RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|255764515|ref|YP_003065608.2| SNF2 related [Candidatus
Liberibacter asiaticus str. psy62]
(458 letters)
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 67.9 bits (166), Expect = 5e-12
Identities = 38/176 (21%), Positives = 67/176 (38%), Gaps = 13/176 (7%)
Query: 3 LAPHQTKIVDWILDHKR-CAIWASMGSGKT-VSVLTALSYIHLWGEKSVLVIAPLRVAQS 60
L P+Q + ++ +L R + A GSGKT ++L AL + K VLV+ P R
Sbjct: 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAE 68
Query: 61 VWTSEVQRWSNFSHMNISVITG---TVKQRTKVLKTPAVLYVINFENL-GWLVQELKGTW 116
W E+++ + + + G +Q K+ + V L L +L
Sbjct: 69 QWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELS 128
Query: 117 PFATIVVDES--TKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLW 170
+++DE+ F L K ++ + + L+ TP L
Sbjct: 129 NVDLVILDEAHRLLDGGFG-----DQLEKLLKLLPKNVQLLLLSATPPEEIENLLE 179
>gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 36.0 bits (84), Expect = 0.022
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 353 TIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIG 405
++++N GKI +L A GL+L G ++++ + L W + Q I R G
Sbjct: 29 ILEKFNNGKIKVLVA-TDVAERGLDLP-GVDLVIIYDLPWSPASYIQRIGRAG 79
>gnl|CDD|161952 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University).
Length = 732
Score = 34.4 bits (79), Expect = 0.059
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 27 GSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITGTVKQ 86
G+GK++ +TA + +KS LV+ V+ W + + WS I T K+
Sbjct: 283 GAGKSLVGVTAACTV----KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQICRFTSDAKE 338
Query: 87 R 87
R
Sbjct: 339 R 339
>gnl|CDD|134340 PRK00650, PRK00650, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 288
Score = 30.2 bits (68), Expect = 1.1
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 5/95 (5%)
Query: 366 FAHPASCGHGLNLQYGGNIL--VFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA---VFV 420
+ P+ C NL+Y N L F L DL+E + +E + G + +FV
Sbjct: 179 YVQPSDCSSRKNLEYTQNDLEKPVFRLRLDLKEKKHWLESLWAELPVHVGLTGSGATLFV 238
Query: 421 YYLIAQNTIDELVLQRLRTKSTIQDLLLNALKKET 455
Y Q R + LL + ++++
Sbjct: 239 RYPEILEKDPSYAAQIQRAITLSGGLLTSPIRRDP 273
>gnl|CDD|152224 pfam11788, MRP-L46, 39S mitochondrial ribosomal protein L46. This
is the L46 subunit of the mammalian mitochondrial
ribosome, conserved from plants and fungi.
Length = 113
Score = 30.3 bits (68), Expect = 1.2
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 17/78 (21%)
Query: 240 PILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEK 299
P++ P P P K ++K+Q EL L + F T+ E
Sbjct: 13 PVVT----PDPSPFEKAFYKYQAELLERLMWPFPKYFYFKKGTL-------------AEL 55
Query: 300 HWKEVHDEKIKALEVIIE 317
++E+ + ++ +
Sbjct: 56 RFRELQKKPVERDPGVAF 73
>gnl|CDD|178687 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 29.4 bits (66), Expect = 1.9
Identities = 53/210 (25%), Positives = 92/210 (43%), Gaps = 45/210 (21%)
Query: 26 MGSGKTVSVLTALSYIHLWGEKS--VLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITGT 83
MG GKT+ ++ L Y+H + + +V+AP + W +E++R+ + G
Sbjct: 197 MGLGKTLQTISLLGYLHEYRGITGPHMVVAP-KSTLGNWMNEIRRFCPV--LRAVKFHGN 253
Query: 84 VKQRTKVLKTPAV-----LYVINFENLGWLVQE----LKGTWPFATIVVDESTKLKSFRL 134
++R + V + V +FE ++E + +W + I++DE+ ++K+
Sbjct: 254 PEERAHQREELLVAGKFDVCVTSFE---MAIKEKTALKRFSWRY--IIIDEAHRIKNENS 308
Query: 135 RQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLGRVFQSF--VAR 192
SKT R + + R + +TGTP N L +LW + FL L +F S
Sbjct: 309 LL-SKTMRLFST----NYRLL-ITGTPLQNNLHELWALLNFL-----LPEIFSSAETFDE 357
Query: 193 WFNTTQIGSHIGAVRYTAKETAQKEIEAQL 222
WF QI E Q+E+ QL
Sbjct: 358 WF---QISG----------ENDQQEVVQQL 374
>gnl|CDD|171518 PRK12463, PRK12463, chorismate synthase; Reviewed.
Length = 390
Score = 29.3 bits (65), Expect = 2.2
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 312 LEVIIEKANAAPIIVAYHFNSDLARLQKAFPQGRTLDKDPCTIQ 355
L VI+E A + A H N +L R QK +GR + + T++
Sbjct: 14 LTVILEGVPAGLTLAAEHINKELLRRQKGHGRGRRMQIETDTVE 57
>gnl|CDD|162681 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions.
