RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2305
(334 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 = 62.7 bits (153), Expect = 3e-11
Identities = 69/305 (22%), Positives = 108/305 (35%), Gaps = 52/305 (17%)
Query: 7 VDEAPDGTCLLTNSNDNHLRTFDLPSELHCKSVWRPSNQRPKLNYTLKIKEGGIIYDYVW 66
V +PDG L T S D ++ VW TLK G + D
Sbjct: 15 VAFSPDGKLLATGSGDGTIK------------VWDLETGELL--RTLKGHTGPV-RDVAA 59
Query: 67 YPKTSSIDGFTSYFLCSSMYAPIHLWDSVGGEIKATYRPYNQVDEVTHAYSLAFSLDGNK 126
+Y S I LWD GE T + V S+AFS DG
Sbjct: 60 SA-------DGTYLASGSSDKTIRLWDLETGECVRTLTGHTS--YV---SSVAFSPDGRI 107
Query: 127 IYAGFL-SEVKIFSTDRPGRECVSRNLKPWFRKNIVSAIAINPVHPDICALGTYSKIIGL 185
+ + +K++ G+ + + V+++A +P + + + I L
Sbjct: 108 LSSSSRDKTIKVWDV-ETGKCLTTLR----GHTDWVNSVAFSPDGTFVAS-SSQDGTIKL 161
Query: 186 FSDSDGRPLFFLKGHNGGITHLEFSSNGILLFSGARKDCEIICWDLRNPGCILHTFPRQV 245
+ G+ + L GH G + + FS +G L S + D I WDL C+ T
Sbjct: 162 WDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSS-DGTIKLWDLSTGKCL-GTLRGH- 218
Query: 246 STNQRVYFDLTSCSNYLL-SGNTNGDLSIWNVNTSNLPSSPYEESVQEPLYKFSAHQDCT 304
V S YLL SG+ +G + +W++ T E + S H +
Sbjct: 219 --ENGVNSVAFSPDGYLLASGSEDGTIRVWDLRT------------GECVQTLSGHTNSV 264
Query: 305 NGVRW 309
+ W
Sbjct: 265 TSLAW 269
Score = 53.1 bits (128), Expect = 6e-08
Identities = 39/199 (19%), Positives = 74/199 (37%), Gaps = 31/199 (15%)
Query: 116 YSLAFSLDGNKIYAGFLSE---VKIFSTDRPGRECVSRNLKPWFRKNIVSAIAINPVHPD 172
+AFS DG + G S +K++ + + R V+A A
Sbjct: 13 TCVAFSPDGKLLATG--SGDGTIKVWDLETGELLRTLKGHTGPVRD--VAASADGTY--- 65
Query: 173 ICALGTYSKIIGLFSDSDGRPLFFLKGHNGGITHLEFSSNGILLFSGARKDCEIICWDLR 232
A G+ K I L+ G + L GH ++ + FS +G + S + +D I WD+
Sbjct: 66 -LASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDG-RILSSSSRDKTIKVWDVE 123
Query: 233 NPGCI--LHTFPRQVSTNQRVYFDLTSCSNYLLSGNTNGDLSIWNVNTSNLPSSPYEESV 290
C+ L V++ + ++ S + +G + +W++ T
Sbjct: 124 TGKCLTTLRGHTDWVNS-----VAFSPDGTFVASSSQDGTIKLWDLRT------------ 166
Query: 291 QEPLYKFSAHQDCTNGVRW 309
+ + + H N V +
Sbjct: 167 GKCVATLTGHTGEVNSVAF 185
Score = 52.0 bits (125), Expect = 1e-07
Identities = 41/145 (28%), Positives = 63/145 (43%), Gaps = 17/145 (11%)
Query: 89 IHLWDSVGGEIKATYRPYNQVDEVTHAYSLAFSLDGNKIYAGFL-SEVKIF--STDRPGR 145
I LWD G+ AT + EV S+AFS DG K+ + +K++ ST +
Sbjct: 159 IKLWDLRTGKCVATLTGHT--GEV---NSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLG 213
Query: 146 ECVSRNLKPWFRKNIVSAIAINPVHPDICALGTYSKIIGLFSDSDGRPLFFLKGHNGGIT 205
N V+++A +P + A G+ I ++ G + L GH +T
Sbjct: 214 TLRGHE-------NGVNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVT 265
Query: 206 HLEFSSNGILLFSGARKDCEIICWD 230
L +S +G L SG+ D I WD
Sbjct: 266 SLAWSPDGKRLASGS-ADGTIRIWD 289
Score = 50.4 bits (121), Expect = 4e-07
Identities = 34/132 (25%), Positives = 56/132 (42%), Gaps = 22/132 (16%)
Query: 197 LKGHNGGITHLEFSSNGILLFSGARKDCEIICWDLRNPGCILHTFPRQVSTNQRVYFDLT 256
