RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6415
(174 letters)
>gnl|CDD|199834 cd10276, BamB_YfgL, Beta-barrel assembly machinery (Bam) complex
component B and related proteins. BamB (YflG) is a
non-essential component of the beta-barrel assembly
machinery (Bam), a multi-subunit complex that inserts
proteins with beta-barrel topology into the outer
membrane. BamB has been found to interact with BamA,
which in turn binds and stabilizes pre-folded
beta-barrel proteins; it has been suggested that BamB
participates in the stabilization.
Length = 358
Score = 36.9 bits (86), Expect = 0.003
Identities = 17/72 (23%), Positives = 23/72 (31%), Gaps = 16/72 (22%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWETNLK-------NGVCGVDFDRRDIPMNKLVATTLEA 53
MV A NG + F+ T + WET+L G K+ T
Sbjct: 40 MVYAADANGQVSAFNATTGKIIWETSLSGKGFLGGTPAVGNG---------KIFVGTESG 90
Query: 54 KLFVFDLKTLHR 65
L+ D K
Sbjct: 91 YLYALDAKDGSE 102
Score = 26.5 bits (59), Expect = 9.3
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWETNL 27
+ G ++G L D K S W T +
Sbjct: 82 KIFVGTESGYLYALDAKDGSELWRTEV 108
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 34.2 bits (79), Expect = 0.022
Identities = 28/138 (20%), Positives = 55/138 (39%), Gaps = 18/138 (13%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWE-TNLKNGVCGVDFDRRDIPMN-KLVATTLEAKLFVF 58
V + +G +K++DL+T T V V F P KL++++ + + ++
Sbjct: 149 FVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFS----PDGEKLLSSSSDGTIKLW 204
Query: 59 DLKTLHREKGFAYLSEKAHKATTVWAAKHLPQNRDLFVTCGGSGSLNLW-----QLVSAL 113
DL T G + + H+ V + P + L + G++ +W + V L
Sbjct: 205 DLST-----GKCLGTLRGHENG-VNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTL 257
Query: 114 RADTNLCSIFRYSSNYPT 131
TN + +S +
Sbjct: 258 SGHTNSVTSLAWSPDGKR 275
Score = 28.5 bits (64), Expect = 1.8
Identities = 16/110 (14%), Positives = 39/110 (35%), Gaps = 11/110 (10%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWE-TNLKNGVCGVDFDRRDIPMNKLVATTLEAKLFVFD 59
++ G +G +K++DL+T L V V L + + + + ++D
Sbjct: 23 LLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADG---TYLASGSSDKTIRLWD 79
Query: 60 LKTLHREKGFAYLSEKAHKATTVWAAKHLPQNRDLFVTCGGSGSLNLWQL 109
L+T + H + A + + + ++ +W +
Sbjct: 80 LETGECVRTL-----TGHTSYVSSVAFS--PDGRILSSSSRDKTIKVWDV 122
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 31.2 bits (71), Expect = 0.19
Identities = 12/21 (57%), Positives = 18/21 (85%), Gaps = 1/21 (4%)
Query: 11 LKMFDLKTMSLKWETNLKNGV 31
L MF LKT+S++W+ +LK+GV
Sbjct: 155 LNMF-LKTLSIEWQRSLKHGV 174
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 31.2 bits (69), Expect = 0.25
Identities = 35/177 (19%), Positives = 74/177 (41%), Gaps = 15/177 (8%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWETNLKNG--VCGVDFDRRDIPMNKLVATTLEAKLFVF 58
++ +G +G ++++DL++ S T + V V F L + + + + ++
Sbjct: 255 LLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDG---KLLASGSSDGTVRLW 311
Query: 59 DLKTLHREKGFAYLSEKAHKATTVWAAKHLPQNRDLFVTCGGSGSLNLWQL-----VSAL 113
DL+T K + L+ K H+ V + P L G++ LW L + L
Sbjct: 312 DLETG---KLLSSLTLKGHEGP-VSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTL 367
Query: 114 RADTNLCSIFRYSSNYPTQRTKPDIDDIPMGVPGSLTLLQEATLSSQPINSLDWSAD 170
+N+ S+ +S + + + + + +LL+ + + SLD+S D
Sbjct: 368 EGHSNVLSV-SFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPD 423
>gnl|CDD|235957 PRK07193, fliF, flagellar MS-ring protein; Reviewed.
