RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11015
(360 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 = 114 bits (287), Expect = 2e-29
Identities = 54/195 (27%), Positives = 85/195 (43%), Gaps = 42/195 (21%)
Query: 161 SSFKTSLLSC--------------YKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRL 206
S+ T L S +R+ +GH V VA P +L S+S D+T+++
Sbjct: 60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKV 119
Query: 207 WSTQTGKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIWQAVINWECLVSNNDNDS 266
W +TGKC+ GH+ VNSV F P+ V S+S D ++ +W
Sbjct: 120 WDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLW----------------- 162
Query: 267 DLDESKEPDESSITLRTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTI 326
DL K V L GH+ V + + DGE+++++S D L+D+ TG
Sbjct: 163 DLRTGK-----------CVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKC 211
Query: 327 LQSLTEPGEAIRAAA 341
L +L + + A
Sbjct: 212 LGTLRGHENGVNSVA 226
Score = 112 bits (283), Expect = 7e-29
Identities = 50/169 (29%), Positives = 80/169 (47%), Gaps = 28/169 (16%)
Query: 173 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLP 232
+ + GH D V VA P + S+S D T++LW +TGKCV +GH+G VNSV F P
Sbjct: 128 LTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSP 187
Query: 233 NKDLVLSASGDKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLRTPVKELLGHS 292
+ + +LS+S D ++ +W DL K + L GH
Sbjct: 188 DGEKLLSSSSDGTIKLW-----------------DLSTGKC-----------LGTLRGHE 219
Query: 293 NVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTEPGEAIRAAA 341
N V + + DG + + S D ++D+ TG +Q+L+ ++ + A
Sbjct: 220 NGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLA 268
Score = 104 bits (262), Expect = 7e-26
Identities = 42/152 (27%), Positives = 66/152 (43%), Gaps = 28/152 (18%)
Query: 169 SCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSV 228
+ + + +GH V VA P L S+S+D T++LW TGKC+ GH VNSV
Sbjct: 166 TGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSV 225
Query: 229 RFLPNKDLVLSASGDKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLRTPVKEL 288
F P+ L+ S S D ++ +W + V+ L
Sbjct: 226 AFSPDGYLLASGSEDGTIRVW----------------------------DLRTGECVQTL 257
Query: 289 LGHSNVVIAADWLSDGEQVITASWDRVANLFD 320
GH+N V + W DG+++ + S D ++D
Sbjct: 258 SGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 101 bits (254), Expect = 9e-25
Identities = 41/159 (25%), Positives = 69/159 (43%), Gaps = 28/159 (17%)
Query: 173 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLP 232
R+ GH GV VA P +L + S D T+++W +TG+ + GH+G V V
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASA 61
Query: 233 NKDLVLSASGDKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLRTPVKELLGHS 292
+ + S S DK++ +W + V+ L GH+
Sbjct: 62 DGTYLASGSSDKTIRLW----------------------------DLETGECVRTLTGHT 93
Query: 293 NVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLT 331
+ V + + DG + ++S D+ ++DVETG L +L
Sbjct: 94 SYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLR 132
Score = 101 bits (253), Expect = 1e-24
Identities = 48/176 (27%), Positives = 80/176 (45%), Gaps = 28/176 (15%)
Query: 166 SLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSV 225
L + +R+ GH V DVA L S S+D+T+RLW +TG+CV +GH+ V
Sbjct: 37 DLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYV 96
Query: 226 NSVRFLPNKDLVLSASGDKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLRTPV 285
+SV F P+ ++ S+S DK++ +W + +
Sbjct: 97 SSVAFSPDGRILSSSSRDKTIKVW----------------------------DVETGKCL 128
Query: 286 KELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTEPGEAIRAAA 341
L GH++ V + + DG V ++S D L+D+ TG + +LT + + A
Sbjct: 129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVA 184
Score = 64.7 bits (158), Expect = 9e-12
Identities = 30/118 (25%), Positives = 48/118 (40%), Gaps = 28/118 (23%)
Query: 214 CVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIWQAVINWECLVSNNDNDSDLDESKE 273
GH+G V V F P+ L+ + SGD ++ +W E
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVW---------------------DLE 39
Query: 274 PDESSITLRTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLT 331
E TL+ GH+ V +DG + + S D+ L+D+ETG +++LT
Sbjct: 40 TGELLRTLK-------GHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLT 90
Score = 42.7 bits (101), Expect = 2e-04
