RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8430
(361 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 116 bits (292), Expect = 4e-30
Identities = 57/188 (30%), Positives = 89/188 (47%), Gaps = 30/188 (15%)
Query: 140 IVSSFKTSLL----SCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKC 195
SS KT L + +R+ +GH V VA P +L S+S D+T+++W +TGKC
Sbjct: 68 SGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKC 127
Query: 196 VLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIWQAVINWECLNNDNDSDLDESKEPDE 255
+ GH+ VNSV F P+ V S+S D ++ +W DL K
Sbjct: 128 LTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLW---------------DLRTGK---- 168
Query: 256 SSITLRTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTGHDEE 315
V L GH+ V + + DGE+++++S D L+D+ TG L +L GH+
Sbjct: 169 -------CVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENG 221
Query: 316 PHILCVSS 323
+ + S
Sbjct: 222 VNSVAFSP 229
Score = 107 bits (268), Expect = 1e-26
Identities = 51/176 (28%), Positives = 83/176 (47%), Gaps = 28/176 (15%)
Query: 147 SLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSV 206
L + +R+ GH V DVA L S S+D+T+RLW +TG+CV +GH+ V
Sbjct: 37 DLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYV 96
Query: 207 NSVRFLPNKDLVLSASGDKSVHIWQAVINWECLNNDNDSDLDESKEPDESSITLRTPVKE 266
+SV F P+ ++ S+S DK++ +W + +
Sbjct: 97 SSVAFSPDGRILSSSSRDKTIKVW--------------------------DVETGKCLTT 130
Query: 267 LLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTGHDEEPHILCVS 322
L GH++ V + + DG V ++S D L+D+ TG + +LTGH E + V+
Sbjct: 131 LRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGE--VNSVA 184
Score = 105 bits (264), Expect = 4e-26
Identities = 43/159 (27%), Positives = 71/159 (44%), Gaps = 26/159 (16%)
Query: 154 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLP 213
R+ GH GV VA P +L + S D T+++W +TG+ + GH+G V V
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASA 61
Query: 214 NKDLVLSASGDKSVHIWQAVINWECLNNDNDSDLDESKEPDESSITLRTPVKELLGHSNV 273
+ + S S DK++ +W + V+ L GH++
Sbjct: 62 DGTYLASGSSDKTIRLW--------------------------DLETGECVRTLTGHTSY 95
Query: 274 VIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTGH 312
V + + DG + ++S D+ ++DVETG L +L GH
Sbjct: 96 VSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGH 134
Score = 102 bits (256), Expect = 4e-25
Identities = 42/150 (28%), Positives = 66/150 (44%), Gaps = 26/150 (17%)
Query: 150 SCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSV 209
+ + + +GH V VA P L S+S+D T++LW TGKC+ GH VNSV
Sbjct: 166 TGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSV 225
Query: 210 RFLPNKDLVLSASGDKSVHIWQAVINWECLNNDNDSDLDESKEPDESSITLRTPVKELLG 269
F P+ L+ S S D ++ +W + V+ L G
Sbjct: 226 AFSPDGYLLASGSEDGTIRVW--------------------------DLRTGECVQTLSG 259
Query: 270 HSNVVIAADWLSDGEQVITASWDRVANLFD 299
H+N V + W DG+++ + S D ++D
Sbjct: 260 HTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 71.6 bits (176), Expect = 4e-14
Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 28/128 (21%)
Query: 195 CVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIWQAVINWECLNNDNDSDLDESKEPD 254
GH+G V V F P+ L+ + SGD ++ +W E
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-------------------DLETG 41
Query: 255 ESSITLRTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTGHDE 314
E TL+ GH+ V +DG + + S D+ L+D+ETG +++LTGH
Sbjct: 42 ELLRTLK-------GHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTS 94
Query: 315 EPHILCVS 322
+ V+
Sbjct: 95 Y--VSSVA 100
Score = 41.6 bits (98), Expect = 3e-04
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 147 SLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWS 189
L + +++ SGH + V +A P L S SAD T+R+W
Sbjct: 247 DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 68.6 bits (166), Expect = 1e-12
Identities = 52/189 (27%), Positives = 88/189 (46%), Gaps = 19/189 (10%)
Query: 153 KIRSFSGHRDGVWDVAVRPGQPVLGSAS-ADRTVRLWSTQTGKCVLQYSGHSGSVNSVRF 211
IR+ GH + V +A P +L S S D T++LW +TGK + +GH+ V+S+ F
Sbjct: 147 LIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAF 206
Query: 212 LPNKD-LVLSASGDKSVHIW------------QAVINWECLNNDNDSDLDESKEPDESSI 258
P+ L+ S S D ++ +W + + D L S D +
Sbjct: 207 SPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIR 266
