Query T0622 3NKL, , 138 residues
Match_columns 138
No_of_seqs 113 out of 1147
Neff 8.0
Searched_HMMs 11830
Date Thu Jul 22 15:03:09 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0622.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0622.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02629 CoA_binding: CoA bind 98.6 4.1E-08 3.5E-12 67.7 6.5 89 1-95 3-92 (96)
2 PF08484 Methyltransf_14: C-me 98.0 2E-05 1.7E-09 51.0 8.9 87 2-94 78-166 (169)
3 PF01408 GFO_IDH_MocA: Oxidore 97.9 7.4E-06 6.3E-10 53.7 5.2 88 3-95 2-92 (120)
4 PF01113 DapB_N: Dihydrodipico 97.2 0.00033 2.8E-08 43.5 5.9 85 3-94 2-96 (124)
5 PF02844 GARS_N: Phosphoribosy 96.5 0.0046 3.9E-07 36.4 7.5 88 3-94 2-91 (100)
6 PF01118 Semialdhyde_dh: Semia 96.2 0.011 8.9E-07 34.1 8.0 90 3-100 1-101 (121)
7 PF10727 Rossmann-like: Rossma 96.0 0.0041 3.5E-07 36.7 4.7 80 1-89 10-92 (127)
8 PF05368 NmrA: NmrA-like famil 95.3 0.018 1.6E-06 32.6 6.1 89 4-95 1-100 (233)
9 PF02571 CbiJ: Precorrin-6x re 95.1 0.09 7.6E-06 28.4 10.1 93 2-95 1-99 (249)
10 PF03435 Saccharop_dh: Sacchar 94.7 0.1 8.5E-06 28.1 8.4 87 4-95 1-97 (386)
11 PF00289 CPSase_L_chain: Carba 94.4 0.073 6.2E-06 28.9 7.3 89 2-93 3-103 (110)
12 PF01210 NAD_Gly3P_dh_N: NAD-d 93.7 0.04 3.4E-06 30.5 4.7 95 2-100 1-108 (159)
13 PF01488 Shikimate_DH: Shikima 92.5 0.1 8.7E-06 28.0 5.4 82 1-85 12-98 (135)
14 PF02254 TrkA_N: TrkA-N domain 91.6 0.27 2.3E-05 25.4 6.7 83 4-90 1-88 (116)
15 PF00743 FMO-like: Flavin-bind 90.2 0.097 8.2E-06 28.2 3.3 28 1-29 1-28 (531)
16 PF04321 RmlD_sub_bind: RmlD s 89.4 0.56 4.7E-05 23.4 7.0 84 3-97 2-101 (286)
17 PF03807 F420_oxidored: NADP o 88.6 0.11 8.9E-06 27.9 2.5 77 3-85 1-81 (96)
18 PF01946 Thi4: Thi4 family; I 88.3 0.32 2.7E-05 24.9 4.8 95 3-102 19-123 (230)
19 PF02826 2-Hacid_dh_C: D-isome 87.5 0.59 5E-05 23.3 5.7 88 2-96 37-127 (178)
20 PF03447 NAD_binding_3: Homose 86.6 0.34 2.9E-05 24.8 4.2 83 8-95 1-89 (117)
21 PF10087 DUF2325: Uncharacteri 86.5 0.85 7.2E-05 22.3 8.9 82 3-96 1-82 (97)
22 PF03721 UDPG_MGDP_dh_N: UDP-g 86.3 0.58 4.9E-05 23.3 5.2 70 2-74 1-88 (185)
23 PF03808 Glyco_tran_WecB: Glyc 84.6 1.1 8.9E-05 21.7 9.1 105 2-117 49-157 (172)
24 PF01248 Ribosomal_L7Ae: Ribos 83.6 0.63 5.3E-05 23.1 4.4 60 43-102 12-71 (95)
25 PF05834 Lycopene_cycl: Lycope 82.0 0.82 7E-05 22.4 4.5 34 4-38 2-36 (374)
26 PF03465 eRF1_3: eRF1 domain 3 77.4 0.55 4.7E-05 23.5 2.4 57 44-100 19-93 (113)
27 PF07991 IlvN: Acetohydroxy ac 77.0 0.82 6.9E-05 22.4 3.1 90 2-98 5-97 (165)
28 PF07992 Pyr_redox_2: Pyridine 76.8 0.8 6.8E-05 22.5 3.0 31 3-35 1-31 (201)
29 PF02558 ApbA: Ketopantoate re 76.7 0.86 7.3E-05 22.3 3.2 92 4-97 1-102 (151)
30 PF00044 Gp_dh_N: Glyceraldehy 75.1 0.87 7.3E-05 22.3 2.9 90 3-95 2-118 (151)
