Query         T0636 YP_108324.1, BURKHOLDERIA PSEUDOMALLEI, 336 residues
Match_columns 336
No_of_seqs    141 out of 7282
Neff          8.0 
Searched_HMMs 11830
Date          Thu Jul 22 15:19:30 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0636.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0636.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF00155 Aminotran_1_2:  Aminot 100.0       0       0  364.6  26.2  315   15-329     1-363 (363)
  2 PF00266 Aminotran_5:  Aminotra  99.9 5.5E-20 4.7E-24  145.9  28.5  303   18-325     1-371 (371)
  3 PF04864 Alliinase_C:  Allinase  99.9 7.5E-23 6.4E-27  164.5   9.9  266   52-332    45-361 (362)
  4 PF01053 Cys_Met_Meta_PP:  Cys/  99.6 2.5E-13 2.2E-17  102.8  18.9  303   14-333    19-385 (386)
  5 PF01041 DegT_DnrJ_EryC1:  DegT  99.5 6.6E-13 5.5E-17  100.1  18.5  262   31-304     5-310 (363)
  6 PF00464 SHMT:  Serine hydroxym  99.5 2.4E-12   2E-16   96.4  18.0  310    2-321     7-382 (399)
  7 PF01212 Beta_elim_lyase:  Beta  99.0 1.1E-12 9.4E-17   98.6  -5.6  243   29-279     7-283 (290)
  8 PF06838 Alum_res:  Aluminium r  99.0 3.1E-08 2.6E-12   69.8  15.6  255   32-294    28-328 (403)
  9 PF01276 OKR_DC_1:  Orn/Lys/Arg  98.9 5.1E-08 4.3E-12   68.4  16.0  220   48-272    64-326 (417)
 10 PF00202 Aminotran_3:  Aminotra  98.8 9.1E-09 7.7E-13   73.3   9.2  226   13-242    14-292 (339)
 11 PF02347 GDC-P:  Glycine cleava  98.8 2.5E-07 2.1E-11   63.9  14.8  285   30-329    80-429 (429)
 12 PF00282 Pyridoxal_deC:  Pyrido  98.3 0.00011 9.4E-09   46.8  17.5  223   55-279    84-368 (373)
 13 PF05889 SLA_LP_auto_ag:  Solub  97.7  0.0017 1.4E-07   39.2  15.0  268   62-334    68-389 (389)
 14 PF03841 SelA:  L-seryl-tRNA se  97.5 1.7E-05 1.4E-09   52.1   1.9  203   29-241    18-257 (367)
 15 PF01282 Ribosomal_S24e:  Ribos  57.1     3.2 0.00027   17.9   2.8   24   50-73     13-36  (84)
 16 PF03786 UxuA:  D-mannonate deh  42.4     5.8 0.00049   16.2   2.2   14  209-222   219-232 (351)
 17 PF00701 DHDPS:  Dihydrodipicol  36.0     9.3 0.00078   14.9   4.8   22  144-166   134-157 (289)
 18 PF07021 MetW:  Methionine bios  32.5      11 0.00089   14.5  10.1  158    5-189     5-184 (193)
 19 PF09581 Spore_III_AF:  Stage I  29.9      12 0.00098   14.3   2.7   16  319-334   163-178 (188)
 20 PF05728 UPF0227:  Uncharacteri  29.2      12   0.001   14.2   8.8  112   16-131     1-122 (187)
 21 PF05848 CtsR:  Firmicute trans  29.0      12   0.001   14.1   5.4   11   59-69     31-41  (152)
 22 PF04392 ABC_sub_bind:  ABC tra  28.4      12   0.001   14.1   2.7  114   51-167    43-163 (294)
 23 PF06252 DUF1018:  Protein of u  27.0      11 0.00092   14.4   1.6   79  255-334    25-117 (119)
 24 PF04914 DltD_C:  DltD C-termin  26.8     4.3 0.00037   17.0  -0.5   84  117-220    33-128 (130)
 25 PF05127 DUF699:  Putative ATPa  25.2      10 0.00085   14.7   1.1   23   89-111    25-48  (174)
 26 PF01974 tRNA_int_endo:  tRNA i  21.8      15  0.0013   13.5   1.5   20  288-307     6-25  (85)
 27 PF05448 AXE1:  Acetyl xylan es  21.7      16  0.0014   13.3   3.2   13   54-66     27-39  (320)
 28 PF02679 ComA:  (2R)-phospho-3-  21.0      17  0.0014   13.2   1.6   51   54-118    55-105 (244)
 29 PF05913 DUF871:  Bacterial pro  20.8      17  0.0014   13.2   2.1   37  121-162    96-132 (357)
 30 PF06153 DUF970:  Protein of un  20.0      18  0.0015   13.1   5.8   17  284-300    11-27  (109)

No 1  
>PF00155 Aminotran_1_2:  Aminotransferase class I and II 1-aminocyclopropane-1-carboxylate synthase signature aspartate aminotransferase signature;  InterPro: IPR004839 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped  into class I and class II. This entry includes proteins from both subfamilies.; GO: 0016769 transferase activity, transferring nitrogenous groups, 0030170 pyridoxal phosphate binding, 0009058 biosynthetic process; PDB: 1u08_A 1v2f_A 1v2d_A 1v2e_B 2r5c_A 2r5e_B 1yiz_B 1yiy_A 3fvx_B 3fvs_B ....
Probab=100.00  E-value=0  Score=364.57  Aligned_cols=315  Identities=26%  Similarity=0.352  Sum_probs=268.6

Q ss_pred             CCCEECCCCCCCCC----CCHHHHHHHHH---HHHHHHCCCCC-CHHHHHHHHHHHHC------CCHH-HEEEECCHHHH
Q ss_conf             55357357654888----76899999999---98750058898-61899999999848------8854-38860778899
Q T0636            15 AQAVCLAFNENPEA----VEPRVQAAIAA---AAARINRYPFD-AEPRVMRKLAEHFS------CPED-NLMLVRGIDEC   79 (336)
Q Consensus        15 ~~~i~L~~Nenp~~----p~~~v~~al~~---~~~~~~~Ypd~-~~~~Lr~aia~~~~------v~~d-~I~~t~Gs~~~   79 (336)
                      +++|+|++|.++++    ++|.+.+++.+   .....++|++. |+++||++++++++      ++++ +|++|+|++++
T Consensus         1 ~~~i~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~G~~~lr~~la~~~~~~~~~~~~~~~~i~~~~G~~~~   80 (363)
T PF00155_consen    1 KDVINLSSGDPLFDSQNPPLPEALKALLDGAADGSSILQYGPPQGYPELREALADFLGRRRGIPLDPDSNILITSGAQAA   80 (363)
T ss_dssp             TEEEBESSSSTSSTTTHHHHHHHHHHHHHHHHHHGGGTSS--TTHHHHHHHHHHHHHHHHHHHHTTGGEGEEEESHHHHH
T ss_pred             CCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEE
T ss_conf             97699859879974444465999999987655444425489942119999999997876059765776228961676223


Q ss_pred             HHHHHHHH---CCCCEEECCCCCHHHHHHHHHHCCCEEEECCC--CCCCCCHHHHHHHC--------CHHHHHHHCCCCC
Q ss_conf             99999984---69925763887356999999818803641554--35677889997300--------0243133036633
Q T0636            80 FDRISAEF---SSMRFVTAWPGFDGYRARIAVSGLRHFEIGLT--DDLLLDPNDLAQVS--------RDDCVVLANPSNP  146 (336)
Q Consensus        80 i~~~~~~~---~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~~--~~~~~d~~~l~~~~--------~~~~i~l~nPnNP  146 (336)
                      +..++.++   +||.|++++|+|+.|...++..|.+++.+|++  ++|++|++++++..        ++++++++|||||
T Consensus        81 ~~~~~~~~~~~~gd~vl~~~p~y~~~~~~~~~~g~~~~~~~~~~~~~~~~d~~~l~~~l~~~~~~~~~~~~i~i~~p~NP  160 (363)
T PF00155_consen   81 LFLLFRLLKLDPGDVVLVPEPTYPSYIRIARLAGAEVVPVPLDSEDDFGLDLDALEAALEEYRKRSPRPKAILIPNPHNP  160 (363)
T ss_dssp             HHHHHHHHHHTTTSEEEEEESSTTHHHHHHHHTTTEEEEEEBEETTTTEETHHHHHHHHHTHHTTTETEEEEEEESS-ST
T ss_pred             EEHHHHCCCCCCCCCCCCCCCCCCCCCCCHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCC
T ss_conf             30002101135644455557755422310103684699995045555576612133333222223455413521465456


Q ss_pred             CCCCCCHHHHHHH---HHHCCC-CCCCCCCCCCCCCCC------CHHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHH
Q ss_conf             2222237999999---973787-202521002588662------003324520012023465233434531311788999
Q T0636           147 TGQALSAGELDQL---RQRAGK-LLIDETYVDYSSFRA------RGLAYGENELVFRSFSKSYGLAGLRLGALFGPSELI  216 (336)
Q Consensus       147 TG~~~~~~~l~~l---~~~~~~-~IvDeaY~~f~~~~~------~~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i  216 (336)
                      ||.+++.+++.++   +++++. +|+||+|.+|.....      ..+...+++|+++||||+||+||+|+||++++++++
T Consensus       161 tG~~~s~~~l~~l~~~~~~~~~~li~De~y~~~~~~~~~~~~~~~~~~~~~~vi~~~S~SK~~g~~GlR~G~v~~~~~~~  240 (363)
T PF00155_consen  161 TGSVLSAEELRELAELARKYNVLLIEDEAYSDLVYGDPDFYSILSLLDEGPNVIVLGSFSKALGLPGLRVGFVVAPPELI  240 (363)
T ss_dssp             T-B---HHHHHHHHHHHHHTTSEEEEEETTTTGSSSSSHTHHHGGGHHTTTTEEEEEESTTTTTBGGGT-EEEEEEHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCHHCHHHH
T ss_conf             31455477655588763022023430441355543897777542235788418994133223333434666400134666


Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHCCCEEECCC-CCEEEEECCC--HHHH
Q ss_conf             9997337877877778999999974599----9999999999999999999985897861698-6478865698--8999
Q T0636           217 AAMKRKQWFCNVGTLDLHALEAALDNDR----AREAHIAKTLAQRRRVADALRGLGYRVASSE-ANFVLVENAA--GERT  289 (336)
Q Consensus       217 ~~l~~~~~~~~~~~~~~~aa~~~l~~~~----~~~~~~~~~~~~r~~l~~~l~~lg~~~~~s~-~~Fi~~~~~~--~~~~  289 (336)
                      +.+++...++..++++|.++.+++.+..    ++.+.++.++++++.+.+.|++.++++.++. +.|+|++...  +.++
T Consensus       241 ~~l~~~~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (363)
T PF00155_consen  241 AALRKLSRPWIISSPLQQAAAAALADPQFYDRHLRELRRRLRERRDRLREALEELGISVLPPPGGFFLWLDLDPLDAMEL  320 (363)
T ss_dssp             HHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSEEEHHSSSEEEEEEETHHHHHHH
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCEEEEEECCCCHHHHH
T ss_conf             54430001223202457899875325432221100256788789999998776206243036885289996565169999


Q ss_pred             HHHHHHC-CCEEEECCCCCCCCEEEEEE--CCHHHHHHHHHHH
Q ss_conf             9999876-93896077888887478874--7989999999999
Q T0636           290 LRFLRER-GIQVKDAGQFGLHHHIRISI--GREEDNDRLLAAL  329 (336)
Q Consensus       290 ~~~L~~~-gi~vr~~~~fg~~~~iRis~--~~~ee~~~l~~aL  329 (336)
                      ++.|.++ ||.++||..|+.++|+|||+  .+++++++++++|
T Consensus       321 ~~~L~~~~gi~v~~g~~f~~~~~iRi~~a~~~~~~~~~~~~~l  363 (363)
T PF00155_consen  321 AQKLLEEHGILVVPGSYFGVPGFIRISLAGLTPEEIEEAVERL  363 (363)
T ss_dssp             HHHHHHHHTEEEBEGGTTSSTTEEEEESSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHCCEEEEECCCCCCCCEEEEEEEECCHHHHHHHHCCC
T ss_conf             9999984999998377789999899996109999999983469


No 2  
>PF00266 Aminotran_5:  Aminotransferase class-V;  InterPro: IPR000192 Aminotransferases share certain mechanistic features with other pyridoxal- phosphate dependent enzymes, such as the covalent binding of the pyridoxal- phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped  into subfamilies. This entry represents the class V aminotransferases and the related, though functionally distinct, cysteine desulphurases.; GO: 0008483 transaminase activity, 0008152 metabolic process; PDB: 2hzp_A 3e9k_A 1qz9_A 1n2t_B 1elu_A 1n31_A 1elq_B 2bkw_A 2yrr_B 2yri_A ....
Probab=99.89  E-value=5.5e-20  Score=145.93  Aligned_cols=303  Identities=20%  Similarity=0.243  Sum_probs=207.1

Q ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC-----C------HHHHHHHHHHHHCCCH-HHEEEECCHHHHHHHHHH
Q ss_conf             573576548887689999999998750058898-----6------1899999999848885-438860778899999999
Q T0636            18 VCLAFNENPEAVEPRVQAAIAAAAARINRYPFD-----A------EPRVMRKLAEHFSCPE-DNLMLVRGIDECFDRISA   85 (336)
Q Consensus        18 i~L~~Nenp~~p~~~v~~al~~~~~~~~~Ypd~-----~------~~~Lr~aia~~~~v~~-d~I~~t~Gs~~~i~~~~~   85 (336)
                      |.|+.+- +=++|+.|++++.+.+.+....|..     +      ..+.|+.+++.+|+++ ++|+++.|+++++..+..
T Consensus         1 iYld~ag-~~~~p~~v~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~r~~la~ll~~~~~~~i~f~~~~t~~~~~~~~   79 (371)
T PF00266_consen    1 IYLDNAG-TGPLPPSVLEAISEYLEEFFGNPHSSIHHRSQEFQEIVEEAREKLARLLGAPPPEEIAFTSNTTEALNAVLR   79 (371)
T ss_dssp             EBBBTTT-S---BHHHHHHHHHHHHSTTTCTTTCSCTTSHHHHHHHHHHHHHHHHHHTSSGTGEEEEESSHHHHHHHHHH
T ss_pred             CEEECCC-CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             9703677-366979999999999987624876656753399999999999999997199853332322466554323300


Q ss_pred             HH-----CCCCEEECCCCCHHHH----HHHHHHCCCEEEECCCCCCCCCHHHHHHH--CCHHHHHHHCCCCCCCCCCCHH
Q ss_conf             84-----6992576388735699----99998188036415543567788999730--0024313303663322222379
Q T0636            86 EF-----SSMRFVTAWPGFDGYR----ARIAVSGLRHFEIGLTDDLLLDPNDLAQV--SRDDCVVLANPSNPTGQALSAG  154 (336)
Q Consensus        86 ~~-----~~~~vii~~P~y~~y~----~~~~~~g~~~~~vp~~~~~~~d~~~l~~~--~~~~~i~l~nPnNPTG~~~~~~  154 (336)
                      .+     +|++|++..-.|+...    ...+..|.++..++.+.+..+|++++++.  .++++++++.-+|-||...+.+
T Consensus        80 ~l~~~~~~g~~il~~~~e~~s~~~~~~~~~~~~g~~v~~~~~~~~~~~~~~~l~~~i~~~~~lv~~s~~~~~tG~~~pi~  159 (371)
T PF00266_consen   80 SLRRNLKPGDEILVTNNEHPSNRLPWEELAERKGAEVREIPVDPGGEVDLEELEEAIDPRTRLVSISHVETSTGVRNPIE  159 (371)
T ss_dssp             HHHHHTTSSSEEEEECTSHHHHHHHHHHHHHHCCEEEEEEEBGTTSSBSHHHHHHHHHTTEEEEEEESBETTTTEBSSHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCEEECHH
T ss_conf             01134455421022233562046799875430530269941333210114667776346862698622677775883058


