RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780430|ref|YP_003064843.1| nitrogen fixation protein
[Candidatus Liberibacter asiaticus str. psy62]
(189 letters)
>gnl|CDD|149691 pfam08712, Nfu_N, Scaffold protein Nfu/NifU N terminal. This
domain is found at the N terminus of NifU and NifU
related proteins, and in the human Nfu protein. Both of
these proteins are thought to be involved in the the
assembly of iron-sulphur clusters.
Length = 87
Score = 142 bits (360), Expect = 6e-35
Identities = 55/87 (63%), Positives = 63/87 (72%), Gaps = 1/87 (1%)
Query: 3 IQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFIT 62
IQTE TPNP TLKF+PG+ VL EG F NA EAE SPLA ++F IPG+ SV+FG DFIT
Sbjct: 1 IQTESTPNPNTLKFLPGKEVLPEGTFEFKNADEAEGSPLAQKLFKIPGVKSVFFGDDFIT 60
Query: 63 VGK-DQYDWEHLRPPVLGMIMEHFISG 88
V K D DW+ L+P VL IMEH SG
Sbjct: 61 VTKADDADWDDLKPEVLEAIMEHLESG 87
>gnl|CDD|162652 TIGR02000, NifU_proper, Fe-S cluster assembly protein NifU. Three
different but partially homologous Fe-S cluster assembly
systems have been described: Isc, Suf, and Nif. The
latter is associated with donation of an Fe-S cluster to
nitrogenase in a number of nitrogen-fixing species.
NifU, described here, consists of an N-terminal domain
(pfam01592) and a C-terminal domain (pfam01106).
Homologs with an equivalent domain archictecture from
Helicobacter and Campylobacter, however, are excluded
from this model by a high trusted cutoff. The model,
therefore, is specific for NifU involved in nitrogenase
maturation. The related model TIGR01999 homologous to
the N-terminus of this model describes IscU from the Isc
system as in E. coli, Saccharomyces cerevisiae, and Homo
sapiens.
Length = 290
Score = 46.0 bits (109), Expect = 5e-06
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 118 VQRIKEVLD--NRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLK 169
VQRI+ + VRP + DGGD+ IV++ + GACSGC ++ TLK
Sbjct: 218 VQRIQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLK 271
>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI. IscR
(TIGR02010) is an iron-sulfur cluster-binding
transcriptional regulator (see Genome Property
GenProp0138). Members of this protein family include
YhgI, whose expression is under control of IscR, and
show sequence similarity to IscA, a known protein of
iron-sulfur cluster biosynthesis. These two lines of
evidence strongly suggest a role as an iron-sulfur
cluster biosynthesis protein. An older study designated
this protein GntY and suggested a role for it and for
the product of an adjacent gene, based on
complementation studies, in gluconate utilization.
Length = 190
Score = 45.4 bits (108), Expect = 9e-06
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 111 IESDSAVVQRIKEVLDNRVRPAVARDGGDI-VFKGYRDGIVFLSMRGACSGCPSASETLK 169
+ D+ + +RI VL + + P +A GG + + + DG+ L G C+GC TLK
Sbjct: 100 VADDAPLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLK 159
Query: 170 YGVANILNHFVPEVKDIR 187
GV L PE+K +R
Sbjct: 160 DGVEKTLLERFPELKGVR 177
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional.
Length = 192
Score = 38.5 bits (90), Expect = 0.001
Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 111 IESDSAVVQRIKEVLDNRVRPAVARDGGDIVF-KGYRDGIVFLSMRGACSGCPSASETLK 169
+ D+ +++R++ VL +++ P +A GG + + DG L G C+GC TLK
Sbjct: 101 VADDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLK 160
Query: 170 YGV-ANILNHFVPEVKDIRTV 189
G+ +LN F E+K +R +
Sbjct: 161 EGIEKQLLNEFPGELKGVRDL 181
>gnl|CDD|166487 PLN02846, PLN02846, digalactosyldiacylglycerol synthase.
