RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy677
(451 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 42.8 bits (101), Expect = 4e-06
Identities = 15/26 (57%), Positives = 20/26 (76%)
Query: 360 HLTTHIRTHTGEKPFSCDVCGRKFAR 385
+L H+RTHTGEKP+ C VCG+ F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 42.4 bits (100), Expect = 6e-06
Identities = 14/26 (53%), Positives = 20/26 (76%)
Query: 332 ELTRHIRIHTGQKPFQCRICMRSFSR 357
L RH+R HTG+KP++C +C +SFS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 40.9 bits (95), Expect = 0.001
Identities = 26/98 (26%), Positives = 40/98 (40%), Gaps = 18/98 (18%)
Query: 301 KYPNRPSKTPVHERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCR----ICMRSFS 356
P+R K +PY CPVE C++++ + L H +H Q M FS
Sbjct: 336 DTPSRMLKV-KDGKPYKCPVEGCNKKYKNQNGLKYH-MLHGHQNQKLHENPSPEKMNIFS 393
Query: 357 RSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAK 394
D KP+ C+VC +++ + K H K
Sbjct: 394 AKD------------KPYRCEVCDKRYKNLNGLKYHRK 419
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 36.8 bits (85), Expect = 0.005
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRH 392
P+ C +C+ FS S L HIR K C VCG++F +D H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDH 118
Score = 35.2 bits (81), Expect = 0.015
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 315 PYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHI 365
PY CP+ C FS S L +HIR K C +C + F +D H+
Sbjct: 73 PYVCPL--CLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDHV 119
>gnl|CDD|236641 PRK10019, PRK10019, nickel/cobalt efflux protein RcnA; Provisional.
Length = 279
Score = 38.2 bits (89), Expect = 0.006
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 413 QQQAQQQQQQNHVHQQQQHHHHHHHHPNMEGMP 445
+ +H H + HH H HHH + G
Sbjct: 118 ENMHHHDHDHDHDHDHEHHHDHGHHHHHEHGAT 150
Score = 34.8 bits (80), Expect = 0.067
Identities = 7/27 (25%), Positives = 10/27 (37%)
Query: 412 SQQQAQQQQQQNHVHQQQQHHHHHHHH 438
+ + +H H H HHH H
Sbjct: 113 ERNWLENMHHHDHDHDHDHDHEHHHDH 139
Score = 31.3 bits (71), Expect = 0.96
Identities = 6/23 (26%), Positives = 8/23 (34%)
Query: 417 QQQQQQNHVHQQQQHHHHHHHHP 439
+ + H H H H H H
Sbjct: 114 RNWLENMHHHDHDHDHDHDHEHH 136
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 37.8 bits (87), Expect = 0.011
Identities = 22/50 (44%), Positives = 27/50 (54%)
Query: 343 QKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRH 392
+P C C SFSR +HLT HIR+HTGEKP C G + S +
Sbjct: 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELS 80
Score = 33.1 bits (75), Expect = 0.33
Identities = 31/68 (45%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 312 HERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMR--SFSRSDHLTTHIRTHT 369
RP +CP NC FSR + LTRHIR HTG+KP QC SFSR L+ H+RTH
Sbjct: 30 APRPDSCP--NCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHH 87
Query: 370 GEKPFSCD 377
Sbjct: 88 NNPSDLNS 95
Score = 31.2 bits (70), Expect = 1.1
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 314 RPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRS 358
+P++CP C + FSR+D L RHI +HT P + ++ S S
Sbjct: 320 KPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFS 364
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 32.1 bits (73), Expect = 0.027
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 346 FQCRICMRSFSRSDHLTTHIRTH 368
++C C + F L H+RTH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 29.7 bits (67), Expect = 0.16
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 316 YACPVENCDRRFSRSDELTRHIRIH 340
Y CP C + F L H+R H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 29.7 bits (67), Expect = 0.20
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 374 FSCDVCGRKFARSDEKKRHAKVH 396
+ C CG+ F + H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 31.8 bits (72), Expect = 0.030
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 346 FQCRICMRSFSRSDHLTTHIRTH 368
F+C +C +SFS D L H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 28.0 bits (62), Expect = 0.70
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 316 YACPVENCDRRFSRSDELTRHIRIH 340
+ CP+ C + FS D L RH+R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
Score = 27.6 bits (61), Expect = 1.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 374 FSCDVCGRKFARSDEKKRHAKVH 396
F C +CG+ F+ D KRH + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>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 = 31.5 bits (72), Expect = 0.034
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 321 ENCDRRFSRSDELTRHIRIH 340
+C + FSR L RH+R H
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
Score = 31.2 bits (71), Expect = 0.053
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 347 QCRICMRSFSRSDHLTTHIRTH 368
+C C +SFSR +L H+RTH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.5 bits (64), Expect = 0.42
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 375 SCDVCGRKFARSDEKKRHAKVH 396
C CG+ F+R KRH + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO. This family
contains the bacterial type III secretion protein YscO,
which is approximately 150 residues long. YscO has been
shown to be required for high-level expression and
secretion of the anti-host proteins V antigen and Yops
in Yersinia pestis.
