RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13945
(86 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 = 50.4 bits (121), Expect = 6e-09
Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 1/86 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVTADDGTLI-SSSL 60
+ +A S G + + G + L DL TG L + +GHE + + + DG L+ S S
Sbjct: 180 VNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSE 239
Query: 61 DQTISAWHTNDGSLKCNIQGPTEPVH 86
D TI W G + G T V
Sbjct: 240 DGTIRVWDLRTGECVQTLSGHTNSVT 265
Score = 46.2 bits (110), Expect = 2e-07
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVT-ADDGTLISSSL 60
+ C+A S G +A G G + + DL TG L + KGH G + + AD L S S
Sbjct: 12 VTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSS 71
Query: 61 DQTISAWHTNDGSLKCNIQGPTEPV 85
D+TI W G + G T V
Sbjct: 72 DKTIRLWDLETGECVRTLTGHTSYV 96
Score = 45.0 bits (107), Expect = 4e-07
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVTADDGTLI-SSSL 60
+R +A S+ G+++A G + + L DL TG + + GH + + + DG ++ SSS
Sbjct: 54 VRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSR 113
Query: 61 DQTISAWHTNDGSLKCNIQGPTEPV 85
D+TI W G ++G T+ V
Sbjct: 114 DKTIKVWDVETGKCLTTLRGHTDWV 138
Score = 44.2 bits (105), Expect = 8e-07
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 1/86 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVTADDGTLI-SSSL 60
+ +A S G ++ + + D+ TG L + +GH + + + DGT + SSS
Sbjct: 96 VSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQ 155
Query: 61 DQTISAWHTNDGSLKCNIQGPTEPVH 86
D TI W G + G T V+
Sbjct: 156 DGTIKLWDLRTGKCVATLTGHTGEVN 181
Score = 43.1 bits (102), Expect = 2e-06
Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVTADDG-TLISSSL 60
+ +A S G+++A G + L DLRTG +A+ GH GE+ + + DG L+SSS
Sbjct: 138 VNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSS 197
Query: 61 DQTISAWHTNDGSLKCNIQGPTEPVH 86
D TI W + G ++G V+
Sbjct: 198 DGTIKLWDLSTGKCLGTLRGHENGVN 223
Score = 38.5 bits (90), Expect = 1e-04
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVTADDG-TLISSSL 60
+ +A S G +A G G + + DLRTG + + GH + L + DG L S S
Sbjct: 222 VNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSA 281
Query: 61 DQTISAW 67
D TI W
Sbjct: 282 DGTIRIW 288
Score = 33.8 bits (78), Expect = 0.005
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 33 SLASWKGHEGEILQLVTADDG-TLISSSLDQTISAWHTNDGSLKCNIQGPTEPV 85
+ KGH G + + + DG L + S D TI W G L ++G T PV
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPV 54
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 34.3 bits (77), Expect = 0.004
Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 3/87 (3%)
Query: 2 IRCIAVSSSGSWIAIGQAS-GVLTLLDLRTGTSLAS-WKGHEGEILQLVTADDGTLISSS 59
+ +A S G + +S G + L DL TG L S GH ++ + D L S S
Sbjct: 201 VSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGS 260
Query: 60 LDQTISAWHT-NDGSLKCNIQGPTEPV 85
D TI W + SL + G + V
Sbjct: 261 SDGTIRLWDLRSSSSLLRTLSGHSSSV 287
Score = 32.4 bits (72), Expect = 0.014
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 1/77 (1%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQL-VTADDGTLISSSL 60
+ ++ S G ++ G G + L DL TG+ L + GH + L + D +L S S
Sbjct: 373 VLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSS 432
Query: 61 DQTISAWHTNDGSLKCN 77
D TI W +
Sbjct: 433 DNTIRLWDLKTSLKSVS 449
Score = 29.7 bits (65), Expect = 0.17
Identities = 28/86 (32%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 2 IRCIAVSSSGSWIAIGQASGVLTLLDLRTG--TSLASWKGHEGEILQLVTADDGTLISSS 59
