RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18141
(113 letters)
>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 97
Score = 44.0 bits (104), Expect = 6e-07
Identities = 23/75 (30%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 17 LGHQYVRDEFRRHKGCNPSE-AQVFMNEWAKYAVNLAEQLGIRGPKFAKPLGQSLDEQAL 75
LG +YVR EFRRH G E A+ F+ E Y L Q G + E
Sbjct: 27 LGRRYVRKEFRRHAGATDDELAKEFLQEAENYLAYLKAQRHYLELLERYNPGLDMSE--- 83
Query: 76 NDLRDDQIAQLYELM 90
+ + Q A L
Sbjct: 84 -EEKVRQTANRVGLD 97
>gnl|CDD|240092 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 294
Score = 30.8 bits (70), Expect = 0.12
Identities = 19/60 (31%), Positives = 23/60 (38%), Gaps = 14/60 (23%)
Query: 4 ATLHRGLPPELQILGHQYVRD--EFRRHKGCNPSEAQVFMNEWAKYAVNLAEQLGIRGPK 61
T R LP E+QI+G V D R + S AV + LG GPK
Sbjct: 234 RTFRRLLPSEIQIIGVGGVLDGRGAFRMRLAGAS------------AVQVGTALGKEGPK 281
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup has
a fairly well conserved active site tetrad and domain
size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes 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 (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 28.8 bits (65), Expect = 0.44
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 37 AQVFMNEWAKYA----VNLAEQLGIRGPKF 62
+Q F+ + K +N+A G+ P F
Sbjct: 122 SQAFIKLFKKQGKGSIINIASIYGVIAPDF 151
>gnl|CDD|200587 cd10965, CE4_IcaB_5s, Putative catalytic polysaccharide deacetylase
domain of bacterial intercellular adhesion protein IcaB
and similar proteins. The family is represented by the
surface-attached protein intercellular adhesion protein
IcaB (Poly-beta-1,6-N-acetyl-D-glucosamine
N-deacetylase, EC 3.5.1.-), encoded by Staphylococcus
epidermidis icaB gene from the icaABC gene cluster that
is involved in the synthesis of polysaccharide
intercellular adhesin (PIA), which is located mainly on
the cell surface. IcaB is a secreted, cell
wall-associated protein that plays a crucial role in
exopolysaccharide modification in bacterial biofilm
formation. It catalyzes the N-deacetylation of
poly-beta-1,6-N-acetyl-D-glucosamine (PNAG, also
referred to as PIA), a biofilm adhesin polysaccharide.
IcaB shows high homology to the N-terminal NodB homology
domain of Escherichia coli PgaB. At this point, they are
classified in the same family.
Length = 172
Score = 27.7 bits (62), Expect = 1.1
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 34 PSEAQVFMNEWAKYAVNLAEQLGIRGPKFAKPLGQSLDEQALNDLRDDQIAQLYEL 89
P+ F ++AK L E+LG + FA P G+ ++ L+ I + L
Sbjct: 86 PASYSRFAEDYAKSQKCLKEKLGKKTRYFAYPYGEG-NKDTQKILKKQGIQYGFTL 140
>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family).
Proteins in this family have been identified as a
component of the higher eukaryotic NADH complex. In
Saccharomyces cerevisiae, the Isd11 protein has been
shown to play a role in Fe/S cluster biogenesis in
mitochondria. We have named this family LYR after a
highly conserved tripeptide motif close to the
N-terminus of these proteins.
