RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026229
(241 letters)
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 32.4 bits (75), Expect = 0.22
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 174 RSKARAERNYEQADALHQKIINAGYRL 200
R +AR +++ ADA+ ++ G L
Sbjct: 425 RQEARKAKDFALADAIRDELAALGIVL 451
>gnl|CDD|178337 PLN02736, PLN02736, long-chain acyl-CoA synthetase.
Length = 651
Score = 32.0 bits (73), Expect = 0.31
Identities = 24/77 (31%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 114 YGLPLPHTLIPVSTAEPTTLPAGVDARAIPDGDTITVYVSAADPRESACVPGDVQMAAVR 173
YG L +L+ V +P L A + I D + DPR A V D M AV
Sbjct: 542 YGDSLNSSLVAVVVVDPEVLKAWAASEGIKYEDLKQL---CNDPRVRAAVLAD--MDAVG 596
Query: 174 RSKARAERNYEQADALH 190
R R +E A A+
Sbjct: 597 REAQL--RGFEFAKAVT 611
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 31.8 bits (73), Expect = 0.33
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 174 RSKARAERNYEQADALHQKIINAGYRL 200
R +AR +N+ AD + +++ G L
Sbjct: 426 RLEARKAKNWALADEIRDELLALGIIL 452
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 29.8 bits (67), Expect = 0.96
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 62 SSKKAQANWYRKLSEA--WREAK----PPPTTAEEA 91
+K Q NW RK++ W+ + P P+T +EA
Sbjct: 149 ITKALQVNWKRKVATPANWQPGQEGIVPAPSTLDEA 184
>gnl|CDD|187684 cd09626, DOMON_glucodextranase_like, DOMON-like domain of various
glycoside hydrolases. This DOMON-like domain is found
at the C-terminus of various bacterial proteins that
play roles in metabolizing carbohydrates, such as
glucodextranase (hydrolyzes alpha-1,6-glucosidic
linkages of dextran from the non-reducing end), glucan
alpha-1,4-glucosidase, pullulanase (degrades pullulan, a
polysaccharide built from maltotriose units),
arabinogalactan endo-1,4-beta-galactosidase, and others.
Consequently, the DOMON-like domains in this family
co-occur with catalytic domains from various glycosyl
hydrolase families. The precise function of the DOMON
domains in these proteins is not clear, they may be
involved in interactions with carbohydrates.
Length = 220
Score = 29.2 bits (66), Expect = 1.4
Identities = 12/34 (35%), Positives = 13/34 (38%)
Query: 124 PVSTAEPTTLPAGVDARAIPDGDTITVYVSAADP 157
P L A A PDG+TITV V
Sbjct: 112 PEGEESAADLLAAPSVYADPDGNTITVTVPKKLL 145
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 29.8 bits (68), Expect = 1.6
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 130 PTTLPAGVDARAIPDGDTITVYVSAADPRESACVPGDVQMAAVRRSKARAERNYEQADAL 189
P L V+ A P +++ ++ A RE +P V+ R +A+ E N + A+
Sbjct: 437 PDGL---VEGLAQPPEESVAGFLGARFSREKHFLPEIVERLWEGRDEAKREMNKPLSQAI 493
Query: 190 HQKII-NAGY 198
KII NA Y
Sbjct: 494 --KIIMNAFY 501
>gnl|CDD|237018 PRK11905, PRK11905, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1208
Score = 29.4 bits (67), Expect = 2.0
Identities = 25/82 (30%), Positives = 30/82 (36%), Gaps = 27/82 (32%)
Query: 74 LSEAWREAKPPPTTAEEAARLVIQTLSRHKKADVEGLLAFYGLPLPHTLIPVSTAEPTTL 133
LS+ R A E A +LV ++ K VE LL Y L S+ E
Sbjct: 40 LSDEARAA-----IRERARKLVEALRAKRKGTGVEALLQEYSL---------SSQE---- 81
Query: 134 PAGVD----ARA---IPDGDTI 148
GV A A IPD T
Sbjct: 82 --GVALMCLAEALLRIPDTATR 101
>gnl|CDD|232974 TIGR00435, cysS, cysteinyl-tRNA synthetase. This model finds the
cysteinyl-tRNA synthetase from most but not from all
species. The enzyme from one archaeal species,
Archaeoglobus fulgidus, is found but the equivalent
enzymes from some other Archaea, including Methanococcus
jannaschii, are not found, although biochemical evidence
suggests that tRNA(Cys) in these species are charged
directly with Cys rather than through a misacylation and
correction pathway as for tRNA(Gln) [Protein synthesis,
tRNA aminoacylation].
