RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy179
(359 letters)
>gnl|CDD|216494 pfam01425, Amidase, Amidase.
Length = 431
Score = 58.1 bits (141), Expect = 2e-09
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 190 VLIYPTFPAQAQRHGEILLTTSGVYYAM-------LANVIGFPSTNVPLGLGSNGLPVGL 242
VL+ PT P A R GE + + +Y + AN+ G P+ ++P G +GLPVGL
Sbjct: 359 VLLSPTTPTPAPRLGEAADSPTVLYNLLDFTANTVPANLAGLPAISLPAGFSEDGLPVGL 418
Query: 243 QV 244
Q+
Sbjct: 419 QI 420
>gnl|CDD|223232 COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit
and related amidases [Translation, ribosomal structure
and biogenesis].
Length = 475
Score = 52.7 bits (127), Expect = 1e-07
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 181 LKEILGTDGVLIYPTFPAQAQRHGEILLTTSGVYYAM-------LANVIGFPSTNVPLGL 233
++ VL+ PT P A + GE AN+ G P+ +VP G
Sbjct: 376 FDKLFEEVDVLLTPTTPTPAPKIGESESDGDDPLEMYLLDVFTVPANLAGLPAISVPAGF 435
Query: 234 GSNGLPVGLQV 244
++GLPVGLQ+
Sbjct: 436 TADGLPVGLQL 446
>gnl|CDD|235723 PRK06170, PRK06170, amidase; Provisional.
Length = 490
Score = 45.4 bits (108), Expect = 3e-05
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 14/69 (20%)
Query: 190 VLIYPTFPAQAQRHG------EILLTTSGVYYAM--------LANVIGFPSTNVPLGLGS 235
V++ P P A H E + GV Y LA + G P+T +P+GL +
Sbjct: 393 VVLCPVTPTPAFPHDHAPDPLERRIDIDGVSYPYWDQLVWAGLATLPGLPATAIPIGLSA 452
Query: 236 NGLPVGLQV 244
GLPVG+Q+
Sbjct: 453 TGLPVGVQI 461
>gnl|CDD|232842 TIGR00132, gatA, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
A subunit. In many species, Gln--tRNA ligase is
missing. tRNA(Gln) is misacylated with Glu after which a
heterotrimeric amidotransferase converts Glu to Gln.
This model represents the amidase chain of that
heterotrimer, encoded by the gatA gene. In the Archaea,
Asn--tRNA ligase is also missing. This amidase subunit
may also function in the conversion of Asp-tRNA(Asn) to
Asn-tRNA(Asn), presumably with a different recognition
unit to replace gatB. Both Methanococcus jannaschii and
Methanobacterium thermoautotrophicum have both authentic
gatB and a gatB-related gene, but only one gene like
gatA. It has been shown that gatA can be expressed only
when gatC is also expressed. In most species expressing
the amidotransferase, the gatC ortholog is about 90
residues in length, but in Mycoplasma genitalium and
Mycoplasma pneumoniae the gatC equivalent is as the
C-terminal domain of a much longer protein. Not
surprisingly, the Mycoplasmas also represent the most
atypical lineage of gatA orthology. This orthology group
is more narrowly defined here than in Proc Natl Acad Aci
USA 94, 11819-11826 (1997). In particular, a Rhodococcus
homolog found in association with nitrile hydratase
genes and described as an enantiomer-selective amidase
active on several 2-aryl propionamides, is excluded
here. It is likely, however, that the amidase subunit
GatA is not exclusively a part of the Glu-tRNA(Gln)
amidotransferase heterotrimer and restricted to that
function in all species [Protein synthesis, tRNA
aminoacylation].
Length = 460
Score = 43.5 bits (103), Expect = 1e-04
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 190 VLIYPTFPAQAQRHGEILLTTSGVYYA----MLANVIGFPSTNVPLGLGSNGLPVGLQV 244
V++ PT P + GE L +Y + + AN+ G P+ +VP G+ GLP+GLQ+
Sbjct: 382 VIVSPTAPTLPFKIGEKLDDPLEMYLSDILTVPANLAGLPAISVPCGVKEKGLPIGLQI 440
>gnl|CDD|235686 PRK06061, PRK06061, amidase; Provisional.
Length = 483
Score = 42.8 bits (101), Expect = 2e-04
Identities = 25/69 (36%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 184 ILGTDGVLIYPTFPAQAQRHGEIL-LTTSGVYYAMLA--------NVIGFPSTNVPLGLG 234
I V++ PT R G L AM+A NV+G+PS NVP G
Sbjct: 378 IFDIVDVVLAPTTAQPPPRVGAFDRLGGWATDRAMIAACPYTWPWNVLGWPSINVPAGFT 437
Query: 235 SNGLPVGLQ 243
S+GLP+G Q
Sbjct: 438 SDGLPIGAQ 446
>gnl|CDD|234572 PRK00012, gatA, aspartyl/glutamyl-tRNA amidotransferase subunit A;
Reviewed.