Q ss_pred             HHHHHHHHCCC-CCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCCCC-------
Q ss_conf             99999973787-2025210025886620033245200120234652334345313117889999997337877-------
Q T0636           155 ELDQLRQRAGK-LLIDETYVDYSSFRARGLAYGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMKRKQWFC-------  226 (336)
Q Consensus       155 ~l~~l~~~~~~-~IvDeaY~~f~~~~~~~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~~~~~~~-------  226 (336)
                      +|.+++++++. +++|.+.. ++.... .+...+--+++.|.-|.+|-+|  +|+++.+++.++.++.....|       
T Consensus       160 ~i~~~~~~~g~~~~vD~~~~-~g~~~i-d~~~~~~D~~~~s~~Kl~gp~G--~g~l~v~~~~~~~~~~~~~~~~~~~~~~  235 (371)
T PF00266_consen  160 EIAALAREYGALVVVDAAQS-AGAIPI-DLDELGVDFLVFSSHKLFGPPG--LGFLYVSPRAIEKLEPPFPGWGYVDDPS  235 (371)
T ss_dssp             HHHHHHHHTTSEEEEE-TTT-TTSS----TTTTTESEEEEESTSTTS------EEEEEEHHHHHHHHSSTCSSCTTTHTH
T ss_pred             HHHHHHHCCCCEEEEECCCC-CCCCCC-CCCCCCCCEEEECCCCCCCCCC--HHHHHCCHHHHHCCCCCCCCCCCCCCCC
T ss_conf             86566620697699831356-665555-5553322468755877778973--7787705987722487457887555643


Q ss_pred             ----------------CCCHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHCCC-EEECC-----CCCEEE--
Q ss_conf             ----------------87777899999997459--99999999999999999999985897-86169-----864788--
Q T0636           227 ----------------NVGTLDLHALEAALDND--RAREAHIAKTLAQRRRVADALRGLGY-RVASS-----EANFVL--  280 (336)
Q Consensus       227 ----------------~~~~~~~~aa~~~l~~~--~~~~~~~~~~~~~r~~l~~~l~~lg~-~~~~s-----~~~Fi~--  280 (336)
                                      +.+.++..+...+++..  .-++...++.....+++.+.|++++. .++.+     .++.+.  
T Consensus       236 ~~~~~~~~~~~~f~~GT~~~~~~~al~~al~~~~~~g~~~i~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~iv~~~  315 (371)
T PF00266_consen  236 LQEYGFKDDAQRFEPGTPNVPSIYALGEALKLLQEGGLEAIRERIRELAQYLREALEEIGGVRLLGPDDEPRSPSIVSFN  315 (371)
T ss_dssp             HHHHHHHHTTGGSSSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTEEESSCSGGGGGTTSEEEE
T ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCEEEEE
T ss_conf             54420235642223555205789999999999876304789999999999999999867866994353344556548999


Q ss_pred             EECCCHHHHHHHHHHCCCEEEECCCC--------CCCCEEEEEEC---CHHHHHHH
Q ss_conf             65698899999998769389607788--------88874788747---98999999
Q T0636           281 VENAAGERTLRFLRERGIQVKDAGQF--------GLHHHIRISIG---REEDNDRL  325 (336)
Q Consensus       281 ~~~~~~~~~~~~L~~~gi~vr~~~~f--------g~~~~iRis~~---~~ee~~~l  325 (336)
                      ++..+++++.+.|.++||.++.|...        +.++++|+|++   |++|+++|
T Consensus       316 ~~~~~~~~~~~~L~~~gI~~~~G~~~~~~~~~~~~~~~~iRvS~~~~nt~~dvd~l  371 (371)
T PF00266_consen  316 LPGIDAEDLVKALKERGIIISAGSACAGPSLRLLGLGGVIRVSLHYYNTEEDVDRL  371 (371)
T ss_dssp             ETTSSHHHHHHHHHHHHEBEBETTTTCHHHHHHTTTTTEEEEE--TTSSHHHHHHH
T ss_pred             ECCCCHHHHHHHHHCCCCEEECCCCCCHHHHHHCCCCCEEEEECCCCCCHHHHHHC
T ss_conf             64568999999985289817546640427888707998899858888999999539


No 3  
>PF04864 Alliinase_C:  Allinase;  InterPro: IPR006948 Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system .; GO: 0016846 carbon-sulfur lyase activity; PDB: 2hor_A 2hox_C 1lk9_A 3bwo_E 3bwn_B.
Probab=99.88  E-value=7.5e-23  Score=164.48  Aligned_cols=266  Identities=19%  Similarity=0.275  Sum_probs=179.7

Q ss_pred             HHHHHHHHHHHHC-----CCHH-HEEEECCHHHHHHHHHHHHCCC--------CEEECCCCCHHHHHHHHHHCCCEEEEC
Q ss_conf             1899999999848-----8854-3886077889999999984699--------257638873569999998188036415
Q T0636            52 EPRVMRKLAEHFS-----CPED-NLMLVRGIDECFDRISAEFSSM--------RFVTAWPGFDGYRARIAVSGLRHFEIG  117 (336)
Q Consensus        52 ~~~Lr~aia~~~~-----v~~d-~I~~t~Gs~~~i~~~~~~~~~~--------~vii~~P~y~~y~~~~~~~g~~~~~vp  117 (336)
                      .++|.+.|.+.|+     +..+ .|+++.|++|+|+.+..++..+        +|+...|.|+.|....+.+......  
T Consensus        45 s~eLe~~Ir~LH~~VGNAvtdgr~IV~GtGsTQL~~AavyALSp~~~~~~~p~~VVa~aPyY~~y~~qT~~~~s~~y~--  122 (362)
T PF04864_consen   45 SPELERHIRRLHRVVGNAVTDGRYIVFGTGSTQLLNAAVYALSPPATNSSPPASVVAAAPYYSVYKEQTDFFDSGLYK--  122 (362)
T ss_dssp             -HHHHHHHHHHHHH---B--TTSEEE-----HHHHHHHHHHHCHHT-TTSSSEEEEE-SS--CHHHHHCCCT-B--EE--
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCHHHHHHHCCCCCE--
T ss_conf             699999999999873452016737999277999999999970888788899631574488674328888761466833--


Q ss_pred             CCCCCCCCHHHHHHHC-CHHHH-HHHCCCCCCCCCCCHHHHHHHHHH-CCCCCCCCCCC--CCCCCCCCHHHHCCCHHHH
Q ss_conf             5435677889997300-02431-330366332222237999999973-78720252100--2588662003324520012
Q T0636           118 LTDDLLLDPNDLAQVS-RDDCV-VLANPSNPTGQALSAGELDQLRQR-AGKLLIDETYV--DYSSFRARGLAYGENELVF  192 (336)
Q Consensus       118 ~~~~~~~d~~~l~~~~-~~~~i-~l~nPnNPTG~~~~~~~l~~l~~~-~~~~IvDeaY~--~f~~~~~~~l~~~~n~iv~  192 (336)
                          |.-|........ ....| ++|+||||.|.+-  +.   .++. .+.+|.|-||.  .|++-+.    -.+.-|.+
T Consensus       123 ----w~Gda~~~~~~~~~~~~IElVTSPNNPDG~lr--~a---V~~g~~~k~I~D~AYYWPhyTpI~~----~aD~DiML  189 (362)
T PF04864_consen  123 ----WAGDASTFVNSDTPGPYIELVTSPNNPDGQLR--EA---VLNGSSGKAIHDLAYYWPHYTPITA----PADHDIML  189 (362)
T ss_dssp             ----E---GGGGTT-S-GGGEEEEEESS-S-------------S--TTEEEEEEE-TT-STTTS---S-----B--SEEE
T ss_pred             ----ECCCHHHHCCCCCCCCEEEEEECCCCCCCCHH--HH---HCCCCCCCEEEEEEEECCCCCCCCC----CCCCCEEE
T ss_conf             ----42578996578998873899838999851021--45---4069975314320000555566577----66675589


Q ss_pred             HHHHHHHCCCCCCCEEEC-CCHHHHHHHHHCC--CCCCCCHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHH
Q ss_conf             023465233434531311-7889999997337--87787777899999997459----------9999999999999999
Q T0636           193 RSFSKSYGLAGLRLGALF-GPSELIAAMKRKQ--WFCNVGTLDLHALEAALDND----------RAREAHIAKTLAQRRR  259 (336)
Q Consensus       193 ~S~SK~~gl~GlRiG~~i-~~~~~i~~l~~~~--~~~~~~~~~~~aa~~~l~~~----------~~~~~~~~~~~~~r~~  259 (336)
                      .|+||.-|.+|-|+||++ -++++.++|.+..  ++.++|.=+|.-+...|+..          +.+.--.+.++++.++
T Consensus       190 FTlSK~TGHAGsR~GWAlVKD~~Va~km~~y~~lnt~GvS~dsQLRa~kiLk~v~~~~~~~~g~~~F~fg~~~m~~RW~~  269 (362)
T PF04864_consen  190 FTLSKLTGHAGSRFGWALVKDEEVAKKMLKYMELNTIGVSRDSQLRALKILKVVLDGYKTNPGTEIFEFGYEVMRERWER  269 (362)
T ss_dssp             --HHHH----------EEES-HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHHCCHHSTTTTTT---HHHHHHHHH
T ss_pred             EEEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99731357664511046762399999999999761555768899999999999985116788624789999999999999


Q ss_pred             HHHHHHHCC-C--------------EEECCCCCEEEEECC--CHHHHHHHHHHCCCEEEECCCCCC-CCEEEEE-ECCHH
Q ss_conf             999998589-7--------------861698647886569--889999999876938960778888-8747887-47989
Q T0636           260 VADALRGLG-Y--------------RVASSEANFVLVENA--AGERTLRFLRERGIQVKDAGQFGL-HHHIRIS-IGREE  320 (336)
Q Consensus       260 l~~~l~~lg-~--------------~~~~s~~~Fi~~~~~--~~~~~~~~L~~~gi~vr~~~~fg~-~~~iRis-~~~~e  320 (336)
                      |.+.++.-+ +              ++.++.-.|-|++..  ..+++.+.|+++||.-|.|..||. ..|+|+| +.+.+
T Consensus       270 L~~~~~~S~rFSLq~~~~~yC~ff~~~~~psPafaWlkCe~eed~DC~~~L~~~~Iitr~G~~Fga~~ryvRlSll~~~d  349 (362)
T PF04864_consen  270 LRAAVSNSDRFSLQEIPPQYCNFFGKVREPSPAFAWLKCEWEEDEDCYAVLREAKIITRSGVLFGADSRYVRLSLLKRQD  349 (362)
T ss_dssp             HHHHHCCSSSEEE---SCEEETTTTEEEE---SEEEEEE-SCGGSSHHHHHHTTTEEEB------S-TTEEEEESSS-HH
T ss_pred             HHHHHHHCCCEECCCCCCHHCHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCHH
T ss_conf             99999637847558788221200053148998768886386441059999986881057887448887569987157675


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q T0636           321 DNDRLLAALAEY  332 (336)
Q Consensus       321 e~~~l~~aL~~~  332 (336)
                      +.+.|++.|++.
T Consensus       350 ~Fd~l~~rL~~l  361 (362)
T PF04864_consen  350 DFDQLLERLSKL  361 (362)
T ss_dssp             HHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHH
T ss_conf             699999999844


No 4  
>PF01053 Cys_Met_Meta_PP:  Cys/Met metabolism PLP-dependent enzyme;  InterPro: IPR000277    Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .   PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic .   A number of pyridoxal-dependent enzymes involved in the metabolism of cysteine, homocysteine and methionine have been shown ,  to be evolutionary related. These enzymes are proteins of about 400 amino-acid residues. The pyridoxal-P group is attached to a lysine residue located in the central section of these enzymes.; GO: 0030170 pyridoxal phosphate binding, 0006520 amino acid metabolic process; PDB: 1pff_B 1e5f_A 1e5e_A 1gc0_B 1gc2_C 1ukj_C 1pg8_D 2o7c_B 1y4i_A 2rfv_A ....
Probab=99.58  E-value=2.5e-13  Score=102.75  Aligned_cols=303  Identities=18%  Similarity=0.209  Sum_probs=180.3

Q ss_pred             CCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH--C
Q ss_conf             655357357654888768999999999875005889861---89999999984888543886077889999999984--6
Q T0636            14 AAQAVCLAFNENPEAVEPRVQAAIAAAAARINRYPFDAE---PRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF--S   88 (336)
Q Consensus        14 ~~~~i~L~~Nenp~~p~~~v~~al~~~~~~~~~Ypd~~~---~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~--~   88 (336)
                      ..-.|..++. -.|+.....  ++...-..-..|.-.+.   ..|.+++|+.-|-  +..++++.+..+|..++.++  +
T Consensus        19 v~pPI~~sst-f~~~~~~~~--~~~~~~~~~~~Y~R~gnPt~~~le~~la~LEg~--~~a~~~sSGmaAi~~~~~~ll~~   93 (386)
T PF01053_consen   19 VNPPIYQSST-FAFDSAEEL--DAFAGESKGYIYSRYGNPTVRALEERLAALEGG--EAALLFSSGMAAITAALLALLRP   93 (386)
T ss_dssp             SS--B---SB-BBBSSSHHH--HHHCTTT-S-SBTTTB-HHHHHHHHHHHHHHT---SEEE-B----HHHHHHHHHHS--
T ss_pred             CCCCEECCCC-CCCCCHHHH--HHHCCCCCCCCEECCCCCHHHHHHHHHHHHHCC--CCEEEECCHHHHHHHHHHHHCCC
T ss_conf             3288606666-337765777--865698778724089993157999999998576--53488636089999999974789


Q ss_pred             CCCEEECCCCCHHHHHHHH----HHCCCEEEECCCCCCCCCHHHHHHH--CCHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             9925763887356999999----8188036415543567788999730--002431330366332222237999999973
Q T0636            89 SMRFVTAWPGFDGYRARIA----VSGLRHFEIGLTDDLLLDPNDLAQV--SRDDCVVLANPSNPTGQALSAGELDQLRQR  162 (336)
Q Consensus        89 ~~~vii~~P~y~~y~~~~~----~~g~~~~~vp~~~~~~~d~~~l~~~--~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~  162 (336)
                      ||+|+++...|.+....++    .+|+++..+..     -|++++++.  .++++||+-+|.|||-.+.+.+.|.+++++
T Consensus        94 Gd~vv~~~~~Yg~t~~~l~~~~~~~gv~v~~~d~-----~d~~~~~~~i~~~t~~v~~EspsNP~l~v~Di~~i~~~a~~  168 (386)
T PF01053_consen   94 GDHVVASDDLYGGTRRLLREFLPRFGVEVTFVDP-----SDLDALEAAIDPNTKLVFLESPSNPTLEVPDIEAIAEIAHE  168 (386)
T ss_dssp             --EEEEESSS-HHHHHHHHHCHHH---EEEEEST-----TSHHHHHHHHCTTEEEEEEESSBTTTTB---HHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHCCCCCCEEEEEECC-----CCHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHHHHHHH
T ss_conf             9979995775431767656336678859999688-----68899999853577589998788777524678999999998