Length = 464
Score = 29.3 bits (66), Expect = 2.2
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 174 RSKARAERNYEQADALHQKIINAGYRL 200
RS AR E+++ +AD + ++ G L
Sbjct: 427 RSIARKEKDFAKADEIRDELAKKGIVL 453
>gnl|CDD|218441 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 = 28.4 bits (64), Expect = 3.3
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 19/72 (26%)
Query: 180 ERNYEQADALHQ--------KIINAGYRLAIHLG-DKSSKQRG----------SSSTKVS 220
ER YE L Q K+I +G + D + RG SS T +S
Sbjct: 134 ERGYEDHYTLGQQLSIRITTKLIQSGLDFKHQVDNDATVAVRGWNDKAFEKLLSSITSIS 193
Query: 221 NSTKRHRCTREF 232
+ KRH+ ++++
Sbjct: 194 DVIKRHKSSKKY 205
>gnl|CDD|233454 TIGR01536, asn_synth_AEB, asparagine synthase
(glutamine-hydrolyzing). This model describes the
glutamine-hydrolysing asparagine synthase. A poorly
conserved C-terminal extension was removed from the
model. Bacterial members of the family tend to have a
long, poorly conserved insert lacking from archaeal and
eukaryotic sequences. Multiple isozymes have been
demonstrated, such as in Bacillus subtilis. Long-branch
members of the phylogenetic tree (which typically were
also second or third candidate members from their
genomes) were removed from the seed alignment and score
below trusted cutoff [Amino acid biosynthesis, Aspartate
family].
Length = 466
Score = 28.5 bits (64), Expect = 3.7
Identities = 17/95 (17%), Positives = 26/95 (27%), Gaps = 11/95 (11%)
Query: 23 SLGPHGVSAATVGVSALAQDLYHFEITSQVPEGLTRHVTSSKKAQANWYRKLSEA----W 78
+L H +ALA + P R V + +
Sbjct: 162 ALLAHPNIKPFPDGAALAP--GFGFVRVPPPSTFFRGVFELEPGHDLPLDDDGLNIERYY 219
Query: 79 REAKPPPTTAEEAA-----RLVIQTLSRHKKADVE 108
E + T +EE L+ + R ADV
Sbjct: 220 WERRDEHTDSEEDLVDELRSLLEDAVKRRLVADVP 254
>gnl|CDD|153417 cd07963, Anticodon_Ia_Cys, Anticodon-binding domain of cysteinyl
tRNA synthetases. This domain is found in cysteinyl
tRNA synthetases (CysRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. CysRS catalyzes the
transfer of cysteine to the 3'-end of its tRNA.
Length = 156
Score = 27.5 bits (62), Expect = 4.1
Identities = 6/26 (23%), Positives = 16/26 (61%)
Query: 172 VRRSKARAERNYEQADALHQKIINAG 197
+R++AR +++ +AD + ++ G
Sbjct: 117 AQRNQARKAKDWAEADRIRDELAAQG 142
>gnl|CDD|144538 pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).
This protein is also known as NSP1. NS53 is encoded by
gene 5. It is made in low levels in the infected cells
and is a component of early replication. The protein is
known to accumulate on the cytoskeleton of the infected
cell. NS53 is an RNA binding protein that contains a
characteristic cysteine rich region.
