- 77
Query: 475 FCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQI 533
L++LRK + E D E + +L +L + ++ +
Sbjct: 78 ---------------LEELRKLMQKV-----EYESDEESEKQAQLLHELGREKPKVLGL 116
>gnl|CDD|128764 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 31.2 bits (71), Expect = 2.4
Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 31/119 (26%)
Query: 418 NGKNLIIEGPPGTGKSQT-ITNIIAAAMLHGKKILFCAQKMAAIEVVR--HRLEKAGLGE 474
GK I+E P GTGK+ + + + ++I QK+ I + R +EK
Sbjct: 26 RGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI----QKIKLIYLSRTVSEIEKR---- 77
Query: 475 FCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQI 533
L++LRK + E D E + +L +L + ++ +
Sbjct: 78 ---------------LEELRKLMQKV-----EYESDEESEKQAQLLHELGREKPKVLGL 116
>gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional.
Length = 188
Score = 31.4 bits (72), Expect = 2.4
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 439 IIAAAMLHGKKILFC--------AQKMAAIEVVRHRLEKAGL 472
+ A+ +G KIL C AQ +AA V R + E+ L
Sbjct: 30 ALIEALANGGKILLCGNGGSAADAQHIAAELVGRFKKERPAL 71
>gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model.
Length = 586
Score = 30.9 bits (70), Expect = 3.1
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAA 442
Q AV + +I G PGTGK+ T+ ++ A
Sbjct: 150 QKVAVALALKSNFSLITGGPGTGKTTTVARLLLA 183
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 30.9 bits (70), Expect = 3.4
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
+ G G GKS T+ NI AA GKK+L
Sbjct: 2 RKFCFYGKGGIGKSTTVCNIAAALAESGKKVL 33
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 30.8 bits (70), Expect = 3.7
Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 22/105 (20%)
Query: 1135 HTIYNSFIKDLKNLRMIWQQQVKTQEDFIEDTQLDMAQWAARCNDELVKLISRNSEAIKK 1194
H Y D ++ + W LD+ ++ +K +S +
Sbjct: 30 HATYRHHKPDFQHDNVQWHA-------------LDV------TDEAEIKQLSEQFTQLD- 69
Query: 1195 PRWLNGWVNLMHMVQDMQDKGLKEIQAAIFNNSLDVKYLESSLLA 1239
WL V ++H +K L+ + A F ++ + L S LLA
Sbjct: 70 --WLINCVGMLHTQDKGPEKSLQALDADFFLQNITLNTLPSLLLA 112
>gnl|CDD|153048 pfam12614, RRF_GI, Ribosome recycling factor. This family of
proteins is found in bacteria and viruses. Proteins in
this family are approximately 130 amino acids in length.
There are two conserved sequence motifs: LPS and LKR.
Overproduction of ribosome recycling factor (RRF) reduces
tna operon expression and increases the rate of cleavage
of TnaC-tRNA(2)(Pro), relieving the growth inhibition
associated with plasmid-mediated tnaC overexpression.
Length = 128
Score = 30.4 bits (69), Expect = 3.9
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 1725 DRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELRELISQKSSST 1773
D+L+ E E + IR+I + + +EP+ +L LI Q + T
Sbjct: 58 DQLKTEEYEEFRYLIRKIEAA--LLLHSDKLEPLEDKLIRLIPQNPNIT 104
>gnl|CDD|161955 TIGR00608, radc, DNA repair protein radc. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 218
Score = 30.5 bits (69), Expect = 4.2
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 15/69 (21%)
Query: 627 SSLENWQSALIKWQKD--HE-------VFLNRYGVQNQRQRLLYWQGQLLAAVDQVPSLP 677
+ + ++A D HE +FL+R + RL+ + + V+ VP P
Sbjct: 95 PVIRSPEAAAEFLHTDLAHETREHFMVLFLDR------KNRLIAKEVVFIGTVNHVPVHP 148
Query: 678 RVICFKAFK 686
R I +A K
Sbjct: 149 REIFKEALK 157
>gnl|CDD|162286 TIGR01287, nifH, nitrogenase iron protein. This model describes
nitrogenase (EC 1.18.6.1) iron protein, also called
nitrogenase reductase or nitrogenase component II. This
model includes molybdenum-iron nitrogenase reductase
(nifH), vanadium-iron nitrogenase reductase (vnfH), and
iron-iron nitrogenase reductase (anfH). The model
excludes the homologous protein from the
light-independent protochlorophyllide reductase.