31 PF05913 DUF871: Bacterial pro 74.7 2.2 0.00019 19.7 5.7 77 20-96 164-247 (357)
32 PF00899 ThiF: ThiF family; I 74.2 2.3 0.00019 19.7 10.3 89 1-94 2-122 (135)
33 PF10100 DUF2338: Uncharacteri 73.6 1.3 0.00011 21.1 3.5 31 2-33 2-32 (429)
34 PF03949 Malic_M: Malic enzyme 70.1 2.8 0.00024 19.1 6.3 85 2-87 26-130 (255)
35 PF01370 Epimerase: NAD depend 70.0 2.8 0.00024 19.1 7.4 96 4-100 1-120 (238)
36 PF00732 GMC_oxred_N: GMC oxid 68.3 1.6 0.00013 20.7 2.9 26 4-29 3-28 (298)
37 PF03446 NAD_binding_2: NAD bi 67.0 3.3 0.00028 18.7 8.7 93 2-96 2-120 (163)
38 PF00070 Pyr_redox: Pyridine n 65.2 3.6 0.0003 18.4 7.6 25 3-28 1-25 (81)
39 PF00106 adh_short: short chai 65.0 3.6 0.0003 18.4 7.4 72 2-86 1-75 (167)
40 PF04244 DPRP: Deoxyribodipyri 64.1 3.7 0.00032 18.3 9.6 66 23-97 60-125 (224)
41 PF02423 OCD_Mu_crystall: Orni 63.3 3.3 0.00028 18.6 3.8 71 2-74 129-204 (313)
42 PF01494 FAD_binding_3: FAD bi 62.1 3.3 0.00028 18.6 3.6 34 2-37 2-35 (356)
43 PF02737 3HCDH_N: 3-hydroxyacy 58.6 4.7 0.00039 17.7 4.0 34 3-38 1-34 (180)
44 PF00551 Formyl_trans_N: Formy 58.3 4.7 0.0004 17.7 7.0 69 2-70 1-87 (181)
45 PF00056 Ldh_1_N: lactate/mala 55.3 5.3 0.00045 17.4 4.7 66 3-70 2-77 (142)
46 PF01266 DAO: FAD dependent ox 53.8 4.2 0.00036 18.0 3.0 91 4-96 2-117 (358)
47 PF04412 DUF521: Protein of un 53.2 5.7 0.00048 17.2 7.2 75 14-89 230-316 (400)
48 PF04016 DUF364: Domain of unk 52.2 5.9 0.0005 17.1 6.8 86 2-97 113-198 (232)
49 PF07075 DUF1343: Protein of u 48.9 6.7 0.00057 16.7 6.2 117 8-127 9-148 (362)
50 PF08032 SpoU_sub_bind: RNA 2' 48.7 5.3 0.00045 17.4 2.8 49 48-97 2-51 (76)
51 PF02670 DXP_reductoisom: 1-de 44.2 7.9 0.00067 16.3 8.7 52 4-69 1-54 (129)
52 PF09445 Methyltransf_15: RNA 40.4 4.7 0.00039 17.7 1.5 88 7-100 8-124 (163)
53 PF00290 Trp_syntA: Tryptophan 34.0 11 0.00097 15.3 4.1 39 47-85 124-162 (259)
54 PF02310 B12-binding: B12 bind 33.8 12 0.00097 15.3 4.9 68 12-93 15-83 (121)
55 PF05049 IIGP: Interferon-indu 31.7 12 0.0011 15.1 6.2 95 3-97 37-149 (376)
56 PF08915 tRNA-Thr_ED: Archaea- 24.7 14 0.0012 14.7 1.8 71 27-98 36-116 (137)
57 PF00218 IGPS: Indole-3-glycer 22.3 18 0.0016 14.0 5.5 58 45-102 110-173 (255)
58 PF00670 AdoHcyase_NAD: S-aden 22.1 17 0.0014 14.2 1.8 51 2-54 24-75 (162)
59 PF01262 AlaDh_PNT_C: Alanine 21.3 19 0.0016 13.9 3.9 64 2-69 21-109 (168)
60 PF00875 DNA_photolyase: DNA p 20.8 20 0.0017 13.8 5.4 47 52-98 78-126 (166)
61 PF00208 ELFV_dehydrog: Glutam 20.6 20 0.0017 13.8 4.0 31 2-33 33-63 (244)
62 PF09822 ABC_transp_aux: ABC-t 20.0 21 0.0017 13.7 8.4 117 14-131 132-268 (271)
No 1
>PF02629 CoA_binding: CoA binding domain; InterPro: IPR003781 This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.; PDB: 2fpp_A 2fpi_A 1euc_A 1eud_A 2fpg_A 2fp4_A 2yv2_A 2dt5_A 1xcb_F 2vt3_A ....
