Query T0599 IDP1205, , 399 residues Match_columns 399 No_of_seqs 147 out of 1826 Neff 6.5 Searched_HMMs 11830 Date Mon Jul 5 09:10:19 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0599.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0599.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF00425 Chorismate_bind: chor 100.0 0 0 575.3 29.7 253 120-381 1-257 (257) 2 PF04715 Anth_synt_I_N: Anthra 96.9 0.00031 2.6E-08 40.9 4.0 55 22-86 84-140 (140) 3 PF04928 PAP_central: Poly(A) 64.7 0.19 1.6E-05 24.7 -2.4 122 208-336 6-134 (254) 4 PF03367 zf-ZPR1: ZPR1 zinc-fi 18.4 15 0.0013 13.7 0.9 62 257-323 75-139 (161) 5 PF04963 Sigma54_CBD: Sigma-54 16.6 22 0.0019 12.7 2.0 81 124-218 107-187 (195) 6 PF09754 PAC2: PAC2 family; PD 16.2 23 0.0019 12.7 1.7 32 121-152 80-111 (220) 7 PF12112 DUF3579: Protein of u 15.7 3 0.00025 17.7 -3.2 60 121-182 22-81 (92) 8 PF11590 DNAPolymera_Pol: DNA 14.4 25 0.0021 12.4 2.2 27 358-389 14-40 (41) 9 PF03668 ATP_bind_2: P-loop AT 12.9 28 0.0024 12.1 4.6 96 126-240 35-132 (284) 10 PF07598 DUF1561: Protein of u 12.7 28 0.0024 12.1 3.5 56 292-348 376-437 (633) No 1 >PF00425 Chorismate_bind: chorismate binding enzyme; InterPro: IPR015890 This entry represents the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase. Anthranilate synthase catalyses the reaction:chorismate + l-glutamine = anthranilate + pyruvate + l-glutamate. The enzyme is a tetramer comprising 2 I and 2 II components: this entry is restricted to component I that catalyses the formation of anthranilate using ammonia rather than glutamine, while component II provides glutamine amidotransferase activity IPR006220 from INTERPRO.; PDB: 1k0g_A 1k0e_A 1i7s_C 1i7q_C 1i1q_A 2eua_A 3bzm_A 3bzn_A 3gse_A 2fn1_A .... Probab=100.00 E-value=0 Score=575.28 Aligned_cols=253 Identities=45% Similarity=0.738 Sum_probs=247.3 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEECCCEE Q ss_conf 98999999999999986299506875358999627999989999999973898349988547666678627996278300 Q T0599 120 DHEVYMKGVKQGIEKIKDGDLKKIVLSRSLDVKSSGKIDKQKLLRELAEHNKHGYTFAVNLPKDENENSKTLIGASPELL 199 (399) Q Consensus 120 ~~~~y~~~v~~~~~~I~~Gd~~kvvLsr~~~~~~~~~~d~~~~~~~L~~~~p~~y~f~~~~~~~~~~~~~~~~gaSPE~l 199 (399) ++++|.++|++++++|++|+++||||||++.+++..++|++.+|++|++.||++|+|+++++ .|+|+|||+| T Consensus 1 ~~~~y~~~v~~~~~~I~~G~~~kvvLsr~~~~~~~~~~~~~~l~~~L~~~~p~~y~~~~~~~--------~~vgaSPE~l 72 (257) T PF00425_consen 1 SKEEYKEAVERAKEHIRAGDLYKVVLSRRFELKLPSPIDPLALYRRLRRRNPSPYSFYFEFG--------TFVGASPERL 72 (257) T ss_dssp -TTHHHHHHHHHHHHHH----SBEEEEEEEEEEESSEB-HHHHHHHHHHHSTTSBEEEEEES--------EEEEEBSSEE T ss_pred CHHHHHHHHHHHHHHHHCCCCEEEECCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEECC--------CEEECCHHHH T ss_conf 