RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8036
(194 letters)
>gnl|CDD|161920 TIGR00545, lipoyltrans, lipoyltransferase and lipoate-protein
ligase. One member of this group of proteins is bovine
lipoyltransferase, which transfers the lipoyl group from
lipoyl-AMP to the specific Lys of lipoate-dependent
enzymes. However, it does not first activate lipoic acid
with ATP to create lipoyl-AMP and pyrophosphate. Another
member of this group, lipoate-protein ligase A from E.
coli, catalyzes both the activation and the transfer of
lipoate. Homology between the two is full-length, except
for the bovine mitochondrial targeting signal, but is
strongest toward the N-terminus [Protein fate, Protein
modification and repair].
Length = 324
Score = 37.9 bits (88), Expect = 0.002
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 84 KIQSEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIE 132
+ + +QSWEW +G TPKF +F A G + +++ KG I
Sbjct: 229 RAKERFQSWEWNFGKTPKF----NFKNKKRFTA-GGFELHVQVEKGKIV 272
>gnl|CDD|233176 TIGR00898, 2A0119, cation transport protein. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 505
Score = 31.1 bits (71), Expect = 0.36
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 1/63 (1%)
Query: 74 PTDDWFPGLAKIQSEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIES 133
P GLA + WE+ Y + TI +D+ E L S V L+ S
Sbjct: 86 PLKLSDLGLAATEPCLDGWEYSYDTFSS-TIVTEWDLVCEDAWKVDLTQSCFFVGVLLGS 144
Query: 134 VCF 136
F
Sbjct: 145 FVF 147
>gnl|CDD|179655 PRK03822, lplA, lipoate-protein ligase A; Provisional.
Length = 338
Score = 30.8 bits (70), Expect = 0.39
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 80 PGLAKIQSEYQSWEWRYGSTPKFT 103
PG A+ + SWEW +G P F+
Sbjct: 230 PGFAETFARQSSWEWNFGQAPAFS 253
>gnl|CDD|223173 COG0095, LplA, Lipoate-protein ligase A [Coenzyme metabolism].
Length = 248
Score = 30.4 bits (69), Expect = 0.40
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 76 DDWFPGLAKIQSEYQSWEWRYG 97
++ + +Y SWEW +G
Sbjct: 226 EELELAEKLAEEKYSSWEWNFG 247
>gnl|CDD|172552 PRK14061, PRK14061, unknown domain/lipoate-protein ligase A fusion
protein; Provisional.
Length = 562
Score = 30.1 bits (67), Expect = 0.78
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 79 FPGLAKIQSEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLI 131
P A+ + SWEW +G P F+ + DE + G + + ++ KG I
Sbjct: 453 LPNFAETFARQSSWEWNFGQAPAFS-----HLLDERFSWGGVELHFDVEKGHI 500
>gnl|CDD|232831 TIGR00115, tig, trigger factor. Trigger factor is a
ribosome-associated molecular chaperone and is the first
chaperone to interact with nascent polypeptide. Trigger
factor can bind at the same time as the signal
recognition particle (SRP), but is excluded by the SRP
receptor (FtsY). The central domain of trigger factor
has peptidyl-prolyl cis/trans isomerase activity. This
protein is found in a single copy in virtually every
bacterial genome [Protein fate, Protein folding and
stabilization].
Length = 408
Score = 29.4 bits (67), Expect = 1.1
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 125 EIVKGLIESVCFKIPPALVNDE--HFLQDAELLCSVQGRKFTETALDDLKEAL 175
+++ L+E+ F++P +LV E L+ A QG E L D +E L
Sbjct: 278 QLLDKLVENNEFELPESLVEQEIDRLLEQALQQLQQQGIDL-EEYLKDTEEEL 329
>gnl|CDD|220157 pfam09261, Alpha-mann_mid, Alpha mannosidase, middle domain.
Members of this family adopt a structure consisting of
three alpha helices, in an
immunoglobulin/albumin-binding domain-like fold. They
are predominantly found in the enzyme alpha-mannosidase.
Length = 82
Score = 26.8 bits (60), Expect = 2.4
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 146 EHFLQDAELLCSVQGRKFTETALDDLKEALT 176
E L+ AELL S+ + LDD E L
Sbjct: 21 ESLLRAAELLASLASLLGNKGELDDYYEELD 51
>gnl|CDD|232946 TIGR00379, cobB, cobyrinic acid a,c-diamide synthase. This model
describes cobyrinic acid a,c-diamide synthase, the cobB
(cbiA in Salmonella) protein of cobalamin biosynthesis.
