RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6442
(231 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 = 89.3 bits (222), Expect = 2e-21
Identities = 51/214 (23%), Positives = 89/214 (41%), Gaps = 38/214 (17%)
Query: 13 DTGDWIGTFEGHKGCVWGVDINKDASKAASGAADFQAK---------------------- 50
+TG+ + T GH V V + D +S + D K
Sbjct: 81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNS 140
Query: 51 -----NNTRLISCAEDKTVRLWDVSASAEVQKLEF--GAVPNSLEISRDGTT-ITVTHGS 102
+ T + S ++D T++LWD+ V L G V NS+ S DG ++ +
Sbjct: 141 VAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEV-NSVAFSPDGEKLLSSSSDG 199
Query: 103 CVTFLDANSLELIKEHKVPAQVHSA---SLLLNSERPIFVCGGEDLKMYKFDYSTGAEIE 159
+ D ++ + + + H S+ + + + G ED + +D TG ++
Sbjct: 200 TIKLWDLSTGKCLGTL----RGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQ 255
Query: 160 SFKGHFGPIHCVKFSPDGELYASGSEDGTLRLWQ 193
+ GH + + +SPDG+ ASGS DGT+R+W
Sbjct: 256 TLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 85.8 bits (213), Expect = 4e-20
Identities = 55/218 (25%), Positives = 88/218 (40%), Gaps = 38/218 (17%)
Query: 18 IGTFEGHKGCVWGVDINKDASKAASGAADFQAK--------------------------- 50
T +GH G V V + D A+G+ D K
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASA 61
Query: 51 NNTRLISCAEDKTVRLWDVSASAEVQKLE--FGAVPNSLEISRDGTTITVTHG-SCVTFL 107
+ T L S + DKT+RLWD+ V+ L V +S+ S DG ++ + +
Sbjct: 62 DGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYV-SSVAFSPDGRILSSSSRDKTIKVW 120
Query: 108 DANSLELIKEHKVPAQVHSA---SLLLNSERPIFVCGGEDLKMYKFDYSTGAEIESFKGH 164
D + + + + H+ S+ + + +D + +D TG + + GH
Sbjct: 121 DVETGKCLTT----LRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGH 176
Query: 165 FGPIHCVKFSPDGELYASGSEDGTLRLWQTNVGKTYGL 202
G ++ V FSPDGE S S DGT++LW + GK G
Sbjct: 177 TGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGT 214
Score = 85.1 bits (211), Expect = 9e-20
Identities = 60/229 (26%), Positives = 102/229 (44%), Gaps = 41/229 (17%)
Query: 13 DTGDWIGTFEGHKGCVWGVDINKDASKAASGAADFQAK---------------------- 50
+TG+ + T +GH G V V + D + ASG++D +
Sbjct: 39 ETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSS 98
Query: 51 ----NNTRLI-SCAEDKTVRLWDVSASAEVQKLEF--GAVPNSLEISRDGTTITVTHG-S 102
+ R++ S + DKT+++WDV + L V NS+ S DGT + +
Sbjct: 99 VAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWV-NSVAFSPDGTFVASSSQDG 157
Query: 103 CVTFLDANSLELIKE---HKVPAQVHSASLLLNSERPIFVCGGEDLKMYKFDYSTGAEIE 159
+ D + + + H +V+S + + E+ + D + +D STG +
Sbjct: 158 TIKLWDLRTGKCVATLTGHT--GEVNSVAFSPDGEK--LLSSSSDGTIKLWDLSTGKCLG 213
Query: 160 SFKGHFGPIHCVKFSPDGELYASGSEDGTLRLWQTNVGKTYGLWKCIEG 208
+ +GH ++ V FSPDG L ASGSEDGT+R+W G+ + + G
Sbjct: 214 TLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGE---CVQTLSG 259
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 70.1 bits (170), Expect = 6e-14
Identities = 46/191 (24%), Positives = 75/191 (39%), Gaps = 19/191 (9%)
Query: 18 IGTFEGHKGCVWGVDINKDASKAASGAADFQAKNNTRLISCAEDKTVRLWDVSASAEVQK 77
I T EGH V + + D + D T++LWD+ +
Sbjct: 148 IRTLEGHSESVTSLAFSPD--------------GKLLASGSSLDGTIKLWDLRTGKPLST 193
