Query 028937
Match_columns 201
No_of_seqs 113 out of 130
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 04:54:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028937hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05542 DUF760: Protein of un 100.0 4E-36 8.7E-41 223.7 9.8 85 81-165 1-86 (86)
2 COG4694 Uncharacterized protei 35.1 45 0.00098 34.3 3.8 93 19-123 590-683 (758)
3 PF14969 DUF4508: Domain of un 34.5 27 0.00059 27.7 1.8 35 67-101 49-96 (98)
4 PF02258 SLT_beta: Shiga-like 33.8 26 0.00057 26.5 1.5 19 131-149 31-49 (70)
5 PRK00084 ispF 2-C-methyl-D-ery 32.0 51 0.0011 28.0 3.1 28 105-133 109-136 (159)
6 PHA02993 hypothetical protein; 28.8 27 0.00058 29.6 0.9 12 46-57 132-143 (147)
7 PF03800 Nuf2: Nuf2 family; I 27.7 80 0.0017 24.9 3.4 56 70-126 4-60 (146)
8 TIGR00151 ispF 2C-methyl-D-ery 27.7 70 0.0015 27.1 3.2 28 105-133 106-133 (155)
9 PF07531 TAFH: NHR1 homology t 26.5 61 0.0013 25.6 2.5 27 94-120 12-39 (96)
10 PF13877 RPAP3_C: Potential Mo 26.2 69 0.0015 23.4 2.6 38 78-115 19-57 (94)
11 PF04596 Pox_F15: Poxvirus pro 23.9 29 0.00063 29.1 0.3 12 46-57 121-132 (136)
12 cd05538 POLBc_Pol_II_B DNA pol 23.6 92 0.002 28.7 3.5 59 76-134 203-262 (347)
13 COG4698 Uncharacterized protei 22.5 86 0.0019 27.8 2.9 22 124-145 50-71 (197)
14 PF02590 SPOUT_MTase: Predicte 22.3 1.1E+02 0.0024 25.3 3.4 70 80-149 17-97 (155)
15 cd00554 MECDP_synthase MECDP_s 21.7 1.1E+02 0.0024 25.8 3.3 31 105-137 106-136 (153)
No 1
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=100.00 E-value=4e-36 Score=223.67 Aligned_cols=85 Identities=44% Similarity=0.733 Sum_probs=83.5
Q ss_pred hHHHHHHHhcCchHHHHHhccCCHHHHHHHHHHHHHhhcCC-CCCCcceEEEecHHhHHHHHHHHHhHhHhhchhHHHHH
Q 028937 81 DILLEYVKNVQPEFMELFVKRAPEQVVDAMRQTVTNMIGTL-PPQFFAVTVTTVAENLAQLMYSVMMTGYMFKNAQYRLE 159 (201)
Q Consensus 81 N~LleYLqsl~PE~is~lsk~ASpeV~eaM~qtV~gLLG~L-P~~~F~VtItTsrE~LArLLaSaMMTGYfLRNAEqRLe 159 (201)
|.||+|||+++||.+++|++++||||+|+|+++|+++||.+ |+++|+++|+|+||+||+|++|+|||||||||||||++
T Consensus 1 n~L~~yi~~l~pe~~~~l~~~~s~ev~e~m~~~v~~llG~l~p~~~~~~~i~~s~~~La~L~~~~mm~GYfLr~~E~R~~ 80 (86)
T PF05542_consen 1 NDLLQYIQSLKPERIQQLSEPASPEVLEAMKQHVSGLLGNLSPSDQFNVTIQTSRENLAQLLAWSMMTGYFLRNAEQRLE 80 (86)
T ss_pred ChHHHHHHHCCHHHHHHhhccCCHHHHHHHHHHHHHHHcCCCCcccCcceeEECHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred HHHhhh
Q 028937 160 LQQSLE 165 (201)
Q Consensus 160 LErsL~ 165 (201)
||++|.