Probab=98.59 E-value=4.1e-08 Score=67.75 Aligned_cols=89 Identities=25% Similarity=0.336 Sum_probs=76.2
Q ss_pred CCCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECC-HHHHHHHHHHCCCCEEEEECCCCCHHHHH
Q ss_conf 95179983376899999999718994489986078536485028812507-88999999854998999965899989999
Q T0622 1 KKKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYR-PKYLERLIKKHCISTVLLAVPSASQVQKK 79 (138)
Q Consensus 1 ~krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~-~~dl~~~i~~~~i~~iiia~~~~~~~~~~ 79 (138)
.++++|+|+|..+.++...+.+..++...++++.||.+.+..+.|+++|+ .+++++.. ++|.++++.| .+...
T Consensus 3 ~~~VavvGas~~~~~~~~~~~~~~~~~~~~v~~vnp~~~g~~i~G~~vy~~l~~l~~~~---~id~aii~vP---~~~v~ 76 (96)
T PF02629_consen 3 PKSVAVVGASNRGGKLGYVLRNLLGFGFVGVFPVNPKKIGEEIEGVPVYPSLDDLPEKI---EIDLAIIAVP---AESVP 76 (96)
T ss_dssp TBEEEEE---S-TTCHHHHHHHHHHBEEEEEEEC-TTTTSSB----BCESSHHHHHHHC---TTSEEEEES----HHHHH
T ss_pred CCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCCEECCEEEECCHHHHCCCC---CCCEEEEECC---HHHHH
T ss_conf 87899995898616799999999769983999818850386898998235598732544---9989999668---89999
Q ss_pred HHHHHHHHCCCEEEEC
Q ss_conf 9999998579829980
Q T0622 80 VIIESLAKLHVEVLTI 95 (138)
Q Consensus 80 ~i~~~~~~~~v~v~~i 95 (138)
+.++.|.+.|++-.++
T Consensus 77 ~~~~~~~~~gvk~i~~ 92 (96)
T PF02629_consen 77 DVVEECIEAGVKAIVI 92 (96)
T ss_dssp HHHHHHHHCT-SEEEE
T ss_pred HHHHHHHHCCCCEEEE
T ss_conf 9999999879988999
No 2
>PF08484 Methyltransf_14: C-methyltransferase; InterPro: IPR013691 This domain is found in bacterial C-methyltransferase proteins, often together with other methyltransferase domains such as IPR013216 from INTERPRO or IPR013217 from INTERPRO.
Probab=97.98 E-value=2e-05 Score=51.03 Aligned_cols=87 Identities=21% Similarity=0.255 Sum_probs=64.4
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCC--EEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHH
Q ss_conf 51799833768999999997189944899860785364850288--1250788999999854998999965899989999
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQG--ITIYRPKYLERLIKKHCISTVLLAVPSASQVQKK 79 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g--~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~ 79 (138)
|+|++|||+..|..+.+.+--+++ .+..++|+||.|+|+++-| +||++.+++. +.+.|.+++..+....+.++
T Consensus 78 k~I~~yGA~~kg~tlLn~~gl~~~-~I~~vvD~np~KqG~~~PGt~ipI~spe~l~----~~~pD~vlil~w~y~~EI~~ 152 (169)
T PF08484_consen 78 KRIAGYGAGAKGNTLLNYCGLDND-LIDYVVDDNPNKQGKFLPGTHIPIVSPEELK----ERKPDYVLILAWNYADEIME 152 (169)
T ss_pred CEEEEECCCHHHHHHHHHHCCCCC-EEEEEEECCCCCCCCCCCCCCCEECCHHHHH----HCCCCEEEECCHHHHHHHHH
T ss_conf 979999962489999998499870-1579996895527731599987086989995----37999999957255899999
Q ss_pred HHHHHHHHCCCEEEE
Q ss_conf 999999857982998
Q T0622 80 VIIESLAKLHVEVLT 94 (138)
Q Consensus 80 ~i~~~~~~~~v~v~~ 94 (138)
++ ....+.|-++.+
T Consensus 153 ~~-~~~~~~Gg~fi~ 166 (169)
T PF08484_consen 153 QL-AEYREWGGKFIV 166 (169)
T ss_pred HH-HHHHHCCCEEEE
T ss_conf 99-999966998999
No 3
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyze the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 3cea_A 3ec7_D 3euw_A 3ezy_B 3e18_A 2p2s_A 3dty_B 1tlt_B 1xea_D 3bio_A ....
Probab=97.88 E-value=7.4e-06 Score=53.71 Aligned_cols=88 Identities=28% Similarity=0.405 Sum_probs=70.6
Q ss_pred CEEEEECCHHHHHHHHHHHHC-CCCEEEEEECCCHHHCCC--CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHH
Q ss_conf 179983376899999999718-994489986078536485--02881250788999999854998999965899989999
Q T0622 3 KVLIYGAGSAGLQLANMLRQG-KEFHPIAFIDDDRKKHKT--TMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKK 79 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~-~~y~ivGfiDd~~~~~g~--~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~ 79 (138)
|+.|+|+|..|...+..+.+. ++++++|++|.++.+... .-.+.+.+ .++.+++...++|.++++.|...+.