LKGH GG+T + FS +G LL +G+ D I WDL G +L T + T +
Sbjct: 5 LKGHTGGVTCVAFSPDGKLLATGSG-DGTIKVWDL-ETGELLRTL--KGHTGPVRDVAAS 60
Query: 257 SCSNYLLSGNTNGDLSIWNVNTSNLPSSPYEESVQEPLYKFSAHQDCTNGVRWKHHKFER 316
+ YL SG+++ + +W++ T E + + H + V +
Sbjct: 61 ADGTYLASGSSDKTIRLWDLETG------------ECVRTLTGHTSYVSSVAFSPD---G 105
Query: 317 DLLVA---DATC 325
+L + D T
Sbjct: 106 RILSSSSRDKTI 117
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 61.3 bits (147), Expect = 2e-10
Identities = 50/239 (20%), Positives = 86/239 (35%), Gaps = 19/239 (7%)
Query: 72 SIDGFTSYFLCSSMYAPIHLWDSVGGEIKATYRPYNQVDEVTHAYSLAFSLDGNKIYAGF 131
+ L S I LWD G + + + + + + S DGN I
Sbjct: 72 AFSPDGELLLSGSSDGTIKLWDLDNG--EKLIKSLEGLHDSSVSKLALSSPDGNSILLAS 129
Query: 132 LSEVK-IFSTDRPGRECVSRNLKPWFRKNIVSAIAINPVHPDICALGTYSKIIGLFSDSD 190
S + D + R L+ V+++A +P + + + I L+
Sbjct: 130 SSLDGTVKLWDLSTPGKLIRTLEG--HSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRT 187
Query: 191 GRPLFFLKGHNGGITHLEFSSNGILLFSGARKDCEIICWDLRNPGCILHTFPRQVSTNQR 250
G+PL L GH ++ L FS +G LL + D I WDL + T
Sbjct: 188 GKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSD---S 244
Query: 251 VYFDLTSCSNYLLSGNTNGDLSIWNVNTSNLPSSPYEESVQEPLYKFSAHQDCTNGVRW 309
V + + L SG+++G + +W++ +S+ L S H V +
Sbjct: 245 VVSSFSPDGSLLASGSSDGTIRLWDLRSSS-----------SLLRTLSGHSSSVLSVAF 292
Score = 57.8 bits (138), Expect = 3e-09
Identities = 74/302 (24%), Positives = 119/302 (39%), Gaps = 33/302 (10%)
Query: 6 DVDEAPDGTCLLTNSNDNHLRTFDLPSELHCKSVWRPSNQRPKLNYTLKIKEGGIIYDYV 65
+ +PDG LL+ S+D ++ +DL + KL +L+ +
Sbjct: 70 SIAFSPDGELLLSGSSDGTIKLWDL-------------DNGEKLIKSLEGLHDSSVSKLA 116
Query: 66 WYPKTSSIDGFTSYFLCSSMYAPIHLWDSVGGEIKATYRPYNQVDEVTHAYSLAFSLDGN 125
SS DG + SS+ + LWD + SLAFS DG
Sbjct: 117 L----SSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHS----ESVTSLAFSPDGK 168
Query: 126 KIYAG--FLSEVKIFSTDRPGRECVSRNLKPWFRKNIVSAIAINPVHPDICALGTYSKII 183
+ +G +K++ VS++A +P + A G+ I
Sbjct: 169 LLASGSSLDGTIKLWDLRTGKPLSTLAGHTDP-----VSSLAFSPDGGLLIASGSSDGTI 223
Query: 184 GLFSDSDGRPLFF-LKGHNGGITHLEFSSNGILLFSGARKDCEIICWDLRNPGCILHTFP 242
L+ S G+ L L GH+ + FS +G LL SG+ D I WDLR+ +L T
Sbjct: 224 RLWDLSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSS-DGTIRLWDLRSSSSLLRTLS 281
Query: 243 RQVSTNQRVYFDLTSCSNYLLSGNTNGDLSIWNVNTSNLPSSPYEESVQEPLYKFSAHQD 302
S+ V F L SG+++G + +W++ T L SS + + P+ S D
Sbjct: 282 GHSSSVLSVAFS--PDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPD 339
Query: 303 CT 304
+
Sbjct: 340 GS 341
Score = 51.2 bits (121), Expect = 3e-07
Identities = 55/283 (19%), Positives = 107/283 (37%), Gaps = 39/283 (13%)
Query: 6 DVDEAPDGTCLLTNSN-DNHLRTFDLPSELHCKSVWRPSNQRPKLNYTLKIKEGGIIYDY 64
+ +PDG L + S+ D ++ +DL + ++ + +
Sbjct: 160 SLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHT---------------DPVSSL 204
Query: 65 VWYPKTSSIDGFTSYFLCSSMYAPIHLWDSVGGEIKATYRPYNQVDEVTHAYSLAFSLDG 124
