RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14031
(280 letters)
>gnl|CDD|214566 smart00216, VWD, von Willebrand factor (vWF) type D domain. Von
Willebrand factor contains several type D domains: D1
and D2 are present within the N-terminal propeptide
whereas the remaining D domains are required for
multimerisation.
Length = 163
Score = 127 bits (322), Expect = 9e-37
Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 7/157 (4%)
Query: 6 GVCTVFGDPHYRTFDGKFYSFQGSCKYQLTADCT-GGAFSIRVTNDARDTKTSSWTKTVS 64
C+V GDPHY TFDG Y+F G+C Y L DC+ FS+ + N ++ K+V
Sbjct: 10 PTCSVSGDPHYTTFDGVAYTFPGNCYYVLAQDCSSEPTFSVLLKNVPCGG-GATCLKSVK 68
Query: 65 IRIGDMKV-NLGEKLRVKIDGQRVALPYDLPSKVIVTKTAES-VLVETAIGI-KVLWDGN 121
+ + ++ + +V ++GQ+V+LPY I +++ ++V T++G+ +V +DG
Sbjct: 69 VELNGDEIELKDDNGKVTVNGQQVSLPYKTSDGSIQIRSSGGYLVVITSLGLIQVTFDGL 128
Query: 122 SFLEVSAPAKFKILDRLCGLCGNFNGISSDDLTTKRG 158
+ L V P+K++ + CGLCGNF+G DD T G
Sbjct: 129 TLLSVQLPSKYR--GKTCGLCGNFDGEPEDDFRTPDG 163
>gnl|CDD|215713 pfam00094, VWD, von Willebrand factor type D domain.
Luciferin-2-monooxygenase from Vargula hilgendorfii
contains a vwd domain. Its function is unrelated but the
similarity is very strong by several methods.
Length = 159
Score = 127 bits (322), Expect = 1e-36
Identities = 56/161 (34%), Positives = 89/161 (55%), Gaps = 11/161 (6%)
Query: 8 CTVFGDPHYRTFDGKFYSFQGSCKYQ--LTADCTG---GAFSIRVTNDARDTKTSSWTKT 62
C+V GDPHY TFDG Y+F G+C Y L DC+ FS+ N + + K+
Sbjct: 1 CSVSGDPHYTTFDGVSYTFPGNCSYVLVLAQDCSSEPSFKFSVLNKNVNDGAEGVTCLKS 60
Query: 63 VSIRIGDMKVNL--GEKLRVKIDGQRVALPYDLPSKVIVTKTAESVLVETAIGIKV--LW 118
V++ +G++++ L G +++V ++GQ V+LPY + +I + VLV +G+ +
Sbjct: 61 VTVILGNLEIELVPGNQVKVLVNGQEVSLPYSSDNGLIEILGSGFVLVTLRLGVTLQFDG 120
Query: 119 DGNSFLEVSAPAKFKILDRLCGLCGNFNGISSDDLTTKRGR 159
DG + L VS ++ + CGLCGNF+G +DD T G
Sbjct: 121 DGRTQLFVSLSPMYR--GKTCGLCGNFDGEPADDFRTPDGS 159
>gnl|CDD|219998 pfam08742, C8, C8 domain. This domain contains 8 conserved
cysteine residues, but this family only contains 7 of
them to overlaps with other domains. It is found in
disease-related proteins including von Willebrand
factor, Alpha tectorin, Zonadhesin and Mucin. It is
often found on proteins containing pfam00094 and
pfam01826.
Length = 74
Score = 76.7 bits (189), Expect = 4e-18
Identities = 24/68 (35%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 207 KKCKPLRSDVFSACHARLNHLMYFKSCLVDMCECP-LKNCHCESFTAYARECSRLGVQLG 265
++C L S VF+ CH+ ++ ++++C+ D+C C + C C + AYAR C++ GV +
Sbjct: 6 EQCGILLSPVFAECHSVVDPEPFYEACVYDLCACGGGEECLCSALAAYARACAQAGVCVD 65
Query: 266 DWRKLTGC 273
WR T C
Sbjct: 66 GWRTPTFC 73
>gnl|CDD|214843 smart00832, C8, This domain contains 8 conserved cysteine residues.
Not all of the conserved cysteines have been included
in the alignment model. It is found in disease-related
proteins including von Willebrand factor, Alpha
tectorin, Zonadhesin and Mucin.
Length = 76
Score = 65.8 bits (161), Expect = 4e-14
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 203 KYRDKKCKPLRSD--VFSACHARLNHLMYFKSCLVDMCECP-LKNCHCESFTAYARECSR 259
Y +C L S F+ACH+ ++ +F++C+ D C C C C++ AYA C+
Sbjct: 2 YYACSQCGILLSPRGPFAACHSVVDPEPFFENCVYDTCACGGDCECLCDALAAYAAACAE 61
Query: 260 LGVQLGDWRKLTGC 273
GV + WR T C
Sbjct: 62 AGVCISPWRTPTFC 75
>gnl|CDD|219076 pfam06535, RGM_N, Repulsive guidance molecule (RGM) N-terminus.
