RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17186
(100 letters)
>gnl|CDD|202808 pfam03920, TLE_N, Groucho/TLE N-terminal Q-rich domain. The
N-terminal domain of the Grouch/TLE co-repressor
proteins are involved in oligomerisation.
Length = 134
Score = 155 bits (394), Expect = 1e-50
Identities = 83/115 (72%), Positives = 88/115 (76%), Gaps = 15/115 (13%)
Query: 1 GPPQPGQPFKFTVSESCDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHYVM------ 54
GP QPGQPFKFT+ ESCDRIKEEF FLQAQYH+ K+E EKL EKTEMQRHYVM
Sbjct: 9 GPGQPGQPFKFTILESCDRIKEEFQFLQAQYHSLKLECEKLASEKTEMQRHYVMYYEMSY 68
Query: 55 ---------TEIAKRLNAIIVQIMPFLSQEHQQQVATALERAKQVTMTELNAIIG 100
EIAKRLNAI QI+PFLSQEHQQQVA A+ERAKQVTM ELNAIIG
Sbjct: 69 GLNIEMHKQAEIAKRLNAICAQILPFLSQEHQQQVAQAVERAKQVTMAELNAIIG 123
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 29.1 bits (66), Expect = 0.29
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 27 LQAQYHNAKMEVEKLIQEKTEMQRHYVMTEIAKR 60
A+Y +A E+ L E+ E+ R Y E A R
Sbjct: 344 RGAKYGDALDELAALYAERRELARRYFYLEEAFR 377
>gnl|CDD|202143 pfam02183, HALZ, Homeobox associated leucine zipper.
Length = 45
Score = 27.1 bits (61), Expect = 0.37
Identities = 8/33 (24%), Positives = 18/33 (54%)
Query: 17 CDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQ 49
+ +K ++ L+A+ + + E EKL E ++
Sbjct: 7 YEVLKRCYDALKAENDSLQKENEKLRAEVLSLK 39
>gnl|CDD|232851 TIGR00165, S18, ribosomal protein S18. This ribosomal small
subunit protein is found in all eubacteria so far, as
well as in chloroplasts. YER050C from Saccharomyces
cerevisiae and a related protein from Caenorhabditis
elegans appear to be homologous and may represent
mitochondrial forms. The trusted cutoff is set high
enough that these two candidate S18 proteins are not
categorized automatically [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 70
Score = 27.4 bits (61), Expect = 0.52
Identities = 10/51 (19%), Positives = 27/51 (52%), Gaps = 13/51 (25%)
Query: 46 TEMQRHYVMTEIAKRLNAIIVQIMPF----LSQEHQQQVATALERAKQVTM 92
++ + ++ +E K I+P S ++Q+++A A++RA+ + +
Sbjct: 23 LDLLKKFI-SERGK--------ILPRRITGTSAKYQRRLAVAIKRARYLAL 64
>gnl|CDD|223316 COG0238, RpsR, Ribosomal protein S18 [Translation, ribosomal
structure and biogenesis].
Length = 75
Score = 25.7 bits (57), Expect = 2.0
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 13/49 (26%)
Query: 46 TEMQRHYVMTEIAKRLNAIIVQIMPF----LSQEHQQQVATALERAKQV 90
E+ + ++ +E K I+P S +HQ+++A A++RA+ +
Sbjct: 33 VELLKRFI-SERGK--------ILPRRITGTSAKHQRRLARAIKRARYL 72
>gnl|CDD|225519 COG2972, COG2972, Predicted signal transduction protein with a
C-terminal ATPase domain [Signal transduction
mechanisms].
Length = 456
Score = 26.6 bits (59), Expect = 2.3
Identities = 8/46 (17%), Positives = 13/46 (28%)
Query: 4 QPGQPFKFTVSESCDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQ 49
I E N ++ + E L QE+ E +
Sbjct: 212 LLLSRIALGYLSELKEISETINEMEERLEYLIEENYSLEQEQLEAE 257
>gnl|CDD|153414 cd07960, Anticodon_Ia_Ile_BEm, Anticodon-binding domain of
bacterial and eukaryotic mitochondrial isoleucyl tRNA
synthetases. This domain is found in isoleucyl tRNA
synthetases (IleRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. This family includes
bacterial and eukaryotic mitochondrial members. IleRS
catalyzes the transfer of isoleucine to the 3'-end of
its tRNA.