It is responsible for the amidation of carboxylic groups
at positions A and C of either cobyrinic acid or
hydrogenobrynic acid. NH(2) groups are provided by
glutamine and one molecule of ATP hydrogenolyzed for
each amidation [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 449
Score = 28.6 bits (64), Expect = 2.5
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 33 EVSMDRLI-----KSLGYEYLRTKAITMEDGGEGQIA--KQRGFQTINPTDDWFPGLAKI 85
EV D LI K G+E+ ++ M Q A +RG I+ D G +
Sbjct: 370 EVVNDCLILWQGEKFRGHEFHYSR---MTKLPNAQFAYRVERGRGIIDQLDGICVG--SV 424
Query: 86 QSEYQSWEWRYGSTPKF 102
+ Y GS PKF
Sbjct: 425 LASYLHLHA--GSVPKF 439
>gnl|CDD|200511 cd11250, Sema_3B, The Sema domain, a protein interacting module, of
semaphorin 3B (Sema3B). Sema3B is coexpressed with
semaphorin 3F and both proteins are candidate tumor
suppressors. Both Sema3B and Sema3F show high levels of
expression in normal tissues and low-grade tumors but
are down-regulated in highly metastatic tumors in the
lung, melanoma cells, bladder carcinoma cells and
prostate carcinoma. They are upregulated by estrogen and
inhibit cell motility and invasiveness through decreased
FAK phosphorylation and inhibition of MMP-2 and MMP-9
expression. Two receptor families, the neuropilins (NP)
and plexins, have been implicated in mediating the
actions of semaphorins 3B and 3F. Sema3B is a member of
the class 3 semaphorin family of 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 = 471
Score = 28.3 bits (63), Expect = 2.5
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 141 ALVNDEHFLQDAELLCSVQGRKFTETALDDLKE 173
+LVN A L+CSV G + +T D+L++
Sbjct: 232 SLVNKWTTFLKARLVCSVPGNEGGDTHFDELRD 264
>gnl|CDD|177475 PHA02693, PHA02693, hypothetical protein; Provisional.
Length = 710
Score = 27.7 bits (61), Expect = 4.4
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 116 APGQLVISLEIVKGLIESVCFKIPPALVND 145
AP L++ + IE+VC I PALVN+
Sbjct: 137 APWTACPQLKLSRTEIETVCRAIDPALVNE 166
>gnl|CDD|214836 smart00825, PKS_KS, Beta-ketoacyl synthase. The structure of
beta-ketoacyl synthase is similar to that of the
thiolase family and also chalcone synthase. The active
site of beta-ketoacyl synthase is located between the N
and C-terminal domains.
Length = 298
Score = 26.9 bits (61), Expect = 6.5
Identities = 9/35 (25%), Positives = 13/35 (37%)
Query: 61 GQIAKQRGFQTINPTDDWFPGLAKIQSEYQSWEWR 95
G I F+T NP D ++ +E W
Sbjct: 240 GVIPPTLHFETPNPHIDLEESPLRVPTELTPWPPP 274
>gnl|CDD|238429 cd00833, PKS, polyketide synthases (PKSs) polymerize simple fatty
acids into a large variety of different products, called
polyketides, by successive decarboxylating Claisen
condensations. PKSs can be divided into 2 groups,
modular type I PKSs consisting of one or more large
multifunctional proteins and iterative type II PKSs,
complexes of several monofunctional subunits.
Length = 421
Score = 27.1 bits (61), Expect = 6.5
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 61 GQIAKQRGFQTINPTDDWFPGLAKIQSEYQSWE 93
G I F+T NP D+ ++ +E + W
Sbjct: 365 GVIPPNLHFETPNPKIDFEESPLRVPTEARPWP 397
>gnl|CDD|205259 pfam13078, DUF3942, Protein of unknown function (DUF3942). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 130 amino acids in length.
Length = 126
Score = 26.3 bits (58), Expect = 7.5
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 145 DEHFLQDAELLCSVQGRKFTETALDD 170
DE LQ+ EL + KFTE L+D
Sbjct: 91 DEIILQEGELFALGRNEKFTEDILED 116
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
0.317 0.134 0.394
Gapped
Lambda K H
0.267 0.0940 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,749,679
Number of extensions: 888385
Number of successful extensions: 710
Number of sequences better than 10.0: 1
Number of HSP's gapped: 710
Number of HSP's successfully gapped: 23
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
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 (21.6 bits)
S2: 56 (25.0 bits)