Q ss_pred             CC--CCCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHHCCCC-CCCEEECCC--HHHHHHHHHCCCCCC--CCHHHHHH
Q ss_conf             78--720252100258866200332452001202346523343-453131178--899999973378778--77778999
Q T0636           163 AG--KLLIDETYVDYSSFRARGLAYGENELVFRSFSKSYGLAG-LRLGALFGP--SELIAAMKRKQWFCN--VGTLDLHA  235 (336)
Q Consensus       163 ~~--~~IvDeaY~~f~~~~~~~l~~~~n~iv~~S~SK~~gl~G-lRiG~~i~~--~~~i~~l~~~~~~~~--~~~~~~~a  235 (336)
                      ++  .+|||..+...  .-..++... --||+.|.||.++-.| +=.|.++.+  +++.+.++..+..++  ++......
T Consensus       169 ~g~~~vvVDnT~atp--~~~~Pl~~G-aDivv~S~TKyl~Ghsdv~~G~vv~~~~~~~~~~~~~~~~~~G~~l~p~da~l  245 (386)
T PF01053_consen  169 HGDILVVVDNTFATP--VLQRPLELG-ADIVVHSATKYLSGHSDVMGGAVVTNGSEELIERLRFLRRLLGATLSPFDAWL  245 (386)
T ss_dssp             HST-EEEEEGTTTHT--TTS-GGG-----EEEEETTTTT----S--E-EEEESHHHHHHHHHHHHHHH---B--HHHHHH
T ss_pred             HCCEEEEEECCCCCC--CEECCCCCC-CCEEEEECCEEECCCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             597499980642276--050366567-82899847677238877435999988717889887777875388878799999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-C-EE-ECC----------------CCCEEEEECCCHH-HHHHHHHH
Q ss_conf             999974599999999999999999999998589-7-86-169----------------8647886569889-99999987
Q T0636           236 LEAALDNDRAREAHIAKTLAQRRRVADALRGLG-Y-RV-ASS----------------EANFVLVENAAGE-RTLRFLRE  295 (336)
Q Consensus       236 a~~~l~~~~~~~~~~~~~~~~r~~l~~~l~~lg-~-~~-~~s----------------~~~Fi~~~~~~~~-~~~~~L~~  295 (336)
                      ...-|   +-+.-+.++..++...+.+.|++.. + +| ||+                .|..+-+++.+.. .+.+++..
T Consensus       246 l~rgl---~TL~lR~~~~~~nA~~lA~~L~~hp~V~~V~yPgl~s~p~h~~~~~~~~g~gg~~sf~l~~~~~~~~~f~~~  322 (386)
T PF01053_consen  246 LLRGL---RTLALRMERHNENALALAEFLEAHPKVKRVNYPGLPSHPQHELAKRQMTGGGGMLSFELKGGEEAARRFIDA  322 (386)
T ss_dssp             HH------TTHHHHHHHHHHHHHHHHHHHHTSTTEEEEEETTSTTSTTHHHHHHHCSGG--EEEEEESSHHHHHHHHHHC
T ss_pred             HHHCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHH
T ss_conf             98058---989999999999999999998517998889974778871588886023688833899928847999999984


Q ss_pred             CCCE------------E-EECCC------------CCC-CCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             6938------------9-60778------------888-8747887479899999999999998
Q T0636           296 RGIQ------------V-KDAGQ------------FGL-HHHIRISIGREEDNDRLLAALAEYS  333 (336)
Q Consensus       296 ~gi~------------v-r~~~~------------fg~-~~~iRis~~~~ee~~~l~~aL~~~~  333 (336)
                      -.++            + .|...            .|. ++.+|+|+|.+ +.+.|++-|++-+
T Consensus       323 l~l~~~~~slGg~~SLi~~p~~~~h~~~~~e~~~~~Gi~~~lvRlsvGlE-d~~DLi~Dl~~AL  385 (386)
T PF01053_consen  323 LKLFKIAVSLGGVESLISHPASTTHRSMPEEERAAAGIPDGLVRLSVGLE-DPEDLIADLEQAL  385 (386)
T ss_dssp             -SSSEESS-----S-EEEETTTTTTTTSCHHHHHH----TTEEEEE------HHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCCCCCCCCCCHHHHCCCHHHHHHCCCCCCEEEEEECCC-CHHHHHHHHHHHH
T ss_conf             35405864678777455577523231299989975699999599994579-9999999999850


No 5  
>PF01041 DegT_DnrJ_EryC1:  DegT/DnrJ/EryC1/StrS aminotransferase family;  InterPro: IPR000653 The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA P72454 from SWISSPROT, StsC P77952 from SWISSPROT and StsS . The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase 2.6.1.50 from EC, which catalyzes the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin .; PDB: 3gr9_D 3b8x_A 2gms_B 2gmu_B 2r0t_A 3bb8_B 3bcx_A 3dr7_C 3dr4_B 3bn1_C ....
Probab=99.55  E-value=6.6e-13  Score=100.09  Aligned_cols=262  Identities=16%  Similarity=0.183  Sum_probs=168.2

Q ss_pred             HHHHHHHHHHHHHHHCCCC-C-CHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH---CCCCEEECCCCCHHHHHH
Q ss_conf             8999999999875005889-8-6189999999984888543886077889999999984---699257638873569999
Q T0636            31 PRVQAAIAAAAARINRYPF-D-AEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF---SSMRFVTAWPGFDGYRAR  105 (336)
Q Consensus        31 ~~v~~al~~~~~~~~~Ypd-~-~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~---~~~~vii~~P~y~~y~~~  105 (336)
                      ...++++.+.+..- .|.. . .-.++.+++|+++|+  ...+.++.++.|+.+++.++   +||+|+++.-+|......
T Consensus         5 ~~~~~~v~~vl~sg-~~~~~g~~~~~fE~~~a~~~g~--~~av~~~sgt~AL~~al~al~~~~gdeVi~p~~t~~at~~a   81 (363)
T PF01041_consen    5 EEELEAVLEVLRSG-WLTNYGPEVREFEKEFAEYFGV--KYAVAVSSGTSALHLALRALGVGPGDEVIVPAFTFPATASA   81 (363)
T ss_dssp             HHHHHHHHHHHHHT-TCB----HHHHHHHHHHHHCTS--SEEE-BSSCHHHHHHHHHH-S-BTT-EEEEESSS-THHHHH
T ss_pred             HHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHHCC--CEEEEECCHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHH
T ss_conf             99999999999809-9626998999999999998497--96999679999999999984178999899788655777999


Q ss_pred             HHHHCCCEEEECCC-CCCCCCHHHHHHH--CCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC-CCCCCCCCCCCCC
Q ss_conf             99818803641554-3567788999730--002431330366332222237999999973787202-5210025886620
Q T0636           106 IAVSGLRHFEIGLT-DDLLLDPNDLAQV--SRDDCVVLANPSNPTGQALSAGELDQLRQRAGKLLI-DETYVDYSSFRAR  181 (336)
Q Consensus       106 ~~~~g~~~~~vp~~-~~~~~d~~~l~~~--~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~Iv-DeaY~~f~~~~~~  181 (336)
                      +...|..++.+..+ ++|.+|++++++.  .++|+|++.   +.-|...+.++|.++++++++.|| |.+..-.+...-.
T Consensus        82 i~~~G~~pv~~Dvd~~t~~~d~~~~~~~i~~~t~aii~v---h~~G~~~d~~~i~~~~~~~~i~vIEDaa~a~g~~~~g~  158 (363)
T PF01041_consen   82 ILQAGAKPVFVDVDPDTLNIDPEALEKAITPKTKAIIPV---HLFGQPADMDEIREIARKHGIPVIEDAAQALGATYKGK  158 (363)
T ss_dssp             HHHTT-EEEEE-BETTTSSB-HHHHHHHHHTTEEEEEEE-----------HHHHHHHHHHCT-EEEEE-TT----EETTE
T ss_pred             HHHCCCEEEEEECCCCCCCCCHHHHHHHHHCCCEEEEEE---CCCCCCCCHHHHHHHHHHHCCEEEECCCCCCCCEECCE
T ss_conf             998299899982698989839999997621698799998---88678148999999999959999871757656725997


Q ss_pred             HHHHCCCHHHHHHH--HHHHCCCCCCCEEECC-CHHHHHHHHHCCCCC-------------------CCCHHHHHHHHHH
Q ss_conf             03324520012023--4652334345313117-889999997337877-------------------8777789999999
Q T0636           182 GLAYGENELVFRSF--SKSYGLAGLRLGALFG-PSELIAAMKRKQWFC-------------------NVGTLDLHALEAA  239 (336)
Q Consensus       182 ~l~~~~n~iv~~S~--SK~~gl~GlRiG~~i~-~~~~i~~l~~~~~~~-------------------~~~~~~~~aa~~~  239 (336)
                      .+-... .+.+.||  +|.+...  -=|.++. ++++.++++.++...                   .++.+....+...
T Consensus       159 ~~G~~g-d~~~fSF~~~K~i~~g--eGG~v~t~d~~~~~~~~~lr~~G~~~~~~~~~~~~~~~G~n~rm~~~~AAig~~Q  235 (363)
T PF01041_consen  159 KVGTFG-DAGVFSFHPTKNITTG--EGGAVVTNDEELAERARSLRNHGRSRDSFDRYEHELPIGYNYRMSELQAAIGLAQ  235 (363)
T ss_dssp             B----S-SBEE---STTSSS-S-------EEES-HHHHHHHHHHCBTCEETSSSSTTB-S-S---B-B-BHHHHHHHHHH
T ss_pred             ECCCCC-CEEEEECCCCCCCEEC--CCCCEEECCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHH
T ss_conf             556888-8899968998766106--9980653749999986577745876566652332105865567668999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CEEE--CCCC---C---E-EEEECC---CHHHHHHHHHHCCCEEEECC
Q ss_conf             74599999999999999999999998589-7861--6986---4---7-886569---88999999987693896077
Q T0636           240 LDNDRAREAHIAKTLAQRRRVADALRGLG-YRVA--SSEA---N---F-VLVENA---AGERTLRFLRERGIQVKDAG  304 (336)
Q Consensus       240 l~~~~~~~~~~~~~~~~r~~l~~~l~~lg-~~~~--~s~~---~---F-i~~~~~---~~~~~~~~L~~~gi~vr~~~  304 (336)
                      |+.   +.+.+++-++..+++.+.|+++. +...  +.+.   .   | +.++..   +-+.+.+.|.++||-++...
T Consensus       236 L~~---l~~~~~~R~~~a~~y~~~L~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~Rd~l~~~L~~~GI~t~~~y  310 (363)
T PF01041_consen  236 LKR---LDEIIARRRENAERYREALADLPGLRPLPIPPGNSEHSYHRYPIRLPEEALADRDELIEALRARGIETRVHY  310 (363)
T ss_dssp             HHC---HHHHHHHHHHHHHHHHHHHTTGSSEEEEGCGTTTEEEEESSEEEEETTTCHHCHHHHHHHHHHTTEB-BSST
T ss_pred             HHH---HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHCCCCEECCC
T ss_conf             999---999999999999999998558999656777888765212799999545322579999999998799634115


No 6  
>PF00464 SHMT:  Serine hydroxymethyltransferase;  InterPro: IPR001085 Synonym(s): Serine hydroxymethyltransferase, Serine aldolase, Threonine aldolase   Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme and belongs to the aspartate aminotransferase superfamily (fold type I) . The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme . The enzyme carries out interconversion of serine and glycine using PLP as the cofactor. SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer , . PLP dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalysed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V) , .   In vertebrates, glycine hydroxymethyltransferase exists in a cytoplasmic and a mitochondrial form whereas only one form is found in prokaryotes.; GO: 0004372 glycine hydroxymethyltransferase activity, 0006544 glycine metabolic process, 0006563 L-serine metabolic process; PDB: 3ecd_D 2dkj_A 2a7v_A 1bj4_A 1eji_C 1rv3_A 1ls3_C 1cj0_B 1rvu_A 1rvy_A ....
Probab=99.50  E-value=2.4e-12  Score=96.43  Aligned_cols=310  Identities=19%  Similarity=0.249  Sum_probs=195.4

Q ss_pred             CHHHHHHHHHCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHH--HHCCCCC------CHHHHHHHHH-----HHHCCCHH
Q ss_conf             511578975036655357357654888768999999999875--0058898------6189999999-----98488854
Q T0636             2 SVGEAMDTEVRAAAQAVCLAFNENPEAVEPRVQAAIAAAAAR--INRYPFD------AEPRVMRKLA-----EHFSCPED   68 (336)
Q Consensus         2 ~~~~~~~~~~~~~~~~i~L~~Nenp~~p~~~v~~al~~~~~~--~~~Ypd~------~~~~Lr~aia-----~~~~v~~d   68 (336)
                      +|.++++++...-...|.|--.||-  .+|.+++++...+..  ...||..      .+....|.+|     +.++.+++
T Consensus         7 ei~~~i~~e~~rq~~~l~LIASEN~--~S~~v~~algS~ltnkYaeG~pg~ryy~G~~~vD~iE~la~~ra~~lF~a~~~   84 (399)
T PF00464_consen    7 EIFELIEKEEERQRDTLNLIASENF--TSPAVLEALGSDLTNKYAEGYPGKRYYGGCEYVDEIEELAIERAKKLFGAEPK   84 (399)
T ss_dssp             HHHHHHHHHHHHHHHSEB--TT-------HHHHHH---GGGGS--------------HHHHHHHHHHHHHHHHHTT--TT
T ss_pred             HHHHHHHHHHHHHHCCEEEECCCCC--CCHHHHHHHCCCHHCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999988658657557565--89999998637130447788898677688774999999999999998599854


Q ss_pred             ----HEEEECCHHHHHHHHHHHH-CCCCEEECCCCCHHHHHHHHH----------HCCCEEEECCC-CCCCCCHHHHHHH
Q ss_conf             ----3886077889999999984-699257638873569999998----------18803641554-3567788999730
Q T0636            69 ----NLMLVRGIDECFDRISAEF-SSMRFVTAWPGFDGYRARIAV----------SGLRHFEIGLT-DDLLLDPNDLAQV  132 (336)
Q Consensus        69 ----~I~~t~Gs~~~i~~~~~~~-~~~~vii~~P~y~~y~~~~~~----------~g~~~~~vp~~-~~~~~d~~~l~~~  132 (336)
                          +|-.-+|++..+...+..+ +||+|+.+.+...++...-..          ...+.+.++.+ ++..+|.+++++.
T Consensus        85 ~w~anVqp~SGs~An~av~~ALl~pgD~im~l~l~~GGHlthg~~~~~~k~~~~g~~~~~~~Y~~d~~~~~IDyd~l~~~  164 (399)
T PF00464_consen   85 EWYANVQPHSGSQANLAVYFALLKPGDRIMGLSLPHGGHLTHGYKVNFKKVSASGKFYESVPYGVDPETGLIDYDELEKL  164 (399)
T ss_dssp             T-EEE-------HHHHHHHHHHT-S-EEEE---TT----TT---TTSSSBSSHHHHHSEE----B-TTTSSB-HHHHHHH
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCHHHHHHH
T ss_conf             55378845875899999999975347838953655687767676666532344354379998652466796679999999


Q ss_pred             ---CCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCC-CCCCCCCC-CC--CCCCCCHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf             ---002431330366332222237999999973787-20252100-25--886620033245200120234652334345
Q T0636           133 ---SRDDCVVLANPSNPTGQALSAGELDQLRQRAGK-LLIDETYV-DY--SSFRARGLAYGENELVFRSFSKSYGLAGLR  205 (336)
Q Consensus       133 ---~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~~~~-~IvDeaY~-~f--~~~~~~~l~~~~n~iv~~S~SK~~gl~GlR  205 (336)
                         .++|+|++.-=+.|  ..++-++++++++..+. +++|-+.. .+  ++..+.++.. -+ ||..|.-|+|  +|=|
T Consensus       165 a~~~kPklIi~G~S~y~--r~~d~~~~reIad~vga~l~~D~aH~aGLIA~g~~p~P~~~-AD-vVt~tTHKTl--rGPr  238 (399)
T PF00464_consen  165 AKEFKPKLIICGASAYP--RPIDFKRFREIADEVGAYLMADIAHIAGLIAGGLFPSPLPY-AD-VVTTTTHKTL--RGPR  238 (399)
T ss_dssp             HHHH--SEEEE--TS-S--S---HHHHHHHHHHTT-EEEEE-TTT---TTTTSS--GTTT-SS-EEE--SSGGG------
T ss_pred             HHHCCCCEEEECCHHCC--CCCCHHHHHHHHHHCCCEEEEEHHHHHHHEECCCCCCCCCC-CC-EEECCCCCCC--CCCC
T ss_conf             98769999998904437--77799999999987798999614556665127777998787-72-8976666566--6887


Q ss_pred             CEEECCC--------------HHHHHHHHHCCCCCCCCH--HHHHHHHH-HHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3131178--------------899999973378778777--78999999-9745--999999999999999999999985
Q T0636           206 LGALFGP--------------SELIAAMKRKQWFCNVGT--LDLHALEA-ALDN--DRAREAHIAKTLAQRRRVADALRG  266 (336)
Q Consensus       206 iG~~i~~--------------~~~i~~l~~~~~~~~~~~--~~~~aa~~-~l~~--~~~~~~~~~~~~~~r~~l~~~l~~  266 (336)
                      -|.++.+              +++.+++++..-|...+.  ....++++ ++..  ...++++.+++..+.+.|.+.|.+
T Consensus       239 gGiIl~~~g~~~~~~~~~~~~~~~~~kI~~avFPg~qggp~~h~iAa~Ava~~Ea~~~~fk~Ya~qVv~NAkaLA~~L~~  318 (399)
T PF00464_consen  239 GGIILTNKGYKNVDKQGKEIDEELAKKIDSAVFPGLQGGPHMHRIAALAVAFKEALSPEFKEYAKQVVKNAKALAEALNE  318 (399)
T ss_dssp             ---EEES----EE-T---EE-HHHHHHHHHHHTTTT-----HHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             06999805655555555521799999873241876434640768999999999865843899999999999999999976


