RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14285
(443 letters)
>gnl|CDD|221593 pfam12473, DUF3694, Kinesin protein. This domain family is found
in eukaryotes, and is typically between 131 and 151
amino acids in length. The family is found in
association with pfam00225, pfam00498. There is a single
completely conserved residue W that may be functionally
important.
Length = 142
Score = 53.5 bits (129), Expect = 1e-08
Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 11/96 (11%)
Query: 165 DYTPVEVTPSRAPDMLTGGTYQLRQGQQRRIQVLVRPVTNSGTLPIICES--VGSIA--- 219
+Y PV V A D GT++LRQG QRRI V ++ + VG +
Sbjct: 1 EYVPVPVDQLNALDA---GTFKLRQGLQRRIVVTLKQESGEQLPWEDITRLVVGLVRKAG 57
Query: 220 --VGSVCLRSRLQKPLDSYQEEDLAV-LREKWSDAL 252
+ L L S ++ V + +W +L
Sbjct: 58 KQPDMGLVDPVLSLKLLSGPDDGTNVVIEAQWDSSL 93
Score = 40.4 bits (95), Expect = 3e-04
Identities = 23/106 (21%), Positives = 37/106 (34%), Gaps = 35/106 (33%)
Query: 369 HIPVLFLDLNADDLSASNSGPELDYPVA-GLHSILPKEHGTKF----------------- 410
++PV LNA D +L + + L +E G +
Sbjct: 2 YVPVPVDQLNALDAGT----FKLRQGLQRRIVVTLKQESGEQLPWEDITRLVVGLVRKAG 57
Query: 411 -----------YNLPLVRHLNQE--VGAVATWDSSVHDSQHLNKIT 443
+L L+ + V A WDSS+H+S LN++T
Sbjct: 58 KQPDMGLVDPVLSLKLLSGPDDGTNVVIEAQWDSSLHNSLLLNRVT 103
>gnl|CDD|221433 pfam12130, DUF3585, Protein of unknown function (DUF3585). This
domain is found in eukaryotes. This domain is typically
between 135 and 149 amino acids in length and is found
associated with pfam00307.
Length = 142
Score = 33.0 bits (76), Expect = 0.098
Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 42/116 (36%)
Query: 237 QEEDLAV-----LREKWSDALVRRR---QYLDQQIQRLINKQDKSEQDIEREQSLEEQWV 288
+EE+L V +REK +ALVRR YL Q++Q E Q+ EQ
Sbjct: 41 EEEELMVEWFKLVREK--NALVRRESELMYLAQELQL------------EERQADLEQ-- 84
Query: 289 NLTEERNAVLVPAPGSGIPGAPADWNPPSDKSEQDIEREQSLVEQWVNLTEERNAV 344
E R + P + K+E+D +RE+ L+++ V L ++R+A+
Sbjct: 85 ---ELRALLSKP-----------EH----LKTEEDRQREEELLQELVKLVQKRDAL 122
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 33.3 bits (77), Expect = 0.17
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 244 LREKWSDALVRRRQYLDQQIQRLINKQ---DKSEQDIE-REQSLEEQWVNLTEER 294
LR + L RR L +Q +RL+ K+ D+ ++ +E +E+SLEE+ L +
Sbjct: 65 LRAEAERELKERRNELQRQEKRLLQKEETLDRKDESLEKKEESLEEKEKELAARQ 119
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 33.6 bits (78), Expect = 0.21
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 244 LREKWSDALVRRRQYLDQQIQRLINKQ---DKSEQDIE-REQSLEEQWVNLTEERNAV 297
LR ++ L RR L + +RL+ K+ D+ + +E RE+ LE++ L +++ +
Sbjct: 69 LRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQEL 126
>gnl|CDD|153271 cd07307, BAR, The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization
module that binds membranes and detects membrane
curvature. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions including organelle
biogenesis, membrane trafficking or remodeling, and cell
division and migration. Mutations in BAR containing
proteins have been linked to diseases and their
inactivation in cells leads to altered membrane
dynamics. A BAR domain with an additional N-terminal
amphipathic helix (an N-BAR) can drive membrane
curvature. These N-BAR domains are found in amphiphysins
and endophilins, among others. BAR domains are also
frequently found alongside domains that determine lipid
specificity, such as the Pleckstrin Homology (PH) and
Phox Homology (PX) domains which are present in beta
centaurins (ACAPs and ASAPs) and sorting nexins,
respectively. A FES-CIP4 Homology (FCH) domain together
with a coiled coil region is called the F-BAR domain and
is present in Pombe/Cdc15 homology (PCH) family
proteins, which include Fes/Fes tyrosine kinases, PACSIN
or syndapin, CIP4-like proteins, and srGAPs, among
others. The Inverse (I)-BAR or IRSp53/MIM homology
Domain (IMD) is found in multi-domain proteins, such as
IRSp53 and MIM, that act as scaffolding proteins and
transducers of a variety of signaling pathways that link
membrane dynamics and the underlying actin cytoskeleton.
