RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15612
(131 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 = 52.3 bits (126), Expect = 6e-09
Identities = 28/123 (22%), Positives = 49/123 (39%), Gaps = 4/123 (3%)
Query: 10 RQLQQHDFSSQIFSLGYCPSGEWLAVGMENSNVEVLH-ALKPDKYQLHLHESCVLSLRFA 68
R L+ H + + + + P G+ LA G + ++V L H V + +
Sbjct: 3 RTLKGH--TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAAS 60
Query: 69 ACGKWFVSTGKDNLLNAWRTPYGASIFQ-SKESSSVLSCDISADDKYIVTGSGDKKATVY 127
A G + S D + W G + + +S V S S D + + + S DK V+
Sbjct: 61 ADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVW 120
Query: 128 EVI 130
+V
Sbjct: 121 DVE 123
Score = 47.3 bits (113), Expect = 3e-07
Identities = 30/125 (24%), Positives = 51/125 (40%), Gaps = 6/125 (4%)
Query: 7 SPGRQLQQHDFSSQIFSLGYCPSGEWLAVGMENSNVEV--LHALKPDKYQLHLHESCVLS 64
L H ++ S+ + P GE L + +++ L K L HE+ V S
Sbjct: 168 KCVATLTGHT--GEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKC-LGTLRGHENGVNS 224
Query: 65 LRFAACGKWFVSTGKDNLLNAWRTPYGASIFQ-SKESSSVLSCDISADDKYIVTGSGDKK 123
+ F+ G S +D + W G + S ++SV S S D K + +GS D
Sbjct: 225 VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGT 284
Query: 124 ATVYE 128
+++
Sbjct: 285 IRIWD 289
Score = 45.0 bits (107), Expect = 2e-06
Identities = 26/131 (19%), Positives = 52/131 (39%), Gaps = 8/131 (6%)
Query: 3 LQSVSPGRQLQQHDFSSQIFSLGYCPSGEWLAVGMENSNVEV--LHALKPDKYQLHLHES 60
L++ R L+ H + + + G +LA G + + + L + L H S
Sbjct: 38 LETGELLRTLKGH--TGPVRDVAASADGTYLASGSSDKTIRLWDLETGEC-VRTLTGHTS 94
Query: 61 CVLSLRFAACGKWFVSTGKDNLLNAWRTPYGASI--FQSKESSSVLSCDISADDKYIVTG 118
V S+ F+ G+ S+ +D + W G + + V S S D ++ +
Sbjct: 95 YVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDW-VNSVAFSPDGTFVASS 153
Query: 119 SGDKKATVYEV 129
S D ++++
Sbjct: 154 SQDGTIKLWDL 164
Score = 36.2 bits (84), Expect = 0.002
Identities = 27/130 (20%), Positives = 53/130 (40%), Gaps = 6/130 (4%)
Query: 3 LQSVSPGRQLQQHDFSSQIFSLGYCPSGEWLAVGMENSNVEVLHALKPD-KYQLHLHESC 61
L++ R L H +S + S+ + P G L+ + ++V L H
Sbjct: 80 LETGECVRTLTGH--TSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDW 137
Query: 62 VLSLRFAACGKWFVSTGK-DNLLNAWRTPYGASIFQ-SKESSSVLSCDISADDKYIVTGS 119
V S+ F+ G FV++ D + W G + + + V S S D + +++ S
Sbjct: 138 VNSVAFSPDGT-FVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSS 196
Query: 120 GDKKATVYEV 129
D ++++
Sbjct: 197 SDGTIKLWDL 206
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 48.5 bits (114), Expect = 1e-07
Identities = 31/116 (26%), Positives = 49/116 (42%), Gaps = 4/116 (3%)
Query: 18 SSQIFSLGYCPSGEWLAVGMENSNVEVLHALKPDKYQLH---LHESCVLSLRFAACGKWF 74
SS + S+ + P G+ LA G + V + HE V SL F+ G
Sbjct: 284 SSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLL 343
Query: 75 VSTG-KDNLLNAWRTPYGASIFQSKESSSVLSCDISADDKYIVTGSGDKKATVYEV 129
VS G D + W G + + S+VLS S D + + +GS D ++++
Sbjct: 344 VSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDL 399
Score = 41.2 bits (95), Expect = 5e-05
Identities = 26/114 (22%), Positives = 46/114 (40%), Gaps = 2/114 (1%)
Query: 18 SSQIFSLGYCPSGEWLAVG-MENSNVEVLHALKPDKYQLHLHESCVLSLRFAACGKWFVS 76
+ SL + P G L G ++ + + + S VLS+ F+ G+ S