Length = 152
Score = 34.7 bits (80), Expect = 0.039
Identities = 13/78 (16%), Positives = 31/78 (39%)
Query: 360 HLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAKVHLKQRSKKESKMAVMMSQQQAQQQ 419
+R + ++ ++ R A+ L++ K + K A + Q+QA+ Q
Sbjct: 74 QQVGLLRENEASLEQQLAEAKQRLEAERQRLRQARQQLQEARKAQEKFAELARQEQAEAQ 133
Query: 420 QQQNHVHQQQQHHHHHHH 437
Q+ ++ + +Q
Sbjct: 134 AQRQYLEELEQEEFRTVS 151
>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3. The
C.elegans Notch pathway, involved in the control of
growth, differentiation and patterning in animal
development, relies on either of the receptors GLP-1 or
LIN-12. Both these receptors promote signalling by the
recruitment of LAG-3 to target promoters, where it then
acts as a transcriptional activator. LAG-3 works as a
ternary complex together with the DNA binding protein,
LAG-1.
Length = 476
Score = 34.2 bits (77), Expect = 0.14
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 398 KQRSKKESKMAVMMSQQQAQQQQQQNHVHQQ--QQHHHHHHHHPNMEGMP 445
Q + +M M Q+Q Q QQQQ HQQ QQH H G+P
Sbjct: 398 HQHAAYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQHQQPAQHGQMGYGIP 447
Score = 30.3 bits (67), Expect = 2.1
Identities = 13/39 (33%), Positives = 17/39 (43%)
Query: 395 VHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHH 433
+L+Q + + QQQAQ QQ HQQ H
Sbjct: 402 AYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQHQQPAQHG 440
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing archaeal-type
C2H2 Zn-finger [General function prediction only].
Length = 65
Score = 30.7 bits (69), Expect = 0.18
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 365 IRTHTGEKPFSCDVCGRKFARSDEKKRH---AKVHLKQRSKKESK 406
+R GE+ C CG F R + RH A L R K + K
Sbjct: 9 VRDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHGWLFGRGKPKGK 53
>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage [Cellular processes, DNA transformation].
Length = 410
Score = 33.6 bits (77), Expect = 0.23
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 225 VQAQPGIIPKQEPVYGNTNLSGCGSLVNLSDPNNPGSSYPVQLAEYN 271
+QA +IPK +YG + G + +S G+ PV+L+ Y+
Sbjct: 282 IQAGDLVIPKGTVLYGTAKIQGERLDIKISSIEYNGTILPVELSVYD 328
>gnl|CDD|221930 pfam13135, DUF3947, Protein of unknown function (DUF3947). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 80 amino acids in length.
Length = 76
Score = 30.6 bits (69), Expect = 0.23
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 414 QQAQQQQQQNHVHQQQQHHHHHHHHPNM 441
QA Q QQQ QQQ ++
Sbjct: 28 HQAMQMQQQMQPAMQQQGQQPYYPSVEY 55
>gnl|CDD|181000 PRK07492, PRK07492, adenylosuccinate lyase; Provisional.
Length = 435
Score = 33.0 bits (76), Expect = 0.29
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 196 YARVNQSLMHSPNNKYQ-WLDSPVEYSASIVQAQPGIIPKQ 235
Y+R + P K++ W + +E A QA+ G+IPK+
Sbjct: 5 YSRPEMVAIWEPETKFRIWFE--IEAHACEAQAELGVIPKE 43
>gnl|CDD|236558 PRK09545, znuA, high-affinity zinc transporter periplasmic
component; Reviewed.
