RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17688
(349 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 = 66.2 bits (162), Expect = 3e-12
Identities = 60/313 (19%), Positives = 107/313 (34%), Gaps = 69/313 (22%)
Query: 24 PLYSMNWSVRPDKLFRLAIGSYVEEYNNKVQIVALNEDISEFGPKSTIDHPYPTTKIMWI 83
+ + +S LA GS + +++ L K H P +
Sbjct: 11 GVTCVAFSPDGK---LLATGSG----DGTIKVWDLETGELLRTLKG---HTGPVRDVAAS 60
Query: 84 PDRKGVFPDLLATSGD--YLRVW--RAGEPETRLECILNNNKNSDFCAPLTSFDWNEVDP 139
D LA+ +R+W GE L + ++S ++ D
Sbjct: 61 ADGT-----YLASGSSDKTIRLWDLETGECVRTLTG---------HTSYVSSVAFS-PDG 105
Query: 140 NLLGTSSIDTTCTIWCLETNQVV-------GRVNSV------------------------ 168
+L +SS D T +W +ET + + VNSV
Sbjct: 106 RILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLR 165
Query: 169 SGHVKTQLIAHDKEVYDIAFSRAGGGRDMFASVGAEGSVRMFDLRHLEHSTIIYEDPQHT 228
+G L H EV +AFS G + +S ++G+++++DL + +
Sbjct: 166 TGKCVATLTGHTGEVNSVAFS--PDGEKLLSS-SSDGTIKLWDLSTGKCLGTLRGHEN-- 220
Query: 229 PLLRLAWNKQDPNYLAMVAMNACEVIILDVRVPCTPVARLNNHRACVNGIAWAPHSSCHI 288
+ +A++ YL + + D+R V L+ H V +AW+P +
Sbjct: 221 GVNSVAFS--PDGYLLASGSEDGTIRVWDLR-TGECVQTLSGHTNSVTSLAWSP-DGKRL 276
Query: 289 CTAGDDHQALIWD 301
+ D IWD
Sbjct: 277 ASGSADGTIRIWD 289
Score = 63.9 bits (156), Expect = 1e-11
Identities = 43/209 (20%), Positives = 81/209 (38%), Gaps = 43/209 (20%)
Query: 127 APLTSFDWNEVDPNLLGTSSIDTTCTIWCLETNQV----------VGRVNSVS------- 169
+T ++ D LL T S D T +W LET ++ V V + +
Sbjct: 10 GGVTCVAFSP-DGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLAS 68
Query: 170 --------------GHVKTQLIAHDKEVYDIAFSRAGGGRDMFASVGAEGSVRMFDLRHL 215
G L H V +AFS G + +S + +++++D+
Sbjct: 69 GSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDG---RILSSSSRDKTIKVWDVETG 125
Query: 216 EHSTIIYEDPQHT-PLLRLAWNKQDPNYLAMVAMNACEVIILDVRVPCTPVARLNNHRAC 274
+ T + HT + +A++ D ++A + + + D+R VA L H
Sbjct: 126 KCLTTL---RGHTDWVNSVAFS-PDGTFVA-SSSQDGTIKLWDLR-TGKCVATLTGHTGE 179
Query: 275 VNGIAWAPHSSCHICTAGDDHQALIWDIQ 303
VN +A++P + ++ D +WD+
Sbjct: 180 VNSVAFSP-DGEKLLSSSSDGTIKLWDLS 207
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 61.3 bits (147), Expect = 2e-10
Identities = 53/277 (19%), Positives = 107/277 (38%), Gaps = 38/277 (13%)
Query: 34 PDKLFRLAIGSYVEEYNNKVQIVALNEDISEFGPKSTIDHPYPTTKIMWIPDRKGVFPDL 93
PD L S + V++ L+ ++ H T + + PD L
Sbjct: 120 PDGNSILLASSS---LDGTVKLWDLSTPGKL--IRTLEGHSESVTSLAFSPD-----GKL 169
Query: 94 LATSGDY---LRVWRAGEPETRLECILNNNKNSDFCAPLTSFDWNEVDPNLLGTSSIDTT 150
LA+ +++W + L + P++S ++ L+ + S D T
Sbjct: 170 LASGSSLDGTIKLWDLRTGK--PLSTLAGHT-----DPVSSLAFSPDGGLLIASGSSDGT 222
Query: 151 CTIWCLETNQVVGRVNSVSGHVKTQLIAHDKEVYDIAFSRAGGGRDMFASVGAEGSVRMF 210
+W L T +++ +++SGH + + + FS G + AS ++G++R++