BAR domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions. The I-BAR domain
induces membrane protrusions in the opposite direction
compared to classical BAR and F-BAR domains, which
produce membrane invaginations. BAR domains that also
serve as protein interaction domains include those of
arfaptin and OPHN1-like proteins, among others, which
bind to Rac and Rho GAP domains, respectively.
Length = 194
Score = 32.0 bits (73), Expect = 0.38
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 10/91 (10%)
Query: 204 NSGTLPIICESVGSIA--VGSV--CLRSRLQ----KPLDSYQEEDLAVLREKWSDALVRR 255
++ L E G I + L +L+ +PL Y ++DL ++++ L +
Sbjct: 48 SNTDLGEALEKFGKIQKELEEFRDQLEQKLENKVIEPLKEYLKKDLKEIKKR-RKKLDKA 106
Query: 256 RQYLDQQIQRLINKQDKSEQDIEREQSLEEQ 286
R D ++L K K ++D + EE+
Sbjct: 107 RLDYDAAREKL-KKLRKKKKDSSKLAEAEEE 136
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 31.3 bits (71), Expect = 0.60
Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 9/108 (8%)
Query: 195 IQVLVRPVTNSGTLPIICESVGSIAVGSVCL-----RSRLQKPLDSYQEEDLAVLREKWS 249
I +LV G L + +A+G V L L+ P+ S + + L L+ + S
Sbjct: 23 IALLVLFGAGLGALISTLLGIALLALGLVLLALGLLCLLLKAPVQSVRPQKLEELQGELS 82
Query: 250 DALVRRRQYLDQQIQRLINKQDKSEQDIEREQSLEEQWVNLTEERNAV 297
+ L ++ L ++++ L + + E ++E L+E L E ++
Sbjct: 83 E-LKQQLSELQEELEDLEERIAELESELE---DLKEDLQLLRELLKSL 126
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 31.6 bits (72), Expect = 0.82
Identities = 13/87 (14%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 208 LPIICESVGSIAVGSVCLRSRLQKPLDSYQEEDLAVLREKWSDALVRRRQYLDQQIQRL- 266
+ + V + + L+K + +E R+K + L++++++L
Sbjct: 242 PNYYYKDEKYLDVVPLKAYADLEKLFNEALDE--KFERDKIKQLASELEKKLEKELKKLE 299
Query: 267 --INKQDKSEQDIEREQSLEEQWVNLT 291
+ KQ+ +++E+ Q L
Sbjct: 300 NKLEKQEDELEELEKAAEELRQKGELL 326
>gnl|CDD|236798 PRK10929, PRK10929, putative mechanosensitive channel protein;
Provisional.
Length = 1109
Score = 31.6 bits (72), Expect = 0.92
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 239 EDLAVLREKWSDALVRRRQYLDQQIQRLIN-----KQDKSEQDIEREQSLEEQWVNL 290
++LA LR S+ +R Q LD +Q L N +Q ++E+ +E + L EQ +L
Sbjct: 203 QELARLR---SELAKKRSQQLDAYLQALRNQLNSQRQREAERALESTELLAEQSGDL 256
>gnl|CDD|233947 TIGR02600, Verru_Chthon_A, Verru_Chthon cassette protein A. In
Verrucomicrobium spinosum and Chthoniobacter flavus, a
four-gene operon that includes proteins with an
N-terminal signal sequence for cleavage and methylation
recurs many times. Each operon is likely to encode a
membrane complex, the function of which is unknown. This
model represents a long protein from this putative
membrame complex, with members averaging about 1300
amino acids. The N-terminal region includes an apparent
signal sequence. The function is unknown. Most cassettes
are adjacent to an unusually large protein with both an
outer membrane autotransporter region and PEP-CTERM
putative protein-sorting motif [Cell envelope, Surface
structures].