T Consensus 81 Le~sL~ 86 (86)
T PF05542_consen 81 LERSLK 86 (86)
T ss_pred HHHhcC
Confidence 999984
No 2
>COG4694 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.06 E-value=45 Score=34.26 Aligned_cols=93 Identities=19% Similarity=0.313 Sum_probs=57.5
Q ss_pred eeeeecCCCcccceeeccCCccCCCCceeE-EEeeecCCCCCCCCCCCCCCCCCCCCCCCCchhHHHHHHHhcCchHHHH
Q 028937 19 VTVVSCRPKLFSSVRCPIKTKKNNNGRLAL-RIQAYDSSKNESNNNGSNDSKPPNGALPKGRRDILLEYVKNVQPEFMEL 97 (201)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~-r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~LleYLqsl~PE~is~ 97 (201)
+++.++.--..--+.--.+++|+|+|...| |+++-.+ +++.-...++..|--+. ..-.||+|+..--...-+.
T Consensus 590 viVLtHntYF~rd~~~~~~~~RyNkgk~~f~~ik~~~n--~~~~~~~~ad~d~ikns----py~lly~~v~~~~~n~~e~ 663 (758)
T COG4694 590 VIVLTHNTYFYRDITLELDLKRYNKGKYSFWIIKKDNN--VSKIKVYKADEDPIKNS----PYELLYQEVKQAKENNAEW 663 (758)
T ss_pred EEEEeccceehHHHHhhhccccccccceEEEEEeCCCC--CCceeehhccccchhcc----HHHHHHHHHHHHhccchhH
Confidence 444555544455556667889999999997 6665322 22222222222232222 1557999998766555555
Q ss_pred HhccCCHHHHHHHHHHHHHhhcCCCC
Q 028937 98 FVKRAPEQVVDAMRQTVTNMIGTLPP 123 (201)
Q Consensus 98 lsk~ASpeV~eaM~qtV~gLLG~LP~ 123 (201)
+. +.-+||+.|-+.+.-+||
T Consensus 664 ~l------~an~~R~lVE~ffrf~~p 683 (758)
T COG4694 664 VL------LANAMRRLVEYFFRFLGP 683 (758)
T ss_pred HH------HHHHHHHHHHHHHHhcCc
Confidence 44 788999999999877776
No 3
>PF14969 DUF4508: Domain of unknown function (DUF4508)
Probab=34.54 E-value=27 Score=27.71 Aligned_cols=35 Identities=26% Similarity=0.586 Sum_probs=30.2
Q ss_pred CCCCCCC-------------CCCCCchhHHHHHHHhcCchHHHHHhcc
Q 028937 67 DSKPPNG-------------ALPKGRRDILLEYVKNVQPEFMELFVKR 101 (201)
Q Consensus 67 ~~~~~~~-------------~~~~~~~N~LleYLqsl~PE~is~lsk~ 101 (201)
.+||++. +-+.++||.+++-|..++|+++++|-+.
T Consensus 49 ~dkppsiFqCqlkLf~qWf~~W~~~ern~fl~~Lee~D~~f~~k~~~~ 96 (98)
T PF14969_consen 49 QDKPPSIFQCQLKLFRQWFPKWSEEERNKFLEQLEEIDPDFVAKFYQE 96 (98)
T ss_pred CCCCCcHHHHhHHHHHHHHhhccHHHHHHHHHHHHHhChHHHHHHHHh
Confidence 6789886 5578999999999999999999988653
No 4
>PF02258 SLT_beta: Shiga-like toxin beta subunit; InterPro: IPR003189 This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of Escherichia coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT s are composed of one enzymatic A subunit and five cell binding B subunits.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2GA4_B 1R4P_D 1BOS_I 4ULL_A 2C5C_I 1QNU_C 1CZW_F 1D1I_C 1CZG_D 2XSC_D ....
