RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11588
(459 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 34.7 bits (80), Expect = 0.003
Identities = 15/26 (57%), Positives = 17/26 (65%)
Query: 335 NMKVHMRIHTGEKKYVCETCGASFVQ 360
N++ HMR HTGEK Y C CG SF
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.5 bits (64), Expect = 0.46
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 420 LKEHMAVHTTDRPFVCDMCPSAFK 443
L+ HM HT ++P+ C +C +F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 26.2 bits (58), Expect = 3.4
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 281 SHLDIHSGEKDHCCHICKKVFLR 303
H+ H+GEK + C +C K F
Sbjct: 4 RHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 33.7 bits (77), Expect = 0.053
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 349 YVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIRYAHTI 401
YVC C F SL QH + +T + VC CG ++N S H+ H I
Sbjct: 74 YVCPLCLMPFSSSVSLKQH-IRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125
Score = 33.3 bits (76), Expect = 0.091
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 377 VCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHM 424
VC C + + SL+ HIRY +C VCGKEF+ +H+
Sbjct: 75 VCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTDSTLDHV 119
>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 30.0 bits (68), Expect = 0.59
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 11/48 (22%)
Query: 312 KAVHEKVRD-HQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASF 358
K + + R H C CG+ RI TG + C CGA F
Sbjct: 26 KEIEAQQRAKHVCPFCGR--------TTVKRIATG--IWKCRKCGAKF 63
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 31.3 bits (72), Expect = 0.79
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 18/55 (32%)
Query: 377 VCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFK---------MKKRLKE 422
+C CG TY H+++ + + CDVCG+E ++KRL+
Sbjct: 129 ICPACGRTY--------HVKFNPP-KVEGKCDVCGEELIQRADDNEETVRKRLEV 174
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.2 bits (70), Expect = 1.3
Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 3/83 (3%)
Query: 321 HQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASFVQWGSLN---QHNLVHTAVNVV 377
C C +F+ + ++ H+R HTGEK C G L H + +
Sbjct: 34 DSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDL 93
Query: 378 CSYCGNTYKNPKSLESHIRYAHT 400
S + S S +
Sbjct: 94 NSKSLPLSNSKASSSSLSSSSSN 116
Score = 28.5 bits (63), Expect = 8.7
Identities = 33/183 (18%), Positives = 56/183 (30%), Gaps = 18/183 (9%)
Query: 182 HSCQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHSKVLVRYVHSAVRHMKKHHKLQL 241
++C SF + L H+ + + + + +S + + +K+H L
Sbjct: 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRND--ALKRHILLHT 347
Query: 242 SIPKAHNYFRKKTVIHVNKKVNYKCPDCSAILLSYGGFTSHLDIHSGEKDHCC--HICKK 299
SI A + N +K + C +
Sbjct: 348 SISPAKEKLLNSSSKFSPLLNNEP-----------PQSLQQYKDLKNDKKSETLSNSCIR 396
Query: 300 VFLRYRNLVCHIKAVHEKVRDHQC--SVCGKAFADITNMKVHMRIHTGEKKYVCETCGAS 357
F R NL HI H R + C C K+F N+ H +IHT +C +
Sbjct: 397 NFKRDSNLSLHII-THLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSF 455
Query: 358 FVQ 360
Sbjct: 456 RRD 458
>gnl|CDD|181283 PRK08197, PRK08197, threonine synthase; Validated.
Length = 394
Score = 30.4 bits (69), Expect = 2.3
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 15/49 (30%)
Query: 184 CQKCEESFDNCNNLWSHMFIKHENSDFVCNLCPSHSKVLVRYVHSAVRH 232
C KC E++D +D V NLC +LVRY AV+
Sbjct: 10 CSKCGETYD---------------ADQVHNLCKCGKPLLVRYDLEAVKQ 43
>gnl|CDD|145933 pfam03048, Herpes_UL92, UL92 family. Members of this family, found
in several herpesviruses, include EBV BDLF4, HCMV UL92,
HHV8 31, HSV6 U63. Their function is unknown. The N
terminus of this protein contains 6 conserved cysteines
and histidines that might form a zinc binding domain (A
Bateman pers. obs.).
Length = 192
Score = 29.5 bits (67), Expect = 2.5
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 349 YVCETCGASFVQWGSLNQHNLVHTAVNVVCSYCGNTY 385
YVC C V G LV+T VVC+ G Y
Sbjct: 21 YVCVRCDRYHVCDGGSECV-LVNTGEGVVCALTGLCY 56
>gnl|CDD|235183 PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed.
Length = 90
Score = 28.0 bits (63), Expect = 2.5
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 11/49 (22%)
Query: 311 IKAVHEKVR-DHQCSVCGKAFADITNMKVHMRIHTGEKKYVCETCGASF 358
+ + EK+R H C VCG+ KV R+ TG + C CGA F
Sbjct: 26 VADIEEKMRAKHVCPVCGR-------PKVK-RVGTG--IWECRKCGAKF 64
>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 = 28.7 bits (65), Expect = 3.0
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 406 ICDVCGKEFKMKKRLKEHMAVH 427
IC GK+FK LK H+ H
Sbjct: 72 ICLEDGKKFKT---LKRHLRTH 90
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.3 bits (58), Expect = 3.1
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 321 HQCSVCGKAFADITNMKVHMRIH 343
++C CGK F + ++ HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.7 bits (54), Expect = 9.7
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 407 CDVCGKEFKMKKRLKEHMAVH 427
C CGK FK K L+EHM H
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
>gnl|CDD|237659 PRK14287, PRK14287, chaperone protein DnaJ; Provisional.
