RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780776|ref|YP_003065189.1| ribosome recycling factor
[Candidatus Liberibacter asiaticus str. psy62]
(186 letters)
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 259 bits (664), Expect = 3e-70
Identities = 85/181 (46%), Positives = 123/181 (67%)
Query: 6 DLQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRM 65
L++ ++RM + LK+++ +RTGR +PS+LD +KV+ YGS PLNQVA+++V E R
Sbjct: 5 ILKDAEERMEKAVEALKRELAKIRTGRANPSLLDGIKVDYYGSPTPLNQVASISVPEART 64
Query: 66 LVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKS 125
L++ WDK M+ ++E+ I S+LGLNP +G V+R+P+P TEERR LVK AE++
Sbjct: 65 LLIQPWDKSMLKAIEKAIRASDLGLNPSNDGTVIRLPIPPLTEERRKELVKQVKKEAEEA 124
Query: 126 KISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMH 185
K+++RNIRRD D LKK K + SED + E++IQK+TD IK ID K+KEIM
Sbjct: 125 KVAIRNIRRDANDKLKKLEKDKEISEDELKRAEDEIQKLTDKYIKKIDELLAAKEKEIME 184
Query: 186 F 186
Sbjct: 185 V 185
>gnl|CDD|129587 TIGR00496, frr, ribosome recycling factor. This model finds only
eubacterial proteins. Mitochondrial and/or chloroplast
forms might be expected but are not currently known.
This protein was previously called ribosome releasing
factor. By releasing ribosomes from mRNA at the end of
protein biosynthesis, it prevents inappropriate
translation from 3-prime regions of the mRNA and frees
the ribosome for new rounds of translation.
EGAD|53116|YHR038W is part of the frr superfamily.
Length = 176
Score = 181 bits (461), Expect = 9e-47
Identities = 81/176 (46%), Positives = 118/176 (67%)
Query: 11 KDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSV 70
K+RM +I LK+++ +RTGR +PS+LD + VE YG+ PL Q+A+VTV + R LV+
Sbjct: 1 KERMDKSIQALKRELSKIRTGRANPSLLDRILVEYYGAPTPLRQLASVTVPDARTLVIQP 60
Query: 71 WDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVR 130
+DK + ++E+ I S+LGLNP +G V+R+ P TEERR LVK A AE++K++VR
Sbjct: 61 FDKSNINAIEKAIQRSDLGLNPNNDGSVIRVNFPPLTEERRKELVKHAKKIAEQAKVAVR 120
Query: 131 NIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMHF 186
N+RRD D +KK K + SED L+ +IQK+TD IK ID ++K+KE+M
Sbjct: 121 NVRRDANDKVKKLEKDKEISEDEERRLQEEIQKLTDEYIKKIDEILKDKEKELMEV 176
>gnl|CDD|180891 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 31.5 bits (72), Expect = 0.14
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 13/48 (27%)
Query: 149 ASEDMVASLENDIQKITDSTIK-------------NIDSFFEEKKKEI 183
SE+M A LE D+Q I D K I S +EK+KEI
Sbjct: 537 VSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEI 584
>gnl|CDD|185113 PRK15191, PRK15191, fimbrial protein BcfF; Provisional.
Length = 172
Score = 28.5 bits (63), Expect = 0.97
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 5 IDLQNIKDRM-GDTISF------LKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVAN 57
IDLQN G T+SF D++ L G S + + + + +PL Q ++
Sbjct: 71 IDLQNCGSTASGVTVSFSGAADSRNTDLLALTAGESDASGIGIALYDQNKTLIPLGQESD 130
Query: 58 VTVLEP 63
V L P
Sbjct: 131 VVTLSP 136
>gnl|CDD|162969 TIGR02670, cas_csx8, CRISPR-associated protein Csx8 (provisional).
In three genomes so far, a member of this protein
appears in the midst of a CRISPR-associated (cas) gene
operon, immediately upstream of a member of family
TIGR01875 (CRISPR-associated autoregulator, DevR
family). The genomes so far are Nocardia farcinica
IFM10152, Clostridium perfringens SM101, and Clostridium
tetani E88.
