RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1285
(118 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 = 52.7 bits (127), Expect = 2e-09
Identities = 30/100 (30%), Positives = 39/100 (39%), Gaps = 28/100 (28%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWD------V 65
T VWD T K + L GH D + + D + S+S+D TIKLWD V
Sbjct: 116 TIKVWDVET-----GKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCV 170
Query: 66 RKFNG-----------------AANSKDQTIKLWDVRKFS 88
G ++S D TIKLWD+
Sbjct: 171 ATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGK 210
Score = 52.3 bits (126), Expect = 3e-09
Identities = 28/98 (28%), Positives = 38/98 (38%), Gaps = 28/98 (28%)
Query: 14 FVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDVRKF----- 68
+WD RT K V L GH + + D L+S+S D TIKLWD+
Sbjct: 160 KLWDLRTG-----KCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGT 214
Query: 69 ----NGAANS--------------KDQTIKLWDVRKFS 88
NS +D TI++WD+R
Sbjct: 215 LRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGE 252
Score = 50.4 bits (121), Expect = 1e-08
Identities = 30/100 (30%), Positives = 43/100 (43%), Gaps = 28/100 (28%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDVRKFN-- 69
T +WD T + V L GH ++ + D R L S+S+D+TIK+WDV
Sbjct: 74 TIRLWDLETG-----ECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCL 128
Query: 70 ---------------------GAANSKDQTIKLWDVRKFS 88
A++S+D TIKLWD+R
Sbjct: 129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGK 168
Score = 45.8 bits (109), Expect = 6e-07
Identities = 31/106 (29%), Positives = 44/106 (41%), Gaps = 28/106 (26%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWD------V 65
T VWD T + + L GH + + D +L S S D+TI+LWD V
Sbjct: 32 TIKVWDL-----ETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECV 86
Query: 66 RKFNG-----------------AANSKDQTIKLWDVRKFSNKTAQR 94
R G +++S+D+TIK+WDV T R
Sbjct: 87 RTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLR 132
Score = 44.2 bits (105), Expect = 3e-06
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 23/82 (28%)
Query: 28 PVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDV------RKFNG----------- 70
L GH G+T + D + L + S D TIK+WD+ R G
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAAS 60
Query: 71 ------AANSKDQTIKLWDVRK 86
A+ S D+TI+LWD+
Sbjct: 61 ADGTYLASGSSDKTIRLWDLET 82
Score = 40.0 bits (94), Expect = 7e-05
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWD 64
T VWD RT + V L+GH + +T + D + L S S D TI++WD
Sbjct: 242 TIRVWDLRT-----GECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 41.6 bits (98), Expect = 2e-06
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 27 KPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWD 64
K + L GH +T + D L S S D T+++WD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 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 = 40.4 bits (95), Expect = 4e-06
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 25 TAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWD 64
+ + + L GH +T + D ++L S S D TIKLWD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 38.1 bits (87), Expect = 4e-04
Identities = 34/105 (32%), Positives = 46/105 (43%), Gaps = 29/105 (27%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLI-SNSKDQTIKLWDVRK--- 67
T +WD RT KP+ LAGH D ++ + D LI S S D TI+LWD+
Sbjct: 179 TIKLWDLRT-----GKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKL 233
Query: 68 ----FNG----------------AANSKDQTIKLWDVRKFSNKTA 92
+G A+ S D TI+LWD+R S+
Sbjct: 234 LRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLR 278
Score = 36.6 bits (83), Expect = 0.001
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDVRK 67
T +WD R+ + + L+GH + + D + L S S D T++LWD+
Sbjct: 264 TIRLWDLRSSS----SLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLET 315
Score = 35.4 bits (80), Expect = 0.003
Identities = 30/119 (25%), Positives = 44/119 (36%), Gaps = 29/119 (24%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNS-KDQTIKLWDVRK--- 67
T +WD T K + L GH + +T + D + L S S D TIKLWD+R
Sbjct: 135 TVKLWDLSTPG----KLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKP 190
Query: 68 ---FNG------------------AANSKDQTIKLWDVRKFSNKTAQRNTFRAVCEQNW 105
G A+ S D TI+LWD+ + + ++
Sbjct: 191 LSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSF 249
Score = 34.7 bits (78), Expect = 0.006
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDVRKF 68
T +WD T + L GH +T +D D + L S S D TI+LWD++
Sbjct: 393 TVRLWDLSTG-----SLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTS 444