Q ss_pred             CCCEEECCC--CCEEEEECC----CHHHHHHHHHHCCCEEE----ECCCCC-CCCEEEEEECCHHH
Q ss_conf             897861698--647886569----88999999987693896----077888-88747887479899
Q T0636           267 LGYRVASSE--ANFVLVENA----AGERTLRFLRERGIQVK----DAGQFG-LHHHIRISIGREED  321 (336)
Q Consensus       267 lg~~~~~s~--~~Fi~~~~~----~~~~~~~~L~~~gi~vr----~~~~fg-~~~~iRis~~~~ee  321 (336)
                      .|+++...+  ...+|+++.    ++..+.+.|.+.||.+.    |++... .+..|||  ||++-
T Consensus       319 ~G~~vv~ggTdnHlvlvD~~~~g~~g~~a~~~L~~agI~~Nkn~iP~d~~~~~~sGiRi--GT~~~  382 (399)
T PF00464_consen  319 RGFRVVSGGTDNHLVLVDLRSKGLTGKEAEKLLEEAGITVNKNTIPGDKSPFVPSGIRI--GTPAL  382 (399)
T ss_dssp             ---EE------SS-EEEEGGGGT----HHHHHHHHTTEB-B----TT-STTTT----EE----HHH
T ss_pred             CCCEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEE--CCHHH
T ss_conf             79748616987737999755356899999999997794760451578776768886896--88789


No 7  
>PF01212 Beta_elim_lyase:  Beta-eliminating lyase;  InterPro: IPR001597   This family includes tryptophanase (tryptophan indole-lyase, TNase) (4.1.99.1 from EC), tyrosine phenol-lyase (TPL) (4.1.99.2 from EC), threonine aldolase (4.1.2.5 from EC).; GO: 0016829 lyase activity, 0006520 amino acid metabolic process; PDB: 1svv_B 1v72_A 1c7g_A 1tpl_B 2vlh_B 2vlf_B 2tpl_B 2ez2_A 2ez1_A 1ax4_B ....
Probab=99.01  E-value=1.1e-12  Score=98.62  Aligned_cols=243  Identities=24%  Similarity=0.239  Sum_probs=141.0

Q ss_pred             CCHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH--CCCCEEECCCCCH-HHH-
Q ss_conf             76899999999987500588-986189999999984888543886077889999999984--6992576388735-699-
Q T0636            29 VEPRVQAAIAAAAARINRYP-FDAEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF--SSMRFVTAWPGFD-GYR-  103 (336)
Q Consensus        29 p~~~v~~al~~~~~~~~~Yp-d~~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~--~~~~vii~~P~y~-~y~-  103 (336)
                      |.|.++++|.++...-..|. |+...+|.+.+++.+|.+. -+++.+| +.+=.++++++  +++.|+...++-. .++ 
T Consensus         7 ~t~~m~~a~a~a~~gd~~Yg~D~~~~~le~~ia~l~g~e~-a~f~~sG-T~AN~lal~~~~~~~~~vi~~~~~Hi~~~E~   84 (290)
T PF01212_consen    7 PTPAMLEAMAAANVGDDAYGEDPTTNRLEERIAELFGKEA-ALFVPSG-TMANQLALRAHCRPGQSVICHDPAHIHFDET   84 (290)
T ss_dssp             --HHEEHHHHHTT---TT----HHHHHHHHHHHHHHTSTE-EEEE-----HHHHHHHHHHHHHHHEEEEETTESSHHCHH
T ss_pred             CCHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHCCCE-EEECCCC-HHHHHHHHHHHHCCCCEEEECCCCCCCEECC
T ss_conf             6799999997203453220679889999999999859986-9996885-6899999999606698899745761321174


Q ss_pred             -HHHHHHCCCEEEECCCCCCCCCHHHHHHHC--------CHHHHHHHCCCCCC-CCCCCHHHHHHH---HHHCCC-CCCC
Q ss_conf             -999981880364155435677889997300--------02431330366332-222237999999---973787-2025
Q T0636           104 -ARIAVSGLRHFEIGLTDDLLLDPNDLAQVS--------RDDCVVLANPSNPT-GQALSAGELDQL---RQRAGK-LLID  169 (336)
Q Consensus       104 -~~~~~~g~~~~~vp~~~~~~~d~~~l~~~~--------~~~~i~l~nPnNPT-G~~~~~~~l~~l---~~~~~~-~IvD  169 (336)
                       ....+.|.+++.++-+++..++++++++..        ++++|+|.||+|-- |++++.++|+++   ++++++ +.+|
T Consensus        85 ga~~~~~G~~~~~l~~~~~G~l~~~~l~~~~~~~~~h~~~~~~v~le~t~~~~gG~v~~~~el~~i~~~a~~~gl~lhmD  164 (290)
T PF01212_consen   85 GAPEELSGAKLVPLPGDDDGKLTPEDLEAAIEEHGDHAPQPALVSLENTTNSAGGTVYSLEELRAISELAREHGLPLHMD  164 (290)
T ss_dssp             HHHHHH---EEEEEB-GCGT-B-HHHHHHHHHHS-TTSTTEEEEEEESS-ST-------HHHHHHHHHHHHHTT-EEEEE
T ss_pred             CHHHHHHCCEEEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCEECCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             68999829789970785457769999999833566767874079998077687988588999999999999829989997


Q ss_pred             CCCCC----CCCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCCCC--CCC---HHH-----HHH
Q ss_conf             21002----5886620033245200120234652334345313117889999997337877--877---778-----999
Q T0636           170 ETYVD----YSSFRARGLAYGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMKRKQWFC--NVG---TLD-----LHA  235 (336)
Q Consensus       170 eaY~~----f~~~~~~~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~~~~~~~--~~~---~~~-----~~a  235 (336)
                      .|=.-    ....+...+..+-+.++ -|+||..|+|+=  +.++++++.++..++.+...  .+.   .++     +.+
T Consensus       165 GARl~na~~~~~~~~~e~~~~~D~v~-~~~tK~~ga~~G--avl~~~~~~i~~~~~~~k~~Gg~m~q~G~laa~~~~~~~  241 (290)
T PF01212_consen  165 GARLANAAAALGCTLAELAAGADSVS-FSLTKGGGAPGG--AVLAGSDDFIEEARRQRKRLGGGMRQAGILAAAELYQEA  241 (290)
T ss_dssp             -TTHHHHHSHHHHHHHHHHGG-SEEE-E-TTSTT-SS-E--EEEEESSGHHHHHHHHHHHHH-HHHHTHHCBCHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHCCCCEEE-EEEEECCCCCCC--EEEECCHHHHHHHHHHHHHHCCCEEECCCEEEECHHHHH
T ss_conf             23377654330579999960789999-961704766644--599827899999999999965870205611331012688


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEE-ECCCCCEE
Q ss_conf             999974599999999999999999999998589786-16986478
Q T0636           236 LEAALDNDRAREAHIAKTLAQRRRVADALRGLGYRV-ASSEANFV  279 (336)
Q Consensus       236 a~~~l~~~~~~~~~~~~~~~~r~~l~~~l~~lg~~~-~~s~~~Fi  279 (336)
                      +..++++.   .....+-.+.-+++.+.|+.++... .|+++|-+
T Consensus       242 ~l~~le~~---~~~~~~~~~~A~~la~~l~~~~~~~~~~~~tn~~  283 (290)
T PF01212_consen  242 GLRALELW---LERLAHDHAMAKRLAEGLEELGGALPRPVETNQV  283 (290)
T ss_dssp             HHBCEEEC---CTTHHHHSHHHHHHHHSHHEEEEEEETTSS-HHH
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCEE
T ss_conf             88888741---6889999999999999999789811189977557


No 8  
>PF06838 Alum_res:  Aluminium resistance protein ;  InterPro: IPR009651   This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria .; PDB: 3ht4_A 3gwp_B 3fd0_B.
Probab=98.96  E-value=3.1e-08  Score=69.82  Aligned_cols=255  Identities=15%  Similarity=0.214  Sum_probs=148.7

Q ss_pred             HHHHHHHHH-HHHH-----HCC--CCCCHHHHHHHHHHHHCCCHH--HEEEECCHHHHHHHHH-HHH-CCCCEEEC--CC
Q ss_conf             999999999-8750-----058--898618999999998488854--3886077889999999-984-69925763--88
Q T0636            32 RVQAAIAAA-AARI-----NRY--PFDAEPRVMRKLAEHFSCPED--NLMLVRGIDECFDRIS-AEF-SSMRFVTA--WP   97 (336)
Q Consensus        32 ~v~~al~~~-~~~~-----~~Y--pd~~~~~Lr~aia~~~~v~~d--~I~~t~Gs~~~i~~~~-~~~-~~~~vii~--~P   97 (336)
                      .|++|+++. +.+.     ..|  -|.|...|-+..|+.++-..-  +..+.+|+ ++|..++ ..+ +||+.+..  .|
T Consensus        28 KVL~Af~~~~vs~~hf~~stGYGy~D~GRd~Le~vyA~vfgaE~ALVR~q~vSGT-HAi~~aLfg~LrPGD~ll~itG~P  106 (403)
T PF06838_consen   28 KVLKAFQEHRVSESHFNGSTGYGYDDIGRDKLERVYADVFGAEDALVRPQFVSGT-HAIATALFGVLRPGDELLSITGKP  106 (403)
T ss_dssp             HHHHHHHHTT--GGGSS------------HHHHHHHHHHCT-S--B-STTS-----HHHHHHH--------EEEE-----
T ss_pred             HHHHHHHHCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHCCCCCCHH-HHHHHHHHHCCCCCCEEEECCCCC
T ss_conf             9999999839787666888867878756899999999995635553012004408-899999973678998688716997


Q ss_pred             CCHHHH----------HHHHHHCCCEEEECCCCCCCCCHHHHHHH--CCHHHHHHH-CCCCCCCCCCCHHHHHHHHH---
Q ss_conf             735699----------99998188036415543567788999730--002431330-36633222223799999997---
Q T0636            98 GFDGYR----------ARIAVSGLRHFEIGLTDDLLLDPNDLAQV--SRDDCVVLA-NPSNPTGQALSAGELDQLRQ---  161 (336)
Q Consensus        98 ~y~~y~----------~~~~~~g~~~~~vp~~~~~~~d~~~l~~~--~~~~~i~l~-nPnNPTG~~~~~~~l~~l~~---  161 (336)
                       |.-.+          -.++-+|+.+.++|+.+|..+|.+.+.+.  .++|++.|- +.---+=..++.++|.++++   
T Consensus       107 -YDTL~eVIGi~g~~~GSL~e~GI~Y~~v~L~~dg~~D~~~i~~~i~~~tk~v~IQRS~GYs~R~slsi~~I~~~i~~ik  185 (403)
T PF06838_consen  107 -YDTLEEVIGIRGSGQGSLKEFGIKYDEVDLTEDGEIDYEAIKKAIKPKTKMVLIQRSRGYSWRPSLSIEEIKEIIKFIK  185 (403)
T ss_dssp             --CCHHHH----S-----TGGGT-EEEE--B-----B-HHHHHHHHHTTEEEEEEE------SS----HHHHHHHHHHHH
T ss_pred             -CHHHHHHHCCCCCCCCCHHHHCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             -0767987287999988889939752899753799828999998617565599995278876789859999999999999


Q ss_pred             -H--CCCCCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHHCCCCC-C-CEEECCCHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf             -3--787202521002588662003324520012023465233434-5-3131178899999973378778777789999
Q T0636           162 -R--AGKLLIDETYVDYSSFRARGLAYGENELVFRSFSKSYGLAGL-R-LGALFGPSELIAAMKRKQWFCNVGTLDLHAL  236 (336)
Q Consensus       162 -~--~~~~IvDeaY~~f~~~~~~~l~~~~n~iv~~S~SK~~gl~Gl-R-iG~~i~~~~~i~~l~~~~~~~~~~~~~~~aa  236 (336)
                       .  +.++.||..|.||.....+.-...|  ++.+|+=|.-| .|+ . =||+++.++++++...+..   ...++-..+
T Consensus       186 ~~~p~~ivfVDNCYGEFvE~~EP~~vGAD--liaGSLIKNpG-GgiAptGGYIaGr~dlVe~aa~RLT---aPGiG~e~G  259 (403)
T PF06838_consen  186 EINPDVIVFVDNCYGEFVETKEPTEVGAD--LIAGSLIKNPG-GGIAPTGGYIAGRKDLVEQAAYRLT---APGIGKEVG  259 (403)
T ss_dssp             HH-TTSEEEEE------SSSS-GGG------EEE--TTS-------------BB--HHHHHHHHHHHS------------
T ss_pred             HHCCCEEEEEECCCCCCCCCCCCCCCCHH--HEECCCEECCC-CCCCCCCCEEECHHHHHHHHHHHCC---CCCCCCCCC
T ss_conf             75898399997886120156585301644--40120124798-8736757778536999999864005---885564457


Q ss_pred             HHHHHHHH-----HHH-HHHHHHHHHHHHHHHHHHHCCCEEECCCC----CE-EEEECCCHHHHHHHHH
Q ss_conf             99974599-----999-99999999999999999858978616986----47-8865698899999998
Q T0636           237 EAALDNDR-----ARE-AHIAKTLAQRRRVADALRGLGYRVASSEA----NF-VLVENAAGERTLRFLR  294 (336)
Q Consensus       237 ~~~l~~~~-----~~~-~~~~~~~~~r~~l~~~l~~lg~~~~~s~~----~F-i~~~~~~~~~~~~~L~  294 (336)
                      ...-....     ++. ....+-.+........|+++|+++.|.-.    -- --+++.+.+.+..+++
T Consensus       260 at~~~~r~~~QGlFlAP~vv~eAlKgAif~A~~~e~lG~~v~P~~~~~R~DiIQav~lg~~e~liaFC~  328 (403)
T PF06838_consen  260 ATLGSNRLMYQGLFLAPHVVGEALKGAIFAAALFEKLGFEVSPKPDEPRTDIIQAVKLGSPEKLIAFCQ  328 (403)
T ss_dssp             --TTTHHHHH---TSHHHHHHHHH---HHHHHHHHH---EEES-TTS--SSS-EEEE-SSHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCHHHHHHHHH
T ss_conf             680378999878600249999999999999999998499568999998672578886799899999999


No 9  
>PF01276 OKR_DC_1:  Orn/Lys/Arg decarboxylase, major domain;  InterPro: IPR000310 Pyridoxal-dependent decarboxylases are bacterial proteins acting on ornithine, lysine, arginine and related substrates . One of the regions of sequence similarity contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group.; GO: 0003824 catalytic activity; PDB: 2vyc_G 1ord_A 1c4k_A.
Probab=98.94  E-value=5.1e-08  Score=68.39  Aligned_cols=220  Identities=17%  Similarity=0.222  Sum_probs=129.6

Q ss_pred             CCCCHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH--CCCCEEECCCCCHHHHHHHHHHCCCEEEECCC-CCC--
Q ss_conf             8986189999999984888543886077889999999984--69925763887356999999818803641554-356--
Q T0636            48 PFDAEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF--SSMRFVTAWPGFDGYRARIAVSGLRHFEIGLT-DDL--  122 (336)
Q Consensus        48 pd~~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~--~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~~-~~~--  122 (336)
                      |+.--.+..+..|+.||.+ ...+++||++.++..++.+.  +||.|+++--+=-.....+.+.|...++++.+ +++  
T Consensus        64 p~G~I~eaq~~aA~~fgad-~t~f~vnGsT~~n~a~i~a~~~~gd~vLv~RN~HKSv~~alil~ga~Pvyl~p~~~~~Gi  142 (417)
T PF01276_consen   64 PEGIIKEAQELAARAFGAD-RTYFLVNGSTGGNQAMIMALCRPGDKVLVDRNCHKSVYHALILSGAKPVYLYPERNEYGI  142 (417)
T ss_dssp             T---HHHHHHHHHHHHT-S-EEEEE----HHHHHHHHHHH--TT-EEEEETT--HHHHHHTTT---EEEEE---------
T ss_pred             CCCHHHHHHHHHHHHCCCC-CEEEEECCCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHCCCEEEEECCCCCCCCC
T ss_conf             8719999999999863998-379995782189999999842899989970764899999999879978994378667886