Length = 441
Score = 28.3 bits (63), Expect = 1.2
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 116 KVAHAYAEKSKISVRN-IRRDGM---DHLKKSRKSGKASEDMVASLENDI----QKITDS 167
K +++YA I + IR G ++LKK++ KA N + QK+ S
Sbjct: 334 KNSYSYAINELIKINQLIRNGGKEMDENLKKAKACAKAVVKKFIKENNKLASYKQKLLSS 393
Query: 168 TI-KNIDSFFE 177
+ K+ D +
Sbjct: 394 VVFKDHDRICD 404
>gnl|CDD|147910 pfam06007, PhnJ, Phosphonate metabolism protein PhnJ. This family
consists of several bacterial phosphonate metabolism
(PhnJ) sequences. The exact role that PhnJ plays in
phosphonate utilisation is unknown.
Length = 279
Score = 27.2 bits (61), Expect = 2.6
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 92 PIVEGQ--VLRIPVPE--TTEERRLALVKVAHAYAEKSKISVR 130
P+ E Q VL++P+PE E A + HA A+ + V+
Sbjct: 112 PLTEDQILVLQVPIPEPLRFVEPSEAETRKMHAEADYGLMWVK 154
>gnl|CDD|117664 pfam09104, BRCA-2_OB3, BRCA2,
oligonucleotide/oligosaccharide-binding, domain 3.
Members of this family assume an OB fold, which consists
of a highly curved five-stranded beta-sheet that closes
on itself to form a beta-barrel. OB3 has a pronounced
groove formed by one face of the curved sheet and is
demarcated by two loops, one between beta 1 and beta 2
and another between beta 4 and beta 5, which allows for
strong ssDNA binding.
Length = 143
Score = 27.1 bits (60), Expect = 2.8
Identities = 9/18 (50%), Positives = 16/18 (88%)
Query: 168 TIKNIDSFFEEKKKEIMH 185
TI+NID+F++E +K++ H
Sbjct: 118 TIENIDTFYKEAEKKLAH 135
>gnl|CDD|118189 pfam09657, Cas_Csx8, CRISPR-associated protein Csx8 (Cas_Csx8).
Clusters of short DNA repeats with nonhomologous
spacers, which are found at regular intervals in the
genomes of phylogenetically distinct prokaryotic
species, comprise a family with recognisable features.
This family is known as CRISPR (short for Clustered,
Regularly Interspaced Short Palindromic Repeats). A
number of protein families appear only in association
with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry describes
proteins of unknown function which are encoded in the
midst of a cas gene operon.
Length = 441
Score = 26.8 bits (59), Expect = 3.8
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 116 KVAHAYAEKSKISVRNIRRDG----MDHLKKSRKSGKASEDMVASLENDI----QKITDS 167
K +++YA I + + R+G ++LKK+ KA + N + QK+ S
Sbjct: 334 KNSYSYAINELIKINQLIRNGGKEMDENLKKAIACAKAVVKKFENSLNKLASYKQKLLSS 393
Query: 168 TI-KNIDSFFE 177
+ K+ D +
Sbjct: 394 VVFKDHDRICD 404
>gnl|CDD|180569 PRK06456, PRK06456, acetolactate synthase catalytic subunit;
Reviewed.
Length = 572
Score = 26.3 bits (58), Expect = 4.3
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 147 GKASEDMVASLENDIQ-----KITDSTIKNIDSFFEEKKKEIM 184
G+A M A+LE+D + +D T + D E +KK IM
Sbjct: 263 GRAEASM-AALESDAMLVVGARFSDRTFTSYDEMVETRKKFIM 304
>gnl|CDD|182685 PRK10735, tldD, protease TldD; Provisional.