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 166 SLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWS 208
L + +++ SGH + V +A P L S SAD T+R+W
Sbjct: 247 DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 41.6 bits (98), Expect = 4e-04
Identities = 17/58 (29%), Positives = 29/58 (50%)
Query: 284 PVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTEPGEAIRAAA 341
+ L GH+ V + DG+ + T S D ++D+ETG +L++L +R A
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVA 58
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 72.4 bits (176), Expect = 6e-14
Identities = 72/329 (21%), Positives = 126/329 (38%), Gaps = 22/329 (6%)
Query: 23 SDTMSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIER 82
++ + K K +L + + S + L S L L S + R
Sbjct: 3 DNSSTSSENKSKLLKKSELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLR 62
Query: 83 EFELLYLENLNLQDKIDMLMEKLDRESIINEKYPECNDMECVTNMNKNFNKQKVLASNPS 142
E D +L D +I + + + K+ S+P
Sbjct: 63 GHEDSITSIAFSPDGELLLSGSSDG-TIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPD 121
Query: 143 AQKLKTTNKLKVQTSKIVSSFKTSLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSAS-AD 201
+ + T K+ L IR+ GH + V +A P +L S S D
Sbjct: 122 GNSILLASSSLDGTVKLWDLSTPGKL----IRTLEGHSESVTSLAFSPDGKLLASGSSLD 177
Query: 202 RTVRLWSTQTGKCVLQYSGHSGSVNSVRFLPNKD-LVLSASGDKSVHIWQAVINWECLVS 260
T++LW +TGK + +GH+ V+S+ F P+ L+ S S D ++ +W +
Sbjct: 178 GTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRST 237
Query: 261 NNDNDSDLDESKEPDESSI---------------TLRTPVKELLGHSNVVIAADWLSDGE 305
+ + + S PD S + + + ++ L GHS+ V++ + DG+
Sbjct: 238 LSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGK 297
Query: 306 QVITASWDRVANLFDVETGTILQSLTEPG 334
+ + S D L+D+ETG +L SLT G
Sbjct: 298 LLASGSSDGTVRLWDLETGKLLSSLTLKG 326
Score = 62.8 bits (151), Expect = 7e-11
Identities = 51/180 (28%), Positives = 86/180 (47%), Gaps = 18/180 (10%)
Query: 173 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYS--GHSGSVNSVRF 230
+R+ SGH V VA P +L S S+D TVRLW +TGK + + GH G V+S+ F
Sbjct: 277 LRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSF 336
Query: 231 LPN-KDLVLSASGDKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLR------- 282
P+ LV S D ++ +W + + L + + + L S PD ++
Sbjct: 337 SPDGSLLVSGGSDDGTIRLWD-LRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVR 395
Query: 283 -------TPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQSLTEPGE 335
+ ++ L GH++ V + D+ DG+ + + S D L+D++T S + G+
Sbjct: 396 LWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPDGK 455
Score = 47.0 bits (110), Expect = 1e-05
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 166 SLLSCYKIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSV 225
L + +++ GH V V+ P V+ S S D TVRLW TG + GH+ V
Sbjct: 357 DLRTGKPLKTLEGH-SNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRV 415
Query: 226 NSVRFLPNKDLVLSASGDKSVHIW 249
S+ F P+ + S S D ++ +W
Sbjct: 416 TSLDFSPDGKSLASGSSDNTIRLW 439
Score = 46.6 bits (109), Expect = 1e-05
Identities = 47/230 (20%), Positives = 88/230 (38%), Gaps = 35/230 (15%)
Query: 120 DMECVTNMNKNFNKQKVLASNPSAQKLKTTNKLKVQTSKIVSSFKTSLLSCYKIRS--FS 177
D ++ NK+ +K + +++ SL+S + S
Sbjct: 3 DNSSTSSENKSKLLKKSELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLR 62
Query: 178 GHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQ--YSGHSGSVNSVRFL-PNK 234
GH D + +A P +L S S+D T++LW G+ +++ H SV+ + P+
Sbjct: 63 GHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDG 122
Query: 235 DLVLSASG--DKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLRTPVKELLGHS 292
+ +L AS D +V +W + ++ L GHS
Sbjct: 123 NSILLASSSLDGTVKLWDLSTPGKL---------------------------IRTLEGHS 155
Query: 293 NVVIAADWLSDGEQVITAS-WDRVANLFDVETGTILQSLTEPGEAIRAAA 341
V + + DG+ + + S D L+D+ TG L +L + + + A
Sbjct: 156 ESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLA 205
Score = 32.0 bits (71), Expect = 0.51
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 12/74 (16%)
Query: 173 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLP 232
+R+ GH V + P L S S+D T+RLW +T S+ SV F P
Sbjct: 405 LRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKT------------SLKSVSFSP 452
Query: 233 NKDLVLSASGDKSV 246
+ ++ S S D SV
Sbjct: 453 DGKVLASKSSDLSV 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 = 51.2 bits (123), Expect = 5e-09
