RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1434
(357 letters)
>gnl|CDD|214549 smart00191, Int_alpha, Integrin alpha (beta-propellor repeats).
Integrins are cell adhesion molecules that mediate
cell-extracellular matrix and cell-cell interactions.
They contain both alpha and beta subunits. Alpha
integrins are proposed to contain a domain containing a
7-fold repeat that adopts a beta-propellor fold. Some of
these domains contain an inserted von Willebrand factor
type-A domain. Some repeats contain putative
calcium-binding sites. The 7-fold repeat domain is
homologous to a similar domain in
phosphatidylinositol-glycan-specific phospholipase D.
Length = 57
Score = 63.5 bits (155), Expect = 2e-13
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 148 ARFGLSLCNLGDINKDGFGDFAVGAP-YDGPNERGVVYIYHGSPIGARENPSQII 201
+ FG S+ +GD+N DG+ D VGAP + E G VY+Y GS G P Q +
Sbjct: 3 SYFGYSVAGVGDVNGDGYPDLLVGAPRANDAGETGAVYVYFGSSGGGNSIPLQNL 57
Score = 49.7 bits (119), Expect = 2e-08
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 12/65 (18%)
Query: 217 FGFSLAGGVDLDENQYPDLVIGAYESNTAFVLRSTAPYDGPNERGVVYIYHGSPIGAREN 276
FG+S+AG D++ + YPDL++GA + E G VY+Y GS G
Sbjct: 5 FGYSVAGVGDVNGDGYPDLLVGAPR------------ANDAGETGAVYVYFGSSGGGNSI 52
Query: 277 PSQII 281
P Q +
Sbjct: 53 PLQNL 57
Score = 46.6 bits (111), Expect = 3e-07
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 81 GAYFAYAVT-TSDVDGDGADDLIIGAPLYTNPTNNVGHYETGRIYVVYQGKET 132
G+YF Y+V DV+GDG DL++GAP + ETG +YV +
Sbjct: 2 GSYFGYSVAGVGDVNGDGYPDLLVGAPRANDAG------ETGAVYVYFGSSGG 48
>gnl|CDD|219842 pfam08441, Integrin_alpha2, Integrin alpha. This domain is found
in integrin alpha and integrin alpha precursors to the C
terminus of a number of pfam01839 repeats and to the
N-terminus of the pfam00357 cytoplasmic region. This
region is composed of three immunoglobulin-like domains.
Length = 440
Score = 44.7 bits (106), Expect = 5e-05
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 292 ELNVQILLDSKKPKSPRMFFLSDEGKNVINQTLLLIKGTQFCKSTVDMVCEAERPLCTPI 351
LN + LD+KK + R FL E ++ +LL G + C++ + + R TPI
Sbjct: 55 TLNYTLTLDTKKRQISRALFLDSETSSLTRTLVLLSGGQEVCRTLTAYLRDEVRDKLTPI 114
Query: 352 T 352
Sbjct: 115 A 115
>gnl|CDD|216733 pfam01839, FG-GAP, FG-GAP repeat. This family contains the
extracellular repeat that is found in up to seven copies
in alpha integrins. This repeat has been predicted to
fold into a beta propeller structure. The repeat is
called the FG-GAP repeat after two conserved motifs in
the repeat. The FG-GAP repeats are found in the N
terminus of integrin alpha chains, a region that has
been shown to be important for ligand binding. A
putative Ca2+ binding motif is found in some of the
repeats.
Length = 30
Score = 34.7 bits (81), Expect = 0.003
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 84 FAYAVTTSDVDGDGADDLIIGAP 106
F +V D++GDG DL++GAP
Sbjct: 1 FGSSVALGDLNGDGRPDLVVGAP 23
Score = 34.0 bits (79), Expect = 0.004
Identities = 18/37 (48%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 150 FGLSLCNLGDINKDGFGDFAVGAPYDGPNERGVVYIY 186
FG S+ LGD+N DG D VGAP G VY+Y
Sbjct: 1 FGSSVA-LGDLNGDGRPDLVVGAP------GGAVYVY 30
Score = 27.0 bits (61), Expect = 1.5
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 217 FGFSLAGGVDLDENQYPDLVIGAY 240
FG S+A G DL+ + PDLV+GA
Sbjct: 1 FGSSVALG-DLNGDGRPDLVVGAP 23
>gnl|CDD|222190 pfam13517, VCBS, Family description. This domain of about 100
residues is found in multiple (up to 35) copies in long
proteins from several species of Vibrio, Colwellia,
Bradyrhizobium, and Shewanella (hence the name VCBS) and
in smaller copy numbers in proteins from several other
bacteria. The large protein size and repeat copy
numbers, species distribution, and suggested activities
of several member proteins suggests a role for this
domain in adhesion (TIGR).
Length = 61
Score = 31.5 bits (72), Expect = 0.067
Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 18/79 (22%)
Query: 92 DVDGDGADDLIIGAPLYTNPTNNVGHYETGRIYVVYQGKETYKFRRLHTRDGKNSKARFG 151
D+DGDG DL+ V R+Y + G T+ F
Sbjct: 1 DLDGDGRLDLV------------VASDGGVRLY-LNNGDGTFTFVTSTLLGTGGGGTSVA 47
Query: 152 LSLCNLGDINKDGFGDFAV 170
+ D++ DG D V
Sbjct: 48 -----VADLDGDGDLDLLV 61
Score = 27.2 bits (61), Expect = 2.7
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 81 GAYFAYAVTTSDVDGDGADDLII 103
+V +D+DGDG DL++
Sbjct: 39 TGGGGTSVAVADLDGDGDLDLLV 61
>gnl|CDD|173195 PRK14733, coaE, dephospho-CoA kinase; Provisional.
