RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11590
(555 letters)
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 33.9 bits (78), Expect = 0.28
Identities = 23/103 (22%), Positives = 36/103 (34%), Gaps = 39/103 (37%)
Query: 386 CPHCPSLLKTFWTLKEHFNIHTSEKKY-----VCELCGAYFIHKSSLV-------AHTTT 433
C C L+E F+ + ++Y C CG F +++ +T+
Sbjct: 104 CEDC---------LEEIFD--PNSRRYLYPFINCTNCGPRF----TIIEALPYDRENTSM 148
Query: 434 HSNVKFK-CDFCEKVYSHRNRLRYHISTVHENKWKSAACDICG 475
F C FC+K Y R+H + AC CG
Sbjct: 149 ---ADFPLCPFCDKEYKDPLNRRFHAQPI--------ACPKCG 180
Score = 32.7 bits (75), Expect = 0.56
Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 10/58 (17%)
Query: 471 CDICGRVFLDSKNMKKHAAVHSTERPFVCKLCGIAYKWRKNLVRHQKNCKASAKCSLM 528
C C + + D N + HA +P C CG LV H A A ++
Sbjct: 154 CPFCDKEYKDPLNRRFHA------QPIACPKCGPHL----FLVNHDGEAIAEANEAIR 201
>gnl|CDD|234198 TIGR03400, 18S_RNA_Rcl1p, 18S rRNA biogenesis protein RCL1.
Members of this strictly eukaryotic protein family are
not RNA 3'-phosphate cyclase (6.5.1.4), but rather a
homolog with a distinct function, found in the nucleolus
and required for ribosomal RNA processing. Homo sapiens
has both a member of this RCL (RNA terminal phosphate
cyclase like) family and EC 6.5.1.4, while Saccharomyces
has a member of this family only.
Length = 360
Score = 33.0 bits (76), Expect = 0.37
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 475 GRVFLDSKNMKKHAAVHSTERPFVCKLCGIAY 506
G V L +K+ +H TER V ++ G+AY
Sbjct: 158 GEVELRCPVIKQLKTIHLTERGRVKRIRGVAY 189
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 33.2 bits (75), Expect = 0.37
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 439 FKCDF--CEKVYSHRNRLRYHISTVHENKWKSAACDICGRVFLDSKNMKKHAAVHSTERP 496
+KC C K Y ++N L+YH+ H + ++ + +K + ++P
Sbjct: 350 YKCPVEGCNKKYKNQNGLKYHMLHGH-----------QNQKLHENPSPEKMNIFSAKDKP 398
Query: 497 FVCKLCGIAYKWRKNLVRHQKN 518
+ C++C YK L H+K+
Sbjct: 399 YRCEVCDKRYKNLNGLKYHRKH 420
Score = 32.0 bits (72), Expect = 0.74
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 221 SHKYSHDDRKFSCS--HCGNSYKNPIFLKRHFRESH---LKHSKSNPEQYAVKSLQDIMY 275
D + + C C YKN LK H H H +PE+ + S +D Y
Sbjct: 340 RMLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPY 399
Query: 276 WCNVCSQR 283
C VC +R
Sbjct: 400 RCEVCDKR 407
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 32.7 bits (74), Expect = 0.59
Identities = 32/130 (24%), Positives = 46/130 (35%), Gaps = 23/130 (17%)
Query: 148 MNNITQYKCPD--CPAILQTFKNLKCHLDIHSG----------EKDFSCHINSNLSEHIR 195
M ++ +KCP C + K LK H G +KDF I S +R
Sbjct: 146 MEDLLSFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLR 205
Query: 196 MHHT---EEKKY----ICEVCGTSFLTWSSLNSHKYSHDDRKFSCSHCGNS----YKNPI 244
H EE+ + +C C F L H + C G +K+
Sbjct: 206 DHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYE 265
Query: 245 FLKRHFRESH 254
L+ HFR +H
Sbjct: 266 DLEAHFRNAH 275
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 28.1 bits (63), Expect = 0.86
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 399 LKEHFNIHTSEKKYVCELCGAYF 421
L+ H HT EK Y C +CG F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSF 24
Score = 26.6 bits (59), Expect = 2.8
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 189 NLSEHIRMHHTEEKKYICEVCGTSFLT 215
NL H+R H EK Y C VCG SF +
Sbjct: 1 NLRRHMRTHT-GEKPYKCPVCGKSFSS 26
Score = 25.8 bits (57), Expect = 5.9
Identities = 8/25 (32%), Positives = 17/25 (68%)
Query: 483 NMKKHAAVHSTERPFVCKLCGIAYK 507
N+++H H+ E+P+ C +CG ++
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
>gnl|CDD|238596 cd01191, INT_phiCTX_C, phiCTX phage and phage-related integrases,
site-specific recombinases, DNA breaking-rejoining
enzymes, C-terminal catalytic domain. This CD includes
various phage and bacterial integrases, including those
similar to phage integrases: Bordetella and Pseudomonas
phiCTX; E. coli Rac, Qin, and Shiga toxin 2 933W; and
Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a
putative pore-forming cytotoxin integrase from Vibrio
parahaemolyticus O3:K6.