Length = 311
Score = 32.7 bits (75), Expect = 0.33
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 406 KMAVMMSQQQAQQQQQQNHVHQQQQHHHHHHHHPNM 441
K +M +H ++ HHH NM
Sbjct: 110 KPLLMKGAHDDHHDDDHDHAGHEKSDEDHHHGEYNM 145
>gnl|CDD|197698 smart00396, ZnF_UBR1, Putative zinc finger in N-recognin, a
recognition component of the N-end rule pathway. Domain
is involved in recognition of N-end rule substrates in
yeast Ubr1p.
Length = 71
Score = 30.1 bits (68), Expect = 0.36
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 348 CRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKK 390
C +C F S H + T CD CG K A +++ K
Sbjct: 25 CVLCSDCFRPSCHKGHDVSLKTSRGSGICD-CGDKEAWNEDLK 66
>gnl|CDD|151765 pfam11324, DUF3126, Protein of unknown function (DUF3126). This
family of proteins with unknown function appear to be
restricted to Alphaproteobacteria.
Length = 63
Score = 29.9 bits (68), Expect = 0.39
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 33 LETEELSVGSPSTKDDSGELCQPKTELITDSPLG-LHEEEEETSLSSTISM 82
L V + K DS E+ I D +G L ++E+E S + M
Sbjct: 13 FGNPTLRVKARPKKGDSAEV------YIGDEFIGVLFKDEDEGETSYSFEM 57
>gnl|CDD|234354 TIGR03789, pdsO, proteobacterial sortase system OmpA family
protein. A newly defined histidine kinase (TIGR03785)
and response regulator (TIGR03787) gene pair occurs
exclusively in Proteobacteria, mostly of marine origin,
nearly all of which contain a subfamily 6 sortase
(TIGR03784) and its single dedicated target protein
(TIGR03788) adjacent to to the sortase. This protein
family shows up in only in those species with the
histidine kinase/response regulator gene pair, and often
adjacent to that pair. It belongs to the OmpA protein
family (pfam00691). Its function is unknown. We assign
the gene symbol pdsO, for Proteobacterial Dedicated
Sortase system OmpA family protein.
Length = 239
Score = 32.1 bits (73), Expect = 0.41
Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 397 LKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHHHHHHH 438
+ +++ +M + +Q+Q +Q + Q Q H
Sbjct: 83 QQHIAQQRQQMVAL-TQKQQALEQLEAEYQQAQVHLETLQQD 123
>gnl|CDD|177648 PHA03420, PHA03420, E4 protein; Provisional.
Length = 137
Score = 31.1 bits (70), Expect = 0.53
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 422 QNHVHQQQQHHHHHHHHPNMEGMPVVTTPL 451
H HQQ HH H + + PL
Sbjct: 55 HPHRHQQDDHHLQDRQHLPQQHLQRPHHPL 84
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 31.3 bits (71), Expect = 1.1
Identities = 13/46 (28%), Positives = 28/46 (60%)
Query: 385 RSDEKKRHAKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQ 430
R ++++ AK +QR KKE + A + Q+QA +Q++ + +++
Sbjct: 66 RQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERL 111
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.5 bits (71), Expect = 1.1
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 7/63 (11%)
Query: 176 CGALKQPSSSYSSCSGEQDVYARVNQSLMHSPNNKYQWLDSPVEYSASIVQAQPGIIPKQ 235
LK S G V Q + + KY + E S++ + A +I
Sbjct: 3311 RDVLKMSKVIVSE--GSIFV-----QRYLDTFPFKYCIISGVDELSSTFIMALSTLIMSL 3363
Query: 236 EPV 238
PV
Sbjct: 3364 VPV 3366
>gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional.