Length = 462
Score = 32.5 bits (74), Expect = 0.071
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 93 HNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFL 152
H L +++D GSG+ DS V+ E L+ VR RD D +F Y+ VFL
Sbjct: 253 HQKELSGLEVDLYGSGE----DSDEVKAAAEKLELDVRVYPGRDHADPLFHDYK---VFL 305
Query: 153 SMRGACSGCPSASETLKYG 171
+ C + +E L G
Sbjct: 306 NPSTTDVVCTTTAEALAMG 324
>gnl|CDD|132152 TIGR03108, eps_aminotran_1, exosortase 1 system-associated
amidotransferase 1. The predicted protein-sorting
transpeptidase that we call exosortase (see TIGR02602)
has distinct subclasses that associated with different
types of exopolysaccharide production loci. This model
represents a distinct clade among a set of
amidotransferases largely annotated (not necessarily
accurately) as glutatime-hydrolyzing asparagine
synthases. Members of this clade are essentially
restricted to the characteristic exopolysaccharide (EPS)
regions that contain the exosortase 1 genome (xrtA), in
genomes that also have numbers of PEP-CTERM domain
(TIGR02595) proteins.
Length = 628
Score = 27.4 bits (61), Expect = 2.5
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 120 RIKEVLDNRVRPAVARDGGDIVFKGYR 146
R+ E+ RV A++ DGGD +F GYR
Sbjct: 349 RVCELARKRVTVALSGDGGDELFAGYR 375
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 27.0 bits (60), Expect = 2.9
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 19 GQVVLVEGAIHFSNAKEAEISPLASRIFSIPG 50
G + +E + S + A SPLA ++F + G
Sbjct: 355 GAISAIEDGLRASGSSPASGSPLAGKLFVVIG 386
>gnl|CDD|179616 PRK03635, PRK03635, chromosome replication initiation inhibitor
protein; Validated.
Length = 294
Score = 25.9 bits (58), Expect = 5.9
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 7/39 (17%)
Query: 115 SAVVQRIK-------EVLDNRVRPAVARDGGDIVFKGYR 146
SAV QRIK +VL R +P + G + + R
Sbjct: 31 SAVSQRIKALEERVGQVLLVRTQPCRPTEAGQRLLRHAR 69
>gnl|CDD|180801 PRK07033, PRK07033, hypothetical protein; Provisional.
Length = 427
Score = 25.8 bits (57), Expect = 6.5
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 106 GSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMR 155
G G F S S V+ + + RV A+ + G+++ GY D + + R
Sbjct: 314 GDGLF-ASASTSVRDRYQPVLARVADALNQVKGNVLVTGYSDNVPIRTAR 362
>gnl|CDD|177938 PLN02303, PLN02303, urease.
Length = 837
Score = 25.9 bits (57), Expect = 7.2
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 102 LDDMGSGDFIESDSAVVQRIKEVL 125
L DMG+ I SDS + RI EV+
Sbjct: 618 LHDMGAISIISSDSQAMGRIGEVI 641
>gnl|CDD|179209 PRK01029, tolB, translocation protein TolB; Provisional.
Length = 428
Score = 25.9 bits (57), Expect = 7.4
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 11/42 (26%)
Query: 45 IFSIPGIASVYFGYDFITVGKDQ-----------YDWEHLRP 75
+ +PGI+S + T D YD ++LRP
Sbjct: 138 LTGVPGISSGKIIFSLSTTNSDTELKQGELWSVDYDGQNLRP 179
>gnl|CDD|179115 PRK00767, PRK00767, transcriptional regulator BetI; Validated.
Length = 197
Score = 25.6 bits (57), Expect = 9.1
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 15/35 (42%)
Query: 33 AKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQ 67
A+ A +S GI S YFG GKD
Sbjct: 36 ARRAGVST---------GIISHYFG------GKDG 55
>gnl|CDD|152009 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex
that regulates RNA polymerase II activity. Med23 is
required for heat-shock-specific gene expression, and
has been shown to mediate transcriptional activation of
E1A in mice.
Length = 1341
Score = 25.2 bits (55), Expect = 9.6
Identities = 6/27 (22%), Positives = 14/27 (51%)
Query: 67 QYDWEHLRPPVLGMIMEHFISGDPIIH 93
Q+ W HL ++ ++ F + I++
Sbjct: 337 QWQWLHLSSQLIYFVLFQFANFKNIVN 363
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 0.142 0.424
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,229,020
Number of extensions: 207983
Number of successful extensions: 411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 21
Length of query: 189
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 101
Effective length of database: 4,092,969
Effective search space: 413389869
Effective search space used: 413389869
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: 54 (24.6 bits)