Length = 371
Score = 29.6 bits (66), Expect = 3.4
Identities = 28/85 (32%), Positives = 36/85 (42%), Gaps = 22/85 (25%)
Query: 345 GEKKYVCETCGASFVQWGSLN--QHNLVHTAVNV-VCSYCGNTYKNPKSLESHIRYAHTI 401
G K C CG S G LN Q+ VN VC +C T K I
Sbjct: 152 GTKPETCSHCGGS----GQLNVEQNTPFGRVVNRRVCHHCEGTGK-------------II 194
Query: 402 RQKSICDVCGKEFKMKKRLKEHMAV 426
+QK C CG + K++KR K ++ V
Sbjct: 195 KQK--CATCGGKGKVRKRKKINVKV 217
>gnl|CDD|130625 TIGR01562, FdhE, formate dehydrogenase accessory protein FdhE.
This model describes an accessory protein required for
the assembly of formate dehydrogenase of certain
proteobacteria although not present in the final
complex. The exact nature of the function of FdhE in the
assembly of the complex is unknown, but considering the
presence of selenocysteine, molybdopterin, iron-sulfur
clusters and cytochrome b556, it is likely to have
something to do with the insertion of cofactors. The
only sequence scoring between trusted and noise is that
from Aquifex aeolicus, which shows certain structural
differences from the proteobacterial forms in the
alignment. However it is notable that A. aeolicus also
has a sequence scoring above trusted to the alpha
subunit of formate dehydrogenase (TIGR01553).
Length = 305
Score = 29.5 bits (66), Expect = 3.9
Identities = 24/108 (22%), Positives = 35/108 (32%), Gaps = 24/108 (22%)
Query: 341 RIHTGEKKYVCETCG----ASFVQWGSLNQHNLVHTAVNVVCSYCGNTYKNPKSLESHIR 396
+ T E + +C CG AS V+ G + CS C +
Sbjct: 177 VVETRESRTLCPACGSPPVASMVRQGGKET-----GLRYLSCSLCATEW----------- 220
Query: 397 YAHTIRQKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMCPSAFKL 444
H +R K C C + + EH A + CD C K+
Sbjct: 221 --HYVRVK--CSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKI 264
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 29.6 bits (67), Expect = 4.0
Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 16/75 (21%)
Query: 379 SYCGNTYKNPKSLESHIRYAHTIRQKSICDVCGKEFKMKKRLKEHMAVHTTDRPFVCDMC 438
SY NP+ + + C VCG+E + + E +C C
Sbjct: 373 SYLELAALNPRDSKEGSKGTR------ECKVCGREEPIAEDEDEG----------LCPTC 416
Query: 439 PSAFKLKKHLQQHYK 453
++L K L +
Sbjct: 417 ERLYELGKELLKDDS 431
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 29.6 bits (66), Expect = 4.0
Identities = 35/219 (15%), Positives = 56/219 (25%), Gaps = 54/219 (24%)
Query: 142 ELCVLSKYCIKHQDCSKAMSTPAPSSESVCIKHSNLIPKCHSCQKCEESFDNCNNLWSHM 201
+ + K ++ + E V + +L+ KC + L H
Sbjct: 117 PADITDRRQWKGREEKVGIFY---EGEDVRDEMEDLLSFKCPKSKCHRRCGSLKELKKHY 173
Query: 202 FIKHENSDFVCNLCPSHSKVLVRYVHSAVRHMKKHHKLQLSIPKAHNYFRKKTVIHVNKK 261
+H +C+ C + K FR T+
Sbjct: 174 KAQHGF--VLCSECIGNKKDF---------------------WNEIRLFRSSTLRDHKNG 210
Query: 262 VNY--------KCPDCSAILLSYGGFTSHLDIHSGEKDHCCHICKKV-------FLRYRN 306
C C L H + CHIC V F Y +
Sbjct: 211 GLEEEGFKGHPLCIFCKIYFYD----DDELRRHCRLRHEACHICDMVGPIRYQYFKSYED 266
Query: 307 LVCHIKAVH-----EKVRDHQCSVCGKAFADITNMKVHM 340
L H + H + R +C V F T + H+
Sbjct: 267 LEAHFRNAHYCCTFQTCRVGKCYV----FPYHTELLEHL 301
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 28.7 bits (64), Expect = 4.9
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 18/56 (32%)
Query: 377 VCSYCGNTYKNPKSLESHIRYAHTIRQKSICDVCG---------KEFKMKKRLKEH 423
+C C N + Y ++K ICDVC KE +K RL+E+
Sbjct: 124 ICKSCNNIFN---------IYTLPTKEKGICDVCKGDLYQRKDDKEESLKTRLQEY 170
>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 = 6.3
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 322 QCSVCGKAFADITNMKVHMRIH 343
+C CGK+F+ +N+K H+R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 28.9 bits (64), Expect = 8.0
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 5 CCKCIAKYTSRSHLSLHLLSHSSDADEIKQELSCEQC 41
C CI K R+H S L+ +DE ++ L C+ C
Sbjct: 492 CVFCITK---RAHYSFAKLAKPGSSDEAEERLVCDTC 525
>gnl|CDD|234663 PRK00142, PRK00142, putative rhodanese-related sulfurtransferase;
Provisional.
Length = 314
Score = 28.3 bits (64), Expect = 8.3
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 169 SVCIKHSNLIPKCHSCQKCEESFDNCNN 196
+V I I CH C + + NC N
Sbjct: 232 AVPINDEVPIGHCHQCGTPCDRYVNCAN 259
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
0.326 0.135 0.454
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,576,153
Number of extensions: 1935954
Number of successful extensions: 2776
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2758
Number of HSP's successfully gapped: 95
Length of query: 459
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 359
Effective length of database: 6,502,202
Effective search space: 2334290518
Effective search space used: 2334290518
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 61 (27.3 bits)