Query: 78 LEF-GAVPNSLEISRDGTTITVTHGS--CVTFLDANSLELIKEHKVPAQVHSASLLLNSE 134
L +SL S DG + + S + D ++ +L++ + S + +
Sbjct: 194 LAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRS-TLSGHSDSVVSSFSPD 252
Query: 135 RPIFVCGGEDLKMYKFDYSTGA-EIESFKGHFGPIHCVKFSPDGELYASGSEDGTLRLWQ 193
+ G D + +D + + + + GH + V FSPDG+L ASGS DGT+RLW
Sbjct: 253 GSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWD 312
Query: 194 TNVGKTYGLWK 204
GK
Sbjct: 313 LETGKLLSSLT 323
Score = 67.0 bits (162), Expect = 6e-13
Identities = 48/178 (26%), Positives = 72/178 (40%), Gaps = 22/178 (12%)
Query: 20 TFEGHKGCVWGVDINKDASKAASGAADFQAKNNTRLISCAEDKTVRLWDVSASAEVQKLE 79
T GH V V + D L S + D TVRLWD+ + L
Sbjct: 279 TLSGHSSSVLSVAFSPD---------------GKLLASGSSDGTVRLWDLETGKLLSSLT 323
Query: 80 F---GAVPNSLEISRDGTTITVTHGS--CVTFLDANSLELIKEHKVPAQVHSASLLLNSE 134
+SL S DG+ + + D + + +K + + V S S +
Sbjct: 324 LKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGR 383
Query: 135 RPIFVCGGEDLKMYKFDYSTGAEIESFKGHFGPIHCVKFSPDGELYASGSEDGTLRLW 192
+ G D + +D STG+ + + GH + + FSPDG+ ASGS D T+RLW
Sbjct: 384 --VVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLW 439
Score = 65.9 bits (159), Expect = 1e-12
Identities = 52/207 (25%), Positives = 80/207 (38%), Gaps = 19/207 (9%)
Query: 4 DGKPMLRQGDTGDWIGTFEGHKGCVWGVDINKDASKAASGAADFQAKNNTRLISCAEDKT 63
DG L TG + T GH V + + D + S + D T
Sbjct: 177 DGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPD--------------GGLLIASGSSDGT 222
Query: 64 VRLWDVSASAEVQKLEFG-AVPNSLEISRDGTT-ITVTHGSCVTFLDANSLELIKEHKVP 121
+RLWD+S ++ G + S DG+ + + + D S +
Sbjct: 223 IRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSG 282
Query: 122 AQVHSASLLLNSERPIFVCGGEDLKMYKFDYSTGAEIE--SFKGHFGPIHCVKFSPDGEL 179
S+ + + + G D + +D TG + + KGH GP+ + FSPDG L
Sbjct: 283 HSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSL 342
Query: 180 YASG-SEDGTLRLWQTNVGKTYGLWKC 205
SG S+DGT+RLW GK +
Sbjct: 343 LVSGGSDDGTIRLWDLRTGKPLKTLEG 369
Score = 60.9 bits (146), Expect = 8e-11
Identities = 46/188 (24%), Positives = 78/188 (41%), Gaps = 24/188 (12%)
Query: 20 TFEGHKGCVWGVDINKDASKAASGAADFQAKNNTRLISCAEDKTVRLWDVSAS----AEV 75
GH+ + + + D L+S + D T++LWD+ +
Sbjct: 60 LLRGHEDSITSIAFSPD---------------GELLLSGSSDGTIKLWDLDNGEKLIKSL 104
Query: 76 QKLEFGAVPNSLEISRDGTTITVTHGSC---VTFLD-ANSLELIKEHKVPAQVHSASLLL 131
+ L +V S DG +I + S V D + +LI+ + ++ ++
Sbjct: 105 EGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFS 164
Query: 132 NSERPIFVCGGEDLKMYKFDYSTGAEIESFKGHFGPIHCVKFSPDGELY-ASGSEDGTLR 190
+ + D + +D TG + + GH P+ + FSPDG L ASGS DGT+R
Sbjct: 165 PDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIR 224
Query: 191 LWQTNVGK 198
LW + GK
Sbjct: 225 LWDLSTGK 232
Score = 40.1 bits (92), Expect = 6e-04
Identities = 19/40 (47%), Positives = 25/40 (62%)
Query: 161 FKGHFGPIHCVKFSPDGELYASGSEDGTLRLWQTNVGKTY 200
+GH I + FSPDGEL SGS DGT++LW + G+
Sbjct: 61 LRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKL 100
>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 = 52.3 bits (126), Expect = 9e-10
Identities = 21/39 (53%), Positives = 30/39 (76%)
Query: 154 TGAEIESFKGHFGPIHCVKFSPDGELYASGSEDGTLRLW 192