97899999999999997699669992379999768899999999999976999789999589--------4882694681 Q ss_pred EEEECC--EEEEEECCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC--CCCEECCCCCCCCCCCEE Q ss_conf 677488--7999863677889779899999999985071000356899999999888645--852215543202267346 Q T0599 200 VSRHGM--QVISNPLAGSRPRSDDPVEDKRRAEELLSSPKDLHEHAVVVEAVAAALRPYC--HTLYVPEKPSVIHSEAMW 275 (399) Q Consensus 200 ~~~~~~--~v~t~plaGT~~r~~~~~~D~~~~~~Ll~s~Ke~~Eh~mvvd~ir~~L~~~c--~sv~v~~~~~i~~~~~v~ 275 (399) ++++++ ++.|+|||||+||+.++++|..++++|++|+||++||.||||++||||+++| ++|+|++.|.|+++++|| T Consensus 73 ~~~~~~~~~v~t~plaGT~~r~~~~~~d~~~~~~L~~s~Ke~~Eh~mvvd~irn~L~~~~~~~sv~v~~~~~i~~~~~v~ 152 (257) T PF00425_consen 73 LRVDGGGRRVETRPLAGTRPRGADPEEDAELAEELLNSEKERAEHQMVVDLIRNDLSRICKPGSVKVPELPEIERYSNVQ 152 (257) T ss_dssp EEEETTTTEEEEEEBE-EEE--SSHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHTTEEESEEEEEEEEEEEE-SSEE T ss_pred EEEECCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCEE T ss_conf 89989552899964899868999968869999998748411689999999999988755279972357751664508689 Q ss_pred EEEEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECC Q ss_conf 89999999963889998999998488876588877999999998638999630333576528987210463567778988 Q T0599 276 HLSTEVKGELKNPNTSSLELAIALHPTPAVCGTPMEEAREAIQKIEPFDREFFTGMLGWSDLNGDGEWIVTIRCAEVQEN 355 (399) Q Consensus 276 HL~s~v~g~L~~~~~~~~~ll~~l~Pt~av~G~Pk~~A~~~I~~lE~~~Rg~Y~G~vG~~~~~G~~~~~V~IRsa~~~~~ 355 (399) ||+|.|+|+|+ ++.+.+|+++++||||||||+||.+||++|+++|+++||+|||+|||++.+|+++|+|+|||++++++ T Consensus 153 HL~s~i~g~l~-~~~~~~dll~al~Pt~av~G~Pk~~A~~~I~~~E~~~Rg~Y~G~vG~~~~~g~~~~~V~IRs~~~~~~ 231 (257) T PF00425_consen 153 HLVSRITGRLK-PGVSLLDLLRALHPTPAVTGAPKERAMEIIRELEPFPRGWYAGAVGWIDPDGDGDFAVAIRSAQIDGG 231 (257) T ss_dssp EEEEEEEEEES-TTS-HHHHHHHHSS-GGG----HHHHHHHHHHHSSSB-TT----EEEEETTCEEEEEE--SEEEEETT T ss_pred EEEEEEEEEEC-CCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCEEEEEEEEEEEEECC T ss_conf 98778999985-89998999997099976789716999999998669987434042689975798799999768999899 Q ss_pred EEEEEECCEEECCCCHHHHHHHHHHH Q ss_conf 89999731770268878999999999 Q T0599 356 TLRLYAGAGVVAESKPEDELAETSAK 381 (399) Q Consensus 356 ~~~l~AGaGIv~~S~p~~E~~Et~~K 381 (399) .++++||||||++|+|+.||+||.+| T Consensus 232 ~~~l~aG~GIv~~S~p~~E~~Et~~K 257 (257) T PF00425_consen 232 RARLYAGAGIVADSDPEKEWEETELK 257 (257) T ss_dssp EEEEEE-EEEBTT--HHHHHHHHHHH T ss_pred EEEEEECEEEECCCCHHHHHHHHHCC T ss_conf 99999542896899847899998449 No 2 >PF04715 Anth_synt_I_N: Anthranilate synthase component I, N terminal region; InterPro: IPR006805 Anthranilate synthase catalyses the first step in the biosynthesis of tryptophan. Component I catalyses the formation of anthranilate using ammonia and chorismate. The catalytic site lies in the adjacent