+ P + S I LWD G++ + + V+ +FS DG
Sbjct: 205 AFSPDGGLL------IASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVS-----SFSPDG 253
Query: 125 NKIYAGFL-SEVKIFSTDRPGRECVSRNLKPWFRKNIVSAIAINPVHPDICALGTYSKII 183
+ + +G ++++ R + V ++A +P + A G+ +
Sbjct: 254 SLLASGSSDGTIRLWDL-RSSSSLLRTLSGHSSS---VLSVAFSPDG-KLLASGSSDGTV 308
Query: 184 GLFSDSDGR--PLFFLKGHNGGITHLEFSSNGILLFSGARKDCEIICWDLRNPGCILHTF 241
L+ G+ LKGH G ++ L FS +G LL SG D I WDLR +
Sbjct: 309 RLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLE 368
Query: 242 PRQVSTNQRVYFDLTSCSNYLLSGNTNGDLSIWNVNTSNLPSS 284
+ + + SG+T+G + +W+++T +L +
Sbjct: 369 GHSNVLS----VSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRN 407
>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 = 38.4 bits (90), Expect = 1e-04
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 190 DGRPLFFLKGHNGGITHLEFSSNGILLFSGARKDCEIICWD 230
G L LKGH G +T + FS +G L SG+ D I WD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSD-DGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 38.1 bits (89), Expect = 2e-04
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 191 GRPLFFLKGHNGGITHLEFSSNGILLFSGARKDCEIICWD 230
G+ L LKGH G +T + FS +G LL SG+ D + WD
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSD-DGTVRVWD 39
>gnl|CDD|227282 COG4946, COG4946, Uncharacterized protein related to the
periplasmic component of the Tol biopolymer transport
system [Function unknown].
Length = 668
Score = 32.9 bits (75), Expect = 0.28
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 13/78 (16%)
Query: 57 EGGIIYDYVWYPKTSSIDGFTSYFLCSSMYA-PIHLWDSVGGEIKATYRPYNQVDEVTHA 115
E G+I D+ W+P + + +Y Y I L+D GG+I P +
Sbjct: 442 EYGLITDFDWHPNSR----WIAYAFPEGYYTQSIKLYDMDGGKIYDVTTPT------AYD 491
Query: 116 YSLAFSLDGNKIYAGFLS 133
+S AF DG +Y FLS
Sbjct: 492 FSPAFDPDGRYLY--FLS 507
>gnl|CDD|214519 smart00108, B_lectin, Bulb-type mannose-specific lectin.
Length = 114
Score = 30.4 bits (69), Expect = 0.46
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 13 GTCLLTNSNDNHLRTFDLPSELHCKSVWRPSNQRPKLNYTLKIKEGG--IIYD----YVW 66
+C LT +D +L +D + VW + NY L + + G +IYD ++W
Sbjct: 54 DSCTLTLQSDGNLVLYDGDG----RVVWSSNTTGANGNYVLVLLDDGNLVIYDSDGNFLW 109
>gnl|CDD|236623 PRK09775, PRK09775, putative DNA-binding transcriptional regulator;
Provisional.
Length = 442
Score = 30.3 bits (69), Expect = 1.5
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 294 LYKFSAHQDCTNGVRWKHHKFERDLLVADA 323
+ KFSA D RW RDLL+A+
Sbjct: 225 IVKFSAADDNPVSQRW------RDLLIAEH 248
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 26.6 bits (59), Expect = 4.4
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 275 NVNTSNLPSSPYEESVQEPLYKFSAHQDCTNGVRWKHHKFERDLLVADA 323
NV NLP S EE ++E L KF D V+ K+ F L +A+A
Sbjct: 5 NVYIGNLPESYSEEELREDLEKFGP-IDQIKIVKEKNIAFVHFLSIANA 52
>gnl|CDD|146175 pfam03397, Rhabdo_matrix, Rhabdovirus matrix protein.
