RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16373
(166 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 = 71.2 bits (175), Expect = 2e-15
Identities = 28/101 (27%), Positives = 51/101 (50%), Gaps = 2/101 (1%)
Query: 54 SNRVITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWDT 113
++++ S D T+K++ L + L TL GH + ++ + SGS+DG + VWD
Sbjct: 189 GEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDL 248
Query: 114 VTGACMYSIQAHDGCIHALTYSDS--YVISLGQDERLCVWD 152
TG C+ ++ H + +L +S + S D + +WD
Sbjct: 249 RTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 70.8 bits (174), Expect = 3e-15
Identities = 38/127 (29%), Positives = 63/127 (49%), Gaps = 4/127 (3%)
Query: 41 RAHHQPITVLEC--VSNRVITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTLFIDGVSMM 98
+ H +T + + TGS D T+KV+ LE +LL TL GH GP+ +
Sbjct: 6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTY 65
Query: 99 SGSGSQDGLLCVWDTVTGACMYSIQAHDGCIHALTYSDS--YVISLGQDERLCVWDRFQG 156
SGS D + +WD TG C+ ++ H + ++ +S + S +D+ + VWD G
Sbjct: 66 LASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETG 125
Query: 157 HLLSTIQ 163
L+T++
Sbjct: 126 KCLTTLR 132
Score = 66.2 bits (162), Expect = 1e-13
Identities = 31/109 (28%), Positives = 57/109 (52%), Gaps = 2/109 (1%)
Query: 57 VITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWDTVTG 116
+ + S+D T+KV+ +E + L TL GH + ++ S SQDG + +WD TG
Sbjct: 108 LSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTG 167
Query: 117 ACMYSIQAHDGCIHALTYSDSY--VISLGQDERLCVWDRFQGHLLSTIQ 163
C+ ++ H G ++++ +S ++S D + +WD G L T++
Sbjct: 168 KCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLR 216
Score = 66.2 bits (162), Expect = 1e-13
Identities = 32/111 (28%), Positives = 60/111 (54%), Gaps = 6/111 (5%)
Query: 57 VITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTL--FIDGVSMMSGSGSQDGLLCVWDTV 114
V + SQD T+K++ L + + TL GH G + ++ DG ++S S DG + +WD
Sbjct: 150 VASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSS--DGTIKLWDLS 207
Query: 115 TGACMYSIQAHDGCIHALTYSDS--YVISLGQDERLCVWDRFQGHLLSTIQ 163
TG C+ +++ H+ ++++ +S + S +D + VWD G + T+
Sbjct: 208 TGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLS 258
Score = 65.0 bits (159), Expect = 3e-13
Identities = 33/128 (25%), Positives = 64/128 (50%), Gaps = 14/128 (10%)
Query: 43 HHQPITVLECV--SNRVITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTL-FIDGVSMMS 99
H P+ + + +GS D T++++ LE + + TL GH ++++ F ++S
Sbjct: 50 HTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILS 109
Query: 100 GSGSQDGLLCVWDTVTGACMYSIQAHDGCIHALTYS--DSYVISLGQDERLCVWD----- 152
S S+D + VWD TG C+ +++ H ++++ +S ++V S QD + +WD
Sbjct: 110 SS-SRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGK 168
Query: 153 ---RFQGH 157
GH
Sbjct: 169 CVATLTGH 176
Score = 50.0 bits (120), Expect = 7e-08
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 76 LLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWDTVTGACMYSIQAHDGCIHALTYS 135
L TL GH G +T + + +GS DG + VWD TG + +++ H G + + S
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAAS 60
Query: 136 --DSYVISLGQDERLCVWDRFQGHLLSTI 162
+Y+ S D+ + +WD G + T+
Sbjct: 61 ADGTYLASGSSDKTIRLWDLETGECVRTL 89
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 63.2 bits (152), Expect = 3e-12
Identities = 31/115 (26%), Positives = 55/115 (47%), Gaps = 6/115 (5%)
Query: 54 SNRVITGSQDHTLKVYKLE-DQQLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWD 112
+ + +GS D T++++ L LL TL GH + ++ + SGS DG + +WD
Sbjct: 253 GSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWD 312
Query: 113 TVTGAC--MYSIQAHDGCIHALTYSDS---YVISLGQDERLCVWDRFQGHLLSTI 162
TG +++ H+G + +L++S V D + +WD G L T+
Sbjct: 313 LETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTL 367