region, described in the chorismate binding enzyme family (IPR005801 from INTERPRO). This region is involved in feedback inhibition by tryptophan . This family also contains a region of Para-aminobenzoate synthase component I.; GO: 0016833 oxo-acid-lyase activity, 0009058 biosynthetic process; PDB: 1k0g_A 1k0e_A 1i7s_C 1i7q_C 1i1q_A 1qdl_A. Probab=96.95 E-value=0.00031 Score=40.86 Aligned_cols=55 Identities=18% Similarity=0.184 Sum_probs=34.7 Q ss_pred CCCCCCCCCCCEEEEEEEHHHHHHHHH-CCHHHHHHHHCCCC-CCCCCCEEEEEEEEEECCCCEEEE Q ss_conf 786313788542775661122157673-01333377624632-234444068888998467870899 Q T0599 22 SSFFFASPTRTILAEGEFTTVKHHEIE-SFPELVQAVLRNAK-QAGNPNPIVVGALPFDRRKEVQLI 86 (399) Q Consensus 22 ~~f~F~~~~~~~~a~G~~~~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~~i~fD~~~~~~l~ 86 (399) ..++|.++ ..|+++|+....++ .++. .+... .|+..+.++..+++|||.++..++ T Consensus 84 ~~~pf~gG-----~~Gy~sYd~~~~~ep~l~~-----~~~~~~~Pd~~~~~~~~~iv~Dh~~~~~~l 140 (140) T PF04715_consen 84 SDLPFTGG-----LVGYFSYDLVRYIEPKLPS-----PDDPDELPDAAFGFYDRVIVFDHQKGRLYL 140 (140) T ss_dssp TTBTTSSE-----EE-EB-GGGGGGTS-S--------CBSSS---SEEEEEECEEEEEETTTTEEEE T ss_pred CCCCCCCE-----EEEEECHHHHHHHHCCCCC-----CCCCCCCCCEEEEECCEEEEEECCCCEEEC T ss_conf 78981440-----7888748776556423899-----777889986998831779999989995969 No 3 >PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined . The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006350 transcription; PDB: 1f5a_A 1q79_A 1q78_A 3c66_A 2o1p_A 1fa0_A 2q66_A 2hhp_A. Probab=64.71 E-value=0.19 Score=24.74 Aligned_cols=122 Identities=18% Similarity=0.321 Sum_probs=52.4 Q ss_pred EEEECCCCCCCCCCHHHHHHHHHHHH-----HCHHHHHHHHHHHHHHHHHHHHHCC--CCEECCCCCCCCCCCEEEEEEE Q ss_conf 99863677889779899999999985-----0710003568999999998886458--5221554320226734689999 Q T0599 208 ISNPLAGSRPRSDDPVEDKRRAEELL-----SSPKDLHEHAVVVEAVAAALRPYCH--TLYVPEKPSVIHSEAMWHLSTE 280 (399) Q Consensus 208 ~t~plaGT~~r~~~~~~D~~~~~~Ll-----~s~Ke~~Eh~mvvd~ir~~L~~~c~--sv~v~~~~~i~~~~~v~HL~s~ 280 (399) .|.||.-..|-..|......+.+.|. .|+.|..--.-|++.+++-+.+... --.+|+...+..-.-+..|--. T Consensus 6 ~t~pis~~~pt~~d~~~s~~L~~~L~~~~~~~s~ee~~~R~~vl~~l~~iv~~~v~~~~~~vp~~l~l~~~~~L~~ld~~ 85 (254) T PF04928_consen 6 VTKPISTAGPTEADLERSDSLEEFLKDQGLFESEEEEEKREEVLEKLQQIVKEWVKRALPSVPEDLDLLDDNLLRNLDEK 85 (254) T ss_dssp ----S------HHHHHHHHHHHHHHCC------HHHHHHHHHHHHHHHHHHHHHHHHSSSS--TT--TT-GGGGTT--HH T ss_pred CCCCCCCCCCCHHHHHCCHHHHHHHHHCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHCCCHH T ss_conf 88885589998155654099999999858988857751499999999999999975245779824478981465567988 Q ss_pred EEEEECCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEEEEEC Q ss_conf 99996388999899999848887658887799999999863899963033357652 Q T0599 281 VKGELKNPNTSSLELAIALHPTPAVCGTPMEEAREAIQKIEPFDREFFTGMLGWSD 336 (399) Q Consensus 281 v~g~L~~~~~~~~~ll~~l~Pt~av~G~Pk~~A~~~I~~lE~~~Rg~Y~G~vG~~~ 336 (399) =...