Length = 552
Score = 29.6 bits (67), Expect = 0.90
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 8/32 (25%)
Query: 132 QRTKPDIDDIPMGVPGSLTLLQEATLSSQPIN 163
+ DD+ +G+PGS LS++P
Sbjct: 300 TSQENSNDDMALGIPGS--------LSNRPPP 323
>gnl|CDD|224437 COG1520, COG1520, FOG: WD40-like repeat [Function unknown].
Length = 370
Score = 28.3 bits (63), Expect = 2.0
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 1/62 (1%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWETNLKNGVCGVDFDRRDIPMNKLVATTLEAKLFVFDL 60
V G +G++ + T +KW L V K+ + + KL+ D
Sbjct: 70 TVYVGTRDGNIFALNPDTGLVKWSYPLLGAV-AQLSGPILGSDGKIYVGSWDGKLYALDA 128
Query: 61 KT 62
T
Sbjct: 129 ST 130
>gnl|CDD|234163 TIGR03300, assembly_YfgL, outer membrane assembly lipoprotein YfgL.
Members of this protein family are YfgL, a lipoprotein
component of a complex that acts protein insertion into
the bacterial outer membrane. Other members of this
complex are NlpB, YfiO, and YaeT. This protein contains
multiple copies of a repeat that, in other contexts, are
associated with binding of the coenzyme PQQ [Protein
fate, Protein and peptide secretion and trafficking].
Length = 377
Score = 28.0 bits (63), Expect = 2.7
Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 7/62 (11%)
Query: 2 VVAGYDNGDLKMFDLKTMSLKWETNLKNGVC-GVDFDRRDIPMNKLVATTLEAKLFVFDL 60
A D G + D +T W +L + GV D + T + ++ D
Sbjct: 69 YAADAD-GTVVALDAETGKRLWRVDLDERLSGGVGAD-----GGLVFVGTEKGEVIALDA 122
Query: 61 KT 62
+
Sbjct: 123 ED 124
Score = 26.8 bits (60), Expect = 6.6
Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 1 MVVAGYDNGDLKMFDLKTMSLKWETNLKNGVCGVDFDR-RDI---PM---NKLVATTLEA 53
V+ G+ G L +L+T WE + + +R D+ P+ ++ A + +
Sbjct: 192 GVLVGFAGGKLVALNLQTGQPLWEQRVALPKGRTELERLVDVDGDPVVDGGQVYAVSYQG 251
Query: 54 KLFVFDLKT 62
++ DL++
Sbjct: 252 RVAALDLRS 260
>gnl|CDD|234102 TIGR03075, PQQ_enz_alc_DH, PQQ-dependent dehydrogenase,
methanol/ethanol family. This protein family has a
phylogenetic distribution very similar to that coenzyme
PQQ biosynthesis enzymes, as shown by partial
phylogenetic profiling. Genes in this family often are
found adjacent to the PQQ biosynthesis genes themselves.
An unusual, strained disulfide bond between adjacent Cys
residues contributes to PQQ-binding, as does a Trp
residue that is part of a PQQ enzyme repeat (see
pfam01011). Characterized members include the
dehydrogenase subunit of a membrane-anchored, three
subunit alcohol (ethanol) dehydrogenase of Gluconobacter
suboxydans, a homodimeric ethanol dehydrogenase in
Pseudomonas aeruginosa, and the large subunit of an
alpha2/beta2 heterotetrameric methanol dehydrogenase in
Methylobacterium extorquens.