Query: 259 -----TLRTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTGHD 313
+ + ++ L GHS+ V++ + DG+ + + S D L+D+ETG +L SLT
Sbjct: 267 LWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKG 326
Query: 314 EEPHILCVS 322
E + +S
Sbjct: 327 HEGPVSSLS 335
Score = 57.8 bits (138), Expect = 4e-09
Identities = 47/167 (28%), Positives = 78/167 (46%), Gaps = 18/167 (10%)
Query: 154 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYS--GHSGSVNSVRF 211
+R+ SGH V VA P +L S S+D TVRLW +TGK + + GH G V+S+ F
Sbjct: 277 LRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSF 336
Query: 212 LPN-KDLVLSASGDKSVHIWQ-----AVINWECLNNDNDSDLDESKE-----PDESSITL 260
P+ LV S D ++ +W + E +N + ++ L
Sbjct: 337 SPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRL 396
Query: 261 R-----TPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVET 302
+ ++ L GH++ V + D+ DG+ + + S D L+D++T
Sbjct: 397 WDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKT 443
Score = 47.0 bits (110), Expect = 1e-05
Identities = 32/111 (28%), Positives = 51/111 (45%), Gaps = 1/111 (0%)
Query: 147 SLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSV 206
L + +++ GH V V+ P V+ S S D TVRLW TG + GH+ V
Sbjct: 357 DLRTGKPLKTLEGH-SNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRV 415
Query: 207 NSVRFLPNKDLVLSASGDKSVHIWQAVINWECLNNDNDSDLDESKEPDESS 257
S+ F P+ + S S D ++ +W + + ++ D + SK D S
Sbjct: 416 TSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPDGKVLASKSSDLSV 466
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats (blades)
of the beta propeller domain.
Length = 40
Score = 49.2 bits (118), Expect = 2e-08
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 192 TGKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIW 230
+G+ + GH+G V SV F P+ + S S D ++ +W
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 41.9 bits (99), Expect = 8e-06
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 154 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWS 189
+++ GH V VA P L S S D T++LW
Sbjct: 5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 35.0 bits (81), Expect = 0.002
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 261 RTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFD 299
+K L GH+ V + + DG+ + + S D L+D
Sbjct: 2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 48.1 bits (115), Expect = 5e-08
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 193 GKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIW 230
GK + GH+G V SV F P+ +L+ S S D +V +W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 42.7 bits (101), Expect = 5e-06
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 153 KIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWS 189
+R+ GH V VA P +L S S D TVR+W
Sbjct: 3 LLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 35.8 bits (83), Expect = 0.001
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 261 RTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFD 299
++ L GH+ V + + DG + + S D ++D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 38.3 bits (89), Expect = 0.005
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 159 GHRDGVWDVAVRP-GQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLPNKDL 217
GH V V+ P VL SA AD V +W + GK V HS + S+ + + L
Sbjct: 123 GHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSL 182
Query: 218 VLSASGDKSVHI 229
+ + S DK ++I
Sbjct: 183 LCTTSKDKKLNI 194
Score = 35.3 bits (81), Expect = 0.044
Identities = 42/163 (25%), Positives = 68/163 (41%), Gaps = 35/163 (21%)
Query: 159 GHRDGVWDVAVRPGQPV-LGSASADRTVRLW-------STQTGKCVLQYSGHSGSVNSVR 210
G + DVA P P L +AS D T+ W + ++ GH+ V V
Sbjct: 73 GQEGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVS 132
Query: 211 FLPNKDLVLSASG-DKSVHIWQAVINWECLNNDNDSDLDESKEPDESSITLRTPVKELLG 269
F P+ VL+++G D V++W D++ K V+ +
Sbjct: 133 FHPSAMNVLASAGADMVVNVW---------------DVERGK-----------AVEVIKC 166
Query: 270 HSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTGH 312
HS+ + + +W DG + T S D+ N+ D GTI+ S+ H
Sbjct: 167 HSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSSVEAH 209
>gnl|CDD|222731 pfam14393, DUF4422, Domain of unknown function (DUF4422). This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 255 and
371 amino acids in length.
