RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12378
(260 letters)
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of
two alpha chains, one beta chain, and one beta' subunit
[Transcription, DNA-dependent RNA polymerase].
Length = 1065
Score = 33.9 bits (78), Expect = 0.091
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 161 VYFRFDIVDVVGTVVDRNRAICVQPFLMAEGYVIFDIKIGEG 202
+ F D D+V +DR R + L A GY I +K+
Sbjct: 176 LEFETDKKDLVYVRIDRKRKLPATVLLRALGYTIDTLKLNRV 217
>gnl|CDD|131325 TIGR02272, gentisate_1_2, gentisate 1,2-dioxygenase. This family
consists of gentisate 1,2-dioxygenases. This
ring-opening enzyme acts in salicylate degradation that
goes via gentisate rather than via catechol. It converts
gentisate to maleylpyruvate. Some putative gentisate
1,2-dioxygenases are excluded by a relatively high
trusted cutoff score because they are too closely
related to known examples of 1-hydroxy-2-naphthoate
dioxygenase. Therefore some homologs may be bona fide
gentisate 1,2-dioxygenases even if they score below the
given cutoffs.
Length = 335
Score = 30.5 bits (69), Expect = 0.89
Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 4/90 (4%)
Query: 68 EGDY-QKDIHNSSPQIHKNFNFQLPFFGFRFNYTRVSRHGYLEFSDPPDHFTYPLSFPNK 126
EGD + HN P HK + P F + + +R + + L + N
Sbjct: 181 EGDSLARYGHNMLPVRHKRSDRSSPIFNYPYERSREALDDLTRTGEWDPWHGLKLRYVNP 240
Query: 127 ---DWPKKNDPSFIGIFYSKCRIGSIRTTD 153
+P +FI + R + R+TD
Sbjct: 241 ATGGYPMPTIGAFIQLLPKGFRTATYRSTD 270
>gnl|CDD|184851 PRK14849, PRK14849, putative lipoprotein/autotransporter
domain-containing protein; Provisional.
Length = 1806
Score = 29.7 bits (66), Expect = 1.7
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 1 MAEGYVIFD-IKIGEGQYNWKGKYFVVPQQG 30
+AEGY+ D + +G G Y WKG+ + V G
Sbjct: 861 LAEGYISVDTLVVGAGDYTWKGRNYQVNGTG 891
Score = 28.5 bits (63), Expect = 3.9
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 188 MAEGYVIFD-IKIGEGQYNWKGKYF 211
+AEGY+ D + +G G Y WKG+ +
Sbjct: 861 LAEGYISVDTLVVGAGDYTWKGRNY 885
>gnl|CDD|227116 COG4775, COG4775, Outer membrane protein/protective antigen OMA87
[Cell envelope biogenesis, outer membrane].
Length = 766
Score = 29.6 bits (67), Expect = 1.9
Identities = 11/56 (19%), Positives = 16/56 (28%), Gaps = 7/56 (12%)
Query: 52 ENLWFVWFFDRGGDDNEGDYQKDIHNSSPQIHKNFN-------FQLPFFGFRFNYT 100
+ FFD G N G + N + + P RF+Y
Sbjct: 689 SGVRGALFFDAGSVWNTGTDPSTVRNFYGSGSELRASAGVGLRWASPLGPLRFDYA 744
>gnl|CDD|241425 cd13271, PH2_TAPP1_2, Tandem PH-domain-containing proteins 1 and
2 Pleckstrin homology (PH) domain, C-terminal repeat.
The binding of TAPP1 (also called PLEKHA1/pleckstrin
homology domain containing, family A (phosphoinositide
binding specific) member 1) and TAPP2 (also called
PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4,
5)P3, function as negative regulators of insulin and
PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin
complex). TAPP1 and TAPP2 contain two sequential PH
domains in which the C-terminal PH domain specifically
binds PtdIns(3,4)P2 with high affinity. The N-terminal
PH domain does not interact with any phosphoinositide
tested. They also contain a C-terminal PDZ-binding
motif that interacts with several PDZ-binding proteins,
including PTPN13 (known previously as PTPL1 or FAP-1)
as well as the scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 114
Score = 28.1 bits (63), Expect = 1.9
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 18 NWKGKYFVVPQQGLGIFTSET 38
NWK +YF++ + + SET
Sbjct: 23 NWKRRYFILDDNTISYYKSET 43
>gnl|CDD|182040 PRK09707, PRK09707, putative lipoprotein; Provisional.