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 211 TGKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIW 249
+G+ + GH+G V SV F P+ + S S D ++ +W
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 43.5 bits (103), Expect = 2e-06
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 173 IRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWS 208
+++ GH V VA P L S S D T++LW
Sbjct: 5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 36.1 bits (84), Expect = 9e-04
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 282 RTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFD 320
+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 = 49.7 bits (119), Expect = 1e-08
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 212 GKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIW 249
GK + GH+G V SV F P+ +L+ S S D +V +W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 43.9 bits (104), Expect = 2e-06
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 172 KIRSFSGHRDGVWDVAVRPGQPVLGSASADRTVRLWS 208
+R+ GH V VA P +L S S D TVR+W
Sbjct: 3 LLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.6 bits (85), Expect = 6e-04
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 282 RTPVKELLGHSNVVIAADWLSDGEQVITASWDRVANLFD 320
++ 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: 178 GHRDGVWDVAVRP-GQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLPNKDL 236
GH V V+ P VL SA AD V +W + GK V HS + S+ + + L
Sbjct: 123 GHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSL 182
Query: 237 VLSASGDKSVHI 248
+ + S DK ++I
Sbjct: 183 LCTTSKDKKLNI 194
Score = 32.6 bits (74), Expect = 0.31
Identities = 40/161 (24%), Positives = 65/161 (40%), Gaps = 37/161 (22%)
Query: 178 GHRDGVWDVAVRPGQPV-LGSASADRTVRLW-------STQTGKCVLQYSGHSGSVNSVR 229
G + DVA P P L +AS D T+ W + ++ GH+ V V
Sbjct: 73 GQEGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVS 132
Query: 230 FLPNKDLVLSASG-DKSVHIWQAVINWECLVSNNDNDSDLDESKEPDESSITLRTPVKEL 288
F P+ VL+++G D V++W D++ V+ +
Sbjct: 133 FHPSAMNVLASAGADMVVNVW-----------------DVERG-----------KAVEVI 164
Query: 289 LGHSNVVIAADWLSDGEQVITASWDRVANLFDVETGTILQS 329
HS+ + + +W DG + T S D+ N+ D GTI+ S
Sbjct: 165 KCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSS 205
>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 = 35.9 bits (83), Expect = 0.026
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 12/85 (14%)
Query: 191 GQPVLGSASADRTVRLWSTQTGKCVLQYSGHSGSVNSVRFLPNKDLVLSASGDKSVHIWQ 250
GQ L + S D T+R+W+ TG+C + R+L + S +
Sbjct: 231 GQTFLFTLSLDGTLRVWNLDTGQCA--FLPSRADSGGSRYLC---VTYSPFSSGEFKFFS 285
Query: 251 AVINWECLVSNNDNDSDLDESKEPD 275
+ S DS + E PD
Sbjct: 286 -------VKSGALVDSSVIEDSFPD 303
>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 = 34.1 bits (79), Expect = 0.074
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 21/89 (23%)
Query: 30 STKHKRTASGKLSN-LGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFELLY 88
K + A K L ++++ L +YD ++LP + + +L+S Y
Sbjct: 82 KKKKHKDAEYKKEFILSEEEIE----KLLKKYD-IILPKKRNYYIETLYSH--------Y 128
Query: 89 LENLNLQDKIDMLMEKLDRESIINEKYPE 117
+ +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 = 0.11
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 178 GHRDGVWDVAVRPG-QPVLGSASADRTVRLW----------STQTGKCVLQYSGHSGSVN 226
GH + D+ P +L S S D T+R+W + +C+L+ GH ++
Sbjct: 72 GHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILK--GHKKKIS 129
Query: 227 SVRFLPNKDLVLSASG-DKSVHIW 249
+ + P ++ +SG D V+IW
Sbjct: 130 IIDWNPMNYYIMCSSGFDSFVNIW 153
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 33.6 bits (77), Expect = 0.20
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 26 MSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFE 85
+S T H R A L L QDL + T + Y DVVLP+S + + F+ ER +
Sbjct: 661 LSDPDTNHVRAALEALDFLVVQDLFLTET---ANYADVVLPASASLEKDGTFTNTERRIQ 717
Query: 86 LLY 88
LY
Sbjct: 718 RLY 720
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.3 bits (75), Expect = 0.31
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 319 FDVETGTILQSLTEPGEAIRAAAGRTGG 346
+D +TG ++ LTE G+ A G GG
Sbjct: 96 YDADTGELIADLTEHGQRFLVAKGGKGG 123
>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 = 30.3 bits (69), Expect = 0.57
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 79 QIEREFELLYLENLNLQDKIDMLMEKLDRESIINEK 114
Q+ +++E LY EN L+++I+ L EKL+ + E