Q ss_pred             --CCCH-----HHHHHH----CCHHH---HHHHCCCCCCCCCCCHHHHHHHHHHCC-CCCCCCCCCC---CCCCCCCHH-
Q ss_conf             --7788-----999730----00243---133036633222223799999997378-7202521002---588662003-
Q T0636           123 --LLDP-----NDLAQV----SRDDC---VVLANPSNPTGQALSAGELDQLRQRAG-KLLIDETYVD---YSSFRARGL-  183 (336)
Q Consensus       123 --~~d~-----~~l~~~----~~~~~---i~l~nPnNPTG~~~~~~~l~~l~~~~~-~~IvDeaY~~---f~~~~~~~l-  183 (336)
                        .+++     +.+++.    ...+.   ++|+||+- -|.+.+.++|.+++++.+ .++||||...   |.+.....+ 
T Consensus       143 ~~~i~~~~~~~e~i~~~l~~~p~~ka~~~vvlt~pTY-~G~~~d~~~i~~~~h~~~~~llvDEAhGah~~F~~lp~~a~~  221 (417)
T PF01276_consen  143 IGGIPPSEFTPESIEKALAEHPDAKAPRAVVLTSPTY-DGVCYDLKEIADICHKYGIPLLVDEAHGAHFRFHPLPKSALA  221 (417)
T ss_dssp             -----GGGCSHHHHHHHHHHGCCCHCECEEEEESS------EE-HHHHHHHHTTTECEEEEE-TT---CCCSGGGCCCSS
T ss_pred             CCCCCHHHCCHHHHHHHHHHCCCCCCCEEEEEECCCC-CEEEECHHHHHHHHHHCCCEEEEECCCHHHHCCCCCCCCHHH
T ss_conf             0477836437999999998486435831899977986-637408999999985459959997857676553867547756


Q ss_pred             -----HHCCCHHHHHHHHHHHCCCCCCCE-EECCC-H-----HHH-HHHHHCCCCCCCCH--HHHHHHHHHH---HHHHH
Q ss_conf             -----324520012023465233434531-31178-8-----999-99973378778777--7899999997---45999
Q T0636           184 -----AYGENELVFRSFSKSYGLAGLRLG-ALFGP-S-----ELI-AAMKRKQWFCNVGT--LDLHALEAAL---DNDRA  245 (336)
Q Consensus       184 -----~~~~n~iv~~S~SK~~gl~GlRiG-~~i~~-~-----~~i-~~l~~~~~~~~~~~--~~~~aa~~~l---~~~~~  245 (336)
                           ...+.++++.|.=|+.  |++.-+ |+... .     +.+ +.+...+.+.+...  .|.-++.+.+   ...+.
T Consensus       222 ~gaD~~~~~~~~vvqS~HKtL--~alTQ~S~LH~~~~~~vd~~~~~~al~~~qTTSPSY~LmASLD~A~~~m~~~~G~~l  299 (417)
T PF01276_consen  222 MGADDPEDPAILVVQSTHKTL--PALTQASMLHVKGDRIVDHERVNEALMMLQTTSPSYLLMASLDVARAMMEAEEGREL  299 (417)
T ss_dssp             TT-------EEEEEEEHHHHS--S--TT-EEEEEE-GGG--HHHHHHHHHHCS-SS--CHHHHHHHHHHHHH------HH
T ss_pred             CCCCCCCCCCEEEEEEHHHCC--CCCCHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             479655676326886221125--674600377877997777999999999875888389999999999999750451999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHC-CCEEE
Q ss_conf             9999999999999999999858-97861
Q T0636           246 REAHIAKTLAQRRRVADALRGL-GYRVA  272 (336)
Q Consensus       246 ~~~~~~~~~~~r~~l~~~l~~l-g~~~~  272 (336)
                      +++.++....-|+++.. +++. +++++
T Consensus       300 ~~~~i~~a~~~R~~l~~-~~~~~~f~~~  326 (417)
T PF01276_consen  300 LEEAIELAIDFRKKLAR-LNDIWGFKPW  326 (417)
T ss_dssp             HHHHHHHHHHHHHHHHH-HH----SEES
T ss_pred             HHHHHHHHHHHHHHHHC-CCCCCEEEEC
T ss_conf             99999999999997513-3568867747


No 10 
>PF00202 Aminotran_3:  Aminotransferase class-III;  InterPro: IPR005814   Aminotransferases share certain mechanistic features with other pyridoxalphosphate-dependent enzymes, such as the covalent binding of the pyridoxalphosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped  into subfamilies. One of these, called class-III, includes acetylornithine aminotransferase (2.6.1.11 from EC), which catalyzes the transfer of an amino group from acetylornithine to alpha-ketoglutarate, yielding N-acetyl-glutamic-5-semi-aldehyde and glutamic acid; ornithine aminotransferase (2.6.1.13 from EC), which catalyzes the transfer of an amino group from ornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde and glutamic acid; omega-amino acid--pyruvate aminotransferase (2.6.1.18 from EC), which catalyzes transamination between a variety of omega-amino acids, mono- and diamines, and pyruvate; 4-aminobutyrate aminotransferase (2.6.1.19 from EC) (GABA transaminase), which catalyzes the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid; DAPA aminotransferase (2.6.1.62 from EC), a bacterial enzyme (bioA), which catalyzes an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid; 2,2-dialkylglycine decarboxylase (4.1.1.64 from EC), a Burkholderia cepacia (Pseudomonas cepacia) enzyme (dgdA) that catalyzes the decarboxylating amino transfer of 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbon dioxide; glutamate-1-semialdehyde aminotransferase (5.4.3.8 from EC) (GSA); Bacillus subtilis aminotransferases yhxA and yodT; Haemophilus influenzae aminotransferase HI0949; and Caenorhabditis elegans aminotransferase T01B11.2.; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding; PDB: 2pb2_A 2pb0_B 1wkg_A 1wkh_B 1vef_B 2can_A 1gbn_B 1oat_C 2byj_A 2byl_B ....
Probab=98.83  E-value=9.1e-09  Score=73.27  Aligned_cols=226  Identities=19%  Similarity=0.230  Sum_probs=130.2

Q ss_pred             CCCCCEECCCC--CCCCC-CCHHHHHHHHHHHHHHHC-----CCCCCHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHH
Q ss_conf             66553573576--54888-768999999999875005-----88986189999999984888543886077889999999
Q T0636            13 AAAQAVCLAFN--ENPEA-VEPRVQAAIAAAAARINR-----YPFDAEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRIS   84 (336)
Q Consensus        13 ~~~~~i~L~~N--enp~~-p~~~v~~al~~~~~~~~~-----Ypd~~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~   84 (336)
                      .+++.||+.++  -+.+| -.|.+.+|+.+.+.++..     ++.+...+|-+.|++...-..++++.+++++|+...++
T Consensus        14 dG~~ylD~~~g~~~~~lGh~~p~v~~ai~~q~~~~~~~~~~~~~~~~~~~lae~L~~~~p~~~~~v~f~~SGseAve~Ai   93 (339)
T PF00202_consen   14 DGNEYLDFTSGYGVVNLGHNHPEVVEAIKEQLERLNHVSFFGFPHPPAVELAEKLAELAPPGLDRVFFANSGSEAVEAAI   93 (339)
T ss_dssp             TEEEEEBSSHHHHTT------HHHHHHHHHHHHHCSHHSTTTSEEHHHHHHHHHHHHHS-TTESEEEEE----HHHHHHH
T ss_pred             CCCEEEECCCCHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHH
T ss_conf             99999986655230057888199999999999753234322457679999999997108997567987568857999999


Q ss_pred             H---------HHCCC-CEEECCCCCHHHHHHHHH-HCC------------CEEEECCCCCCC-----CCHHHH---H-HH
Q ss_conf             9---------84699-257638873569999998-188------------036415543567-----788999---7-30
Q T0636            85 A---------EFSSM-RFVTAWPGFDGYRARIAV-SGL------------RHFEIGLTDDLL-----LDPNDL---A-QV  132 (336)
Q Consensus        85 ~---------~~~~~-~vii~~P~y~~y~~~~~~-~g~------------~~~~vp~~~~~~-----~d~~~l---~-~~  132 (336)
                      +         ...+. +|+...-+|-+....+.. .+.            .+..+|..+...     ...+.+   . +.
T Consensus        94 klAr~y~~~~~~tgr~~ii~~~~~yHG~t~~~~s~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~  173 (339)
T PF00202_consen   94 KLARQYHKKRGYTGRSKIISFEGSYHGRTLGALSVTGNPGYRKPFGPLLPGVIFVPFPDLYADEEEQACLEYLEELIAAL  173 (339)
T ss_dssp             HHHHHHHHHHHHTT--EEEEECT------HHHCTTTTSHHHHGCCSSSSS-EEEEETTEHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99866400247888747999368657787461565578755566545676530013797134567888899999999974


Q ss_pred             CCHH-HHHHHCCC-CCCCCCCCHH----HHHHHHHHCCCCC-CCCCCCCCCCCCC----CHHHHCCCHHHHHHHHHHHCC
Q ss_conf             0024-31330366-3322222379----9999997378720-2521002588662----003324520012023465233
Q T0636           133 SRDD-CVVLANPS-NPTGQALSAG----ELDQLRQRAGKLL-IDETYVDYSSFRA----RGLAYGENELVFRSFSKSYGL  201 (336)
Q Consensus       133 ~~~~-~i~l~nPn-NPTG~~~~~~----~l~~l~~~~~~~I-vDeaY~~f~~~~~----~~l~~~~n~iv~~S~SK~~gl  201 (336)
                      ...+ +.+|.-|= ...|.....+    .+.+++++++.++ +||+...|+..-.    ......|+++   +|||..| 
T Consensus       174 ~~~~iAAviiEPiqg~gG~~~~~~~yl~~lr~lc~~~g~llI~DEV~tG~GRtG~~~a~~~~gv~PDiv---~~gK~l~-  249 (339)
T PF00202_consen  174 GPDDIAAVIIEPIQGEGGVIPPPPGYLQALRELCREHGILLIFDEVQTGFGRTGKMFAFEHFGVEPDIV---TFGKGLG-  249 (339)
T ss_dssp             CCTTEEEEEEESEE-----EEB-HHHHHHHHHHHHHTT-EEEEE-S------SSTTSGGGGGT--SSEE---EE-TTT--
T ss_pred             CCCCEEEEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCHHHCCCCCCHHH---HHHHHCC-
T ss_conf             799789999940124689626898999858987356727999976886765767862200248711499---9876426-


Q ss_pred             CCCCCEEECCCHHHHHHHHHCC--CCCCCCHHHHHHHHHHHHH
Q ss_conf             4345313117889999997337--8778777789999999745
Q T0636           202 AGLRLGALFGPSELIAAMKRKQ--WFCNVGTLDLHALEAALDN  242 (336)
Q Consensus       202 ~GlRiG~~i~~~~~i~~l~~~~--~~~~~~~~~~~aa~~~l~~  242 (336)
                      .|+-+|.+++.+++.+.+....  .+|+-|.++..++.+.|+.
T Consensus       250 gG~P~sav~~~~~i~~~~~~~~~~~T~~gnpl~~aaa~a~L~~  292 (339)
T PF00202_consen  250 GGLPISAVVGREEIMDAFDPGSHGSTFGGNPLACAAALATLDI  292 (339)
T ss_dssp             E-EEEEEEEEEHHHHTTCTTTSS--TTTT-HHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             8613422440488887751488666467896999889999999


No 11 
>PF02347 GDC-P:  Glycine cleavage system P-protein;  InterPro: IPR003437   This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T . The reaction catalysed by this protein is:    Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0006544 glycine metabolic process, 0005961 glycine dehydrogenase complex (decarboxylating); PDB: 1wyv_A 1wyu_E 1wyt_C.
Probab=98.77  E-value=2.5e-07  Score=63.92  Aligned_cols=285  Identities=17%  Similarity=0.193  Sum_probs=148.4

Q ss_pred             CHHHHHHHHHHHHHHHCC-CC-----CCHH----HHHHHHHHHHCCCHHHEEEECCH---HHHHHHHHHHHCCC--CEEE
Q ss_conf             689999999998750058-89-----8618----99999999848885438860778---89999999984699--2576
Q T0636            30 EPRVQAAIAAAAARINRY-PF-----DAEP----RVMRKLAEHFSCPEDNLMLVRGI---DECFDRISAEFSSM--RFVT   94 (336)
Q Consensus        30 ~~~v~~al~~~~~~~~~Y-pd-----~~~~----~Lr~aia~~~~v~~d~I~~t~Gs---~~~i~~~~~~~~~~--~vii   94 (336)
                      |+.+.+.+.+...-+..| |-     .|..    ++-..|++..|.+.-+.-+-.|+   -|++.++.+...+.  ++++
T Consensus        80 P~~i~~~i~~~~ef~TaytPYQpEisQG~Lq~l~e~Qt~i~eLTGmdvanaSl~d~atA~aEa~~ma~r~~~~~~~kvlv  159 (429)
T PF02347_consen   80 PAVIDRNILSRPEFYTAYTPYQPEISQGRLQALFEYQTMICELTGMDVANASLYDGATAAAEAMLMAVRITRRKRNKVLV  159 (429)
T ss_dssp             -HHHHH-HHCHHHTTTS-STTSGGGB---HHHHHHHHHHHHHH----EE-SB-----HHHH---HHHHHHH-----EEEE
T ss_pred             CHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             77772243346210015799994788999999999999999976978557788860679999999999983788738997


Q ss_pred             CCCCCHHHHH----HHHHHCCCEEEECCCCCCCCCHHHHHHHCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf             3887356999----999818803641554356778899973000243133036633222223799999997378720252
Q T0636            95 AWPGFDGYRA----RIAVSGLRHFEIGLTDDLLLDPNDLAQVSRDDCVVLANPSNPTGQALSAGELDQLRQRAGKLLIDE  170 (336)
Q Consensus        95 ~~P~y~~y~~----~~~~~g~~~~~vp~~~~~~~d~~~l~~~~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~IvDe  170 (336)
                      +.-..+.+..    .++..|.+++.++.+++...|      ..++.++++.|||. .|.+-+.+++.++++.++-+++-.
T Consensus       160 ~~~~hp~~~~v~~t~a~~~g~~iv~~~~~~~~~~d------~~~~a~v~vq~Pn~-~G~~ed~~~i~~~~h~~gal~~~~  232 (429)
T PF02347_consen  160 PDSVHPQNRAVLRTYAEGAGIEIVTVPLDDDGMDD------DDDTAAVMVQYPNT-FGVFEDIEEIAEIAHEAGALVYVG  232 (429)
T ss_dssp             ETT--HHHHHHHHHHHHHEEEEEEEE------------------EEEEEEESS--------THHHHHHHHHH---EEEEE
T ss_pred             CCCCCCCCHHHHHHHEEECCCEEEEECCCCCCCCC------CCCEEEEEEECCCC-CEEEEEHHHHHHHHHHCCCEEEEE
T ss_conf             68889888999984045068189997630147776------63748998746998-747801999999999859999999


Q ss_pred             CCC-CCCCCCCCHHHHCCCHHHHHHHHHHHCCC----CCCCEEECCCHHHH----------------------------H
Q ss_conf             100-25886620033245200120234652334----34531311788999----------------------------9
Q T0636           171 TYV-DYSSFRARGLAYGENELVFRSFSKSYGLA----GLRLGALFGPSELI----------------------------A  217 (336)
Q Consensus       171 aY~-~f~~~~~~~l~~~~n~iv~~S~SK~~gl~----GlRiG~~i~~~~~i----------------------------~  217 (336)
                      +.. -.+....+. ...-+++ +++ +|.||+|    |=-.|++...++++                            +
T Consensus       233 an~~Al~~l~~Pg-e~GADI~-vg~-~Q~fgiP~g~GGP~~G~~a~~~~l~r~lPGRiVG~t~D~~G~~~~~LtLqtREQ  309 (429)
T PF02347_consen  233 ANPNALGGLKSPG-EMGADIA-VGE-HQTFGIPHGFGGPGAGFFAVRKELVRQLPGRIVGVTKDADGKRAYRLTLQTREQ  309 (429)
T ss_dssp             --CCCT--B----------EE-E-T-TTTT-------------BEE-GGGGGGS-S-EEEB--BE------EEE-GGGTC
T ss_pred             ECHHHHCCCCCHH-HCCCCEE-EEC-CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCC
T ss_conf             5878870878831-1676679-407-987776767888760167658988866898845531136677136753256765