Length = 196
Score = 31.3 bits (71), Expect = 0.87
Identities = 18/77 (23%), Positives = 24/77 (31%), Gaps = 4/77 (5%)
Query: 448 YSHRNRLRYHISTVHENKWKSAACDICGRVFLDSK-NMKKHAAVHSTERPFV--CKLCGI 504
R H TV E ++ VF D K AV S + + K GI
Sbjct: 91 AKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGI 150
Query: 505 AYKWRKNLVRHQKNCKA 521
Y+ +RH
Sbjct: 151 RYR-NPYQMRHTFASWM 166
>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase,
Saccharomyces cerevisiae Pus3 like. This group consists
of eukaryotic pseudouridine synthases similar to S.
cerevisiae Pus3p, mouse Pus3p and, human PUS2.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse
Pus3p has been shown to makes psi38 and, possibly also
psi 39, in tRNAs. Psi38 and psi39 are highly conserved
in tRNAs from eubacteria, archea and eukarya.
Length = 256
Score = 31.1 bits (71), Expect = 1.2
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 166 FKNLKCHLDIHSGEKDFSCHINSNLSEHIRMHHTEEKKYICEVCGTSFL 214
F+N C +D+ + ++ + S E + H + Y EV G++FL
Sbjct: 155 FRNF-CKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFL 202
>gnl|CDD|223425 COG0348, NapH, Polyferredoxin [Energy production and conversion].
Length = 386
Score = 30.9 bits (70), Expect = 2.0
Identities = 15/82 (18%), Positives = 24/82 (29%), Gaps = 7/82 (8%)
Query: 268 KSLQDIMYWCNVCSQRCYLSATCSIHRPSNCKDQYKMSVSISNECDQHMECHTCNEC-DS 326
KSL + Y RC + I + +EC C C D+
Sbjct: 201 KSLLKVNYDDKRGCPRCKRCKKVCPEPIPLWVQVCPAGIDIRDG----LECIGCGRCIDA 256
Query: 327 KHND--CQSLWDHVFSEHKNML 346
+D +L + + M
Sbjct: 257 CDDDMLKFNLPFGLIAYSTFMA 278
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 30.6 bits (70), Expect = 2.2
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 9/71 (12%)
Query: 356 NKISKVAEKQYWKDVEEKCRIIVEDTMRYQCPHCPSLLKTFWTLKEHFNIHTSEKKYVCE 415
N+I ++ Y D + + QC +C L K+ K +CE
Sbjct: 11 NQIFEIDNDSYMYDTKYSWNTQKYKHLWVQCENCYGLN-----YKKFL----KSKMNICE 61
Query: 416 LCGAYFIHKSS 426
CG + SS
Sbjct: 62 QCGYHLKMSSS 72
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 30.6 bits (70), Expect = 2.7
Identities = 18/73 (24%), Positives = 20/73 (27%), Gaps = 3/73 (4%)
Query: 383 RYQCPHCPSLLKTFWTLKEHFNIHTSEKKYVCELCGAYFIHKSSLVAHTTTHSNVKFKCD 442
R +CP C TF+ HT E Y C CG K K D
Sbjct: 626 RRKCPSCGKE--TFYRRCPFCGTHT-EPVYRCPRCGIEVEEDECEKCGREPTPYSKRKID 682
Query: 443 FCEKVYSHRNRLR 455
E L
Sbjct: 683 LKELYDRALENLG 695
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 30.1 bits (68), Expect = 3.3
Identities = 19/81 (23%), Positives = 27/81 (33%), Gaps = 12/81 (14%)
Query: 414 CELCGAYFIHKSSLVAHTTTHSNVKFK-CDFCEKVYSHRNRLRYHISTVHENKWKSAACD 472
C CG F +L S F C C K Y R+H + AC
Sbjct: 93 CTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPI--------ACP 144
Query: 473 ICG--RVFL-DSKNMKKHAAV 490
CG F+ + ++ A+
Sbjct: 145 RCGPQLNFVSRGGHAEQDDAL 165
Score = 29.7 bits (67), Expect = 4.6
Identities = 10/53 (18%), Positives = 18/53 (33%), Gaps = 10/53 (18%)
Query: 471 CDICGRVFLDSKNMKKHAAVHSTERPFVCKLCGIAYKWRKNLVRHQKNCKASA 523
C C + + D + + HA +P C CG + V + +
Sbjct: 121 CPDCAKEYKDPLDRRFHA------QPIACPRCGPQLNF----VSRGGHAEQDD 163
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 28.7 bits (64), Expect = 3.4
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 384 YQCPHCPSLLKTFWTLKEHFNIHTSEKKYVCELCGAYFIHKSSLVAHTTTHSNV 437
Y CP C + +LK+H I +E VC +CG F + S + H N+
Sbjct: 74 YVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.3 bits (58), Expect = 4.0
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 204 YICEVCGTSFLTWSSLNSHKYSH 226
Y C CG F + S+L H +H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|226826 COG4391, COG4391, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 62
Score = 27.1 bits (60), Expect = 4.7
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 160 PAILQTFKNLKCHLDIHSGEKDFSCHINSNLSEHIRMH--HTEEKKYICEVCGTSF 213
I+ F+N H I G+ C ++H R+ +E + +C C T +
Sbjct: 3 GMIIPHFQNDGGHETIEIGDLPLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRY 58
>gnl|CDD|224693 COG1779, COG1779, C4-type Zn-finger protein [General function
prediction only].