Length = 864
Score = 29.0 bits (65), Expect = 2.8
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 2/39 (5%)
Query: 215 QKEIEAQLSD--CCLSLDIADYQNIDKPILITKKVPLPQ 251
QK I+A +D ++++IA +++ K IL VP+P+
Sbjct: 192 QKRIQATETDRTSAIAVEIACDKDLTKEILSDAGVPVPE 230
>gnl|CDD|132509 TIGR03469, HonB, hopene-associated glycosyltransferase HpnB. This
family of genes include a glycosyl transferase, group 2
domain (pfam00535) which are responsible, generally for
the transfer of nucleotide-diphosphate sugars to
substrates such as polysaccharides and lipids. The genes
of this family are often found in the same genetic locus
with squalene-hopene cyclase genes, and are never
associated with genes for the metabolism of phytoene.
Indeed, the members of this family appear to never be
found in a genome lacking squalene-hopene cyclase (SHC),
although not all genomes encoding SHC have this glycosyl
transferase. In the organism Zymomonas mobilis the
linkage of this gene to hopanoid biosynthesis has been
noted and the gene named HpnB. Hopanoids are known to
feature polar glycosyl head groups in many organisms.
Length = 384
Score = 28.9 bits (65), Expect = 3.2
Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 11/81 (13%)
Query: 117 PFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLW-GQIWF 175
I+VD+ + + + ARA A+ +R ++G P P G W G++W
Sbjct: 70 KLHVILVDDHSTDGT------ADIARAAARAYGRGDRLTVVSGQPLPPG----WSGKLWA 119
Query: 176 LDKGKRLGRVFQSFVARWFNT 196
+ +G R T
Sbjct: 120 VSQGIAAARTLAPPADYLLLT 140
>gnl|CDD|179286 PRK01368, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 454
Score = 28.7 bits (64), Expect = 3.7
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 229 LDIADYQNIDKPILITKKVPLPQPVMKQYHKF 260
L + +QN+DK I+++ +PL ++K F
Sbjct: 56 LSDSRWQNLDK-IVLSPGIPLTHEIVKIAKNF 86
>gnl|CDD|177632 PHA03396, lef-9, late expression factor 9; Provisional.
Length = 493
Score = 27.6 bits (62), Expect = 6.4
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 231 IADYQNIDKPILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNS 278
+ D +D I ++++ KF R L DL+ I FNS
Sbjct: 18 LTDPNKLDNVFFIN---------IEEFKKFLRNLISDLKKIKINYFNS 56
>gnl|CDD|162908 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems.
Length = 564
Score = 27.3 bits (61), Expect = 7.9
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 27 GSGKTVSVLTALS 39
GSGKTVS+ TAL+
Sbjct: 326 GSGKTVSLYTALN 338
>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 = 27.2 bits (60), Expect = 8.1
Identities = 32/169 (18%), Positives = 52/169 (30%), Gaps = 13/169 (7%)
Query: 2 NLAPHQ-TKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVL--VIAPLRVA 58
N ++ T +D+ I G+GKT ++L A++Y L+G+ VI L
Sbjct: 10 NFGSYKGTHTIDFTALGPIFLICGKTGAGKT-TLLDAITYA-LYGKLPRRSEVIRSLNSL 67
Query: 59 QSVWTSEVQRWSNFSHMN-----ISVITGTVKQRTKVLKTPAVLYVINFENLGWLVQELK 113
+ + FS + T R L L +
Sbjct: 68 YAAPSEAAFAELEFSLGTKIYRVHRTLRCTRSHRKTEQPEQLYLEQKKGRG-RILAAKKS 126
Query: 114 GT--WPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGT 160
T + +D T + L QG AK + E + L
Sbjct: 127 ETEEVIHDLLKLDYKTFTRVVLLPQGEFAQFLKAKSKEKKELLMNLFPL 175
>gnl|CDD|184796 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 27.2 bits (60), Expect = 8.5
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 309 IKALEVIIEKANAAPIIVAYHFNSDLARLQK 339
++ +E EKAN +V YH S+L + +K
Sbjct: 139 VEKIESFCEKANLDVRLVYYH--SNLRKKEK 167
>gnl|CDD|131121 TIGR02066, dsrB, sulfite reductase, dissimilatory-type beta
subunit. This model describes the beta subunit of
sulfite reductase.
Length = 341
Score = 27.1 bits (60), Expect = 9.3
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 116 WPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLW 170
WP V + + ++ + + + WE RF EL G P ID W
Sbjct: 271 WPELVAYVKKILEAWKANAKKHERLIEWVERIGWE--RFFELVGLPFTQHHIDDW 323
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.321 0.135 0.416
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,486,531
Number of extensions: 482126
Number of successful extensions: 802
Number of sequences better than 10.0: 1
Number of HSP's gapped: 800
Number of HSP's successfully gapped: 17
Length of query: 458
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 361
Effective length of database: 3,898,497
Effective search space: 1407357417
Effective search space used: 1407357417
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: 59 (26.6 bits)