Query T0630 NP_001128980.1, , 132 residues
Match_columns 132
No_of_seqs 106 out of 428
Neff 7.3
Searched_HMMs 11830
Date Thu Jul 22 14:59:35 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0630.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0630.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04970 NC: NC domain; Inter 99.9 9.4E-24 8E-28 164.0 7.0 73 58-132 1-73 (74)
2 PF08405 Calici_PP_N: Viral po 99.2 8.5E-12 7.2E-16 90.3 7.4 96 2-121 3-98 (358)
3 PF00877 NLPC_P60: NlpC/P60 fa 97.6 1.3E-05 1.1E-09 52.1 3.2 35 3-37 47-82 (105)
4 PF05708 DUF830: Orthopoxvirus 97.5 1.6E-05 1.4E-09 51.5 2.3 92 7-121 1-116 (155)
5 PF05608 DUF778: Protein of un 96.0 0.0032 2.7E-07 37.3 4.4 98 19-124 9-113 (136)
6 PF05903 DUF862: PPPDE putativ 94.1 0.012 1.1E-06 33.7 2.7 36 85-121 79-117 (150)
7 PF08007 Cupin_4: Cupin superf 91.1 0.073 6.2E-06 28.9 3.4 29 6-37 178-206 (319)
8 PF06672 DUF1175: Protein of u 85.0 0.43 3.7E-05 24.2 4.0 34 5-38 133-173 (216)
9 PF05382 Amidase_5: Bacterioph 84.6 0.42 3.5E-05 24.3 3.8 32 6-37 74-110 (145)
10 PF10030 DUF2272: Uncharacteri 84.1 0.53 4.5E-05 23.6 4.1 36 6-41 92-146 (183)
11 PF05257 CHAP: CHAP domain; I 78.9 0.42 3.5E-05 24.3 2.1 27 4-30 59-88 (124)
12 PF07313 DUF1460: Protein of u 69.3 0.54 4.6E-05 23.6 0.7 55 5-71 151-209 (216)
13 PF03079 ARD: ARD/ARD' family; 66.8 1.1 9.5E-05 21.6 1.9 19 7-26 118-136 (157)
14 PF11948 DUF3465: Protein of u 61.2 2.8 0.00024 19.1 3.1 32 3-39 81-112 (131)
15 PF11649 T4_neck-protein: Viru 57.1 1.8 0.00015 20.4 1.5 14 6-19 112-125 (230)
16 PF01052 SpoA: Surface present 40.6 8.1 0.00069 16.3 2.7 28 6-33 27-54 (77)
17 PF10077 DUF2314: Uncharacteri 35.8 10 0.00088 15.6 2.7 20 8-27 80-99 (133)
18 PF06248 Zw10: Centromere/kine 29.6 7.5 0.00064 16.5 1.1 17 106-122 513-529 (595)
19 PF00122 E1-E2_ATPase: E1-E2 A 27.9 5 0.00042 17.6 -0.0 19 2-20 46-64 (228)
20 PF05820 DUF845: Baculovirus p 26.6 16 0.0013 14.6 5.2 22 94-115 93-114 (119)
21 PF06251 DUF1017: SLBB-domain 23.0 16 0.0013 14.5 1.8 16 4-19 56-71 (173)
22 PF06819 Arc_PepC: Archaeal Pe 21.0 11 0.00093 15.5 0.6 14 2-15 28-41 (110)
23 PF01245 Ribosomal_L19: Riboso 20.2 17 0.0014 14.4 1.4 18 1-18 12-29 (113)
No 1
>PF04970 NC: NC domain; InterPro: IPR007053 This domain is found in proteins from viruses, bacteria and the eukayota. The domain contains a well-conserved NCEHF motif. The function of this domain is unknown.