Score = 54.7 bits (130), Expect = 3e-09
Identities = 33/124 (26%), Positives = 57/124 (45%), Gaps = 6/124 (4%)
Query: 35 CKVESTRAHHQPITVLECVSN---RVITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTL- 90
+ + H + +T L + S D T+K++ L + L TL GH P+++L
Sbjct: 146 KLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLA 205
Query: 91 FIDGVSMMSGSGSQDGLLCVWDTVTGACMYS-IQAH-DGCIHALTYSDSYVISLGQDERL 148
F ++ SGS DG + +WD TG + S + H D + + + S + S D +
Sbjct: 206 FSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTI 265
Query: 149 CVWD 152
+WD
Sbjct: 266 RLWD 269
Score = 48.9 bits (115), Expect = 2e-07
Identities = 32/124 (25%), Positives = 57/124 (45%), Gaps = 6/124 (4%)
Query: 35 CKVESTRAHHQPITVLEC--VSNRVITGSQDHTLKVYKLE--DQQLLFTLHGHCGPITTL 90
+ + H + + + +GS D T++++ LE TL GH GP+++L
Sbjct: 275 SLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSL 334
Query: 91 -FIDGVSMMSGSGSQDGLLCVWDTVTGACMYSIQAHDGCIHALTYSDSYVISLG-QDERL 148
F S++ GS DG + +WD TG + +++ H + D V+S G D +
Sbjct: 335 SFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTV 394
Query: 149 CVWD 152
+WD
Sbjct: 395 RLWD 398
Score = 48.2 bits (113), Expect = 5e-07
Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 5/110 (4%)
Query: 57 VITGSQDHTLKVYKLEDQ-QLLFTLHGHCGPITTL-FIDGVSMMSGSGSQDGLLCVWDTV 114
+ + S D T+K++ L +L+ TL GH +T+L F +++ S DG + +WD
Sbjct: 127 LASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLR 186
Query: 115 TGACMYSIQAHDGCIHALTYS---DSYVISLGQDERLCVWDRFQGHLLST 161
TG + ++ H + +L +S + S D + +WD G LL +
Sbjct: 187 TGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRS 236
Score = 33.1 bits (74), Expect = 0.047
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 54 SNRVITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWD 112
V +GS D T++++ L LL L GH +T+L SGS D + +WD
Sbjct: 382 GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWD 440
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 34.3 bits (79), Expect = 0.002
Identities = 17/38 (44%), Positives = 23/38 (60%)
Query: 75 QLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWD 112
+LL TL GH GP+T++ + SGS DG + VWD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 27.3 bits (61), Expect = 0.65
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 116 GACMYSIQAHDGCIHALTYSDS--YVISLGQDERLCVWD 152
G + +++ H G + ++ +S + S D + VWD
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 25.0 bits (55), Expect = 4.3
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 34 CCKVESTRAHHQPITVLECV--SNRVITGSQDHTLKVYK 70
+ + + H P+T + N + +GS D T++V+
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>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 = 34.2 bits (79), Expect = 0.002
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 73 DQQLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWD 112
+LL TL GH GP+T++ SGS DG + +WD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 31.1 bits (71), Expect = 0.025
Identities = 9/40 (22%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 115 TGACMYSIQAHDGCIHALTYS--DSYVISLGQDERLCVWD 152
+G + +++ H G + ++ +S Y+ S D + +WD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 24.6 bits (54), Expect = 5.5
Identities = 8/32 (25%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 41 RAHHQPITVLECV--SNRVITGSQDHTLKVYK 70
+ H P+T + + +GS D T+K++
Sbjct: 9 KGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|217353 pfam03072, DUF237, MG032/MG096/MG288 family 1. This family
consists entirely of mycoplasmal proteins. Their
function is unknown. Another related family, pfam03086,
also consists entirely of mycoplasmal proteins of the
MG032/MG096/MG288 family. Some proteins are included in
both families, but of course differ in the aligned
residues.
