RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7157
(167 letters)
>gnl|CDD|218954 pfam06246, Isy1, Isy1-like splicing family. Isy1 protein is
important in the optimisation of splicing.
Length = 253
Score = 218 bits (558), Expect = 1e-72
Identities = 82/133 (61%), Positives = 99/133 (74%), Gaps = 4/133 (3%)
Query: 34 ARNAEKAMTTLARWRAAHE----HTDQVKDRRPYLASECKSLPAAEKWRSQIIREISRKV 89
ARN+EKA + L R+R A D + RRP L SE SLP AEKWRSQII+EISRKV
Sbjct: 2 ARNSEKAQSMLNRFREAKAAEAGGLDSNRTRRPKLISEVTSLPEAEKWRSQIIKEISRKV 61
Query: 90 AQIQNAGLGEFRIRDLNDEINKLLREKSHWEAQIKELDGPDYARVGPRMLDHDGKEVPGN 149
+IQ+ LGE++IRDLNDEINKL REK HWE +I+EL GPDY R+ ++ D +GKEVPG
Sbjct: 62 TEIQDPSLGEYQIRDLNDEINKLFREKRHWEDRIRELGGPDYRRLSGKLNDAEGKEVPGG 121
Query: 150 RGYKYFGAAKDLP 162
RGY+YFG AK+LP
Sbjct: 122 RGYRYFGRAKELP 134
Score = 47.3 bits (113), Expect = 6e-07
Identities = 18/28 (64%), Positives = 22/28 (78%)
Query: 1 MKDIDADYYGYRDDDDGVLIPLEMKEEK 28
K IDADYYGYRD++DGVL+ E + EK
Sbjct: 159 YKRIDADYYGYRDEEDGVLLEYEAEREK 186
>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 = 32.0 bits (73), Expect = 0.14
Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 69 KSLPAAEKWRSQIIREISRKVAQIQNAGLGEFRIRDLNDEINKLLREKSHWEAQIKELDG 128
K A E+ + I R+++ +++ I +L + ++ + +IK+L
Sbjct: 230 KEKEALERQKEAIERQLASLEEELEKL---TEEISELEKRLEEIEQLLEELNKKIKDLGE 286
Query: 129 PDYARVGPRMLD 140
+ RV ++ +
Sbjct: 287 EEQLRVKEKIGE 298
>gnl|CDD|236165 PRK08147, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 547
Score = 28.9 bits (65), Expect = 1.4
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 78 RSQIIREISRKVAQIQNAGLGEFRIRDLNDEINKL 112
+ I V QI N +I LND+I +L
Sbjct: 155 DKGVNTAIGSSVDQINNYAK---QIASLNDQITRL 186
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 28.7 bits (65), Expect = 1.4
Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 52 EHTDQVKDRRPYLASECKSLPAAEKWRS-QIIREISRKVAQIQNAGLGEFRIRDLNDEIN 110
E D+++ P L + ++I+++ ++ +I E I++L +EI+
Sbjct: 57 EALDKLRSYLPKLNPLREEKKKVSVKSLEELIKDVEEELEKI------EKEIKELEEEIS 110
Query: 111 KLLREKSHWEAQIKEL 126
+L E E +I+ L
Sbjct: 111 ELENEIKELEQEIERL 126
>gnl|CDD|185129 PRK15207, PRK15207, long polar fimbrial outer membrane usher
protein LpfC; Provisional.
Length = 842
Score = 28.7 bits (64), Expect = 1.7
Identities = 29/109 (26%), Positives = 47/109 (43%), Gaps = 16/109 (14%)
Query: 39 KAMTTLARWRAAHEHTDQVKDRRPYLASECKSLPAAEKWRSQIIREISRKVAQI---QNA 95
K+ TL A + D V+ R LAS+ + LP +++ + ++R I++ A++ QN
Sbjct: 252 KSQLTLGDTATAGDIFDSVQMRGALLASDEEMLPDSQRGFAPVVRGIAKSNAEVSIEQNG 311
Query: 96 GL--------GEFRIRDLNDEINKLLREKSHWEAQIKELDGPDYARVGP 136
+ G F I DL N IKE DG + + P
Sbjct: 312 YVIYRTFVQPGAFEINDLYPTSN-----SGDLTVIIKEADGSEQRFIQP 355
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 28.3 bits (64), Expect = 2.4
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 78 RSQIIREISRKVAQIQNAGLGEFRIRDL-NDEINKLLREKSHWEAQIKEL 126
+ ++I E+S A L + R+R L +EI KL +E E +I EL
Sbjct: 366 KKELIEELSEIQAD----YLLDMRLRRLTKEEIEKLEKEIEELEKEIAEL 411
>gnl|CDD|222255 pfam13600, DUF4140, N-terminal domain of unknown function
(DUF4140). This family is often found at the N-terminus
of its member proteins, with DUF4139, pfam13598, at the
C-terminus.