Length = 110
Score = 29.5 bits (67), Expect = 1.2
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 403 KESKMAVMMSQQQAQQQQQQNHVHQQQQ 430
+ K+ + Q Q QQQ Q+ Q Q
Sbjct: 7 RRRKLEELQKQAQEQQQAQEEQEEAQAQ 34
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 30.8 bits (69), Expect = 1.7
Identities = 24/88 (27%), Positives = 29/88 (32%), Gaps = 15/88 (17%)
Query: 318 CPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMR---------SFSRSDHLTTHIRTH 368
CP C RR EL +H + G C C+ RS L H
Sbjct: 154 CPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGG 211
Query: 369 TGEKPFS----CDVCGRKFARSDEKKRH 392
E+ F C C F DE +RH
Sbjct: 212 LEEEGFKGHPLCIFCKIYFYDDDELRRH 239
>gnl|CDD|204848 pfam12203, HDAC4_Gln, Glutamine rich N terminal domain of histone
deacetylase 4. This domain is found in eukaryotes, and
is approximately 90 amino acids in length. The family is
found in association with pfam00850. The domain forms an
alpha helix which complexes to form a tetramer. The
glutamine rich domains have many intra- and
inter-helical interactions which are thought to be
involved in reversible assembly and disassembly of
proteins. The domain is part of histone deacetylase 4
(HDAC4) which removes acetyl groups from histones. This
restores their positive charge to allow stronger DNA
binding thus restricting transcriptional activity.
Length = 92
Score = 28.8 bits (64), Expect = 1.8
Identities = 9/46 (19%), Positives = 24/46 (52%)
Query: 391 RHAKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHHHHH 436
R + L++ K++ ++ M QQ+ +++++ +Q+Q H
Sbjct: 42 RQHEAQLQEHLKQQQELLAMKRQQELLEKERKLEQQRQEQELEKHR 87
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 30.3 bits (69), Expect = 2.1
Identities = 8/44 (18%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 387 DEKKRHAKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQ 430
+ K+R K++ + E + Q+A+++Q + + Q+
Sbjct: 214 ERKERQ-----KEKEEAEKRRRQKQELQRAREEQIEEKEERLQE 252
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 30.5 bits (69), Expect = 2.2
Identities = 9/49 (18%), Positives = 14/49 (28%)
Query: 393 AKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHHHHHHHPNM 441
+ ++ E A + +QQA Q Q Q P
Sbjct: 146 PQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQ 194
Score = 29.7 bits (67), Expect = 4.3
Identities = 6/31 (19%), Positives = 9/31 (29%)
Query: 412 SQQQAQQQQQQNHVHQQQQHHHHHHHHPNME 442
QQ Q QQ+ +Q +
Sbjct: 307 LVQQPQGQQRGPQFREQLVQLSQQQREALSQ 337
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 27.4 bits (61), Expect = 2.2
Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 347 QCRICMRSFSRSDHL-TTHIRTH 368
+C+ C + SRS T+++R H
Sbjct: 20 KCKYCGKKLSRSSKGGTSNLRRH 42
>gnl|CDD|215943 pfam00487, FA_desaturase, Fatty acid desaturase.
Length = 251
Score = 30.0 bits (67), Expect = 2.4
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 421 QQNHVHQQQQHHHHHHHHPNMEGMP 445
++ + H HHHH N P
Sbjct: 51 GISYSAWRISHLRHHHHTNNPGKDP 75
>gnl|CDD|197397 cd10149, ClassIIa_HDAC_Gln-rich-N, Glutamine-rich N-terminal
helical domain of various Class IIa histone deacetylases
(HDAC4, HDAC5 and HDCA9). This superfamily consists of
a glutamine-rich N-terminal helical extension to certain
Class IIa histone deacetylases (HDACs), including HDAC4,
HDAC5 and HDAC9; it is missing in HDAC7. It is referred
to as the glutamine-rich domain, and confers
responsiveness to calcium signals and mediates
interactions with transcription factors and cofactors.
This domain is able to repress transcription
independently of the HDAC's C-terminal, zinc-dependent
catalytic domain. It has many intra- and inter-helical
interactions which are possibly involved in reversible
assembly and disassembly of proteins. HDACs regulate
diverse cellular processes through enzymatic
deacetylation of histone as well as non-histone
proteins, in particular deacetylating N(6)-acetyl-lysine
residues.
Length = 90
Score = 28.1 bits (62), Expect = 2.4
Identities = 9/50 (18%), Positives = 24/50 (48%)
Query: 387 DEKKRHAKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHHHHH 436
+ R + L++ K++ +M + QQ+ ++Q++ +Q+Q
Sbjct: 36 ENLTRQHEAQLQEHIKQQQEMLAIKQQQELLEKQRKLEQQRQEQELEKQR 85
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 29.3 bits (66), Expect = 3.0
Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 399 QRSKKESK-MAVMMSQQQ-AQQQQQQNHVHQQQQHHHHHH 436
+RS+ +K +A ++ + QQQQ+Q+ + Q+ HH
Sbjct: 147 ERSQHANKRLARLLIAWKLEQQQQEQSAALKSQRRMFHHQ 186
>gnl|CDD|215173 PLN02304, PLN02304, probable pectinesterase.