Probab=33.79 E-value=26 Score=26.46 Aligned_cols=19 Identities=32% Similarity=0.249 Sum_probs=16.4
Q ss_pred EecHHhHHHHHHHHHhHhH
Q 028937 131 TTVAENLAQLMYSVMMTGY 149 (201)
Q Consensus 131 tTsrE~LArLLaSaMMTGY 149 (201)
-|+|=||+.+|.|+.++|-
T Consensus 31 ~Ts~wnL~~~L~sa~~~G~ 49 (70)
T PF02258_consen 31 WTSRWNLQSPLLSAQITGM 49 (70)
T ss_dssp EE-STTHHHHHHHHHHHTS
T ss_pred eccCcccccceeeeEEcce
Confidence 4899999999999999993
No 5
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=32.02 E-value=51 Score=27.96 Aligned_cols=28 Identities=25% Similarity=0.399 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHhhcCCCCCCcceEEEec
Q 028937 105 QVVDAMRQTVTNMIGTLPPQFFAVTVTTV 133 (201)
Q Consensus 105 eV~eaM~qtV~gLLG~LP~~~F~VtItTs 133 (201)
.-+++|++++..+||. |.+..+++.||+
T Consensus 109 p~~~~m~~~la~~L~i-~~~~V~iKatT~ 136 (159)
T PRK00084 109 PHIEEMRANIAEDLGI-PLDDVNVKATTT 136 (159)
T ss_pred HHHHHHHHHHHHHhCC-CcceEEEEEecC
Confidence 4789999999999994 777777777654
No 6
>PHA02993 hypothetical protein; Provisional
Probab=28.79 E-value=27 Score=29.65 Aligned_cols=12 Identities=42% Similarity=0.637 Sum_probs=10.6
Q ss_pred eeEEEeeecCCC
Q 028937 46 LALRIQAYDSSK 57 (201)
Q Consensus 46 ~~~r~~~~~~~~ 57 (201)
+|||+|.||+++
T Consensus 132 IGLRIK~fWs~~ 143 (147)
T PHA02993 132 IGLRIKDFWSPK 143 (147)
T ss_pred EEEEehhcccce
Confidence 599999999975
No 7
>PF03800 Nuf2: Nuf2 family; InterPro: IPR005549 Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Q9C953 from SWISSPROT. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.; GO: 0007067 mitosis, 0000775 chromosome, centromeric region; PDB: 2VE7_D 3IZ0_D.
Probab=27.74 E-value=80 Score=24.94 Aligned_cols=56 Identities=18% Similarity=0.248 Sum_probs=34.8
Q ss_pred CCCCCCCCCchhHHHHHHHhcC-chHHHHHhccCCHHHHHHHHHHHHHhhcCCCCCCc
Q 028937 70 PPNGALPKGRRDILLEYVKNVQ-PEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQFF 126 (201)
Q Consensus 70 ~~~~~~~~~~~N~LleYLqsl~-PE~is~lsk~ASpeV~eaM~qtV~gLLG~LP~~~F 126 (201)
+.+.+.|.=+.+++.+.++... +-.-+.+.||.+.-|+.+-.+.+..++|. +.+.+
T Consensus 4 ~~~~~FP~L~~~eIv~~L~~~~~~~t~~dl~kPt~e~v~~ly~~~L~~~~g~-~~e~~ 60 (146)
T PF03800_consen 4 QNKYSFPLLSPDEIVNCLQECGIPVTEEDLKKPTPEFVQKLYERFLETFLGI-SPEDI 60 (146)
T ss_dssp -------S--HHHHHHHHHHHT--HHHHC--G--HHHHHHHHHHHHHHHHT---CGGG
T ss_pred cccCCCCCCCHHHHHHHHHHCCCCcCHHHHcCCCHHHHHHHHHHHHHHHHCc-CHHHH
Confidence 3445667777889999999986 57778899999999999999999999998 55544
No 8
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=27.66 E-value=70 Score=27.06 Aligned_cols=28 Identities=29% Similarity=0.539 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHhhcCCCCCCcceEEEec
Q 028937 105 QVVDAMRQTVTNMIGTLPPQFFAVTVTTV 133 (201)
Q Consensus 105 eV~eaM~qtV~gLLG~LP~~~F~VtItTs 133 (201)
.-+++|++++..+|| +|.+..+++.+|+
T Consensus 106 p~~~~m~~~la~~L~-~~~~~V~iKatT~ 133 (155)
T TIGR00151 106 PHIPAMRENIAELLG-IPLDSVNVKATTT 133 (155)
T ss_pred HHHHHHHHHHHHHhC-CCcceEEEEEecC
Confidence 478999999999999 4878888777754
No 9
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=26.52 E-value=61 Score=25.56 Aligned_cols=27 Identities=15% Similarity=0.260 Sum_probs=23.0
Q ss_pred HHHHHhcc-CCHHHHHHHHHHHHHhhcC
Q 028937 94 FMELFVKR-APEQVVDAMRQTVTNMIGT 120 (201)
Q Consensus 94 ~is~lsk~-ASpeV~eaM~qtV~gLLG~ 120 (201)
++.+|++. .||||-+.++.-|++++-.
