Query T0515 putative carboxynorspermidine decarboxylase, Sinorhizobium meliloti, 365 residues
Match_columns 365
No_of_seqs 121 out of 2790
Neff 8.5
Searched_HMMs 11830
Date Fri May 21 18:08:21 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0515.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0515.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02784 Orn_Arg_deC_N: Pyrido 100.0 0 0 323.7 20.5 229 10-238 1-251 (251)
2 PF00278 Orn_DAP_Arg_deC: Pyri 99.9 9.3E-23 7.8E-27 162.1 6.6 102 241-343 1-116 (116)
3 PF01168 Ala_racemase_N: Alani 99.1 1.4E-09 1.2E-13 77.5 14.0 198 9-238 1-212 (214)
4 PF00842 Ala_racemase_C: Alani 92.1 0.25 2.1E-05 24.6 6.9 77 240-322 2-96 (129)
5 PF03851 UvdE: UV-endonuclease 87.6 0.57 4.8E-05 22.3 5.8 134 96-233 39-187 (275)
6 PF01136 Peptidase_U32: Peptid 69.6 2.4 0.00021 18.2 9.8 74 42-115 5-86 (233)
7 PF02424 ApbE: ApbE family; I 66.9 1.9 0.00016 18.9 3.1 121 168-312 107-237 (252)
8 PF02738 Ald_Xan_dh_C2: Molybd 65.8 2.9 0.00025 17.7 5.8 16 339-354 467-483 (543)
9 PF01261 AP_endonuc_2: Xylose 63.7 3.2 0.00027 17.5 7.1 28 209-236 106-136 (211)
10 PF05114 DUF692: Protein of un 53.2 1.5 0.00012 19.6 0.6 143 154-301 56-214 (274)
11 PF09675 Chlamy_scaf: Chlamydi 46.8 4 0.00034 16.9 1.9 36 35-70 5-40 (114)
12 PF02261 Asp_decarbox: Asparta 44.2 6.6 0.00056 15.5 3.7 67 279-350 49-115 (116)
13 PF01081 Aldolase: KDPG and KH 36.3 8.7 0.00073 14.7 4.6 67 32-98 13-85 (196)
14 PF03060 NPD: 2-nitropropane d 35.9 8.8 0.00074 14.7 6.3 97 9-111 45-152 (323)
15 PF01455 HupF_HypC: HupF/HypC 32.0 7.9 0.00067 14.9 1.6 16 305-320 33-48 (68)
16 PF06258 DUF1022: Protein of u 31.0 11 0.00089 14.1 7.1 70 168-239 126-198 (312)
17 PF09561 RE_HpaII: HpaII restr 30.3 8.5 0.00072 14.8 1.5 13 42-54 35-47 (355)
18 PF02812 ELFV_dehydrog_N: Glu/ 27.4 12 0.001 13.7 1.9 46 191-238 63-111 (131)
19 PF00351 Biopterin_H: Biopteri 27.3 5.8 0.00049 15.8 0.2 14 218-233 208-221 (332)
20 PF01079 Hint: Hint module; I 26.1 10 0.00087 14.2 1.3 13 306-318 102-114 (217)
21 PF11213 DUF3006: Protein of u 25.1 13 0.0011 13.7 1.6 25 302-326 26-50 (71)
22 PF08886 GshA: Glutamate-cyste 20.6 16 0.0014 12.9 2.6 83 167-251 192-281 (404)
No 1
>PF02784 Orn_Arg_deC_N: Pyridoxal-dependent decarboxylase, pyridoxal binding domain; InterPro: IPR000183 These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities , . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region .; GO: 0003824 catalytic activity; PDB: 2nv9_A 2nva_H 1szr_B 1qu4_B 2tod_C 1f3t_D 3btn_B 7odc_A 1d7k_B 2oo0_A ....
Probab=100.00 E-value=0 Score=323.67 Aligned_cols=229 Identities=21% Similarity=0.295 Sum_probs=199.6
Q ss_pred CHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHCCCCEEEECHHHHHHHHHCC--CCCCEEECCCCCHHHHH
Q ss_conf 5899999999999997217987987202158989999999808826772889999999707--98727704778866899
Q T0515 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERF--GKETHAYSVAYGDNEID 87 (365)
Q Consensus 10 d~~~i~~n~~~~~~~~~~~~~~i~yAvKaN~~~~vl~~l~~~g~g~dv~S~~El~~a~~~~--~~~~i~~~~~k~~~~i~ 87 (365)
|++.++++++++.+++...+++++||+||||++.||+.+.++|+|+||+|++|+++|++.| ++++++++|.|++++++
T Consensus 1 d~~~~~~~~~~~~~~~~~~~~~~~YA~KaN~~~~il~~l~~~g~g~dv~S~~El~~al~~g~~~~~ii~~gp~k~~~~l~ 80 (251)
T PF02784_consen 1 DEDTIIERIRELLRAFLPYNVQVFYAVKANPNPAILKLLAEEGCGFDVASPGELELALAAGFPPDRIIFTGPAKSDEELE 80 (251)
T ss_dssp EHHHHHHHHHHHHHHHSTT-EEEEEBGGGS--HHHHHHHHHTT-EEEESSHHHHHHHHHTTT-GGGEEEE-SS--HHHHH
T ss_pred CCHHHHHHHHHHHHHCCCCCEEEEEEEECCCCHHHHHHHHHCCCCEEECCHHHHHHHHHCCCCCHHEEECCCCCCHHHHH
T ss_conf 93799999999998628675489999702898999999998399869868999999997699920367628999999999
Q ss_pred HHHHCCC-EECCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCHHCCCCHHH-H------HHHHHCCCEEE
Q ss_conf 9997288-00218989999999972588711311567774554344667887101314899-9------99973690489
Q T0515 88 EVVSHAD-KIIFNSISQLERFADKAAGIARGLRLNPQVSSSSFDLADPARPFSRLGEWDVP-K------VERVMDRINGF 159 (365)
Q Consensus 88 ~a~~~g~-~i~iDs~~el~~i~~~~~~~~v~iRi~p~~~~~~~~~~~~~~~~~kfg~~~~~-~------~~~~~~~i~Gi 159 (365)
.|++.++ .+++||++||+++.+.+++.++++||||++....+....+++..+|||++..+ . +.....++.|+
T Consensus 81 ~a~~~~~~~i~iDs~~el~~l~~~~~~~~v~lRin~~~~~~~~~~~~~g~~~skFGi~~~~~~~~~~~~~~~~~l~l~Gl 160 (251)
T PF02784_consen 81 EAIEYGVATINIDSLDELERLAALAPGARVGLRINPGVGIGAHSKLSTGGKESKFGIDIEEEAEEALDRAKELGLRLVGL 160 (251)
T ss_dssp HHHHTT-SEEEESSHHHHHHHHHHHTTHEEEEB-B-S-STTTSCHCCCSSTSST---BGGG-HHHHHHHHHHTTEEEEEE
T ss_pred HHHHCCCCEEEECCHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHCCCCEEEEE
T ss_conf 99984999899479899999999747063789981487766776421331121057672588999998640148518999
Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHHH----CCC-CCEEEECCCCCCCCC-CCCHHHHHHHHHHHHHC------CCEEE
Q ss_conf 9850678767799999999999999984----456-516650477789888-97889999999998612------66089
Q T0515 160 MIHNNCENKDFGLFDRMLGEIEERFGAL----IAR-VDWVSLGGGIHFTGD-DYPVDAFSARLRAFSDR------YGVQI 227 (365)