Length = 168
Score = 27.9 bits (62), Expect = 5.9
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 97 GEIKAT-YRPYNQVDEVTHAYSLAFSLDGNKIYAGFLSEVKIFS 139
G + T P N V+++ A LA ++ G + F V +F
Sbjct: 26 GTLTITGPPPGNLVEKICMAMKLARAILGGDQHPAFNPLVHLFQ 69
>gnl|CDD|237995 cd00028, B_lectin, Bulb-type mannose-specific lectin. The domain
contains a three-fold internal repeat (beta-prism
architecture). The consensus sequence motif QXDXNXVXY is
involved in alpha-D-mannose recognition. Lectins are
carbohydrate-binding proteins which specifically
recognize diverse carbohydrates and mediate a wide
variety of biological processes, such as cell-cell and
host-pathogen interactions, serum glycoprotein turnover,
and innate immune responses.
Length = 116
Score = 26.9 bits (60), Expect = 7.4
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 10/58 (17%)
Query: 15 CLLTNSNDNHLRTFDLPSELHCKSVWRPSNQRPKLNYTLKIKEGG--IIYD----YVW 66
C LT +D +L +D VW + R NY L + + G ++YD ++W
Sbjct: 57 CTLTLQSDGNLVIYDGSG----TVVWSSNTTRVNGNYVLVLLDDGNLVLYDSDGNFLW 110
>gnl|CDD|237138 PRK12563, PRK12563, sulfate adenylyltransferase subunit 2;
Provisional.
Length = 312
Score = 27.8 bits (62), Expect = 7.8
Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 26 RTFDLPSELHCKSVWRPSNQRPKL 49
R F S H W P QRP+L
Sbjct: 157 RIFSFRSAFH---RWDPKAQRPEL 177
>gnl|CDD|219469 pfam07569, Hira, TUP1-like enhancer of split. The Hira proteins
are found in a range of eukaryotes and are implicated in
the assembly of repressive chromatin. These proteins
also contain pfam00400.
Length = 214
Score = 27.6 bits (62), Expect = 8.2
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 255 LTSCSNYLLSGNTNGDLSIWNVNTSNLPSSP 285
L S +YLL + G L +WNV T P
Sbjct: 18 LESNGSYLLCITSVGLLYVWNVKTKKAILPP 48
>gnl|CDD|221863 pfam12931, Sec16_C, Sec23-binding domain of Sec16. Sec16 is a
multi-domain vesicle coat protein. The C-terminal region
is the part that binds to Sec23, a COPII vesicle coat
protein. This association is part of the transport
vesicle coat structure.
Length = 274
Score = 27.6 bits (62), Expect = 8.4
Identities = 23/126 (18%), Positives = 40/126 (31%), Gaps = 25/126 (19%)
Query: 106 YNQVDEVTHAYSLAFSLDGNKIYAGFLSE-VKIFSTDRPGRECVSRNLKPWFRKNIVSAI 164
+ TH +L + +++AG E + E +N W + V+ I
Sbjct: 51 FPVGKNNTHLLALIY-----QVFAGNSKESIDELVPPNAEGEWALQN---W--RETVALI 100
Query: 165 AINPVHPD---ICALG----TYSKIIG-----LFSDSDGRPLFFLKGHNGGITHLEF--S 210
N D + LG +Y + + + P+ L + L F
Sbjct: 101 LSNRSSDDHEALLELGKLLSSYGRTEAAHICFILAGVPLSPIPVLPDSDVLFVLLGFLND 160
Query: 211 SNGILL 216
ILL
Sbjct: 161 LESILL 166
>gnl|CDD|176211 cd08249, enoyl_reductase_like, enoyl_reductase_like. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H)-binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 339
Score = 27.5 bits (62), Expect = 9.5
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 161 VSAIAINPV---HPDICALGTYSKIIG 184
V A+A+NPV H D + +Y I+G
Sbjct: 33 VKAVALNPVDWKHQDYGFIPSYPAILG 59
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
0.320 0.137 0.436
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: 16,887,500
Number of extensions: 1570173
Number of successful extensions: 993
Number of sequences better than 10.0: 1
Number of HSP's gapped: 969
Number of HSP's successfully gapped: 21
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)