Length = 137
Score = 31.2 bits (71), Expect = 0.13
Identities = 10/25 (40%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 58 ITGSQDHTLKVYKLEDQ-QLLFTLH 81
I G +D+ +++ D+ +LLFTLH
Sbjct: 104 IVGKKDYPGSLFQFTDKDKLLFTLH 128
>gnl|CDD|222615 pfam14238, DUF4340, Domain of unknown function (DUF4340). This
domain is found in bacteria, and is typically between
183 and 196 amino acids in length.
Length = 189
Score = 28.9 bits (65), Expect = 1.0
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 55 NRVITGSQDHTLKVYKLEDQQLLFTLHGHCGPITTLFI 92
R + + + L Y L+D L TL G + TL++
Sbjct: 30 ERPVATNPE-DLAEYGLDDPSLTITLSTGDGELATLYV 66
>gnl|CDD|153108 cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subunit,
ferritin-like diiron-binding domain. Ribonucleotide
Reductase, R2/beta subunit (RNRR2) is a member of a
broad superfamily of ferritin-like diiron-carboxylate
proteins. The RNR protein catalyzes the conversion of
ribonucleotides to deoxyribonucleotides and is found in
all eukaryotes, many prokaryotes, several viruses, and
few archaea. The catalytically active form of RNR is a
proposed alpha2-beta2 tetramer. The homodimeric alpha
subunit (R1) contains the active site and redox active
cysteines as well as the allosteric binding sites. The
beta subunit (R2) contains a diiron cluster that, in its
reduced state, reacts with dioxygen to form a stable
tyrosyl radical and a diiron(III) cluster. This
essential tyrosyl radical is proposed to generate a
thiyl radical, located on a cysteine residue in the R1
active site that initiates ribonucleotide reduction. The
beta subunit is composed of 10-13 helices, the 8 longest
helices form an alpha-helical bundle; some have 2
addition beta strands. Yeast is unique in that it
assembles both homodimers and heterodimers of RNRR2. The
yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2
homolog (Y4) that lacks the diiron center and is
proposed to only assist in cofactor assembly, and
perhaps stabilize R1 (Y1) in its active conformation.
Length = 288
Score = 28.4 bits (64), Expect = 1.6
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 118 CMYSIQAHDGCIHALTYS---DSYVISLGQDE 146
Y QA IH+ +YS D+ +DE
Sbjct: 81 AFYGFQAFMENIHSESYSYILDTLGKDEERDE 112
>gnl|CDD|215945 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.
Length = 322
Score = 27.0 bits (61), Expect = 4.6
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 78 FTLHGHCGPITTLFID 93
+T HGHCG + +D
Sbjct: 124 YTSHGHCGILEDGEVD 139
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 27.3 bits (60), Expect = 5.0
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 20 DFKKMQVEEEMTLT------CCKVESTRAHHQPITVLECVSNRVITGSQDHTLKVYKLE- 72
D+K++ + TLT CC+++ +HH + L C +N + T+K+ K+
Sbjct: 1186 DYKEIYMNIMDTLTSEDIAYCCELKLRYSHHMSVKKLFCCNNNFNSIISVDTIKIPKIRH 1245
Query: 73 DQQLLFTLH 81
DQ F L+
Sbjct: 1246 DQTFAFLLN 1254
>gnl|CDD|130586 TIGR01523, ATPase-IID_K-Na, potassium and/or sodium efflux P-type
ATPase, fungal-type. Initially described as a calcium
efflux ATPase , more recent work has shown that the S.
pombe CTA3 gene is in fact a potassium ion efflux pump.