Sbjct: 328 EGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSS 387
Query: 77 TGKDNLLNAWRTPYGASI-FQSKESSSVLSCDISADDKYIVTGSGDKKATVYEV 129
D + W G+ + +S V S D S D K + +GS D ++++
Sbjct: 388 GSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
Score = 38.9 bits (89), Expect = 3e-04
Identities = 33/134 (24%), Positives = 52/134 (38%), Gaps = 7/134 (5%)
Query: 2 YLQSVSPGRQLQQHDF-SSQIFSLGYCPSGEWLAVGMENSNVEVLHALKPDKY---QLHL 57
L + G+ L + + SL + P G L + L L K L
Sbjct: 181 KLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSG 240
Query: 58 HESCVLSLRFAACGKWFVSTGKDNLLNAWRTPYGASIFQS--KESSSVLSCDISADDKYI 115
H V+S F+ G S D + W +S+ ++ SSSVLS S D K +
Sbjct: 241 HSDSVVSS-FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLL 299
Query: 116 VTGSGDKKATVYEV 129
+GS D ++++
Sbjct: 300 ASGSSDGTVRLWDL 313
Score = 38.1 bits (87), Expect = 6e-04
Identities = 26/103 (25%), Positives = 37/103 (35%), Gaps = 5/103 (4%)
Query: 26 YCPSGEWLAVGMENSNVEV--LHALKPDKYQLHLHESCVLSLRFAACGKWFVSTGKDNLL 83
+ P G LA G + + + L + L H S VLS+ F+ GK S D +
Sbjct: 249 FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTV 308
Query: 84 NAWRTPYGASIFQSKE---SSSVLSCDISADDKYIVTGSGDKK 123
W G + V S S D +V+G D
Sbjct: 309 RLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDG 351
Score = 35.1 bits (79), Expect = 0.006
Identities = 29/125 (23%), Positives = 47/125 (37%), Gaps = 12/125 (9%)
Query: 1 MYLQSVSPGRQLQQHDFSSQIFSLGYCPSGEWLAVGMENSNVEVLHALKPD-KYQLHLHE 59
+ L + G+ L+ + S + S+ + P G ++ G + V + L H
Sbjct: 353 IRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHT 412
Query: 60 SCVLSLRFAACGKWFVSTGKDNLLNAWRTPYGASIFQSKESSSVLSCDISADDKYIVTGS 119
S V SL F+ GK S DN + W +S+ S S D K + + S
Sbjct: 413 SRVTSLDFSPDGKSLASGSSDNTIRLWDL-----------KTSLKSVSFSPDGKVLASKS 461
Query: 120 GDKKA 124
D
Sbjct: 462 SDLSV 466
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 31.2 bits (71), Expect = 0.016
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 100 SSSVLSCDISADDKYIVTGSGDKKATVY 127
+ V S S D + +GS D V+
Sbjct: 11 TGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 30.0 bits (68), Expect = 0.048
Identities = 9/34 (26%), Positives = 12/34 (35%)
Query: 53 YQLHLHESCVLSLRFAACGKWFVSTGKDNLLNAW 86
L H V S+ F+ G S D + W
Sbjct: 5 RTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
>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 = 30.0 bits (68), Expect = 0.044
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 100 SSSVLSCDISADDKYIVTGSGDKKATVYE 128
+ V S S D KY+ +GS D +++
Sbjct: 12 TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 29.6 bits (67), Expect = 0.065
Identities = 10/34 (29%), Positives = 14/34 (41%)
Query: 53 YQLHLHESCVLSLRFAACGKWFVSTGKDNLLNAW 86
L H V S+ F+ GK+ S D + W
Sbjct: 6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|202169 pfam02239, Cytochrom_D1, Cytochrome D1 heme domain. Cytochrome cd1
(nitrite reductase) catalyzes the conversion of nitrite
to nitric oxide in the nitrogen cycle. This family
represents the d1 heme binding domain of cytochrome cd1,
in which His/Tyr side chains ligate the d1 heme iron of
the active site in the oxidized state.