Length = 459
Score = 41.6 bits (99), Expect = 5e-04
Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 190 VLIYPTFPAQAQRHGEILLTTSGVYYA----MLANVIGFPSTNVPLGLGSNGLPVGLQV 244
V++ PT P A + GE +Y + + AN+ G P+ +VP G GLPVGLQ+
Sbjct: 383 VILGPTAPTTAFKIGEKTDDPLAMYLSDIFTVPANLAGLPAISVPAGFDDGGLPVGLQL 441
>gnl|CDD|235979 PRK07235, PRK07235, amidase; Provisional.
Length = 502
Score = 38.8 bits (91), Expect = 0.003
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 190 VLIYPTFPAQAQRHGE---ILLTTSGVYYAMLAN-----VIGFPSTNVPLGLGSNGLPVG 241
+L+ PT P A M+AN V G P+ +VP GL +GLPVG
Sbjct: 419 LLVMPTTPMVATPLPAPDASREEYVSRALEMIANTAPFDVTGHPAMSVPCGL-VDGLPVG 477
Query: 242 LQV 244
L +
Sbjct: 478 LML 480
>gnl|CDD|236030 PRK07488, PRK07488, indole acetimide hydrolase; Validated.
Length = 472
Score = 37.6 bits (88), Expect = 0.007
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 10/63 (15%)
Query: 191 LIYPTFPAQAQRHGE-ILLTTSGVYYAMLANVI---------GFPSTNVPLGLGSNGLPV 240
+++PT P A G+ + +G A VI G P ++P GL +GLPV
Sbjct: 381 ILFPTTPLTAPPIGDDDTVILNGAAVPTFARVIRNTDPASNAGLPGLSLPAGLTPHGLPV 440
Query: 241 GLQ 243
GL+
Sbjct: 441 GLE 443
>gnl|CDD|181375 PRK08310, PRK08310, amidase; Provisional.
Length = 395
Score = 37.7 bits (88), Expect = 0.008
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 181 LKEILGTDGVLIYPTFPAQAQRHGEILLTTSGV-YYAM----LANVIGFPSTNVPLGLGS 235
L +LG D VL+ PT P A G A+ +A + G P ++PL
Sbjct: 306 LAALLGPDAVLLLPTVPGAAPLRGAPFEALEAYRERALRLLCIAGLAGLPQISLPLA-SV 364
Query: 236 NGLPVGL 242
+G P GL
Sbjct: 365 DGAPFGL 371
>gnl|CDD|236028 PRK07486, PRK07486, amidase; Provisional.
Length = 484
Score = 36.5 bits (85), Expect = 0.020
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 219 ANVIGFPSTNVPLGLGSNGLPVGLQV 244
A + G P+ +VP+G + GLP+G+Q+
Sbjct: 425 ATLAGLPAISVPVGFNAAGLPMGMQI 450
>gnl|CDD|171524 PRK12470, PRK12470, amidase; Provisional.
Length = 462
Score = 36.0 bits (83), Expect = 0.024
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 190 VLIYPTFPAQAQRHGE---------ILLTTSGVYYAMLANVIGFPSTNVPLGLGSNGLPV 240
V++ P R G +LL V Y + N+ G P+ VP +GLP+
Sbjct: 368 VVVTPGTATGPSRIGAYQRRGAVSTLLLVVQRVPYFQVWNLTGQPAAVVPWDFDGDGLPM 427
Query: 241 GLQV 244
+Q+
Sbjct: 428 SVQL 431
>gnl|CDD|181154 PRK07869, PRK07869, amidase; Provisional.
Length = 468
Score = 34.6 bits (80), Expect = 0.083
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 218 LANVIGFPSTNVPLGLGSNGLPVGLQ 243
L N G P+ ++PLG S+GLPVG+
Sbjct: 415 LQNATGEPAISLPLGQSSDGLPVGMM 440
>gnl|CDD|236409 PRK09201, PRK09201, amidase; Provisional.
Length = 465
Score = 34.2 bits (79), Expect = 0.088
Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 190 VLIYPTFPAQAQRHGEILLTTSGVYYAMLANV---------IGFPSTNVPLGLGSNGLPV 240
VLI P P A G+ + GV + AN+ IG P VPL GLP+
Sbjct: 372 VLIAPATPCSAPLIGQETMRIDGVELPVRANLGILTQPISFIGLPVVAVPLRT-PGGLPI 430
Query: 241 GLQV 244
G+Q+
Sbjct: 431 GVQL 434
>gnl|CDD|180437 PRK06169, PRK06169, putative amidase; Provisional.
Length = 466
Score = 33.8 bits (78), Expect = 0.14
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 220 NVIGFPSTNVPLGLGSNGLPVGLQV 244
N+ P+ +VP G + GLPVGLQ+
Sbjct: 411 NLTQQPAASVPCGFTAAGLPVGLQI 435
>gnl|CDD|236029 PRK07487, PRK07487, amidase; Provisional.
