RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2875
(693 letters)
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 38.5 bits (89), Expect = 0.012
Identities = 38/170 (22%), Positives = 59/170 (34%), Gaps = 27/170 (15%)
Query: 120 IFEDDEVLEEHVKSHQNRRFKCP--CCERIFTSETRMRNHIDMKHADENLFKCKKCLKVF 177
+E ++V +E FKCP C R S ++ H +H +C K F
Sbjct: 136 FYEGEDVRDE---MEDLLSFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDF 192
Query: 178 SDEIKFH------------LHGRAHAKFYRCSECEKRFATEDIMRQHFRNYHNKEDAYVC 225
+EI+ L C C+ F +D +R+H R H E ++C
Sbjct: 193 WNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH--EACHIC 250
Query: 226 NYC----YDSFETKSTLVDHFFHHGNPYMCNHC----FLMFPDEKNLRNH 267
+ Y F++ L HF + C +FP L H
Sbjct: 251 DMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEH 300
Score = 31.1 bits (70), Expect = 2.3
Identities = 36/147 (24%), Positives = 49/147 (33%), Gaps = 25/147 (17%)
Query: 426 CEESFKNKKHLKQHLLA-HEKVKVFHCPKCPKLFRHESHLQNHVIVHDESEVHKCLYCFK 484
C + K LK+H A H V C K F +E L + D FK
Sbjct: 159 CHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFK 218
Query: 485 VFVHKAHLDKHLILHETSEMHNCDFCHLTFTTDNDLIRHMRSHEEYHTKHTCDICG---- 540
C FC + F D++L RH R + H CD+ G
Sbjct: 219 GHPL------------------CIFCKIYFYDDDELRRHCR--LRHEACHICDMVGPIRY 258
Query: 541 EKFINDLKLKAHIKIIHNLFTCIHCGD 567
+ F + L+AH + H T C
Sbjct: 259 QYFKSYEDLEAHFRNAHYCCTFQTCRV 285
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 34.6 bits (80), Expect = 0.19
Identities = 13/71 (18%), Positives = 22/71 (30%), Gaps = 25/71 (35%)
Query: 391 RRSF----RCKSCGRRFESEELLIVHQVIHERKFHKCTQCEESF---KNKKHLKQHLLAH 443
RR + C+ CG +C C+ K L+ H +
Sbjct: 429 RRGYAPLLLCRDCGYIA------------------ECPNCDSPLTLHKATGQLRCHYCGY 470
Query: 444 EKVKVFHCPKC 454
++ CP+C
Sbjct: 471 QEPIPQSCPEC 481
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 31.5 bits (72), Expect = 0.33
Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 507 CDFCHLTFTTDNDLIRHMRSHEEYHTKHTCDICGEKFINDLK--LKAHIKIIHNLFTCIH 564
C FC+ T T + + HM H I +++ DL+ L + IH C++
Sbjct: 2 CLFCNHTSDTVEENLEHMF------KSHGFFIPEREYLVDLEGLLNYLREKIHEGNECLY 55
Query: 565 CGDTLNNAKDYASHLL 580
CG + + H+
Sbjct: 56 CGKQFKSLEALRQHMR 71
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 29.3 bits (66), Expect = 0.43
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 71 NLKAHLKMHKGPKIFTCAQCDKAFS 95
NL+ H++ H G K + C C K+FS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 28.1 bits (63), Expect = 0.95
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 380 NLDRHLLTHNVRRSFRCKSCGRRFES 405
NL RH+ TH + ++C CG+ F S
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 25.8 bits (57), Expect = 6.7
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 435 HLKQHLLAHEKVKVFHCPKCPKLFRH 460
+L++H+ H K + CP C K F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|220362 pfam09723, CxxC_CxxC_SSSS, Zinc ribbon domain. This entry
represents a region of about 41 amino acids found in a
number of small proteins in a wide range of bacteria.
The region usually begins with the initiator Met and
contains two CxxC motifs separated by 17 amino acids.
One protein in this entry has been noted as a putative
regulatory protein, designated FmdB. Most proteins in
this entry have a C-terminal region containing highly
degenerate sequence.