Length = 1265
Score = 31.4 bits (71), Expect = 1.1
Identities = 14/73 (19%), Positives = 20/73 (27%), Gaps = 6/73 (8%)
Query: 326 REQSLVEQWVNLTEERNAVLVPAPGSGIPGAPADWNPP------SGMEPHIPVLFLDLNA 379
+V T VPA D N P +G H+P ++
Sbjct: 91 SSDQMVVGAAFATALALESDVPATWDAPKALYTDLNEPVATLADNGTRGHVPTDEPGMDT 150
Query: 380 DDLSASNSGPELD 392
AS G +
Sbjct: 151 PAYPASTGGYPVK 163
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 29.5 bits (67), Expect = 1.6
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 228 RLQKPLDSYQEE---DLAVLREKWSDALVRRRQYLDQQIQRLINKQDKSEQDIEREQ 281
+L+K L +E+ D A L E A ++ + L +++Q KQ K +QD+++ Q
Sbjct: 36 KLEKELQKLKEKLQKDAATLSE---AAREKKEKELQKKVQEFQRKQQKLQQDLQKRQ 89
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 30.7 bits (69), Expect = 1.7
Identities = 24/139 (17%), Positives = 56/139 (40%), Gaps = 5/139 (3%)
Query: 198 LVRPVTN---SGTLPIICESVGSIAVGSVCLRSRLQKPLDSYQEEDLAVLREKWSDALVR 254
+V P+ SG + + SI+ V R D+ L+E+ S +
Sbjct: 156 IVIPLKKNILSGNVSDV--DTDSISDKKVVEALREDNEKGVNFRRDMTDLKERESQEDAK 213
Query: 255 RRQYLDQQIQRLINKQDKSEQDIEREQSLEEQWVNLTEERNAVLVPAPGSGIPGAPADWN 314
R Q L +++ + DK++Q + Q ++ + ++ P +P +
Sbjct: 214 RAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDK 273
Query: 315 PPSDKSEQDIEREQSLVEQ 333
++ +++IE+ Q +++
Sbjct: 274 QVAENQKREIEKAQIEIKK 292
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 30.3 bits (69), Expect = 2.4
Identities = 20/112 (17%), Positives = 41/112 (36%), Gaps = 9/112 (8%)
Query: 183 GTYQLRQGQQRRIQVLVRPVTNSGTLPIICESVGSIAVGSVCLRSRLQKPLDSY------ 236
G Y + QQ + L + ++ S L +LQ+ L+
Sbjct: 521 GGYHDARQQQAQYLAL-KQPAVKKKEEAAAPKAETVKRSSKKLSYKLQRELEQLPQLLED 579
Query: 237 QEEDLAVLREKWSDA--LVRRRQYLDQQIQRLINKQDKSEQDIEREQSLEEQ 286
E ++ L+ + +DA + + + + L + + + E ER + LE
Sbjct: 580 LEAEIEALQAQVADADFFSQPHEQTQKVLADLADAEQELEVAFERWEELEAL 631
>gnl|CDD|217779 pfam03885, DUF327, Protein of unknown function (DUF327). The
proteins in this family are around 140-170 residues in
length. The proteins contain many conserved residues.
with the most conserved motifs found in the central and
C-terminal region. The function of these proteins is
unknown.
Length = 146
Score = 28.7 bits (65), Expect = 3.2
Identities = 7/31 (22%), Positives = 21/31 (67%)
Query: 255 RRQYLDQQIQRLINKQDKSEQDIEREQSLEE 285
R++ +++++ L+++ DK+ + R +LE+
Sbjct: 36 RKKKSEERLKELLDEIDKAGNRLARSPTLED 66
>gnl|CDD|214458 MTH00206, ND4, NADH dehydrogenase subunit 4; Provisional.
Length = 450
Score = 29.9 bits (68), Expect = 3.3
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 194 RIQVLVRPVTNSGTLPIICESV-GSIAVGSVCLRS 227
RI +++ P T + I + GSI S+CLR
Sbjct: 241 RIILILGPSTKLSSYFFIILGLWGSIMTSSICLRQ 275
>gnl|CDD|227654 COG5351, COG5351, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 367
Score = 29.5 bits (66), Expect = 3.8
Identities = 19/60 (31%), Positives = 22/60 (36%), Gaps = 6/60 (10%)
Query: 301 APGSGIPGAPADWNPPSDKSEQDIEREQSLVEQWVNLTEERNAVLVPAPGSGIPGAPADW 360
A G IPG P P D+ R L WV L + V AP + PG D
Sbjct: 144 AFGGTIPGTPDTETPA------DVYRRNPLGCGWVRLDMPADIPGVRAPQTTSPGERLDS 197
>gnl|CDD|222707 pfam14357, DUF4404, Domain of unknown function (DUF4404). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 90 amino acids in length.