Q ss_pred             HHHHCCCCCCCCH---H-HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCC--CEEEEECCCHHH--
Q ss_conf             9973378778777---7-89999999-7459999999999999999999999858978616986--478865698899--
Q T0636           218 AMKRKQWFCNVGT---L-DLHALEAA-LDNDRAREAHIAKTLAQRRRVADALRGLGYRVASSEA--NFVLVENAAGER--  288 (336)
Q Consensus       218 ~l~~~~~~~~~~~---~-~~~aa~~~-l~~~~~~~~~~~~~~~~r~~l~~~l~~lg~~~~~s~~--~Fi~~~~~~~~~--  288 (336)
                      .+++-+...|+.+   + +..++..+ +..++=+.+.-+.......++.+.|+++.-..+++..  .|+.....+ ..  
T Consensus       310 hIrReKAtSNIctnqaL~A~~A~~Y~~~~Gp~GL~~iA~~~~~~A~yl~~~L~~~~~~~~~~~~f~e~v~~~~~~-~~~~  388 (429)
T PF02347_consen  310 HIRREKATSNICTNQALLALAAAMYASYHGPEGLKEIAERIHLNANYLAKRLKEIFGLPFPGPFFFEFVTVFPKD-KKVE  388 (429)
T ss_dssp             HHHGGCSS----S--HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHCC--BECTS-SS-SSEEEEESS--HHHH
T ss_pred             CCHHCCCEECCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCC-HHHH
T ss_conf             210000000024418999999999999879789999999999999999999887538666797811144212873-6699


Q ss_pred             -HHHHHHHCCCEEEECCCCCCCCEEEEEEC---CHHHHHHHHHHH
Q ss_conf             -99999876938960778888874788747---989999999999
Q T0636           289 -TLRFLRERGIQVKDAGQFGLHHHIRISIG---REEDNDRLLAAL  329 (336)
Q Consensus       289 -~~~~L~~~gi~vr~~~~fg~~~~iRis~~---~~ee~~~l~~aL  329 (336)
                       +.+.+.+.|+-.+    +-..+.+-+|+.   |++|+++|+++|
T Consensus       389 ~l~~~~~~~gl~~~----~~~~~~~~i~~tE~~t~~~id~l~~~~  429 (429)
T PF02347_consen  389 ELLKRGIAGGLNLR----YPDDGALLICVTETRTKEDIDALVQAF  429 (429)
T ss_dssp             HHHH------EEET----T----EEEEE--TT--HHHHHHHHH--
T ss_pred             HHHHHHHHCCCCCC----CCCCCEEEEEECCCCCHHHHHHHHHCC
T ss_conf             99999996698754----058997999834799999999998539


No 12 
>PF00282 Pyridoxal_deC:  Pyridoxal-dependent decarboxylase conserved domain;  InterPro: IPR002129    Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .   PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . A number of pyridoxal-dependent decarboxylases share regions of sequence similarity, particularly in the vicinity of a conserved lysine residue, which provides the attachment site for the pyridoxal-phosphate (PLP) group , . Among these enzymes are aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase), which catalyses the decarboxylation of tryptophan to tryptamine ; tyrosine decarboxylase, which converts tyrosine into tyramine; and histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine . These enzymes belong to the group II decarboxylases , .; GO: 0016831 carboxy-lyase activity, 0030170 pyridoxal phosphate binding, 0019752 carboxylic acid metabolic process; PDB: 2qma_B 2okk_A 1es0_B 2okj_A 2jis_B 1xey_B 2dgk_D 1pmm_F 3fz6_E 2dgl_C ....
Probab=98.27  E-value=0.00011  Score=46.77  Aligned_cols=223  Identities=17%  Similarity=0.143  Sum_probs=126.0

Q ss_pred             HHHHHHHHHCCCHHH-------EEEECCHHHHHHHHHHHH----------CC----C--CEEECC-CCCHHHHHHHHHHC
Q ss_conf             999999984888543-------886077889999999984----------69----9--257638-87356999999818
Q T0636            55 VMRKLAEHFSCPEDN-------LMLVRGIDECFDRISAEF----------SS----M--RFVTAW-PGFDGYRARIAVSG  110 (336)
Q Consensus        55 Lr~aia~~~~v~~d~-------I~~t~Gs~~~i~~~~~~~----------~~----~--~vii~~-P~y~~y~~~~~~~g  110 (336)
                      ..+.+++.+|.+.+.       =++|+|++++.-..+.+.          .+    .  .+++.+ .-| ....++...|
T Consensus        84 vi~wl~~l~g~~~~~~~~~~~~G~~tsGgs~anl~al~aAR~~~~~~~~~~~~~~~~~~~i~~s~~aH~-s~~Kaa~~lG  162 (373)
T PF00282_consen   84 VIDWLAELLGLPASFYDSGEAGGIFTSGGSEANLTALLAARDRALPRVKAEGVREIGRPVIYCSEQAHY-SIKKAARILG  162 (373)
T ss_dssp             HHHHHHHHTT--GGG-TTTT-B--EE--HHHHHHHHHHHHHHHHHHHHHCH-TTTSSSEEEEEETTS-T-HHHHHHHHTT
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECHHHH-HHHHHHHHCC
T ss_conf             999999995897420025788428835538999999999999986654214665567605876212147-9999998579


Q ss_pred             CCEEEECCCCCCCCCHHHHHHHCC---HH-----HHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC-CCCCCCCC---CCC
Q ss_conf             803641554356778899973000---24-----3133036633222223799999997378720-25210025---886
Q T0636           111 LRHFEIGLTDDLLLDPNDLAQVSR---DD-----CVVLANPSNPTGQALSAGELDQLRQRAGKLL-IDETYVDY---SSF  178 (336)
Q Consensus       111 ~~~~~vp~~~~~~~d~~~l~~~~~---~~-----~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~I-vDeaY~~f---~~~  178 (336)
                      ..++.||.++++++|++++++..+   .+     +|+.+-..-.||.+=+.++|.+++++++.++ ||-||..+   +++
T Consensus       163 lgv~~Vp~d~~~~md~~~L~~~i~~~~~~G~~p~~VvataGtT~~GaiD~l~~i~~i~~~~~~wlHVDaA~GG~~~~~~~  242 (373)
T PF00282_consen  163 LGVRVVPTDENGRMDVDALEKAIEEDRAAGKTPFAVVATAGTTNTGAIDPLEEIADICRKYNLWLHVDAAYGGSALLSPF  242 (373)
T ss_dssp             -EEEEE-B-TTSSB-HHHHHHHHHHHHHT--EEEEEEEE---TTT-----HHHHHHHHHHHT-EEEEEES----GGGHTT
T ss_pred             CCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHCCC
T ss_conf             73289323866573899999998873025665358885268866553200999988986369756862354552443023


Q ss_pred             CCCHHHHCCCH-HHHHHHHHHHCCCCCCCEEECC-CHHHHH-HHHH----CC----------CC--CCC--CH-HHHHHH
Q ss_conf             62003324520-0120234652334345313117-889999-9973----37----------87--787--77-789999
Q T0636           179 RARGLAYGENE-LVFRSFSKSYGLAGLRLGALFG-PSELIA-AMKR----KQ----------WF--CNV--GT-LDLHAL  236 (336)
Q Consensus       179 ~~~~l~~~~n~-iv~~S~SK~~gl~GlRiG~~i~-~~~~i~-~l~~----~~----------~~--~~~--~~-~~~~aa  236 (336)
                      ....+..-+.. -+.-.+-|..+.| .-+|+++. +++... .+..    +.          ..  +++  +. ......
T Consensus       243 ~r~~~~gle~aDSit~d~HK~l~~p-~~~~~ll~r~~~~l~~~~~~~a~Yl~~~~~~~~~~~d~~~~tl~~sR~~~alk~  321 (373)
T PF00282_consen  243 YRHLLFGLERADSITIDPHKWLYVP-YGCGVLLVRDKELLRSAFSINADYLFHPDRESDDSYDYGDWTLEGSRRFRALKL  321 (373)
T ss_dssp             TGGGGTTSTTESEEEE-TTSTTS---SS-EEEEESSGGGHHGGG-EEBTTSS-S-SSS-GGGSBCCTSS--S-B-CHHHH
T ss_pred             CCHHHCCCCCCEEEEECHHHHCCCC-CCCEEEEECCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             1011048744405888828845666-146577744777777765269230257410044777736756899832379999


Q ss_pred             HHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHCC-CEEE-CCCCCEE
Q ss_conf             99974--599999999999999999999998589-7861-6986478
Q T0636           237 EAALD--NDRAREAHIAKTLAQRRRVADALRGLG-YRVA-SSEANFV  279 (336)
Q Consensus       237 ~~~l~--~~~~~~~~~~~~~~~r~~l~~~l~~lg-~~~~-~s~~~Fi  279 (336)
                      ...|+  ..+-+.+.+++..+..+++.+.+++.+ +.+. +++-+-+
T Consensus       322 W~~l~~~G~~g~~~~i~~~~~~A~~~~~~i~~~~~~el~~~~~l~~V  368 (373)
T PF00282_consen  322 WASLRSLGREGYREMIERCIELARYFAELIRASPDFELVNPPELNIV  368 (373)
T ss_dssp             HHHHHH------HHHHHHHHHHHHHHHHHHHTTTTEEESST-SSSEE
T ss_pred             HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCEEE
T ss_conf             99999968998999999999999999999974889799758983189


No 13 
>PF05889 SLA_LP_auto_ag:  Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen);  InterPro: IPR008829 This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis . The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway . The archaeal sequences Q8TXK0 from SWISSPROT and Q8TYR3 from SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.; PDB: 2e7j_B 2e7i_B 2z67_B 3bcb_A 3bc8_A 3bca_A.
Probab=97.68  E-value=0.0017  Score=39.15  Aligned_cols=268  Identities=15%  Similarity=0.112  Sum_probs=136.4

Q ss_pred             HHCCC-HHHEEEECCHHH-HHHHHHHHHC----CCCEEECC-CCCHHHHHHHHHHCCCEEEECC--CCC-CCCCHHHHHH
Q ss_conf             84888-543886077889-9999999846----99257638-8735699999981880364155--435-6778899973
Q T0636            62 HFSCP-EDNLMLVRGIDE-CFDRISAEFS----SMRFVTAW-PGFDGYRARIAVSGLRHFEIGL--TDD-LLLDPNDLAQ  131 (336)
Q Consensus        62 ~~~v~-~d~I~~t~Gs~~-~i~~~~~~~~----~~~vii~~-P~y~~y~~~~~~~g~~~~~vp~--~~~-~~~d~~~l~~  131 (336)
                      ..|++ ....++.+-++. .|.++++++.    ++-|+.+. =-|..|. ++...|.+++.+|.  ..| ...|.+++++
T Consensus        68 ~~G~~~~~~~~~vP~aTGm~l~l~l~a~~~~~~a~~ViwsridqkSc~k-ai~~AGl~~~vV~~~~~~d~l~td~~~ie~  146 (389)
T PF05889_consen   68 IAGLRSCKSCFVVPMATGMSLTLCLLALRKRPKADYVIWSRIDQKSCFK-AIERAGLEPVVVPTVLEGDELITDEEAIEK  146 (389)
T ss_dssp             H---CCHC-EECHSS----HHHHHHHHHHHHCC--EEEEEEEETHHHHH-HHHH---EEEEE-BEETTT-EE-HHHHHHH
T ss_pred             HCCCCCCCEEEEEECCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCHHH-HHHHCCCEEEEEECCCCCCCCCCCHHHHHH
T ss_conf             7498510306884033423299999997435788679995036520689-999669727996535678700585899999


Q ss_pred             HCCH-----HHHHHHCCCCCCCCCCC-HHHHHHHHHHCC-CCCCCCCCCCCCCCCCCHHHH---CCCH-HHHHHHHHHHC
Q ss_conf             0002-----43133036633222223-799999997378-720252100258866200332---4520-01202346523
Q T0636           132 VSRD-----DCVVLANPSNPTGQALS-AGELDQLRQRAG-KLLIDETYVDYSSFRARGLAY---GENE-LVFRSFSKSYG  200 (336)
Q Consensus       132 ~~~~-----~~i~l~nPnNPTG~~~~-~~~l~~l~~~~~-~~IvDeaY~~f~~~~~~~l~~---~~n~-iv~~S~SK~~g  200 (336)
                      ..+.     .+++++.+.---+..-+ .++|.++|++.+ ..|+..||.==.......+..   ..++ +++.|.-|.|=
T Consensus       147 ~ie~~g~~~ilcvltttscfapr~~D~i~~Iaklc~~~~IPhlvNnAYgvQ~~~~~~~l~~a~~~GRvD~~vqStDKNFl  226 (389)
T PF05889_consen  147 AIEELGADNILCVLTTTSCFAPRNPDDIEEIAKLCKEYDIPHLVNNAYGVQSSYIMHLLEKAWRVGRVDAVVQSTDKNFL  226 (389)
T ss_dssp             HHHHCH-TCEEEEEEESS--TTB----HHHHHHHHHHHT--EEEE---TTT-HHHHHHHHHHTTS---SEEECTHHHHHC
T ss_pred             HHHHHCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEE
T ss_conf             99972888768999804765888874199999999981997697251111259899999876441322237873598868


Q ss_pred             CCCCCCE--EEC-CCHHHHHHHHHCCCCCCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCEE
Q ss_conf             3434531--311-78899999973378778777789999--9997459999999999999999999999----8589786
Q T0636           201 LAGLRLG--ALF-GPSELIAAMKRKQWFCNVGTLDLHAL--EAALDNDRAREAHIAKTLAQRRRVADAL----RGLGYRV  271 (336)
Q Consensus       201 l~GlRiG--~~i-~~~~~i~~l~~~~~~~~~~~~~~~aa--~~~l~~~~~~~~~~~~~~~~r~~l~~~l----~~lg~~~  271 (336)
                      .|   +|  -+. .++..++.+.+....=-..++.....  +-.|.... +...+....+...++.+.|    ++.|.++
T Consensus       227 Vp---vGgai~as~~~~~v~~is~~YpgRas~s~~ld~fitLlsLG~tg-~~~ll~~r~~~f~~l~erl~~~a~e~~e~l  302 (389)
T PF05889_consen  227 VP---VGGAIMASSDPSGVLAISKEYPGRASRSPILDLFITLLSLGCTG-YGALLKERMASFPYLKERLKKWAEEVGERL  302 (389)
T ss_dssp             ---------CEEES-HHHHHHHCCCGHHHHTSHHHHHHHHHHHH---HH-HHHHHHHHHHHHHHHHHHHHHHHHHCCEEB
T ss_pred             EE---CCCCEEEECCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_conf             20---49838882587899999866799541565079999999860556-778999999999999999999999860314


Q ss_pred             ECCCCCEEEEE--CC--------CHHHHHHHHHHCCCE----EEECCCCC---C----CCEEEE-E-EC-CHHHHHHHHH
Q ss_conf             16986478865--69--------889999999876938----96077888---8----874788-7-47-9899999999
Q T0636           272 ASSEANFVLVE--NA--------AGERTLRFLRERGIQ----VKDAGQFG---L----HHHIRI-S-IG-REEDNDRLLA  327 (336)
Q Consensus       272 ~~s~~~Fi~~~--~~--------~~~~~~~~L~~~gi~----vr~~~~fg---~----~~~iRi-s-~~-~~ee~~~l~~  327 (336)
                      ...--|.+.+.  ++        +...+...|..+||.    |.+...+.   .    -.|+-+ | +| +.||++.+++
T Consensus       303 ~~~p~N~is~aitl~~l~~~~~k~~~~lgs~L~~RgVsG~RvV~~~~~~~ts~~~~~~~~Yl~~asaiG~t~eevd~~~~  382 (389)
T PF05889_consen  303 LETPRNHISIAITLPTLDEISQKDITFLGSMLFSRGVSGIRVVTPTWKKQTSHLDEYPVPYLTAASAIGLTREEVDYFVD  382 (389)
T ss_dssp             ---TT-SSEEEEE-CCCHHHCCSHHHHHHHHHHHTTEE--E-EETT---EESSSS--SSSEEEEEE-----HHHHHHHHH
T ss_pred             HCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf             31578972689965654323211088999999748875551104688855346777773166888880898999999999