Length = 42
Score = 29.1 bits (66), Expect = 0.61
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 394 FRCKSCGRRFESEELLIVHQVIHERKFHKCTQC 426
+RC+ CG FE V Q I + C +C
Sbjct: 6 YRCEDCGHTFE------VLQKISDDPLATCPEC 32
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR transcriptional
regulator proteins. The ros chromosomal gene is present
in octopine and nopaline strains of Agrobacterium
tumefaciens as well as in Rhizobium meliloti. This gene
encodes a 15.5-kDa protein that specifically represses
the virC and virD operons in the virulence region of the
Ti plasmid and is necessary for succinoglycan
production. Sinorhizobium meliloti can produce two types
of acidic exopolysaccharides, succinoglycan and
galactoglucan, that are interchangeable for infection of
alfalfa nodules. MucR from Sinorhizobium meliloti acts
as a transcriptional repressor that blocks the
expression of the exp genes responsible for
galactoglucan production therefore allowing the
exclusive production of succinoglycan.
Length = 130
Score = 31.0 bits (71), Expect = 0.73
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 13/66 (19%)
Query: 11 EQEQQIPAQG--KSIQERKFKCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCARMYRY 68
E+E+ PA KS+ C K F K+ ++RH+ H L YR
Sbjct: 52 EEEKPTPAVPIKKSVTPDYIICLEDGKKF--KT-LKRHLRTHHGLT--------PEEYRA 100
Query: 69 KWNLKA 74
KW L A
Sbjct: 101 KWGLPA 106
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 30.2 bits (68), Expect = 1.3
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 114 CKICLEIFEDDEVLEEHVKSHQNRRFKCPCCERIFTSETRMRNHIDMKH 162
C +CL F L++H++ ++ + CP C + F + +H+ KH
Sbjct: 76 CPLCLMPFSSSVSLKQHIRYTEHSK-VCPVCGKEFRNTDSTLDHVCKKH 123
Score = 29.1 bits (65), Expect = 3.8
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 423 CTQCEESFKNKKHLKQHLLAHEKVKVFHCPKCPKLFRHESHLQNHV 468
C C F + LKQH+ E KV CP C K FR+ +HV
Sbjct: 76 CPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDSTLDHV 119
Score = 28.7 bits (64), Expect = 4.6
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 76 LKMHKGPKIFTCAQCDKAFSLKSNLSKHVRHHMENVKQCKICLEIFEDDEVLEEHVKSHQ 135
L K + C C FS +L +H+R + E+ K C +C + F + + +HV
Sbjct: 65 LLTSKAVSPYVCPLCLMPFSSSVSLKQHIR-YTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
Query: 136 N 136
N
Sbjct: 124 N 124
Score = 28.3 bits (63), Expect = 7.5
Identities = 15/52 (28%), Positives = 22/52 (42%)
Query: 534 HTCDICGEKFINDLKLKAHIKIIHNLFTCIHCGDTLNNAKDYASHLLIIHNI 585
+ C +C F + + LK HI+ + C CG N H+ HNI
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125
>gnl|CDD|234541 TIGR04320, Surf_Exclu_PgrA, SEC10/PgrA surface exclusion domain.
This model describes a conserved domain found in surface
proteins of a number of Firmutes. Many members have
LPXTG C-terminal anchoring motifs and a substantial
number have the KxYKxGKxW putative sorting signal at the
N-terminus. The tetracycline resistance plasmid pCF10 in
Enterococcus faecalis promotes conjugal plasmid transfer
in response to sex pheromones, but PgrA/Sec10 encoded by
that plasmid, a member of this family, specifically
inhibits the ability of cells to receive homologous
plasmids. The phenomenon is called surface exclusion.
Length = 356
Score = 31.2 bits (71), Expect = 1.7
Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 11/67 (16%)
Query: 624 GFMYNDETSSYSHIKQ----EDDSCDTYM-------DDTTENSNTYLKQETPDNEDIDTT 672
G ++ND S++ H + + Y+ + + D D T
Sbjct: 188 GMLFNDAGSNWGHAQNLLGDGKGNPGAYLGVSISNDGGVNIHFVNFNDSYIADGNKFDKT 247
Query: 673 PVPESSD 679
P+P + +
Sbjct: 248 PIPNTPN 254
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 31.7 bits (72), Expect = 1.9
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 393 SFRCKSCGRRFESEELLIVHQ 413
S+ C C F S + L HQ
Sbjct: 73 SYVCNVCMAEFSSMDQLAEHQ 93
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 31.2 bits (70), Expect = 2.1
Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 14/96 (14%)
Query: 152 TRMRNHIDMKHADENLFKCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEKRFATEDIM-R 210
T++ ++ + DE+ C C + F + L RAH C C R I R
Sbjct: 445 TKLLHNPSWQKDDESSDSCPSCGRAFI-SLSRPLGTRAH----HCRSCGIRLCVFCITKR 499
Query: 211 QHFR--------NYHNKEDAYVCNYCYDSFETKSTL 238
H+ + E+ VC+ CY +ET S L
Sbjct: 500 AHYSFAKLAKPGSSDEAEERLVCDTCYKEYETVSQL 535
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 30.7 bits (70), Expect = 2.5
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 14/63 (22%)
Query: 181 IKFHLHGRAHAKFYRCSECEKRFATEDIMRQHFRNY-HNKEDAYVCNYCYDSFETKSTLV 239
I L G A+AK Y+C +C + +++Y +K D C C K TL
Sbjct: 70 ITIKL-GYANAKIYKCPKCPR--------PTCYQSYGSSKPDNPPCPGC----GHKMTLK 116
Query: 240 DHF 242
H
Sbjct: 117 RHV 119
>gnl|CDD|215642 PLN03238, PLN03238, probable histone acetyltransferase MYST;
Provisional.