T Consensus 2 rv~iIG~G~~~~~~~~~~~~~~~~~~v~av~d~~~~~~~~~~~~~~~~~~--~~~~~~l~~~~~D~v~I~tp~~~h~--- 76 (120)
T PF01408_consen 2 RVGIIGAGRIGKRHLRALRRSPPGVEVVAVVDPDPERAEAFAKEFGIPVY--TDLEELLEDPKIDAVIIATPPSSHA--- 76 (120)
T ss_dssp EEEEECE-THHHHHHHHHHHTTTTEEEEEEESSSHHHHHHHHHHTTSEEE--SSHHHHHTHTTESEEEEES-GGGHH---
T ss_pred EEEEECCCHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCCCC--CCHHHHHHCCCCCEEEEECCCCCHH---
T ss_conf 89999383999999999996499938999987999999999998299742--8899997255889899957953499---
Q ss_pred HHHHHHHHCCCEEEEC
Q ss_conf 9999998579829980
Q T0622 80 VIIESLAKLHVEVLTI 95 (138)
Q Consensus 80 ~i~~~~~~~~v~v~~i 95 (138)
+++..|.+.|+.|+.=
T Consensus 77 ~~~~~~l~~g~~V~~E 92 (120)
T PF01408_consen 77 EIALAALEAGKHVLVE 92 (120)
T ss_dssp HHHHHHHHCTCEEEEE
T ss_pred HHHHHHHHHCCEEEEE
T ss_conf 9999999829979998
No 4
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase (1.3.1.26 from EC) catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate; PDB: 1vm6_B 3dap_B 1f06_A 2dap_A 1dap_A 1yl7_B 1yl5_B 1p9l_B 1c3v_B 1yl6_A ....
Probab=97.17 E-value=0.00033 Score=43.45 Aligned_cols=85 Identities=19% Similarity=0.287 Sum_probs=63.3
Q ss_pred CEEEEEC-CHHHHHHHHHHHHCCCCEEEEEECCCH-HHCCCCCC--------CEEECCHHHHHHHHHHCCCCEEEEECCC
Q ss_conf 1799833-768999999997189944899860785-36485028--------8125078899999985499899996589
Q T0622 3 KVLIYGA-GSAGLQLANMLRQGKEFHPIAFIDDDR-KKHKTTMQ--------GITIYRPKYLERLIKKHCISTVLLAVPS 72 (138)
Q Consensus 3 rvlIvGa-g~~a~~l~~~l~~~~~y~ivGfiDd~~-~~~g~~i~--------g~~v~~~~dl~~~i~~~~i~~iiia~~~ 72 (138)
|++|+|+ |+.|..+++.+.+++++.++|.+|..+ ...|+.+. |+++. +++.+++.+ .|.++ ..
T Consensus 2 kV~v~G~~GrMG~~i~~~i~~~~~~elv~~~~~~~~~~~g~d~g~~~g~~~~~v~v~--~dl~~~~~~--~DVvI---DF 74 (124)
T PF01113_consen 2 KVAVIGASGRMGRAIAKAILESPDFELVGAVDRSPSPLVGKDIGELLGLGPLGVPVT--DDLEEVLEE--ADVVI---DF 74 (124)
T ss_dssp EEEEB--------HHHHHHHHSTTCEE-EEEESSS-TT---B------------BEB--S-HCHHCCS---SEEE---B-
T ss_pred EEEEECCCCHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCHHHHCCCCCCCCCCC--CCHHHHCCC--CEEEE---EC
T ss_conf 899999999799999999975899799999906985324643677608787544565--899895065--60999---89
Q ss_pred CCHHHHHHHHHHHHHCCCEEEE
Q ss_conf 9989999999999857982998
Q T0622 73 ASQVQKKVIIESLAKLHVEVLT 94 (138)
Q Consensus 73 ~~~~~~~~i~~~~~~~~v~v~~ 94 (138)
+.++.....+..|.++++.+.+
T Consensus 75 T~p~~~~~~~~~~~~~g~~~Vi 96 (124)
T PF01113_consen 75 THPEAVLDNLKAAAKHGVPLVI 96 (124)
T ss_dssp S-HHHHHHHHHHHHHHT-EEEE
T ss_pred CCHHHHHHHHHHHHHCCCCEEE
T ss_conf 9878999999999978999999
No 5
>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR000115 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) catalyzes the second step in the de novo biosynthesis of purine: ATP + 5-phosphoribosylamine + glycine = ADP + P_i + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART.; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 1gso_A 1vkz_B 2qk4_A 2ys6_A 2yrw_A 2ys7_A 2yrx_A 2ip4_B 2yw2_A 2yya_A ....