T Consensus 12 tLi~las~~~spev~~~Vr~LV~~L~~~ 39 (96)
T PF07531_consen 12 TLIQLASDKQSPEVGENVRELVQNLVDG 39 (96)
T ss_dssp HHHHHHCCSC-CCHHHHHHHHHHHHHTT
T ss_pred HHHHHhcCCCChHHHHHHHHHHHHHHcC
Confidence 56788888 9999999999999999865
No 10
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=26.24 E-value=69 Score=23.37 Aligned_cols=38 Identities=13% Similarity=0.307 Sum_probs=26.2
Q ss_pred CchhHHHHHHHhcCchHHHHHhcc-CCHHHHHHHHHHHH
Q 028937 78 GRRDILLEYVKNVQPEFMELFVKR-APEQVVDAMRQTVT 115 (201)
Q Consensus 78 ~~~N~LleYLqsl~PE~is~lsk~-ASpeV~eaM~qtV~ 115 (201)
+..+..++||++++|+.+..+-+. -++++..-|=+.+.
T Consensus 19 ~~~~~~~~yL~~i~p~~l~~if~~~l~~~~L~~il~~l~ 57 (94)
T PF13877_consen 19 KDPEERYEYLKSIPPDSLPKIFKNSLEPEFLSEILEALN 57 (94)
T ss_pred CCHHHHHHHHHhCChHHHHHHHHccCCHHHHHHHHHHHH
Confidence 455689999999999988877664 44555544444443
No 11
>PF04596 Pox_F15: Poxvirus protein F15; InterPro: IPR007675 Protein F15 is found in a number of Poxviruses.
Probab=23.87 E-value=29 Score=29.10 Aligned_cols=12 Identities=50% Similarity=0.686 Sum_probs=10.6
Q ss_pred eeEEEeeecCCC
Q 028937 46 LALRIQAYDSSK 57 (201)
Q Consensus 46 ~~~r~~~~~~~~ 57 (201)
+|||+|.||+++
T Consensus 121 IGLRIK~fWs~~ 132 (136)
T PF04596_consen 121 IGLRIKDFWSSK 132 (136)
T ss_pred EEEchhhcccee
Confidence 599999999975
No 12
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=23.59 E-value=92 Score=28.68 Aligned_cols=59 Identities=17% Similarity=0.131 Sum_probs=50.3
Q ss_pred CCCchhHHHHHHHhcCchHHHHHhccCCHHHHHHHHHHHHHhh-cCCCCCCcceEEEecH
Q 028937 76 PKGRRDILLEYVKNVQPEFMELFVKRAPEQVVDAMRQTVTNMI-GTLPPQFFAVTVTTVA 134 (201)
Q Consensus 76 ~~~~~N~LleYLqsl~PE~is~lsk~ASpeV~eaM~qtV~gLL-G~LP~~~F~VtItTsr 134 (201)
.+-.|.+--+++|...-+.+..+.+...+++.+.+++.+..|. |.+|-+.|-++.+.++
T Consensus 203 ~e~vRrD~~~~~k~~~~~vl~~ll~~~~~~~~~~~~~~~~~l~~~~~~~~~l~i~k~l~k 262 (347)
T cd05538 203 SAFRSRGIEPFLREFLREAVRLLLQGDGAGVHDLYEDYLRRLRSHELPISDLARTETLKE 262 (347)
T ss_pred CCcccCCchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHcCCCCHHHEEEEeecCC
Confidence 3455556778899999999999998888899999999999988 7899999988877765
No 13
>COG4698 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.47 E-value=86 Score=27.80 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=18.1
Q ss_pred CCcceEEEecHHhHHHHHHHHH
Q 028937 124 QFFAVTVTTVAENLAQLMYSVM 145 (201)
Q Consensus 124 ~~F~VtItTsrE~LArLLaSaM 145 (201)
..-..+|||+|+.|++|+.|=+
T Consensus 50 ~~~~fqitttr~~LN~li~syl 71 (197)
T COG4698 50 SEKSFQITTTRSQLNELINSYL 71 (197)
T ss_pred cceeEEEEccHHHHHHHHHHHH
Confidence 3456799999999999998754
No 14
>PF02590 SPOUT_MTase: Predicted SPOUT methyltransferase; InterPro: IPR003742 This family of proteins are predicted to be SPOUT methyltransferases []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1VH0_E 4FAK_A 1TO0_G 1O6D_A 1NS5_B.