Length = 275
Score = 30.4 bits (69), Expect = 4.3
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
+ + I G G GKS T NI AA GKK++
Sbjct: 1 RQIAIYGKGGIGKSTTTQNIAAALAEMGKKVM 32
>gnl|CDD|183073 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 30.3 bits (69), Expect = 4.4
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 12/50 (24%)
Query: 15 DMRRKLLDCSVQ-NKLL--------NFRMDQQSVLRIFNTSPNQLYQQIF 55
D RR+LLD Q NK L N +++QQ +L + ++ + L QQIF
Sbjct: 410 DERRELLD---QLNKQLNNQLNLAINLQLNQQQLLSVSDSLQSTLTQQIF 456
>gnl|CDD|178717 PLN03173, PLN03173, chalcone synthase; Provisional.
Length = 391
Score = 30.4 bits (68), Expect = 4.5
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 1234 ESSLLAAIYHQLSQEILTEKPHLMHYSAVQFTAKQE 1269
E S++ Y L++EIL E P + Y A A+Q+
Sbjct: 61 EKSMIKKRYMHLTEEILKENPSVCEYMAPSLDARQD 96
>gnl|CDD|182067 PRK09767, PRK09767, hypothetical protein; Provisional.
Length = 117
Score = 30.4 bits (68), Expect = 4.6
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIREL 1762
+E DG ++ A + R R LE GW + R W+ + N + V+E I++EL
Sbjct: 59 VELDGGQHDLAVAYDTR---RTSWLESQGWTVLRFWNNEIDCNEEAVLEIILQEL 110
>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 30.0 bits (68), Expect = 5.0
Identities = 19/91 (20%), Positives = 47/91 (51%), Gaps = 17/91 (18%)
Query: 107 EYDSDDEKKNYQVLQKVRDL----------IVEDIKTSNDLV-DIREIEKKI---EISLQ 152
+Y+ ++ +K + +K+++ + ++++ +L + E+EKK+ E L
Sbjct: 514 KYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELA 573
Query: 153 KLTSIIQNYGYADIEDLERAIKENKPLKPPH 183
+L ++ G+ +E+LE +KE L+P +
Sbjct: 574 ELLKELEELGFESVEELEERLKE---LEPFY 601
>gnl|CDD|185348 PRK15451, PRK15451, tRNA cmo(5)U34 methyltransferase; Provisional.
Length = 247
Score = 30.0 bits (67), Expect = 5.6
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 1100 NKSLAVINSTLEFAHSIRERVLFDELIQGIN 1130
N S+ V+N TL+F + L D++ QG+N
Sbjct: 125 NASMVVLNFTLQFLEPSERQALLDKIYQGLN 155
>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 = 29.9 bits (68), Expect = 5.7
Identities = 8/32 (25%), Positives = 18/32 (56%)
Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
++++I G GTGK+Q + ++ G + +
Sbjct: 16 QHILIVGTTGTGKTQALRELLDQIRARGDRAI 47
>gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide
reductase, iron-sulfur ATP-binding protein. The BchL
peptide (ChlL in chloroplast and cyanobacteria) is an
ATP-binding iron-sulfur protein of the dark form
protochlorophyllide reductase, an enzyme similar to
nitrogenase. This subunit resembles the nitrogenase NifH
subunit.
