Query 002781
Match_columns 882
No_of_seqs 6 out of 8
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 06:59:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002781.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002781hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05077 DUF678: Protein of un 21.0 40 0.00088 30.7 0.6 20 859-878 7-29 (74)
2 COG0523 Putative GTPases (G3E 9.9 1.1E+02 0.0024 33.0 0.4 7 872-878 60-66 (323)
3 PF13186 SPASM: Iron-sulfur cl 9.3 96 0.0021 23.8 -0.2 38 832-877 26-63 (64)
4 COG2265 TrmA SAM-dependent met 8.2 1.6E+02 0.0034 33.1 0.7 30 849-878 50-79 (432)
5 KOG3802 Transcription factor O 7.1 1.8E+02 0.0039 33.1 0.6 14 856-870 288-301 (398)
6 PF09111 SLIDE: SLIDE; InterP 6.3 1.2E+02 0.0026 28.8 -1.0 23 731-753 77-99 (118)
7 PF15085 NPFF: Neuropeptide FF 5.9 1.4E+02 0.003 29.0 -0.9 38 589-626 37-74 (110)
8 PF02492 cobW: CobW/HypB/UreG, 5.1 2.4E+02 0.0052 26.8 0.1 11 868-878 55-65 (178)
9 KOG2743 Cobalamin synthesis pr 5.0 2.7E+02 0.0059 31.5 0.5 10 870-879 119-128 (391)
10 COG0381 WecB UDP-N-acetylgluco 4.8 6.8E+02 0.015 28.5 3.3 72 515-590 256-359 (383)
No 1
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=21.03 E-value=40 Score=30.66 Aligned_cols=20 Identities=30% Similarity=0.806 Sum_probs=15.9
Q ss_pred ccccccCCCCcccc---ccceee
Q 002781 859 TSKEKRKPRSSLFT---TCMCCT 878 (882)
Q Consensus 859 ~sk~K~K~RSSLF~---~CMCCa 878 (882)
+.|+|||+|+.+=. .||=|-
T Consensus 7 ~Krrkrk~~t~v~~~~d~c~tCS 29 (74)
T PF05077_consen 7 KKRRKRKPKTTVDDEEDDCTTCS 29 (74)
T ss_pred chhcccCCCceeecCCCCccchh
Confidence 56799999999877 687774
No 2
>COG0523 Putative GTPases (G3E family) [General function prediction only]
Probab=9.86 E-value=1.1e+02 Score=33.04 Aligned_cols=7 Identities=57% Similarity=1.848 Sum_probs=5.4
Q ss_pred cccceee
Q 002781 872 TTCMCCT 878 (882)
Q Consensus 872 ~~CMCCa 878 (882)
.-||||+
T Consensus 60 nGCICCT 66 (323)
T COG0523 60 NGCICCT 66 (323)
T ss_pred CceEEEe
Confidence 4588887
No 3
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=9.35 E-value=96 Score=23.84 Aligned_cols=38 Identities=24% Similarity=0.236 Sum_probs=22.2
Q ss_pred CcccccchhhcccchhhccccchhhhcccccccCCCCcccccccee
Q 002781 832 PQVHGNNAAAKREDKESSNLHAKEVTATSKEKRKPRSSLFTTCMCC 877 (882)
Q Consensus 832 ~~~q~n~aA~KKa~ke~~Ns~tkeV~s~sk~K~K~RSSLF~~CMCC 877 (882)
.-..+|. +...+++||+... +..++..... ++..|.-|
T Consensus 26 ~~~~Gni---~~~l~eiw~s~~~----~~~r~~~~~~-~~~~C~~C 63 (64)
T PF13186_consen 26 EFKIGNI---EDSLEEIWNSPKF----REFRKRHKKN-NFEPCKNC 63 (64)
T ss_pred CeEEeec---CCCHHHHHCCHHH----HHHHHHHhCC-CCCcCCCC
Confidence 3445664 4578999988655 2222222222 88888776
No 4
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=8.18 E-value=1.6e+02 Score=33.11 Aligned_cols=30 Identities=20% Similarity=0.406 Sum_probs=23.0
Q ss_pred ccccchhhhcccccccCCCCccccccceee
Q 002781 849 SNLHAKEVTATSKEKRKPRSSLFTTCMCCT 878 (882)
Q Consensus 849 ~Ns~tkeV~s~sk~K~K~RSSLF~~CMCCa 878 (882)
|--.-+++-.+|..+.+++-..|+.|++|.
T Consensus 50 ~~a~~~~i~~~Sp~R~~~~c~~~g~cggC~ 79 (432)
T COG2265 50 AEAKLVKVLEASPDRVDPPCPHFGRCGGCQ 79 (432)
T ss_pred eeeEeeeeccCChhhcCCCCcccccccccc
Confidence 333334455578888999999999999996
No 5
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=7.13 E-value=1.8e+02 Score=33.11 Aligned_cols=14 Identities=50% Similarity=0.684 Sum_probs=10.3
Q ss_pred hhcccccccCCCCcc
Q 002781 856 VTATSKEKRKPRSSL 870 (882)
Q Consensus 856 V~s~sk~K~K~RSSL 870 (882)
|++.+ ||||+|+||
T Consensus 288 i~a~~-RkRKKRTSi 301 (398)
T KOG3802|consen 288 IGAQS-RKRKKRTSI 301 (398)
T ss_pred hhccc-cccccccce
Confidence 44444 888999997
No 6
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=6.33 E-value=1.2e+02 Score=28.82 Aligned_cols=23 Identities=30% Similarity=0.538 Sum_probs=17.8
Q ss_pred ccccccccccccccccccccccc
Q 002781 731 NTQAQIQKSPSFDLDLRIEARTE 753 (882)
Q Consensus 731 ni~~qmrKsPSFd~dLriEaR~e 753 (882)
.|..+||.+|-|-||.-+-+|+.
