RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 035377
(66 letters)
>gnl|CDD|223162 COG0084, TatD, Mg-dependent DNase [DNA replication,
recombination, and repair].
Length = 256
Score = 64.5 bits (158), Expect = 1e-14
Identities = 22/66 (33%), Positives = 32/66 (48%)
Query: 1 MKLFDAHCHLQDPRIFHKAPQLIATTVNSGVLHFAVNGVSEEDWNLVKDMSERHPSVIPC 60
M L D HCHL ++IA +GV V G ED+ +++E++P+V
Sbjct: 1 MMLIDTHCHLDFEEFDEDRDEVIARAREAGVKKMVVVGTDLEDFKRALELAEKYPNVYAA 60
Query: 61 FGVHPW 66
GVHP
Sbjct: 61 VGVHPL 66
>gnl|CDD|238635 cd01310, TatD_DNAse, TatD like proteins; E.coli TatD is a
cytoplasmic protein, shown to have magnesium dependent
DNase activity.
Length = 251
Score = 63.4 bits (155), Expect = 5e-14
Identities = 16/64 (25%), Positives = 30/64 (46%)
Query: 3 LFDAHCHLQDPRIFHKAPQLIATTVNSGVLHFAVNGVSEEDWNLVKDMSERHPSVIPCFG 62
L D HCHL P+ ++A +GV+ V G + ++++++ +V G
Sbjct: 1 LIDTHCHLDFPQFDADRDDVLARAREAGVIKIIVVGTDLKSSKRALELAKKYDNVYAAVG 60
Query: 63 VHPW 66
+HP
Sbjct: 61 LHPH 64
>gnl|CDD|216250 pfam01026, TatD_DNase, TatD related DNase. This family of
proteins are related to a large superfamily of
metalloenzymes. TatD, a member of this family has been
shown experimentally to be a DNase enzyme.
Length = 255
Score = 56.1 bits (136), Expect = 2e-11
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 4 FDAHCHLQDPRIFHKAPQLIATTVNSGVLHFAVNGVSEEDWNLVKDMSERHPS-VIPCFG 62
DAHCHL ++I +GV V G ED+ +++ ++P V G
Sbjct: 1 IDAHCHLDFKDFDEDRDEVIERAREAGVTAVVVVGTDLEDFLRALELARKYPGKVYAAVG 60
Query: 63 VHPW 66
VHP
Sbjct: 61 VHPH 64
>gnl|CDD|232780 TIGR00010, TIGR00010, hydrolase, TatD family. PSI-BLAST,
starting with a urease alpha subunit, finds a large
superfamily of proteins, including a number of
different enzymes that act as hydrolases at C-N bonds
other than peptide bonds (EC 3.5.-.-), many
uncharacterized proteins, and the members of this
family. Several genomes have multiple paralogs related
to this family. However, a set of 17 proteins can be
found, one each from 17 of the first 20 genomes, such
that each member forms a bidirectional best hit across
genomes with all other members of the set. This core
set (and one other near-perfect member), but not the
other paralogs, form the seed for this model.
Additionally, members of the seed alignment and all
trusted hits, but not all paralogs, have a conserved
motif DxHxH near the amino end. The member from E. coli
was recently shown to have DNase activity [Unknown
function, Enzymes of unknown specificity].
Length = 252
Score = 45.7 bits (109), Expect = 1e-07
Identities = 20/64 (31%), Positives = 30/64 (46%)
Query: 3 LFDAHCHLQDPRIFHKAPQLIATTVNSGVLHFAVNGVSEEDWNLVKDMSERHPSVIPCFG 62
L DAHCHL ++I +GV G ED+ +++E++P+V G
Sbjct: 1 LIDAHCHLDFLDFEEDVEEVIERAKAAGVTAVVAVGTDLEDFLRALELAEKYPNVYAAVG 60
Query: 63 VHPW 66
VHP
Sbjct: 61 VHPL 64
>gnl|CDD|171118 PRK11449, PRK11449, putative deoxyribonuclease YjjV; Provisional.