Length = 230
Score = 33.3 bits (77), Expect = 0.12
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 21/89 (23%)
Query: 11 STKHKRTASGKLSN-LGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFELLY 69
K + A K L ++++ L +YD ++LP + + +L+S Y
Sbjct: 82 KKKKHKDAEYKKEFILSEEEIE----KLLKKYD-IILPKKRNYYIETLYSH--------Y 128
Query: 70 LENLNLQDKIDMLMEKLDRESIINEKYPE 98
+ +D +D+ E +I EKYPE
Sbjct: 129 AHAHHKED-LDLTRE------VIAEKYPE 150
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 34.2 bits (78), Expect = 0.12
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 159 GHRDGVWDVAVRPG-QPVLGSASADRTVRLW----------STQTGKCVLQYSGHSGSVN 207
GH + D+ P +L S S D T+R+W + +C+L+ GH ++
Sbjct: 72 GHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILK--GHKKKIS 129
Query: 208 SVRFLPNKDLVLSASG-DKSVHIW 230
+ + P ++ +SG D V+IW
Sbjct: 130 IIDWNPMNYYIMCSSGFDSFVNIW 153
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 33.6 bits (77), Expect = 0.15
Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 172 GQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIWQ 231
GQ L + S D T+R+W+ TG+C + R+L + S +
Sbjct: 231 GQTFLFTLSLDGTLRVWNLDTGQCA--FLPSRADSGGSRYLC---VTYSPFSSGEFKFFS 285
Query: 232 AVINWECLNNDNDSDLDESKEPD 254
DS + E PD
Sbjct: 286 VKS-----GALVDSSVIEDSFPD 303
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 33.6 bits (77), Expect = 0.19
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 7 MSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFE 66
+S T H R A L L QDL + T + Y DVVLP+S + + F+ ER +
Sbjct: 661 LSDPDTNHVRAALEALDFLVVQDLFLTET---ANYADVVLPASASLEKDGTFTNTERRIQ 717
Query: 67 LLY 69
LY
Sbjct: 718 RLY 720
>gnl|CDD|218434 pfam05103, DivIVA, DivIVA protein. The Bacillus subtilis divIVA1
mutation causes misplacement of the septum during cell
division, resulting in the formation of small,
circular, anucleate mini-cells. Inactivation of divIVA
produces a mini-cell phenotype, whereas overproduction
of DivIVA results in a filamentation phenotype. These
proteins appear to contain coiled-coils.
Length = 131
Score = 31.1 bits (71), Expect = 0.39
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 60 QIEREFELLYLENLNLQDKIDMLMEKLDRESIINEK 95
Q+ +++E LY EN L+++I+ L EKL+ + E
Sbjct: 29 QVIKDYEALYKENEELKEEIERLEEKLEEYKELEET 64
>gnl|CDD|130652 TIGR01591, Fdh-alpha, formate dehydrogenase, alpha subunit,
archaeal-type. This model describes a subset of formate
dehydrogenase alpha chains found mainly archaea but also
in alpha and gamma proteobacteria and a small number of
gram positive bacteria. The alpha chain contains domains
for molybdopterin dinucleotide binding and molybdopterin
oxidoreductase (pfam01568 and pfam00384, respectively).
The holo-enzyme also contains beta and gamma subunits.
The enzyme catalyzes the oxidation of formate (produced
from pyruvate during anaerobic growth) to carbon dioxide
with the concomitant release of two electrons and two
protons. The enzyme's purpose is to allow growth on
formate in some circumstances and, in the case of FdhH
in gamma proteobacteria, to pass electrons to
hydrogenase (by which process acid is neutralized). This
model is well-defined, with only a single fragmentary
sequence falling between trusted and noise. The alpha
subunit of a version of nitrate reductase is closely
related.