Probab=99.88 E-value=9.4e-24 Score=164.03 Aligned_cols=73 Identities=44% Similarity=0.683 Sum_probs=69.8
Q ss_pred CCEEEEEEEEEECCCCEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHCCCCCCCCCCC
Q ss_conf 525787723353588279843437653788989999999997068877204342858999988738850101169
Q T0630 58 AIVKKELLYDVAGSDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNELRYGVARSDQVRD 132 (132)
Q Consensus 58 ~~v~~~~l~~~~~~~~~~v~n~~d~~~~~~~~~~iv~rA~~~lg~~~~Y~l~~nNCEHFa~~cr~G~~~S~Qv~~ 132 (132)
+.|+.++|++|++|++++|+|.+| .+.|+++++|++||+++||+ .+|||++|||||||+|||||+++|.||++
T Consensus 1 a~V~~~~l~~~~~g~~~~v~n~~~-~~~~~~~~~iv~rA~~~lG~-~~Y~l~~nNCEHFa~~c~~G~~~S~Qv~~ 73 (74)
T PF04970_consen 1 ASVKRDSLEDFAGGSKIRVNNSDD-RHQPLPPEEIVERARSRLGE-REYNLLFNNCEHFATWCRYGKSESQQVEK 73 (74)
T ss_pred CEEEEEEHHHEECCCEEEEEECCC-CCCCCCHHHHHHHHHHHHCC-CCCCCCCCCHHHHHHHHHCCCCCCHHHHC
T ss_conf 908998763241797799961687-65789989999999998398-73156533759999999669930112014
No 2
>PF08405 Calici_PP_N: Viral polyprotein N-terminal; InterPro: IPR013614 This domain is found at the N terminus of non-structural viral polyproteins of the Caliciviridae subfamily.
Probab=99.24 E-value=8.5e-12 Score=90.26 Aligned_cols=96 Identities=26% Similarity=0.417 Sum_probs=67.6
Q ss_pred CCCCCCCCCCCEEEEECCCEEEEEEEECCCEEEEEECCCCCCCCCCEEEEECCCCCCCEEEEEEEEEECCCCEEEECCCC
Q ss_conf 88810057786798726975589998779179985267664346611331002678525787723353588279843437
Q T0630 2 RAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIVKKELLYDVAGSDKYQVNNKHD 81 (132)
Q Consensus 2 ~~~~~~~k~GDlI~~~r~~y~H~GIYvGdg~ViH~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~~~v~n~~d 81 (132)
..|.+||.+||+||++.+...|||||+|.|+++-.+.+....+. +.+...+|. .-||+.-.+.
T Consensus 3 ~~~a~EP~~G~ilE~~eG~iyHYaiYig~G~~~gvhsp~aais~------------a~i~l~~ls-----~~WR~~y~P~ 65 (358)
T PF08405_consen 3 AGPAKEPLPGSILEMDEGDIYHYAIYIGQGKVLGVHSPQAAISN------------ATIELTPLS-----LWWRVVYTPR 65 (358)
T ss_pred CCCCCCCCCCCEEEEECCEEEEEEEEECCCEEEEECCCCHHCEE------------EEEEEEECC-----CCCCCCCCCC
T ss_conf 88899998774589716704899999628769741175021212------------159986435-----2101114777
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHH
Q ss_conf 6537889899999999970688772043428589999887
Q T0630 82 DKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNELR 121 (132)
Q Consensus 82 ~~~~~~~~~~iv~rA~~~lg~~~~Y~l~~nNCEHFa~~cr 121 (132)
.+.++++ .+++.|++.+|..+.|||-||+-|..
T Consensus 66 ---~~~~~d~----L~~l~gE~~PYaa~~nNCy~fcc~il 98 (358)
T PF08405_consen 66 ---QRLSYDQ----LRKLEGEKWPYAAFTNNCYHFCCWIL 98 (358)
T ss_pred ---CCCCHHH----HHHHCCCCCCHHHHCCCHHHHHHHHC
T ss_conf ---7799899----98744998881666043798988735
No 3
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The Escherichia coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3h41_A 2fg0_B 2evr_A 2hbw_A 2k1g_A.
Probab=97.63 E-value=1.3e-05 Score=52.08 Aligned_cols=35 Identities=31% Similarity=0.544 Sum_probs=31.0
Q ss_pred CCCCCCCCCCEEEEEC-CCEEEEEEEECCCEEEEEE
Q ss_conf 8810057786798726-9755899987791799852
Q T0630 3 APIPEPKPGDLIEIFR-PFYRHWAIYVGDGYVVHLA 37 (132)
Q Consensus 3 ~~~~~~k~GDlI~~~r-~~y~H~GIYvGdg~ViH~~ 37 (132)
.+..+|+|||||.+.. ..-.|.|||+|++++||-.