Length = 59
Score = 26.0 bits (58), Expect = 1.6
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 20 QYVRDEFRRHKGC-NPSEAQVFMNEWAKY 47
+ +RDEFR++K +P + + + E K
Sbjct: 28 RRIRDEFRKNKNLTDPEKIEALLKEGKKQ 56
>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 61
Score = 25.6 bits (57), Expect = 2.0
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 20 QYVRDEFRRHKGC-NPSEAQVFMNEWAKY 47
+ +RDEFR++K +P + + + E K
Sbjct: 28 RRIRDEFRKNKDLTDPEKIEKLLKEGKKQ 56
>gnl|CDD|226097 COG3567, COG3567, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 452
Score = 26.8 bits (59), Expect = 2.7
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 70 LDEQALNDLRDDQIAQLYELMLAATQPEVLEAEEAQAKAAQ 110
L+++ ++L + E A P+VLE E A A+
Sbjct: 411 LEQKTFSNLTGLDVRLAAEGSQAEEPPDVLEVVETTAPASN 451
>gnl|CDD|239940 cd04494, BRCA2DBD_OB2, BRCA2DBD_OB2: A subfamily of OB folds
corresponding to the second OB fold (OB2) of the
800-amino acid C-terminal ssDNA binding domain (DBD) of
BRCA2 (breast cancer susceptibility gene 2) protein,
called BRCA2DBD. BRCA2 participates in homologous
recombination-mediated repair of double-strand DNA
breaks. It stimulates the displacement of Replication
protein A (RPA), the most abundant eukaryotic ssDNA
binding protein. It also facilitates filament formation.
Mutations that map throughout the BRCA2 protein are
associated with breast cancer susceptibility. BRCA2 is a
large nuclear protein and its most conserved region is
the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro,
and is composed of five structural domains, three of
which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and
OB3 are arranged in tandem, and their mode of binding
can be considered qualitatively similar to two OB folds
of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Length = 251
Score = 26.3 bits (58), Expect = 3.4
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 58 RGPKFAKPLGQSLDEQALNDLRDDQIAQLYELMLAATQPEVLEAE--EAQAKAAQA 111
+P ++ Q + DL+D A+LYE + AA P LEAE E Q +A
Sbjct: 75 EDNNQRRPRSRTRTRQNVTDLQDG--AELYEALEAAADPSFLEAELSEEQLEALSN 128
>gnl|CDD|227282 COG4946, COG4946, Uncharacterized protein related to the
periplasmic component of the Tol biopolymer transport
system [Function unknown].
Length = 668
Score = 26.3 bits (58), Expect = 3.8
Identities = 7/25 (28%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 35 SEAQVF-MNEWAKYAVNLAEQLGIR 58
S + F M W Y++ + ++ G+R
Sbjct: 339 SRGKAFIMRPWDGYSIQVGKKGGVR 363
>gnl|CDD|226428 COG3914, Spy, Predicted O-linked N-acetylglucosamine transferase,
SPINDLY family [Posttranslational modification, protein
turnover, chaperones].
Length = 620
Score = 26.3 bits (58), Expect = 4.8
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 63 AKPLGQSLDEQALNDLRDDQIAQLYELMLAATQPEVLEAEEAQAKAAQA 111
D+ L ++ + +A L+ A E L AE QA A A
Sbjct: 6 DYQTVLIADQAIL-EILPNALAGHLSLLDLAIVLEWLNAEGLQALAIYA 53
>gnl|CDD|235832 PRK06567, PRK06567, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase; Validated.
Length = 1028
Score = 26.0 bits (57), Expect = 5.6
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 72 EQALNDLRDDQIAQLYELMLAATQPEVLEAEEAQAKAAQAA 112
EQA DL D IA + A QP+VL+ E +AK + A
Sbjct: 491 EQAF-DLGFDHIA----FCIGAGQPKVLDIENFEAKGVKTA 526
>gnl|CDD|219361 pfam07277, SapC, SapC. This family contains a number of bacterial
SapC proteins approximately 250 residues long. In
Campylobacter fetus, SapC forms part of a
paracrystalline surface layer (S-layer) that confers
serum resistance.
Length = 220
Score = 25.6 bits (57), Expect = 5.6
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 71 DEQALNDLRDDQIAQL 86
DE+ LN L D+ + +L
Sbjct: 183 DEEKLNALSDEALLEL 198
>gnl|CDD|235550 PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
Length = 378
Score = 25.6 bits (57), Expect = 5.9
Identities = 19/40 (47%), Positives = 23/40 (57%), Gaps = 8/40 (20%)
Query: 45 AKYAVNLAEQLGIRGPKFAKPL-----GQSLDEQALNDLR 79
AK A LA+ LG+R F L QSL E+AL+DLR
Sbjct: 145 AKRAAKLAQGLGLR--SFNLDLMHGLPDQSL-EEALDDLR 181
>gnl|CDD|234178 TIGR03354, VI_FHA, type VI secretion system FHA domain protein.