Score = 32.0 bits (71), Expect = 0.054
Identities = 27/100 (27%), Positives = 38/100 (38%), Gaps = 31/100 (31%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDG-ITFIDPKGDSRHLISNSKDQTIKLWDVRKFNG 70
T +WD T L+GH D ++ P D L S S D TI+LWD+R +
Sbjct: 222 TIRLWDLSTGKLLR----STLSGHSDSVVSSFSP--DGSLLASGSSDGTIRLWDLRSSSS 275
Query: 71 ------------------------AANSKDQTIKLWDVRK 86
A+ S D T++LWD+
Sbjct: 276 LLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLET 315
Score = 30.4 bits (67), Expect = 0.18
Identities = 18/37 (48%), Positives = 20/37 (54%)
Query: 32 LAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDVRKF 68
L GH D IT I D L+S S D TIKLWD+
Sbjct: 61 LRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNG 97
Score = 30.4 bits (67), Expect = 0.20
Identities = 27/100 (27%), Positives = 38/100 (38%), Gaps = 25/100 (25%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWD------- 64
T +WD + G+ + P G+S L S+S D T+KLWD
Sbjct: 88 TIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKL 147
Query: 65 VRKFNG------------------AANSKDQTIKLWDVRK 86
+R G + +S D TIKLWD+R
Sbjct: 148 IRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRT 187
Score = 29.3 bits (64), Expect = 0.41
Identities = 28/111 (25%), Positives = 43/111 (38%), Gaps = 26/111 (23%)
Query: 5 PQVASLVTCFVWDR--RTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKL 62
P + LV+ D R + T KP+ L GH + + D R + S S D T++L
Sbjct: 338 PDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPDGRVVSSGSTDGTVRL 396
Query: 63 WDVRKFNG-----------------------AANSKDQTIKLWDVRKFSNK 90
WD+ + A+ S D TI+LWD++
Sbjct: 397 WDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKS 447
Score = 28.5 bits (62), Expect = 0.97
Identities = 24/103 (23%), Positives = 37/103 (35%), Gaps = 26/103 (25%)
Query: 12 TCFVWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHL-ISNSKDQTIKLWDVRKFNG 70
T +WD T ++ L GH ++ + D L S D TI+LWD+R
Sbjct: 307 TVRLWDLETGKLLSSLT---LKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKP 363
Query: 71 ----------------------AANSKDQTIKLWDVRKFSNKT 91
++ S D T++LWD+ S
Sbjct: 364 LKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLR 406
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 31.2 bits (70), Expect = 0.094
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 28 PVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDV 65
P+ + GH ++++ DS L+S+S D T+KLWD+
Sbjct: 653 PLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDL 689
>gnl|CDD|173427 PTZ00137, PTZ00137, 2-Cys peroxiredoxin; Provisional.
Length = 261
Score = 29.5 bits (66), Expect = 0.28
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 70 GAANSKDQTIKLWDVRKFSNKTAQRNTFRAVCEQNWE 106
G S D+T++L+D +F+ KT VC NW+
Sbjct: 209 GLGRSVDETLRLFDAVQFAEKTGN------VCPVNWK 239
>gnl|CDD|185120 PRK15198, PRK15198, outer membrane usher protein FimD; Provisional.
Length = 860
Score = 29.1 bits (65), Expect = 0.57
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 30 GVLAGHRDGITFIDPKGDSRHLI 52
G + GH DGITF P GD+ LI
Sbjct: 677 GGVVGHEDGITFSQPLGDTNVLI 699
>gnl|CDD|183906 PRK13234, nifH, nitrogenase reductase; Reviewed.
Length = 295
Score = 28.2 bits (63), Expect = 0.97
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 34 GHRDGITFIDPKGDSRHLISNSKDQ 58
G + I DPK DS LI N+K Q
Sbjct: 32 GQKILIVGCDPKADSTRLILNAKAQ 56
>gnl|CDD|237312 PRK13236, PRK13236, nitrogenase reductase; Reviewed.
Length = 296
Score = 26.9 bits (59), Expect = 2.4
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 34 GHRDGITFIDPKGDSRHLISNSKDQTIKL 62
G R I DPK DS L+ +SK QT L
Sbjct: 34 GQRILIVGCDPKADSTRLMLHSKAQTTVL 62
>gnl|CDD|183905 PRK13233, nifH, nitrogenase reductase; Reviewed.
Length = 275
Score = 27.1 bits (60), Expect = 2.5
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 24 TTAKPVGVLAGHRDGITFI---DPKGDSRHLISNSKDQTIKLWDVRKFNGAANSKDQTIK 80
TT +A D FI DPK DS LI K QT + +R+ + D+ IK
Sbjct: 18 TTQNTAAAMAYFHDKKVFIHGCDPKADSTRLILGGKPQTTMMDTLRELGEEKVTPDKVIK 77
>gnl|CDD|216272 pfam01060, DUF290, Transthyretin-like family. This family called
family 2 in, has weak similarity to transthyretin
(formerly called pre-albumin) which transports thyroid
hormones. The specific function of this protein is
unknown.
Length = 81
Score = 25.7 bits (57), Expect = 2.8
Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 14 FVWDRRTLNETTAKPVG--VLAGHRDGITFIDPK 45
D L+ET G L+G IT IDP
Sbjct: 25 IDPDD-LLDETKTDSDGTFRLSGSTTEITSIDPY 57
>gnl|CDD|182644 PRK10681, PRK10681, DNA-binding transcriptional repressor DeoR;
Provisional.
