RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7189
(120 letters)
>gnl|CDD|152604 pfam12169, DNA_pol3_gamma3, DNA polymerase III subunits gamma and
tau domain III. This domain family is found in
bacteria, and is approximately 110 amino acids in
length. The family is found in association with
pfam00004. Domains I-III are shared between the tau and
the gamma subunits, while most of the DnaB-binding
Domain IV and all of the alpha-interacting Domain V are
unique to tau.
Length = 143
Score = 28.0 bits (63), Expect = 0.81
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 20 RDFAEYLRELTRAQFV--SNNKFTIEEEETLK-KNLASLKRLS 59
RD E L LTR + + + ++ EEE + LA K+LS
Sbjct: 52 RDLLELLHLLTRLKIAPDAADDLSLPEEERERIAALA--KKLS 92
>gnl|CDD|173547 PTZ00354, PTZ00354, alcohol dehydrogenase; Provisional.
Length = 334
Score = 26.9 bits (60), Expect = 2.8
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 95 MREDSKGMFSKLFKRKDKYKKDLKSS 120
+R+ + +FS L R D+YK DL +S
Sbjct: 256 LRKRASIIFSTLRSRSDEYKADLVAS 281
>gnl|CDD|215974 pfam00529, HlyD, HlyD family secretion protein.
Length = 304
Score = 26.7 bits (59), Expect = 3.3
Identities = 7/35 (20%), Positives = 12/35 (34%)
Query: 20 RDFAEYLRELTRAQFVSNNKFTIEEEETLKKNLAS 54
++ L A S + + E + NL S
Sbjct: 81 QEADAARAALREALAASRGAASKAQLEAARDNLRS 115
>gnl|CDD|217990 pfam04257, Exonuc_V_gamma, Exodeoxyribonuclease V, gamma subunit.
The Exodeoxyribonuclease V enzyme is a multi-subunit
enzyme comprised of the proteins RecB, RecC (this
family) and RecD. This enzyme plays an important role in
homologous genetic recombination, repair of double
strand DNA breaks resistance to UV irradiation and
chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyzes
ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of
ssDNA or dsDNA and unwinding of dsDNA. This family
consists of two AAA domains.
Length = 756
Score = 26.4 bits (59), Expect = 4.4
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 8 VVIYWVGEGKKYRDFAEYLRELTRAQFVSNNKFTIEEEETLKKNLASLKRLSEDIYNKKY 67
V ++ + GK+ RDF + L EL + + F + ++L L +L DI N
Sbjct: 232 VHLFLLNPGKQGRDFQDLLEELEEGEAREIDLFVDPKPDSL------LHQLQNDILNLAE 285
Query: 68 P 68
Sbjct: 286 D 286
>gnl|CDD|234779 PRK00485, fumC, fumarate hydratase; Reviewed.
Length = 464
Score = 26.2 bits (59), Expect = 4.9
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 20 RDFAEYLRELTRAQFVSN-NKF 40
AE L ELT FV+ NKF
Sbjct: 244 ERVAEELAELTGLPFVTAPNKF 265
>gnl|CDD|193559 cd08011, M20_ArgE_DapE_like6, M20 Peptidases with similarity to
acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. This group includes the
hypothetical protein ygeY from Escherichia coli, a
putative deacetylase, but many in this subfamily are
classified as unassigned peptidases. ArgE/DapE enzymes
catalyze analogous reactions and share a common
activator, the metal ion (usually Co2+ or Zn2+). ArgE
catalyzes a broad range of substrates, including
N-acetylornithine, alpha-N-acetylmethionine and
alpha-N-formylmethionine, while DapE catalyzes the
hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP)
to L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly archaeal, and have been inferred
by homology as being related to both ArgE and DapE.
Length = 390
Score = 26.2 bits (58), Expect = 4.9
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 14 GEGKKYRDFAEYLREL 29
G+ Y + AEYL+E
Sbjct: 15 PPGENYEECAEYLKER 30
>gnl|CDD|224625 COG1711, COG1711, DNA replication initiation complex subunit,
GINS family [Replication, recombination, and
repair].
Length = 223
Score = 25.9 bits (57), Expect = 5.1
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 19 YRDFAEYLRELTRAQFVSNNKFTIEEEETLKKNLASLKRLSEDIYNKKY 67
YRD +++EL + IE+ + + + K + I+ ++Y
Sbjct: 27 YRDVRSFIKELEDEAGRAEEARDIEKYLLTDR-IETAKSDARSIFQRRY 74
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 26.0 bits (58), Expect = 5.4
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 18 KYRDFAEYLRELTRAQFVSNNKFTIEEEETL-------KKNLASLK-RLSEDIYNKKYP 68
DF + ++V K IE++ T+ + N A L +++E + +KK
Sbjct: 204 WGPDFPTGGEIVGPGKYVVRGKIEIEDDNTIVITELPYQVNTADLIEKIAELVKDKKIE 262
>gnl|CDD|223192 COG0114, FumC, Fumarase [Energy production and conversion].