Sbjct: 29 QVIKDYEALYKENEELKEEIERLEEKLEEYKELEET 64
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 31.8 bits (73), Expect = 0.59
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 318 LFDVETGTILQSLTEPGEAIRAAAGRTGG 346
+ D +TG +L LTE G+ A G GG
Sbjct: 96 VRDEDTGELLADLTEHGQRFLVAKGGRGG 124
>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 = 31.7 bits (72), Expect = 0.70
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 26 MSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFE 85
S +T R A KL L QD+ M T ++Y DVVLP++ + F+ ER +
Sbjct: 396 QSDPNTSKVRKALEKLELLVVQDIFMTET---AKYADVVLPAAAWLEKEGTFTNAERRIQ 452
Query: 86 LLY 88
+
Sbjct: 453 RFF 455
>gnl|CDD|236270 PRK08471, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 613
Score = 31.6 bits (72), Expect = 0.78
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 111 INEKYPECNDMECVTNMNKNFNKQKVLASNPS--AQKLKTTNKLKVQTSKIVSSFKT 165
++ +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 = 30.3 bits (69), Expect = 0.86
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 72 KLNSLFSQIEREFELLYLENLNLQDKIDMLMEKLD-RESIINEKYPECNDME 122
+LN L +E E LE D L + ++ ++ + Y E E
Sbjct: 67 ELNELAELLE-ELGEDGLEAFAALDHFGSLEDLIELKDDFEDAYYGEYESEE 117
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 30.5 bits (70), Expect = 1.2
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 319 FDVETGTILQSLTEPGEAIRAAAGRTGG 346
+D +TG +L LTEPG+ A G GG
Sbjct: 95 YDADTGELLADLTEPGQRFLVAKGGRGG 122
>gnl|CDD|110047 pfam01018, GTP1_OBG, GTP1/OBG. The N-terminal domain of B.
subtilis GTPase obgE has the OBG fold, which is formed
by three glycine-rich regions inserted into a small
8-stranded beta-sandwich these regions form six
left-handed collagen-like helices packed and H-bonded
together.
Length = 156
Score = 28.4 bits (64), Expect = 3.5
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 319 FDVETGTILQSLTEPGEAIRAAAGRTGG 346
D++ G +L L G+ + AA G GG
Sbjct: 95 LDLDNGELLADLVHHGQRLLAAKGGKGG 122
>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 = 3.6
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 8/64 (12%)
Query: 43 NLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFELLYLENLNLQDKIDMLM 102
QD L T L + V +P K + ER +E LQDKID ++
Sbjct: 420 GWSPQDWDNLYTDLPNRQLKVKVPDRSVIK----TTDAERRL----VEPKGLQDKIDAIV 471
Query: 103 EKLD 106
K +
Sbjct: 472 AKYN 475
>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 = 28.7 bits (65), Expect = 4.0
Identities = 8/19 (42%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 276 ESSITLRTPVKELLGHSNV 294
+ LR V+ELLGH+++
Sbjct: 251 NNGADLRA-VQELLGHASL 268
>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 = 4.2
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 24 DTMSQKSTKHKRTASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIERE 83
D + +++ +K+ +GKL L ++ LR + + L V F + L ++ +
Sbjct: 297 DRLKEETVLYKKLLAGKLVELQEKIFKYLRLLDKGKVSEEELEEIVDFLEDELCIKLPED 356
Query: 84 FELLYLENLNLQDKIDMLMEKLDR 107
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 = 4.4
Identities = 14/70 (20%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 37 ASGKLSNLGDQDLSMLRTHLNSEYDDVVLPSSVKFKLNSLFSQIEREFELLYLENLNLQD 96
A KL+ + +L L +++++ + + + +E ++L EN+ L+D
Sbjct: 184 ARIKLAAQEKIHVEILEEQLEKLRNELLIRGATE---GLCVHSLSKELDVLKEENMLLKD 240
Query: 97 KIDMLMEKLD 106
I L +L
Sbjct: 241 DIQFLKAELI 250
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 28.1 bits (62), Expect = 9.7
Identities = 28/115 (24%), Positives = 42/115 (36%), Gaps = 45/115 (39%)
Query: 179 HRDGVWDVAVRPGQP-VLGSASADRTVRLWSTQTGK-----------CVLQYS------- 219
H VW + P +L S S D +V+LWS G C +Q+
Sbjct: 574 HEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSL 633
Query: 220 -------------------------GHSGSVNSVRFLPNKDLVLSASGDKSVHIW 249
GHS +V+ VRF+ + LV S+S D ++ +W
Sbjct: 634 AFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFVDSSTLV-SSSTDNTLKLW 687
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
0.313 0.129 0.367
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: 17,325,620
Number of extensions: 1596741
Number of successful extensions: 1165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1140
Number of HSP's successfully gapped: 50
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
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 (21.9 bits)
S2: 60 (26.9 bits)