| + +.-..|.|..+-|.. .==..|+++|.-+-. .||+|+-.+||++ T Consensus 86 s~rsL-n-G~Rv~d~Il~lVP~~----~~Fr~alR~IKlWAk-rRgIYsn~~GylG 134 (254) T PF04928_consen 86 SVRSL-N-GCRVTDEILRLVPNP----ETFRTALRAIKLWAK-RRGIYSNVFGYLG 134 (254) T ss_dssp HHHHH-----HHHHHHHCTSS-H----HHHHHHHHHHHHHHH-HTT-B-TT---B- T ss_pred HHHHH-H-HHHHHHHHHHHCCCH----HHHHHHHHHHHHHHH-HCCCCHHCCCCCC T ss_conf 98765-2-066899999978888----999999999999999-8375200025630 No 4 >PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0005515 protein binding, 0008270 zinc ion binding; PDB: 2qkd_A. Probab=18.37 E-value=15 Score=13.67 Aligned_cols=62 Identities=19% Similarity=0.243 Sum_probs=43.3 Q ss_pred CCCCEECCCCCCCC--CCCEEEEEEEEEEEECCCCCCHHHHHHHHCC-CCCCCCCCHHHHHHHHHHHCCC Q ss_conf 58522155432022--6734689999999963889998999998488-8765888779999999986389 Q T0599 257 CHTLYVPEKPSVIH--SEAMWHLSTEVKGELKNPNTSSLELAIALHP-TPAVCGTPMEEAREAIQKIEPF 323 (399) Q Consensus 257 c~sv~v~~~~~i~~--~~~v~HL~s~v~g~L~~~~~~~~~ll~~l~P-t~av~G~Pk~~A~~~I~~lE~~ 323 (399) ..++.+|++ .++- .+...-..|+|+|-|.+ ..+.|....| .-+....-+....++|++++.. T Consensus 75 ta~i~IPEl-~~ei~P~~~~~g~iTTVEGlL~~----i~~~L~~~~~~~~~~~~e~~~k~~~~~~~L~~~ 139 (161) T PF03367_consen 75 TATIEIPEL-GLEIEPGGTLGGFITTVEGLLTR----IIDNLERLQPERDSMDPEEKEKIEEFLEKLREI 139 (161) T ss_dssp T-EEEEGGG-TEEE--TTS----EEE----HHH----HHHHHHTTHHHHHHH-GGHHHHHHHHHHHTGGG T ss_pred CEEEEEECC-CEEECCCCCCCCEEEEHHHHHHH----HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 769999315-53985687776169869999999----999997532034358999999999999999999 No 5 >PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme . The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation; PDB: 2k9l_A 2k9m_A. Probab=16.62 E-value=22 Score=12.73 Aligned_cols=81 Identities=16% Similarity=0.157 Sum_probs=53.6 Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEECCCEEEEEE Q ss_conf 99999999999862995068753589996279999899999999738983499885476666786279962783006774 Q T0599 124 YMKGVKQGIEKIKDGDLKKIVLSRSLDVKSSGKIDKQKLLRELAEHNKHGYTFAVNLPKDENENSKTLIGASPELLVSRH 203 (399) Q Consensus 124 y~~~v~~~~~~I~~Gd~~kvvLsr~~~~~~~~~~d~~~~~~~L~~~~p~~y~f~~~~~~~~~~~~~~~~gaSPE~l~~~~ 203 (399) -...|..-.+.+..+++.++ ++.+.+... +....+..+++.||.|-..|-.- .---..|+.+++.. T Consensus 107 a~~ii~~~l~~l~~~~~~~i--ak~l~~s~e---~v~~a~~~I~~L~P~Pg~~f~~~---------~~~yi~PDv~V~~~ 172 (195) T PF04963_consen 107 AYRIIEEHLEDLAKRDYKKI--AKKLGISLE---EVQEALDLIRSLNPKPGRAFSSE---------EAEYIIPDVIVKKD 172 (195) T ss_dssp THHHHHHHHHHHH------------------------------------------------------------------- T ss_pred HHHHHHHHHHHHHHHHHCCC--CCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCC T ss_conf 99999999999987640121--000000000---00000000000000000000000---------00000000000000 Q ss_pred CCEEEEEECCCCCCC Q ss_conf 887999863677889 Q T0599 204 GMQVISNPLAGSRPR 218 (399) Q Consensus 204 ~~~v~t~plaGT~~r 218 (399) ++.