Length = 1343
Score = 29.7 bits (66), Expect = 2.0
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 1 MAEGYVIFD-IKIGEGQYNWKGKYFVVPQQG 30
+AEGY+ D + +G Y WKG+ + V G
Sbjct: 861 LAEGYISVDTLVVGASDYTWKGRNYQVNGTG 891
Score = 28.5 bits (63), Expect = 4.5
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 188 MAEGYVIFD-IKIGEGQYNWKGKYF 211
+AEGY+ D + +G Y WKG+ +
Sbjct: 861 LAEGYISVDTLVVGASDYTWKGRNY 885
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 29.3 bits (67), Expect = 2.2
Identities = 26/115 (22%), Positives = 38/115 (33%), Gaps = 34/115 (29%)
Query: 157 RTPGVYFR----------------------------FDIVDVVGTVVDRNRAICVQPFLM 188
R+PGVYF FD D++ +DR R + V L
Sbjct: 145 RSPGVYFDHDKDKTSSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLR 204
Query: 189 AEGYV------IFDIKIGEGQYNWKGKYFVETPATATERIYFETDAVHERYPEEI 237
A GY +F K G+ ++ A + + ET V +EI
Sbjct: 205 ALGYSDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEI 259
>gnl|CDD|224369 COG1452, Imp, Organic solvent tolerance protein OstA [Cell envelope
biogenesis, outer membrane].
Length = 784
Score = 28.2 bits (63), Expect = 5.0
Identities = 19/109 (17%), Positives = 28/109 (25%), Gaps = 24/109 (22%)
Query: 79 SPQIHKNFNFQL-PFFGFRF-NYTRVSRHGYLEFSDPPDHFTYPLSFPNKDW-------- 128
+PQ F L F + F N R L D +F W
Sbjct: 255 TPQYMSKRGFGLEGEFRYLFSNGAGQLRGAGL-PQDDSYYFGDDTRGNEVRWRYYWNHSG 313
Query: 129 -------------PKKNDPSFIGIFYSKCRIGSIRTTDIDQRTPGVYFR 164
+ +DP++ F + S + Q YF
Sbjct: 314 DFDQNRWKFGVDVERVSDPNYFNDFDIRYSSVSTSDGYLTQLGRRNYFA 362
>gnl|CDD|236409 PRK09201, PRK09201, amidase; Provisional.
Length = 465
Score = 28.0 bits (63), Expect = 5.1
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 93 FGFRFNYTRVSRHGYLEFSDPPDH 116
FG + Y R+SR G F DH
Sbjct: 191 FGLKPTYGRLSRAGSFPFVASLDH 214
>gnl|CDD|187565 cd05255, SQD1_like_SDR_e, UDP_sulfoquinovose_synthase (Arabidopsis
thaliana SQD1 and related proteins), extended (e) SDRs.
Arabidopsis thaliana UDP-sulfoquinovose-synthase (
SQD1), an extended SDR, catalyzes the transfer of
SO(3)(-) to UDP-glucose in the biosynthesis of plant
sulfolipids. Members of this subgroup share the
conserved SDR catalytic residues, and a partial match to
the characteristic extended-SDR NAD-binding motif.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 382
Score = 27.7 bits (62), Expect = 6.2
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 15/53 (28%)
Query: 144 CRIGSIRTTDIDQ------------RTPGVYFRFDIVDVVGTVVDRNRAICVQ 184
C+ IR TD++Q + RFD V GTV++R CVQ
Sbjct: 196 CKAWGIRITDLNQGVVYGTKTEETEADERLINRFDYDGVFGTVLNR---FCVQ 245
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
0.322 0.141 0.452
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,906,219
Number of extensions: 1336995
Number of successful extensions: 896
Number of sequences better than 10.0: 1
Number of HSP's gapped: 894
Number of HSP's successfully gapped: 21
Length of query: 260
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 165
Effective length of database: 6,723,972
Effective search space: 1109455380
Effective search space used: 1109455380
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 (21.8 bits)
S2: 58 (26.1 bits)