There are two completely conserved residues (P and G)
that may be functionally important.
Length = 85
Score = 27.2 bits (61), Expect = 4.4
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 17/70 (24%)
Query: 225 LRSRLQKPLDSYQEEDLAVLREKWSDALVRRRQYLDQQIQRLINKQDKSEQDIEREQSLE 284
L L++ DS EE A+L E L I+ + ++D +E ++SL
Sbjct: 9 LHEELEQ-TDSLDEETRALLSE------------LIDDIEAQLAEEDATE---AEDESLA 52
Query: 285 EQWVNLTEER 294
++ +NL ER
Sbjct: 53 DR-LNLAVER 61
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 29.6 bits (67), Expect = 4.4
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 227 SRLQKPLDSYQEEDLAVLREKWSDALVRRRQYLDQQIQRLINKQDKS--EQDIEREQSLE 284
S L+K Y +D + K S RR + + ++ QR + +S EQ E E+SL
Sbjct: 547 SWLKKYYKKYSVKDS---KLKPSALFKRRFRKIVEKAQRASEDKGESAREQTNEFEESLS 603
Query: 285 EQWVNLTEERNAVL 298
Q N+ ERN ++
Sbjct: 604 IQRENIYAERNRLI 617
>gnl|CDD|217789 pfam03915, AIP3, Actin interacting protein 3.
Length = 424
Score = 29.2 bits (66), Expect = 4.8
Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 1/76 (1%)
Query: 259 LDQQIQRLINKQDKSEQDIEREQSLEEQWVNLTEERNAVLVPAPGSGIPGAPADWNPPSD 318
L ++I+ L D + I + S +Q R A P + D P+
Sbjct: 90 LSEKIKSLKQALDDQQSTILQRLSELQQNTAKEVARPAAAPPPSSLPNSSSSPDSINPAG 149
Query: 319 KSE-QDIEREQSLVEQ 333
E Q + RE +++ Q
Sbjct: 150 LKELQSLRRELAVLRQ 165
>gnl|CDD|173104 PRK14641, PRK14641, hypothetical protein; Provisional.
Length = 173
Score = 28.6 bits (64), Expect = 5.2
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 240 DLAVLREKWSDALVRRRQYLDQQIQRLINKQDKSEQDIEREQSLEEQWVNLTEERNAVLV 299
DL V + ++ RQY + + RL+ + E+ E E + Q V+LTE A +V
Sbjct: 81 DLMVSSPGLGEPIILPRQYG-RHVGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIV 139
Query: 300 PAP 302
P
Sbjct: 140 LKP 142
>gnl|CDD|221069 pfam11304, DUF3106, Protein of unknown function (DUF3106). Some
members in this family of proteins are annotated as
transmembrane proteins however this cannot be confirmed.
Currently no function is known.
Length = 107
Score = 27.7 bits (62), Expect = 5.5
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 233 LDSYQEEDLAVLREKWSDALVRRRQYLDQQIQRLINKQDKSEQDIEREQSLEEQWVNLT- 291
L Q+E LA L E+W +RQ + +R S ++ +R Q +W L+
Sbjct: 5 LTPEQQEALAPLAERWDSLSPEQRQKWLRIAERY---PKMSPEEQKRLQERMTRWAKLSP 61
Query: 292 EERNAV 297
E+R
Sbjct: 62 EQREQA 67
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 29.1 bits (66), Expect = 5.5
Identities = 26/107 (24%), Positives = 38/107 (35%), Gaps = 25/107 (23%)
Query: 255 RRQYLDQQIQRL--INKQDKSEQDIEREQSLEEQWVNLTEERNAVLVPAP-GS-----GI 306
RQ + R+ +NK D+ D +E+ L N V V P G+ G+
Sbjct: 121 WRQADKYGVPRILFVNKMDRLGADFYL--VVEQLKERLG--ANPVPVQLPIGAEEEFEGV 176
Query: 307 ------------PGAPADWNP-PSDKSEQDIEREQSLVEQWVNLTEE 340
GA +W P+D E E + L+E EE
Sbjct: 177 IDLVEMKAVAFGDGAKYEWIEIPADLKEIAEEAREKLLEALAEFDEE 223
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.1 bits (66), Expect = 5.6
Identities = 18/91 (19%), Positives = 29/91 (31%), Gaps = 23/91 (25%)
Query: 250 DALVRRRQYLDQQIQRLINKQDKSEQDIEREQSLEEQWVNLTEERNAVLVPAPGSGIPGA 309
+ L RR L+ ++ L + ER L + L E A+
Sbjct: 422 EDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAAL------------ 469
Query: 310 PADWNPPSDKSEQDIEREQSLVEQWVNLTEE 340
E ++E+ LVE + L E
Sbjct: 470 -----------EARWQQEKELVEAILALRAE 489
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 29.2 bits (65), Expect = 6.1
Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 4/59 (6%)
Query: 229 LQKPLDSYQEEDLAVLREKWSDALVRRRQYLDQQIQRLINKQDKS--EQDIEREQSLEE 285
LQ Q+ + + A + Q + + QD Q +E +L+
Sbjct: 589 LQNITVRLQDLTEKLSEAEDMLACEQHALLRKLQPE--QDLQDVRLHLQQCSQELALKL 645
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, 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 KRs 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 = 436
Score = 28.9 bits (65), Expect = 6.2
Identities = 25/129 (19%), Positives = 37/129 (28%), Gaps = 21/129 (16%)
Query: 277 IEREQSLEEQWVNLTEERNAVLVPAPGSGIPGAPADWNPPSDK-SEQDIEREQSLVEQWV 335
+E SL+ W A L A + + G A D S D L+E
Sbjct: 30 LEALASLQPVWAPAALAS-AFLALAYEAALLGLAAAEAALLDALSALDPAAALQLLESLQ 88
Query: 336 NLTE--------ERNAVLVPAPGSGIPGAPADWNPPSGM-----------EPHIPVLFLD 376
L + A+L G +P P + +D
Sbjct: 89 RLLKAGLLAARASGRALLQVVTGLPGALGLDALDPAGAGLAGLLRTLAQEYPGLTCRLID 148
Query: 377 LNADDLSAS 385
L+A + SA
Sbjct: 149 LDAGEASAE 157
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.9 bits (65), Expect = 6.9
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 225 LRSRLQKPLDSYQE--EDLAVLREKWSDALVRRRQYLDQQIQRLINKQDKSEQDIEREQ- 281
LR +L++ +E +LA L E+ L R + L+++++ L + ++ ++ +E +
Sbjct: 707 LRRQLEELERQLEELKRELAALEEELEQ-LQSRLEELEEELEELEEELEELQERLEELEE 765
Query: 282 ---SLEEQWVNLTEERNAV 297
SLEE L EE +
Sbjct: 766 ELESLEEALAKLKEEIEEL 784
>gnl|CDD|223771 COG0699, COG0699, Predicted GTPases (dynamin-related) [General
function prediction only].
Length = 546
Score = 28.3 bits (63), Expect = 8.8
Identities = 11/49 (22%), Positives = 15/49 (30%), Gaps = 3/49 (6%)
Query: 235 SYQEEDLAVLREKWS---DALVRRRQYLDQQIQRLINKQDKSEQDIERE 280
+ LA L E L R+ Q I+ L+ Q I
Sbjct: 434 KKLDALLATLGEALRRLTGLLPERKTLEKQLIKSLLESLLILAQKIRDS 482
>gnl|CDD|219776 pfam08278, DnaG_DnaB_bind, DNA primase DnaG DnaB-binding.
Eubacterial DnaG primases interact with several factors
to from the replisome. One of these factors in DnaB, a
helicase. This domain has been demonstrated to be
responsible for the interaction between DnaG and DnaB.
Length = 126
Score = 27.2 bits (61), Expect = 9.0
Identities = 12/40 (30%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 244 LREKWSDALVR-RRQYLDQQIQRLINKQDKSE-QDIEREQ 281
+ +++ D L R + Q L+++I+ LI K +S D E+++
Sbjct: 82 IEQEFDDTLARLQEQLLERRIEELIAKSRRSGLTDEEKQE 121
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 27.6 bits (62), Expect = 9.1
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 225 LRSRLQKPLDSYQ--EEDLAVLREKWSDALVRRRQYLDQQIQRLINKQDKSEQDIEREQS 282
L++ LQK Q E+ L S+ + +Q Q++Q+ + + +Q ++E
Sbjct: 47 LQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQ---QELQQKQQELQQKQQAAQQELQ 103
Query: 283 LEEQ 286
++Q
Sbjct: 104 QKQQ 107
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
0.316 0.134 0.404
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,178,418
Number of extensions: 2271029
Number of successful extensions: 2313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2302
Number of HSP's successfully gapped: 56
Length of query: 443
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 343
Effective length of database: 6,502,202
Effective search space: 2230255286
Effective search space used: 2230255286
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 (21.6 bits)
S2: 61 (27.2 bits)