T Consensus 47 ~~~~~~~pGDlvf~~~~~~~~HVgIy~g~~~~iha~ 82 (105)
T PF00877_consen 47 VSVDELQPGDLVFFKGGGGPSHVGIYIGNGKMIHAS 82 (105)
T ss_dssp E-GGG-----EEEEESTS-EEBEEEB----EEEE--
T ss_pred CCHHHCCCCCEEEECCCCCCCEEEEEECCCEEEEEC
T ss_conf 824418997889968998987889995699899989
No 4
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); InterPro: IPR008548 This family contains the G6 protein from Vaccinia virus (strain Copenhagen) and related proteins from other Orthopoxvirus. The proteins are uncharacterised.; PDB: 2if6_A.
Probab=97.50 E-value=1.6e-05 Score=51.46 Aligned_cols=92 Identities=28% Similarity=0.401 Sum_probs=61.2
Q ss_pred CCCCCCEEEEEC-------------CCEEEEEEEECCC----EEEEEECCCCCCCCCCEEEEECCCCCCCEEEEEEEEEE
Q ss_conf 057786798726-------------9755899987791----79985267664346611331002678525787723353
Q T0630 7 EPKPGDLIEIFR-------------PFYRHWAIYVGDG----YVVHLAPPSEVAGAGAASVMSALTDKAIVKKELLYDVA 69 (132)
Q Consensus 7 ~~k~GDlI~~~r-------------~~y~H~GIYvGdg----~ViH~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~ 69 (132)
++|+||+|.+.- ..|.|.|||+|++ .|+|.. . ..|+..+|.+|.
T Consensus 1 ~l~~GDIi~~~~~~~~s~~i~~~t~~~~sHvgI~~~~~~~~~~viea~-~------------------~Gv~~~~l~~~~ 61 (155)
T PF05708_consen 1 QLQPGDIIFRRGKSRLSKAIRPVTSSPYSHVGIVVGEGGQEPYVIEAP-G------------------PGVRIEPLSDFL 61 (155)
T ss_dssp ------EEEB---STTHHHHHHHHTSS--B---EEEETTE-EEEEEE-----------------------EEEEEHHHHH
T ss_pred CCCCCCEEEEECCCCHHHHHHHHCCCCCCEEEEEEECCCCCEEEEEEC-C------------------CCEEEEEHHHHH
T ss_conf 998851899967973888998760899877999993389736999823-7------------------986997889997
Q ss_pred C-CCCEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEE------ECCHHHHHHHHH
Q ss_conf 5-882798434376537889899999999970688772043------428589999887
Q T0630 70 G-SDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLT------SENCEHFVNELR 121 (132)
Q Consensus 70 ~-~~~~~v~n~~d~~~~~~~~~~iv~rA~~~lg~~~~Y~l~------~nNCEHFa~~cr 121 (132)
. +..+.|....+. .+...+.+++.|..++|. +|+.. ...|=.|+.++-
T Consensus 62 ~~~~~~~v~r~~~~--~~~~~~~~~~~a~~~~g~--~Y~~~~~~~~~~~yCSelV~~ay 116 (155)
T PF05708_consen 62 ERNRKIAVYRLKDP--TDEQREKAIAYAKNYIGK--PYDISFNLNDKKYYCSELVAQAY 116 (155)
T ss_dssp H----EEEEEE------HHHHHHHHHHHHCC------B-TT--SSSSSB-HHHHHHHHH
T ss_pred HCCCCEEEEEECCC--CHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCEEHHHHHHHHH
T ss_conf 36896999993899--999999999999996499--87765447999779899999999
No 5
>PF05608 DUF778: Protein of unknown function (DUF778); InterPro: IPR008496 This family consists of several eukaryotic proteins of unknown function.
Probab=96.01 E-value=0.0032 Score=37.31 Aligned_cols=98 Identities=18% Similarity=0.239 Sum_probs=51.3
Q ss_pred CCEEEEEEEECCCEEEEEECCCCCCCCCCEEEEECCCCCCCEEEEEEEE----EE---CCCCEEEECCCCCCCCCCCHHH
Q ss_conf 9755899987791799852676643466113310026785257877233----53---5882798434376537889899
Q T0630 19 PFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIVKKELLYD----VA---GSDKYQVNNKHDDKYSPLPCSK 91 (132)
Q Consensus 19 ~~y~H~GIYvGdg~ViH~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~----~~---~~~~~~v~n~~d~~~~~~~~~~ 91 (132)
+..-|.||---+|-|--|.++--... ..+...+..+.-.|.. +. .+...+-.-..........=|.