Probab=22.35 E-value=1.1e+02 Score=25.29 Aligned_cols=70 Identities=17% Similarity=0.356 Sum_probs=51.0
Q ss_pred hhHHHHHHHhcCc----hHHHHHhc--cCCHHHHHHHHHHHHHhhcCCCCCCcceEEE-----ecHHhHHHHHHHHHhHh
Q 028937 80 RDILLEYVKNVQP----EFMELFVK--RAPEQVVDAMRQTVTNMIGTLPPQFFAVTVT-----TVAENLAQLMYSVMMTG 148 (201)
Q Consensus 80 ~N~LleYLqsl~P----E~is~lsk--~ASpeV~eaM~qtV~gLLG~LP~~~F~VtIt-----TsrE~LArLLaSaMMTG 148 (201)
+...-+|++.+.+ |++..-.+ ..+.++.++++.--..++..+|++.+-|... .+-+.||+.+...+..|
T Consensus 17 ~~~~~eY~kRl~~~~~~e~~e~~~~~~~~~~~~~~~~~~E~~~il~~i~~~~~~i~Ld~~Gk~~sS~~fA~~l~~~~~~g 96 (155)
T PF02590_consen 17 KELIEEYLKRLSRYAKLEIIELKEEKIAKAQSIEKIKEKEGERILKKIPPNDYVILLDERGKQLSSEEFAKKLERWMNQG 96 (155)
T ss_dssp HHHHHHHHHHHCTTSEEEEEEE------TCHHHHHHHHHHHHHHHCTSHTTSEEEEE-TTSEE--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCccCceeEEEeccccccccccHHHHHHHHHHHHHhhccCCCEEEEEcCCCccCChHHHHHHHHHHHhcC
Confidence 3466788888876 22322222 2467888899999999999999999877665 67899999999999999
Q ss_pred H
Q 028937 149 Y 149 (201)
Q Consensus 149 Y 149 (201)
.
T Consensus 97 ~ 97 (155)
T PF02590_consen 97 K 97 (155)
T ss_dssp S
T ss_pred C
Confidence 6
No 15
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=21.72 E-value=1.1e+02 Score=25.81 Aligned_cols=31 Identities=32% Similarity=0.627 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHhhcCCCCCCcceEEEecHHhH
Q 028937 105 QVVDAMRQTVTNMIGTLPPQFFAVTVTTVAENL 137 (201)
Q Consensus 105 eV~eaM~qtV~gLLG~LP~~~F~VtItTsrE~L 137 (201)
..+++|++++..+|| ++.+...++.+| .|.|
T Consensus 106 p~~~~m~~~ls~~L~-~~~~~V~iKatT-~E~l 136 (153)
T cd00554 106 PYREAMRANLAELLG-IPPSRVNIKATT-TEGL 136 (153)
T ss_pred HHHHHHHHHHHHHhC-CCCceEEEEEec-CCCC
Confidence 478999999999999 667777777664 3443
Done!