Length = 462
Score = 26.0 bits (58), Expect = 5.6
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 22 FAEYLRELTRAQFVS-NNKFT--------IEEEETLKKNLASLKRLSEDI 62
AE L ELT FV+ NKF +E L+ SL +++ DI
Sbjct: 245 VAEELAELTGLPFVTAPNKFEALAAHDALVEASGALRTLAVSLMKIANDI 294
>gnl|CDD|211789 TIGR03137, AhpC, peroxiredoxin. This peroxiredoxin (AhpC,
alkylhydroperoxide reductase subunit C) is one subunit
of a two-subunit complex with subunit F(TIGR03140).
Usually these are found as an apparent operon. The gene
has been characterized in Bacteroides fragilis where it
is important in oxidative stress defense. This gene
contains two invariant cysteine residues, one near the
N-terminus and one near the C-terminus, each followed
immediately by a proline residue [Cellular processes,
Detoxification, Cellular processes, Adaptations to
atypical conditions].
Length = 187
Score = 25.8 bits (57), Expect = 5.6
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 6/39 (15%)
Query: 20 RDFAEYLRELTRAQFVSNNKFTI------EEEETLKKNL 52
RD +E LR++ AQ+V+ + + E ETLK +L
Sbjct: 143 RDASELLRKIKAAQYVAAHPGEVCPAKWKEGAETLKPSL 181
>gnl|CDD|131515 TIGR02462, pyranose_ox, pyranose oxidase. Pyranose oxidase (also
called glucose 2-oxidase) converts D-glucose and
molecular oxygen to 2-dehydro-D-glucose and hydrogen
peroxide. Peroxide production is believed to be
important to the wood rot fungi in which this enzyme is
found for lignin degradation.
Length = 544
Score = 26.0 bits (57), Expect = 5.9
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 83 CNTLLSQEFLDAMREDSKGM 102
C +LS E +D++R D +G+
Sbjct: 319 CQIVLSTELVDSVRSDPRGL 338
>gnl|CDD|130052 TIGR00979, fumC_II, fumarate hydratase, class II. Putative
fumarases from several species (Mycobacterium
tuberculosis, Streptomyces coelicolor, Pseudomonas
aeruginosa) branch deeply, although within the same
branch of a phylogenetic tree rooted by aspartate
ammonia-lyase sequences, and score between the trusted
and noise cutoffs [Energy metabolism, TCA cycle].
Length = 458
Score = 25.8 bits (57), Expect = 6.3
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 22 FAEYLRELTRAQFVS-NNKFT--------IEEEETLKKNLASLKRLSEDI 62
AE + + T FV+ NKF +E LK ASL +++ DI
Sbjct: 243 VAEEIAKETGLPFVTAPNKFEALAAHDAIVEAHGALKTLAASLMKIANDI 292
>gnl|CDD|153304 cd07620, BAR_SH3BP1, The Bin/Amphiphysin/Rvs (BAR) domain of
SH3-domain Binding Protein 1. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions. SH3-domain binding protein 1 (SH3BP1 or
3BP-1) is a Rac GTPase activating protein that inhibits
Rac-mediated platelet-derived growth factor
(PDGF)-induced membrane ruffling. SH3BP1 contains an
N-terminal BAR domain followed by a GAP domain for Rho
and Rac GTPases and a C-terminal proline-rich domain.
BAR domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 257
Score = 25.3 bits (55), Expect = 8.3
Identities = 20/105 (19%), Positives = 42/105 (40%), Gaps = 8/105 (7%)
Query: 20 RDFAEYLRELTRAQFVSNNKFTIEEEETLKKNLASLKRLSEDIYNKKYPRTFQTSASGLN 79
A++ ++ + NK + E+ + KN +L+ D +N R+ Q +
Sbjct: 95 NILADFEMKVEKDVLQPLNKLSEEDLPEILKNKKQFAKLTTD-WNSAKSRSPQAAGRSPR 153
Query: 80 GK-------ECNTLLSQEFLDAMREDSKGMFSKLFKRKDKYKKDL 117
E + + ++E+ + + KL + KD+Y DL
Sbjct: 154 SGGRSEEVGEHQGIRRANKGEPLKEEEEECWRKLEQCKDQYSADL 198
>gnl|CDD|182988 PRK11133, serB, phosphoserine phosphatase; Provisional.
Length = 322
Score = 25.3 bits (56), Expect = 9.8
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 22 FAEYLRELTRAQFVSNNKFTIEE 44
FA+YLR+ R N+ I +
Sbjct: 210 FADYLRDKLRLDAAVANELEIMD 232
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
0.316 0.132 0.371
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,006,279
Number of extensions: 512096
Number of successful extensions: 703
Number of sequences better than 10.0: 1
Number of HSP's gapped: 703
Number of HSP's successfully gapped: 49
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
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: 53 (24.1 bits)