Probab=96.53 E-value=0.0046 Score=36.35 Aligned_cols=88 Identities=17% Similarity=0.204 Sum_probs=64.8
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHH
Q ss_conf 17998337689999999971899448998607853648502881--2507889999998549989999658999899999
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGI--TIYRPKYLERLIKKHCISTVLLAVPSASQVQKKV 80 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~--~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~ 80 (138)
+|||+|+|...-+++..+.+++...-+-+..-|+..... ...+ .....+.+.+++++++||-+++-.. ..-..-
T Consensus 2 kVLviGsGgREHAla~~l~~S~~v~~v~~apGN~G~~~~-~~~~~i~~~d~~~i~~~a~~~~idlvvvGPE---~pL~~G 77 (100)
T PF02844_consen 2 KVLVIGSGGREHALAWALAQSPRVDEVYVAPGNPGTARL-AENVNIDITDIEEIVDFAKENNIDLVVVGPE---APLVAG 77 (100)
T ss_dssp EEEE------HHHHHHHHTTCTTEEEEEEE------TTT-SEEE-S-TT-HHHHHHHHHHTTESEEE---H---HHHH--
T ss_pred EEEEECCCHHHHHHHHHHHCCCCCCEEEEECCCHHHHHH-CCCCCCCCCCHHHHHHHHHHCCCCEEEECCH---HHHHHH
T ss_conf 799987885999999999629987889992898477763-4211789689999999999849998998961---888876
Q ss_pred HHHHHHHCCCEEEE
Q ss_conf 99999857982998
Q T0622 81 IIESLAKLHVEVLT 94 (138)
Q Consensus 81 i~~~~~~~~v~v~~ 94 (138)
+.+.+++.|+.+.=
T Consensus 78 l~D~l~~~gi~vfG 91 (100)
T PF02844_consen 78 LADALRAAGIPVFG 91 (100)
T ss_dssp -HHHHHH---TEE-
T ss_pred HHHHHHHCCCCEEC
T ss_conf 79999878996689
No 6
>PF01118 Semialdhyde_dh: Semialdehyde dehydrogenase, NAD binding domain; InterPro: IPR000534 The semialdehyde dehydrogenase family is found in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), which is involved in arginine biosynthesis, and aspartate-semialdehyde dehydrogenase , an enzyme involved in the biosynthesis of various amino acids from aspartate. This family is also found in yeast and fungal Arg5,6 protein, which is cleaved into the enzymes N-acety-gamma-glutamyl-phosphate reductase and acetylglutamate kinase. These are also involved in arginine biosynthesis. All proteins in this entry contain a NAD binding region of semialdehyde dehydrogenase.; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0006520 amino acid metabolic process, 0005737 cytoplasm; PDB: 2hjs_A 2qz9_B 2r00_B 2fmu_A 2bka_A 1mb4_A 1mc4_A 1t4b_B 1t4d_A 1brm_C ....
Probab=96.25 E-value=0.011 Score=34.14 Aligned_cols=90 Identities=20% Similarity=0.295 Sum_probs=64.1
Q ss_pred CEEEEE-CCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCC----------CCEEECCHHHHHHHHHHCCCCEEEEECC
Q ss_conf 179983-37689999999971899448998607853648502----------8812507889999998549989999658
Q T0622 3 KVLIYG-AGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTM----------QGITIYRPKYLERLIKKHCISTVLLAVP 71 (138)
Q Consensus 3 rvlIvG-ag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i----------~g~~v~~~~dl~~~i~~~~i~~iiia~~ 71 (138)
|+.|+| +|..|..+++.+.+++.+.++.++.... ..|..+ ....+.. .+...+ .++|.+++|.|
T Consensus 1 kv~IvGAtG~vG~~ll~~L~~~p~~e~~~~~~~~~-~~g~~~~~~~~~~~~~~~~~~~~-~~~~~~---~~~Dvvf~al~ 75 (121)
T PF01118_consen 1 KVAIVGATGYVGRELLRLLAEHPDFEIVALVSRSR-SAGKPLSEVHPHLTGVEDLDLED-FDPEDF---ADADVVFFALP 75 (121)
T ss_dssp EEEEE--------HHHHHHHHTSSEEEEEEEESTT-T---BHHHHCGGGTTCTCEBEEE-GGGGGG---TTESEEEE-SS
T ss_pred CEEEECCCCHHHHHHHHHHHCCCCEEEEEEEECCH-HCCCCHHHHCCCCCCCCCCCCCC-CCHHHH---CCCCEEEECCC
T ss_conf 99999998979999999996599955999885052-12877544003211111210133-786575---39978998588
Q ss_pred CCCHHHHHHHHHHHHHCCCEEEECCCHHH
Q ss_conf 99989999999999857982998068366
Q T0622 72 SASQVQKKVIIESLAKLHVEVLTIPNLDD 100 (138)
Q Consensus 72 ~~~~~~~~~i~~~~~~~~v~v~~iP~~~~ 100 (138)
.....++...+...|+.|.-...-+-
T Consensus 76 ---~~~s~~~~~~~~~~g~~ViD~S~~~R 101 (121)
T PF01118_consen 76 ---HGASKELAPALLAAGCRVIDLSGDFR 101 (121)
T ss_dssp ---HHHHHHHHHHHHHTTSEEEESSSTTT
T ss_pred ---HHHHHHHHHHHHHCCEEEEECCHHHH
T ss_conf ---00789999997429909997878872
No 7
>PF10727 Rossmann-like: Rossmann-like domain; PDB: 3dfu_A 3c24_B.