Length = 268
Score = 29.8 bits (67), Expect = 5.9
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
L + G G GKS T +N+ A GK++L
Sbjct: 3 LAVYGKGGIGKSTTSSNLSVAFAKLGKRVL 32
>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 = 29.9 bits (67), Expect = 6.0
Identities = 24/176 (13%), Positives = 51/176 (28%), Gaps = 8/176 (4%)
Query: 515 RYEELKGQLNQYAQEINQIWKNTELSIHQILMGAARYRHNLPLDPVQLHVEGLSGENADR 574
K Q Q Q++ + + L + L + V+ H + R
Sbjct: 615 HALLRKLQPEQDLQDVRLHLQQCSQELALKLTALHALQLTLTQERVREHAL------SIR 668
Query: 575 LLRSRLEDQIKAFKDVIVEFHKQAGESMELMNHPWYGVHSSDIHILNYNKALSSLENWQS 634
+L L + + +Q E++ + + HI Y++ + +EN S
Sbjct: 669 VLPKELLASRQLALQKMQSEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFNEIENASS 728
Query: 635 ALIKWQKDHEVFLNRYGVQNQRQRLLYWQGQLLAAVDQVPSLPRVICFKAFKKLED 690
+L E LN+ + + + + +L
Sbjct: 729 SLGSDLAAREDALNQ--SLKELMHQARTVLKARTEAHFNNNEEVTAALQTGAELSH 782
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 30.0 bits (68), Expect = 6.0
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 421 NLIIEGPPGTGKSQTITNIIAAAM 444
+++ GPPGTGKS + +AAA+
Sbjct: 1 GVLLVGPPGTGKS-ELAERLAAAL 23
>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.9 bits (68), Expect = 6.8
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 386 EYKIDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNLI--IEGPPGTGKSQTITNIIAAA 443
+Y+ +EIE +H+ PL+ + A + + I I GPPG GKS T+ + A
Sbjct: 6 QYRDEEIEAVHK--PLL------RRLAALQAEPQRRTIVGIAGPPGAGKS-TLAEFLEAL 56
>gnl|CDD|182715 PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA;
Provisional.
Length = 413
Score = 29.7 bits (67), Expect = 7.0
Identities = 34/133 (25%), Positives = 54/133 (40%), Gaps = 38/133 (28%)
Query: 434 QTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAILDDL 493
Q I NI AQ ++ +R RL GL + +++ K I+ ++
Sbjct: 80 QAIANI-------------AAQNNMTLDQMRSRLAYDGLN---YNTYRNQIRKEMIISEV 123
Query: 494 RKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEI-NQIWKNTELSIHQILMGAARYR 552
R R I +PQE+D A++I NQ +TEL++ IL+
Sbjct: 124 RNNEVRRRITILPQEVD--------------SLAKQIGNQNDASTELNLSHILI------ 163
Query: 553 HNLPLDPVQLHVE 565
LP +P Q V+
Sbjct: 164 -PLPENPTQDQVD 175
>gnl|CDD|181881 PRK09466, metL, bifunctional aspartate kinase II/homoserine
dehydrogenase II; Provisional.
Length = 810
Score = 29.5 bits (67), Expect = 7.1
Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 25/115 (21%)
Query: 950 YRKVHQIWKDNSSLDDALINGFLMLDS-------QLFKRIQKLHCDELSKKITKVFGRIQ 1002
YR+V I + S DD L++ S QL ++ D LS Q
Sbjct: 28 YRRVAGILAEYSQPDD------LVVVSAAGKTTNQLISWLKLSQTDRLSAHQV-----QQ 76
Query: 1003 ELEQFLPKQKELQNRSALFVGEGNVFDSLIQRLSHNFDPWQNWFKEDEILLQEAQ 1057
L ++ Q++L L SL+ RL + + Q A+
Sbjct: 77 TLRRY---QQDLI--EGLL--PAEQARSLLSRLISDLERLAALLDGGINDAQYAE 124
>gnl|CDD|163318 TIGR03545, TIGR03545, conserved hypothetical protein TIGR03545. This
model represents a relatively rare but broadly
distributed uncharacterized protein family, distributed
in 1-2 percent of bacterial genomes, all of which have
outer membranes. In many of these genomes, it is part of
a two-gene pair.
Length = 555
Score = 29.7 bits (67), Expect = 7.7
Identities = 23/125 (18%), Positives = 42/125 (33%), Gaps = 16/125 (12%)
Query: 900 WKKLYAQLPNAYQFAVEKEKLEKRNFGNTLGEHYRGLSTDIVALKNIREWYRKVHQIWKD 959
WKK LPN K++LE + + DI +++ + ++ K+
Sbjct: 180 WKKRKKDLPNKQDLEEYKKRLE------AIKK------KDIKNPLELQKIKEEFDKLKKE 227
Query: 960 NSSLDDALINGFLMLDSQLFKRIQKLHCDELSKKITKVFGRIQELEQFLPKQKELQNRSA 1019
D I K+++ EL K R++ K +L+N +
Sbjct: 228 -GKADKQKIKSAKNDLQNDKKQLKAD-LAELKKAPQNDLKRLENKYAI--KSGDLKNFAV 283
Query: 1020 LFVGE 1024
G
Sbjct: 284 DLFGP 288
>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 29.6 bits (67), Expect = 7.8
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 418 NGKNLIIEGPPGTGKSQTI 436
N +L+++GPPG+GK+ +
Sbjct: 35 NLPHLLVQGPPGSGKTAAV 53
>gnl|CDD|140295 PTZ00269, PTZ00269, variant surface glycoprotein; Provisional.