Length = 379
Score = 29.8 bits (67), Expect = 3.3
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 424 HVHQQQQHHHHHHHHPN 440
H HHHHHH HP+
Sbjct: 35 HSIHHHSHHHHHHKHPD 51
>gnl|CDD|235045 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
Length = 310
Score = 29.5 bits (67), Expect = 3.4
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 10/58 (17%)
Query: 243 NLSGCGSLV--NLSDPNNPGSSYPVQLAEYNPSTSKGHEILSQV--YQQSPLPLKLVP 296
S LV NLS PN PG Q+A Y+ T++ +IL +V Y PL +KL P
Sbjct: 115 QASDFNGLVELNLSCPNVPGKP---QIA-YDFETTE--QILEEVFTYFTKPLGVKLPP 166
>gnl|CDD|236005 PRK07376, PRK07376, NAD(P)H-quinone oxidoreductase subunit F;
Validated.
Length = 673
Score = 30.0 bits (68), Expect = 3.5
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 416 AQQQQQQNHVHQQQQHHHHHHHHPNMEGMPVVTTPL 451
A + H ++ HHHH E +T PL
Sbjct: 472 AADAPGHHEGHHEEHGEHHHHSGSPHESPWTMTLPL 507
>gnl|CDD|237323 PRK13263, ureE, urease accessory protein UreE; Provisional.
Length = 206
Score = 29.0 bits (65), Expect = 3.8
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 422 QNHVHQQQQHHHHHHHH 438
+HVH H HHHHH
Sbjct: 189 HDHVHGPGCGHGHHHHH 205
>gnl|CDD|204935 pfam12474, PKK, Polo kinase kinase. This domain family is found in
eukaryotes, and is approximately 140 amino acids in
length. The family is found in association with
pfam00069. Polo-like kinase 1 (Plx1) is essential during
mitosis for the activation of Cdc25C, for spindle
assembly, and for cyclin B degradation. This family is
Polo kinase kinase (PKK) which phosphorylates Polo
kinase and Polo-like kinase to activate them. PKK is a
serine/threonine kinase.
Length = 142
Score = 28.4 bits (64), Expect = 4.0
Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 385 RSDEKKRHAKV--HLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHH 433
R+++K R LK K+ + + + Q Q++++ ++Q+ H
Sbjct: 58 RAEQKTRLKMFKESLKIEKKELKQEVEKLPRFQEQEKKRMKAEKEEQEQKH 108
>gnl|CDD|218163 pfam04592, SelP_N, Selenoprotein P, N terminal region. SelP is the
only known eukaryotic selenoprotein that contains
multiple selenocysteine (Sec) residues, and accounts for
more than 50% of the selenium content of rat and human
plasma. It is thought to be glycosylated. SelP may have
antioxidant properties. It can attach to epithelial
cells, and may protect vascular endothelial cells
against peroxynitrite toxicity. The high selenium
content of SelP suggests that it may be involved in
selenium intercellular transport or storage. The
promoter structure of bovine SelP suggest that it may be
involved in countering heavy metal intoxication, and may
also have a developmental function. The N-terminal
region of SelP can exist independently of the C terminal
region. Zebrafish selenoprotein Pb lacks the C terminal
Sec-rich region, and a protein encoded by the rat SelP
gene and lacking this region has also been reported.
N-terminal region contains a conserved SecxxCys motif,
which is similar to the CysxxCys found in thioredoxins.
It is speculated that the N terminal region may adopt a
thioredoxin fold and catalyze redox reactions. The
N-terminal region also contains a His-rich region, which
is thought to mediate heparin binding. Binding to
heparan proteoglycans could account for the membrane
binding properties of SelP. The function of the
bacterial members of this family is uncharcterised.