Length = 204
Score = 31.5 bits (71), Expect = 0.40
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 114 NVGHYETGRIYVVYQGKETYKFRRLHTRDGKNSKARFGLSLCNLGDINKDGFGDFAV 170
N HY+ + +V + + RRL RDGKN + + D ++ DF +
Sbjct: 122 NFRHYDYLKKVIVIKADLETRIRRLMERDGKNRQQAVAFINLQISDKEREKIADFVI 178
>gnl|CDD|217782 pfam03895, YadA, YadA-like C-terminal region. This region
represents the C-terminal 120 amino acids of a family
of surface-exposed bacterial proteins. YadA, an adhesin
from Yersinia, was the first member of this family to
be characterized. UspA2 from Moraxella was second. The
Eib immunoglobulin-binding proteins from E. coli were
third, followed by the DsrA proteins of Haemophilus
ducreyi and others. These proteins are homologous at
their C-terminal and have predicted signal sequences,
but they diverge elsewhere. The C-terminal 9 amino
acids, consisting of alternating hydrophobic amino
acids ending in F or W, comprise a targeting motif for
the outer membrane of the Gram negative cell envelope.
This region is important for oligomerisation.
Length = 78
Score = 27.8 bits (63), Expect = 2.1
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 26 PTDDGSYMGYSVASGFFSGESGVAVGIPRGARLLGKVAL 64
P G G + GES VAVG R G V +
Sbjct: 21 PDAPGKSS-VGAGVGTYRGESAVAVGA--SYRSNGNVVV 56
>gnl|CDD|234000 TIGR02760, TraI_TIGR, conjugative transfer relaxase protein TraI.
This protein is a component of the relaxosome complex.
In the process of conjugative plasmid transfer the
realaxosome binds to the plasmid at the oriT (origin of
transfer) site. The relaxase protein TraI mediates the
single-strand nicking and ATP-dependent unwinding
(relaxation, helicase activity) of the plasmid molecule.
These two activities reside in separate domains of the
protein.
Length = 1960
Score = 29.5 bits (66), Expect = 3.6
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 289 GLQELNVQILLDSKKPKSPRMFFLSDEG-KNVINQTLLLIKGTQ 331
Q+ VQ LLD P S + F+ DE K N+ L LI +
Sbjct: 511 DDQDHTVQGLLDKSSPFSNKDIFVVDEANKLSNNELLKLIDKAE 554
>gnl|CDD|234108 TIGR03104, trio_amidotrans, asparagine synthase family
amidotransferase. Members of this protein family are
closely related to several isoforms of asparagine
synthetase (glutamine amidotransferase) and typically
have been given this name in genome annotation to date.
Each is part of a conserved three-gene cassette sparsely
distributed across at least twenty different species
known so far, including alpha, beta, and gamma
Proteobacteria, Mycobacterium, and Prosthecochloris,
which is a member of the Chlorobi. The other two members
of the cassette are a probable protease and a member of
the GNAT family of acetyltransferases.
Length = 589
Score = 28.9 bits (65), Expect = 4.5
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 211 QGSLTTF--GFSLAGGVDLDENQYPDLVIGAYESN 243
L TF GF GG DE +Y D++ + +
Sbjct: 285 VDGLRTFSIGFEDVGGEKGDEFEYSDIIAERFHTR 319
>gnl|CDD|219249 pfam06980, DUF1302, Protein of unknown function (DUF1302). This
family contains a number of hypothetical bacterial
proteins of unknown function that are approximately 600
residues long. Most family members seem to be from
Pseudomonas.
Length = 543
Score = 28.7 bits (65), Expect = 5.9
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 12/74 (16%)
Query: 81 GAYFAYAVTTSDVDGDGADDLIIGAPLYTNPTNNVGHYETGRIYVVYQGKETYKFRRLHT 140
G YF+ TSD G+G D L + A NP T R
Sbjct: 213 GTYFS----TSDFAGEGGDALNVNAGALGNPG-------TIAALANALVGGGVGIPRGPD 261
Query: 141 RDGKNSKARFGLSL 154
+ +S +FGL+L
Sbjct: 262 DEPSDS-GQFGLAL 274
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 28.2 bits (63), Expect = 8.3
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 272 GARENPSQI--ITAEEVNFGLQELNVQI-LLDSKKPKSPRMFFLSDEGKN------VINQ 322
G RE+ + + E+ +++ ++ I +LD+ +P + F + D K+ V+N+
Sbjct: 260 GIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNKSKKPFILVLNK 319
Query: 323 TLLLIKGTQFCKS 335
L I +F S
Sbjct: 320 IDLKINSLEFFVS 332
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
0.316 0.137 0.402
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,434,922
Number of extensions: 1809993
Number of successful extensions: 1235
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1232
Number of HSP's successfully gapped: 20
Length of query: 357
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 259
Effective length of database: 6,590,910
Effective search space: 1707045690
Effective search space used: 1707045690
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 (21.5 bits)
S2: 60 (27.0 bits)