T Consensus 9 PfIGHvGIc~s~GvI~DFaG~y~V~~-------d~~aFG~p~rY~qLd~~~~~~~~~~~~~~~~~~~~~~~~g~~~~wD~ 81 (136)
T PF05608_consen 9 PFIGHVGICRSDGVILDFAGPYFVSV-------DNMAFGRPTRYWQLDRDKCCSPPNLSGHTCEEGYEHVERGGAETWDD 81 (136)
T ss_pred HHCCCEEEECCCCEEEECCCCCEECC-------CCCCCCCCEEEEEECHHHCCCCCCCCCCCCCCCHHCCCCCCHHHHHH
T ss_conf 31770377548952886278848701-------76265781389871878765666645445432100014565878999
Q ss_pred HHHHHHHHCCCCCCCEEEECCHHHHHHHHHCCC
Q ss_conf 999999970688772043428589999887388
Q T0630 92 IIQRAEELVGQEVLYKLTSENCEHFVNELRYGV 124 (132)
Q Consensus 92 iv~rA~~~lg~~~~Y~l~~nNCEHFa~~cr~G~ 124 (132)
.|++|.+..+ ...||||.+||++||.-|.+-.
T Consensus 82 Av~~a~~~F~-~r~yNLft~NCHSfVA~~LN~m 113 (136)
T PF05608_consen 82 AVSKASREFK-HRMYNLFTCNCHSFVANALNRM 113 (136)
T ss_pred HHHHHHHHHH-CCCCCEECCCHHHHHHHHHHHC
T ss_conf 9999999861-3745564258389999999865
No 6
>PF05903 DUF862: PPPDE putative peptidase domain; InterPro: IPR008580 This domain consists of the N-terminal portion of several eukaryotic sequences. The function of this domain is unknown.; PDB: 3ebq_A.
Probab=94.07 E-value=0.012 Score=33.68 Aligned_cols=36 Identities=22% Similarity=0.376 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHHHHHCCC---CCCCEEEECCHHHHHHHHH
Q ss_conf 788989999999997068---8772043428589999887
Q T0630 85 SPLPCSKIIQRAEELVGQ---EVLYKLTSENCEHFVNELR 121 (132)
Q Consensus 85 ~~~~~~~iv~rA~~~lg~---~~~Y~l~~nNCEHFa~~cr 121 (132)
+.++.+++.+-. ..|.. ...|||+.+||-||+..+.
T Consensus 79 T~~~~~~~~~~l-~~l~~~~~~~~Y~Ll~~NCnhFs~~l~ 117 (150)
T PF05903_consen 79 TTLSQEEFEEIL-RSLSAEFTGDSYHLLNRNCNHFSDALC 117 (150)
T ss_dssp B---HHHHHHHH-HH----------BTTTB-HHHHHHHHH
T ss_pred CCCCHHHHHHHH-HHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 748999999999-999855165532566652788999999
No 7
>PF08007 Cupin_4: Cupin superfamily protein; InterPro: IPR013109 This family contains many hypothetical proteins that belong to the cupin superfamily.; PDB: 2ilm_A 1h2k_A 1h2m_A 1mze_A 2cgn_A 1yci_A 1mzf_A 1iz3_A 3d8c_A 1h2l_A ....
