RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7602
(95 letters)
>gnl|CDD|223207 COG0129, IlvD, Dihydroxyacid dehydratase/phosphogluconate
dehydratase [Amino acid transport and metabolism /
Carbohydrate transport and metabolism].
Length = 575
Score = 28.3 bits (64), Expect = 0.62
Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 22/68 (32%)
Query: 23 YLTTKIIQEGMGQTIAC---------------------AAHGCNI-LVDDGKPIEFDVYQ 60
T+ + +G+G+ +A AA G I LV DG I D+
Sbjct: 460 KPTSALKGKGLGKKVALITDGRFSGASRGPSIGHVSPEAAEGGPIALVRDGDIIRIDIPN 519
Query: 61 GILSNQVT 68
L V+
Sbjct: 520 RTLDLLVS 527
>gnl|CDD|235809 PRK06464, PRK06464, phosphoenolpyruvate synthase; Validated.
Length = 795
Score = 27.8 bits (63), Expect = 0.83
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 26 TKIIQEGMGQTIACAAHGCNILVDDGKPIEFDVYQGILSNQVTNCRLASLVP 77
T+++++G T++C A G D G VY+G+L +V L +
Sbjct: 438 TEVLKDGQEVTVSC-AEG-----DTGY-----VYEGLLEFEVEEVSLEEMPE 478
>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 155
Score = 27.5 bits (62), Expect = 0.84
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 46 ILVDDGKPIEFD 57
ILV++G+P+EF
Sbjct: 137 ILVENGQPVEFG 148
>gnl|CDD|201633 pfam01163, RIO1, RIO1 family. This is a family of atypical serine
kinases which are found in archaea, bacteria and
eukaryotes. Activity of Rio1 is vital in Saccharomyces
cerevisiae for the processing of ribosomal RNA, as well
as for proper cell cycle progression and chromosome
maintenance. The structure of RIO1 has been determined.
Length = 186
Score = 26.8 bits (60), Expect = 1.6
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 45 NILVDDGKPIEFDVYQ 60
N+LVDD KP+ DV Q
Sbjct: 134 NVLVDDDKPVIIDVPQ 149
>gnl|CDD|226921 COG4548, NorD, Nitric oxide reductase activation protein [Inorganic
ion transport and metabolism].
Length = 637
Score = 26.7 bits (59), Expect = 2.1
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 46 ILVDDGKPIEFDVYQG 61
I++ DGKP +FD Y+G
Sbjct: 557 IVLSDGKPNDFDHYEG 572
>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional.
Length = 73
Score = 25.4 bits (55), Expect = 2.7
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 28 IIQEGMGQTIACAAHGCNILVDD------GKPIEFDVYQGILSNQVT 68
I EG G+ I AH I +D G+ + FDV+QG N +
Sbjct: 18 ICPEGGGEDIF--AHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
>gnl|CDD|173798 cd05562, Peptidases_S53_like, Peptidase domain in the S53 family.
Members of the peptidase S53 (sedolisin) family
include endopeptidases and exopeptidases. The S53
family contains a catalytic triad Glu/Asp/Ser with an
additional acidic residue Asp in the oxyanion hole,
similar to that of Asn in subtilisin. The stability of
these enzymes may be enhanced by calcium, some members
have been shown to bind up to 4 ions via binding sites
with different affinity. Some members of this clan
contain disulfide bonds. These enzymes can be intra-
and extracellular, some function at extreme
temperatures and pH values. Characterized sedolisins
include Kumamolisin, an extracellular calcium-dependent
thermostable endopeptidase from Bacillus. The enzyme is
synthesized with a 188 amino acid N-terminal preprotein
region which is cleaved after the extraction into the
extracellular space with low pH. One kumamolysin
paralog, kumamolisin-As, is believed to be a
collagenase. TPP1 is a serine protease that functions
as a tripeptidyl exopeptidase as well as an
endopeptidase. Less is known about PSCP from
Pseudomonas which is thought to be an aspartic
proteinase.
Length = 275
Score = 26.1 bits (58), Expect = 2.8
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 40 AAHGCNILVDD 50
AA G +I+VDD
Sbjct: 87 AAAGADIIVDD 97
>gnl|CDD|238839 cd01681, aeEF2_snRNP_like_IV, This family represents domain IV of
archaeal and eukaryotic elongation factor 2 (aeEF-2) and
of an evolutionarily conserved U5 snRNP-specific
protein. U5 snRNP is a GTP-binding factor closely
related to the ribosomal translocase EF-2. In complex
with GTP, EF-2 promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site of the small subunit
of ribosome and the mRNA is shifted one codon relative
to the ribosome. It has been shown that EF-2_IV domain
mimics the shape of anticodon arm of the tRNA in the
structurally homologous ternary complex of Phe-tRNA,
EF-1 (another transcriptional elongation factor) and GTP
analog. The tip portion of this domain is found in a
position that overlaps the anticodon arm of the A-site
tRNA, implying that EF-2 displaces the A-site tRNA to
the P-site by physical interaction with the anticodon
arm.
Length = 177
Score = 26.0 bits (58), Expect = 2.9
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 42 HGCNILVDDGKPIEFDV 58
G NILVDD K +++D
Sbjct: 84 TGPNILVDDTKGVQYDK 100
>gnl|CDD|238840 cd01683, EF2_IV_snRNP, EF-2_domain IV_snRNP domain is a part of
116kD U5-specific protein of the U5 small nucleoprotein
(snRNP) particle, essential component of the
spliceosome. The protein is structurally closely
related to the eukaryotic translational elongation
factor EF2. This domain has been also identified in
114kD U5-specific protein of Saccharomyces cerevisiae
and may play an important role either in splicing
process itself or the recycling of spliceosomal snRNP.