This model describes the clade of fungal P-type ATPases
responsible for potassium and sodium efflux. The degree
to which these pumps show preference for sodium or
potassium varies. This group of ATPases has been
classified by phylogentic analysis as type IID. The
Leishmania sequence (GP|3192903), which falls between
trusted and noise in this model, may very well turn out
to be an active potassium pump.
Length = 1053
Score = 26.9 bits (59), Expect = 7.3
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 10/87 (11%)
Query: 11 RTGSAGSLLDFKKMQVEEEMTLTCCKVESTRAHHQPITVL---------ECVSNRVITGS 61
R SAG++ + + M LT E+ +A Q + ++ E + + V+TGS
Sbjct: 648 RNESAGAVEKCHQAGINVHM-LTGDFPETAKAIAQEVGIIPPNFIHDRDEIMDSMVMTGS 706
Query: 62 QDHTLKVYKLEDQQLLFTLHGHCGPIT 88
Q L +++D + L + C P T
Sbjct: 707 QFDALSDEEVDDLKALCLVIARCAPQT 733
>gnl|CDD|235995 PRK07338, PRK07338, hypothetical protein; Provisional.
Length = 402
Score = 26.5 bits (59), Expect = 7.4
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 72 EDQQLLFTLHGHCGPITTLFIDGVSMMSGSGSQDGLLCVWDT 113
E++ +L + P+ I ++ SGS + DGL + +
Sbjct: 4 EERAVLDLIDDRQAPMLEQLIAWAAINSGSRNLDGLARMAEL 45
>gnl|CDD|131710 TIGR02662, dinitro_DRAG, ADP-ribosyl-[dinitrogen reductase]
hydrolase. Members of this family are the enzyme
ADP-ribosyl-[dinitrogen reductase] hydrolase (EC
3.2.2.24), better known as Dinitrogenase Reductase
Activating Glycohydrolase, DRAG. This enzyme reverses a
regulatory inactivation of dinitrogen reductase caused
by the action of NAD(+)--dinitrogen-reductase
ADP-D-ribosyltransferase (EC 2.4.2.37) (DRAT). This
enzyme is restricted to nitrogen-fixing bacteria and
belongs to the larger family of
ADP-ribosylglycohydrolases described by pfam03747
[Central intermediary metabolism, Nitrogen fixation].
Length = 287
Score = 26.3 bits (58), Expect = 7.6
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 13/48 (27%)
Query: 111 WDTVTGACMYSIQAHDGCIHALTYSDSYVISLGQDERLCVWDRFQGHL 158
WD GA M ++ A AL +LG D W Q H+
Sbjct: 117 WDAGNGAAMRNLPA------ALA-------TLGDDAAFERWSVEQAHI 151
>gnl|CDD|236038 PRK07521, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 483
Score = 26.4 bits (59), Expect = 8.5
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 7/33 (21%)
Query: 90 LFIDGV-------SMMSGSGSQDGLLCVWDTVT 115
++IDGV M GS LL + D +
Sbjct: 252 VYIDGVPLTGGSGVMPLAGGSLAALLQLRDEIA 284
>gnl|CDD|215596 PLN03133, PLN03133, beta-1,3-galactosyltransferase; Provisional.
Length = 636
Score = 26.3 bits (58), Expect = 8.8
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 126 DGCIHALTYSDSYVISLGQDER--LCVWDRFQ 155
DG I+ D YV++ Q R LC+W + Q
Sbjct: 594 DGRIYNEGCKDGYVVAHYQSPREMLCLWQKLQ 625
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
0.323 0.135 0.420
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: 7,814,807
Number of extensions: 654556
Number of successful extensions: 432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 33
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
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 (22.0 bits)
S2: 55 (25.0 bits)