RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1555
(271 letters)
>gnl|CDD|150854 pfam10245, MRP-S22, Mitochondrial 28S ribosomal protein S22. This
is the conserved N-terminus and central portion of the
mitochondrial small subunit 28S ribosomal protein S22.
Mammalian mitochondria carry out the synthesis of 13
polypeptides that are essential for oxidative
phosphorylation and, hence, for the synthesis of the
majority of the ATP used by eukaryotic organisms. The
number of proteins produced by prokaryotes is smaller,
reflected in the lower number of ribosomal proteins
present in them.
Length = 243
Score = 253 bits (649), Expect = 5e-85
Identities = 116/244 (47%), Positives = 160/244 (65%), Gaps = 3/244 (1%)
Query: 13 LFFKPEVQELLLKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEEAYNRAIKKM 72
LF EVQ+LL +TR+DL KVFRK+ EYK +T E++E+ K ++ A + +
Sbjct: 3 LFVDEEVQKLLTSMTRLDLDKVFRKRS--VRDNRSEYKLMTDEQLEREKLQSIEFAKQML 60
Query: 73 QMPPIVPARDDSKLEVLSNDKELLGHDVCKYVFTDITFGISDAKRIIVVREPDGLLREAN 132
QMPP+V R +S +VL+ D L G KYVFTDITFG+ ++R IVVREPDG LREAN
Sbjct: 61 QMPPVVEPRQES-NDVLAKDLALKGFSTSKYVFTDITFGLPHSERTIVVREPDGTLREAN 119
Query: 133 TNERHRMNNIYFSRPGATYKHPDMFEEENLKALCDRKEYVFILDRAATQYEPDDQLYHNI 192
ER RMN IYF G P MFE+ENLK L ++ +Y F+LDRA Q+EPD+ YH +
Sbjct: 120 YEERDRMNQIYFPLEGRKVFPPPMFEDENLKKLLEQGKYEFVLDRACVQFEPDEPEYHRL 179
Query: 193 LNTTFTHIHENNGFDHLRSTRHFGCLVFFLANNNIIDNLLLQNLHCNMIEDAVWLIKVYQ 252
+ HI+E+ FD LRSTRHFG + F+LA + +ID+LL + + +++AV LI++
Sbjct: 180 SARVYEHINESGKFDKLRSTRHFGPMAFYLAWHKLIDDLLYDMIKRDYLDNAVELIRLTC 239
Query: 253 IVNP 256
I++P
Sbjct: 240 ILHP 243
>gnl|CDD|178234 PLN02627, PLN02627, glutamyl-tRNA synthetase.
Length = 535
Score = 30.1 bits (68), Expect = 1.2
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 5/27 (18%)
Query: 51 FLTTEEVEKLKEEAYNRAIKKMQMPPI 77
F T EE+E +KEEA + ++PP
Sbjct: 150 FCTDEELEAMKEEA-----ELKKLPPR 171
>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A. GidA, the
longer of two forms of GidA-related proteins, appears to
be present in all complete eubacterial genomes so far,
as well as Saccharomyces cerevisiae. A subset of these
organisms have a closely related protein. GidA is absent
in the Archaea. It appears to act with MnmE, in an
alpha2/beta2 heterotetramer, in the
5-carboxymethylaminomethyl modification of uridine 34 in
certain tRNAs. The shorter, related protein, previously
called gid or gidA(S), is now called TrmFO (see model
TIGR00137) [Protein synthesis, tRNA and rRNA base
modification].
Length = 617
Score = 29.3 bits (66), Expect = 2.4
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 15/72 (20%)
Query: 66 NRAIKKMQMPPIVPARDDSKLEVLSNDKELLGHDVCKYVFTDITFGISDAKRIIVVR-EP 124
N A+K P + R ++ + VL +D +T G + R+ R E
Sbjct: 385 NAALKLQNKEPFILKRSEAYIGVLIDDL--------------VTKGTKEPYRMFTSRAEY 430
Query: 125 DGLLREANTNER 136
LLRE N + R
Sbjct: 431 RLLLREDNADFR 442
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 27.1 bits (61), Expect = 9.3
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 45 KPPEYKFLTTEEVEKLKEEA---YNRAIKK 71
KPPE K EE +++EEA Y A ++
Sbjct: 35 KPPELKAEEIEERREVREEAEEKYEEAKEE 64
>gnl|CDD|233443 TIGR01509, HAD-SF-IA-v3, haloacid dehalogenase superfamily,
subfamily IA, variant 3 with third motif having DD or
ED. This model represents part of one structural
subfamily of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The subfamilies are defined based on the location and
the observed or predicted fold of a so-called "capping
domain", or the absence of such a domain. Subfamily I
consists of sequences in which the capping domain is
found in between the first and second catalytic motifs.