Length = 258
Score = 31.5 bits (71), Expect = 0.017
Identities = 15/64 (23%), Positives = 25/64 (39%)
Query: 2 KLFDAHCHLQDPRIFHKAPQLIATTVNSGVLHFAVNGVSEEDWNLVKDMSERHPSVIPCF 61
+ D HCH P + +GV V E++ V ++ER+ +
Sbjct: 4 RFIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAERYQPLYAAL 63
Query: 62 GVHP 65
G+HP
Sbjct: 64 GLHP 67
>gnl|CDD|233323 TIGR01230, agmatinase, agmatinase. Members of this family include
known and predicted examples of agmatinase (agmatine
ureohydrolase). The seed includes members of archaea,
for which no definitive agmatinase sequence has yet been
made available. However, archaeal sequences are
phylogenetically close to the experimentally verified B.
subtilis sequence. One species of Halobacterium has been
demonstrated in vitro to produce agmatine from arginine,
but no putrescine from ornithine, suggesting that
arginine decarboxylase and agmatinase, rather than
arginase and ornithine decarboxylase, lead from Arg to
polyamine biosynthesis. Note: a history of early
misannotation of members of this family is detailed in
PUBMED:10931887.
Length = 275
Score = 28.2 bits (63), Expect = 0.24
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 4 FDAHCHLQDP----RIFHKAPQLIATTVNSGVLHFAVNGVSEEDWNLVK 48
FDAH L+D + H P + V+ F + +E+ + +
Sbjct: 125 FDAHTDLRDEFDGGTLNHACPMRRVIELGLNVVQFGIRSGFKEENDFAR 173
>gnl|CDD|222250 pfam13594, Amidohydro_5, Amidohydrolase. This family of enzymes
are a part of a large metal dependent hydrolase
superfamily. The family includes Adenine deaminase
EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine
and ammonia. Adenine deaminases reaction is important
for adenine utilisation as a purine and also as a
nitrogen source. This family also includes
dihydroorotase and N-acetylglucosamine-6-phosphate
deacetylases, EC:3.5.1.25 These enzymes catalyze the
reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=>
D-glucosamine 6-phosphate + acetate. This family
includes the catalytic domain of urease alpha subunit.
Dihydroorotases (EC:3.5.2.3) are also included.
Length = 66
Score = 25.7 bits (57), Expect = 0.92
Identities = 8/29 (27%), Positives = 10/29 (34%)
Query: 3 LFDAHCHLQDPRIFHKAPQLIATTVNSGV 31
L D H HL + A + GV
Sbjct: 35 LIDMHVHLGEEPGRETLETGAAAALAGGV 63
>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
protein; Provisional.
Length = 697
Score = 24.8 bits (54), Expect = 3.3
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 14 RIFHKAPQLIATTV--NSGVLHFAVNGVSEEDWNLVKDMSE 52
+F P+ TTV NS + +A++G SEE L +M +
Sbjct: 280 CVFDGMPE--KTTVAWNSMLAGYALHGYSEEALCLYYEMRD 318
>gnl|CDD|233724 TIGR02095, glgA, glycogen/starch synthase, ADP-glucose type. This
family consists of glycogen (or starch) synthases that
use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose
(EC 2.4.1.11) as in animals, as the glucose donor. This
enzyme is found in bacteria and plants. Whether the name
given is glycogen synthase or starch synthase depends on
context, and therefore on substrate [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 473
Score = 24.9 bits (55), Expect = 3.8
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 28 NSGVLHFAVNGVSEEDWNLVKD 49
SG L +NG+ E WN D
Sbjct: 236 RSGKLRGILNGIDTEVWNPATD 257
>gnl|CDD|238624 cd01299, Met_dep_hydrolase_A, Metallo-dependent hydrolases,
subgroup A is part of the superfamily of
metallo-dependent hydrolases, a large group of proteins
that show conservation in their 3-dimensional fold (TIM
barrel) and in details of their active site. The vast
majority of the members have a conserved metal binding
site, involving four histidines and one aspartic acid
residue. In the common reaction mechanism, the metal
ion (or ions) deprotonate a water molecule for a
nucleophilic attack on the substrate. The function of
this subgroup is unknown.
Length = 342
Score = 24.6 bits (54), Expect = 4.3
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 19/75 (25%)
Query: 3 LFDAHCHL-----------QDPRIFH--KAPQLIATTVNSGVLHFAVNGVSEEDWNLVKD 49
L DAH HL P + +A + + +G V D+ L++D
Sbjct: 15 LIDAHTHLGSDPGDLPLDLALPVEYRTIRATRQARAALRAGFT--TVRDAGGADYGLLRD 72
Query: 50 MSERH----PSVIPC 60
+ P V
Sbjct: 73 AIDAGLIPGPRVFAS 87
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
0.325 0.138 0.470
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,254,321
Number of extensions: 223627
Number of successful extensions: 352
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 11
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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: 40 (21.6 bits)
S2: 53 (24.2 bits)