Q Consensus 160 h~H~gs~~~~~~~~~~~l~~~~~~~~~~----~~~-~~~idiGGG~~~~~~-~~~~~~~~~~i~~~~~~------~~~~l 227 (365)
|||+|||+.+.+.|.++++.+.+++.++ +.+ +++||+|||||++|. +++++.+++.++..+++ .+++|
T Consensus 161 H~H~GS~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~idiGGG~~v~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 240 (251)
T PF02784_consen 161 HFHIGSQIRDPEAFREAIARLLDLIDELRRELGFEDLEWIDIGGGFGVPYDDDYDFEDYADLIRAALKEFFPSGFPGPKL 240 (251)
T ss_dssp B----TTBSSTHHHHHHHHHHHHHHHHHHHH---TT-SEEE--------SSSSSCHHHHHHHHHHHHHHHCTTTTTTSEE
T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEE
T ss_conf 98768788887999999999999999876611987687898549978888875564459999999999987404899589
Q ss_pred EEECCCEEEEC
Q ss_conf 99716200105
Q T0515 228 YLEPGEASITK 238 (365)
Q Consensus 228 ~~EpGR~lva~ 238 (365)
|+|||||+||+
T Consensus 241 ~~EpGR~lva~ 251 (251)
T PF02784_consen 241 IIEPGRYLVAN 251 (251)
T ss_dssp EEEE--TTTGG
T ss_pred EEECCHHHHCC
T ss_conf 99707898679
No 2
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR000183 These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities , . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region .; GO: 0003824 catalytic activity; PDB: 2qgh_A 3c5q_A 2yxx_A 1knw_A 1ko0_A 1hkw_B 1hkv_B 2o0t_B 1f3t_A 1szr_B ....
Probab=99.86 E-value=9.3e-23 Score=162.11 Aligned_cols=102 Identities=29% Similarity=0.389 Sum_probs=88.2
Q ss_pred EEEEEEEEECCCC--------CEEEEECCCCCCCCCCHHCCCCCCCC-----CCCCCCEEEEEEECCCCCCCEEECCCCC
Q ss_conf 8999999740477--------46999826543102420102453233-----7799943799970666876354304538
Q T0515 241 TLEVTVLDTLYNG--------KNLAIVDSSIEAHMLDLLIYRETAKV-----LPNEGSHSYMICGKSCLAGDVFGEFRFA 307 (365)
Q Consensus 241 ~lit~V~~~k~~~--------~~~~i~d~g~~~~~~~~~~~~~~~~~-----~~~~~~~~~~i~G~~C~~~D~~~~~~~l 307 (365)
+|+|+|+++|+.. ++|+++|+|++++ .+++.++...+. .+.++.+++.|+||||++.|++.++..+
T Consensus 1 ~Lvt~Vi~~k~~~~~~~~~~~~~~~~vd~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~G~tC~~~D~i~~~~~l 79 (116)
T PF00278_consen 1 TLVTRVIDVKRRRDSDDGNDDKTWYYVDDGIYGS-PDPWLYDQYFPILPLNRDNEGPEEPYTVWGPTCDSGDVIARDVPL 79 (116)
T ss_dssp EEEEEEEEEEEECS---SSS-EEEEEES----SS-THHHHHS----EEEESS-TTSSEEEEEEE---SSTT--SEEEEEE
T ss_pred CEEEEEEEEEECCCCCCCCCCCEEEEECCCHHHC-HHHHHHCCCCCEEECCCCCCCCCEEEEEEECCCCCCCEEEEECCC
T ss_conf 9698999999748976654210399993794669-787961987516872456777857899994676899999265367
Q ss_pred C-CCCCCCEEEEECCCHHHHHHHCCCCCCCCCEEEEE
Q ss_conf 9-88977789982788455132136788678808999
Q T0515 308 E-ELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIR 343 (365)
Q Consensus 308 p-~l~~GD~l~~~~~GAY~~~~~s~fn~~~~p~~v~~ 343 (365)
| ++++||||+|+++|||+++++++||++++|++|++
T Consensus 80 P~~l~~GD~l~f~~~GAYt~~~s~~Fn~~~~p~~v~v 116 (116)
T PF00278_consen 80 PKELEVGDWLVFENMGAYTMSLSSNFNGFPPPAEVYV 116 (116)
T ss_dssp ETT-----EEEES-----SGTTSBCCCTT--EEEEEE
T ss_pred CCCCCCCCEEEEEECCCCHHHHCCCCCCCCCCCEEEC
T ss_conf 8888999899999256031655674669899879979
No 3
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes ,. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A . The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C-terminus of the first beta-strand of the alpha/beta barrel. This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alenine racemase activity.; PDB: 3cpg_A 1b54_A 1ct5_A 1w8g_A 3gwq_B 1rcq_A 2odo_D 2rjg_B 3b8u_D 2rjh_A ....
Probab=99.11 E-value=1.4e-09 Score=77.48 Aligned_cols=198 Identities=19% Similarity=0.128 Sum_probs=133.4
Q ss_pred ECHHHHHHHHHHHHHHHHCCCCEEEEEECCC-CCHHHHHHHH-HC-CC-CEEEECHHHHHHHHHCCCCCCEEECCCCCHH
Q ss_conf 5589999999999999721798798720215-8989999999-80-88-2677288999999970798727704778866
Q T0515 9 IDKAKLTRNMERIAHVREKSGAKALLALKCF-ATWSVFDLMR-DY-MD-GTTSSSLFEVRLGRERFGKETHAYSVAYGDN 84 (365)
Q Consensus 9 ~d~~~i~~n~~~~~~~~~~~~~~i~yAvKaN-~~~~vl~~l~-~~-g~-g~dv~S~~El~~a~~~~~~~~i~~~~~k~~~ 84 (365)
+|++++++|++.+++.. . .++.-.+|+| +...+.+.+. .. |+ +|-|++..|....+.. ++.+.++ ..++
T Consensus 1 Idl~~l~~Ni~~~~~~~-~--~~i~~vvK~~a~g~g~~~~~~~~~~g~~~~~va~~~Ea~~l~~~---~il~~~~-~~~~ 73 (214)
T PF01168_consen 1 IDLDALRHNIKKIRQRA-P--KKIRAVVKANAYGHGIVRVAKALAEGVDGFGVATLQEAEELREA---PILVLGP-PPPE 73 (214)
T ss_dssp EEHHHHHHHHHHHHHHS-T--SEEEEB-HHHHSCHHHHHHHHHHHHTSSEEEESSHHHHHHHHHG---GEEE-C---SGG
T ss_pred CCHHHHHHHHHHHHHHC-C--CCEEEEECCCCCCCCHHHHHHHHHHCCCCHHCCCHHHHHHHHHC---CEEEECC-CCHH
T ss_conf 98899999999999865-8--86899986887782299999999975976240849899999838---5854638-8888
Q ss_pred HHHHHHHCCCEECCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCHHCCCCH---HHHHHH----HHCCCE
Q ss_conf 8999997288002189899999999725887113115677745543446678871013148---999999----736904
Q T0515 85 EIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQVSSSSFDLADPARPFSRLGEWD---VPKVER----VMDRIN 157 (365)
Q Consensus 85 ~i~~a~~~g~~i~iDs~~el~~i~~~~~~~~v~iRi~p~~~~~~~~~~~~~~~~~kfg~~~---~~~~~~----~~~~i~ 157 (365)
++..++++++...+||.+.++.+.+.+......++|...++.+.+ |.|+.. .+.++. .+.++.