+...-=..+.|+ T Consensus 173 ~g~~~V~ln~~~~P~ 187 (195) T PF04963_consen 173 DGEWEVELNDENLPR 187 (195) T ss_dssp --------------- T ss_pred CCCCCCCCCCCCCCC T ss_conf 000000000000000 No 6 >PF09754 PAC2: PAC2 family; PDB: 3gaa_B 3e35_A 2p90_B. Probab=16.22 E-value=23 Score=12.67 Aligned_cols=32 Identities=9% Similarity=0.087 Sum_probs=21.1 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEE Q ss_conf 89999999999999862995068753589996 Q T0599 121 HEVYMKGVKQGIEKIKDGDLKKIVLSRSLDVK 152 (399) Q Consensus 121 ~~~y~~~v~~~~~~I~~Gd~~kvvLsr~~~~~ 152 (399) ...|..-.++..+.+++-.+.+|++--.+... T Consensus 80 ~~~~~~~~~~l~~~~~~~gv~~Vi~L~g~~~~ 111 (220) T PF09754_consen 80 PGRWYEFAEELLDWAKELGVKEVITLGGLPAG 111 (220) T ss_dssp SCGHHHHHHHHHHHHHH----EEEEEEEEEES T ss_pred CHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC T ss_conf 16899999999999998199889998275389 No 7 >PF12112 DUF3579: Protein of unknown function (DUF3579) Probab=15.74 E-value=3 Score=17.73 Aligned_cols=60 Identities=10% Similarity=0.146 Sum_probs=37.1 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCC Q ss_conf 89999999999999862995068753589996279999899999999738983499885476 Q T0599 121 HEVYMKGVKQGIEKIKDGDLKKIVLSRSLDVKSSGKIDKQKLLRELAEHNKHGYTFAVNLPK 182 (399) Q Consensus 121 ~~~y~~~v~~~~~~I~~Gd~~kvvLsr~~~~~~~~~~d~~~~~~~L~~~~p~~y~f~~~~~~ 182 (399) +.+|.+++.-+...++.|- +++.|.-..=...+.+--..+=.+|+..+|.+|-|.++|.. T Consensus 22 PSDWaERL~gv~a~F~~~~--~l~ysp~v~P~~~~g~Kcv~Vd~~L~~~~P~afdfvm~FA~ 81 (92) T PF12112_consen 22 PSDWAERLCGVMASFRPGH--RLHYSPYVRPVVINGVKCVVVDPRLRDIEPMAFDFVMNFAK 81 (92) T ss_pred CCHHHHHHHHHHHHCCCCC--CEEECCCCCCEEECCEEEEEECHHHHHHCCHHHHHHHHHHH T ss_conf 7359999865886028998--42555631550318826999872864509189999997887 No 8 >PF11590 DNAPolymera_Pol: DNA polymerase catalytic subunit Pol; PDB: 1dml_B. Probab=14.38 E-value=25 Score=12.38 Aligned_cols=27 Identities=33% Similarity=0.586 Sum_probs=18.9 Q ss_pred EEEECCEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 99973177026887899999999999999984 Q T0599 358 RLYAGAGVVAESKPEDELAETSAKFQTMLKAL 389 (399) Q Consensus 358 ~l~AGaGIv~~S~p~~E~~Et~~K~~~ll~al 389 (399) .+.+|+|+ |..|-+||..|++.-...