Length = 201
Score = 28.8 bits (65), Expect = 5.9
Identities = 14/43 (32%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 378 VEDTMRYQCPHCPSLLKTFWTLKE--HFNIHTSEKKYVCELCG 418
E R CP C LK L + +F VCE CG
Sbjct: 9 EEFETRIDCPVCGGTLKAHMYLYDIPYFG-EVLISTGVCERCG 50
>gnl|CDD|182045 PRK09718, PRK09718, hypothetical protein; Validated.
Length = 512
Score = 28.9 bits (64), Expect = 7.6
Identities = 50/196 (25%), Positives = 75/196 (38%), Gaps = 40/196 (20%)
Query: 6 CEFHFDV---ESCAVSRLQDITFPCEE-----------------CKEL--CVLSKYCIKH 43
C F DV S S LQ +TF C+E C+ L + K ++
Sbjct: 100 CHFKGDVISKVSFLSSNLQHVTFECKEIGDCNFTTAIVDNVIFKCRRLHNVIFIKASGEY 159
Query: 44 KDCSKAMSTPAPSSESVCTEHSNLFPKCHSCQKCEESFDNCNNLWSHM----FIKHENSD 99
D SK + S+S T HSN CQ +FDNC SH F+ +
Sbjct: 160 VDFSKNILDTVDFSQSQLT-HSNF----RECQIRNSNFDNCYLYASHFTRAEFLSAKEIS 214
Query: 100 FV-CNLCPPDSKIMIKYAHLLVRHMKQCHTMQVHIPAVYKNFRSVTSFT--MNNITQY-- 154
F+ NL + +M + + + K C T Q+ + Y + +NNI +
Sbjct: 215 FIKSNL----TAVMFDHVRISTGNFKDCITEQLELTIDYSDIFGNEDLDGYINNIIKMID 270
Query: 155 KCPDCPAILQTFKNLK 170
PD IL++ +K
Sbjct: 271 TLPDNAMILKSVLAVK 286
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 26.2 bits (57), Expect = 7.7
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 412 YVCELCGAYFIHKSSLVAHTTTHSNVKFKCDFCEKV 447
Y C +CG +I + S++ H H N K C+++
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH-NTNLKLSNCKRI 40
>gnl|CDD|217312 pfam03000, NPH3, NPH3 family. Phototropism of Arabidopsis thaliana
seedlings in response to a blue light source is
initiated by nonphototropic hypocotyl 1 (NPH1), a
light-activated serine-threonine protein kinase.
Mutations in NPH3 disrupt early signaling occurring
downstream of the NPH1 photoreceptor. The NPH3 gene
encodes a NPH1-interacting protein. NPH3 is a member of
a large protein family, apparently specific to higher
plants, and may function as an adapter or scaffold
protein to bring together the enzymatic components of a
NPH1-activated phosphorelay.
Length = 249
Score = 28.7 bits (65), Expect = 7.9
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 399 LKEHFNIHTSEKKYVCEL 416
LK H N+ SEKK +C L
Sbjct: 221 LKAHPNLSESEKKRLCRL 238
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 0.131 0.438
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,400,545
Number of extensions: 2220756
Number of successful extensions: 2966
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2949
Number of HSP's successfully gapped: 79
Length of query: 555
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 453
Effective length of database: 6,413,494
Effective search space: 2905312782
Effective search space used: 2905312782
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: 40 (21.5 bits)
S2: 62 (27.7 bits)