Length = 526
Score = 28.0 bits (63), Expect = 2.8
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 2 VVAGYDNGDLKMFDLKTMSLKWETNLKNGVCG 33
V G G K FD KT W+ +G+ G
Sbjct: 475 VFTGTLEGYFKAFDAKTGEELWKFKTGSGIVG 506
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 27.7 bits (62), Expect = 2.8
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 2 VVAGYDNGDLKMFDLKTMSLKWETNLKNGVCGVDFDRR-DIPM------NKLVATTLEAK 54
V+ G+ +G L D KT + WE + G + +R DI ++ A++ + +
Sbjct: 122 VIVGFSSGKLVALDPKTGKVLWEAPVAAPRGGSEIERLVDITGTPVVDGGRVYASSYQGR 181
Query: 55 LFVFDLKT 62
L DL T
Sbjct: 182 LVALDLAT 189
Score = 27.4 bits (61), Expect = 3.5
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 7/58 (12%)
Query: 7 DNGDLKMFDLKTMSLKWETNL--KNGVCGVDFDRRDIPMNKLVATTLEAKLFVFDLKT 62
+G + D T + W +L GV D +L T + +L D T
Sbjct: 1 ADGVVAALDAATGKVLWRVDLGGTALGGGVAVDG-----GRLYVATGKGELVALDAAT 53
Score = 26.2 bits (58), Expect = 8.9
Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 8/66 (12%)
Query: 2 VVAGYDNGDLKMFDLKTMSLKWETNLKNGVCG--VDFDRRDIPMNKLVATTLEAKLFVFD 59
+ G+L D T L W +L + G +V T + L+ D
Sbjct: 37 LYVATGKGELVALDAATGKLLWRKDLSGEILGAPTVAGGV------VVVVTADGSLYALD 90
Query: 60 LKTLHR 65
+T
Sbjct: 91 AETGKL 96
>gnl|CDD|235817 PRK06501, PRK06501, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 425
Score = 27.7 bits (62), Expect = 3.3
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 84 AAKHLPQNRDLFVTCGGSGSLNLWQLVSALRADTNLCSIFR----YSSNYPTQRTKPD 137
A+K ++RD FV G+G+L L L SA+ + I + ++ R+ PD
Sbjct: 230 ASKPFSKDRDGFVMAEGAGALVLESLESAVARGAKILGIVAGCGEKADSFHRTRSSPD 287
>gnl|CDD|213618 TIGR01424, gluta_reduc_2, glutathione-disulfide reductase, plant.
The tripeptide glutathione is an important reductant,
e.g., for maintaining the cellular thiol/disulfide
status and for protecting against reactive oxygen
species such as hydrogen peroxide. Glutathione-disulfide
reductase regenerates reduced glutathione from oxidized
glutathione (glutathione disulfide) + NADPH. This model
represents one of two closely related subfamilies of
glutathione-disulfide reductase. Both are closely
related to trypanothione reductase, and separate models
are built so each of the three can describe proteins
with conserved function. This model describes
glutathione-disulfide reductases of plants and some
bacteria, including cyanobacteria [Energy metabolism,
Electron transport].
Length = 446
Score = 27.1 bits (60), Expect = 6.3
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 93 DLFVTCGGSGSLNLWQLVSALRADTNLCSIFRY 125
DLFV GSG + +L +AL A + FR
Sbjct: 4 DLFVIGAGSGGVRAARLAAALGAKVAIAEEFRV 36
>gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Ornithine and Diaminopimelate
Decarboxylases, and Related Enzymes. This family
includes eukaryotic ornithine decarboxylase (ODC, EC
4.1.1.17), diaminopimelate decarboxylase (DapDC, EC
4.1.1.20), plant and prokaryotic biosynthetic arginine
decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine
decarboxylase (CANSDC), and ODC-like enzymes from
diverse bacterial species. These proteins are fold type
III PLP-dependent enzymes that catalyze essential steps
in the biosynthesis of polyamine and lysine. ODC and
ADC participate in alternative pathways of the
biosynthesis of putrescine, which is the precursor of
aliphatic polyamines in many organisms. ODC catalyzes
the direct synthesis of putrescine from L-ornithine,
while ADC converts L-arginine to agmatine, which is
hydrolysed to putrescine by agmatinase in a pathway that
exists only in plants and bacteria. DapDC converts
meso-2,6-diaminoheptanedioate to L-lysine, which is the
final step of lysine biosynthesis. CANSDC catalyzes the
decarboxylation of carboxynorspermidine, which is the
last step in the synthesis of norspermidine. The
PLP-dependent decarboxylases in this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. Prokaryotic ornithine, lysine and
biodegradative arginine decarboxylases are fold type I
PLP-dependent enzymes and are not included in this
family.
Length = 368
Score = 26.9 bits (60), Expect = 6.6
Identities = 24/121 (19%), Positives = 39/121 (32%), Gaps = 21/121 (17%)
Query: 33 GVDFDRRDIPMNKL---VATTLEAKLFVFDLKTLHREKGFAYLSEKAHKATTVWAAKHLP 89
G+ +D + + + + L+ TL E G +++ T V A K
Sbjct: 212 GIPYDEQPLDFEEYAALINPLLKKYFPNDPGVTLILEPGRYIVAQAGVLVTRVVAVKVN- 270
Query: 90 QNRDLFVTCGG-SGSLNLWQLVSALRADTNLCSIFRYSSNYPTQRTKPDIDDIPMGVPGS 148
R V GG + S Y + +P K D P+ VP +
Sbjct: 271 GGRFFAVVDGGMNHSFRPA---------------LAYDAYHPITPLKAPGPDEPL-VPAT 314
Query: 149 L 149
L
Sbjct: 315 L 315
>gnl|CDD|221098 pfam11376, DUF3179, Protein of unknown function (DUF3179). This
family of proteins has no known function.