Probab=91.13 E-value=0.073 Score=28.93 Aligned_cols=29 Identities=31% Similarity=0.521 Sum_probs=23.8
Q ss_pred CCCCCCCEEEEECCCEEEEEEEECCCEEEEEE
Q ss_conf 00577867987269755899987791799852
Q T0630 6 PEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLA 37 (132)
Q Consensus 6 ~~~k~GDlI~~~r~~y~H~GIYvGdg~ViH~~ 37 (132)
-.++|||++|+|++.+ |+|+..+ .-+|++
T Consensus 178 ~~L~pGD~LYiP~g~~-H~~~~~~--~s~~~s 206 (319)
T PF08007_consen 178 VVLEPGDVLYIPRGWW-HYAEALD--PSLHLS 206 (319)
T ss_dssp EEE----EEEE-TT-E-EEEEESS---EEEEE
T ss_pred EEECCCCEEEECCCCE-EEEEECC--CCEEEE
T ss_conf 9988998899789965-9879889--967999
No 8
>PF06672 DUF1175: Protein of unknown function (DUF1175); InterPro: IPR009558 This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=85.01 E-value=0.43 Score=24.18 Aligned_cols=34 Identities=32% Similarity=0.543 Sum_probs=25.8
Q ss_pred CCCCCCCCEEEEECCC---EEEEEEEECC----CEEEEEEC
Q ss_conf 1005778679872697---5589998779----17998526
Q T0630 5 IPEPKPGDLIEIFRPF---YRHWAIYVGD----GYVVHLAP 38 (132)
Q Consensus 5 ~~~~k~GDlI~~~r~~---y~H~GIYvGd----g~ViH~~~ 38 (132)
....+|||||.|.-.. +.|-=||+|+ .-|.|-.+
T Consensus 133 ~~~A~PGDL~Ff~q~d~~~pyHlMI~~g~~~~~~~vYHtG~ 173 (216)
T PF06672_consen 133 VSQARPGDLLFFHQEDDQMPYHLMIWVGRDAENYIVYHTGP 173 (216)
T ss_pred HHHCCCCCEEEECCCCCCCCEEEEEEEECCCCEEEEEECCC
T ss_conf 75459876788647887641379999605651369983378
No 9
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 At least one of the members of this domain, the Pal protein from the pneumococcal bacteriophage Dp-1 O03979 from SWISSPROT has been shown to be an N-acetylmuramoyl-L-alanine amidase . According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside in the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids , .
Probab=84.61 E-value=0.42 Score=24.26 Aligned_cols=32 Identities=16% Similarity=0.166 Sum_probs=25.9
Q ss_pred CCCCCCCEEEEECC-----CEEEEEEEECCCEEEEEE
Q ss_conf 00577867987269-----755899987791799852
Q T0630 6 PEPKPGDLIEIFRP-----FYRHWAIYVGDGYVVHLA 37 (132)
Q Consensus 6 ~~~k~GDlI~~~r~-----~y~H~GIYvGdg~ViH~~ 37 (132)
.++|+||++-+-.. -+-|.||+.+...+||-.
T Consensus 74 ~~~q~GDI~I~g~~g~S~Ga~GHtgi~~~~~~~ihc~ 110 (145)
T PF05382_consen 74 WDLQRGDIVIWGKRGQSGGAGGHTGIFMDWDNIIHCN 110 (145)
T ss_pred CCCCCCCEEEECCCCCCCCCCCEEEEEECCCEEEEEC
T ss_conf 7777789999827777789897379996698088723
No 10
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272)
Probab=84.06 E-value=0.53 Score=23.64 Aligned_cols=36 Identities=31% Similarity=0.325 Sum_probs=24.3
Q ss_pred CCCCCCCEEEEECCC--------------E-EEEEEEEC----CCEEEEEECCCC
Q ss_conf 005778679872697--------------5-58999877----917998526766
Q T0630 6 PEPKPGDLIEIFRPF--------------Y-RHWAIYVG----DGYVVHLAPPSE 41 (132)
Q Consensus 6 ~~~k~GDlI~~~r~~--------------y-~H~GIYvG----dg~ViH~~~~~~ 41 (132)
-.|+|||||...|+. | .|-+|.|- |...|...+.+.
T Consensus 92 ~~P~~GDlic~~R~~~~~~~~~~~~~~~~~~sHcdiVVa~n~~d~~~i~~IGGNv 146 (183)
T PF10030_consen 92 YAPAPGDLICADRGRDKSLDYAGLITAGGFPSHCDIVVAANVVDPREISTIGGNV 146 (183)
T ss_pred CCCCCCCEEECCCCCCCCCCCHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCCC
T ss_conf 6899876786158877513612202355652333479986026877158843754
No 11
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism , . The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands , . Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigene putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2vpm_B 2vps_A 2vob_A 2io8_B 2ioa_A 2iob_B 2io9_B 2io7_A 2k3a_A.