T Consensus 74 ~~~~~~~~~~~~~v~s~~~~~~l~~~~~~~~~~~~v~l~idtG~~----------R~G~~~~~~~~l~~~i~~~~~l~l~ 143 (214)
T PF01168_consen 74 ELEELVEYNIIPTVDSPEQLEALNKAARKQGKPLPVHLKIDTGMG----------RLGVRPEELEELARAIKALPGLRLE 143 (214)
T ss_dssp GHHHHHHTTEEEEE-SHHHHHHHHHHHHHTSS-EEEEEBE--SST---------------HHHHHHHHHHHHCTTTEEEE
T ss_pred HHHHHHHCCEEEEECCHHHHHHHHHHHHHCCCCCEEEEEECCCCC----------CCCCCHHHHHHHHHHHHHCCCCCEE
T ss_conf 999987398999999899999999998985997349999998688----------6887999999999999857998667
Q ss_pred EEEEEECCCCCCHHH---HHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCE
Q ss_conf 899850678767799---99999999999998445651665047778988897889999999998612660899971620
Q T0515 158 GFMIHNNCENKDFGL---FDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEA 234 (365)
Q Consensus 158 Gih~H~gs~~~~~~~---~~~~l~~~~~~~~~~~~~~~~idiGGG~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~EpGR~ 234 (365)
|+..|.+.-...... ..+.+..+.+.+...+.++..+++|+- ..+... ....+.+ ++.||.+
T Consensus 144 Gi~th~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~s~g~S----------~~~~~~----~~~~~~~-~vR~G~~ 208 (214)
T PF01168_consen 144 GIMTHFGHADDPDATRRAQFERFRRLVEALEKAGIKPPIVSMGNS----------AAILRA----PAEEGYT-EVRPGSA 208 (214)
T ss_dssp EEBE--SSTTSSCHHHHHHHHHHHHHHHHHHHTTTTSSCEBEEBH----------HHHHHH----GGHCSTT-EEEE--T
T ss_pred EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCC----------CCHHHC----CCCCCCC-EEEECHH
T ss_conf 899631677880177999999999999999860899988965698----------564322----3114897-8983322
Q ss_pred EEEC
Q ss_conf 0105
Q T0515 235 SITK 238 (365)
Q Consensus 235 lva~ 238 (365)
+-+.
T Consensus 209 lyG~ 212 (214)
T PF01168_consen 209 LYGY 212 (214)
T ss_dssp T---
T ss_pred HHCC
T ss_conf 2286
No 4
>PF00842 Ala_racemase_C: Alanine racemase, C-terminal domain; InterPro: IPR011079 Alanine racemase (5.1.1.1 from EC) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins ,. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A . The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C-terminus of the first beta-strand of the alpha/beta barrel.; GO: 0008784 alanine racemase activity, 0006522 alanine metabolic process; PDB: 2odo_D 1rcq_A 2rjg_B 3b8u_D 2rjh_A 3b8v_B 3b8t_C 3b8w_D 2vd8_B 2vd9_A ....
Probab=92.08 E-value=0.25 Score=24.55 Aligned_cols=77 Identities=16% Similarity=0.180 Sum_probs=44.7
Q ss_pred EEEEEEEEEECCC----------------CCEEEEECCCCCCCCCCHHCCCCCCCCCCCCCCEEEEEEECCCCCCCEEEC
Q ss_conf 0899999974047----------------746999826543102420102453233779994379997066687635430
Q T0515 240 TTLEVTVLDTLYN----------------GKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 303 (365)
Q Consensus 240 g~lit~V~~~k~~----------------~~~~~i~d~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~C~~~D~~~~ 303 (365)
..+-++|+.+|.- +...+++..|+...+.+.+........ ..+.+-+.|..| +|.+.-
T Consensus 2 ~~l~a~i~~vr~l~~G~~VgYg~t~~~~~~~~iavv~iGYaDG~~R~~s~~~~vli----~G~~~piiGrV~--MD~~~v 75 (129)
T PF00842_consen 2 MSLKARIIQVRTLPAGEGVGYGRTYRAPRDTRIAVVPIGYADGYPRALSNKGYVLI----NGKRCPIIGRVC--MDMTMV 75 (129)
T ss_dssp EEEEEEEEEEEEE----EE-GGG-EE-SSSEEEEEE---------GGGCC--EEEE-------EEEEE------SS-BEE
T ss_pred EEEEEEEEEEEECCCCCCCCCCCEEECCCCCEEEEEEEECCCCCCCCCCCCCEEEE----CCEEEEEEEEEE--CCEEEE
T ss_conf 89999997999819989272799788899839999841020475300389848999----999957876874--018999
Q ss_pred CCC-C-CCCCCCCEEEEECCC
Q ss_conf 453-8-988977789982788
Q T0515 304 FRF-A-EELKVGDRISFQDAA 322 (365)
Q Consensus 304 ~~~-l-p~l~~GD~l~~~~~G 322 (365)
+.. . ++.++||.+.++.-.
T Consensus 76 dl~~~~~~~~~Gd~V~l~G~~ 96 (129)
T PF00842_consen 76 DLTDIEPDVKVGDEVVLFGDQ 96 (129)
T ss_dssp EBSTS-TT-----EEEEE--T
T ss_pred ECCCCCCCCCCCCEEEEECCC
T ss_conf 976876679999999998898
No 5
>PF03851 UvdE: UV-endonuclease UvdE; InterPro: IPR004601 Schizosaccharomyces pombe ultraviolet damage endonuclease (UVDE or Uve1p) performs the initial step in an alternative excision repair pathway for UV-induced DNA damage. This DNA repair pathway was originally thought to be specific for UV damage, however Uve1p also recognises UV-induced bipyrimidine photoadducts and other non-UV-induced DNA adducts . The Deinococcus radiodurans UVSE protein has also shown to be a UV DNA damage endonuclease that catalyzes repair of UV-induced DNA damage by a similar mechanism .; GO: 0004519 endonuclease activity, 0006289 nucleotide-excision repair; PDB: 3bzj_A 3bzg_A 3c0q_A 3c0s_A 3c0l_A.