Length = 178
Score = 25.7 bits (57), Expect = 3.4
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 42 HGCNILVDDGKPIEFD 57
G N+L+DD P E D
Sbjct: 84 KGPNVLIDDTLPEEVD 99
>gnl|CDD|129252 TIGR00148, TIGR00148, UbiD family decarboxylase. The member of
this family in E. coli is UbiD,
3-octaprenyl-4-hydroxybenzoate carboxy-lyase. The family
described by This model, however, is broad enough that
it is likely to contain several different
decarboxylases. Found in bacteria, archaea, and yeast,
with two members in A. fulgidus. No homologs were
detected besides those classified as orthologs. The
member from H. pylori has a C-terminal extension of just
over 100 residues that is shared in part by the Aquifex
aeolicus homolog [Unknown function, General].
Length = 438
Score = 25.8 bits (57), Expect = 4.1
Identities = 8/41 (19%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 55 EFDVYQGILSNQVTNCRLASLVPCKCSWVRFPPGADFILNG 95
E++ I ++ +V C+ + + P A+ +L G
Sbjct: 222 EYEFAGAIRGEKLR------VVKCETNDLEVPADAEIVLEG 256
>gnl|CDD|225057 COG2146, {NirD}, Ferredoxin subunits of nitrite reductase and
ring-hydroxylating dioxygenases [Inorganic ion
transport and metabolism / General function prediction
only].
Length = 106
Score = 25.4 bits (56), Expect = 4.2
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 34 GQTIACAAHGCNILVDDGKPIE 55
+T+ C HG + G+ +E
Sbjct: 61 DETVVCPLHGARFDLRTGECLE 82
>gnl|CDD|240158 cd05119, RIO, RIO kinase family, catalytic domain. The RIO kinase
catalytic domain family is part of a larger superfamily,
that includes the catalytic domains of other kinases
such as the typical serine/threonine/tyrosine protein
kinases (PKs), aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase (PI3K).
RIO kinases are atypical protein serine kinases present
in archaea, bacteria and eukaryotes. Serine kinases
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine residues in protein substrates. RIO
kinases contain a kinase catalytic signature, but
otherwise show very little sequence similarity to
typical PKs. The RIO catalytic domain is truncated
compared to the catalytic domains of typical PKs, with
deletions of the loops responsible for substrate
binding. Most organisms contain at least two RIO
kinases, RIO1 and RIO2. A third protein, RIO3, is
present in multicellular eukaryotes. In yeast, RIO1 and
RIO2 are essential for survival. They function as
non-ribosomal factors necessary for late 18S rRNA
processing. RIO1 is also required for proper cell cycle
progression and chromosome maintenance. The biological
substrates for RIO kinases are still unknown.
Length = 187
Score = 25.5 bits (57), Expect = 4.2
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 45 NILVDDGKPIEFDVYQ 60
NILVDDGK DV Q
Sbjct: 145 NILVDDGKVYIIDVPQ 160
>gnl|CDD|201234 pfam00449, Urease_alpha, Urease alpha-subunit, N-terminal domain.
The N-terminal domain is a composite domain and plays
a major trimer stabilising role by contacting the
catalytic domain of the symmetry related alpha-subunit.
Length = 121
Score = 25.1 bits (56), Expect = 4.3
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 14/42 (33%)
Query: 27 KIIQEGMGQTIACAAHGC------NILVDDGKPIEFDVYQGI 62
K+I++GMGQ+ G N L+ D Y GI
Sbjct: 48 KVIRDGMGQSQGATRDGALDLVITNALIID--------YWGI 81
>gnl|CDD|181274 PRK08184, PRK08184, benzoyl-CoA-dihydrodiol lyase; Provisional.
Length = 550
Score = 25.7 bits (57), Expect = 4.5
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 6 MTGLECSHRFCTQCWCEYLTTKI 28
+TG+E + RF E + T+I
Sbjct: 491 LTGMEANLRFAGP---ETMETRI 510
>gnl|CDD|237104 PRK12448, PRK12448, dihydroxy-acid dehydratase; Provisional.
Length = 615
Score = 25.2 bits (56), Expect = 6.2
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 40 AAHGCNI-LVDDGKPIEFDV 58
AA G I LV+DG IE D+
Sbjct: 531 AASGGAIGLVEDGDIIEIDI 550
>gnl|CDD|225386 COG2830, COG2830, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 214
Score = 24.9 bits (54), Expect = 8.1
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 38 ACAAHGCNILVDDGKPIEFDVYQGILSNQVTNCRL 72
A A +G + DD I +++G L N N RL
Sbjct: 83 ATAINGTGLPCDDSFGIPPAIFKGTLENLTENNRL 117
>gnl|CDD|215172 PLN02303, PLN02303, urease.
Length = 837
Score = 24.7 bits (54), Expect = 9.2
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 21 CEYLTTKIIQEGMGQTIACAAHGC 44
C++ K++++GMGQ A
Sbjct: 310 CKFGGGKVLRDGMGQATGYGAADS 333
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
0.326 0.140 0.485
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,514,858
Number of extensions: 342012
Number of successful extensions: 400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 25
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.4 bits)