Length = 671
Score = 32.1 bits (73), Expect = 0.59
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 7 MSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFE 66
S +T R A KL L QD+ M T ++Y DVVLP++ + F+ ER +
Sbjct: 396 QSDPNTSKVRKALEKLELLVVQDIFMTET---AKYADVVLPAAAWLEKEGTFTNAERRIQ 452
Query: 67 LLY 69
+
Sbjct: 453 RFF 455
>gnl|CDD|236270 PRK08471, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 613
Score = 31.6 bits (72), Expect = 0.77
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 92 INEKYPECNDMECVTNMNKNFNKQKVLASNPS--AQKLKTTNKLKVQTSKIVSSFKT 146
++ +P+ +D + ++ FN ASNP AQK K + T+ I + +
Sbjct: 98 ASQYFPDLDDTGILKDLQDYFNAWNDFASNPKDSAQKQALAQKTETLTNNIKDTRER 154
>gnl|CDD|219360 pfam07275, ArdA, Antirestriction protein (ArdA). This family
consists of several bacterial antirestriction (ArdA)
proteins. ArdA functions in bacterial conjugation to
allow an unmodified plasmid to evade restriction in the
recipient bacterium and yet acquire cognate
modification.
Length = 166
Score = 29.5 bits (67), Expect = 1.4
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 53 KLNSLFSQIEREFELLYLENLNLQDKIDMLMEKLD-RESIINEKYPECNDME 103
+LN L +E E LE D L + ++ ++ + Y E E
Sbjct: 67 ELNELAELLE-ELGEDGLEAFAALDHFGSLEDLIELKDDFEDAYYGEYESEE 117
>gnl|CDD|233788 TIGR02224, recomb_XerC, tyrosine recombinase XerC. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerC, one of two closely related
chromosomal proteins along with XerD (TIGR02225). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and homologs of XerC on other replicons, the
chomosomal copy was preferred for building this model.
This model does not detect all XerC, as some apparent
XerC examples score in the gray zone between trusted
(450) and noise (410) cutoffs, along with some XerD
examples. XerC and XerD interact with cell division
protein FtsK [DNA metabolism, DNA replication,
recombination, and repair].
Length = 295
Score = 29.5 bits (67), Expect = 2.9
Identities = 8/19 (42%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 255 ESSITLRTPVKELLGHSNV 273
+ LR V+ELLGH+++
Sbjct: 251 NNGADLRA-VQELLGHASL 268
>gnl|CDD|100088 cd03086, PGM3, PGM3 (phosphoglucomutase 3), also known as PAGM
(phosphoacetylglucosamine mutase) and AGM1
(N-acetylglucosamine-phosphate mutase), is an essential
enzyme found in eukaryotes that reversibly catalyzes the
conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate
as part of the UDP-N-acetylglucosamine (UDP-GlcNAc)
biosynthetic pathway. UDP-GlcNAc is an essential
metabolite that serves as the biosynthetic precursor of
many glycoproteins and mucopolysaccharides. AGM1 is a
member of the alpha-D-phosphohexomutase superfamily,
which catalyzes the intramolecular phosphoryl transfer
of sugar substrates. The alpha-D-phosphohexomutases have
four domains with a centrally located active site formed
by four loops, one from each domain. All four domains
are included in this alignment model.