Length = 101
Score = 26.1 bits (58), Expect = 4.8
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 76 KWRSQII--REISRKVAQIQNAGLGEFRIRDLNDEINKLLREKSHWEAQIKELD 127
R + S +A+++ +R L DE+ L EK EAQIK L
Sbjct: 54 SVRRDYLPDEATSPALAELEE------ELRALEDELAALEAEKEALEAQIKFLS 101
>gnl|CDD|176449 cd00281, DAP_dppA, Peptidase M55, D-aminopeptidase
dipeptide-binding protein family. M55 Peptidase,
D-Aminopeptidase dipeptide-binding protein (dppA; DAP
dppA; EC 3.4.11.-) domain: Peptide transport systems are
found in many bacterial species and generally function
to accumulate intact peptides in the cell, where they
are hydrolyzed. The dipeptide-binding protein (dppA) of
Bacillus subtilis belongs to the dipeptide ABC transport
(dpp) operon expressed early during sporulation. It is a
binuclear zinc-dependent, D-specific aminopeptidase. The
biologically active enzyme is a homodecamer with active
sites buried in its channel. These
self-compartmentalizing proteases are characterized by a
SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the
preferred substrates. Bacillus subtilis dppA is thought
to function as an adaptation to nutrient deficiency;
hydrolysis of its substrate releases D-Ala which can be
used subsequently as metabolic fuel. This family also
contains a number of uncharacterized putative
peptidases.
Length = 265
Score = 26.8 bits (59), Expect = 5.3
Identities = 14/63 (22%), Positives = 24/63 (38%)
Query: 72 PAAEKWRSQIIREISRKVAQIQNAGLGEFRIRDLNDEINKLLREKSHWEAQIKELDGPDY 131
P E +R Q+ + AG + ++D +D L+ E+ Q+ G Y
Sbjct: 26 PGYEAFREQMTEAVIAACEGSLAAGATQVLVKDSHDSGRNLIPERLPEPVQLISGSGHPY 85
Query: 132 ARV 134
V
Sbjct: 86 CMV 88
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 26.9 bits (60), Expect = 5.7
Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 64 LASECKSLPAAEKWR-----SQIIREISRKVAQIQNAGLGEFRIRDLNDEINKLLREKSH 118
L E + E R ++++EI KV +++ E +++L +I L +KS
Sbjct: 194 LEDELEDCDPTELDRAKEKLKKLLQEIMIKVKKLEEL---EEELQELESKIEDLTNKKSE 250
Query: 119 WEAQIKELDG 128
+I E +
Sbjct: 251 LNTEIAEAEK 260
>gnl|CDD|239460 cd03344, GroEL, GroEL_like type I chaperonin. Chaperonins are
involved in productive folding of proteins. They share a
common general morphology, a double toroid of 2 stacked
rings, each composed of 7-9 subunits. The symmetry of
type I is seven-fold and they are found in eubacteria
(GroEL) and in organelles of eubacterial descent (hsp60
and RBP). With the aid of cochaperonin GroES, GroEL
encapsulates non-native substrate proteins inside the
cavity of the GroEL-ES complex and promotes folding by
using energy derived from ATP hydrolysis.
Length = 520
Score = 27.0 bits (61), Expect = 5.9
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 21 PLEMKEEKHRYCHARNAEKA 40
+E+KE+K R A NA +A
Sbjct: 383 EVELKEKKDRVEDALNATRA 402
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 26.8 bits (59), Expect = 7.0
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 55 DQVKDRRPYLASECKSLPAAEKWRSQIIREISRKVAQIQNAGLGEFRIRDLNDEINKLLR 114
+++K L + K + EK S ++EI R + NA ++ +E++ L
Sbjct: 190 EKLKSSNLELENIKKQIADDEKSHSITLKEIERLSIEYNNAMDDYNNLKSALNELSSLED 249
Query: 115 EKSHWEAQIKELDG 128
K+ +E++IK +
Sbjct: 250 MKNRYESEIKTAES 263
>gnl|CDD|234450 TIGR04056, OMP_RagA_SusC, TonB-linked outer membrane protein,
SusC/RagA family. This model describes a distinctive
clade among the TonB-linked outer membrane proteins
(OMP). Members of this family are restricted to the
Bacteriodetes lineage (except for Gemmatimonas
aurantiaca T-27 from the novel phylum Gemmatimonadetes)
and occur in high copy numbers, with over 100 members
from Bacteroides thetaiotaomicron VPI-5482 alone.