+G +++ KGH GP+ V FSPDG+ ASGS+DGT++LW
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 38.1 bits (89), Expect = 1e-04
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 15/55 (27%)
Query: 14 TGDWIGTFEGHKGCVWGVDINKDASKAASGAADFQAKNNTRLISCAEDKTVRLWD 68
+G+ + T +GH G V V + D L S ++D T++LWD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPD---------------GKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 50.0 bits (120), Expect = 6e-09
Identities = 22/38 (57%), Positives = 28/38 (73%)
Query: 155 GAEIESFKGHFGPIHCVKFSPDGELYASGSEDGTLRLW 192
G + + KGH GP+ V FSPDG L ASGS+DGT+R+W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 37.7 bits (88), Expect = 2e-04
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 15/51 (29%)
Query: 18 IGTFEGHKGCVWGVDINKDASKAASGAADFQAKNNTRLISCAEDKTVRLWD 68
+ T +GH G V V + D L S ++D TVR+WD
Sbjct: 4 LRTLKGHTGPVTSVAFSPD---------------GNLLASGSDDGTVRVWD 39
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 34.5 bits (79), Expect = 0.040
Identities = 16/34 (47%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 161 FKGHFGPIHCVKFSP-DGELYASGSEDGTLRLWQ 193
KGH I ++F+P E+ ASGSED T+R+W+
Sbjct: 70 LKGHTSSILDLQFNPCFSEILASGSEDLTIRVWE 103
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 32.8 bits (74), Expect = 0.18
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 174 SPDGELYASGSEDGTLRLWQTNVGKTYGLWK 204
S D L ASGS+DG+++LW N G + G K
Sbjct: 585 SADPTLLASGSDDGSVKLWSINQGVSIGTIK 615
Score = 28.1 bits (62), Expect = 5.1
Identities = 41/168 (24%), Positives = 66/168 (39%), Gaps = 17/168 (10%)
Query: 61 DKTVRLWDVSASAEVQKL-EFGAVPNSLEISRDGTTITVTHGS---CVTFLDANSLELIK 116
+ V++WDV+ S V ++ E S++ S T+ + GS V N I
Sbjct: 554 EGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLAS-GSDDGSVKLWSINQGVSIG 612
Query: 117 EHKVPAQVHSASLLLNSERPIFVCGGEDLKMYKFDY-STGAEIESFKGHFGPIHCVKFSP 175
K A + S R + G D K+Y +D + + + GH + V+F
Sbjct: 613 TIKTKANICCVQFPSESGRSL-AFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFV- 670
Query: 176 DGELYASGSEDGTLRLWQTNVGKTYGLWKCIEGGLNNSLGLDSSGHLN 223
D S S D TL+LW ++ + G+N + GH N
Sbjct: 671 DSSTLVSSSTDNTLKLWDLSMSIS---------GINETPLHSFMGHTN 709
Score = 27.0 bits (59), Expect = 9.6
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 51 NNTRLISCAEDKTVRLWDVSASA 73
+++ L+S + D T++LWD+S S
Sbjct: 671 DSSTLVSSSTDNTLKLWDLSMSI 693
>gnl|CDD|176120 cd08429, PBP2_NhaR, The C-terminal substrate binding domain of
LysR-type transcriptional activator of the nhaA gene,
encoding Na+/H+ antiporter, contains the type 2
periplasmic binding fold. NhaR is a positive regulator
of the LysR family and is known to be an activator of
the nhaA gene encoding a Na(+)/H(+) antiporter. In
Escherichia coli, NhaA is the vital antiporter that
protects against high sodium stress, and it is essential
for growth in high sodium levels, while NhaB becomes
essential only if NhaA is not available. The nhaA gene
of nhaAR operon is induced by monovalent cations. The
nhaR of the operon activates nhaAR, as well as the osmC
transcription which is induced at elevated osmolarity.