Length = 290
Score = 30.6 bits (69), Expect = 2.7
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 334 EKTLYKCLYCHKVFKKSTSFDKHMEH 359
LY C YC K +K S +H+
Sbjct: 45 CTKLYICEYCLKYMRKKKSLLRHLAK 70
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.8 bits (69), Expect = 2.8
Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 10/83 (12%)
Query: 137 RRFKCPC--CERIFTSETRMRNHIDMKHADENLFKCKKCLKVFSDEIKFHLHGRAHAKFY 194
+ +KCP C + + ++ ++ H M H + L K A K Y
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYH--MLHG-----HQNQKLHENPSPEK-MNIFSAKDKPY 399
Query: 195 RCSECEKRFATEDIMRQHFRNYH 217
RC C+KR+ + ++ H ++ H
Sbjct: 400 RCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 30.8 bits (69), Expect = 3.0
Identities = 70/448 (15%), Positives = 115/448 (25%), Gaps = 68/448 (15%)
Query: 164 DENLFKCKKCLKVFSDEIKFHLHGRAHAKFYRC----SECEKRFATEDIMRQHFRNYHNK 219
C C FS H R+H S C+K F+ + +H R +HN
Sbjct: 30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89
Query: 220 EDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRNHECTSCFTCPFCQ 279
S S+ + P
Sbjct: 90 PSDLNSKSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDP-------QLPDLLS 142
Query: 280 RKYKIEKHLEKHIESCIQLNPTTTVLKTLQKCRYCQRMFRNEDKLTAHELSHTMEKTLYK 339
L + S + + ++ L + N L + +S + + +
Sbjct: 143 ISNLRNNPLPGNNSSSVNTPQSNSLHPPLPANSLSKDPSSNLSLLISSNVSTS-IPSSSE 201
Query: 340 CLYCHKVFKKSTSFDKHMEHHNRNVLHKCHLCTKAYPSEKNLDRHLLTHNVRRSFRCKSC 399
+ +S ++ + L ++ P + S
Sbjct: 202 NSPLSSSYSIPSSSSDQNLENSSSSL-PLTTNSQLSPKSLLSQSPSSLSSSDSSSSASES 260
Query: 400 GRRFESEELLIVHQVIH--------ERKFHKCTQCEESFKNKKHLKQHLLAH----EKVK 447
R K QC SF L +HL + E +K
Sbjct: 261 PRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLK 320
Query: 448 VFHCPK--CPKLFRHESHLQNHVIVHDESEVHKCLY------------------------ 481
F CP C KLF L+ H+++H K
Sbjct: 321 PFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKD 380
Query: 482 -------------CFKVFVHKAHLDKHLILHETSEMHNCDF--CHLTFTTDNDLIRHMRS 526
C + F ++L H+I H + +NC C +F +LI H +
Sbjct: 381 LKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKI 440
Query: 527 HEEYHTKHTCDICGEKFINDLKLKAHIK 554
H + + F DL L H K
Sbjct: 441 HTNHAPLLCSILK--SFRRDLDLSNHGK 466
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 30.5 bits (70), Expect = 3.5
Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 21/62 (33%)
Query: 396 CKSCGRRFESEELLIVHQVIHERKFHKCTQCEESF---KNKKHLKQHLLAHEKVKVFHCP 452
C+ CG E C C+ S + ++ L+ H +++ CP
Sbjct: 384 CRDCGWVAE------------------CPHCDASLTLHRFQRRLRCHHCGYQEPIPKACP 425
Query: 453 KC 454
+C
Sbjct: 426 EC 427
>gnl|CDD|217969 pfam04216, FdhE, Protein involved in formate dehydrogenase
formation. The function of these proteins is unknown.