Length = 369
Score = 28.2 bits (63), Expect = 1.1
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 53 YQLHLHESCVLSLRFAACGKWFVSTGKD---NLLNAWRTPYGASIFQSKESSSVLSCDIS 109
Y LH+ S F++ G++ G+D ++ W A + Q + SV +S
Sbjct: 36 YALHI------SRMFSSDGRYVYVIGRDGGLTKIDLWNLEIVAEVRQGGNARSV---AVS 86
Query: 110 ADDKYIVTGS 119
+ +Y++ G+
Sbjct: 87 YEGRYVIVGN 96
>gnl|CDD|215805 pfam00227, Proteasome, Proteasome subunit. The proteasome is a
multisubunit structure that degrades proteins. Protein
degradation is an essential component of regulation
because proteins can become misfolded, damaged, or
unnecessary. Proteasomes and their homologues vary
greatly in complexity: from HslV (heat shock locus v),
which is encoded by 1 gene in bacteria, to the
eukaryotic 20S proteasome, which is encoded by more than
14 genes. Recently evidence of two novel groups of
bacterial proteasomes was proposed. The first is Anbu,
which is sparsely distributed among cyanobacteria and
proteobacteria. The second is call beta-proteobacteria
proteasome homologue (BPH).
Length = 188
Score = 27.5 bits (62), Expect = 1.8
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 7/47 (14%)
Query: 81 NLLNAWRTPYGASI----FQSKESSSVLSCDISA---DDKYIVTGSG 120
+ R PYG S+ + + S D S + K GSG
Sbjct: 94 YTQYSGRRPYGVSLLIAGYDEDGGPHLYSIDPSGSVIEYKATAIGSG 140
>gnl|CDD|185174 PRK15267, PRK15267, subtilase cytotoxin subunit B-like protein;
Provisional.
Length = 141
Score = 26.6 bits (58), Expect = 3.0
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 71 GKWFVSTGKDNLL----NAWRTPYGASIFQSKESSSVLSCDISA 110
K++ +TG D + N WR P S F S+E ++ +C S+
Sbjct: 89 AKYYYTTGGDVRIYYKENVWRDPDFKSAFSSRELIAITTCSSSS 132
>gnl|CDD|185515 PTZ00213, PTZ00213, asparagine synthetase A; Provisional.
Length = 348
Score = 25.9 bits (57), Expect = 7.5
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 36 GMENSNVEVLHAL-KPDKYQLHLHE 59
G+ NS EV+H+L K + L H+
Sbjct: 64 GIPNSVFEVVHSLAKWKRLTLGEHK 88
>gnl|CDD|215493 PLN02910, PLN02910, polygalacturonate
4-alpha-galacturonosyltransferase.
Length = 657
Score = 26.1 bits (57), Expect = 8.2
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 41 NVEVLHALKPDKYQLHLHESCVLSLRFAACGKWFV 75
N VLHA +P K+ H+ L FAA WF+
Sbjct: 363 NSTVLHAKEPQKHVFHIVTD---KLNFAAMKMWFI 394
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 26.0 bits (58), Expect = 8.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 45 LHALKPDKYQLHLHESCVLSL 65
LHA P K+ H H ++++
Sbjct: 118 LHAFLPFKHVDHTHPDAIIAI 138
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
0.318 0.132 0.405
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: 6,287,296
Number of extensions: 501755
Number of successful extensions: 415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 24
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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 (21.7 bits)
S2: 53 (24.2 bits)