Probab=87.63 E-value=0.57 Score=22.29 Aligned_cols=134 Identities=10% Similarity=0.163 Sum_probs=69.6
Q ss_pred ECCCCHHHHHHHHHHHCCCCC-EEECCCCCCC-CCCCCCCCCCCCHHCCCCHHHHHHHH-HCCCEEEEEEECC----CCC
Q ss_conf 021898999999997258871-1311567774-55434466788710131489999997-3690489985067----876
Q T0515 96 IIFNSISQLERFADKAAGIAR-GLRLNPQVSS-SSFDLADPARPFSRLGEWDVPKVERV-MDRINGFMIHNNC----ENK 168 (365)
Q Consensus 96 i~iDs~~el~~i~~~~~~~~v-~iRi~p~~~~-~~~~~~~~~~~~~kfg~~~~~~~~~~-~~~i~Gih~H~gs----~~~ 168 (365)
+...|+..|.++.+......+ ..|+.-.+-+ .+|+.. +-.+.++....++.+... ...=.-+.||.|. +..
T Consensus 39 l~~~Nl~~l~~~l~~n~~~~I~~~RisS~l~P~ashp~~--~~~~~~~~~~~l~~iG~~ak~~~iRls~HP~qf~vLnSp 116 (275)
T PF03851_consen 39 LALSNLRDLLRILRYNEAHGIRFYRISSDLFPFASHPEV--GYDWEEEFAEELAEIGRLAKEHGIRLSMHPGQFTVLNSP 116 (275)
T ss_dssp HHHHHHHHHHHHHHHHHH----EEE---TSSTTTTSTT----S------HHHHHH---HHHH---EEEB-----------
T ss_pred HHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCCEECCCC
T ss_conf 999999999999999998699779647364788888554--732699999999999999998498688569974428999
Q ss_pred CHHHHHHHHHHHH---HHHHHHCCC-----CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 7799999999999---999984456-----5166504777898889788999999999861266089997162
Q T0515 169 DFGLFDRMLGEIE---ERFGALIAR-----VDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGE 233 (365)
Q Consensus 169 ~~~~~~~~l~~~~---~~~~~~~~~-----~~~idiGGG~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~EpGR 233 (365)
+++.....++++. ++++.++.. .=.|.+||.++ ..+..++.|.+.++.+.+...-.|.+|-.-
T Consensus 117 ~~eVv~~Si~~L~yha~~l~~mg~~~~~~~~iviH~GG~yg--dK~~al~Rf~~n~~~L~~~ir~rL~lENDd 187 (275)
T PF03851_consen 117 RPEVVENSIRDLEYHAELLDLMGLPPSQDSVIVIHIGGVYG--DKEAALERFIENFKRLPESIRRRLTLENDD 187 (275)
T ss_dssp SHHHHHHHHHHHHHHHHHHHH----------EEEE------------HHHHHHHHH----HHHHTTEEEE--S
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCC--CHHHHHHHHHHHHHHCCHHHHHHEEEECCC
T ss_conf 87999999999999999999859995555079996177767--689999999999841789877444660587
No 6
>PF01136 Peptidase_U32: Peptidase family U32 This is family U32 in the peptidase classification. ; InterPro: IPR001539 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belonging to MEROPS peptidase family U32 (clan U-). The type example is collagenase (gene prtC) from Porphyromonas gingivalis (Bacteroides gingivalis) , which is an enzyme that degrades type I collagen and that seems to require a metal cofactor. The product of PrtC is evolutionary related to a number of uncharacterised proteins with a well conserved region containing two cysteines.; GO: 0008233 peptidase activity, 0006508 proteolysis
Probab=69.57 E-value=2.4 Score=18.22 Aligned_cols=74 Identities=12% Similarity=0.167 Sum_probs=56.4
Q ss_pred HHHHHHHHHCCC-CEEEECHHHHHHHHHCCCCC-CEEE--CCCCCHHHHHHHHHCCC-EECCC---CHHHHHHHHHHHCC
Q ss_conf 899999998088-26772889999999707987-2770--47788668999997288-00218---98999999997258
Q T0515 42 WSVFDLMRDYMD-GTTSSSLFEVRLGRERFGKE-THAY--SVAYGDNEIDEVVSHAD-KIIFN---SISQLERFADKAAG 113 (365)
Q Consensus 42 ~~vl~~l~~~g~-g~dv~S~~El~~a~~~~~~~-~i~~--~~~k~~~~i~~a~~~g~-~i~iD---s~~el~~i~~~~~~ 113 (365)
...++.+.+.|. |+-|++++-+++++..+++- ++.. .+..+...++...+.|+ ++++. |++|+..|.+..++
T Consensus 5 ~~~l~~l~~~g~d~i~v~d~g~~~~~~~~~~~~~i~~~~~~nv~N~~~~~~~~~~G~~~v~ls~ELs~~ei~~i~~~~~~ 84 (233)
T PF01136_consen 5 EKYLDQLKELGVDGIIVADPGAIELAKELGPDLPIHADTSLNVFNSESARFLKELGASRVTLSRELSLEEIKEIAENSPN 84 (233)
T ss_pred HHHHHHHHHCCCCEEEEECHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHCCC
T ss_conf 99999999769999999599999999972899749997245678799999999879979998987999999999743789
Q ss_pred CC
Q ss_conf 87
Q T0515 114 IA 115 (365)
Q Consensus 114 ~~ 115 (365)
.+
T Consensus 85 ~~ 86 (233)
T PF01136_consen 85 IE 86 (233)
T ss_pred CE
T ss_conf 73
No 7
>PF02424 ApbE: ApbE family; InterPro: IPR003374 This prokaryotic family of lipoproteins are related to ApbE, from Salmonella typhimurium. ApbE is involved in thiamine synthesis . More specifically is may be involved in the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) during the biosynthesis of the pyrimidine moiety of thiamine.; GO: 0009228 thiamin biosynthetic process; PDB: 2o34_B 2o18_C 1vrm_A.
Probab=66.87 E-value=1.9 Score=18.91 Aligned_cols=121 Identities=17% Similarity=0.126 Sum_probs=61.3
Q ss_pred CCHHHHHH--HHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEE-CCCEEEECCEEEEE
Q ss_conf 67799999--9999999999844565166504777898889788999999999861266089997-16200105508999
Q T0515 168 KDFGLFDR--MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLE-PGEASITKSTTLEV 244 (365)
Q Consensus 168 ~~~~~~~~--~l~~~~~~~~~~~~~~~~idiGGG~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~E-pGR~lva~ag~lit 244 (365)
.|+....| +++.+.+.+++.+.+--+||+||-+-.-....+ ..+-++-++ | + +...++.