This family consists of the N-terminal region of several
mammalian and one bird sequence from Gallus gallus
(Chicken). All of the mammalian proteins are
hypothetical and have no known function but RGMA from
the chicken is annotated as being a repulsive guidance
molecule (RGM). RGM is a GPI-linked axon guidance
molecule of the retinotectal system. RGM is repulsive
for a subset of axons, those from the temporal half of
the retina. Temporal retinal axons invade the anterior
optic tectum in a superficial layer, and encounter RGM
expressed in a gradient with increasing concentration
along the anterior-posterior axis. Temporal axons are
able to receive posterior-dependent information by
sensing gradients or concentrations of guidance cues.
Thus, RGM is likely to provide positional information
for temporal axons invading the optic tectum in the
stratum opticum.
Length = 207
Score = 31.7 bits (72), Expect = 0.27
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 8 CTVFGDPHYRTFDGKFYSFQGSCKYQ 33
C +FGDPH RTF+ F +CK Q
Sbjct: 147 CGLFGDPHLRTFNDHFQ----TCKVQ 168
>gnl|CDD|222521 pfam14066, DUF4256, Protein of unknown function (DUF4256). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 190 amino acids in length.
Length = 173
Score = 29.1 bits (66), Expect = 1.5
Identities = 10/15 (66%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 53 DTKTSSWTKT-VSIR 66
D KTSSW KT IR
Sbjct: 122 DLKTSSWIKTPADIR 136
>gnl|CDD|111086 pfam02154, FliM, Flagellar motor switch protein FliM.
Length = 192
Score = 29.3 bits (66), Expect = 1.7
Identities = 15/43 (34%), Positives = 19/43 (44%)
Query: 119 DGNSFLEVSAPAKFKILDRLCGLCGNFNGISSDDLTTKRGRVV 161
G LEV F I+DRL G G F+ + T RV+
Sbjct: 74 KGTGLLEVDPSIAFIIVDRLFGGDGRFHAKEGREFTDIERRVI 116
>gnl|CDD|226628 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 29.6 bits (67), Expect = 1.8
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 11/67 (16%)
Query: 63 VSIRIGDMKVNLGEKLRVKIDGQRVALPYD----------LPSKVI-VTKTAESVLVETA 111
+ + + +G +LR++I + V+L LP KV+ + V V+
Sbjct: 256 QHLWVPKLDAPVGARLRIRIQARDVSLALQKPEQTSIRNILPGKVVGIEDDDGQVDVQLD 315
Query: 112 IGIKVLW 118
G K LW
Sbjct: 316 CGGKTLW 322
>gnl|CDD|224781 COG1868, FliM, Flagellar motor switch protein [Cell motility and
secretion].
Length = 332
Score = 29.2 bits (66), Expect = 2.1
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 118 WDGNSFLEVSAPAKFKILDRLCGLCGNFNG-ISSDDLT 154
G + LE F ++DRL G G F +LT
Sbjct: 107 LKGTALLEFDPSLVFIMVDRLFGGDGRFPAKPEGRELT 144
>gnl|CDD|212703 cd11769, SH3_CSK, Src Homology 3 domain of C-terminal Src kinase.
CSK is a cytoplasmic (or nonreceptor) tyr kinase
containing the Src homology domains, SH3 and SH2,
N-terminal to the catalytic tyr kinase domain. They
negatively regulate the activity of Src kinases that are
anchored to the plasma membrane. To inhibit Src kinases,
CSK is translocated to the membrane via binding to
specific transmembrane proteins, G-proteins, or adaptor
proteins near the membrane. CSK catalyzes the tyr
phosphorylation of the regulatory C-terminal tail of Src
kinases, resulting in their inactivation. It is
expressed in a wide variety of tissues and plays a role,
as a regulator of Src, in cell proliferation, survival,
and differentiation, and consequently, in cancer
development and progression. In addition, CSK also shows
Src-independent functions. It is a critical component in
G-protein signaling, and plays a role in cytoskeletal
reorganization and cell migration. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 57
Score = 26.9 bits (60), Expect = 2.3
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 144 NFNGISSDDLTTKRGRVVT 162
NFNG S +DL K+G ++T
Sbjct: 9 NFNGASEEDLPFKKGDILT 27
>gnl|CDD|222656 pfam14292, SusE, SusE outer membrane protein. This family includes
the SusE outer membrane protein from Bacteroides
thetaiotaomicron. This protein has a role in starch
utilisation, but is not essential for growth on starch.
