RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy64
(115 letters)
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit
4. Members of this family function as part of the
Mediator (Med) complex, which links DNA-bound
transcriptional regulators and the general
transcription machinery, particularly the RNA
polymerase II enzyme. They play a role in basal
transcription by mediating activation or repression
according to the specific complement of transcriptional
regulators bound to the promoter.
Length = 176
Score = 31.2 bits (71), Expect = 0.057
Identities = 8/35 (22%), Positives = 17/35 (48%)
Query: 27 FKLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQ 61
K L +H + ++ L ++++ EKI+D
Sbjct: 15 KSALKELEEHQENQQRILELRAEVESLDEKIKDIL 49
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 29.3 bits (66), Expect = 0.062
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 5 LKEHMAVHTTDRPFVCNMCPSTFK 28
L+ HM HT ++P+ C +C +F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 24.7 bits (54), Expect = 2.5
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 74 NLKLHMRIHTGEKKY 88
NL+ HMR HTGEK Y
Sbjct: 1 NLRRHMRTHTGEKPY 15
Score = 24.3 bits (53), Expect = 3.4
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 46 LENHMKAVHEKIRDFQCKVCDRAF 69
L HM+ H + ++C VC ++F
Sbjct: 2 LRRHMR-THTGEKPYKCPVCGKSF 24
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional.
Length = 325
Score = 30.0 bits (68), Expect = 0.21
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 8 HMAVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLKMDTLENHMKAVH 54
HMAVH +P V + +++ +H R H ++ L+++T H VH
Sbjct: 198 HMAVHPMGKPAVTH-----YRIMEHFRVHTRLRLRLETGRTHQIRVH 239
>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 = 27.7 bits (62), Expect = 0.23
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 61 QCKVCDRAFFDVYNLKLHMRIH 82
+C C ++F NLK H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 2.0
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 19 VCNMCPSTFKLKKHLRQHYKVH 40
C C +F K +L++H + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.4 bits (61), Expect = 0.28
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 60 FQCKVCDRAFFDVYNLKLHMRIH 82
++C C + F L+ HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 0.77
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 18 FVCNMCPSTFKLKKHLRQHYKVH 40
+ C C FK K LR+H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.5 bits (63), Expect = 0.74
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 16 RPFVCNM--CPSTFK----LKKH-LRQHYKVHLKMDTLENHMKAVHEKIRDFQCKVCDRA 68
+P+ C + C +K LK H L H L + M K + ++C+VCD+
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407
Query: 69 FFDVYNLKLH 78
+ ++ LK H
Sbjct: 408 YKNLNGLKYH 417
>gnl|CDD|216090 pfam00733, Asn_synthase, Asparagine synthase. This family is
always found associated with pfam00310. Members of this
family catalyze the conversion of aspartate to
asparagine.
Length = 195
Score = 28.0 bits (63), Expect = 0.95
Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 11/90 (12%)
Query: 10 AVHTTDRPFVCNMCPSTFKLKKHLRQHYKVHLK---MDTL-----ENHMKAVHEKIRDFQ 61
++ + PF + + L + R+ KV L D L ++ M H + +
Sbjct: 91 VIYHLEEPFGDSSAIPLYLLSRLARKGVKVVLSGEGADELFGGYRDDRMSMAHGL--EVR 148
Query: 62 CKVCDRAFFD-VYNLKLHMRIHTGEKKYIF 90
D + +L +++ GE+KYI
Sbjct: 149 VPFLDHRLVEFALSLPPELKLRDGEEKYIL 178
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 27.6 bits (61), Expect = 1.5
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 19 VCNMCPSTFKLKK--HLRQHY-----KVHLKMDTLENHMKAVHEKIRD 59
VC +C +T +K H+ HY ++ K+ +E +K + EKI D
Sbjct: 454 VCPVCGTTLGEEKSNHIINHYNEKKSRLEEKIREIEIEVKDIDEKIVD 501
>gnl|CDD|131979 TIGR02933, nifM_nitrog, nitrogen fixation protein NifM. Members of
this protein family, found in a subset of
nitrogen-fixing bacteria, are the nitrogen fixation
protein NifM. NifM, homologous to peptidyl-prolyl
cis-trans isomerases, appears to be an accessory protein
for NifH, the Fe protein, also called component II or
dinitrogenase reductase, of nitrogenase [Central
intermediary metabolism, Nitrogen fixation].