Length = 261
Score = 26.4 bits (59), Expect = 7.2
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 8 NGDLKMFDLKTMSLKWETNLKNGVCG 33
N +L M+D +T SL W+ + G
Sbjct: 93 NSNLVMYDRETESL-WQQATGEAIVG 117
>gnl|CDD|199899 cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA alpha and beta
subunits and similar proteins. Transcription factor II
A (TFIIA) is one of the general transcription factors
for RNA polymerase II. TFIIA increases the affinity of
TATA-binding protein (TBP) for DNA in order to assemble
the initiation complex. TFIIA also functions as an
activator during development and differentiation, and
is involved in transcription from TATA-less promoters.
TFIIA is composed of more than one subunit in various
organisms. Mammalian TFIIA large subunits (TFIIA alpha
and beta) and the smaller subunit (TFIIA gamma) form a
heterotrimer. TFIIA alpha and beta are encoded by a
single gene (TFIIA_alpha_beta), its protein product is
post-translationally processed and cleaved. TOA1 and
TOA2 are the two subunits of Yeast TFIIA which
correspond to Mammalian TFIIA_alpha_beta and TFIIA
gamma, respectively. TOA1 and TOA2 form a heterodimeric
protein complex. TFIIA_alpha_beta alone is sufficient
for transcription in early embryogenesis, but the
cleaved forms, TFIIA alpha and TFIIA beta, represent
the vast majority of TFIIA in most differentiated
cells. The exact functional differences between cleaved
and uncleaved forms are not yet clear. This model also
contains paralogs of the canonical TFIIA_alpha_beta,
such as the human ALF, which may be involved in
gametogenesis and early embryogenesis (and is also
subject to proteolytic cleavage).
Length = 102
Score = 25.6 bits (57), Expect = 7.2
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 22 KWETNLKNGVCGVDFDRRDIPMNK 45
KW+ LK+G+ + + +D K
Sbjct: 74 KWKCTLKDGI--MTLNGKDYVFQK 95
>gnl|CDD|204170 pfam09226, Endonuc-HincII, Restriction endonuclease HincII.
Members of this family of prokaryotic restriction
endonucleases recognise the double-stranded sequence
5'-GTYRAC-3' and cleave after Y-3. They catalyze the
endonucleolytic cleavage of DNA to give specific
double-stranded fragments with terminal 5'-phosphates.
Length = 257
Score = 26.2 bits (57), Expect = 8.5
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 7 DNGDLKMFDLKTMSLKWETNLKNGVC 32
DN + +FD+ + + WE N ++ VC
Sbjct: 156 DNKEFDLFDINYLEVDWELNGEDLVC 181
>gnl|CDD|185420 PTZ00058, PTZ00058, glutathione reductase; Provisional.
Length = 561
Score = 26.5 bits (58), Expect = 8.8
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 67 KGFAYLSEKAHKATTVWAAKHLPQNRDLFVTCGGSGSLNLWQLVSALRADTN 118
+ F++ + K DL V GGSG + +A RA N
Sbjct: 24 RSFSFYHNLEASSAPTHLKKKPRMVYDLIVIGGGSGGMA-----AARRAARN 70
>gnl|CDD|222953 PHA02986, PHA02986, hypothetical protein; Provisional.
Length = 141
Score = 26.0 bits (57), Expect = 9.2
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 117 TNLCSIFRYSSNYPTQRTKPDIDDIPMGVPGSLT 150
+NLC F + T K +I I + +P S+
Sbjct: 33 SNLCKEFISNKK-KTTLIKEEIKKILLEIPDSMI 65
>gnl|CDD|237044 PRK12294, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 272
Score = 26.3 bits (58), Expect = 9.3
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 102 GSLNLWQ---LVSALRAD-TNLCSIFRYSSNYPTQRTK 135
G + WQ + ALR D T+ + RY S YPT TK
Sbjct: 51 GERSFWQHEHQIYALRNDFTD--QLLRYYSMYPTAATK 86
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
0.319 0.134 0.408
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,607,543
Number of extensions: 742611
Number of successful extensions: 553
Number of sequences better than 10.0: 1
Number of HSP's gapped: 550
Number of HSP's successfully gapped: 25
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
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: 56 (25.4 bits)