T Consensus 107 lDlggiaKGyavD~~~~~L~~~gi~~~lVn~GGdi~~~G~~p~-------------g~~W~IgI~~P-~----~~~~~~~ 168 (252)
T PF02424_consen 107 LDLGGIAKGYAVDRAAEVLKAEGITNALVNAGGDIRAIGSKPD-------------GEPWRIGIQDP-Q----DPGELLG 168 (252)
T ss_dssp ---CCG----HHHHHHHHHHHGTTSSEEEE----EEEE-SC----------------B-EEEEEE-S----------EEE
T ss_pred EEECHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEEEECCCCC-------------CCCEEEEEECC-C----CCCCEEE
T ss_conf 7004578999999999999976998699946870899767999-------------99769998047-7----8775258
Q ss_pred EE------EEECCCCCEEEEECCCCCCCCCCHHCCCCCCCCCCC-CCCEEEEEEECCCCCCCEEECCCCCCCCCC
Q ss_conf 99------974047746999826543102420102453233779-994379997066687635430453898897
Q T0515 245 TV------LDTLYNGKNLAIVDSSIEAHMLDLLIYRETAKVLPN-EGSHSYMICGKSCLAGDVFGEFRFAEELKV 312 (365)
Q Consensus 245 ~V------~~~k~~~~~~~i~d~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~G~~C~~~D~~~~~~~lp~l~~ 312 (365)
.| +...-+.++++..++-.++|+.+|.-. .|. .....++|..++|...|.++.-.++-.++.
T Consensus 169 ~v~l~~~avaTSG~y~r~~~~~~~~~~HIidP~tG------~p~~~~~~svTVva~~a~~ADalaTa~~~~~~~~ 237 (252)
T PF02424_consen 169 VVELKNGAVATSGDYERYFEIGGKRYHHIIDPRTG------YPAETDIASVTVVAPDAATADALATALFVMGPEE 237 (252)
T ss_dssp EEEE---EEEEE--TTTCCC-S--EEES-B-TT---------B--SSEEEEEEEESSHHHHHHHHHH----STCH
T ss_pred EEEECCCEEECCCCCEEEEEECCEEEEEEECCCCC------CCCCCCCEEEEEECCCHHHHHHHHHHHHHCCHHH
T ss_conf 99947943974567435787689465204887779------9887997799997898889999999998279999
No 8
>PF02738 Ald_Xan_dh_C2: Molybdopterin-binding domain of aldehyde dehydrogenase; InterPro: IPR008274 Aldehyde oxidase () catalyzes the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase () catalyzes the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase () activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphhydryl groups.; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 3hrd_B 1rm6_D 1sb3_D 1t3q_E 1ffu_B 1ffv_B 1n63_E 1n61_E 1zxi_E 1n5w_E ....
Probab=65.76 E-value=2.9 Score=17.74 Aligned_cols=16 Identities=31% Similarity=0.287 Sum_probs=8.2
Q ss_pred EEEEEE-CCCEEEEEEE
Q ss_conf 089997-7880899983
Q T0515 339 AIAIRE-LDGSVRTVRE 354 (365)
Q Consensus 339 ~~v~~~-~dg~~~~ir~ 354 (365)
++|=++ ..|++++.|-
T Consensus 467 aeVeVD~~tG~v~v~~~ 483 (543)
T PF02738_consen 467 AEVEVDTETGEVRVLRY 483 (543)
T ss_dssp EEEEEETTT--EEEEEE
T ss_pred EEEECCCCCCCCCCEEE
T ss_conf 99730345555331368
No 9
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae . ; PDB: 3cny_B 2q02_B 1i6n_A 1i60_A 2g0w_B 1k77_A 1xp3_A 1qtw_A 2nqj_B 1qum_A ....
Probab=63.75 E-value=3.2 Score=17.50 Aligned_cols=28 Identities=25% Similarity=0.349 Sum_probs=12.4
Q ss_pred HHHHHHHHHHH---HHCCCEEEEEECCCEEE
Q ss_conf 89999999998---61266089997162001
Q T0515 209 VDAFSARLRAF---SDRYGVQIYLEPGEASI 236 (365)
Q Consensus 209 ~~~~~~~i~~~---~~~~~~~l~~EpGR~lv 236 (365)
++.+.+.++++ .++.++++.+|+--...
T Consensus 106 ~~~~~~~l~~~~~~a~~~gv~l~lE~~~~~~ 136 (211)
T PF01261_consen 106 LDRAAEFLRELAEYAEEHGVKLALENHPGEP 136 (211)
T ss_dssp HHHHHHHHHHHHHHHHHTTSEEEEE--SBST
T ss_pred HHHHHHHHHHHHHHHHHHCCEEEEEECCCCC
T ss_conf 9999999999999999739989998156867
No 10
>PF05114 DUF692: Protein of unknown function (DUF692); InterPro: IPR007801 This family consists of uncharacterised bacterial proteins.; PDB: 3bww_A.
Probab=53.19 E-value=1.5 Score=19.63 Aligned_cols=143 Identities=17% Similarity=0.187 Sum_probs=75.7
Q ss_pred CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHH--HCCCCCEEEECCC----CCCCCCCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 690489985067876779999999999999998--4456516650477----7898889788999999999861266089
Q T0515 154 DRINGFMIHNNCENKDFGLFDRMLGEIEERFGA--LIARVDWVSLGGG----IHFTGDDYPVDAFSARLRAFSDRYGVQI 227 (365)
Q Consensus 154 ~~i~Gih~H~gs~~~~~~~~~~~l~~~~~~~~~--~~~~~~~idiGGG----~~~~~~~~~~~~~~~~i~~~~~~~~~~l 227 (365)
.-+.|+++.+||...-...+-+.++.+.+.+.. ..-++.+-..+|- +|.+|.+..+....+.++.+-+..+..|
T Consensus 56 v~~HGv~LSlG~~~~ld~~~L~~l~~l~~~~~~~~~SeHL~~~~~~g~~~dLlPlP~t~eal~~v~~~i~~vQd~L~rpl 135 (274)
T PF05114_consen 56 VVLHGVGLSLGSADPLDRDYLKRLKALADRFQPPWVSEHLCWSSADGHLHDLLPLPYTEEALDRVVDRIRRVQDALGRPL 135 (274)
T ss_dssp EEE--------------HHHHHHHHHHHHHTT----EE-S--------------B---HHHHHHHHHHHHHHHHHHTS--
T ss_pred EEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCE
T ss_conf 88724660057999889999999999999878886875778864898157667888789999999999999999868986
Q ss_pred EEECCCEEEECCEEEEEEEEE----ECCCCCEEEEECCC------CCCCCCCHHCCCCCCCCCCCCCCEEEEEEECCCCC
Q ss_conf 997162001055089999997----40477469998265------43102420102453233779994379997066687
Q T0515 228 YLEPGEASITKSTTLEVTVLD----TLYNGKNLAIVDSS------IEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLA 297 (365)
Q Consensus 228 ~~EpGR~lva~ag~lit~V~~----~k~~~~~~~i~d~g------~~~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~C~~ 297 (365)
.+|--.+.+.....-.++.-. +++.+ -...+|-. .|+ -.++. .+....|-+......++|...+.