Length = 488
Score = 28.1 bits (63), Expect = 4.5
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 218 KVSNSTKRHRCTREFNAIW 236
K N+ K+ +C E+ W
Sbjct: 115 KFINNVKQRKCRNEYLIEW 133
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 28.0 bits (63), Expect = 4.8
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 59 HVTSSKKAQANWYRKLSEA-WREAKPPPTTAEEAARLVIQTLSRHKKADVEGLL 111
+ ++A L E + A PPT + ARL I + H + D++ L
Sbjct: 328 ILGDEERALEASRALLEEGIYVSAIRPPTVPKGTARLRITLTAAHTEEDIDRLA 381
>gnl|CDD|221446 pfam12158, DUF3592, Protein of unknown function (DUF3592). This
family of proteins is functionally uncharacterized.This
family of proteins is found in bacteria, archaea,
eukaryotes and viruses. Proteins in this family are
typically between 150 and 242 amino acids in length.
Length = 134
Score = 26.7 bits (59), Expect = 7.1
Identities = 4/19 (21%), Positives = 9/19 (47%)
Query: 143 PDGDTITVYVSAADPRESA 161
G+ + VY +P ++
Sbjct: 86 RVGERVPVYYDPDNPEQAR 104
>gnl|CDD|131069 TIGR02014, BchZ, chlorophyllide reductase subunit Z. This model
represents the Z subunit of the three-subunit enzyme,
(bacterio)chlorophyllide reductase. This enzyme is
responsible for the reduction of the chlorin B-ring and
is closely related to the protochlorophyllide reductase
complex which reduces the D-ring. Both of these
complexes in turn are homologous to nitrogenase [Energy
metabolism, Photosynthesis].
Length = 468
Score = 27.2 bits (60), Expect = 9.6
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 2/92 (2%)
Query: 150 VYVSAADPRESACVPGDVQMAAVRRSKARAERNYEQADALHQKIINAGYRLAIHLGDKSS 209
+Y++ AD + S +P A +RR+ Y A L Q++ NA + ++ +
Sbjct: 344 IYLAEADAK-SRFIPASFPGAIIRRATGTPFMGYSGATWLVQEVCNALFDTLFNILPITR 402
Query: 210 KQRGSSSTKVSNSTKRHRCTREFNAIWERSTE 241
+Q +++T S E NAI +R E
Sbjct: 403 RQDAAAATP-SRMHDPLPWDPEANAILDRIVE 433
>gnl|CDD|221273 pfam11858, DUF3378, Domain of unknown function (DUF3378). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is about 80
amino acids in length.
Length = 82
Score = 25.3 bits (56), Expect = 9.8
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 126 STAEPTTLPAGVDARAIPDGDTITVYVS 153
+ ++LP G A G TIT Y S
Sbjct: 20 KSYLTSSLPPGAVFAAKVPGATITAYTS 47
>gnl|CDD|116029 pfam07407, Seadorna_VP6, Seadornavirus VP6 protein. This family
consists of several VP6 proteins from the Banna virus as
well as a related protein VP5 from the Kadipiro virus.
Members of this family are typically of around 420
residues in length. The function of this family is
unknown.
Length = 420
Score = 26.9 bits (59), Expect = 10.0
Identities = 19/47 (40%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 79 REAKPPPTTAEEAARLVIQTLSRHKKADVEGLLAFYGLPLPHTLIPV 125
R KP AE A + TL K VEGLL +G P TL+ V
Sbjct: 286 RAYKPIRVMAEYA---IFPTLPHEYKGRVEGLLLLHGGLAPITLVRV 329
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.128 0.374
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,865,737
Number of extensions: 1091430
Number of successful extensions: 1034
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1034
Number of HSP's successfully gapped: 32
Length of query: 241
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 147
Effective length of database: 6,768,326
Effective search space: 994943922
Effective search space used: 994943922
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.0 bits)