Q ss_pred             HHHHHHH
Q ss_conf             9999984
Q T0636           328 ALAEYSD  334 (336)
Q Consensus       328 aL~~~~e  334 (336)
                      .|++..+
T Consensus       383 ~l~k~~~  389 (389)
T PF05889_consen  383 RLDKILK  389 (389)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHC
T ss_conf             9988649


No 14 
>PF03841 SelA:  L-seryl-tRNA selenium transferase;  InterPro: IPR004534 In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.   This family describes SelA. A close homolog of SelA is found in Helicobacter pylori, but all other required elements are missing and the protein is shorter at the N-terminus than SelA from other species. The trusted cut-off is set above the score generated for Helicobacter pyloriputative SelA.; GO: 0004125 L-seryl-tRNASec selenium transferase activity, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2aeu_A 2aev_A.
Probab=97.46  E-value=1.7e-05  Score=52.06  Aligned_cols=203  Identities=23%  Similarity=0.251  Sum_probs=113.9

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC---------CC--HHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHHC-CCCEEECC
Q ss_conf             768999999999875005889---------86--1899999999848885438860778899999999846-99257638
Q T0636            29 VEPRVQAAIAAAAARINRYPF---------DA--EPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEFS-SMRFVTAW   96 (336)
Q Consensus        29 p~~~v~~al~~~~~~~~~Ypd---------~~--~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~~-~~~vii~~   96 (336)
                      .++.+.+++.+....   |.+         .|  +..+.+.++...|.  +..+++|....++.+++.++. +.+|++.-
T Consensus        18 ls~~a~~a~~~~~~~---y~nLE~dL~~G~RG~R~~~v~~ll~~ltgA--EaA~VVNNNAAAV~L~L~~la~~kEVIVSR   92 (367)
T PF03841_consen   18 LSEEAIDAVKEVASG---YSNLEYDLETGKRGSRYSHVEELLCELTGA--EAALVVNNNAAAVLLALNTLAAGKEVIVSR   92 (367)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             222222222222222---222222222222222222222222222222--222222222222222222222222222222


Q ss_pred             C---CCH---HHHHHHHHHCCCEEEECCCCCCCCCHHHHHH--HCCHHHHHHHCCCCCCCC----CCCHHHHHHHHHHCC
Q ss_conf             8---735---6999999818803641554356778899973--000243133036633222----223799999997378
Q T0636            97 P---GFD---GYRARIAVSGLRHFEIGLTDDLLLDPNDLAQ--VSRDDCVVLANPSNPTGQ----ALSAGELDQLRQRAG  164 (336)
Q Consensus        97 P---~y~---~y~~~~~~~g~~~~~vp~~~~~~~d~~~l~~--~~~~~~i~l~nPnNPTG~----~~~~~~l~~l~~~~~  164 (336)
                      =   .+.   ......+..|.++++|-.++.-  .+.+++.  .++|.+++-..+.|-.-.    -.+.+++.+++++++
T Consensus        93 GelVeiGg~FRIpdvm~~sGa~LvEVGtTN~T--~~~Dye~AI~e~Ta~llkVh~Sn~~i~GFt~~~~~~el~~la~~~~  170 (367)
T PF03841_consen   93 GELVEIGGSFRIPDVMRQSGAKLVEVGTTNRT--HLRDYENAINENTAALLKVHTSNFRIQGFTEEVSLEELAELAKEHG  170 (367)
T ss_dssp             ----------------------------------------------------------------------HHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             22222222222222222222222222222222--2222222222222222222222222222234447999999986659


Q ss_pred             -CCCCCCCC---CCCC-----CCCCC--HHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCC--CCCCCHH
Q ss_conf             -72025210---0258-----86620--0332452001202346523343453131178899999973378--7787777
Q T0636           165 -KLLIDETY---VDYS-----SFRAR--GLAYGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMKRKQW--FCNVGTL  231 (336)
Q Consensus       165 -~~IvDeaY---~~f~-----~~~~~--~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~~~~~--~~~~~~~  231 (336)
                       .+++|-.-   .|+.     +++..  .+....+ +|+.|=.|.+|  |-..|.+++.+++|+++++-..  .+-+..+
T Consensus       171 ip~i~DlgSG~l~dl~~~gl~~Ep~v~~~l~~GaD-lV~fSGdKlLg--GPQAGiI~Gkk~lI~~lk~~~l~RalrvdK~  247 (367)
T PF03841_consen  171 IPVIVDLGSGSLVDLSKYGLPDEPTVQEALAAGAD-LVTFSGDKLLG--GPQAGIIVGKKELIEKLKKHPLGRALRVDKE  247 (367)
T ss_dssp             --EEEE------HHHHTT----------CCC-----EEE--TTSS----------EE--HHHHHHHHH----------HH
T ss_pred             CCEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCC-EEEEECCEECC--CCCCEEEEEHHHHHHHHHHCCCCEEEECCHH
T ss_conf             98899899986547751246302559999977999-89988998178--9983699513999999977787640047999


Q ss_pred             HHHHHHHHHH
Q ss_conf             8999999974
Q T0636           232 DLHALEAALD  241 (336)
Q Consensus       232 ~~~aa~~~l~  241 (336)
                      +..+..+.|+
T Consensus       248 tlaaL~atL~  257 (367)
T PF03841_consen  248 TLAALEATLR  257 (367)
T ss_dssp             HH---HHHHH
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 15 
>PF01282 Ribosomal_S24e:  Ribosomal protein S24e;  InterPro: IPR001976   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 , .   This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1ywx_A 1xn9_A 2v94_B 2g1d_A.
Probab=57.14  E-value=3.2  Score=17.87  Aligned_cols=24  Identities=17%  Similarity=0.303  Sum_probs=17.3

Q ss_pred             CCHHHHHHHHHHHHCCCHHHEEEE
Q ss_conf             861899999999848885438860
Q T0636            50 DAEPRVMRKLAEHFSCPEDNLMLV   73 (336)
Q Consensus        50 ~~~~~Lr~aia~~~~v~~d~I~~t   73 (336)
                      +.-.++|+.||+.|++++|.|++.
T Consensus        13 psr~eirekLA~~~~~~~~~vvv~   36 (84)
T PF01282_consen   13 PSRKEIREKLAAMYKVDPDLVVVF   36 (84)
T ss_dssp             --HHHHHHHHHHHHTS-STTEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             899999999999978995859983


No 16 
>PF03786 UxuA:  D-mannonate dehydratase (UxuA);  InterPro: IPR004628   This Fe2+-requiring enzyme plays a role in D-glucuronate catabolism in Escherichia coli. Mannonate dehydratase converts D-mannonate to 2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is found in a glucuronate utilization operon in Bacillus stearothermophilus T-6.; GO: 0008927 mannonate dehydratase activity, 0006064 glucuronate catabolic process; PDB: 3dbn_A 3bdk_B 3ban_A 1tz9_A.
Probab=42.36  E-value=5.8  Score=16.19  Aligned_cols=14  Identities=7%  Similarity=0.003  Sum_probs=6.5

Q ss_pred             ECCCHHHHHHHHHC
Q ss_conf             11788999999733
Q T0636           209 LFGPSELIAAMKRK  222 (336)
Q Consensus       209 ~i~~~~~i~~l~~~  222 (336)
                      ++++.+-++++-+.
T Consensus       219 Iv~~~ed~~~~l~~  232 (351)
T PF03786_consen  219 IVSTEEDYQRLLDL  232 (351)
T ss_dssp             -TTSHHHHHHHHHC
T ss_pred             EECCHHHHHHHHHH
T ss_conf             40799999999974


No 17 
>PF00701 DHDPS:  Dihydrodipicolinate synthetase family;  InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue . Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Sinorhizobium meliloti protein mosA , which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry . Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3e96_B 3d0c_A 3dz1_A 3eb2_C 2r8w_A 2v9d_C 2v8z_B 1nal_3 1fdy_B 1fdz_B ....
Probab=35.97  E-value=9.3  Score=14.89  Aligned_cols=22  Identities=32%  Similarity=0.442  Sum_probs=17.1

Q ss_pred             CCC--CCCCCCHHHHHHHHHHCCCC
Q ss_conf             633--22222379999999737872
Q T0636           144 SNP--TGQALSAGELDQLRQRAGKL  166 (336)
Q Consensus       144 nNP--TG~~~~~~~l~~l~~~~~~~  166 (336)
                      |||  ||..++.+.+.+|++ ++-+
T Consensus       134 n~P~~~g~~ls~~~~~~L~~-~p~v  157 (289)
T PF00701_consen  134 NIPSRTGVDLSPETLARLAE-HPNV  157 (289)
T ss_dssp             E-TTTHSSTS-HHHHHHHHT-STTB
T ss_pred             ECCCCCCCCCCHHHHHHHHC-CCCE
T ss_conf             78866542788999999718-8988


No 18 
>PF07021 MetW:  Methionine biosynthesis protein MetW;  InterPro: IPR010743   This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells . 
Probab=32.47  E-value=11  Score=14.53  Aligned_cols=158  Identities=13%  Similarity=0.175  Sum_probs=80.0

Q ss_pred             HHHHHHHCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHCC-----C------HH---H
Q ss_conf             57897503665535735765488876899999999987500588-98618999999998488-----8------54---3
Q T0636             5 EAMDTEVRAAAQAVCLAFNENPEAVEPRVQAAIAAAAARINRYP-FDAEPRVMRKLAEHFSC-----P------ED---N   69 (336)
Q Consensus         5 ~~~~~~~~~~~~~i~L~~Nenp~~p~~~v~~al~~~~~~~~~Yp-d~~~~~Lr~aia~~~~v-----~------~d---~   69 (336)
                      ..+.+..+++++++||.-+.   |   ...+.+++. .....|. +-.......++++-+.|     +      +|   .
T Consensus         5 ~~I~~~I~pgsrVLDlGCG~---G---~LL~~L~~~-k~~~~~GIEid~~~v~~~~~~Gl~Vi~~die~~l~~f~d~~FD   77 (193)
T PF07021_consen    5 EIIAEWIPPGSRVLDLGCGD---G---ELLAYLKEE-KGVRGYGIEIDEENVAACIARGLNVIQGDIEEGLSDFPDQSFD   77 (193)
T ss_pred             HHHHHHCCCCCEEEEECCCC---C---HHHHHHHHH-CCCCEEEEECCHHHHHHHHHCCCEEEEECHHHHHHHCCCCCCC
T ss_conf             99998638999478748999---7---899999984-5982899963999999999869959992577878648888888


Q ss_pred             EEEECCHHHHHHH---HHHH-H-CCCCEEECCCCCHHHHHHHHHH--CCCEEEECCCCCCCCCHHHHHHHCCHHHHHHHC
Q ss_conf             8860778899999---9998-4-6992576388735699999981--880364155435677889997300024313303
Q T0636            70 LMLVRGIDECFDR---ISAE-F-SSMRFVTAWPGFDGYRARIAVS--GLRHFEIGLTDDLLLDPNDLAQVSRDDCVVLAN  142 (336)
Q Consensus        70 I~~t~Gs~~~i~~---~~~~-~-~~~~vii~~P~y~~y~~~~~~~--g~~~~~vp~~~~~~~d~~~l~~~~~~~~i~l~n  142 (336)
                      .++-+-+-|.+..   ++.. + .|.++++..|.|..+.....+.  |.-.+.--+...|                 ..+
T Consensus        78 ~VIlsqtLqh~~~P~~vL~emLrvg~~~IVsfPNf~~w~~r~~l~~~GrmP~t~~lp~~W-----------------ydT  140 (193)
T PF07021_consen   78 YVILSQTLQHLRNPDKVLREMLRVGREAIVSFPNFGHWRVRLQLLFRGRMPVTEFLPYEW-----------------YDT  140 (193)
T ss_pred             EEEEHHHHHHHHHHHHHHHHHHHHCCEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCC-----------------CCC
T ss_conf             997367888365689999999873897999747737899999999669999788888743-----------------489


Q ss_pred             CCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCH
Q ss_conf             66332222237999999973787202521002588662003324520
Q T0636           143 PSNPTGQALSAGELDQLRQRAGKLLIDETYVDYSSFRARGLAYGENE  189 (336)
Q Consensus       143 PnNPTG~~~~~~~l~~l~~~~~~~IvDeaY~~f~~~~~~~l~~~~n~  189 (336)
                      |   -=+.++..+.++|+++.++-|++..+.+-...........||+
T Consensus       141 p---nIh~~T~~DF~~lc~~~~~~i~~~~~~~~~~~~~~~~~~~pNl  184 (193)
T PF07021_consen  141 P---NIHFCTIKDFEELCRELGIRILERVALDGDHRPSWLVRLWPNL  184 (193)
T ss_pred             C---CCCCEEHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCHH
T ss_conf             9---8030209999999998799899999974888755533236424


No 19 
>PF09581 Spore_III_AF:  Stage III sporulation protein AF (Spore_III_AF)
Probab=29.89  E-value=12  Score=14.25  Aligned_cols=16  Identities=19%  Similarity=0.439  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             8999999999999984
Q T0636           319 EEDNDRLLAALAEYSD  334 (336)
Q Consensus       319 ~ee~~~l~~aL~~~~e  334 (336)
                      .++.+++.+.|.++.+
T Consensus       163 ~~~~~~i~~~la~~~~  178 (188)
T PF09581_consen  163 SEEEEEIKNFLADFYG  178 (188)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             0789999999999959


No 20 
>PF05728 UPF0227:  Uncharacterised protein family (UPF0227);  InterPro: IPR008886 Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes in that they contain a domain distantly related to IPR000073 from INTERPRO.
Probab=29.19  E-value=12  Score=14.18  Aligned_cols=112  Identities=17%  Similarity=0.195  Sum_probs=53.4

Q ss_pred             CCEECC-CCCCCCCCCHHHHHHHHHHHHHH---HCCCCC--C-HHH-HHHHHHHHH-CCCHHHEEEECCHHHHHHHHHHH
Q ss_conf             535735-76548887689999999998750---058898--6-189-999999984-88854388607788999999998
Q T0636            16 QAVCLA-FNENPEAVEPRVQAAIAAAAARI---NRYPFD--A-EPR-VMRKLAEHF-SCPEDNLMLVRGIDECFDRISAE   86 (336)
Q Consensus        16 ~~i~L~-~Nenp~~p~~~v~~al~~~~~~~---~~Ypd~--~-~~~-Lr~aia~~~-~v~~d~I~~t~Gs~~~i~~~~~~   86 (336)
                      +++.|+ ||.+|...-.   +++.+...+.   ..|+++  . .++ ..+.+.+.. ...++++++.-.|-.++.....+
T Consensus         1 ~ilylHGF~Ssp~s~Ka---~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~~~~~~~~LiGSSLGG~~A~~LA   77 (187)
T PF05728_consen    1 MILYLHGFNSSPQSHKA---QALAEYFAEHGPDIEYPDPNLPHFPQQALARLEQLIEQLKDENVVLIGSSLGGYYATYLA   77 (187)
T ss_pred             CEEEECCCCCCCCCHHH---HHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHH
T ss_conf             97994587889875789---999999997598628867999978999999999999853778718999786999999999


Q ss_pred             H-CCCCEEECCCCCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHH
Q ss_conf             4-69925763887356999999818803641554356778899973
Q T0636            87 F-SSMRFVTAWPGFDGYRARIAVSGLRHFEIGLTDDLLLDPNDLAQ  131 (336)
Q Consensus        87 ~-~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~~~~~~~d~~~l~~  131 (336)
                      . .+-..++.+|.+..+.......|-+... ...++|.++...+.+
T Consensus        78 ~~~~~~aVLinPAv~p~~~l~~~lG~~~~~-~~~e~~~l~~~h~~~  122 (187)
T PF05728_consen   78 ERYGIKAVLINPAVRPYELLRDYLGEQTNP-YTGEEYELEEYHYAE  122 (187)
T ss_pred             HHHCCCEEEECCCCCHHHHHHHHCCCCCCC-CCCCEEEEEHHHHHH
T ss_conf             984999799958878789987741876456-778425774789874