Length = 238
Score = 28.7 bits (64), Expect = 5.0
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 422 QNHVHQQQQHHHHHHHHP 439
+ HH H HHHP
Sbjct: 191 HHEHQGHAHHHPHGHHHP 208
Score = 28.3 bits (63), Expect = 6.5
Identities = 6/21 (28%), Positives = 8/21 (38%)
Query: 420 QQQNHVHQQQQHHHHHHHHPN 440
++ H H HHH N
Sbjct: 191 HHEHQGHAHHHPHGHHHPGSN 211
>gnl|CDD|218259 pfam04775, Bile_Hydr_Trans, Acyl-CoA thioester hydrolase/BAAT
N-terminal region. This family consists of the amino
termini of acyl-CoA thioester hydrolase and bile
acid-CoA:amino acid N-acetyltransferase (BAAT). This
region is not thought to contain the active site of
either enzyme. Thioesterase isoforms have been
identified in peroxisomes, cytoplasm and mitochondria,
where they are thought to have distinct functions in
lipid metabolism. For example, in peroxisomes, the
hydrolase acts on bile-CoA esters.
Length = 126
Score = 28.0 bits (63), Expect = 5.0
Identities = 11/43 (25%), Positives = 14/43 (32%)
Query: 294 LVPVKPRKYPNRPSKTPVHERPYACPVENCDRRFSRSDELTRH 336
+ P + R K V PY +E S L RH
Sbjct: 70 MRPEPGGRPGLRLRKRDVVPTPYTVELEVYSGHELASATLERH 112
>gnl|CDD|238501 cd01019, ZnuA, Zinc binding protein ZnuA. These proteins have been
shown to function as initial receptors in the ABC uptake
of Zn2+. They belong to the TroA superfamily of
periplasmic metal binding proteins that share a distinct
fold and ligand binding mechanism. They are comprised
of two globular subdomains connected by a single helix
and bind their specific ligands in the cleft between
these domains. A typical TroA protein is comprised of
two globular subdomains connected by a single helix and
can bind the metal ion in the cleft between these
domains. In addition, these proteins sometimes have a
low complexity region containing a metal-binding
histidine-rich motif (repetitive HDH sequence).
Length = 286
Score = 28.9 bits (65), Expect = 5.0
Identities = 4/18 (22%), Positives = 6/18 (33%)
Query: 424 HVHQQQQHHHHHHHHPNM 441
H H +H H +
Sbjct: 104 HEHAHGEHDGHEEGGLDP 121
>gnl|CDD|237322 PRK13261, ureE, urease accessory protein UreE; Provisional.
Length = 159
Score = 28.4 bits (64), Expect = 5.6
Identities = 5/15 (33%), Positives = 6/15 (40%)
Query: 425 VHQQQQHHHHHHHHP 439
+HH H H H
Sbjct: 144 YGGAFRHHGHSHDHS 158
>gnl|CDD|206084 pfam13913, zf-C2HC_2, zinc-finger of a C2HC-type. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 25
Score = 25.3 bits (56), Expect = 6.3
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 375 SCDVCGRKFARSDEKKRHAKV 395
C +CGRKFA D +H KV
Sbjct: 4 PCPICGRKFA-PDRLAKHEKV 23
>gnl|CDD|183722 PRK12750, cpxP, periplasmic repressor CpxP; Reviewed.
Length = 170
Score = 28.3 bits (63), Expect = 6.5
Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 391 RHAKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQ---QQHHHHHHHHPN 440
+ + +K K+ ++++ +Q+A+ Q+ Q Q+ + H H N
Sbjct: 118 KQVERRVKMLEKRHQMLSILTPEQKAKFQELQQERMQECQDKMHKRMKKHASN 170
>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 = 29.0 bits (65), Expect = 7.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 348 CRICMRSFSRSDHLTTHIRT 367
C +CM FS D L H RT
Sbjct: 76 CNVCMAEFSSMDQLAEHQRT 95
>gnl|CDD|217089 pfam02535, Zip, ZIP Zinc transporter. The ZIP family consists of
zinc transport proteins and many putative metal
transporters. The main contribution to this family is
from the Arabidopsis thaliana ZIP protein family these
proteins are responsible for zinc uptake in the plant.
Also found within this family are C. elegans proteins of
unknown function which are annotated as being similar to
human growth arrest inducible gene product, although
this protein in not found within this family.
