RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4268
(86 letters)
>gnl|CDD|215623 PLN03190, PLN03190, aminophospholipid translocase; Provisional.
Length = 1178
Score = 31.4 bits (71), Expect = 0.040
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 25 SNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKHVGEDGALPPPHEPDY 82
S RS L+ MN E L F LC+ + A+ + R+H E +P D+
Sbjct: 320 SKRSRLETRMNLEIIILSLFLIALCTIV----SVCAAVWLRRHRDELDTIPFYRRKDF 373
>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 = 28.1 bits (63), Expect = 0.076
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 17 CDSCDRTYSNRSSLKRHMN 35
C C +++S +S+LKRH+
Sbjct: 2 CPDCGKSFSRKSNLKRHLR 20
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 26.8 bits (60), Expect = 0.27
Identities = 5/22 (22%), Positives = 15/22 (68%)
Query: 14 RYLCDSCDRTYSNRSSLKRHMN 35
++ C +CD+ + + ++L+ H+
Sbjct: 1 QFYCVACDKYFKSENALENHLK 22
>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 = 26.1 bits (57), Expect = 0.50
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 15 YLCDSCDRTYSNRSSLKRHMN 35
+ C C +++S++ +LKRH+
Sbjct: 1 FKCPLCGKSFSSKDALKRHLR 21
Score = 24.1 bits (52), Expect = 2.4
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 44 FPCTLCSYATKRKTSLASHYYRKH 67
F C LC + K +L H + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 1.1
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 15 YLCDSCDRTYSNRSSLKRHM 34
Y C C + + ++S+L+ HM
Sbjct: 1 YRCPECGKVFKSKSALREHM 20
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 26.7 bits (59), Expect = 1.3
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 4 YYFSAPSGEKRYLCDSCDRTYSNRSSLKR 32
+ F P+ E RY+C S D T + + + R
Sbjct: 240 FLFEHPAAEGRYICSSHDATIHDLAKMLR 268
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 26.2 bits (58), Expect = 1.8
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 15 YLCDSCDRTYSNRSSLKRHMNYECGK 40
Y C SC + Y + ++RH Y CG+
Sbjct: 120 YRCGSCGQLYPRKRRIRRH-KYRCGR 144
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 25.8 bits (56), Expect = 3.1
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 11 GEKRYLCD--SCDRTYSNRSSLKRHM 34
K Y C C++ Y N++ LK HM
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHM 371
Score = 25.8 bits (56), Expect = 3.5
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 12 EKRYLCDSCDRTYSNRSSLKRH 33
+K Y C+ CD+ Y N + LK H
Sbjct: 396 DKPYRCEVCDKRYKNLNGLKYH 417
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 23.9 bits (52), Expect = 3.1
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 29 SLKRHMNYECGKLPAFPCTLCSYATKR 55
+L+RHM G+ P + C +C +
Sbjct: 1 NLRRHMRTHTGEKP-YKCPVCGKSFSS 26
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 25.6 bits (56), Expect = 3.2
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 15 YLCDSCDRTYSNRSSLKRHMNYECGKLPAFPCTLCSYATKRKTSLASHYYRKH 67
Y+C C +S+ SLK+H+ Y + C +C + S H +KH
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRY---TEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 25.9 bits (58), Expect = 3.2
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 78 HEPDYIVPE 86
+PDYIVPE
Sbjct: 74 EKPDYIVPE 82
>gnl|CDD|132854 cd07215, Pat17_PNPLA8_PNPLA9_like2, Patatin-like phospholipase of
bacteria. Patatin is a storage protein of the potato
tuber that shows Phospholipase A2 activity (PLA2; EC
3.1.1.4). Patatin catalyzes the nonspecific hydrolysis
of phospholipids, glycolipids, sulfolipids, and mono-
and diacylglycerols, thereby showing lipid acyl
hydrolase activity. The active site includes an oxyanion
hole with a conserved GGxR motif; it is found in almost
all the members of this family. The catalytic dyad is
formed by a serine and an aspartate. Patatin belongs to
the alpha-beta hydrolase family which is identified by a
characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Members of this family
have been found also in vertebrates. This family
includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9
(iPLA2-beta) like phospholipases from human as well as
the Pat17 isozyme from Solanum cardiophyllum.
Length = 329
Score = 25.1 bits (55), Expect = 4.8
Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 45 PCTLCSYATKRKTSLASHYYRKHVGED 71
PC + SY +R++ H+++ H
Sbjct: 128 PCLITSYDIERRS---PHFFKSHTAIK 151
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 23.2 bits (51), Expect = 4.9
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 15 YLCDSCDRTYSNRSSLKRHMN 35
+ C+ C+ T+++ S LK H+
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 25.2 bits (56), Expect = 5.1
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 56 KTSLASHYYRKHVGEDGALPPPHEPD 81
K A Y KH+G+ L PP + +
Sbjct: 289 KLEKADALYEKHLGD--LLTPPTKEE 312
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type
zinc fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 23.4 bits (51), Expect = 5.4
Identities = 5/23 (21%), Positives = 13/23 (56%)
Query: 13 KRYLCDSCDRTYSNRSSLKRHMN 35
+ C C+ T+++ S++ H+
Sbjct: 2 GGFYCKLCNVTFTDEISVEAHLK 24
>gnl|CDD|177562 PHA03234, PHA03234, DNA packaging protein UL33; Provisional.