Probab=78.86 E-value=0.42 Score=24.27 Aligned_cols=27 Identities=33% Similarity=0.347 Sum_probs=21.5
Q ss_pred CCCCCCCCCEEEE---ECCCEEEEEEEECC
Q ss_conf 8100577867987---26975589998779
Q T0630 4 PIPEPKPGDLIEI---FRPFYRHWAIYVGD 30 (132)
Q Consensus 4 ~~~~~k~GDlI~~---~r~~y~H~GIYvGd 30 (132)
....|||||++.+ ....|-|.||....
T Consensus 59 ~~~~P~~Gdivv~~~~~~~~~GHVaiV~~v 88 (124)
T PF05257_consen 59 TGSTPKPGDIVVFDSGGSGGYGHVAIVEKV 88 (124)
T ss_dssp EES---SSBEEEBEEBTTC----EEEEEEE
T ss_pred CCCCCCCCEEEEECCCCCCCCCCEEEEEEE
T ss_conf 899987366999636789599868989998
No 12
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2im9_A 2p1g_A.
Probab=69.27 E-value=0.54 Score=23.57 Aligned_cols=55 Identities=25% Similarity=0.346 Sum_probs=33.2
Q ss_pred CCCCCCCCEEEEECC----CEEEEEEEECCCEEEEEECCCCCCCCCCEEEEECCCCCCCEEEEEEEEEECC
Q ss_conf 100577867987269----7558999877917998526766434661133100267852578772335358
Q T0630 5 IPEPKPGDLIEIFRP----FYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIVKKELLYDVAGS 71 (132)
Q Consensus 5 ~~~~k~GDlI~~~r~----~y~H~GIYvGdg~ViH~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~ 71 (132)
.+.++.||+|.+-+. -.+|.||.+-.+.-+||-..+ +...+..|.-.+|.+++.+
T Consensus 151 ~~~l~~GDiI~i~t~~~GLDVtH~Gi~i~~~~~~~lrhAS------------s~~~~~~Vvd~pl~~Yv~~ 209 (216)
T PF07313_consen 151 LSQLQTGDIIGIYTNDPGLDVTHVGIAIRTNDGLHLRHAS------------SLKGNVVVVDEPLSDYVKN 209 (216)
T ss_dssp HTTS----EEEEEEEE--EEEEE---EEEETTEEEEEEE-------------S----EEEEEEEHHHHHHC
T ss_pred HHHCCCCCEEEEEECCCCCCEEEEEEEEEECCEEEEEECC------------CCCCCCEEECCCHHHHHHC
T ss_conf 9528999889998069997325788999979935999568------------8678747947568999852
No 13
>PF03079 ARD: ARD/ARD' family; InterPro: IPR004313 The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ . ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions . ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels , . This family also contains other proteins, whose functions are not well characterised.; PDB: 1vr3_A 2hji_A 1zrr_A.
Probab=66.82 E-value=1.1 Score=21.60 Aligned_cols=19 Identities=37% Similarity=0.422 Sum_probs=13.0
Q ss_pred CCCCCCEEEEECCCEEEEEE
Q ss_conf 05778679872697558999
Q T0630 7 EPKPGDLIEIFRPFYRHWAI 26 (132)
Q Consensus 7 ~~k~GDlI~~~r~~y~H~GI 26 (132)
..++||||.+|.+.| ||--
T Consensus 118 ~~e~GDli~vPag~~-HrF~ 136 (157)
T PF03079_consen 118 EVEKGDLIVVPAGTY-HRFT 136 (157)
T ss_dssp E--TTSEEEE-TT---EEE-
T ss_pred EEECCCEEECCCCCE-EEEE
T ss_conf 992799997399961-8787
No 14
>PF11948 DUF3465: Protein of unknown function (DUF3465)
Probab=61.17 E-value=2.8 Score=19.15 Aligned_cols=32 Identities=31% Similarity=0.491 Sum_probs=19.1
Q ss_pred CCCCCCCCCCEEEEECCCEEEEEEEECCCEEEEEECC
Q ss_conf 8810057786798726975589998779179985267
Q T0630 3 APIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPP 39 (132)
Q Consensus 3 ~~~~~~k~GDlI~~~r~~y~H~GIYvGdg~ViH~~~~ 39 (132)
-..|.+++||.|+|.- -| .|--.|-|||++..