They may possibly be involved in the formation of
formate dehydrogenase.
Length = 283
Score = 30.0 bits (68), Expect = 3.9
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 6/35 (17%)
Query: 422 KCTQCEESFKNKKHLKQHLLAHEK--VKVFHCPKC 454
KCT C + K L L + V+ C C
Sbjct: 207 KCTNCGST----KGLAYWSLEEGEPGVRAETCDTC 237
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.3 bits (58), Expect = 4.0
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 449 FHCPKCPKLFRHESHLQNHVIVH 471
+ CP+C K+F+ +S L+ H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 4.0
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 505 HNCDFCHLTFTTDNDLIRHMRSH 527
+ C C F + + L HMR+H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|173875 cd08510, PBP2_Lactococcal_OppA_like, The substrate binding
component of an ABC-type lactococcal OppA-like transport
system contains. This family represents the substrate
binding domain of an ATP-binding cassette (ABC)-type
oligopeptide import system from Lactococcus lactis and
other gram-positive bacteria, as well as its closet
homologs from gram-negative bacteria.
Oligopeptide-binding protein (OppA) from Lactococcus
lactis can bind peptides of length from 4 to at least 35
residues without sequence preference. The oligopeptide
import system OppABCDEF is consisting of five subunits:
two homologous integral membrane proteins OppB and OppF
that form the translocation pore; two homologous
nucleotide-binding domains OppD and OppF that drive the
transport process through binding and hydrolysis of ATP;
and the substrate-binding protein or receptor OppA that
determines the substrate specificity of the transport
system. The dipeptide (DppA) and oligopeptide (OppA)
binding proteins differ in several ways. The DppA binds
dipeptides and some tripeptides and also is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 residues) and
plays a role in recycling of cell wall peptides, which
precludes any involvement in chemotaxis. Most of other
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the dipeptide/oligopeptide binding proteins. The
structural topology of these domains is most similar to
that of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 516
Score = 29.9 bits (68), Expect = 4.7
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 514 FTTDNDLIRHMRSHEEYHTKHTCDICGEKFINDLKLKAHIK 554
+T I M EEYH I G K I+D ++ K
Sbjct: 103 YTDSFKNIVGM---EEYHDGKADTISGIKKIDDKTVEITFK 140
>gnl|CDD|234972 PRK01688, PRK01688, histidinol-phosphate aminotransferase;
Provisional.
Length = 351
Score = 29.9 bits (68), Expect = 4.8
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 18/60 (30%)
Query: 125 EVLEEHV-KSHQNRRF------KCPCCERIFTSETRMRNHIDMKHADENLFKCKKCLKVF 177
+ E V + + NR++ + PC E++F SET N+I L + VF
Sbjct: 262 AAMRERVAEINANRQWLIAALKEIPCVEQVFDSET---NYI--------LARFTASSAVF 310
>gnl|CDD|225357 COG2766, PrkA, Putative Ser protein kinase [Signal transduction
mechanisms].
Length = 649
Score = 30.1 bits (68), Expect = 5.3
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 549 LKAHIKIIHNLFTCIHCGD---TLNNAKDYASHLLIIHNIESSQQVEKNLNNMYNLL 602
KA IK++H L T G+ T L++ H+ ES Q KN N L
Sbjct: 266 FKAPIKVLHPLLTATQEGNYKGTEGIGAIPFDGLIVAHSNESEWQTFKNNKNNEAFL 322
>gnl|CDD|239139 cd02674, Peptidase_C19R, A subfamily of peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 230
Score = 29.6 bits (67), Expect = 5.3
Identities = 15/69 (21%), Positives = 23/69 (33%), Gaps = 6/69 (8%)
Query: 224 VCNYCYDSFETKSTL---VDHFFHHGNPYMCNHCFLMFPDEKNLRNHECTSCFTCPFCQR 280
C +FE + L + C +F E+ L + CP C++
Sbjct: 56 TCGKTSTTFEPFTYLSLPIPSGSGDAPKVTLEDCLRLFTKEETLDGDN---AWKCPKCKK 112
Query: 281 KYKIEKHLE 289
K K K L
Sbjct: 113 KRKATKKLT 121
>gnl|CDD|227322 COG4989, COG4989, Predicted oxidoreductase [General function
prediction only].
