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!