Probab=95.96 E-value=0.0041 Score=36.68 Aligned_cols=80 Identities=21% Similarity=0.332 Sum_probs=56.7
Q ss_pred CCCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCC---CCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHH
Q ss_conf 9517998337689999999971899448998607853648---5028812507889999998549989999658999899
Q T0622 1 KKKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHK---TTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQ 77 (138)
Q Consensus 1 ~krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g---~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~ 77 (138)
|=++-|+|+|..|..|++.+.+. +|.++|+.+.++...- ..+.+.++.. +.+.++ ..|.++||.|+ ..
T Consensus 10 rl~IgiIGaGrVG~~La~~l~~a-G~~v~~v~srs~~sa~~aa~~~~~~~~~~---~~e~~~--~aDlv~IavpD---d~ 80 (127)
T PF10727_consen 10 RLRIGIIGAGRVGTALARALARA-GHPVVGVYSRSPASAERAAAFLPGVPVLD---PEEVLR--RADLVFIAVPD---DA 80 (127)
T ss_dssp --EEEEEE-----SHHHHHHHHS-SSEEEE-SSCGG---TTT------------------CC--C-SEEEE-S-C---HH
T ss_pred CCEEEEECCCHHHHHHHHHHHHC-CCEEEEEEECCCCCCCCCCCCCCCCCCCC---CCCCCC--CCCEEEEEECC---HH
T ss_conf 63699988898999999999978-99699999668432221111111111100---014556--38899998160---77
Q ss_pred HHHHHHHHHHCC
Q ss_conf 999999998579
Q T0622 78 KKVIIESLAKLH 89 (138)
Q Consensus 78 ~~~i~~~~~~~~ 89 (138)
+..+.+.+...+
T Consensus 81 I~~v~~~La~~~ 92 (127)
T PF10727_consen 81 IAEVAEQLAAAG 92 (127)
T ss_dssp HHHHHHHHHCC-
T ss_pred HHHHHHHHHHHC
T ss_conf 899999998750
No 8
>PF05368 NmrA: NmrA-like family; InterPro: IPR008030 NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi . This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families.; GO: 0016564 transcription repressor activity, 0006808 regulation of nitrogen utilization; PDB: 3ew7_A 1he5_A 1he3_A 1he4_A 1he2_A 1hdo_A 2gas_B 1qyd_A 2qys_B 3c3x_A ....
Probab=95.32 E-value=0.018 Score=32.63 Aligned_cols=89 Identities=19% Similarity=0.282 Sum_probs=60.2
Q ss_pred EEEEEC-CHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCC--CCEEEC-C-HHH---HHHHHHHCCCCEEEEECCCCCH
Q ss_conf 799833-7689999999971899448998607853648502--881250-7-889---9999985499899996589998
Q T0622 4 VLIYGA-GSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTM--QGITIY-R-PKY---LERLIKKHCISTVLLAVPSASQ 75 (138)
Q Consensus 4 vlIvGa-g~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i--~g~~v~-~-~~d---l~~~i~~~~i~~iiia~~~~~~ 75 (138)
|+|+|+ |..|..+++.+.+ .+|.+.++.-+........+ .|..+. + ..+ |.+.++ ++|.++++++....