T Consensus 81 prip~L~~GD~V~f~G-eY----ewn~kggvIHWTH~ 112 (131)
T PF11948_consen 81 PRIPGLKKGDTVEFYG-EY----EWNPKGGVIHWTHH 112 (131)
T ss_pred CCCCCCCCCCEEEEEE-EE----EECCCCCEEEEECC
T ss_conf 6677788899899977-99----87699987980536
No 15
>PF11649 T4_neck-protein: Virus neck protein
Probab=57.12 E-value=1.8 Score=20.42 Aligned_cols=14 Identities=43% Similarity=0.508 Sum_probs=12.0
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 00577867987269
Q T0630 6 PEPKPGDLIEIFRP 19 (132)
Q Consensus 6 ~~~k~GDlI~~~r~ 19 (132)
.+|+.||||+||-+
T Consensus 112 ~rP~eGDLIyfPm~ 125 (230)
T PF11649_consen 112 GRPKEGDLIYFPMT 125 (230)
T ss_pred CCCCCCCEEEEECC
T ss_conf 77775877999757
No 16
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells , .They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins .; PDB: 1yab_B 1o9y_B.
Probab=40.57 E-value=8.1 Score=16.32 Aligned_cols=28 Identities=25% Similarity=0.335 Sum_probs=23.4
Q ss_pred CCCCCCCEEEEECCCEEEEEEEECCCEE
Q ss_conf 0057786798726975589998779179
Q T0630 6 PEPKPGDLIEIFRPFYRHWAIYVGDGYV 33 (132)
Q Consensus 6 ~~~k~GDlI~~~r~~y~H~GIYvGdg~V 33 (132)
-++++||+|.+......+.=+|+++-.+
T Consensus 27 l~L~~Gdvi~l~~~~~~~v~l~v~g~~~ 54 (77)
T PF01052_consen 27 LNLKVGDVIPLDKPADEPVELYVNGRPI 54 (77)
T ss_dssp HC-----EEEESSB-----EEEE---EE
T ss_pred HCCCCCCEEEECCCCCCCEEEEECCEEE
T ss_conf 6689999999189899959999999999
No 17
>PF10077 DUF2314: Uncharacterized protein conserved in bacteria (DUF2314)
Probab=35.83 E-value=10 Score=15.64 Aligned_cols=20 Identities=35% Similarity=0.562 Sum_probs=6.8
Q ss_pred CCCCCEEEEECCCEEEEEEE
Q ss_conf 57786798726975589998
Q T0630 8 PKPGDLIEIFRPFYRHWAIY 27 (132)
Q Consensus 8 ~k~GDlI~~~r~~y~H~GIY 27 (132)
+|.||.|.+++...+-|-++
T Consensus 80 ~k~Gd~v~~~~~~I~DW~~~ 99 (133)
T PF10077_consen 80 VKEGDRVEFPREDISDWMYY 99 (133)
T ss_pred CCCCCEEEECHHHEEEEEEE
T ss_conf 67799898786770667998
No 18
>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zw10 and rough deal proteins are both required for correct metaphase check-pointing during mitosis ,. These proteins bind to the centromere/kinetochore .; GO: 0007067 mitosis, 0000775 chromosome, pericentric region, 0005634 nucleus
Probab=29.56 E-value=7.5 Score=16.52 Aligned_cols=17 Identities=18% Similarity=0.256 Sum_probs=14.5
Q ss_pred CEEEECCHHHHHHHHHC
Q ss_conf 20434285899998873
Q T0630 106 YKLTSENCEHFVNELRY 122 (132)
Q Consensus 106 Y~l~~nNCEHFa~~cr~ 122 (132)
=-+|-|||.++|.|+..
T Consensus 513 aalf~NdC~Ylah~l~~ 529 (595)
T PF06248_consen 513 AALFHNDCMYLAHHLLT 529 (595)
T ss_pred HHHHCCCHHHHHHHHHH
T ss_conf 68441562999999998
No 19
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 P-type (or E1-E2-type) ATPases constitute a superfamily of cation transport enzymes, present both in prokaryota and eukaryota, whose members mediate membrane flux of all common biologically relevant cations . The enzymes, that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups : (1) Ca^2+-transporting ATPases; (2) Na^+/K^+- and gastric H^+/K^+-transporting ATPases; (3) plasma membrane H^+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the Mg^2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. ; GO: 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0016020 membrane; PDB: 2hc8_A 2b8e_A 2voy_F 2zxe_A 3b8e_C 3b8c_A 1mhs_B 2eat_A 2by4_A 3ba6_A ....
