Query 032883
Match_columns 131
No_of_seqs 70 out of 72
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 07:07:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK02724 hypothetical protein; 99.9 6.9E-23 1.5E-27 151.5 4.8 41 89-130 4-44 (104)
2 CHL00163 ycf65 putative riboso 99.9 8.7E-23 1.9E-27 149.8 4.9 39 91-130 1-39 (99)
3 cd00732 CheW CheW, a small reg 21.5 1.5E+02 0.0032 20.8 3.5 25 94-119 72-96 (140)
4 PF14189 DUF4312: Domain of un 20.7 41 0.00089 24.4 0.5 7 124-130 62-68 (85)
5 smart00141 PDGF Platelet-deriv 18.2 51 0.0011 23.3 0.5 8 122-129 20-27 (83)
6 cd00135 PDGF Platelet-derived 17.8 69 0.0015 22.5 1.1 8 122-129 20-27 (86)
7 cd00588 CheW_like CheW-like do 16.0 1.7E+02 0.0036 19.9 2.6 26 93-119 72-97 (136)
8 PF09337 zf-H2C2: His(2)-Cys(2 15.9 39 0.00085 20.8 -0.5 12 118-129 12-23 (39)
9 PRK09455 rseB anti-sigma E fac 15.1 2.6E+02 0.0055 23.9 4.0 26 84-110 145-170 (319)
10 PRK13994 potassium-transportin 13.9 79 0.0017 26.6 0.7 16 115-130 75-90 (222)
No 1
>PRK02724 hypothetical protein; Provisional
Probab=99.87 E-value=6.9e-23 Score=151.48 Aligned_cols=41 Identities=29% Similarity=0.617 Sum_probs=39.5
Q ss_pred CCCCeEEEEEEeeeCceEEEeeeeecCCCcccceeeeecccC
Q 032883 89 LEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVS 130 (131)
Q Consensus 89 ~~~~rfvLK~LWleknIgiAlDQvv~g~~t~PLT~YfFWPr~ 130 (131)
.+++||+||||||||||||||||++ |+|++|||+||||||+
T Consensus 4 ~~~~rfvlKvlWle~~iaiAvDQ~v-g~~t~PLT~yfFWPr~ 44 (104)
T PRK02724 4 ADEGRFILKVLWLDDNVALAVDQIV-GKGTSPLTAYFFWPRN 44 (104)
T ss_pred cccceEEEEEEEeccceeEEeeeec-CCCCCcCcceeecCCc
Confidence 4689999999999999999999999 9999999999999997
No 2
>CHL00163 ycf65 putative ribosomal protein 3; Validated
Probab=99.87 E-value=8.7e-23 Score=149.81 Aligned_cols=39 Identities=36% Similarity=0.657 Sum_probs=37.5
Q ss_pred CCeEEEEEEeeeCceEEEeeeeecCCCcccceeeeecccC
Q 032883 91 KPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVS 130 (131)
Q Consensus 91 ~~rfvLK~LWleknIgiAlDQvv~g~~t~PLT~YfFWPr~ 130 (131)
++||+||||||||||||||||++ |+|++|||+||||||+
T Consensus 1 m~kf~lKvlWl~~~iaiAvDq~v-~~~t~PlT~yfFWPr~ 39 (99)
T CHL00163 1 MQKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRT 39 (99)
T ss_pred CCeEEEEEEEecCceEEEEeeee-CCCCccCcceeecCCc
Confidence 58999999999999999999999 7899999999999997
No 3
>cd00732 CheW CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together with CheA and the methyl-accepting chemotaxis proteins (MCPs), which are involved in response modulation.
Probab=21.47 E-value=1.5e+02 Score=20.75 Aligned_cols=25 Identities=12% Similarity=0.202 Sum_probs=17.5
Q ss_pred EEEEEEeeeCceEEEeeeeecCCCcc
Q 032883 94 LVLKFIWMEKNIGLALDQSIPGAVAI 119 (131)
Q Consensus 94 fvLK~LWleknIgiAlDQvv~g~~t~ 119 (131)
.++=+-+-+..+|+.||++. |-..+
T Consensus 72 ~vli~~~~~~~~gl~Vd~v~-~i~~~ 96 (140)
T cd00732 72 RIIVVEVGDQVVGLLVDSVS-EVLRL 96 (140)
T ss_pred EEEEEEECCEEEEEEEeeEe-eEEEE
Confidence 34445556788999999998 64443
No 4
>PF14189 DUF4312: Domain of unknown function (DUF4312)
Probab=20.72 E-value=41 Score=24.45 Aligned_cols=7 Identities=14% Similarity=0.415 Sum_probs=4.0
Q ss_pred eeecccC
Q 032883 124 WMKIPVS 130 (131)
Q Consensus 124 YfFWPr~ 130 (131)
||||||+
T Consensus 62 ~fF~PR~ 68 (85)
T PF14189_consen 62 FFFFPRE 68 (85)
T ss_pred eeecccc
Confidence 3566664
No 5
>smart00141 PDGF Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.