Published descriptions of members of this family are
available for RagA from Porphyromonas gingivalis, SusC
from Bacteroides thetaiotaomicron, and OmpW from
Bacteroides caccae. Members form pairs with members of
the SusD/RagB family (pfam07980). Transporter complexes
including these outer membrane proteins are likely to
import large degradation products of proteins (e.g.
RagA) or carbohydrates (e.g. SusC) as nutrients, rather
than siderophores [Transport and binding proteins,
Unknown substrate].
Length = 982
Score = 26.8 bits (60), Expect = 7.2
Identities = 13/38 (34%), Positives = 16/38 (42%)
Query: 123 IKELDGPDYARVGPRMLDHDGKEVPGNRGYKYFGAAKD 160
I ELD DY V + +G + GY G KD
Sbjct: 744 ILELDEGDYLPVKYPYISKEGYPIGQIYGYIADGLFKD 781
>gnl|CDD|215951 pfam00498, FHA, FHA domain. The FHA (Forkhead-associated) domain
is a phosphopeptide binding motif.
Length = 67
Score = 24.9 bits (55), Expect = 7.2
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 85 ISRKVAQIQNAGLGEFRIRDLN 106
+SR+ A+I+ G G F + DL
Sbjct: 18 VSRRHAEIRYDGGGRFYLEDLG 39
>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type.
Members of this protein family include secreted (or
membrane-anchored) pullulanases of Gram-negative
bacteria and pullulanase-type starch debranching enzymes
of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
linkages. Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. This
family is closely homologous to, but architecturally
different from, the Gram-positive pullulanases of
Gram-positive bacteria (TIGR02102) [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 898
Score = 26.7 bits (59), Expect = 7.3
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 137 RMLDHDGKEVPGNRGYKYFGAAKDLPVGY 165
+ DH+GK V G Y GA P GY
Sbjct: 621 VLTDHEGKVVTGEE-LDYNGA----PAGY 644
>gnl|CDD|212566 cd11684, DHR2_DOCK, Dock Homology Region 2, a GEF domain, of
Dedicator of Cytokinesis proteins. DOCK proteins
comprise a family of atypical guanine nucleotide
exchange factors (GEFs) that lack the conventional Dbl
homology (DH) domain. As GEFs, they activate the small
GTPases Rac and Cdc42 by exchanging bound GDP for free
GTP. They are also called the CZH (CED-5, Dock180, and
MBC-zizimin homology) family, after the first family
members identified. Dock180 was first isolated as a
binding partner for the adaptor protein Crk. The
Caenorhabditis elegans protein, Ced-5, is essential for
cell migration and phagocytosis, while the Drosophila
ortholog, Myoblast city (MBC), is necessary for myoblast
fusion and dorsal closure. DOCKs are divided into four
classes (A-D) based on sequence similarity and domain
architecture: class A includes Dock1 (or Dock180), 2 and
5; class B includes Dock3 and 4; class C includes Dock6,
7, and 8; and class D includes Dock9, 10 and 11. All
DOCKs contain two homology domains: the DHR-1 (Dock
homology region-1), also called CZH1, and DHR-2 (also
called CZH2 or Docker). This alignment model represents
the DHR-2 domain of DOCK proteins, which contains the
catalytic GEF activity for Rac and/or Cdc42.
Length = 392
Score = 26.5 bits (59), Expect = 7.8
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 13/80 (16%)
Query: 52 EHTDQVKDRRPYLASECKSLPAAEKWRSQIIREISRKVAQIQNAGLGEFRIRDLNDEINK 111
E TDQ K+R E S P + RS+++ +++ I+NA I D+ + +
Sbjct: 238 EITDQWKERTILTTEE--SFPTILR-RSEVVSIEEIELSPIENA------IEDIEKKTEE 288
Query: 112 LLREKSHWEAQIKELDGPDY 131
L + + D P+
Sbjct: 289 LRSL----INKYRSGDSPNV 304
>gnl|CDD|218797 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2. This
family consists of several Eukaryotic rRNA processing
protein EBP2 sequences. Ebp2p is required for the
maturation of 25S rRNA and 60S subunit assembly. Ebp2p
may be one of the target proteins of Rrs1p for executing
the signal to regulate ribosome biogenesis. This family
also plays a role in chromosome segregation.