Length = 481
Score = 25.9 bits (57), Expect = 6.2
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 44 EAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLG 89
E+Y +H+P+ ++ N ML +E++ SVE GI+ N G
Sbjct: 353 ESY-AHLPMPRMTNTY-----MLAGKSTPQEIIESVEYGIYAPNFG 392
>gnl|CDD|152163 pfam11727, ISG65-75, Invariant surface glycoprotein. This family
is found in Trypanosome species, and appears to be one
of two invariant surface glycoproteins, ISG65 and ISG75.
that are found in the mammalian stage of the parasitic
protozoan. the sequence suggests the two families are
polypeptides with N-terminal signal sequences,
hydrophilic extracellular domains, single trans-membrane
alpha-helices and short cytoplasmic domains. they are
both expressed in the bloodstream form but not in the
midgut stage. Both polypeptides are distributed over the
entire surface of the parasite.
Length = 289
Score = 26.0 bits (57), Expect = 6.3
Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 21/69 (30%)
Query: 131 NIRRDGMDHLKKSRKSGKASEDMVASLENDIQKI---------------TDSTIKNIDSF 175
+ + D+L K +E A+++ + ++ +DS K I
Sbjct: 54 KVGNERADYLVKK------TEGFAANIKLALDRVKYYLEKLESRSDSKLSDSDKKKIKEI 107
Query: 176 FEEKKKEIM 184
E+ K +I
Sbjct: 108 CEKAKDKID 116
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. These
proteins are found in P. falciparum, P. vivax and P.
yoelii.
Length = 2757
Score = 25.8 bits (56), Expect = 7.4
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 124 KSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLE---NDIQKITDSTIKNIDSFFEEKK 180
K K ++N+ + H+K + K SE+ + ++ ND++ + D I N D EKK
Sbjct: 1115 KIKDDIKNLDQKIDHHIKALEEIKKKSENYIDEIKAQINDLEDVADKAISNDDPEEIEKK 1174
Query: 181 KE 182
E
Sbjct: 1175 IE 1176
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 25.5 bits (56), Expect = 8.0
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 149 ASEDMVASLENDIQKITDSTIKNIDSFFEE 178
DM + LE D+ KI + IK D+ EE
Sbjct: 528 TKPDMTSRLEEDMDKIAEGKIKE-DAVLEE 556
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 25.7 bits (57), Expect = 8.5
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 4/81 (4%)
Query: 106 TTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKK-SRKSGKASEDMVASL---ENDI 161
T+E+R +A AEK S R +RR+ + L + + + + + A L E +I
Sbjct: 340 KTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLSIIFKHNPELAARLAAFLELTEEEI 399
Query: 162 QKITDSTIKNIDSFFEEKKKE 182
+ +T S +K E
Sbjct: 400 EFLTGSKKATKKIKKIVEKAE 420
>gnl|CDD|184561 PRK14192, PRK14192, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 283
Score = 25.6 bits (56), Expect = 8.8
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 88 LGLNPIVEGQVLRIPVPETTEER 110
L NP V G +L+ PVP +ER
Sbjct: 86 LNANPDVHGILLQHPVPAQIDER 108
>gnl|CDD|151875 pfam11436, DUF3199, Protein of unknown function (DUF3199). Some
members in this family of proteins with unknown function
are annotated as YqbG however this cannot be confirmed.
Currently the proteins has no known function.
Length = 124
Score = 25.5 bits (56), Expect = 9.4
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 101 IPVPETTEERRLALVKVAHAYAEK 124
P+PET RLAL+K+A YA K
Sbjct: 50 RPLPETV---RLALLKLAQYYALK 70
>gnl|CDD|182781 PRK10854, PRK10854, exopolyphosphatase; Provisional.
Length = 513
Score = 25.1 bits (55), Expect = 10.0
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 104 PETTEERRLALVKVAHAYAEKSKISVRNIRR 134
P E RR+ V A Y IS N +R
Sbjct: 159 PILVESRRMGCVSFAQLYFPGGVISKENFQR 189
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
0.316 0.131 0.355
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,923,810
Number of extensions: 177526
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 41
Length of query: 186
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 98
Effective length of database: 4,092,969
Effective search space: 401110962
Effective search space used: 401110962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.5 bits)