Sbjct: 223 IRLWDLSTGKLLR--STLSGHSDSVVSS---------FSPDG---SLLASGSSDGTIRLW 268
Query: 211 DLRHLEHSTIIYEDPQHTPLLRLAWNKQDPNYLAMVAMNACEVIILDVRVP-CTPVARLN 269
DLR +L +A++ D LA + + V + D+ L
Sbjct: 269 DLRSSSSLLRTLSGHSS-SVLSVAFSP-DGKLLASGS-SDGTVRLWDLETGKLLSSLTLK 325
Query: 270 NHRACVNGIAWAPHSSCHICTAGDDHQALIWDIQQMP 306
H V+ ++++P S + DD +WD++
Sbjct: 326 GHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGK 362
Score = 61.3 bits (147), Expect = 2e-10
Identities = 40/188 (21%), Positives = 75/188 (39%), Gaps = 13/188 (6%)
Query: 117 LNNNKNSDFCAPLTSFDWNEVDPNLLGTSSIDTTCTIWCLETNQVVGRVNSVSGHVKTQL 176
L++ +TS ++ LL + S D T +W L+ + + +K+
Sbjct: 56 LSSLLLRGHEDSITSIAFSPDGELLL-SGSSDGTIKLWDLDNGEKL---------IKSLE 105
Query: 177 IAHDKEVYDIAFSRAGGGRDMFASVGAEGSVRMFDLRHLEHSTIIYEDPQHTPLLRLAWN 236
HD V +A S G + AS +G+V+++DL +I H+ +
Sbjct: 106 GLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTP--GKLIRTLEGHSESVTSLAF 163
Query: 237 KQDPNYLAMVAMNACEVIILDVRVPCTPVARLNNHRACVNGIAWAPHSSCHICTAGDDHQ 296
D LA + + + D+R P++ L H V+ +A++P I + D
Sbjct: 164 SPDGKLLASGSSLDGTIKLWDLRTG-KPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGT 222
Query: 297 ALIWDIQQ 304
+WD+
Sbjct: 223 IRLWDLST 230
Score = 50.1 bits (118), Expect = 1e-06
Identities = 52/283 (18%), Positives = 116/283 (40%), Gaps = 41/283 (14%)
Query: 23 WPLYSMNWSVRPDKLFRLAIGSYVEEYNNKVQIVALNEDISEFGPKSTIDHPYPTTKIM- 81
P+ S+ +S PD +A GS + +++ D+S + + + +
Sbjct: 199 DPVSSLAFS--PDGGLLIASGSS----DGTIRLW----DLSTGKLLRSTLSGHSDSVVSS 248
Query: 82 WIPDRKGVFPDLLATSGDY-LRVWRAGEPETRLECILNNNKNSDFCAPLTSFDWNEVDPN 140
+ PD L + S D +R+W + L + ++ + S ++ D
Sbjct: 249 FSPDGS----LLASGSSDGTIRLWDLRSSSSLLRTLSGHSS------SVLSVAFSP-DGK 297
Query: 141 LLGTSSIDTTCTIWCLETNQVVGRVNSVSGHVKTQLIAHDKEVYDIAFSRAGGGRDMFAS 200
LL + S D T +W LET +++ L H+ V ++FS G + +
Sbjct: 298 LLASGSSDGTVRLWDLETGKLL---------SSLTLKGHEGPVSSLSFSP--DGSLLVSG 346
Query: 201 VGAEGSVRMFDLRHLEHSTIIYEDPQHTPLLRLAWNKQDPNYLAMVAMNACEVIILDVRV 260
+G++R++DLR + + H+ +L ++++ D ++ V + D+
Sbjct: 347 GSDDGTIRLWDLRTGKP---LKTLEGHSNVLSVSFSP-DGRVVS-SGSTDGTVRLWDLST 401
Query: 261 PCTPVARLNNHRACVNGIAWAPHSSCHICTAGDDHQALIWDIQ 303
+ + L+ H + V + ++P + + D+ +WD++
Sbjct: 402 G-SLLRNLDGHTSRVTSLDFSP-DGKSLASGSSDNTIRLWDLK 442
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 263 TPVARLNNHRACVNGIAWAPHSSCHICTAGDDHQALIWD 301
+ L H V +A++P ++ + DD +WD
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGK-YLASGSDDGTIKLWD 40
Score = 32.7 bits (75), Expect = 0.016
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 169 SGHVKTQLIAHDKEVYDIAFSRAGGGRDMFASVGAEGSVRMFD 211
SG + L H V +AFS G AS +G+++++D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDG---KYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 37.7 bits (88), Expect = 3e-04