Subfamily II consists of sequences in which the capping
domain is found between the second and third motifs.
Subfamily III sequences have no capping domain in either
of these positions.The Subfamily IA and IB capping
domains are predicted by PSI-PRED to consist of an alpha
helical bundle. Subfamily I encompasses such a wide
region of sequence space (the sequences are highly
divergent) that representing it with a single model is
impossible, resulting in an overly broad description
which allows in many unrelated sequences. Subfamily IA
and IB are separated based on an aparrent phylogenetic
bifurcation. Subfamily IA is still too broad to model,
but cannot be further subdivided into large chunks based
on phylogenetic trees. Of the three motifs defining the
HAD superfamily, the third has three variant forms : (1)
hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s
where _s_ refers to a small amino acid and _h_ to a
hydrophobic one. All three of these variants are found
in subfamily IA. Individual models were made based on
seeds exhibiting only one of the variants each. Variant
3 (this model) is found in the enzymes
beta-phosphoglucomutase (TIGR01990) and
deoxyglucose-6-phosphatase, while many other enzymes of
subfamily IA exhibit this variant as well as variant 1
(TIGR01549). These three variant models were created
withthe knowledge that there will be overlap among them
- this is by design and serves the purpose of
eliminating the overlap with models of more distantly
relatedHAD subfamilies caused by an overly broad single
model [Unknown function, Enzymes of unknown
specificity].
Length = 177
Score = 27.0 bits (60), Expect = 9.3
Identities = 31/180 (17%), Positives = 62/180 (34%), Gaps = 29/180 (16%)
Query: 4 KTITKSTSALFFKPEVQELLLKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEE 63
+ + A+ + E L + +S+V + + K + ++ E+ + L ++
Sbjct: 8 GVLVDTAHAIAKLVDRAEFPLVPDELGVSEVGSLELALRRWKAKYGRTMSAEDAQLLYKQ 67
Query: 64 AYNRAIKKMQMPPIVPARDDSKLEVLSNDKELLGHDVCKYVFTDITFGISDAKRIIVVRE 123
+ A++K + P+ R LE L G + + T+ S +V E
Sbjct: 68 LFYEALEKEGLKPLPGVRA--LLEALRAR----GKKLA--LLTN-----SPRADAKLVLE 114
Query: 124 PDGLLREANTNERHRMNNIYFSRPGATYKHPDMF----EEENLKALCDRKEYVFILDRAA 179
I S G PD++ ++ LK E +F+ D A
Sbjct: 115 LG--------LRALFDVVIDSSDVGLGKPDPDIYLQALKKLGLKP----SECLFVDDSPA 162
>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1. This is
the N-terminal 200 residues of a set of proteins
conserved from yeasts to humans. Most of the proteins in
this entry have an RhoGEF pfam00621 domain at their
C-terminal end.
Length = 158
Score = 26.6 bits (59), Expect = 9.4
Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 16 KPEVQELLLKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEEAYNRAIKKMQ 73
+ EV+ LL+ LS + ++K + K E K L E+ + +++ + I+ ++
Sbjct: 47 ELEVELELLREDNERLSTQYEREK--ELRKQAEQKLLEFEDELEQEKKELQKKIEDLE 102
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 27.5 bits (62), Expect = 9.6
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 120 VVREPDGLLREAN--TNERHRMN 140
VVR+ DG R + RHR+N
Sbjct: 449 VVRDDDGRYRVTDPRIARRHRLN 471
>gnl|CDD|178530 PLN02942, PLN02942, dihydropyrimidinase.
Length = 486
Score = 27.5 bits (61), Expect = 9.7
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 59 KLKEEAYNRAIKKMQMPPIVPARDDSKLE-VLSNDK-ELLGHDVCKYVFTDITFGISDAK 116
KL + + A K + PPI PA L+ LS+ +L+G D C + T FG D +
Sbjct: 277 KLWDPDFTIASKYVMSPPIRPAGHGKALQAALSSGILQLVGTDHCPFNSTQKAFGKDDFR 336
Query: 117 RI 118
+I
Sbjct: 337 KI 338
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
0.320 0.137 0.400
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,080,423
Number of extensions: 1379315
Number of successful extensions: 1311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1308
Number of HSP's successfully gapped: 28
Length of query: 271
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 176
Effective length of database: 6,723,972
Effective search space: 1183419072
Effective search space used: 1183419072
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 (26.2 bits)