T Consensus 77 ~Ik~~Ir~~p~FrFDwf~kSRt~ 99 (118)
T PF09111_consen 77 KIKQEIRESPLFRFDWFFKSRTP 99 (118)
T ss_dssp HHHHHHHH-CGGCT-HHHHTS-H
T ss_pred HHHHHHHhCCCcccchhcccCCH
Confidence 47889999999999999999874
No 7
>PF15085 NPFF: Neuropeptide FF
Probab=5.94 E-value=1.4e+02 Score=29.00 Aligned_cols=38 Identities=26% Similarity=0.366 Sum_probs=26.0
Q ss_pred CCChhhhhcCcccCCcccccccCCCCCccccccccccc
Q 002781 589 ENSKDARENGEQCTPPVEQEVSLTKAPLSLFQPQDNQQ 626 (882)
Q Consensus 589 gn~~eerq~gEq~t~~veae~~lp~aPaslfQsQd~qq 626 (882)
++..+.+--|..+.-..++..-...+|+.|||+|----
T Consensus 37 ~~~~d~~~~~sllralL~~~qR~gRspa~LfQPQRFGR 74 (110)
T PF15085_consen 37 DNRQDAQTPGSLLRALLQAMQRPGRSPAFLFQPQRFGR 74 (110)
T ss_pred CcccccccHHHHHHHHHHhcccCCCCcccccCccccCC
Confidence 44555555555655556666667778999999997543
No 8
>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.
Probab=5.10 E-value=2.4e+02 Score=26.80 Aligned_cols=11 Identities=45% Similarity=1.180 Sum_probs=8.1
Q ss_pred Cccccccceee
Q 002781 868 SSLFTTCMCCT 878 (882)
Q Consensus 868 SSLF~~CMCCa 878 (882)
.-|.+-|+||+
T Consensus 55 ~~l~~gcicc~ 65 (178)
T PF02492_consen 55 VELNNGCICCT 65 (178)
T ss_dssp EEECTTTESS-
T ss_pred EEecCCCcccc
Confidence 35788899997
No 9
>KOG2743 consensus Cobalamin synthesis protein [Coenzyme transport and metabolism]
Probab=5.00 E-value=2.7e+02 Score=31.52 Aligned_cols=10 Identities=50% Similarity=1.331 Sum_probs=7.2
Q ss_pred cccccceeec
Q 002781 870 LFTTCMCCTT 879 (882)
Q Consensus 870 LF~~CMCCaT 879 (882)
|=.-||||+-
T Consensus 119 L~NGClCCtV 128 (391)
T KOG2743|consen 119 LRNGCLCCTV 128 (391)
T ss_pred hcCCeEEEEe
Confidence 3456999974
No 10
>COG0381 WecB UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]
Probab=4.84 E-value=6.8e+02 Score=28.50 Aligned_cols=72 Identities=21% Similarity=0.254 Sum_probs=48.8
Q ss_pred HhhccCCeeeccCCCcccccccchhhhhccc-cccCCCCccccccc-----------------ccccCCc--ccccchhh
Q 002781 515 KVAKNGGLVDEHSNDQNAASVEHSEDSQKEV-EMVPDSGTVSTESA-----------------LVDCKSE--EASEEGQV 574 (882)
Q Consensus 515 Kv~eNgy~Vdl~~~~qn~~~~e~~Ed~cKe~-~~vp~~gtvste~~-----------------~tDc~~e--E~~~E~qi 574 (882)
+.+++.-+|.|+....- ..+=-+.|.. .++.++|.+.+|.. .+|+.-- --+++.+|
T Consensus 256 ~~L~~~~~v~li~pl~~----~~f~~L~~~a~~iltDSGgiqEEAp~lg~Pvl~lR~~TERPE~v~agt~~lvg~~~~~i 331 (383)
T COG0381 256 KRLKNVERVKLIDPLGY----LDFHNLMKNAFLILTDSGGIQEEAPSLGKPVLVLRDTTERPEGVEAGTNILVGTDEENI 331 (383)
T ss_pred HHhCCCCcEEEeCCcch----HHHHHHHHhceEEEecCCchhhhHHhcCCcEEeeccCCCCccceecCceEEeCccHHHH
Confidence 56666666888887766 5555666666 89999999999987 2222222 22456778
Q ss_pred HHHHhhhhc------------cccccCC
Q 002781 575 FEEAEDKTK------------TSYGNEN 590 (882)
Q Consensus 575 vEei~eKte------------~s~avgn 590 (882)
++.++...+ -|||.|+
T Consensus 332 ~~~~~~ll~~~~~~~~m~~~~npYgdg~ 359 (383)
T COG0381 332 LDAATELLEDEEFYERMSNAKNPYGDGN 359 (383)
T ss_pred HHHHHHHhhChHHHHHHhcccCCCcCcc
Confidence 887765444 5888887
Done!