T Consensus 1 I~V~GaTG~~G~~v~~~L~~-~g~~V~~l~R~~~~~~~~~l~~~g~~~v~~d~~d~~~l~~al~--g~d~v~~~~~~~~~ 77 (233)
T PF05368_consen 1 ILVTGATGNVGRAVVRALLA-RGHEVRALVRNPSSARAQELRDQGVEIVQGDLDDPDSLRAALQ--GVDVVFSATGSRHD 77 (233)
T ss_dssp EEEES----HHHHHHHHHHH-TGGEEEEEESSGHHHHHHHHHHSGGEEEEHHTTTHHHHHHHHT--T-SEEEEE--STTH
T ss_pred CEEECCCCHHHHHHHHHHHH-CCCCCEEEECCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHC--CCCEEEEEECCCCH
T ss_conf 98999886799999999983-8998489980353333410124431012123143788888751--56304897156511
Q ss_pred ---HHHHHHHHHHHHCCCEEEEC
Q ss_conf ---99999999998579829980
Q T0622 76 ---VQKKVIIESLAKLHVEVLTI 95 (138)
Q Consensus 76 ---~~~~~i~~~~~~~~v~v~~i 95 (138)
+....+++.|.+.||+-.+.
T Consensus 78 ~~~~~~~~li~Aa~~agVk~~v~ 100 (233)
T PF05368_consen 78 DEIDAQKNLIDAAKEAGVKRFVP 100 (233)
T ss_dssp HHCHHHHHHHHHHHH---SEEEE
T ss_pred HHHHHHHHHHHHHHHCCCCEEEE
T ss_conf 68887677789999839976987
No 9
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y , .; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process
Probab=95.13 E-value=0.09 Score=28.36 Aligned_cols=93 Identities=16% Similarity=0.191 Sum_probs=69.3
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCC-CC--CCCEEECC---HHHHHHHHHHCCCCEEEEECCCCCH
Q ss_conf 517998337689999999971899448998607853648-50--28812507---8899999985499899996589998
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHK-TT--MQGITIYR---PKYLERLIKKHCISTVLLAVPSASQ 75 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g-~~--i~g~~v~~---~~dl~~~i~~~~i~~iiia~~~~~~ 75 (138)
.+++|+|-+..|..++..+.+... -.+-+..+-..... .. ...+.+++ .+++.+++++++|+.||=|......
T Consensus 1 m~IlilgGT~Egr~la~~L~~~g~-v~~~v~t~~g~~~~~~~~~~~~v~~G~lg~~~~l~~~l~~~~i~~vIDATHPfA~ 79 (249)
T PF02571_consen 1 MRILILGGTSEGRKLAEALAEAGW-VIVSVATSYGGELREPEHPPLPVRVGRLGDAEGLAAFLRENGIDAVIDATHPFAA 79 (249)
T ss_pred CEEEEEECHHHHHHHHHHHHHCCC-EEEEEEHHHHHHHCCCCCCCCCEEECCCCCHHHHHHHHHHCCCCEEEECCCCCHH
T ss_conf 979999101899999999986599-8999981212545176678850897899999999999997799899989981089
Q ss_pred HHHHHHHHHHHHCCCEEEEC
Q ss_conf 99999999998579829980
Q T0622 76 VQKKVIIESLAKLHVEVLTI 95 (138)
Q Consensus 76 ~~~~~i~~~~~~~~v~v~~i 95 (138)
.--+...+.|..+++.....
T Consensus 80 ~is~~a~~a~~~~~ipylR~ 99 (249)
T PF02571_consen 80 QISQNAAQACKELGIPYLRF 99 (249)
T ss_pred HHHHHHHHHHHHHCCCEEEE
T ss_conf 99999999999849976999
No 10
>PF03435 Saccharop_dh: Saccharopine dehydrogenase ; InterPro: IPR005097 This family comprised of three structural domains that can not be separated in the linear sequence. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase (PF). The saccharopine dehydrogenase can also function as a saccharopine reductase.; PDB: 2ph5_A 2axq_A 1e5l_B 1e5q_B 1ff9_A 2z2v_A.
Probab=94.69 E-value=0.1 Score=28.07 Aligned_cols=87 Identities=17% Similarity=0.266 Sum_probs=59.0
Q ss_pred EEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCC--------CCCCCEEECC--HHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 7998337689999999971899448998607853648--------5028812507--88999999854998999965899
Q T0622 4 VLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHK--------TTMQGITIYR--PKYLERLIKKHCISTVLLAVPSA 73 (138)
Q Consensus 4 vlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g--------~~i~g~~v~~--~~dl~~~i~~~~i~~iiia~~~~ 73 (138)
|+|+|+|..|..+++.+.+...+.-+-+.|.+..+.- ..+.-..+-- .+++.++++.+ |.|+-+.+..