No 21 
>PF05848 CtsR:  Firmicute transcriptional repressor of class III stress genes (CtsR);  InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon .
Probab=28.96  E-value=12  Score=14.15  Aligned_cols=11  Identities=36%  Similarity=0.836  Sum_probs=3.7

Q ss_pred             HHHHHCCCHHH
Q ss_conf             99984888543
Q T0636            59 LAEHFSCPEDN   69 (336)
Q Consensus        59 ia~~~~v~~d~   69 (336)
                      +|+.++|-|.+
T Consensus        31 LA~~F~CvPSQ   41 (152)
T PF05848_consen   31 LADRFDCVPSQ   41 (152)
T ss_pred             HHHHHCCCHHH
T ss_conf             88871867466


No 22 
>PF04392 ABC_sub_bind:  ABC transporter substrate binding protein;  InterPro: IPR007487   This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 2qh8_A.
Probab=28.42  E-value=12  Score=14.09  Aligned_cols=114  Identities=16%  Similarity=0.170  Sum_probs=51.8

Q ss_pred             CHHHHHHHHHHHH-CCCHHHEEEECCHHHHHHHHHHHHCC-CCEE---ECCCCCHHHHHHHHHHCCCEEEECCCCCCCCC
Q ss_conf             6189999999984-88854388607788999999998469-9257---63887356999999818803641554356778
Q T0636            51 AEPRVMRKLAEHF-SCPEDNLMLVRGIDECFDRISAEFSS-MRFV---TAWPGFDGYRARIAVSGLRHFEIGLTDDLLLD  125 (336)
Q Consensus        51 ~~~~Lr~aia~~~-~v~~d~I~~t~Gs~~~i~~~~~~~~~-~~vi---i~~P~y~~y~~~~~~~g~~~~~vp~~~~~~~d  125 (336)
                      +..+...++++.+ .-.+ +++++.|+..+..+. +...+ -.|+   +.+|...++......-|..+..+.....+.-.
T Consensus        43 ~d~~~~~~i~~~l~~~~~-DlIva~gt~aa~~l~-~~~~~~iPIVf~~V~dp~~~glv~s~~~pg~nvTGv~~~~~~~~~  120 (294)
T PF04392_consen   43 GDPERLAAIARKLVADKP-DLIVAIGTPAAQALA-KAIKDDIPIVFSGVSDPVGAGLVPSLDRPGGNVTGVSEPVPVEKQ  120 (294)
T ss_dssp             --HHHHHHHHHHH------SEEE---HHHHHHHH-HH-SS-S-EEEEEES------S-S-SS-----EE-EE----HHHH
T ss_pred             CCHHHHHHHHHHHHHCCC-CEEEEECCHHHHHHH-HHHCCCCCEEEEECCCHHHCCCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf             899999999999975699-999991849999999-730788649999716834335665566899988999915789999


Q ss_pred             HHHHHHH-CCHH-HHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             8999730-0024-3133036633222223799999997378720
Q T0636           126 PNDLAQV-SRDD-CVVLANPSNPTGQALSAGELDQLRQRAGKLL  167 (336)
Q Consensus       126 ~~~l~~~-~~~~-~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~I  167 (336)
                      ++-+.+. ++.| +-++.||+++++. ...+++.+.++..++-+
T Consensus       121 l~ll~~l~P~~k~igvly~~~~~~~~-~~~~~~~~~a~~~gi~l  163 (294)
T PF04392_consen  121 LELLKELLPDAKRIGVLYDPSEPNSV-AQVEELKAAAKELGIEL  163 (294)
T ss_dssp             HHHHHHHSTT--EE-EEE----HHHH-HHHHHHHHHHHH---EE
T ss_pred             HHHHHHHCCCCCEEEEEECCCCCCHH-HHHHHHHHHHHHCCCEE
T ss_conf             99999868788689999789885469-99999999999869879


No 23 
>PF06252 DUF1018:  Protein of unknown function (DUF1018);  InterPro: IPR009363   This family consists of several bacterial and phage proteins of unknown function.
Probab=26.99  E-value=11  Score=14.44  Aligned_cols=79  Identities=19%  Similarity=0.238  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHCCCEEECCCCCEE-E---EECCCHH---HHHHHHHHCCCEEEECCCCCCCCE-------EEEEECCHH
Q ss_conf             9999999999858978616986478-8---6569889---999999876938960778888874-------788747989
Q T0636           255 AQRRRVADALRGLGYRVASSEANFV-L---VENAAGE---RTLRFLRERGIQVKDAGQFGLHHH-------IRISIGREE  320 (336)
Q Consensus       255 ~~r~~l~~~l~~lg~~~~~s~~~Fi-~---~~~~~~~---~~~~~L~~~gi~vr~~~~fg~~~~-------iRis~~~~e  320 (336)
                      .++..+.+.|+..|++..++....- -   ...+...   .++..+...|+ |+..+.-.+..|       -++-..+.+
T Consensus        25 ~el~~Vl~~l~~~Gfk~~~~~~~~~~~~~~~~~~~~~KI~ALw~~l~~~~~-v~~~s~~al~~~vkr~~gv~~l~wl~~~  103 (119)
T PF06252_consen   25 AELQKVLDHLKAKGFKPRKPAKKPGPRPGMARSAQLRKIRALWIQLGKAGA-VRDRSEAALDAFVKRQFGVDRLRWLDPE  103 (119)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCHHHHCCHH
T ss_conf             999999999997568675433466889888778899999999999775678-6562799999999999685327668999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999984
Q T0636           321 DNDRLLAALAEYSD  334 (336)
Q Consensus       321 e~~~l~~aL~~~~e  334 (336)
                      +..+++++|+.|..
T Consensus       104 qa~~vIeaLk~w~~  117 (119)
T PF06252_consen  104 QASKVIEALKKWQR  117 (119)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999880


No 24 
>PF04914 DltD_C:  DltD C-terminal region;  InterPro: IPR006998   The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation .   These sequences contain the C-terminal region of DltD.; PDB: 3bma_C.
Probab=26.83  E-value=4.3  Score=17.04  Aligned_cols=84  Identities=20%  Similarity=0.162  Sum_probs=38.6

Q ss_pred             CCCCCCCCCHHHHHHHCCHHHHHHHCCCCC-----CCCCCCHHHHH-------HHHHHCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             554356778899973000243133036633-----22222379999-------999737872025210025886620033
Q T0636           117 GLTDDLLLDPNDLAQVSRDDCVVLANPSNP-----TGQALSAGELD-------QLRQRAGKLLIDETYVDYSSFRARGLA  184 (336)
Q Consensus       117 p~~~~~~~d~~~l~~~~~~~~i~l~nPnNP-----TG~~~~~~~l~-------~l~~~~~~~IvDeaY~~f~~~~~~~l~  184 (336)
                      |+-.||++-++.+.+ .+++.++|.-|-|+     ||  ++.+...       ..++.++.=|+     ||+.....+--
T Consensus        33 pEy~DlqllL~~~~~-~~~~vlfIi~PvNgkWydytG--~~~~~r~~~y~kI~~~~~~~Gf~i~-----D~s~~~y~pYf  104 (130)
T PF04914_consen   33 PEYGDLQLLLDQFKE-LGADVLFIIPPVNGKWYDYTG--LSKEMRQQYYKKIKYQLKSQGFNIA-----DLSDDEYEPYF  104 (130)
T ss_dssp             THHHHHHHHHHHHHH-TT-EEEEEE----HHHHHH----B-HHHHHHHHHHHHHHHHT----EE-----E-TT----TTS
T ss_pred             CCHHHHHHHHHHHHH-CCCCCEEEECCCCCHHHHHHC--CCHHHHHHHHHHHHHHHHHCCCCEE-----ECCCCCCCCCE
T ss_conf             234789999999998-399617985578715888808--8999999999999999998799487-----32136898764


Q ss_pred             HCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHH
Q ss_conf             245200120234652334345313117889999997
Q T0636           185 YGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMK  220 (336)
Q Consensus       185 ~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~  220 (336)
                      ..+ +          -..||+ ||+..++.+.+.+.
T Consensus       105 m~D-t----------iHlgw~-GWv~~D~~i~~f~~  128 (130)
T PF04914_consen  105 MQD-T----------IHLGWK-GWVYVDKAIYPFMK  128 (130)
T ss_dssp             -SS-S----------S--------HHHHHHHHHHHH
T ss_pred             EEE-C----------CCCCCH-HHHHHHHHHHHHHH
T ss_conf             744-4----------335601-69999999999973


No 25 
>PF05127 DUF699:  Putative ATPase (DUF699);  InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO.; PDB: 1w36_D 2zpa_B.
Probab=25.21  E-value=10  Score=14.66  Aligned_cols=23  Identities=9%  Similarity=-0.024  Sum_probs=16.1

Q ss_pred             CC-CEEECCCCCHHHHHHHHHHCC
Q ss_conf             99-257638873569999998188
Q T0636            89 SM-RFVTAWPGFDGYRARIAVSGL  111 (336)
Q Consensus        89 ~~-~vii~~P~y~~y~~~~~~~g~  111 (336)
                      +. +|++..|+........+....
T Consensus        25 ~~~~I~vtAPt~~av~~l~~~~~~   48 (174)
T PF05127_consen   25 GKLRILVTAPTGKAVKTLFEFLIK   48 (174)
T ss_dssp             ----EEEEBSS--CHHHHHHC---
T ss_pred             HCCEEEEECCCHHHHHHHHHHHHH
T ss_conf             064389966866899999999875


No 26 
>PF01974 tRNA_int_endo:  tRNA intron endonuclease, catalytic C-terminal domain;  InterPro: IPR006677   tRNA-intron endonucleases (3.1.27.9 from EC) cleave pre-tRNA producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron . This entry is for C-terminal domain of tRNA-intron endonuclease. ; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, 0000214 tRNA-intron endonuclease complex; PDB: 2zyz_A 1a79_A 2ohe_A 2ohc_B 1r11_A 1r0v_A 2gjw_D 1rlv_A 2cv8_B.
Probab=21.81  E-value=15  Score=13.47  Aligned_cols=20  Identities=40%  Similarity=0.564  Sum_probs=10.5

Q ss_pred             HHHHHHHHCCCEEEECCCCC
Q ss_conf             99999987693896077888
Q T0636           288 RTLRFLRERGIQVKDAGQFG  307 (336)
Q Consensus       288 ~~~~~L~~~gi~vr~~~~fg  307 (336)
                      .++..|+++|..+++|..||
T Consensus         6 ~vy~dLr~rG~~v~~G~kfG   25 (85)
T PF01974_consen    6 AVYKDLRSRGYVVKSGIKFG   25 (85)
T ss_dssp             HHHHHHHH---EEEEEEE-T
T ss_pred             HHHHHHHHCCCEECCCCCCC
T ss_conf             99999998888876464368


No 27 
>PF05448 AXE1:  Acetyl xylan esterase (AXE1);  InterPro: IPR008391 This family consists of several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan .; PDB: 1vlq_J 1ods_A 1l7a_B 1odt_C.
Probab=21.73  E-value=16  Score=13.29  Aligned_cols=13  Identities=31%  Similarity=0.261  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             9999999984888
Q T0636            54 RVMRKLAEHFSCP   66 (336)
Q Consensus        54 ~Lr~aia~~~~v~   66 (336)
                      ...+.+++--.++
T Consensus        27 FW~~~~~e~~~~p   39 (320)
T PF05448_consen   27 FWKKTLAELAAVP   39 (320)
T ss_dssp             HHHHHHHHHHTS-
T ss_pred             HHHHHHHHHHCCC
T ss_conf             9999999986389


No 28 
>PF02679 ComA:  (2R)-phospho-3-sulfolactate synthase (ComA);  InterPro: IPR003830   Methanogenic archaea produce methane via the anaerobic reduction of acetate or single carbon compounds . Coenzyme M (CoM; 2-mercaptoethanesulphonic acid) serves as the terminal methyl carrier for this process. Previously thought to be unique to methanogenic archaea, CoM has also been found in methylotrophic bacteria.   Biosynthesis of CoM begins with the Michael addition of sulphite to phosphoenolpyruvate, forming 2-phospho-3-sulpholactate (PSL). This reaction is catalyzed by members of this family, PSL synthase (ComA) . Subsequently, PSL is dephosphorylated by phosphosulpholactate phosphatase (ComB) to form 3-sulpholactate , which is then converted to 3-sulphopyruvate by L-sulpholactate dehydrogenase (ComC; 1.1.1.272 from EC) . Sulphopyruvate decarboxylase (ComDE; 4.1.1.79 from EC) converts 3-sulphopyruvate to sulphoacetaldehyde . Reductive thiolation of sulphoacetaldehyde is the final step.; GO: 0019295 coenzyme M biosynthetic process; PDB: 1u83_A 1qwg_A.
Probab=21.00  E-value=17  Score=13.23  Aligned_cols=51  Identities=18%  Similarity=0.171  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCEEEECC
Q ss_conf             99999999848885438860778899999999846992576388735699999981880364155
Q T0636            54 RVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEFSSMRFVTAWPGFDGYRARIAVSGLRHFEIGL  118 (336)
Q Consensus        54 ~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~  118 (336)
                      .|++.+.-++.   ..|-+..|.+  +.-++..  .+       .+..|...++.+|...+++.-
T Consensus        55 ~l~eki~l~~~---~~V~v~~GGt--lfe~~~~--~~-------~~~~y~~~~k~lGf~~iEiSd  105 (244)
T PF02679_consen   55 ILREKIDLAHD---HGVYVYTGGT--LFEIAIS--QG-------KFDEYLRECKDLGFDAIEISD  105 (244)
T ss_dssp             HHHHHHHHHHC---TT-EEE------HHHHHHH--TT--------HHHHHHHHHH----EEEE--
T ss_pred             HHHHHHHHHHH---CCCEEECCCH--HHHHHHH--CC-------HHHHHHHHHHHCCCCEEEECC
T ss_conf             99999999998---6981707954--9999982--07-------499999999985997899759


No 29 
>PF05913 DUF871:  Bacterial protein of unknown function (DUF871);  InterPro: IPR008589 This family consists of several conserved hypothetical proteins from bacteria and archaea. The function of this family is unknown though a number are annotated as outer surface proteins.; PDB: 1x7f_A 2p0o_A.
Probab=20.77  E-value=17  Score=13.16  Aligned_cols=37  Identities=19%  Similarity=0.293  Sum_probs=15.7

Q ss_pred             CCCCCHHHHHHHCCHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             567788999730002431330366332222237999999973
Q T0636           121 DLLLDPNDLAQVSRDDCVVLANPSNPTGQALSAGELDQLRQR  162 (336)
Q Consensus       121 ~~~~d~~~l~~~~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~  162 (336)
                      |++++.+++++..+..+-+.-|-     ..++.+.|..|...
T Consensus        96 D~Gf~~~e~a~ls~ngl~I~LNa-----Sti~~~~l~~l~~~  132 (357)
T PF05913_consen   96 DYGFSGEEIAELSKNGLKIELNA-----STITEEYLDNLMSY  132 (357)
T ss_dssp             -----HHHHHHHTTT-S-EEEET-----TT--CCHHHHHCCT
T ss_pred             CCCCCHHHHHHHHHCCCEEEEEC-----CCCCHHHHHHHHHH
T ss_conf             59999899999974797899977-----77977899999972


No 30 
>PF06153 DUF970:  Protein of unknown function (DUF970);  InterPro: IPR010375   This is a family of uncharacterised bacterial proteins.
Probab=20.03  E-value=18  Score=13.06  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=7.1

Q ss_pred             CCHHHHHHHHHHCCCEE
Q ss_conf             98899999998769389
Q T0636           284 AAGERTLRFLRERGIQV  300 (336)
Q Consensus       284 ~~~~~~~~~L~~~gi~v  300 (336)
                      .+++.+.+.|.++|+.+
T Consensus        11 ~Da~~l~~aL~~~g~~~   27 (109)
T PF06153_consen   11 EDANRLSDALTENGFRA   27 (109)
T ss_pred             CCHHHHHHHHHHCCCCE
T ss_conf             43799999999879108


Done!