+ +A S G +A G + G + L DL TG S + KGHEG + L + DG+L+ S
Sbjct: 287 VLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSG 346
Query: 60 L--DQTISAWHTNDGSLKCNIQGPTE 83
D TI W G ++G +
Sbjct: 347 GSDDGTIRLWDLRTGKPLKTLEGHSN 372
Score = 28.5 bits (62), Expect = 0.32
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 4 CIAVSSSGSWIAIGQASGVLTLLDLRTGTS-LASWKGHEGEILQL-VTADDGTLISSSLD 61
+ S GS +A G + G + L DLR+ +S L + GH +L + + D L S S D
Sbjct: 246 VSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSD 305
Query: 62 QTISAWHTNDGSLKC 76
T+ W G L
Sbjct: 306 GTVRLWDLETGKLLS 320
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 32.8 bits (74), Expect = 0.011
Identities = 27/81 (33%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 8 SSSGSWIAIGQASGVLTLLDLRT-GTSLASWKGHEGEILQLVTADDGTLISSSLDQTISA 66
S SG +A G A + DLR L + GH + + D TL+SSS D T+
Sbjct: 627 SESGRSLAFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFVDSSTLVSSSTDNTLKL 686
Query: 67 WHTNDGSLKCNIQGPTE-PVH 86
W L +I G E P+H
Sbjct: 687 W-----DLSMSISGINETPLH 702
Score = 26.2 bits (57), Expect = 2.6
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 11/83 (13%)
Query: 12 SWIAIGQASGVLTLLDLRTGTSLASWKGHEGEI--LQLVTADDGTLISSSLDQTISAWHT 69
S +A GV+ + D+ + K HE + + +AD L S S D ++ W
Sbjct: 546 SQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSI 605
Query: 70 ND----GSLK-----CNIQGPTE 83
N G++K C +Q P+E
Sbjct: 606 NQGVSIGTIKTKANICCVQFPSE 628
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 31.6 bits (72), Expect = 0.023
Identities = 22/79 (27%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 7 VSSSGSWIAIGQASGVLTLLDLRTGTSLASWKGH-EGEILQLVTADDGTLISSSLDQTIS 65
V+ G + + G L LD TG L W+ GEIL T G ++ + D ++
Sbjct: 30 VAVDGGRLYVATGKGELVALDAATGKLL--WRKDLSGEILGAPTVAGGVVVVVTADGSLY 87
Query: 66 AWHTNDGSLKCNIQGPTEP 84
A G L + Q P
Sbjct: 88 ALDAETGKLLWSYQRSLPP 106
Score = 31.6 bits (72), Expect = 0.029
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 19 ASGVLTLLDLRTGTSLASWKGH--EGEILQLVTADDGTLISSSLDQTISAWHTNDGSLK 75
A GV+ LD TG L W+ + V D G L ++ + A G L
Sbjct: 1 ADGVVAALDAATGKVL--WRVDLGGTALGGGVAVDGGRLYVATGKGELVALDAATGKLL 57
>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 = 28.4 bits (64), Expect = 0.066
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 30 TGTSLASWKGHEGEILQLVTADDGT-LISSSLDQTISAWH 68
+G L + KGH G + + + DG L S S D TI W
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|227826 COG5539, COG5539, Predicted cysteine protease (OTU family)
[Posttranslational modification, protein turnover,
chaperones].
Length = 306
Score = 28.7 bits (64), Expect = 0.30
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 25 LLDLRTGTSLASWKGHEGEILQLVTADDGTLI-----SSSLDQTISAWHTNDGSLKCNIQ 79
D T + W + E+L A DG I +S L +T S+KCNI
Sbjct: 225 HFDEETLAMV-LWDTYVNEVLF--DASDGITIEIQQLASLLKNPHYYTNTASPSIKCNIC 281
Query: 80 GPT 82
G
Sbjct: 282 GTG 284
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 26.5 bits (59), Expect = 0.41
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 31 GTSLASWKGHEGEILQLVTADDGT-LISSSLDQTISAWH 68
G L + KGH G + + + DG L S S D T+ W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|217296 pfam02941, FeThRed_A, Ferredoxin thioredoxin reductase variable
alpha chain.
Length = 67
Score = 25.7 bits (57), Expect = 1.3
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 38 KGHEGEILQLVTADDGTLISSSL 60
KG EGEI Q VT G IS++L
Sbjct: 27 KGMEGEIKQYVTDWKGRPISANL 49
>gnl|CDD|234163 TIGR03300, assembly_YfgL, outer membrane assembly lipoprotein YfgL.