Length = 472
Score = 29.5 bits (66), Expect = 7.9
Identities = 19/44 (43%), Positives = 27/44 (61%), Gaps = 6/44 (13%)
Query: 1041 PW----QNWFKEDEILLQEAQEFSAKLHKIREKNIVLAEESLIK 1080
PW + E E+LLQ+ Q+ SAKL +I+E + + ESLIK
Sbjct: 325 PWMKALEKVENEMEVLLQDKQDKSAKLERIKELSQEI--ESLIK 366
>gnl|CDD|180003 PRK05302, PRK05302, 30S ribosomal protein S7; Validated.
Length = 156
Score = 29.7 bits (68), Expect = 7.9
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 432 KSQTITNIIAAAMLHGKKILFCAQKM--AAIEVVRHRLEKAGL 472
S +T I ML GKK + A+K+ A++++ + K L
Sbjct: 19 GSVLVTKFINKLMLDGKKSV--AEKIVYGALDIIEEKTGKDPL 59
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 29.3 bits (67), Expect = 8.0
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 426 GPPGTGKSQTITNIIAAAM 444
GPPG GK+ T+ NIIA M
Sbjct: 58 GPPGLGKT-TLANIIANEM 75
>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
Length = 234
Score = 29.6 bits (67), Expect = 8.3
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
++IEG GTGKS + A+ GKK+
Sbjct: 28 ILIEGDHGTGKSVLSQQFVYGALKQGKKVYV 58
>gnl|CDD|162859 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit. A number of
genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside from
the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins, so
do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 29.3 bits (66), Expect = 8.8
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 9/83 (10%)
Query: 1472 VDRYGVGFTHVKNGVVVDQGNPEEARV-------IALAVKDHALRYPEESLGVIAMN-AK 1523
V+R G+ +H V++ NPEE + L V A R PEE + +I A
Sbjct: 157 VEREGLSVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRRRLAF 216
Query: 1524 QRDLIESTINKLCRKDSEVEKAI 1546
D E+ + + E+ I
Sbjct: 217 DADP-EAFAARWAAEQEELRNRI 238
>gnl|CDD|185583 PTZ00375, PTZ00375, dihydroxyacetone kinase-like protein;
Provisional.
Length = 584
Score = 29.4 bits (66), Expect = 9.2
Identities = 11/46 (23%), Positives = 14/46 (30%), Gaps = 3/46 (6%)
Query: 890 LSLAKNPGISWKKLYAQLPN-AYQFAVEKEKLEKRNFGNTLGEHYR 934
L P SW A+ P A Q A + + R R
Sbjct: 336 LLNFHTPQSSWA--TAKGPLSALQLAKPEAEAASRKAATPTNSLLR 379
>gnl|CDD|179887 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 29.2 bits (66), Expect = 9.4
Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 21/100 (21%)
Query: 255 LEKRSSTSQPGLTQYHLRYTGEEIILNLSLKEKLQSDFGIILPAIAEGMWPEDYFLQIQK 314
L R S ++ Q + T E ++ +L +KL+ E DY ++++
Sbjct: 1065 LHARLSANRSRRNQLEKQLTFCEAEMD-NLTKKLRK---------LE----RDYH-EMRE 1109
Query: 315 IIEESKSHW-----AVRRYGVLGLLNFSKMLMYLDLDHLR 349
+ +K+ W V+ GV L+ + L YL D LR
Sbjct: 1110 QVVNAKAGWCAVLRLVKDNGVERRLH-RRELAYLSADELR 1148
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
0.319 0.136 0.397
Gapped
Lambda K H
0.267 0.0681 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 29,648,298
Number of extensions: 2032730
Number of successful extensions: 4945
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4932
Number of HSP's successfully gapped: 97
Length of query: 1775
Length of database: 5,994,473
Length adjustment: 107
Effective length of query: 1668
Effective length of database: 3,682,417
Effective search space: 6142271556
Effective search space used: 6142271556
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: 64 (28.5 bits)