Members of this protein family are FHA
(forkhead-associated) domain-containing proteins that
are part of type VI secretion loci in a considerable
number of bacteria, most of which are known pathogens.
Species include Pseudomonas aeruginosa PAO1, Aeromonas
hydrophila, Yersinia pestis, Burkholderia mallei, etc
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 396
Score = 25.4 bits (56), Expect = 7.1
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 12/70 (17%)
Query: 46 KYAVNLAEQLGI----RGPKFAKPLGQSLDEQALNDLRDDQIAQL------YELMLAATQ 95
K++ + E L + R P ++ E+A DLR Q+A L ML A
Sbjct: 277 KFSADYDEALAVLLAPRSPGHLSA--EAAIEEAFRDLRAHQVALLAAVRAALRRMLDAFS 334
Query: 96 PEVLEAEEAQ 105
PE LEA Q
Sbjct: 335 PEALEARFEQ 344
>gnl|CDD|224226 COG1307, DegV, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 282
Score = 25.3 bits (56), Expect = 8.6
Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 10/66 (15%)
Query: 51 LAEQLGIRGPKFAKPLGQSLDEQALNDLRDDQIAQLYELMLAA------TQPEVLEAEEA 104
LAE+L I PL +D ++ D + Q Y M +QP E EE
Sbjct: 17 LAEKLDI----TVLPLSVIIDGESYFDGVELSPDQFYYEMAEKGELPKTSQPSPGEFEEL 72
Query: 105 QAKAAQ 110
K Q
Sbjct: 73 FEKLLQ 78
>gnl|CDD|220551 pfam10071, DUF2310, Zn-ribbon-containing, possibly
nucleic-acid-binding protein (DUF2310). Members of
this family of proteobacterial zinc ribbon proteins are
thought to bind to nucleic acids, however their exact
function has not as yet been defined.
Length = 259
Score = 25.3 bits (56), Expect = 8.7
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 40 FMNEWAKYAVNLAEQLGIRGPKFAKPLGQSLD 71
+ K A+N E+ G+ PKF K +G+ L+
Sbjct: 67 NNSPQVKEALNQLEEAGLLFPKF-KIIGEDLN 97
>gnl|CDD|232859 TIGR00179, murB, UDP-N-acetylenolpyruvoylglucosamine reductase.
This model describes MurB,
UDP-N-acetylenolpyruvoylglucosamine reductase, which is
also called UDP-N-acetylmuramate dehydrogenase. It is
part of the pathway for the biosynthesis of the
UDP-N-acetylmuramoyl-pentapeptide that is a precursor of
bacterial peptidoglycan [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 284
Score = 25.1 bits (55), Expect = 9.1
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 27 RRHKGCNPSEAQVFMNEWAKYAVNLAEQLGIRG 59
R +P+ F N +A L E+ G++G
Sbjct: 198 RTSHYPDPNAGSFFKNPSPNHAGRLIEECGLKG 230
>gnl|CDD|130585 TIGR01522, ATPase-IIA2_Ca, golgi membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
golgi membrane of fungi and animals , and is of
particular importance in the sarcoplasmic reticulum of
skeletal and cardiac muscle in vertebrates. The calcium
P-type ATPases have been characterized as Type IIA based
on a phylogenetic analysis which distinguishes this
group from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the former of which is
modelled by TIGR01116.
Length = 884
Score = 25.2 bits (55), Expect = 9.4
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 48 AVNLAEQLGIRGPKFAKPLGQSLDEQALNDLRDDQIAQLYE--LMLAATQPE 97
AV++A +LG+ QS+ + L+ + D Q++Q+ + A PE
Sbjct: 558 AVSIARRLGM-----PSKTSQSVSGEKLDAMDDQQLSQIVPKVAVFARASPE 604
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
0.317 0.131 0.374
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,806,554
Number of extensions: 500817
Number of successful extensions: 661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 657
Number of HSP's successfully gapped: 47
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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 (21.7 bits)
S2: 53 (24.3 bits)