Probab=27.87 E-value=5 Score=17.61 Aligned_cols=19 Identities=32% Similarity=0.373 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCEEEEECCC
Q ss_conf 8881005778679872697
Q T0630 2 RAPIPEPKPGDLIEIFRPF 20 (132)
Q Consensus 2 ~~~~~~~k~GDlI~~~r~~ 20 (132)
+.|..+++|||+|.+..+.
T Consensus 46 ~i~~~~L~~GDIi~l~~G~ 64 (228)
T PF00122_consen 46 EIPSSELVPGDIIILKAGD 64 (228)
T ss_dssp EEEGGGT----EEEB----
T ss_pred EECHHHEECCCEEEECCCC
T ss_conf 9628992116378640254
No 20
>PF05820 DUF845: Baculovirus protein of unknown function (DUF845); InterPro: IPR008563 This family consists of several highly related baculovirus proteins of unknown function.
Probab=26.58 E-value=16 Score=14.58 Aligned_cols=22 Identities=23% Similarity=0.462 Sum_probs=15.8
Q ss_pred HHHHHHCCCCCCCEEEECCHHH
Q ss_conf 9999970688772043428589
Q T0630 94 QRAEELVGQEVLYKLTSENCEH 115 (132)
Q Consensus 94 ~rA~~~lg~~~~Y~l~~nNCEH 115 (132)
+..+..+..+..+|+.++|||-
T Consensus 93 ~eL~~~vegEN~FNiaf~NCEs 114 (119)
T PF05820_consen 93 KELRKFVEGENNFNIAFNNCES 114 (119)
T ss_pred HHHHHHHHCCCCCEEEHHCCHH
T ss_conf 9999997222341101003043
No 21
>PF06251 DUF1017: SLBB-domain like (DUF1017); InterPro: IPR010425 This is a family of uncharacterised protein from proteobacteria.
Probab=23.04 E-value=16 Score=14.52 Aligned_cols=16 Identities=25% Similarity=0.208 Sum_probs=12.7
Q ss_pred CCCCCCCCCEEEEECC
Q ss_conf 8100577867987269
Q T0630 4 PIPEPKPGDLIEIFRP 19 (132)
Q Consensus 4 ~~~~~k~GDlI~~~r~ 19 (132)
.-+.++-||.|+++.-
T Consensus 56 ~n~~L~ggd~L~vP~r 71 (173)
T PF06251_consen 56 YNPELEGGDQLYVPPR 71 (173)
T ss_pred CCCCCCCCCEEEECCC
T ss_conf 7984279988997899
No 22
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=20.99 E-value=11 Score=15.50 Aligned_cols=14 Identities=36% Similarity=0.721 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCEEE
Q ss_conf 88810057786798
Q T0630 2 RAPIPEPKPGDLIE 15 (132)
Q Consensus 2 ~~~~~~~k~GDlI~ 15 (132)
.-|++|+++||++.
T Consensus 28 ~k~VeELkEgDIL~ 41 (110)
T PF06819_consen 28 EKPVEELKEGDILG 41 (110)
T ss_pred CCCHHHCCCCCEEE
T ss_conf 26665517643211
No 23
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L19 is one of the proteins from the large ribosomal subunit , . In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1vs8_P 2qox_P 3df4_P 2qam_P 3df2_P 2qbc_P 2qao_P 2gya_N 2j28_P 2qbi_P ....
Probab=20.17 E-value=17 Score=14.41 Aligned_cols=18 Identities=28% Similarity=0.597 Sum_probs=14.2
Q ss_pred CCCCCCCCCCCCEEEEEC
Q ss_conf 988810057786798726
Q T0630 1 MRAPIPEPKPGDLIEIFR 18 (132)
Q Consensus 1 ~~~~~~~~k~GDlI~~~r 18 (132)
++.+.|+.++||.|.+..
T Consensus 12 ~k~~~p~f~~GD~V~V~~ 29 (113)
T PF01245_consen 12 LKKDIPEFRVGDTVKVHY 29 (113)
T ss_dssp CSSSSS-S----BEEEEE
T ss_pred HCCCCCCCCCCCEEEEEE
T ss_conf 425899879998999999
Done!