Length = 314
Score = 28.5 bits (64), Expect = 7.6
Identities = 10/50 (20%), Positives = 14/50 (28%)
Query: 394 KVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQQHHHHHHHHPNMEG 443
+ H + + N VH + HHHHH E
Sbjct: 104 RGHSHGHDHGHDGEHSHTVPDEESGAVESNVVHHEHGEGPHHHHHEGHEK 153
>gnl|CDD|238500 cd01018, ZntC, Metal binding protein ZntC. These proteins are
predicted to function as initial receptors in ABC
transport of metal ions. They belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and bind their specific ligands in
the cleft between these domains. In addition, many of
these proteins possess a metal-binding histidine-rich
motif (repetitive HDH sequence).
Length = 266
Score = 28.5 bits (64), Expect = 7.9
Identities = 10/35 (28%), Positives = 13/35 (37%)
Query: 405 SKMAVMMSQQQAQQQQQQNHVHQQQQHHHHHHHHP 439
KM V+ + +H H H HHHH
Sbjct: 75 PKMQVVNMSKGITLIPMADHHHHHHGEHEHHHHGN 109
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 28.7 bits (65), Expect = 8.0
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 410 MMSQQQAQQQQQQNHVHQQQQ 430
M QQ QQ Q +Q
Sbjct: 739 MAQQQGQQQGGQGQQQGRQGG 759
>gnl|CDD|153362 cd07678, F-BAR_FCHSD1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH and double SH3
domains 1 (FCHSD1). F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. FCH and double SH3 domains 1 (FCHSD1)
contains an N-terminal F-BAR domain and two SH3 domains
at the C-terminus. It has been characterized only in
silico, and its biological function is still unknown.
F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 263
Score = 28.0 bits (62), Expect = 9.5
Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 5/101 (4%)
Query: 352 MRSFSRSDHLTTHI-RTHTGEKPFSCDVCGRKFARSDEKKRHAKVHLKQRSKKESKMAVM 410
++ S+S L + R K + DV R +SD H+K L++ S K S +
Sbjct: 129 VKELSKSKKLYGQLERVSEVAKEKAADVEAR-LNKSDHGIFHSKASLQKLSAKFSAQSAE 187
Query: 411 MSQQQAQQQQQQNHVHQQQQHHHHHHHHPNMEGMPVVTTPL 451
SQQ + + H H++ E +P + L
Sbjct: 188 YSQQLQAARNEYLLNLVAANAHLDHYYQ---EELPAIMKAL 225
>gnl|CDD|221591 pfam12470, SUFU_C, Suppressor of Fused Gli/Ci N terminal binding
domain. This domain family is found in eukaryotes, and
is typically between 192 and 219 amino acids in length.
The family is found in association with pfam05076.
There is a conserved HGRHFT sequence motif. This family
is the C terminal domain of the Suppressor of Fused
protein (Su(fu)). Su(fu) is a repressor of the Gli and
Ci transcription factors of the Hedgehog signalling
cascade. It functions by binding these proteins and
preventing their translocation to the nucleus. The C
terminal domain is only found in eukaryotic Su(fu)
proteins; it is not present in bacterial homologues.
The C terminal domain binds to the N terminal of Gli/Ci
while the N terminal of Su(fu) binds to the C terminal
of Gli/Ci. This dual binding mechanism is likely an
evolutionary advancement in this signalling cascade
which is not present in bacterial homologues.
Length = 201
Score = 27.9 bits (62), Expect = 9.6
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 36 EELSVGSPSTKDDSGELCQPKTELITDSPLGLHEEEEETSLSSTISMYPGSNPSHSDKIS 95
+ELS K+D + TE I E +EE S T+S SNP H S
Sbjct: 25 KELSKP-AIDKEDVDSIEDKDTEQIRSPLSEGLEIKEEPSEPPTLSQ--SSNPLHHSGSS 81
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 28.5 bits (63), Expect = 9.9
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 399 QRSKK----ESKMAVMMSQQQAQQQQQQNHVHQQQQH 431
Q++KK +S V++ Q +A QQQQ + +QQQ
Sbjct: 64 QKAKKYAMEQSIKQVLLKQTKAHQQQQLENQQRQQQR 100
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
0.312 0.127 0.381
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,537,364
Number of extensions: 1943092
Number of successful extensions: 2845
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2530
Number of HSP's successfully gapped: 139
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (27.4 bits)