Length = 469
Score = 33.0 bits (76), Expect = 0.21
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 194 PTFPAQAQRHGEI----LLTTSGVYYAMLANVIGFPSTNVPLGLGSNGLPVGLQV 244
FP R G + A+ +G P +VP GL G+PVG+Q+
Sbjct: 385 LPFPDDLDRQGAEGFRRVWEAQLPQIAL--PFMGLPGLSVPTGL-VGGVPVGVQL 436
>gnl|CDD|236161 PRK08137, PRK08137, amidase; Provisional.
Length = 497
Score = 32.0 bits (73), Expect = 0.50
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 218 LANVIGFPSTNVPLGLGSNGLPVGL 242
A V G+P VP+G GLPVGL
Sbjct: 437 PAAVAGYPHLTVPMGQ-VQGLPVGL 460
>gnl|CDD|235698 PRK06102, PRK06102, hypothetical protein; Provisional.
Length = 452
Score = 31.9 bits (73), Expect = 0.54
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 217 MLANVIGFPSTNVPLGLGSNGLPVGLQVCETA 248
M N + ++P G G+ G+PVGL + A
Sbjct: 401 MPGNFLDMCGVSLPCGTGAAGMPVGLLLSAPA 432
>gnl|CDD|235855 PRK06707, PRK06707, amidase; Provisional.
Length = 536
Score = 31.0 bits (70), Expect = 0.99
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 217 MLANVIGFPSTNVPLGLGSNGLPVGL 242
+L+ V G+P VP G +NG PVG
Sbjct: 480 LLSAVAGYPELAVPAGYDNNGEPVGA 505
>gnl|CDD|180608 PRK06529, PRK06529, amidase; Provisional.
Length = 482
Score = 30.9 bits (70), Expect = 1.0
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 215 YAMLANVIGFPSTNVPLGLGSNGLPVGLQ 243
Y LAN+ G P+ ++P GLP+G+Q
Sbjct: 428 YTALANLTGQPAISLPTYETKEGLPMGVQ 456
>gnl|CDD|180715 PRK06828, PRK06828, amidase; Provisional.
Length = 491
Score = 30.6 bits (69), Expect = 1.4
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 223 GFPSTNVPLGLGSNGLPVGLQVCETA 248
G+PS +P G G P G+ + TA
Sbjct: 440 GYPSIAIPAGYMEGGRPFGITLASTA 465
>gnl|CDD|223351 COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide transport
and metabolism].
Length = 228
Score = 29.5 bits (67), Expect = 2.2
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 185 LGTDGVLIYPTFPAQAQRHGEILLTTSGVYYAMLANVIGFPSTNVPL 231
G V + P++ A+ E L ++ V + VIGFP
Sbjct: 36 YGFAAVCVNPSYVPLAK---EALKGSTVV---RVCTVIGFPLGANTT 76
>gnl|CDD|218994 pfam06333, Med13_C, Mediator complex subunit 13 C-terminal.
Mediator is a large complex of up to 33 proteins that is
conserved from plants through fungi to humans - the
number and representation of individual subunits varying
with species. It is arranged into four different
sections, a core, a head, a tail and a kinase-activity
part, and the number of subunits within each of these is
what varies with species. Overall, Mediator regulates
the transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med13 is part of the
ancillary kinase module, together with Med12, CDK8 and
CycC, which in yeast is implicated in transcriptional
repression, though most of this activity is likely
attributable to the CDK8 kinase. The large Med12 and
Med13 proteins are required for specific developmental
processes in Drosophila, zebrafish, and Caenorhabditis
elegans but their biochemical functions are not
understood.
Length = 406
Score = 28.5 bits (64), Expect = 7.0
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 3 ELVLSPEACMGKVFSIDDMNSL----YSIIEPLSHSKSQPNTVAEFLKSLIGLSSYTPHL 58
+ + SP + V S D+ SL Y+ P S KS N L L+ P
Sbjct: 51 DFIASPNSL--VVPSSDEYLSLALSVYNQCPPKSTVKSPANCAPFTL-----LAKDLPEK 103
Query: 59 LMFQTYIETSGFLSQSD 75
+ F+ Y S L Q D
Sbjct: 104 INFKLYSNPSTSLLQED 120
>gnl|CDD|166363 PLN02722, PLN02722, indole-3-acetamide amidohydrolase.
Length = 422
Score = 28.3 bits (63), Expect = 7.8
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 181 LKEILGTDGVLIYPTFPA---QAQRHGEILLTTSGVYYAML--ANVIGFPSTNVPLGLGS 235
L +LG GVL+ PT P + Q L + +++L A V GF ++PLGL
Sbjct: 334 LTTLLGEFGVLVIPTVPGPPPKLQADPTTLESFRARAFSLLSIAGVSGFCQVSIPLGLHD 393
Query: 236 NGLPVGL 242
N LPV +
Sbjct: 394 N-LPVSV 399
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
0.321 0.136 0.413
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,849,497
Number of extensions: 1665417
Number of successful extensions: 1151
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1148
Number of HSP's successfully gapped: 29
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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: 60 (26.9 bits)