T Consensus 136 llEN~s~Y~~~~~~~m~E~eFl~el~~rtg-c~LLLDvnNvyvna~N~-g~Dp~---~yl~~lPlerV~eiHlAG~~~~~ 210 (274)
T PF05114_consen 136 LLENPSSYLPFPDSEMSEPEFLAELVERTG-CGLLLDVNNVYVNAVNH-GFDPY---EYLDRLPLERVVEIHLAGHSDDE 210 (274)
T ss_dssp EEB----S-B-TT-SS-HHHHHHHHHHHHT----EEEHHHHHHHHHH-----HH---HHHHHS-GGG--EEEE-------
T ss_pred EEECHHHHCCCCCCCCCHHHHHHHHHHHHC-CCEEEEECCCEEECCCC-CCCHH---HHHHHCCHHHEEEEEECCCCCCC
T ss_conf 983707644888576799999999999739-98899722302320107-98999---99973899792888815676788
Q ss_pred CCEE
Q ss_conf 6354
Q T0515 298 GDVF 301 (365)
Q Consensus 298 ~D~~ 301 (365)
.+++
T Consensus 211 ~~~~ 214 (274)
T PF05114_consen 211 GGLL 214 (274)
T ss_dssp ----
T ss_pred CCEE
T ss_conf 9835
No 11
>PF09675 Chlamy_scaf: Chlamydia-phage Chp2 scaffold (Chlamy_scaf)
Probab=46.77 E-value=4 Score=16.86 Aligned_cols=36 Identities=17% Similarity=-0.068 Sum_probs=30.6
Q ss_pred EECCCCCHHHHHHHHHCCCCEEEECHHHHHHHHHCC
Q ss_conf 202158989999999808826772889999999707
Q T0515 35 ALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERF 70 (365)
Q Consensus 35 AvKaN~~~~vl~~l~~~g~g~dv~S~~El~~a~~~~ 70 (365)
+-|.|..+.+.++-+..++..||+|+.+...|+...
T Consensus 5 v~k~na~~~l~hl~~Rs~~y~~c~~p~d~~eAln~V 40 (114)
T PF09675_consen 5 VAKVNATGVLRHLERRSPCYGDCCSPMDYQEALNAV 40 (114)
T ss_pred HHHHHCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf 998853225544665187525479816199999999
No 12
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1vc3_A 2eeo_B 2c45_C 1uhd_A 1uhe_A 1aw8_D 1pqf_B 1pyq_B 1pt0_A 1ppy_B ....
Probab=44.18 E-value=6.6 Score=15.47 Aligned_cols=67 Identities=18% Similarity=0.195 Sum_probs=42.2
Q ss_pred CCCCCCCEEEEEEECCCCCCCEEECCCCCCCCCCCCEEEEECCCHHHHHHHCCCCCCCCCEEEEEECCCEEE
Q ss_conf 377999437999706668763543045389889777899827884551321367886788089997788089
Q T0515 279 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVR 350 (365)
Q Consensus 279 ~~~~~~~~~~~i~G~~C~~~D~~~~~~~lp~l~~GD~l~~~~~GAY~~~~~s~fn~~~~p~~v~~~~dg~~~ 350 (365)
..+.+...+|.|-|+-= |+.+-.....-.-.++||.|+|..-+-|.....-+| .|.+|++++++++.
T Consensus 49 v~NG~Rf~TYvI~g~~G-Sg~i~lNGAAAr~~~~GD~vII~ay~~~~~~e~~~~----~P~vv~vd~~N~i~ 115 (116)
T PF02261_consen 49 VNNGERFETYVIPGERG-SGVICLNGAAARLVQPGDRVIIMAYAQMDEEEAKNH----KPKVVFVDEKNRIK 115 (116)
T ss_dssp ST---EEEEEEEEE-------EEEE--GGGTS----EEEEEEEEEEEHHHHHH-------EEEEEETTSEEE
T ss_pred CCCCCEEEEEEEECCCC-CCEEEECCHHHHCCCCCCEEEEEECCCCCHHHHHCC----CCEEEEECCCCCCC
T ss_conf 99993789999873689-877987788983479999999998845798998338----88699999999895
No 13
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1fq0_B 1eun_C 1fwr_B 1eua_C 2c0a_C 1wbh_C 1wau_A 1mxs_A 2v82_A 2v81_A ....
Probab=36.32 E-value=8.7 Score=14.69 Aligned_cols=67 Identities=3% Similarity=-0.052 Sum_probs=32.3
Q ss_pred EEEEECCCCCHHHHHHHHHCCC-CEEEECHHH--H---HHHHHCCCCCCEEECCCCCHHHHHHHHHCCCEECC
Q ss_conf 9872021589899999998088-267728899--9---99997079872770477886689999972880021
Q T0515 32 ALLALKCFATWSVFDLMRDYMD-GTTSSSLFE--V---RLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIF 98 (365)
Q Consensus 32 i~yAvKaN~~~~vl~~l~~~g~-g~dv~S~~E--l---~~a~~~~~~~~i~~~~~k~~~~i~~a~~~g~~i~i 98 (365)
+....+......+++.+.+.|. .+|+....+ + +..++..++-.+=.+...+.+..+.+++.|..+.+
T Consensus 13 Vir~~~~~~a~~~~~al~~gGi~~iEiT~~t~~a~~~I~~l~~~~p~~~iGAGTV~~~~~~~~a~~aGA~Fiv 85 (196)
T PF01081_consen 13 VIRGDDAEDALPIAEALIEGGIRVIEITLRTPNALEAIEALRKEYPDLLIGAGTVLTAEQAEAAIDAGAEFIV 85 (196)
T ss_dssp EE--SSGGGHHHHHHHHHH----BEEE-TTSTTHHHHHHHHHHHHTTSBEEE-B--SHHHHHHHHH----EEE
T ss_pred EEECCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCCCCEEE
T ss_conf 9977999999999999998799889996898319999999998789978957828589999999985999998
No 14
>PF03060 NPD: 2-nitropropane dioxygenase; InterPro: IPR004136 2-Nitropropane dioxygenase (1.13.11.32 from EC) catalyses the oxidation of nitroalkanes into their corresponding carbonyl compounds and nitrite using eithr FAD or FMN as a cofactor . This entry also includes fatty acid synthase subunit beta (2.3.1.86 from EC), which catalyses the formation of long- chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. The beta subunit contains domains for: [acyl-carrier protein] acetyltransferase and malonyltransferase, S-acyl fatty acid synthase thioesterase, enoyl-[acyl-carrier protein] reductase, and 3-hydroxypalmitoyl-[acyl-carrier protein] dehydratase. ; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2gjn_A 2gjl_A 2z6i_A 2z6j_B 3bo9_A 3bw2_A 3bw4_A 3bw3_A.