Length = 252
Score = 26.2 bits (58), Expect = 3.8
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 18 RRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKL 62
RR LN +A PV VL G G ++P+ S +L+S DQ +L
Sbjct: 39 RRDLNAHSA-PV-VLLG---GYIVLEPRSASHYLLS---DQKSRL 75
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 26.4 bits (58), Expect = 4.2
Identities = 25/100 (25%), Positives = 35/100 (35%), Gaps = 33/100 (33%)
Query: 15 VWDRRTLNETTAKPVGVLAGHRDGITFIDPKGDSRHLISNSKDQTIKLWDVRKFN----- 69
VWD K V V+ H D IT ++ D L + SKD+ + + D R
Sbjct: 152 VWDVER-----GKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSSV 206
Query: 70 -----------------------GAANSKDQTIKLWDVRK 86
G + S+ + I LWD RK
Sbjct: 207 EAHASAKSQRCLWAKRKDLIITLGCSKSQQRQIMLWDTRK 246
>gnl|CDD|235386 PRK05279, PRK05279, N-acetylglutamate synthase; Validated.
Length = 441
Score = 26.3 bits (59), Expect = 4.5
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 12/39 (30%)
Query: 25 TAKPVGVLAGHRDGITF--------IDPKGDSRHLISNS 55
TA+P+GV DG+ + ID + R L S +
Sbjct: 135 TARPLGV----DDGVDYQHTGEVRRIDAEAIRRQLDSGA 169
>gnl|CDD|114764 pfam06060, Mesothelin, Pre-pro-megakaryocyte potentiating factor
precursor (Mesothelin). This family consists of several
mammalian pre-pro-megakaryocyte potentiating factor
precursor (MPF) or mesothelin proteins. Mesothelin is a
glycosylphosphatidylinositol-linked glycoprotein highly
expressed in mesothelial cells, mesotheliomas, and
ovarian cancer, but the biological function of the
protein is not known.
Length = 625
Score = 26.1 bits (57), Expect = 5.5
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 5 PQVASLVTCFVWDRRTLNETTAKPVG 30
QV +LV C++ L+E T K +
Sbjct: 411 AQVIALVACYLRGGGQLDEDTVKALT 436
>gnl|CDD|239770 cd04237, AAK_NAGS-ABP, AAK_NAGS-ABP: N-acetylglutamate (NAG)
kinase-like domain of the NAG Synthase (NAGS) of the
arginine-biosynthesis pathway (ABP) found in gamma- and
beta-proteobacteria and higher plant chloroplasts.
Domain architecture of these NAGS consisted of an
N-terminal NAG kinase-like (ArgB) domain (this CD) and a
C-terminal NAG synthase, acetyltransferase (ArgA)
domain. Both bacterial and plant sequences in this CD
have a conserved N-terminal extension; a similar
sequence in the NAG kinases of the cyclic
arginine-biosynthesis pathway has been implicated in
feedback inhibition sensing. Plant sequences also have
an N-terminal chloroplast transit peptide and an insert
(approx. 70 residues) in the C-terminal region of ArgB.
Members of this CD belong to the Amino Acid Kinase
Superfamily (AAK).
Length = 280
Score = 25.6 bits (57), Expect = 6.4
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 12/42 (28%)
Query: 22 NETTAKPVGVLAGHRDGITF--------IDPKGDSRHLISNS 55
N TA+P+GV DG+ F ID R L S
Sbjct: 125 NFVTARPLGV----VDGVDFGHTGEVRRIDADAIRRQLDQGS 162
>gnl|CDD|211997 TIGR04274, hypoxanDNAglyco, hypoxanthine-DNA glycosylase.
Members of this protein family represent family 6 of
the uracil-DNA glycosylase superfamily, where the five
previously described families all act as uracil-DNA
glycosylase (EC 3.2.2.27) per se. This family, instead,
acts as a hypoxanthine-DNA glycosylase, where
hypoxanthine results from deamination of adenine.
Activity was shown directly for members from
Methanosarcina barkeri and Methanosarcina acetivorans.
Length = 150
Score = 25.4 bits (56), Expect = 6.9
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 5/46 (10%)
Query: 39 ITFIDPKGDSRHLISNSKDQTIKLWDV-----RKFNGAANSKDQTI 79
+ + I K I LWDV R+ + +N KD+
Sbjct: 44 LIGEPHSLNYPTRIELLKRHGIALWDVCAACEREGSLDSNIKDEVP 89
>gnl|CDD|223194 COG0116, COG0116, Predicted N6-adenine-specific DNA methylase [DNA
replication, recombination, and repair].
Length = 381
Score = 25.7 bits (57), Expect = 7.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 21 LNETTAKPVGVLAGHRDGITFIDP 44
L ET A + +LAG + +DP
Sbjct: 175 LKETLAAAILLLAGWKPDEPLLDP 198
>gnl|CDD|225729 COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 835
Score = 25.7 bits (57), Expect = 8.0
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 30 GVLAGHRDGITFIDPKGDSRHLIS 53
G + H G+T P GD+ L+
Sbjct: 656 GGVVAHSGGVTLSQPLGDTFALVD 679
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
0.319 0.132 0.410
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: 5,600,049
Number of extensions: 442455
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 409
Number of HSP's successfully gapped: 39
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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: 53 (24.2 bits)