Length = 270
Score = 26.5 bits (59), Expect = 7.9
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 52 EHTDQVKDRRPYLASECKSLPAAEKWRSQIIREISRKVAQIQNAGLGEFRI---RDLNDE 108
EH +V+ + L +E + A+E+ R Q RE+ + Q+Q L E R +D+ ++
Sbjct: 115 EHMQKVRKK---LLAEAAAKKASEEARKQ--RELKKFGKQVQVEKLQE-RAKEKKDMLEK 168
Query: 109 INKLLREKSHWEAQIKELD 127
I KL +++ + D
Sbjct: 169 IKKLKKKRKGGGDEGDLFD 187
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 26.6 bits (59), Expect = 8.4
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 4/81 (4%)
Query: 51 HEHTDQVKDRRPYLASECKSLPAAEKWRSQIIREISRKVAQIQNAGL----GEFRIRDLN 106
+ + + + + A ++ ++ E+ ++ E R L
Sbjct: 768 ESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLE 827
Query: 107 DEINKLLREKSHWEAQIKELD 127
EI +L E E ++ EL+
Sbjct: 828 QEIEELEEEIEELEEKLDELE 848
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 26.4 bits (59), Expect = 9.6
Identities = 25/149 (16%), Positives = 47/149 (31%), Gaps = 50/149 (33%)
Query: 45 ARWRAAHEHTDQVKDRRPYLASEC-KSLPAAEKWRSQIIREISRKVAQIQNAGLGEFRIR 103
R ++++ R L+ E ++L E ++I E+ +++ E +
Sbjct: 36 EERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKEL---EAALD 92
Query: 104 DLNDEINKLL------------------------------------REKSHWEAQIKELD 127
+L E++ LL K H E ++L
Sbjct: 93 ELEAELDTLLLTIPNIPHESVPVGKDEDDNVEVRRWGEPPVFVFDFEPKDHVEL-GEKLG 151
Query: 128 GPDYARVGPRMLDHDGKEVPGNRGYKYFG 156
D+ R +V G+R Y Y G
Sbjct: 152 LLDFER---------AAKVSGSRFYFYKG 171
>gnl|CDD|220735 pfam10408, Ufd2P_core, Ubiquitin elongating factor core. This is
the most conserved part of the core region of Ufd2P
ubiquitin elongating factor or E4, running from helix
alpha-11 to alpha-38. It consists of 31 helices of
variable length connected by loops of variable size
forming a compact unit; the helical packing pattern of
the compact unit consists of five structural repeats
that resemble tandem Armadillo (ARM) repeats. This
domain is involved in ubiquitination as it binds Cdc48p
and escorts ubiquitinated proteins from Cdc48p to the
proteasome for degradation. The core is structurally
similar to the nuclear transporter protein
importin-alpha. The core is associated with the U-box at
the C-terminus, pfam04564, which has ligase activity.
Length = 625
Score = 26.5 bits (59), Expect = 9.8
Identities = 5/45 (11%), Positives = 21/45 (46%)
Query: 79 SQIIREISRKVAQIQNAGLGEFRIRDLNDEINKLLREKSHWEAQI 123
+ ++ + ++ +++ + +++ L ++ L EK E +
Sbjct: 194 LRELKRLQDELEELEQSRSNWAQLKRLEKQLEILSAEKLSLEGFL 238
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 26.2 bits (58), Expect = 9.9
Identities = 20/106 (18%), Positives = 38/106 (35%), Gaps = 9/106 (8%)
Query: 55 DQVKDRRPYLASECKSLPAAEKWRSQIIREISRKVAQIQNAGLGEFRIRDLNDEINKLLR 114
+ +D+R L + KSL E + + ++ ++ +I DLN +N L
Sbjct: 55 REQQDQRAKLEKQLKSL---ETEIASLEAQLIETADDLKKL---RKQIADLNARLNALEV 108
Query: 115 EKSHWEAQIKELDGPDY---ARVGPRMLDHDGKEVPGNRGYKYFGA 157
++ ++ E P +L R Y+GA
Sbjct: 109 QEREQRRRLAEQLAALQRSGRNPPPALLVSPEDAQRSVRLAIYYGA 154
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
0.318 0.136 0.415
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,005,993
Number of extensions: 822770
Number of successful extensions: 982
Number of sequences better than 10.0: 1
Number of HSP's gapped: 975
Number of HSP's successfully gapped: 62
Length of query: 167
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 77
Effective length of database: 6,945,742
Effective search space: 534822134
Effective search space used: 534822134
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 (21.7 bits)
S2: 55 (25.0 bits)