Length = 256
Score = 27.5 bits (61), Expect = 1.5
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 35 QHYKVHLKMDTLENHMKAVHEKI 57
Q HL + E+ +AV +I
Sbjct: 123 QRLTRHLLLTVNEDDREAVRTRI 145
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 27.0 bits (59), Expect = 2.5
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 40 HLKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLHMRIHTGEKKY 88
+ T ++ +K++ R C C +F + +L H+R HTGEK
Sbjct: 14 SVLSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPS 62
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.9 bits (54), Expect = 2.6
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 60 FQCKVCDRAFFDVYNLKLHMRIH 82
F+C +C ++F LK H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.5 bits (53), Expect = 3.3
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 18 FVCNMCPSTFKLKKHLRQHYKVH 40
F C +C +F K L++H + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>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 = 26.0 bits (58), Expect = 3.7
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 19 VCNMCPSTFK-LKKHLRQHY 37
+C FK LK+HLR H+
Sbjct: 72 ICLEDGKKFKTLKRHLRTHH 91
>gnl|CDD|206532 pfam14364, DUF4408, Domain of unknown function (DUF4408). This
domain is found at the N-terminus of member of the
DUF761 family pfam05553. Many members are plant
proteins.
Length = 34
Score = 24.4 bits (54), Expect = 3.9
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 87 KYIFIVVKKIIVVIYA 102
Y+F+V+ II+ I A
Sbjct: 15 PYLFLVLNLIIITIVA 30
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain
fusion protein; Provisional.
Length = 906
Score = 26.3 bits (58), Expect = 4.1
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 29 LKKHLRQHYKVH------LKMDTLENHMKAVHEKIRDFQCKVCDRAFFDVYNLKLH 78
L + ++ YK H LKM + N+ K V + I DF+ + FD N H
Sbjct: 263 LIRFYKEKYKDHSLLEDYLKMSDIGNNRKPVKDCIADFEKNI----VFDTGNFVYH 314
>gnl|CDD|234038 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs [Cellular processes, Sporulation and
germination].
Length = 764
Score = 26.6 bits (59), Expect = 4.1
Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 15/82 (18%)
Query: 45 TLENHMKAVHEKIRDFQCKVC-------DRAFFDVYNLKLHMRIHTGEKKYIFIVVK--- 94
T++ + E + + C+ C R F Y+ + + EKK +
Sbjct: 341 TMKRKSSYLLENLAERVCQSCNMKHRCWKREFDYTYSAMEELIENLEEKKDPNSKLPDEF 400
Query: 95 -----KIIVVIYAKKFSLDIEI 111
K +I + L+ I
Sbjct: 401 ERKCIKRKELINTTEDILNNYI 422
>gnl|CDD|220807 pfam10552, ORF6C, ORF6C domain. This domain was identified by Iyer
and colleagues.
Length = 114
Score = 25.3 bits (56), Expect = 5.6
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 71 DVYNLKLHMRIHTGEKKYIFIVVKKIIVVIYAKKFS 106
V +L+ +M + GE K I V K +V + K S
Sbjct: 23 KVDDLEENMPLFAGEAKEIQKKVNKRVVELLGGKGS 58
>gnl|CDD|224565 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational
modification, protein turnover, chaperones].
Length = 244
Score = 25.6 bits (56), Expect = 6.0
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 4/35 (11%)
Query: 59 DFQCKVCDRAFFDVYNLKLHMRIHTGEKKYIFIVV 93
D+ C C AF ++ I G+ + +
Sbjct: 93 DYTCPYCKEAFPELKKK----YIDDGKVRLVLREF 123
>gnl|CDD|225935 COG3400, COG3400, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 471
Score = 25.6 bits (56), Expect = 6.8
Identities = 15/90 (16%), Positives = 36/90 (40%), Gaps = 6/90 (6%)
Query: 28 KLKKHLRQHYKVHLKMDTLENHMKAVHEKIRDFQCKV------CDRAFFDVYNLKLHMRI 81
+ + + Q +H K+ + + +++ +H K F K FFD Y ++
Sbjct: 247 AMMRDVYQALFLHKKLKSYKLYIQVLHPKSPKFYHKFLSLETESIEVFFDFYVKSFIQKL 306
Query: 82 HTGEKKYIFIVVKKIIVVIYAKKFSLDIEI 111
H +K + ++V ++ + +D
Sbjct: 307 HEDHQKKMGLIVTELFAREKHRSALVDTAT 336
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
0.332 0.141 0.436
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,841,369
Number of extensions: 498304
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 589
Number of HSP's successfully gapped: 45
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 53 (24.1 bits)