Length = 338
Score = 25.3 bits (55), Expect = 5.4
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 44 FPCTLCSYATKRKTSLASH 62
F C LC+ K+ H
Sbjct: 318 FKCNLCNSQKKKDRDALEH 336
>gnl|CDD|184395 PRK13919, PRK13919, putative RNA polymerase sigma E protein;
Provisional.
Length = 186
Score = 24.9 bits (54), Expect = 5.7
Identities = 13/29 (44%), Positives = 14/29 (48%)
Query: 58 SLASHYYRKHVGEDGALPPPHEPDYIVPE 86
+LA H HV A P P EPD PE
Sbjct: 81 ALAHHAAVDHVRRRAARPQPLEPDEREPE 109
>gnl|CDD|182156 PRK09939, PRK09939, putative oxidoreductase; Provisional.
Length = 759
Score = 25.0 bits (54), Expect = 5.8
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 53 TKRKTSLASHYYRKHVGEDGAL 74
T +T LAS YY +G D AL
Sbjct: 265 TNSETQLASAYYNVRIGGDMAL 286
>gnl|CDD|151999 pfam11563, Protoglobin, Protoglobin. Protoglobin is from
Methanosarcina acetivorans C2A. The protein is part of
the haemoglobin superfamily. Protoglobin has specific
loops and an amino-terminal extension which leads to the
burying of the haem within the matrix of the protein.
Protoglobin-specific apolar tunnels allow the access of
O2, CO and NO to the haem distal site.
Length = 196
Score = 24.7 bits (54), Expect = 6.4
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 13/36 (36%)
Query: 2 LGYYFSAPSGE-------------KRYLCDSCDRTY 24
L YYFS P GE +++ D+C R Y
Sbjct: 71 LLYYFSDPDGEPIQEYLAAVRKRFGQWILDTCRRPY 106
>gnl|CDD|188401 TIGR03886, lyase_spl_fam, spore photoproduct lyase family protein.
This uncharacterized radical SAM domain protein occurs
rarely and sporadically in species that include select
Alphaproteobacteria and Actinobacteria, and in
Deinococcus deserti VCD115. It is a distant but
full-length homolog to the Bacillus subtilis spore
photoproduct lyase (spl), which monomerizes thymine
dimers created as DNA damage by uv radiation.
Length = 346
Score = 24.7 bits (54), Expect = 8.3
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 12/50 (24%)
Query: 43 AFPCTLCSYATKRK------TSLAS-----HYYRKHVGEDGALPPPHEPD 81
A C C Y +RK T + R+HV G P P++ D
Sbjct: 87 AMACAYC-YVPRRKGYANPITVFTNIEQITAALRRHVARQGPKPEPNQCD 135
>gnl|CDD|129843 TIGR00760, araD, L-ribulose-5-phosphate 4-epimerase. E. coli has
two genes, sgaE and sgbE (YiaS), that are very close
homologs of araD, the established L-ribulose-5-phosphate
4-epimerase of E. coli. SgbE, part of an operon for
L-xylulose metabolism, also has L-ribulose-5-phosphate
4-epimerase activity; L-xylulose-5-phosphate may be
converted into L-ribulose-5-phosphate by another product
of that operon. The homolog to this family from
Mycobacterium smegmatis is flanked by putative araB and
araA genes, consistent with it also being araD [Energy
metabolism, Sugars].
Length = 231
Score = 24.4 bits (53), Expect = 9.4
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 37 ECGKLPAFPCTLCSYATK-RKTSLASHYYRKH 67
E + F L ++T L HY RKH
Sbjct: 192 EVAYMALFSRQLNPQLPPMQQTLLDKHYLRKH 223
>gnl|CDD|233808 TIGR02277, PaaX_trns_reg, phenylacetic acid degradation operon
negative regulatory protein PaaX. This transcriptional
regulator is always found in association with operons
believed to be involved in the degradation of
phenylacetic acid. The gene product has been shown to
bind to the promoter sites and repress their
transcription [Regulatory functions, DNA interactions].
Length = 280
Score = 24.4 bits (53), Expect = 9.5
Identities = 8/20 (40%), Positives = 9/20 (45%)
Query: 62 HYYRKHVGEDGALPPPHEPD 81
H YR+ V D LP P
Sbjct: 211 HEYRRVVLRDPLLPEELLPA 230
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 0.136 0.444
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,250,621
Number of extensions: 295812
Number of successful extensions: 293
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 39
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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: 53 (24.3 bits)