Probab=35.94 E-value=8.8 Score=14.65 Aligned_cols=97 Identities=12% Similarity=0.138 Sum_probs=59.3
Q ss_pred ECHHHHHHHHHHHHHHHHCC-CCEEEEEECCCCCH-------HHHHHHHHCCCCEEEECHHHHHHHHHCCCCCCEEECCC
Q ss_conf 55899999999999997217-98798720215898-------99999998088267728899999997079872770477
Q T0515 9 IDKAKLTRNMERIAHVREKS-GAKALLALKCFATW-------SVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVA 80 (365)
Q Consensus 9 ~d~~~i~~n~~~~~~~~~~~-~~~i~yAvKaN~~~-------~vl~~l~~~g~g~dv~S~~El~~a~~~~~~~~i~~~~~ 80 (365)
.+++.+++.++++++..+.+ ++.+++.-+..... .+++.+.+++.- ...++.+++. ..+.+.+.-+
T Consensus 45 ~~~~~l~~~i~~~~~~t~~pfgvnl~~~~~~~~~~~~~~~~~~~~~~~~~~~v~-----~~~~~~~~~~-~~~~v~~~~G 118 (323)
T PF03060_consen 45 LTPEQLREEIRKIRSLTDKPFGVNLFLPPPDPPDEIREKLGKALIDLAIEEGVP-----DEQVEAALKE-KPPVVSFSFG 118 (323)
T ss_dssp SSHHHHHHHHHHHHCC-SS----EEETTSTTHHHHHHHHTHHHCHHHHHHTT-S-----HHHHHHHHHS---SEEEEE--
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHHHCCCC-----CCCCCCCCCH-HHHEEEECCC
T ss_conf 687999999999997403875443102586520333210388999999972997-----3211111100-1220242667
Q ss_pred CC-HHHHHHHHHCCCE--ECCCCHHHHHHHHHHH
Q ss_conf 88-6689999972880--0218989999999972
Q T0515 81 YG-DNEIDEVVSHADK--IIFNSISQLERFADKA 111 (365)
Q Consensus 81 k~-~~~i~~a~~~g~~--i~iDs~~el~~i~~~~ 111 (365)
.. ++.++.+.+.|+. ..+-|..+..+..+..
T Consensus 119 ~p~~~~v~~l~~~g~~v~~~v~s~~~A~~a~~~g 152 (323)
T PF03060_consen 119 LPSEELVERLKAAGIKVIPTVTSVKEARKAAKAG 152 (323)
T ss_dssp -C-HHHHHHHHH---EEEEEESSHHHHHHHHH--
T ss_pred CCHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCC
T ss_conf 9817788998736977999879889998788628
No 15
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HUPF/HYPC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process . They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation , . ; PDB: 2z1c_A 2ot2_A 3d3r_B.
Probab=32.03 E-value=7.9 Score=14.95 Aligned_cols=16 Identities=31% Similarity=0.511 Sum_probs=12.7
Q ss_pred CCCCCCCCCCEEEEEC
Q ss_conf 5389889777899827
Q T0515 305 RFAEELKVGDRISFQD 320 (365)
Q Consensus 305 ~~lp~l~~GD~l~~~~ 320 (365)
.++|++++|||+.++.
T Consensus 33 ~lv~ev~vGD~VLVH~ 48 (68)
T PF01455_consen 33 ALVPEVKVGDYVLVHA 48 (68)
T ss_dssp TTCTTB----EEEEE-
T ss_pred EEECCCCCCCEEEEEC
T ss_conf 8738888898999950
No 16
>PF06258 DUF1022: Protein of unknown function (DUF1022); InterPro: IPR009367 This family consists of several hypothetical eukaryotic and prokaryotic proteins. The function of this family is unknown.
Probab=30.98 E-value=11 Score=14.14 Aligned_cols=70 Identities=11% Similarity=0.115 Sum_probs=47.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCC---HHHHHHHHHHHHHCCCEEEEEECCCEEEECC
Q ss_conf 67799999999999999984456516650477789888978---8999999999861266089997162001055
Q T0515 168 KDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYP---VDAFSARLRAFSDRYGVQIYLEPGEASITKS 239 (365)
Q Consensus 168 ~~~~~~~~~l~~~~~~~~~~~~~~~~idiGGG~~~~~~~~~---~~~~~~~i~~~~~~~~~~l~~EpGR~lva~a 239 (365)
-+++....+...+...++.+....-.+.||| +.....++ ...+...++.+.+..+.++++-+-|=.=...
T Consensus 126 vt~~~l~~a~~~~~~~~~~lp~p~~avlIGG--~s~~~~~~~~~a~~l~~~l~~l~~~~g~~~~iT~SRRTP~~~ 198 (312)
T PF06258_consen 126 VTPARLAEAAAAWAPRLAPLPRPRVAVLIGG--PSKHFRWDEDAARRLLEQLQALARQCGGSLLITTSRRTPPEA 198 (312)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCEEEEEECC--CCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCHHH
T ss_conf 8988887767654455246888759999788--888877799999999999999999679749998379890899
No 17
>PF09561 RE_HpaII: HpaII restriction endonuclease
Probab=30.34 E-value=8.5 Score=14.76 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=7.9
Q ss_pred HHHHHHHHHCCCC
Q ss_conf 8999999980882
Q T0515 42 WSVFDLMRDYMDG 54 (365)
Q Consensus 42 ~~vl~~l~~~g~g 54 (365)
-+|+++++++-.|
T Consensus 35 ~pI~~I~ReE~dg 47 (355)
T PF09561_consen 35 YPIIKIIREEHDG 47 (355)
T ss_pred EEHHHHHHHHCCC
T ss_conf 3266653564598
No 18
>PF02812 ELFV_dehydrog_N: Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; InterPro: IPR006097 Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases (1.4.1.2 from EC, 1.4.1.3 from EC, and 1.4.1.4 from EC) (GluDH) are enzymes that catalyze the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate , . GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids . Leucine dehydrogenase (1.4.1.9 from EC) (LeuDH) is a NAD-dependent enzyme that catalyzes the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues . Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle.; GO: 0016491 oxidoreductase activity, 0006520 amino acid metabolic process; PDB: 1hrd_C 1aup_A 1bgv_A 1k89_A 1v9l_E 1leh_B 1bw9_A 1bxg_A 1c1x_B 1c1d_A ....