| T Consensus 14 ~i~~g~g~-----~~~eEEEtrqkL~~AF~iL 40 (41) T PF11590_consen 14 TIRSGAGL-----PVNEEEETRQKLRRAFRIL 40 (41) T ss_dssp -B---------------HHHHHHHHHHHHHHH T ss_pred HHCCCCCC-----CHHHHHHHHHHHHHHHHHH T ss_conf 74367420-----1012699999999998862 No 9 >PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This is a family of putative P-loop ATPases . Many of the proteins in this family are hypothetical and kinase activity has been proposed for some family members. This family contains an ATP-binding site and could be an ATPase. Probab=12.88 E-value=28 Score=12.13 Aligned_cols=96 Identities=22% Similarity=0.286 Sum_probs=0.0 Q ss_pred HHHHHHHHHHH--CCCCCEEEEEEEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEECCCEEEEEE Q ss_conf 99999999986--2995068753589996279999899999999738983499885476666786279962783006774 Q T0599 126 KGVKQGIEKIK--DGDLKKIVLSRSLDVKSSGKIDKQKLLRELAEHNKHGYTFAVNLPKDENENSKTLIGASPELLVSRH 203 (399) Q Consensus 126 ~~v~~~~~~I~--~Gd~~kvvLsr~~~~~~~~~~d~~~~~~~L~~~~p~~y~f~~~~~~~~~~~~~~~~gaSPE~l~~~~ 203 (399) ..+.+..+.+. .+...++.++-..+-.-.-. +....+..+++.+-..-.- |+-||.|.|+++- T Consensus 35 ~Ll~~l~~~~~~~~~~~~~vAi~iD~R~~~~~~-~~~~~~~~l~~~~~~~~il--------------FLdA~d~~Li~Ry 99 (284) T PF03668_consen 35 SLLPQLIELLSQSDGKIEKVAIVIDIRSREFFD-DLFEVLDELRKQGIDVKIL--------------FLDASDEVLIRRY 99 (284) T ss_pred HHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHH-HHHHHHHHHHHCCCCEEEE--------------EEECCHHHHHHHH T ss_conf 999999999862278888369999688805567-6999999999779963899--------------9979804999876 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHHHHCHHHHH Q ss_conf 8879998636778897798999999999850710003 Q T0599 204 GMQVISNPLAGSRPRSDDPVEDKRRAEELLSSPKDLH 240 (399) Q Consensus 204 ~~~v~t~plaGT~~r~~~~~~D~~~~~~Ll~s~Ke~~ 240 (399) ...=..+||++ ..+..+.-..+.+++..-++++ T Consensus 100 ~eTRR~HPL~~----~~~~le~I~~ER~~L~plr~~A 132 (284) T PF03668_consen 100 SETRRRHPLSK----NGTLLEAIEKERELLAPLRERA 132 (284) T ss_pred HHCCCCCCCCC----CCCCHHHHHHHHHHHHHHHHHC T ss_conf 64378898999----9972899999999999999848 No 10 >PF07598 DUF1561: Protein of unknown function (DUF1560) Protein of unknown function (DUF1561); InterPro: IPR011455 This is a family of paralogous proteins in Leptospira interrogans. Probab=12.74 E-value=28 Score=12.10 Aligned_cols=56 Identities=16% Similarity=0.305 Sum_probs=0.0 Q ss_pred HHHHHHHHCCCCC----CCCCCHHHHHHHHHHHCC-CCCCCEEEEEE-EECCCCCEEEEEEEE Q ss_conf 8999998488876----588877999999998638-99963033357-652898721046356 Q T0599 292 SLELAIALHPTPA----VCGTPMEEAREAIQKIEP-FDREFFTGMLG-WSDLNGDGEWIVTIR 348 (399) Q Consensus 292 ~~~ll~~l~Pt~a----v~G~Pk~~A~~~I~~lE~-~~Rg~Y~G~vG-~~~~~G~~~~~V~IR 348 (399) ++++....-|++. +||.=...++++|+||.. +.||..-+. | +||-..+.+=.|..| T Consensus 376 L~~IA~St~~~~~~~ig~CGvClLht~QMlAELqEyh~~~Plq~G-GYFFdTa~~~dPFiSfr 437 (633) T PF07598_consen 376 LWEIARSTTPGGQESIGICGVCLLHTFQMLAELQEYHSRGPLQSG-GYFFDTAPNRDPFISFR 437 (633) T ss_pred HHHHHHCCCCCCCEEEEECHHHHHHHHHHHHHHHHHCCCCCCCCC-CEEECCCCCCCCEEEHH T ss_conf 999863068887366465160898999999999863479998789-66366899999600344 Done!