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 262 CTPVARLNNHRACVNGIAWAPHSSCHICTAGDDHQALIWD 301
+ L H V +A++P + + + DD +WD
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGN-LLASGSDDGTVRVWD 39
Score = 31.9 bits (73), Expect = 0.027
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 170 GHVKTQLIAHDKEVYDIAFSRAGGGRDMFASVGAEGSVRMFD 211
G + L H V +AFS G ++ AS +G+VR++D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDG---NLLASGSDDGTVRVWD 39
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 35.7 bits (82), Expect = 0.037
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 264 PVARLNNHRACVNGIAWAPHSSCHICTAGDDHQALIWDIQQMPRAIE 310
P L H+ ++ I W P + +C++G D IWDI+ RA +
Sbjct: 117 PQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIENEKRAFQ 163
Score = 29.5 bits (66), Expect = 2.9
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 13/79 (16%)
Query: 90 FPDLLATSGDYL--RVWRAGEPETRL------ECILNNNKNSDFCAPLTSFDWNEVDPNL 141
F ++LA+ + L RVW + + +CIL +K ++ DWN ++ +
Sbjct: 86 FSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHKKK-----ISIIDWNPMNYYI 140
Query: 142 LGTSSIDTTCTIWCLETNQ 160
+ +S D+ IW +E +
Sbjct: 141 MCSSGFDSFVNIWDIENEK 159
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 32.8 bits (74), Expect = 0.35
Identities = 45/244 (18%), Positives = 99/244 (40%), Gaps = 39/244 (15%)
Query: 85 DRKGVFPDLLATSGDYLRVWRAGEPETRLEC--ILNNNKNSDFC-------APLTSFDWN 135
DR G + AT+G ++ EC I+ + ++ + + L+ WN
Sbjct: 492 DRDG---EFFATAGVNKKI-------KIFECESIIKDGRDIHYPVVELASRSKLSGICWN 541
Query: 136 EVDPNLLGTSSIDTTCTIWCLETNQVVGRVNSVSGHVKTQLIAHDKEVYDIAFSRAGGGR 195
+ + +S+ + +W + +Q+V T++ H+K V+ I +S A
Sbjct: 542 SYIKSQVASSNFEGVVQVWDVARSQLV-----------TEMKEHEKRVWSIDYSSA--DP 588
Query: 196 DMFASVGAEGSVRMFDLRHLEHSTIIYEDPQHTPLLRLAWNKQDPNYLAMVAMNACEVII 255
+ AS +GSV+++ + I + + + + LA + + +V
Sbjct: 589 TLLASGSDDGSVKLWS---INQGVSIGTIKTKANICCVQFPSESGRSLAFGSADH-KVYY 644
Query: 256 LDVRVPCTPVARLNNHRACVNGIAWAPHSSCHICTAGDDHQALIWDIQQMPRAI-EDPIL 314
D+R P P+ + H V+ + + S+ + ++ D+ +WD+ I E P+
Sbjct: 645 YDLRNPKLPLCTMIGHSKTVSYVRFVDSST--LVSSSTDNTLKLWDLSMSISGINETPLH 702
Query: 315 AYTA 318
++
Sbjct: 703 SFMG 706
>gnl|CDD|132329 TIGR03286, methan_mark_15, putative methanogenesis marker protein
15. Members of this protein family, to date, are found
in a completed prokaryotic genome if and only if the
species is one of the archaeal methanogens. The exact
function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
Related proteins include the BadF/BadG/BcrA/BcrD ATPase
family (pfam01869), which includes an activator for
(R)-2-hydroxyglutaryl-CoA dehydratase [Energy
metabolism, Methanogenesis].
