RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16704
(146 letters)
>gnl|CDD|214422 MTH00111, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 323
Score = 29.9 bits (68), Expect = 0.38
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 7 MLMLIPMAMPFRLM-----LIFMLMMTFRIVYSLL 36
+ + P+ MPF L L+F+L M+ VYS+L
Sbjct: 88 LTIWTPLPMPFPLADLNLGLLFLLAMSSMAVYSIL 122
>gnl|CDD|227578 COG5253, MSS4, Phosphatidylinositol-4-phosphate 5-kinase [Signal
transduction mechanisms].
Length = 612
Score = 29.9 bits (67), Expect = 0.47
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 10/74 (13%)
Query: 38 YSTGKAATENSLMKYNSKEYFFKAGLCHLCIDLLNCQQALSRYI--DLSP-----AFQDT 90
+ E S Y + + LC L+ LSRYI + + F T
Sbjct: 327 EQFEEGLYEFSCKDYFPEVFRELRALCGCDEALV---SLLSRYILWESNGGKSGSFFLFT 383
Query: 91 REYKFLLKLIESLE 104
R+YKF++K I E
Sbjct: 384 RDYKFIIKTISHSE 397
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 29.5 bits (67), Expect = 0.60
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 72 NCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSIS-RLDQWYTT 130
+ + L +L D E LL+L E EE+D + +E E ++ +L
Sbjct: 60 SLKAKLDTLEELRQRLDDLEE---LLELAE--EEDDEETLAEAEAELKALEKKLAALELE 114
Query: 131 MLLK 134
LL
Sbjct: 115 RLLS 118
>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 = 29.1 bits (66), Expect = 0.95
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 75 QALSRYID-----LSPAFQDTREYKFLLKLIESLEEEDSDAFSET 114
QALSR+ D L+P + R+++ LL+ +E E + D F +
Sbjct: 224 QALSRHTDVHLFLLNPG-KQGRDFQDLLEELEEGEAREIDLFVDP 267
>gnl|CDD|212540 cd11598, HDAC_Hos2, Class I histone deacetylases including ScHos2
and SpPhd1. This subfamily includes Class I histone
deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae
as well as a histone deacetylase Phd1 from
Schizosaccharomyces pombe. Hos2 binds to the coding
regions of genes during gene activation, specifically
it deacetylates the lysines in H3 and H4 histone tails.
It is preferentially associated with genes of high
activity genome-wide and is shown to be necessary for
efficient transcription. Thus, Hos2 is directly
required for gene activation in contrast to other class
I histone deacetylases. Protein encoded by phd1 is
inhibited by trichostatin A (TSA), a specific inhibitor
of histone deacetylase, and is involved in the meiotic
cell cycle in S. pombe. Class 1 HDACs are Zn-dependent
enzymes that catalyze hydrolysis of N(6)-acetyl-lysine
residues in histone amino termini to yield a
deacetylated histone (EC 3.5.1.98).
Length = 311
Score = 28.6 bits (64), Expect = 1.0
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 12 PMAMPFRLMLIFMLMMTFRIVYSLLFYSTGKAATENSLMKYNSKEY 57
PM PFRL L L+M + + ++ Y +AAT L +++ +Y
Sbjct: 19 PMK-PFRLTLTKHLVMGYGLHKAMDTYEA-RAATREELRQFHDADY 62
>gnl|CDD|215477 PLN02882, PLN02882, aminoacyl-tRNA ligase.
Length = 1159
Score = 28.5 bits (64), Expect = 1.3
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 93 YKFLLKLIESLEEEDSDAFS--ETVKEFDSISRLDQWY---TTMLLKIKRQ 138
Y+FL++ + LE E F + K +S + LD+W T L+K R+
Sbjct: 674 YRFLVQNAKRLEVEGGAPFVPLDLAKLQNSANVLDRWINSATQSLVKFVRE 724
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to
EccC in Actinobacteria) and the WXG100 target proteins
are the only homologous parts of type VII secretion
between Firmicutes and Actinobacteria [Protein fate,
Protein and peptide secretion and trafficking].
Length = 1296
Score = 28.0 bits (63), Expect = 2.4
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 2 LMVIFMLMLIPMAMPFRLMLIFML-MMTFRIVYSLLFY 38
L++I + +LI + P + +I + M I++S Y
Sbjct: 45 LVMIAVTVLISIFQPRGIFIIASIAMSLVTIIFSTTTY 82
>gnl|CDD|214418 MTH00071, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 322
Score = 27.3 bits (61), Expect = 3.1
Identities = 11/41 (26%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 1 MLMVIFMLMLIPMAMPF-----RLMLIFMLMMTFRIVYSLL 36
M + + +++ P+ MP L ++F+L ++ VYS+L
Sbjct: 82 MALTLALIIWTPLPMPNNLSNLNLGILFILALSSLAVYSIL 122
>gnl|CDD|177166 MTH00104, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 318
Score = 27.3 bits (61), Expect = 3.2
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 5/37 (13%)
Query: 5 IFMLMLIPMAMPFRLM-----LIFMLMMTFRIVYSLL 36
+ + M IP+ MP+ L+ ++F+L M+ VYS+L
Sbjct: 81 LALTMWIPLPMPYPLINMNLGVLFILAMSSLAVYSIL 117
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily
archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and C-terminal
domains of this protein are well conserved, but the
central hinge region is skewed in composition and highly
divergent [Cellular processes, Cell division, DNA
metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.3 bits (61), Expect = 3.2
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 90 TREYKFLLKLIESLEEEDSDAFSETVKEFDSISR 123
E K +L+ IE E++ + F E F++I+
Sbjct: 999 EEERKAILERIEEYEKKKREVFMEA---FEAINE 1029
>gnl|CDD|234400 TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa. This
model represents the N-terminal domain or EccCa subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 661
Score = 27.2 bits (61), Expect = 4.0
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 5/32 (15%)
Query: 3 MVIFMLM-----LIPMAMPFRLMLIFMLMMTF 29
MV+ M PM + F LM++ ++
Sbjct: 19 MVVMMFASGGRQRNPMFLIFPLMMLVSMLGML 50
>gnl|CDD|217908 pfam04118, Dopey_N, Dopey, N-terminal. DopA is the founding member
of the Dopey family and is required for correct cell
morphology and spatiotemporal organisation of
multicellular structures in the filamentous fungus
Aspergillus nidulans. DopA homologues are found in
mammals. S. cerevisiae DOP1 is essential for viability
and, affects cellular morphogenesis.