OsmC is transcribed from the two overlapping promoters
(osmCp1 and osmP2) and that NhaR is shown to activate
only the expression of osmCp1. NhaR also activates the
transcription of the pgaABCD operon which is required
for production of the biofilm adhesion,
poly-beta-1,6-N-acetyl-d-glucosamine (PGA) .Thus, it is
suggested that NhaR has an extended role in promoting
bacterial survival. This substrate-binding domain has
significant homology to the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 204
Score = 29.2 bits (66), Expect = 1.3
Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 101 GSC-VTFLDANSLELIKEHKVPAQVHSASLLLNSER 135
G C V+F A L E PA + A LLL E
Sbjct: 73 GECGVSFFAAPPLAKRLEKPFPASLDEAPLLLPGED 108
>gnl|CDD|178238 PLN02631, PLN02631, ferric-chelate reductase.
Length = 699
Score = 29.2 bits (65), Expect = 2.1
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 84 PNSLEISRDGTTITVTHGSCVTFLDANSLELIKEHKVPA 122
PNS ++SR + I V+ GS +T + ELI + + P+
Sbjct: 404 PNSFDVSRHNSLILVSGGSGITPFISVIRELIFQSQNPS 442
>gnl|CDD|184619 PRK14322, glmM, phosphoglucosamine mutase; Provisional.
Length = 429
Score = 28.0 bits (62), Expect = 4.4
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 189 LRLWQTNVGKTYGLWKCIEGGLNNSLGLDSSGHL 222
++L +T VG Y L K +E G N LG + SGH+
Sbjct: 289 IKLLRTKVGDKYVLEKMLESGAN--LGGERSGHI 320
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 27.3 bits (61), Expect = 6.9
Identities = 8/33 (24%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 12 GDTGDWIGTF---EGHKGCVWGVDINKDASKAA 41
G G + G + G D + KAA
Sbjct: 12 GLMGGSLARALKEAGLVVRIIGRDRSAATLKAA 44
>gnl|CDD|223107 COG0028, IlvB, Thiamine pyrophosphate-requiring enzymes
[acetolactate synthase, pyruvate dehydrogenase
(cytochrome), glyoxylate carboligase, phosphonopyruvate
decarboxylase] [Amino acid transport and metabolism /
Coenzyme metabolism].
Length = 550
Score = 27.6 bits (62), Expect = 7.3
Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 2/57 (3%)
Query: 87 LEISRDGTTITVTHGSCVTFLDANSLELIKEHKVPAQVHSASLLLNSERPIFVCGGE 143
+++ +D + + + A LL ++RP+ + GG
Sbjct: 156 VDLPKDVLAAEAEEPGPEPAILPPYRPAPPPPEAIRKA--AELLAEAKRPVILAGGG 210
>gnl|CDD|227282 COG4946, COG4946, Uncharacterized protein related to the
periplasmic component of the Tol biopolymer transport
system [Function unknown].
Length = 668
Score = 27.1 bits (60), Expect = 9.3
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 127 ASLLLN----SERPIFVCGGEDLKMYKFDYSTGAEIESFKGHFGPIHCVKFSPDGELYAS 182
+ LN +R IF C + ++++ G + G ++ KFSPDG A
Sbjct: 40 KNYYLNPDIYGDRIIFTCCDD---LWEYSLKDG-KPLRITSGLGVVNNPKFSPDGRKVA- 94
Query: 183 GSEDGTLRLWQTNVGKT 199
R+ + +T
Sbjct: 95 -----FSRVMLGSSLQT 106
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 27.0 bits (60), Expect = 9.9
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 34 NKDASKAASGAADFQAKNNTRLISCAEDKTVRLWDVSASAEVQKLEFGAVPNSLEI 89
N++A + G AD+ +N +++ +D VR+ V+ + G P +E+
Sbjct: 338 NEEALEKLKGIADYFLLHNREIVNRCDDSVVRV--VAGRIAFIRRSRGYAPKPIEL 391
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
0.316 0.134 0.413
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: 11,205,522
Number of extensions: 980766
Number of successful extensions: 886
Number of sequences better than 10.0: 1
Number of HSP's gapped: 853
Number of HSP's successfully gapped: 39
Length of query: 231
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 137
Effective length of database: 6,768,326
Effective search space: 927260662
Effective search space used: 927260662
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 (21.6 bits)
S2: 57 (25.7 bits)