RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4565
(67 letters)
>gnl|CDD|214592 smart00268, ACTIN, Actin. ACTIN subfamily of
ACTIN/mreB/sugarkinase/Hsp70 superfamily.
Length = 373
Score = 58.4 bits (142), Expect = 4e-12
Identities = 25/58 (43%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 8 VCPVQTYVAYGTDYKPSLVITFSGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYL 65
+ Y + LVI SGDGVTH+ PV + + LPH +R+DIAG IT YL
Sbjct: 129 IAIQAVLSLYASGRTTGLVID-SGDGVTHVVPVVDGYVLPHAIKRIDIAGR-DITDYL 184
>gnl|CDD|200935 pfam00022, Actin, Actin.
Length = 367
Score = 57.2 bits (139), Expect = 1e-11
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 24 SLVITFSGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYLLS 67
LV+ SG GVT + PVYE + L RR D+AG+ +T YL
Sbjct: 143 GLVVD-SGAGVTSVVPVYEGYVLQKAIRRSDLAGD-DLTDYLRK 184
>gnl|CDD|240225 PTZ00004, PTZ00004, actin-2; Provisional.
Length = 378
Score = 50.2 bits (120), Expect = 3e-09
Identities = 19/38 (50%), Positives = 27/38 (71%), Gaps = 1/38 (2%)
Query: 30 SGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYLLS 67
SGDGV+H P+YE ++LPH RLD+AG +T Y++
Sbjct: 156 SGDGVSHTVPIYEGYSLPHAIHRLDVAGRD-LTEYMMK 192
>gnl|CDD|173506 PTZ00281, PTZ00281, actin; Provisional.
Length = 376
Score = 47.8 bits (113), Expect = 2e-08
Identities = 20/41 (48%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 26 VITFSGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYLL 66
++ SGDGV+H P+YE +ALPH RLD+AG +T Y++
Sbjct: 152 IVMDSGDGVSHTVPIYEGYALPHAILRLDLAGRD-LTDYMM 191
>gnl|CDD|227602 COG5277, COG5277, Actin and related proteins [Cytoskeleton].
Length = 444
Score = 45.1 bits (107), Expect = 2e-07
Identities = 23/50 (46%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 16 AYGTDYKPSLVITFSGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYL 65
A G+ + LVI SGD VTH+ PV + LP +R+DI G IT YL
Sbjct: 150 ASGSSDETGLVID-SGDSVTHVIPVVDGIVLPKAVKRIDIGGRD-ITDYL 197
>gnl|CDD|240426 PTZ00466, PTZ00466, actin-like protein; Provisional.
Length = 380
Score = 41.9 bits (98), Expect = 3e-06
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 30 SGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYL 65
GDGV H +YE +++ + R D+AG IT YL
Sbjct: 161 CGDGVCHCVSIYEGYSITNTITRTDVAGRD-ITTYL 195
>gnl|CDD|240343 PTZ00280, PTZ00280, Actin-related protein 3; Provisional.
Length = 414
Score = 33.2 bits (76), Expect = 0.004
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 30 SGDGVTHICPVYEQFALPHLTRRLDIAGESHITRYLL 66
SGDGVTH+ PV + + + + + +AG IT ++
Sbjct: 167 SGDGVTHVIPVVDGYVIGSSIKHIPLAGRD-ITNFIQ 202
>gnl|CDD|185631 PTZ00452, PTZ00452, actin; Provisional.
Length = 375
Score = 32.0 bits (72), Expect = 0.009
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 30 SGDGVTHICPVYEQFALPHLTRRLDIAG 57
SG+GVTH PV+E +P ++++AG
Sbjct: 155 SGEGVTHCVPVFEGHQIPQAITKINLAG 182
>gnl|CDD|212657 cd00012, NBD_sugar-kinase_HSP70_actin, Nucleotide-Binding Domain of
the sugar kinase/HSP70/actin superfamily. This
superfamily includes the actin family, the HSP70 family
of molecular chaperones and nucleotide exchange factors,
the ROK (repressor, ORF, kinase) family, the hexokinase
family, the FGGY family (which includes glycerol kinase
and similar carbohydrate kinases such as rhamnulokinase
and xylulokinase), the exopolyphosphatase/guanosine
pentaphosphate phosphohydrolase/nucleoside triphosphate
diphosphohydrolase family, propionate kinase/acetate
kinase family, glycerol dehydratase reactivase,
2-hydroxyglutaryl-CoA dehydratase component A,
N-acetylglucosamine kinase, butyrate kinase 2,
Escherichia coli YeaZ and similar glycoproteases, the
cell shape-determining protein MreB, the plasmid DNA
segregation factor ParM, cell cycle proteins FtsA, Pili
assembly protein PilM, ethanolamine utilization protein
EutJ, and similar proteins. The nucleotide-binding site
residues are conserved; the nucleotide sits in a deep
cleft formed between the two lobes of the
nucleotide-binding domain (NBD). Substrate binding to
superfamily members is associated with closure of this
catalytic site cleft. The functional activities of
several members of the superfamily, including
hexokinases, actin, and HSP70s, are modulated by
allosteric effectors, which may act on the cleft
closure.