Length = 305
Score = 26.8 bits (60), Expect = 4.8
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 95 FLLKLIESLEEEDSDAFSETVKEFDSISRL---DQWYTTMLLKIKR 137
+L L+ LE+E+S+ F +K D + D ++ + L I
Sbjct: 138 LILSLLPGLEDENSEYFERVLKLLDKLKENVGDDLFWQCLWLIIIT 183
>gnl|CDD|165102 PHA02735, PHA02735, putative DNA polymerase type B; Provisional.
Length = 716
Score = 27.0 bits (59), Expect = 4.9
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 81 IDLSPAFQDTREYKFLL-KLIESLEEEDSD 109
IDL PA+Q R+ KF KLI + + E SD
Sbjct: 11 IDLDPAYQAPRKAKFADGKLINAFDTETSD 40
>gnl|CDD|235561 PRK05686, fliG, flagellar motor switch protein G; Validated.
Length = 339
Score = 26.3 bits (59), Expect = 5.9
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 99 LIESLEEEDSDAFSETVKE----FDSISRLDQ 126
++ESLEEED + +E +K+ F+ + LD
Sbjct: 222 ILESLEEEDPEL-AEKIKDLMFVFEDLVDLDD 252
>gnl|CDD|216818 pfam01970, TctA, Tripartite tricarboxylate transporter TctA family.
This family, formerly known as DUF112, is a family of
bacterial and archaeal tripartite tricarboxylate
transporters of the extracytoplasmic solute binding
receptor-dependent transporter group of families,
distinct from the ABC and TRAP-T families. TctA is part
of the tripartite TctABC system which, as characterized
in S. typhimurium, is a secondary carrier that depends
for activity on the extracytoplasmic
tricarboxylate-binding receptor TctC as well as two
integral membrane proteins, TctA and TctB. complete
three-component systems are found only in bacteria. TctA
is a large transmembrane protein with up to 12 predicted
membrane spanning regions in bacteria and up to 11 such
in archaea, with the N-terminal within the cytoplasm.
TctA is thought to be a permease, and in most other
bacteria functions without TctB and TctC molecules.
Length = 418
Score = 26.3 bits (59), Expect = 6.5
Identities = 9/40 (22%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 1 MLMVIFMLMLIP-----MAMPFRLMLIFMLMMTFRIVYSL 35
+L++I L LI + +P+R++ +L+ Y++
Sbjct: 347 LLLLILGLPLIRLFARLLRIPYRILYPIILVFCVVGAYAI 386
>gnl|CDD|214436 MTH00151, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 565
Score = 26.3 bits (59), Expect = 7.5
Identities = 9/54 (16%), Positives = 19/54 (35%)
Query: 6 FMLMLIPMAMPFRLMLIFMLMMTFRIVYSLLFYSTGKAATENSLMKYNSKEYFF 59
+ L + ++ ++ ++ LF S G + S K +FF
Sbjct: 433 LLQSLFEGFSEEFFLPSYLKLLIGFVILLGLFLSFGFWDSGFSSSKMVKLSFFF 486
>gnl|CDD|227734 COG5447, COG5447, Uncharacterized conserved protein [Function
unknown].
Length = 115
Score = 25.6 bits (56), Expect = 8.0
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 84 SPAFQ-----DTREYKFLLKLIESLEEEDSDAFSETVKEFDSISRLDQW 127
SPA Q ++ +F + + ++EE DA E FD D W
Sbjct: 51 SPAPQTSYDEESDGERFFEQRLRGVDEEALDARLEREIRFDP----DIW 95
>gnl|CDD|213564 TIGR00839, aspA, aspartate ammonia-lyase. This enzyme, aspartate
ammonia-lyase, shows local homology to a number of other
lyases, as modeled by Pfam model pfam00206. Fumarate
hydratase scores as high as 570 bits against this model
[Energy metabolism, Amino acids and amines].
Length = 468
Score = 25.9 bits (57), Expect = 8.4
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 93 YKFLLKLIESLEEEDSDAFSETVKEFDSISRL 124
Y L+KL++++ + D F + KEF I ++
Sbjct: 152 YSSLIKLVDAINQL-RDGFEQKAKEFADILKM 182
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 26.2 bits (58), Expect = 8.9
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 79 RYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSISRL 124
Y++L A ++ K ++ LEEE AF E + + L
Sbjct: 603 EYLELKDAEKELER---EEKELKKLEEELDKAFEELAETEKRLEEL 645
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
0.329 0.139 0.400
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,334,783
Number of extensions: 663263
Number of successful extensions: 1640
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1539
Number of HSP's successfully gapped: 149
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.3 bits)