RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780995|ref|YP_003065408.1|
Endonuclease/exonuclease/phosphatase [Candidatus Liberibacter
asiaticus str. psy62]
(125 letters)
>gnl|CDD|146159 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase
family. This large family of proteins includes
magnesium dependent endonucleases and a large number of
phosphatases involved in intracellular signalling. This
family includes: AP endonuclease proteins EC:4.2.99.18,
DNase I proteins EC:3.1.21.1, Synaptojanin an
inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56,
Sphingomyelinase EC:3.1.4.12 and Nocturnin.
Length = 255
Score = 33.0 bits (75), Expect = 0.020
Identities = 22/126 (17%), Positives = 32/126 (25%), Gaps = 25/126 (19%)
Query: 9 LKKWADQKIKTGIPFVIAGDFNRKINSIG---------DTDDFWQKMDPDGLLIRFPQEK 59
L +D +I P ++ GDFN + +S T + D
Sbjct: 139 LDFLSDLRIPKSDPVILCGDFNARPDSWDSALLKSIGKSTLFLLLERDLVFDGFDELPIG 198
Query: 60 -------ESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHC 112
+ K S LD L+ S S L S H
Sbjct: 199 FPPTWWSYRNSSEKKNTGSRLDR---------ILVSGSLLRRVVILSLLLLVIFTGSDHR 249
Query: 113 PLTIEY 118
P+
Sbjct: 250 PVLATL 255
>gnl|CDD|31052 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
repair].
Length = 261
Score = 30.6 bits (69), Expect = 0.12
Identities = 29/143 (20%), Positives = 51/143 (35%), Gaps = 37/143 (25%)
Query: 7 EWLKKWADQKIKTGIPFVIAGDFN--RKINSIGDTDDFWQKMDPDGLLIR---------- 54
+ L+ + ++ +K G P V+ GDFN + + + W G L
Sbjct: 127 DALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEERAWFRRLLN 186
Query: 55 ----------FPQEKESTC-----NVIKRNKSS-LDYFVIDRDNKNFLIDNSFSIVSYDQ 98
P+ ++ T N +RN+ +DY ++ + L D
Sbjct: 187 AGFVDTFRLFHPEPEKYTWWDYRANAARRNRGWRIDYILVSPALADRLKDAGI------- 239
Query: 99 SDLDTRR-SKLSTHCPLTIEYDF 120
D + R K S H P+ +E D
Sbjct: 240 -DREVRGWEKPSDHAPVWVELDL 261
>gnl|CDD|88569 cd05129, RasGAP_RAP6, Rab5-activating protein 6 (RAP6) is an
endosomal protein with a role in the regulation of
receptor-mediated endocytosis. RAP6 contains a Vps9
domain, which is involved in the activation of Rab5, and
a Ras GAP domain (RGD). Rab5 is a small GTPase required
for the control of the endocystic route, and its
activity is regulated by guanine nucleotide exchange
factor, such as Rabex5, and GAPs, such as RN-tre. Human
Rap6 protein is localized on the plasma membrane and on
the endosome. RAP6 binds to Rab5 and Ras through the
Vps9 and RGD domains, respectively..
Length = 353
Score = 28.3 bits (63), Expect = 0.62
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 40 DDFWQKMDPDGLLIRFP---QEKESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSF 91
D+FW +DPD L+ RF +EK K + + + + + K + N F
Sbjct: 118 DEFWLDIDPDKLMERFSPDEREKRFGEKGTKEYERRVQEYRAEVEAKLVALVNKF 172
>gnl|CDD|33370 COG3568, ElsH, Metal-dependent hydrolase [General function
prediction only].
Length = 259
Score = 27.6 bits (61), Expect = 0.89
Identities = 23/122 (18%), Positives = 34/122 (27%), Gaps = 17/122 (13%)
Query: 3 SQQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDP-----DGLLIRFPQ 57
S+ + A + P V+ GDFN + + ++ L F
Sbjct: 147 SRLRQAAALLALAGLPALNPTVLMGDFNNE----PGSAEYRLAARSPLNAQAALTGAFAP 202
Query: 58 EKESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIE 117
T N L +DR + +I S D S H PL E
Sbjct: 203 AVGRTIRTFPSNTPLLR---LDR----IFVSKELAIRSVHVLT-DRLARVASDHLPLLAE 254
Query: 118 YD 119
Sbjct: 255 LR 256
>gnl|CDD|37661 KOG2450, KOG2450, KOG2450, Aldehyde dehydrogenase [Energy
production and conversion].
Length = 501
Score = 26.7 bits (59), Expect = 1.9
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 6 GEWLKKWADQKIKTGIPF 23
E A +K+K G PF
Sbjct: 319 VEKFVAAAKKKLKVGDPF 336
>gnl|CDD|34040 COG4318, COG4318, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 221
Score = 26.1 bits (57), Expect = 2.6
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 14 DQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLL 52
+ +K G+P V+A S DDFW+ MD + +
Sbjct: 92 REGVKQGLPVVVAD------LSPLAKDDFWEVMDENHWV 124
>gnl|CDD|147340 pfam05112, Baculo_p47, Baculovirus P47 protein. This family
consists of several Baculovirus P47 proteins which is
one of the primary components of Baculovirus encoded RNA
polymerase, which initiates transcription from late and
very late promoters.
Length = 313
Score = 26.1 bits (58), Expect = 2.9
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 61 STCNVIKRNKSSLDYFV--IDRDNK----NFLIDNSFSIVSYDQSD 100
S +VIKR+KSS Y V +D +N L+ N+F+++ D
Sbjct: 191 SISDVIKRHKSSKKYIVLELDPNNAAELVKLLLKNNFTVIENAHID 236
>gnl|CDD|176468 cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and
fumarase class II enzymes. This group contains
aspartase (L-aspartate ammonia-lyase), fumarase class II
enzymes, and related proteins. It is a member of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. Aspartase catalyzes the
reversible deamination of aspartic acid. Fumarase
catalyzes the reversible hydration/dehydration of
fumarate to L-malate during the Krebs cycle.
Length = 450
Score = 25.1 bits (56), Expect = 5.3
Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 3/24 (12%)
Query: 19 TGIPFVIAGDFNRKINSIGDTDDF 42
TG+PFV A + + D
Sbjct: 249 TGLPFVTAPN---LFEATAAHDAL 269
>gnl|CDD|31981 COG1796, POL4, DNA polymerase IV (family X) [DNA replication,
recombination, and repair].
Length = 326
Score = 24.4 bits (53), Expect = 7.5
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 16 KIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQ-----------EKESTCN 64
++ I IAG R ++GD D P+ +L + E + +
Sbjct: 176 ELTPIIQASIAGSLRRGRETVGDIDILISTSHPESVLEELLEMPNVQEVIAKGETKVSML 235
Query: 65 VIKRNKSSLDYFVIDRD 81
+I +S+D+ V+ +
Sbjct: 236 LILDEGTSVDFRVVPPE 252
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.137 0.416
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,568,367
Number of extensions: 74458
Number of successful extensions: 180
Number of sequences better than 10.0: 1
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 21
Length of query: 125
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 43
Effective length of database: 4,491,799
Effective search space: 193147357
Effective search space used: 193147357
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 (21.7 bits)
S2: 51 (23.4 bits)