Length = 513
Score = 29.1 bits (66), Expect = 3.7
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 8/64 (12%)
Query: 24 NLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFELLYLENLNLQDKIDMLM 83
QD L T L + V +P K + ER +E LQDKID ++
Sbjct: 420 GWSPQDWDNLYTDLPNRQLKVKVPDRSVIK----TTDAERRL----VEPKGLQDKIDAIV 471
Query: 84 EKLD 87
K +
Sbjct: 472 AKYN 475
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 29.3 bits (65), Expect = 3.8
Identities = 35/158 (22%), Positives = 55/158 (34%), Gaps = 65/158 (41%)
Query: 160 HRDGVWDVAVRPGQP-VLGSASADRTVRLWSTQTGK-----------CVLQYS------- 200
H VW + P +L S S D +V+LWS G C +Q+
Sbjct: 574 HEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSL 633
Query: 201 -------------------------GHSGSVNSVRFLPNKDLVLSASGDKSVHIWQAVIN 235
GHS +V+ VRF+ + LV S+S D ++ +W ++
Sbjct: 634 AFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFVDSSTLV-SSSTDNTLKLWDLSMS 692
Query: 236 WECLNNDNDSDLDESKEPDESSITLRTPVKELLGHSNV 273
+N TP+ +GH+NV
Sbjct: 693 ISGIN--------------------ETPLHSFMGHTNV 710
>gnl|CDD|222566 pfam14134, DUF4301, Domain of unknown function (DUF4301). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 505 and 516 amino
acids in length.
Length = 513
Score = 29.1 bits (66), Expect = 4.0
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 5 DTMSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIERE 64
D + +++ +K+ +GKL L ++ LR + + L V F + L ++ +
Sbjct: 297 DRLKEETVLYKKLLAGKLVELQEKIFKYLRLLDKGKVSEEELEEIVDFLEDELCIKLPED 356
Query: 65 FELLYLENLNLQDKIDMLMEKLDR 88
FE E + I+ L EKL+R
Sbjct: 357 FEKFSDE-----ELIEYLKEKLNR 375
>gnl|CDD|215507 PLN02939, PLN02939, transferase, transferring glycosyl groups.
Length = 977
Score = 29.1 bits (65), Expect = 4.2
Identities = 14/70 (20%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 18 ASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFELLYLENLNLQD 77
A KL+ + +L L +++++ + + + +E ++L EN+ L+D
Sbjct: 184 ARIKLAAQEKIHVEILEEQLEKLRNELLIRGATE---GLCVHSLSKELDVLKEENMLLKD 240
Query: 78 KIDMLMEKLD 87
I L +L
Sbjct: 241 DIQFLKAELI 250
>gnl|CDD|239154 cd02753, MopB_Formate-Dh-H, Formate dehydrogenase H (Formate-Dh-H)
catalyzes the reversible oxidation of formate to CO2
with the release of a proton and two electrons. It is a
component of the anaerobic formate hydrogen lyase
complex. The E. coli formate dehydrogenase H (Fdh-H) is
a monomer composed of a single polypeptide chain with a
Mo active site region and a [4Fe-4S] center. Members of
the MopB_Formate-Dh-H CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 512
Score = 27.9 bits (63), Expect = 9.6
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 7 MSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFE 66
+S +T H R A L L QD+ + T +E DVVLP++ + + F+ ER +
Sbjct: 357 LSDPNTNHVRKALESLEFLVVQDIFLTET---AELADVVLPAASFAEKDGTFTNTERRVQ 413
Query: 67 LLY 69
+
Sbjct: 414 RVR 416
>gnl|CDD|219447 pfam07520, SrfB, Virulence factor SrfB. This family includes
homologues of SsrAB is a two-component regulatory system
encoded within the Salmonella pathogenicity island
SPI-2. Among the products of genes activated by SsrAB
within epithelial and macrophage cells is Salmonella
typhimurium srfB. Homologues are found in several other
proteobacteria.
Length = 999
Score = 28.1 bits (63), Expect = 9.8
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 157 FSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGK-----CVLQYSGHSGSVNSVRF 211
F G + + RP +P A R++R+ S G + Y G +V+
Sbjct: 539 FGGRTEEFFAALARPDRPPAPGAVPGRSLRVASIDIGGGTTDLVITDYYLDDGVGANVKI 598
Query: 212 LP 213
+P
Sbjct: 599 IP 600
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 0.129 0.376
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,066,135
Number of extensions: 1563735
Number of successful extensions: 990
Number of sequences better than 10.0: 1
Number of HSP's gapped: 964
Number of HSP's successfully gapped: 44
Length of query: 361
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 263
Effective length of database: 6,590,910
Effective search space: 1733409330
Effective search space used: 1733409330
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: 60 (26.9 bits)