Members of this protein family are YfgL, a lipoprotein
component of a complex that acts protein insertion into
the bacterial outer membrane. Other members of this
complex are NlpB, YfiO, and YaeT. This protein contains
multiple copies of a repeat that, in other contexts, are
associated with binding of the coenzyme PQQ [Protein
fate, Protein and peptide secretion and trafficking].
Length = 377
Score = 26.4 bits (59), Expect = 2.0
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 11 GSWIAIGQASGVLTLLDLRTGTSLASWK-GHEGEILQLVTADDGTLISSSLDQTISAWH 68
G ++ +G G L L G+ +A K G V DG L+ + D + A+
Sbjct: 320 GGYLVVGDFEGYLHWLSREDGSFVARLKTDGSGIASPPVVVGDGLLVQTR-DGDLYAFR 377
>gnl|CDD|236625 PRK09783, PRK09783, copper/silver efflux system membrane fusion
protein CusB; Provisional.
Length = 409
Score = 26.4 bits (58), Expect = 2.1
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 21 GVLTLLDLRTGTSLASWKGHEGEILQLVTADDGTLISSSLDQTISAWHTNDGSLKCNIQG 80
GV+T DLR G ++A ++ + D +++++ ++I AW D S + +
Sbjct: 218 GVITAFDLRAGMNIAKDN-----VVAKIQGMDPVWVTAAIPESI-AWLVKDAS-QFTLTV 270
Query: 81 PTEP 84
P P
Sbjct: 271 PARP 274
>gnl|CDD|116940 pfam08359, TetR_C_4, YsiA-like protein, C-terminal region. The
members of this family are thought to be TetR-type
transcriptional regulators that bear particular
similarity to YsiA, a hypothetical protein expressed by
B. subtilis.
Length = 133
Score = 25.8 bits (57), Expect = 2.7
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 55 LISSSLDQTISAWHTNDGSLKCNIQGPTEPVH 86
+I +LD+T++ W ND K ++ EPVH
Sbjct: 98 MIFGTLDETVTNWVMNDQ--KYDLVALAEPVH 127
>gnl|CDD|214474 smart00022, PLAc, Cytoplasmic phospholipase A2, catalytic subunit.
Cytosolic phospholipases A2 hydrolyse arachidonyl
phospholipids. Family includes phospholipases B
isoforms.
Length = 549
Score = 25.9 bits (57), Expect = 3.5
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 13/80 (16%)
Query: 5 IAVS-SSGSWIAIGQASGVLTLLDLRTGTSLASWKGHEGEILQLVTADDGTLISSSLDQT 63
IA++ S G + A+ +GVL +D RT G +LQ T G + L T
Sbjct: 78 IAIAGSGGGFRAMVGGAGVLKAMDNRTDGH------GLGGLLQSATYLAGLSGGTWLVGT 131
Query: 64 ISAWHTNDGSLKCNIQGPTE 83
+ A + N ++GP E
Sbjct: 132 L-ASN-NFTP----VKGPEE 145
>gnl|CDD|236089 PRK07761, PRK07761, DNA polymerase III subunit beta; Validated.
Length = 376
Score = 24.8 bits (55), Expect = 7.7
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 47 LVTADDGTLISSSLDQTISAWHT 69
L+ ADDG L S D +SA T
Sbjct: 34 LLEADDGGLTLSGFDYEVSARVT 56
>gnl|CDD|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 24.5 bits (54), Expect = 8.6
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 28 LRTGTSLASWKGHEGEILQLVTADDGTLISSSL 60
+RT T + S + + ++ T L + SL
Sbjct: 125 IRTRTRVLSVEKDDDGRFRVDTDGGEELEADSL 157
>gnl|CDD|221798 pfam12831, FAD_oxidored, FAD dependent oxidoreductase. This family
of proteins contains FAD dependent oxidoreductases and
related proteins.
Length = 415
Score = 24.4 bits (54), Expect = 9.1
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 8/41 (19%)
Query: 3 RCIAVS----SS----GSWIAIGQASGVLTLLDLRTGTSLA 35
RCI+ + S + +A+GQA+G L +R G +
Sbjct: 364 RCISATHIAFGSTRVMPTCMAMGQAAGTAAALAIREGVTPR 404
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 0.130 0.393
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: 3,977,727
Number of extensions: 292667
Number of successful extensions: 238
Number of sequences better than 10.0: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 32
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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: 42 (22.0 bits)
S2: 53 (24.2 bits)