RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17858
(157 letters)
>gnl|CDD|218343 pfam04950, DUF663, Protein of unknown function (DUF663). This
family contains several uncharacterized eukaryotic
proteins.
Length = 293
Score = 171 bits (434), Expect = 1e-53
Identities = 62/137 (45%), Positives = 87/137 (63%)
Query: 20 QARVKKHRWYGKILKSGNPVIMSVGWRRFQTLPIYSKQEDNMRYRMLKYTPQHVACMAHF 79
++KKHRWY K LKS P+I+ VG+RRFQ+ PIYS+ N +++ +Y P H C A F
Sbjct: 113 NFKIKKHRWYKKPLKSKEPLIIQVGFRRFQSQPIYSQNTSNDKHKYERYLPPHKTCNATF 172
Query: 80 WGPITRSGTGFLAVQDVAKREPGFRVIATGTILDANQTAEVTKKLKLTGVPMKIYKKTAF 139
+GPIT + LA + GFR+ ATG IL+ + + KKLKLTG P KI+KKTAF
Sbjct: 173 YGPITFPNSPLLAFKKSFSDTNGFRIAATGCILECDPNRIIAKKLKLTGHPYKIFKKTAF 232
Query: 140 IKDMFNSTLEVAKFEGL 156
++ MF + +V F+ +
Sbjct: 233 VRYMFFNPEDVEWFKPV 249
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 179 bits (454), Expect = 9e-53
Identities = 75/137 (54%), Positives = 97/137 (70%), Gaps = 5/137 (3%)
Query: 20 QARVKKHRWYGKILKSGNPVIMSVGWRRFQTLPIYSKQEDNMRYRMLKYTPQHVACMAHF 79
Q R+K+HRW+ KILK+ +P+I SVGWRRFQ++P+YS ++ R RMLKYTP+H+ C F
Sbjct: 748 QGRIKRHRWHKKILKTNDPLIFSVGWRRFQSIPVYSMKDSRTRNRMLKYTPEHMHCNVSF 807
Query: 80 WGPITRSGTGFLAVQDVAKREPG-FRVIATGTILDANQTAEVTKKLKLTGVPMKIYKKTA 138
+GP+ TGF AVQ E G FRV+A GTI D N A++ KKLKL G P +I + T
Sbjct: 808 YGPVVPPNTGFCAVQS----EKGDFRVLALGTITDVNGDAKLVKKLKLVGYPKQIVQNTV 863
Query: 139 FIKDMFNSTLEVAKFEG 155
F++DMF S LEV KFEG
Sbjct: 864 FVRDMFTSDLEVLKFEG 880
>gnl|CDD|227504 COG5177, COG5177, Uncharacterized conserved protein [Function
unknown].
Length = 769
Score = 65.5 bits (159), Expect = 3e-13
Identities = 33/132 (25%), Positives = 62/132 (46%), Gaps = 2/132 (1%)
Query: 25 KHRWYGKILKSGNPVIMSVGWRRFQTLPIYSKQED--NMRYRMLKYTPQHVACMAHFWGP 82
+H Y LKS +++ +G RR P+ SK + N + + + +A F GP
Sbjct: 581 RHFEYEVPLKSEESMVVQLGHRRVDICPLISKGSNSPNNNQKYFRRLKPLESGVASFIGP 640
Query: 83 ITRSGTGFLAVQDVAKREPGFRVIATGTILDANQTAEVTKKLKLTGVPMKIYKKTAFIKD 142
I+ + + + A E ++A+G + + + + K+ LTG P K +K+ ++
Sbjct: 641 ISFGLSPVIIFKKSALDELSATLLASGGMNNFDGDRVIAKRAVLTGHPFKNHKRYVTVRY 700
Query: 143 MFNSTLEVAKFE 154
MF S +V F+
Sbjct: 701 MFFSPEDVMWFK 712
>gnl|CDD|224742 COG1829, COG1829, Predicted archaeal kinase (sugar kinase
superfamily) [General function prediction only].
Length = 283
Score = 33.9 bits (78), Expect = 0.023
Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 14/78 (17%)
Query: 68 YTPQHVACMAHFWGPITRS--------GTGFL---AVQDVAKREPGFRVIATGTILDANQ 116
+ P H+ F+ P+ G G V + G V G +D
Sbjct: 6 FVPGHITG---FFVPVIGKDPLKSGSIGAGVALERGVTVEVRFGEGTGVRLNGKKIDLPI 62
Query: 117 TAEVTKKLKLTGVPMKIY 134
T +V +KL GV ++I
Sbjct: 63 TRKVIEKLGPDGVGVRIE 80
>gnl|CDD|110106 pfam01081, Aldolase, KDPG and KHG aldolase. This family includes
the following members: 4-hydroxy-2-oxoglutarate aldolase
(KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate
aldolase (KDPG-aldolase).
Length = 196
Score = 30.9 bits (70), Expect = 0.20
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 85 RSGTGFLAVQDVAKREPGFRVIATGTILDANQTAEVTK 122
R+ A++ + K P ++ GT+L+A Q AE +
Sbjct: 42 RTPCALDAIRLLRKNRPDA-LVGAGTVLNAQQLAEAAE 78
>gnl|CDD|216899 pfam02142, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS) where
it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also includes
inosicase. The known structures in this family show a
common phosphate binding site.