Length = 180
Score = 25.6 bits (57), Expect = 4.2
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 52 YVMTEIAKRLNAIIVQIMPFLSQE 75
V+ I L ++ I+PF ++E
Sbjct: 111 TVLYHILDALLKLLAPILPFTAEE 134
>gnl|CDD|235329 PRK05007, PRK05007, PII uridylyl-transferase; Provisional.
Length = 884
Score = 25.7 bits (57), Expect = 4.8
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 2 PPQPGQPFKFTVSE-SCDRIK---EEFNFLQAQYHNAKMEVEKLIQEKTE 47
P QP P + E + +K + F +A + E+L++ +TE
Sbjct: 11 PGQPQSPLTWPDDELTVGGLKQHLDTFQQWLGDAFDAGISAEQLVEARTE 60
>gnl|CDD|173878 cd08513, PBP2_thermophilic_Hb8_like, The substrate-binding
component of ABC-type thermophilic oligopeptide-binding
protein Hb8-like import systems, contains the type 2
periplasmic binding fold. This family includes the
substrate-binding domain of an ABC-type
oligopeptide-binding protein Hb8 from Thermus
thermophilius and its closest homologs from other
bacteria. The structural topology of this
substrate-binding domain is similar to those of DppA
from Escherichia coli and OppA from Salmonella
typhimurium, and thus belongs to the type 2 periplasmic
binding fold protein (PBP2) superfamily. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
The type 2 periplasmic binding proteins are soluble
ligand-binding components of ABC or tripartite
ATP-independent transporters and chemotaxis systems.
Members of the PBP2 superfamily function in uptake of a
variety of metabolites in bacteria such as amino acids,
carbohydrate, ions, and polyamines. Ligands are then
transported across the cytoplasmic membrane energized by
ATP hydrolysis or electrochemical ion gradient. Besides
transport proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 25.7 bits (57), Expect = 5.1
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 25 NFLQAQYHNAKME--VEKLIQEKTEMQRHYVMTEIAKRLNAIIVQIMPFLSQEHQQQVA 81
NF Y N + + ++ E +R + R ++ + +P + + QV+
Sbjct: 421 NF--GGYSNPEADELLDAARTELDPEERK----ALYIRYQDLLAEDLPVIPLYFRNQVS 473
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 25.5 bits (56), Expect = 5.2
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 2 PPQPGQPFKFTVSESCDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHY 52
PP G PF++ + D + + LQ QY + ++L+ E Q Y
Sbjct: 649 PPFLGGPFRYIDTLGADNVVKILERLQTQYGDRFTPCQRLVAMAAEKQSFY 699
>gnl|CDD|220941 pfam11013, DUF2851, Protein of unknown function (DUF2851). This
bacterial family of proteins has no known function.
Length = 377
Score = 25.7 bits (57), Expect = 5.4
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 18 DRIKEEFNFLQAQYHNAKMEVE 39
R+K+E+ +LQ ++ M+V
Sbjct: 238 LRLKKEYRYLQHKFQLQPMDVS 259
>gnl|CDD|183585 PRK12548, PRK12548, shikimate 5-dehydrogenase; Provisional.
Length = 289
Score = 25.5 bits (56), Expect = 6.1
Identities = 12/44 (27%), Positives = 17/44 (38%)
Query: 24 FNFLQAQYHNAKMEVEKLIQEKTEMQRHYVMTEIAKRLNAIIVQ 67
FN Y A+ EK+ QE E + ++L A I
Sbjct: 156 FNIKDDFYERAEQTAEKIKQEVPECIVNVYDLNDTEKLKAEIAS 199
>gnl|CDD|178997 PRK00391, rpsR, 30S ribosomal protein S18; Reviewed.
Length = 79
Score = 24.4 bits (54), Expect = 6.9
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 13/49 (26%)
Query: 46 TEMQRHYVMTEIAKRLNAIIVQIMP----FLSQEHQQQVATALERAKQV 90
E+ + ++ +E K I+P S +HQ+Q+ATA++RA+ +
Sbjct: 32 VELLKKFI-SERGK--------ILPRRITGTSAKHQRQLATAIKRARFL 71
>gnl|CDD|132408 TIGR03365, Bsubt_queE, 7-cyano-7-deazaguanosine (preQ0)
biosynthesis protein QueE. This uncharacterized enzyme,
designated QueE, participates in the biosynthesis, from
GTP, of 7-cyano-7-deazaguanosine, also called preQ0
because in many species it is a precursor of queuosine.