Probab=18.19 E-value=51 Score=23.30 Aligned_cols=8 Identities=13% Similarity=0.268 Sum_probs=6.6
Q ss_pred eeeeeccc
Q 032883 122 LSWMKIPV 129 (131)
Q Consensus 122 T~YfFWPr 129 (131)
++|+|||.
T Consensus 20 ~~~~y~P~ 27 (83)
T smart00141 20 TNFLFKPP 27 (83)
T ss_pred cCcEEecC
Confidence 48999996
No 6
>cd00135 PDGF Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain
Probab=17.78 E-value=69 Score=22.48 Aligned_cols=8 Identities=13% Similarity=-0.039 Sum_probs=6.9
Q ss_pred eeeeeccc
Q 032883 122 LSWMKIPV 129 (131)
Q Consensus 122 T~YfFWPr 129 (131)
++|+|||+
T Consensus 20 ~~~~y~P~ 27 (86)
T cd00135 20 TNTIFKPP 27 (86)
T ss_pred cCCEEECC
Confidence 68999996
No 7
>cd00588 CheW_like CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in the chemotaxis associated histidine kinase CheA binds to CheW, suggesting that these domains can interact with each other.
Probab=15.98 E-value=1.7e+02 Score=19.91 Aligned_cols=26 Identities=15% Similarity=0.414 Sum_probs=17.7
Q ss_pred eEEEEEEeeeCceEEEeeeeecCCCcc
Q 032883 93 RLVLKFIWMEKNIGLALDQSIPGAVAI 119 (131)
Q Consensus 93 rfvLK~LWleknIgiAlDQvv~g~~t~ 119 (131)
..++=+=+-+..+|+.||++. |-...
T Consensus 72 ~~vii~~~~~~~~gl~Vd~i~-~i~~~ 97 (136)
T cd00588 72 TRIVVVEVGDRKVGLVVDSVL-GVLEV 97 (136)
T ss_pred cEEEEEEECCEEEEEEECccc-eEEEE
Confidence 344444456788999999998 54433
No 8
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=15.90 E-value=39 Score=20.83 Aligned_cols=12 Identities=8% Similarity=-0.000 Sum_probs=8.8
Q ss_pred cccceeeeeccc
Q 032883 118 AILLLSWMKIPV 129 (131)
Q Consensus 118 t~PLT~YfFWPr 129 (131)
+.=|..-|+||+
T Consensus 12 ~~~i~~~y~W~g 23 (39)
T PF09337_consen 12 TAKISQRYHWPG 23 (39)
T ss_pred HHHHHHhheecC
Confidence 345678899996
No 9
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=15.06 E-value=2.6e+02 Score=23.94 Aligned_cols=26 Identities=15% Similarity=0.463 Sum_probs=22.4
Q ss_pred eeeecCCCCeEEEEEEeeeCceEEEee
Q 032883 84 VSVKQLEKPRLVLKFIWMEKNIGLALD 110 (131)
Q Consensus 84 ~~v~~~~~~rfvLK~LWleknIgiAlD 110 (131)
+.+.|.+..||. ..||+|+.-|+-|=
T Consensus 145 i~~~PkD~~rY~-~~lwiD~et~llLk 170 (319)
T PRK09455 145 IRIVPKDGTRYS-YIVWIDEESKLPLR 170 (319)
T ss_pred EEEEECCCCCcc-eEEEEEcCCCCEEe
Confidence 344889999999 99999999998876
No 10
>PRK13994 potassium-transporting ATPase subunit C; Provisional
Probab=13.94 E-value=79 Score=26.57 Aligned_cols=16 Identities=13% Similarity=-0.251 Sum_probs=11.4
Q ss_pred CCCcccceeeeecccC
Q 032883 115 GAVAILLLSWMKIPVS 130 (131)
Q Consensus 115 g~~t~PLT~YfFWPr~ 130 (131)
|.++-|-.+.|||||-
T Consensus 75 ~~~~~~~~~~YF~~RP 90 (222)
T PRK13994 75 GEETPEPDLKWFQPRP 90 (222)
T ss_pred ccccCCCCCccccCCC
Confidence 4555455689999993
Done!