Length = 122
Score = 28.1 bits (63), Expect = 2.9
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 9/59 (15%)
Query: 31 KYQLTADCTGGAFSIRVTNDARDTKTSSWTKTV----SIRIGDMKVNLGE----KLRVK 81
Y + D TG FS V D +S + TV I + + + GE ++RVK
Sbjct: 64 TYTVEFDKTGNDFSKPVVLGTTDNGETSLSITVKELNKI-LNKLGIAPGETVTLEVRVK 121
>gnl|CDD|223850 COG0779, COG0779, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 153
Score = 28.0 bits (63), Expect = 3.3
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 75 GEKLRVKIDGQRVALPYDLPSKV 97
GE + +++DG+ V +P+ +K
Sbjct: 125 GETVTLEVDGKEVEIPFSDIAKA 147
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 28.3 bits (64), Expect = 3.6
Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 25/84 (29%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRV-------ALPYDLPSKVIVTKTAESVLVETAIGIKVLW 118
RIG + + + + + V ID Q + L +P + +
Sbjct: 3 RIGKLPIKIPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITIEI----------------- 45
Query: 119 DGNSFLEVSAPAKFKILDRLCGLC 142
++ L VS + K L GL
Sbjct: 46 -QDNSLFVSKKDESKKARALHGLY 68
>gnl|CDD|217656 pfam03644, Glyco_hydro_85, Glycosyl hydrolase family 85. Family of
endo-beta-N-acetylglucosaminidases. These enzymes work
on a broad spectrum of substrates.
Length = 302
Score = 28.5 bits (64), Expect = 4.1
Identities = 11/45 (24%), Positives = 15/45 (33%), Gaps = 11/45 (24%)
Query: 113 GIKVL------WDG-----NSFLEVSAPAKFKILDRLCGLCGNFN 146
G+ VL WDG L+ F D+L L +
Sbjct: 54 GVPVLGTIIFEWDGGVEWLEELLKQDEEGSFPYADKLVELAKYYG 98
>gnl|CDD|145231 pfam01946, Thi4, Thi4 family. This family includes a putative
thiamine biosynthetic enzyme.
Length = 229
Score = 27.8 bits (62), Expect = 5.1
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 95 SKVIVTKTAESVLVETAIGIKVLWDGNSFLEVSAPAKF--KILDRLCGL-CGNFNGISSD 151
S ++V K A+ L E GI+ +G+ + V+ A+F + + FN S +
Sbjct: 64 SAMVVRKPADEFLDE--FGIRYEDEGDYVV-VADAAEFTSTLASKALQPGVKIFNATSVE 120
Query: 152 DLTTKRGRV 160
DL + RV
Sbjct: 121 DLIIRDNRV 129
>gnl|CDD|177178 MTH00117, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 227
Score = 28.0 bits (63), Expect = 5.6
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 86 RVALPYDLPSKVIVTKTAESVLVETAI---GIKV 116
R+ +P + P ++++ TAE VL A+ G+K
Sbjct: 141 RMVIPMESPIRILI--TAEDVLHSWAVPSLGVKT 172
>gnl|CDD|217419 pfam03198, Glyco_hydro_72, Glucanosyltransferase. This is a family
of glycosylphosphatidylinositol-anchored
beta(1-3)glucanosyltransferases. The active site
residues in the Aspergillus fumigatus example are the
two glutamate residues at 160 and 261.
Length = 313
Score = 27.7 bits (62), Expect = 6.5
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 47 VTNDARDTKTSSWTKTVSIRIGDMK 71
V NDA +T S++ K + DMK
Sbjct: 144 VINDASNTDASAYVKAA---VRDMK 165
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type. [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 27.4 bits (62), Expect = 7.2
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 7/51 (13%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRV-------ALPYDLPSKVIVTKTAESVLVE 109
RIG + + + V IDG V L L V V + V
Sbjct: 2 RIGKKPIAIPAGVEVTIDGNVVTVKGPKGELSRTLHPGVTVKVEDGQLTVS 52
>gnl|CDD|200512 cd11251, Sema_3C, The Sema domain, a protein interacting module, of
semaphorin 3C (Sema3C). Sema3C is a secreted semaphorin
expressed in and adjacent to cardiac neural crest cells,
and causes impaired migration of neural crest cells to
the developing cardiac outflow tract, resulting in the
interruption of the aortic arch and persistent truncus
arteriosus. It has been proposed that Sema3C acts as a
guidance molecule, regulating migration of neural crest
cells that express semaphorin receptors such as plexin
A2. Sema3C may also participate in tumor progression.
The cleavage of Sema3C induced by ADAMTS1 promotes the
migration of breast cancer cells. Sema3C is a member of
the class 3 semaphorin family of secreted proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 470
Score = 27.9 bits (62), Expect = 7.4
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 14/62 (22%)
Query: 4 GDGVC--------TVFGDP--HYRTFDGKFYSFQGSCKYQLTADCTGGAFSIRVTNDARD 53
G VC TVF P H + + ++QG Y C GGAF T + +
Sbjct: 290 GSAVCVYHMSDIQTVFNGPFAHKEGPNHQLIAYQGRIPYPRPGTCPGGAF----TPNMQS 345
Query: 54 TK 55
TK
Sbjct: 346 TK 347
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
0.322 0.137 0.441
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,642,909
Number of extensions: 1213580
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 849
Number of HSP's successfully gapped: 21
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
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 (21.9 bits)
S2: 58 (26.1 bits)