In most Archaea, it is instead the precursor of a
different tRNA modified base, archaeosine [Protein
synthesis, tRNA and rRNA base modification].
Length = 238
Score = 25.0 bits (55), Expect = 7.1
Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 1/51 (1%)
Query: 36 MEVEKLIQEKTEM-QRHYVMTEIAKRLNAIIVQIMPFLSQEHQQQVATALE 85
M E++ QE + + ++ A+ + + + ALE
Sbjct: 56 MTAEEVWQELKALGGGTPLHVSLSGGNPALQKPLGELIDLGKAKGYRFALE 106
>gnl|CDD|187803 cd09672, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as TM1802 family.
Length = 545
Score = 25.2 bits (55), Expect = 7.2
Identities = 2/35 (5%), Positives = 12/35 (34%)
Query: 18 DRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHY 52
+ + + + + K++ + L+ +
Sbjct: 349 SKYFKMLDLYEDIFLEGKIDKDLLLDYFVSKIKVD 383
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 25.2 bits (56), Expect = 7.9
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 13/59 (22%)
Query: 18 DRIKEEFNFLQAQY-------HNAKMEVEKLIQEKTEMQRHYVMTEIAKRLNAIIVQIM 69
+ EE + +QA Y K E+EKL +E E++ EIA L I+
Sbjct: 367 KELIEELSEIQADYLLDMRLRRLTKEEIEKLEKEIEELE-----KEIA-ELEKILASEK 419
>gnl|CDD|131502 TIGR02449, TIGR02449, TIGR02449 family protein. Members of this
family are small proteins, typically 73 amino acids in
length, with single copies in each of several
Proteobacteria, including Xylella fastidiosa,
Pseudomonas aeruginosa, and Xanthomonas campestris. The
function is unknown.
Length = 65
Score = 24.0 bits (52), Expect = 8.4
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 15 ESCDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHYVMTEIAK 59
E +R+K E L+AQ + E +L+ EK E R V I +
Sbjct: 14 EYLERLKSENRLLRAQEKTWREERAQLL-EKNEQARQKVEAMITR 57
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 25.1 bits (55), Expect = 8.4
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 18 DRIKEEFNFLQ---AQYHNAKMEVEKLIQEKTEMQRHYVMTE 56
D +++EFN L A+ AK + +LI E E+++ E
Sbjct: 50 DSLRKEFNKLNKEVAKLKIAKEDATELIAETKELKKEITEKE 91
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 25.1 bits (56), Expect = 8.5
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 15/57 (26%)
Query: 18 DRIKEEFNF--LQAQ-------YHNAKMEVEKLIQEKTEMQRHYVMTEIAKRLNAII 65
+ F+ +QA+ AK+E ++ +E+ E+++ EIA+ L AI+
Sbjct: 410 ANLMARFDLSEIQAEAILELRLRRLAKLEEIEIRKEQDELRK-----EIAE-LEAIL 460
>gnl|CDD|234369 TIGR03837, efp_adjacent_2, conserved hypothetical protein, PP_1857
family. This model describes a conserved hypothetical
protein that typically is encoded next to the gene efp
for translation elongation factor P. The function is
unknown.
Length = 371
Score = 24.9 bits (55), Expect = 9.2
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 60 RLNAIIVQIMPFLSQEH 76
R A+ V ++PF+ Q+
Sbjct: 238 RRGALTVAVLPFVPQDD 254
>gnl|CDD|72471 pfam09053, CagZ, CagZ. CagZ is a 23 kDa protein consisting of a
single compact L-shaped domain, composed of seven
alpha-helices that run antiparallel to each other. 70%
of the residues are in alpha-helix conformation and no
beta-sheet is present. CagZ is essential for the
translocation of the pathogenic protein CagA into host
cells.
Length = 198
Score = 24.6 bits (53), Expect = 9.7
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 54 MTEIAKRLNAIIVQI-MPFLSQEHQQQVATALERAKQVTMTELN 96
+ + ++LN I+ I ++ + T+LERAK +T +LN
Sbjct: 153 IDDFGRKLNEIVQDIGTKYIILSKNKTYLTSLERAKLITQLKLN 196
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
0.318 0.130 0.359
Gapped
Lambda K H
0.267 0.0856 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,862,889
Number of extensions: 394466
Number of successful extensions: 670
Number of sequences better than 10.0: 1
Number of HSP's gapped: 669
Number of HSP's successfully gapped: 61
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.0 bits)