Length = 92
Score = 28.6 bits (65), Expect = 0.54
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 11/47 (23%)
Query: 95 DVAKR--EPGFRVIATGTILDANQTAEVTKKLKLTGVPMKIYKKTAF 139
++AK E GF++ ATG TA K LK G+P ++ KT
Sbjct: 4 ELAKALVELGFKLYATGG------TA---KFLKEAGIPTEVVNKTGE 41
>gnl|CDD|183757 PRK12800, fliF, flagellar MS-ring protein; Reviewed.
Length = 574
Score = 27.7 bits (61), Expect = 3.2
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 99 REPGFRVIATGTILDANQTAEVTKKLKLTGVPMKIYKKTAFI----KDMFNSTLEVA 151
++PG++ + TG LD AE L+ +P KI + T I ++++ L++A
Sbjct: 54 QKPGYQSLYTG--LDEKGNAEAADLLRTAQIPFKIDQGTGAISVPQDRLYDARLKLA 108
>gnl|CDD|223322 COG0244, RplJ, Ribosomal protein L10 [Translation, ribosomal
structure and biogenesis].
Length = 175
Score = 26.8 bits (60), Expect = 4.7
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 112 LDANQTAEVTKKLKLTGVPMKIYKKTAFIKDMFNSTLEVAKFEGL 156
L Q E+ KKL+ G +K+ K T + LE A EGL
Sbjct: 33 LTVAQLTELRKKLREAGAKLKVVKNT-----LLRRALEEAGLEGL 72
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 26.8 bits (59), Expect = 4.7
Identities = 17/94 (18%), Positives = 27/94 (28%), Gaps = 5/94 (5%)
Query: 44 GWRRFQTLPIYSKQEDNMRYR---MLKYTPQHVACMAHFWGPITRSGTGFLAVQDVAKRE 100
GW+R IY R R + + + GF A+ + K
Sbjct: 123 GWKRVAL--IYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQALLQLLKAA 180
Query: 101 PGFRVIATGTILDANQTAEVTKKLKLTGVPMKIY 134
P I A + ++ LT + I
Sbjct: 181 PKPDAIFACNDEMAAGALKAAREAGLTPGDISII 214
>gnl|CDD|236758 PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA;
Provisional.
Length = 413
Score = 26.6 bits (59), Expect = 6.2
Identities = 21/67 (31%), Positives = 27/67 (40%), Gaps = 22/67 (32%)
Query: 33 LKSGNPVIMSVGWRRFQTLP-IYSKQEDNMRYRMLKYTPQHVACMAHFWGPITRSGTGF- 90
LK G +GW R Q LP ++++ A GPI RSG GF
Sbjct: 208 LKGGQ-----MGWGRIQELPGLFAQALST-------------AKKGDIVGPI-RSGVGFH 248
Query: 91 -LAVQDV 96
L V D+
Sbjct: 249 ILKVNDL 255
>gnl|CDD|133428 cd05292, LDH_2, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed
predominantly of bacterial LDHs and a few fungal LDHs.
Bacterial LDHs may be non-allosteric or may be activated
by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 308
Score = 26.7 bits (60), Expect = 6.5
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 96 VAKREPGF---RVIATGTILD 113
VA + G RVI +GT+LD
Sbjct: 125 VAYKLSGLPPNRVIGSGTVLD 145
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 26.6 bits (59), Expect = 7.3
Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 3/45 (6%)
Query: 111 ILDANQTAEVTKKLKLTGVPMKIYKKTAFIKDMFNSTLEVAKFEG 155
I T+ L G+P+ T +D + VA+ G
Sbjct: 114 IRRCRNKLYTTQLLAKAGIPV---PPTLITRDPDEAAEFVAEHLG 155
>gnl|CDD|216261 pfam01041, DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS aminotransferase
family. The members of this family are probably all
pyridoxal-phosphate-dependent aminotransferase enzymes
with a variety of molecular functions. The family
includes StsA, StsC and StsS. The aminotransferase
activity was demonstrated for purified StsC protein as
the L-glutamine:scyllo-inosose aminotransferase
EC:2.6.1.50, which catalyzes the first amino transfer in
the biosynthesis of the streptidine subunit of
streptomycin.
Length = 362
Score = 26.4 bits (59), Expect = 7.4
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 6 RLVGTTGNMNCFSFQA 21
+ VGT G+ FSF
Sbjct: 157 KRVGTFGDAATFSFYP 172
>gnl|CDD|234340 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 893
Score = 26.5 bits (59), Expect = 8.7
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 51 LPI-YSKQED-NMRYRMLKYTPQHVACMAHFWGPITRS-GTG 89
LP+ ++ D R+ QH+A + +G RS GTG
Sbjct: 410 LPMNFNPDLDRKSRWYTRLMFAQHIANLLPVFG---RSTGTG 448
>gnl|CDD|214855 smart00851, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS) where
it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also includes
inosicase. The known structures in this family show a
common phosphate binding site.
Length = 91
Score = 25.1 bits (56), Expect = 9.4
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 95 DVAKR--EPGFRVIATGTILDANQTAEVTKKLKLTGVPMKIYK 135
+ AKR E GF ++ATG TA+ ++ L V K
Sbjct: 4 EFAKRLAELGFELLATGG------TAKFLREAGLPVVKTLHPK 40
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
0.324 0.137 0.419
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,814,581
Number of extensions: 685340
Number of successful extensions: 709
Number of sequences better than 10.0: 1
Number of HSP's gapped: 706
Number of HSP's successfully gapped: 25
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (24.7 bits)