Length = 185
Score = 29.1 bits (65), Expect = 0.12
Identities = 8/43 (18%), Positives = 14/43 (32%)
Query: 14 YVAYGTDYKPSLVITFSGDGVTHICPVYEQFALPHLTRRLDIA 56
+ ++++ G G T I V + L IA
Sbjct: 115 AEGLFGKEEDTVLVVDLGTGTTGIAIVEDGKGGVGAAGELGIA 157
>gnl|CDD|232992 TIGR00474, selA, seryl-tRNA(sec) selenium transferase. In
bacteria, the incorporation of selenocysteine as the
21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes SelA.
This model excludes homologs that appear to differ in
function from Frankia alni, Helicobacter pylori,
Methanococcus jannaschii and other archaea, and so on
[Protein synthesis, tRNA aminoacylation].
Length = 454
Score = 27.5 bits (62), Expect = 0.43
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 11 VQTYVAYGTDYKPSLVITFSGD 32
VQ +A G D ++TFSGD
Sbjct: 271 VQEVIAAGVD-----LVTFSGD 287
>gnl|CDD|235278 PRK04311, PRK04311, selenocysteine synthase; Provisional.
Length = 464
Score = 26.7 bits (60), Expect = 0.83
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 11 VQTYVAYGTDYKPSLVITFSGD 32
VQ +A G D ++TFSGD
Sbjct: 276 VQELLAAGVD-----LVTFSGD 292
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 25.7 bits (57), Expect = 1.5
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 12/40 (30%)
Query: 10 PVQTYVAYGTDYKPSLVITFS----------GDGVTHICP 39
P ++ AY T + V+ S G GVT ICP
Sbjct: 458 PSRSLPAYAT--SKAAVLMLSECLRAELAAAGIGVTAICP 495
>gnl|CDD|215237 PLN02433, PLN02433, uroporphyrinogen decarboxylase.
Length = 345
Score = 25.3 bits (56), Expect = 2.7
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 35 THICPV-YEQFALPHLTRRLDIAGESH 60
H+ PV +E+F+ P+L + +D H
Sbjct: 204 GHLSPVDFEEFSKPYLEKIVDEVKARH 230
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 24.6 bits (54), Expect = 3.8
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 39 PVYEQFALPHLTRRLDI 55
P E+++L HL+R L+I
Sbjct: 128 PTLEKYSLSHLSRELNI 144
>gnl|CDD|182937 PRK11061, PRK11061, fused phosphoenolpyruvate-protein
phosphotransferase PtsP/GAF domain; Provisional.
Length = 748
Score = 25.0 bits (55), Expect = 3.9
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 44 FALPHLTRRLDI--AGESHITRYLL 66
F LPHL R+D G + +T+YLL
Sbjct: 603 FMLPHLASRVDFISVGTNDLTQYLL 627
>gnl|CDD|216861 pfam02065, Melibiase, Melibiase.
Length = 395
Score = 24.6 bits (54), Expect = 4.2
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 23 PSLVITFSGDGVTHICPVYEQFALPHLTRR 52
P LV +S G+ + Y HL R
Sbjct: 5 PELVAVYSDKGLNGMSQSYHGLYRDHLVRS 34
>gnl|CDD|234139 TIGR03182, PDH_E1_alph_y, pyruvate dehydrogenase E1 component,
alpha subunit. Members of this protein family are the
alpha subunit of the E1 component of pyruvate
dehydrogenase (PDH). This model represents one branch of
a larger family that E1-alpha proteins from
2-oxoisovalerate dehydrogenase, acetoin dehydrogenase,
another PDH clade, etc [Energy metabolism, Pyruvate
dehydrogenase].
Length = 315
Score = 24.5 bits (54), Expect = 4.4
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 9 CPVQTYVAYGTDYK--PSLVITFSGDGVTHICPVYEQF 44
P+ T +A+ Y+ ++ F GDG + YE F
Sbjct: 116 VPLATGLAFANKYRGNDNVTACFFGDGAANQGQFYESF 153
>gnl|CDD|100086 cd03084, phosphohexomutase, The alpha-D-phosphohexomutase
superfamily includes several related enzymes that
catalyze a reversible intramolecular phosphoryl transfer
on their sugar substrates. Members of this family
include the phosphoglucomutases (PGM1 and PGM2),
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). These
enzymes play important and diverse roles in carbohydrate
metabolism in organisms from bacteria to humans. Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 355
Score = 24.6 bits (54), Expect = 4.6
Identities = 9/44 (20%), Positives = 13/44 (29%), Gaps = 1/44 (2%)
Query: 4 DLEKVCPVQTYVAYGTDYKPSLVITFSGDGVTHICPVYEQFALP 47
D ++ +A K + F GD I V E
Sbjct: 156 DPGSETNLKQLLAVVKAEKADFGVAFDGDADRLIV-VDENGGFL 198
>gnl|CDD|182669 PRK10714, PRK10714, undecaprenyl phosphate
4-deoxy-4-formamido-L-arabinose transferase;
Provisional.
Length = 325
Score = 24.3 bits (53), Expect = 5.5
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 34 VTHICPVY-EQFALPHLTRRLDIAGES 59
V+ + PVY EQ +LP L RR A ES
Sbjct: 8 VSVVIPVYNEQESLPELIRRTTAACES 34
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
0.324 0.141 0.430
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,432,514
Number of extensions: 246743
Number of successful extensions: 186
Number of sequences better than 10.0: 1
Number of HSP's gapped: 186
Number of HSP's successfully gapped: 19
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)