Probab=27.43 E-value=12 Score=13.75 Aligned_cols=46 Identities=20% Similarity=0.165 Sum_probs=19.4
Q ss_pred CCEEEECCCCCCCCCCC---CHHHHHHHHHHHHHCCCEEEEEECCCEEEEC
Q ss_conf 51665047778988897---8899999999986126608999716200105
Q T0515 191 VDWVSLGGGIHFTGDDY---PVDAFSARLRAFSDRYGVQIYLEPGEASITK 238 (365)
Q Consensus 191 ~~~idiGGG~~~~~~~~---~~~~~~~~i~~~~~~~~~~l~~EpGR~lva~ 238 (365)
+--|.+|||-++-..|. +.......++.+...... ++=||+++.|+
T Consensus 63 l~~lp~GG~KggI~~dp~~~s~~e~e~l~r~~~~~l~~--~i~~~~~i~a~ 111 (131)
T PF02812_consen 63 LAGLPFGGGKGGIIVDPKDLSPPERERLLRRFGRALES--IIGPGRDIPAP 111 (131)
T ss_dssp HTTS-----BEEEBSSGGGS-HHHHHHHHHHHHHHHGG--G-BTTSB-B--
T ss_pred HHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH--HHCCCCEEECC
T ss_conf 50389997225553597548888999999999999988--62899689898
No 19
>PF00351 Biopterin_H: Biopterin-dependent aromatic amino acid hydroxylase; InterPro: IPR001273 Phenylalanine, tyrosine and tryptophan hydroxylases constitute a family of tetrahydrobiopterin-dependent aromatic amino acid hydroxylases, all of which are rate-limiting catalysts for important metabolic pathways . The proteins are structurally and functionally related, each containing iron, and catalysing ring hydroxylation of aromatic amino acids, using tetra-hydrobiopterin (BH4) as a substrate. All are regulated by phosphorylation at serines in their N-termini. It has been suggested that the proteins each contain a conserved C-terminal catalytic (C) domain and an unrelated N-terminal regulatory (R) domain. It is possible that the R domains arose from genes that were recruited from different sources to combine with the common gene for the catalytic core. Thus, by combining with the same C domain, the proteins acquired the unique regulatory properties of the separate R domains. A variety of enzymes belong to this family that includes, phenylalanine-4-hydroxylase from Chromobacterium violaceum where it is copper-dependent; it is iron-dependent in Pseudomonas aeruginosa, phenylalanine-4-hydroxylase catalyzes the conversion of phenylalanine to tyrosine. In humans, deficiencies are the cause of phenylketonuria, the most common inborn error of amino acid metabolism , tryptophan 5-hydroxylase catalyzes the rate-limiting step in serotonin biosynthesis: the conversion of tryptophan to 3-hydroxy-anthranilate and tyrosine 3-hydroxylase catalyzes the rate limiting step in catecholamine biosynthesis: the conversion of tyrosine to 3,4-dihydroxy-L-phenylalanine.; GO: 0004497 monooxygenase activity, 0005506 iron ion binding, 0009072 aromatic amino acid family metabolic process; PDB: 3e2t_A 1mlw_A 1ltu_A 1ltz_A 1ltv_A 2phm_A 1phz_A 1mmt_A 4pah_A 3pah_A ....
Probab=27.30 E-value=5.8 Score=15.79 Aligned_cols=14 Identities=36% Similarity=0.646 Sum_probs=5.6
Q ss_pred HHHHCCCEEEEEECCC
Q ss_conf 9861266089997162
Q T0515 218 AFSDRYGVQIYLEPGE 233 (365)
Q Consensus 218 ~~~~~~~~~l~~EpGR 233 (365)
.+.-|+| |+-|+|-
T Consensus 208 WfTVEFG--L~~e~g~ 221 (332)
T PF00351_consen 208 WFTVEFG--LCRENGE 221 (332)
T ss_dssp HTTTT-----EE----
T ss_pred EEEEEEE--EEECCCC
T ss_conf 0124446--7711894
No 20
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signaling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of Drosophila melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain ,.; GO: 0008233 peptidase activity, 0006508 proteolysis, 0007154 cell communication, 0007275 multicellular organismal development; PDB: 2wfx_A 1vhh_A 3ho5_H 2wg3_B 2wfr_A 2wfq_A 1at0_A.
Probab=26.08 E-value=10 Score=14.20 Aligned_cols=13 Identities=31% Similarity=0.646 Sum_probs=6.3
Q ss_pred CCCCCCCCCEEEE
Q ss_conf 3898897778998
Q T0515 306 FAEELKVGDRISF 318 (365)
Q Consensus 306 ~lp~l~~GD~l~~ 318 (365)
+-.++++||.|.+
T Consensus 102 fA~~V~~Gd~v~v 114 (217)
T PF01079_consen 102 FASDVRPGDCVLV 114 (217)
T ss_dssp EGGG--TT-EEEE
T ss_pred EHHHCCCCCEEEE
T ss_conf 6845857888999
No 21
>PF11213 DUF3006: Protein of unknown function (DUF3006)
Probab=25.10 E-value=13 Score=13.67 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=17.0
Q ss_pred ECCCCCCCCCCCCEEEEECCCHHHH
Q ss_conf 3045389889777899827884551
Q T0515 302 GEFRFAEELKVGDRISFQDAAGYTM 326 (365)
Q Consensus 302 ~~~~~lp~l~~GD~l~~~~~GAY~~ 326 (365)
....+++..++||+|.+.+.|.|..
T Consensus 26 p~~~LP~~~keGDvL~i~~~~~~~~ 50 (71)
T PF11213_consen 26 PRSLLPEGAKEGDVLIISEDGEIEI 50 (71)
T ss_pred EHHHCCCCCCCCCEEEECCCCEEEE
T ss_conf 9899998889887999978875999
No 22
>PF08886 GshA: Glutamate-cysteine ligase; InterPro: IPR011718 This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria . It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Probab=20.64 E-value=16 Score=12.92 Aligned_cols=83 Identities=16% Similarity=0.199 Sum_probs=46.6
Q ss_pred CCCHHHHHHHHHHHHHHHH-------HHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCEEEECC
Q ss_conf 7677999999999999999-------844565166504777898889788999999999861266089997162001055
Q T0515 167 NKDFGLFDRMLGEIEERFG-------ALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKS 239 (365)
Q Consensus 167 ~~~~~~~~~~l~~~~~~~~-------~~~~~~~~idiGGG~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~EpGR~lva~a 239 (365)
......|.+...++++.+. .+..+++-+|+..+-+..--....+.+.+.+++..++++++ -.|==++=|++
T Consensus 192 S~hF~~Y~~va~eF~~~~~IDPWlInp~f~~c~~vdF~~~~G~e~la~~Vd~lL~kir~KY~eYgI~--e~PfV~VKADa 269 (404)
T PF08886_consen 192 SNHFSAYEEVAKEFAKLIGIDPWLINPYFSQCGGVDFQEREGEECLASKVDALLAKIRRKYKEYGIK--EKPFVFVKADA 269 (404)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCCEEEEECCC
T ss_conf 6156899999999998739986342676724488577767646899999999999999999973999--99759996479
Q ss_pred EEEEEEEEEECC
Q ss_conf 089999997404
Q T0515 240 TTLEVTVLDTLY 251 (365)
Q Consensus 240 g~lit~V~~~k~ 251 (365)
|++=.-|+.+++
T Consensus 270 GTYGMGImtv~~ 281 (404)
T PF08886_consen 270 GTYGMGIMTVKS 281 (404)
T ss_pred CCCCCEEEEECC
T ss_conf 987733799648
Done!