Length = 298
Score = 29.3 bits (66), Expect = 6.1
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 89 QCDKAFSLKSNLSKHVRHHMENVKQCKICLEIFEDDEV 126
QC+ F L+ +R +E V +C I L E+ +
Sbjct: 58 QCEALFGEALKLAPGLREKIEIVSKCGIRLPSREEPRI 95
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 27.4 bits (61), Expect = 6.7
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 394 FRCKSCGRRFESEELLIVHQVIHERKFHKCTQCEESFKNKKHLKQHL 440
F+C CG F + L + Q H R+ H T+C K+ + L QH
Sbjct: 2 FKCPICG--FTTVTLFALKQ--HARRNHTLTKCPVCNKSYRRLNQHF 44
>gnl|CDD|218613 pfam05502, Dynactin_p62, Dynactin p62 family. Dynactin is a
multi-subunit complex and a required cofactor for most,
or all, of the cellular processes powered by the
microtubule-based motor cytoplasmic dynein. p62 binds
directly to the Arp1 subunit of dynactin.
Length = 456
Score = 29.5 bits (66), Expect = 6.8
Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 7/62 (11%)
Query: 220 EDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHC-FLMFPDEKNLRNHECT-SCFTCPF 277
E C C + + Y C +C F + E + C +CF CP
Sbjct: 3 EQLLFCEDC---HQIRCP--RCVTEEIVCYYCPNCLFEVPSSEVRSEKNRCARNCFDCPI 57
Query: 278 CQ 279
C
Sbjct: 58 CT 59
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 25.6 bits (57), Expect = 7.2
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 505 HNCDFCHLTFTTDNDLIRHMRSH 527
H C C TF++ L H +SH
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|236654 PRK10141, PRK10141, DNA-binding transcriptional repressor ArsR;
Provisional.
Length = 117
Score = 27.9 bits (62), Expect = 7.2
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 483 FKVFVHKAHLDKHLILHETSEMHNCDFCHLTFTTDNDLIRHM 524
FK+ + L L+L E+ E+ CD C + + RH+
Sbjct: 10 FKILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHL 51
>gnl|CDD|203088 pfam04780, DUF629, Protein of unknown function (DUF629). This
family represents a region of several plant proteins of
unknown function. A C2H2 zinc finger is predicted in
this region in some family members, but the spacing
between the cysteine residues is not conserved
throughout the family.
Length = 463
Score = 29.3 bits (66), Expect = 7.3
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 125 EVLEEHVKSHQNRR----FKCPCCERIFTSETRMRNHIDMKHA 163
E LE+ + + R + C C + F+S +NH++ +HA
Sbjct: 40 EALEQVLSFARENRKWRFWMCRTCSKKFSSSEECKNHLEQEHA 82
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 25.4 bits (56), Expect = 7.8
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 86 TCAQCDKAFSLKSNLSKHVRHH 107
C C K+FS KSNL +H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.4 bits (56), Expect = 8.6
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 451 CPKCPKLFRHESHLQNHVIVH 471
CP C K F +S+L+ H+ H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|227252 COG4915, XpaC, 5-bromo-4-chloroindolyl phosphate hydrolysis protein
[General function prediction only].
Length = 204
Score = 28.6 bits (64), Expect = 8.8
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 279 QRKYKIEKHLEKHIESCIQLNPTTTVLKTLQKCRYCQRMFRNEDKLTAHELSHTMEKTLY 338
+R YK E+ H+++ ++L LK +E ++ ELS ++EK L+
Sbjct: 122 KRFYKAEEFFYSHLDNMVELTEKYAFLKKQPVKSKEINQDLSETRILLKELSRSIEKDLH 181
Query: 339 KCL 341
+ L
Sbjct: 182 ELL 184
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 28.6 bits (64), Expect = 9.7
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 185 LHGRAHAKFYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYC 228
LHG ++Y C C KR+ ED++ K D C+ C
Sbjct: 113 LHGNVE-EYY-CVRCGKRYTVEDVI-----EKLEKSDVPRCDDC 149
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
0.323 0.134 0.428
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,956,463
Number of extensions: 3037621
Number of successful extensions: 4871
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4820
Number of HSP's successfully gapped: 223
Length of query: 693
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 589
Effective length of database: 6,324,786
Effective search space: 3725298954
Effective search space used: 3725298954
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 62 (27.5 bits)