Length = 404
Score = 29.4 bits (66), Expect = 2.9
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 142 LGTSSIDTTCTIWCLETNQVVGRVNSVSGHVKT-QLIAHDKEVYDIAFSRAGGGRDMFAS 200
LG S TT +E N+V+G +G V T ++I +E + A AG + +
Sbjct: 147 LGIDSGSTTTKAVVMEDNEVIG-----TGWVPTTKVIESAEEAVERALEEAGVSLEDVEA 201
Query: 201 VGAEGSVRMFDLRH 214
+G G R H
Sbjct: 202 IGTTGYGRFTIGEH 215
>gnl|CDD|173639 cd05066, PTKc_EphR_A, Catalytic domain of the Protein Tyrosine
Kinases, Class EphA Ephrin Receptors. Protein Tyrosine
Kinase (PTK) family; Ephrin Receptor (EphR) subfamily;
most class EphA receptors including EphA3, EphA4, EphA5,
and EphA7, but excluding EphA1, EphA2 and EphA10;
catalytic (c) domain. The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. EphRs comprise the
largest subfamily of receptor tyr kinases (RTKs). In
general, class EphA receptors bind GPI-anchored ephrin-A
ligands. There are ten vertebrate EphA receptors
(EphA1-10), which display promiscuous interactions with
six ephrin-A ligands. One exception is EphA4, which also
binds ephrins-B2/B3. EphRs contain an ephrin-binding
domain and two fibronectin repeats extracellularly, a
transmembrane segment, and a cytoplasmic tyr kinase
domain. Binding of the ephrin ligand to EphR requires
cell-cell contact since both are anchored to the plasma
membrane. The resulting downstream signals occur
bidirectionally in both EphR-expressing cells (forward
signaling) and ephrin-expressing cells (reverse
signaling). Ephrin/EphR interaction mainly results in
cell-cell repulsion or adhesion, making it important in
neural development and plasticity, cell morphogenesis,
cell-fate determination, embryonic development, tissue
patterning, and angiogenesis. EphARs and ephrin-A
ligands are expressed in multiple areas of the
developing brain, especially in the retina and tectum.
They are part of a system controlling retinotectal
mapping.
Length = 267
Score = 28.7 bits (64), Expect = 4.0
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 305 MPRAIED-PILAYTAAGGEINQIQWGATQPDWIAICYNKY 343
+ R +ED P AYT GG+I I+W T P+ AI Y K+
Sbjct: 152 LSRVLEDDPEAAYTTRGGKI-PIRW--TAPE--AIAYRKF 186
>gnl|CDD|239427 cd03311, CIMS_C_terminal_like, CIMS - Cobalamine-independent
methonine synthase, or MetE, C-terminal domain_like.
Many members have been characterized as
5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers the C-terminal barrel, and a few
single-barrel sequences most similar to the C-terminal
barrel. It is assumed that the homologous N-terminal
barrel has evolved from the C-terminus via gene
duplication and has subsequently lost binding sites, and
it seems as if the two barrels forming the active enzyme
may sometimes reside on different polypeptides. The
C-terminal domain incorporates the Zinc ion, which binds
and activates homocysteine. Sidechains from both barrels
contribute to the binding of the folate substrate.
Length = 332
Score = 28.3 bits (64), Expect = 5.8
Identities = 14/68 (20%), Positives = 21/68 (30%), Gaps = 8/68 (11%)
Query: 264 PVARLNNHRACVNGIAWAP-----HSSCHICTAGDDHQALIWDIQQMPRAIEDPILAYTA 318
+A+ H + GI P S + L D+ A+ + I
Sbjct: 110 KIAQSLTHPKPLKGILTGPVTIPSPSFVRFRGYYPSREELAMDLA---LALREEIRDLYD 166
Query: 319 AGGEINQI 326
AG QI
Sbjct: 167 AGCRYIQI 174
>gnl|CDD|176258 cd08298, CAD2, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 329
Score = 27.9 bits (63), Expect = 8.7
Identities = 11/37 (29%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 169 SGHVKTQLIAHD-KEVYDIAFSRAGGGRDMFASVGAE 204
S H+ Q+ + EV+ AF+R+G +++ +GA+
Sbjct: 179 SAHLALQIARYQGAEVF--AFTRSGEHQELARELGAD 213
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 0.136 0.439
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: 18,050,971
Number of extensions: 1705436
Number of successful extensions: 1159
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1130
Number of HSP's successfully gapped: 19
Length of query: 349
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 251
Effective length of database: 6,590,910
Effective search space: 1654318410
Effective search space used: 1654318410
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)