T Consensus 1 IlvlG~G~vG~~v~~~L~~~~~~~~v~va~r~~~~~~~~~~~~~~~~~~~~~~d~~~~~~l~~~~~~~--dvVin~~gp~ 78 (386)
T PF03435_consen 1 ILVLGAGFVGRAVARYLARRGDVSRVTVADRNPEKAEALAAELGGPRIEFVQVDVSDPESLAALLKGC--DVVINCAGPF 78 (386)
T ss_dssp EEEE----THHHHHHHHHCCCCE-EEEEEESSHHHHHHHHC--TTTTEEEEE--TTTHHHHHHHHTTS--SEEEE-S-GG
T ss_pred CEEECCCHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHCC--CEEEECCCCC
T ss_conf 99996839999999999838787538999899999999764203455137998578989999998559--9999906767
Q ss_pred CHHHHHHHHHHHHHCCCEEEEC
Q ss_conf 9899999999998579829980
Q T0622 74 SQVQKKVIIESLAKLHVEVLTI 95 (138)
Q Consensus 74 ~~~~~~~i~~~~~~~~v~v~~i 95 (138)
.-..++..|.++|+...-.
T Consensus 79 ---~~~~v~~ac~~~g~~yvD~ 97 (386)
T PF03435_consen 79 ---FGEPVAKACIEAGVHYVDT 97 (386)
T ss_dssp ---GHHHHHHHHHHHT-EEEES
T ss_pred ---CCHHHHHHHHHHCCCEECC
T ss_conf ---7479999999829988843
No 11
>PF00289 CPSase_L_chain: Carbamoyl-phosphate synthase L chain, N-terminal domain; InterPro: IPR005481 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents the N-terminal domain of the large subunit of carbamoyl phosphate synthase. This domain can also be found in certain other related proteins. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1bxr_G 1m6v_C 1c30_E 1kee_G 1c3o_E 1jdb_B 1ce8_C 1cs0_G 1a9x_A 1t36_G ....
Probab=94.44 E-value=0.073 Score=28.92 Aligned_cols=89 Identities=13% Similarity=0.143 Sum_probs=62.2
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCC--CCCCCEEEC----------CHHHHHHHHHHCCCCEEEEE
Q ss_conf 517998337689999999971899448998607853648--502881250----------78899999985499899996
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHK--TTMQGITIY----------RPKYLERLIKKHCISTVLLA 69 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g--~~i~g~~v~----------~~~dl~~~i~~~~i~~iiia 69 (138)
|++||.|.|+.|..+++++++- +++.|.+..+...... ...+..... ..+.+.+++++.+++.++=-
T Consensus 3 kkvLIanrG~ia~r~~r~~~e~-gi~tv~v~s~~d~~s~~~~~ad~~~~~~~~~~~~~yl~~e~I~~ia~~~g~~ai~pG 81 (110)
T PF00289_consen 3 KKVLIANRGEIAVRIIRALREL-GIETVAVNSNPDTVSTHVRLADELYFEPPGPPAESYLNVERILDIARKEGVDAIHPG 81 (110)
T ss_dssp SEEEES--HHHHHHHHHHHHHH-SSEEEEEESGGGTTGHHHHHSSEEEES---SGGGTTTSHHHHHHHHHHTTESEEE--
T ss_pred CEEEEECCCHHHHHHHHHHHHC-CCEEEEECCHHHHHCCCHHHCCEEEECCCCCHHHHHCCHHHHHHHHHHHCCEEEECC
T ss_conf 6799989889999999999986-994789828588515583115657875886203321589999999987396899879
Q ss_pred CCCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 589998999999999985798299
Q T0622 70 VPSASQVQKKVIIESLAKLHVEVL 93 (138)
Q Consensus 70 ~~~~~~~~~~~i~~~~~~~~v~v~ 93 (138)
.-..+.. .++...|.+.|+.+.
T Consensus 82 ~g~lse~--~~fa~~~~~~gi~fi 103 (110)
T PF00289_consen 82 YGFLSEN--AEFARACEKAGIIFI 103 (110)
T ss_dssp -CCGTTH--HHHHHHHHHTT-EEB
T ss_pred HHHHHHH--HHHHHHHHHCCCEEE
T ss_conf 4898873--999999997899898
No 12
>PF01210 NAD_Gly3P_dh_N: NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; InterPro: IPR011128 NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain . ; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0046168 glycerol-3-phosphate catabolic process, 0005737 cytoplasm; PDB: 1z82_A 1m67_A 1evz_A 1evy_A 1n1g_A 1m66_A 1n1e_A 1jdj_A 3c7d_B 3c7c_B ....
Probab=93.68 E-value=0.04 Score=30.55 Aligned_cols=95 Identities=23% Similarity=0.308 Sum_probs=60.6
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHH---------CCCCCCCEE----ECCHHHHHHHHHHCCCCEEEE
Q ss_conf 5179983376899999999718994489986078536---------485028812----507889999998549989999
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKK---------HKTTMQGIT----IYRPKYLERLIKKHCISTVLL 68 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~---------~g~~i~g~~----v~~~~dl~~~i~~~~i~~iii 68 (138)
++|.|+|+|.-|.+++..+.++. +-|-++..++.. ...++.+++ +.-++|+.+.++ +.|.+++
T Consensus 1 mkI~ViGaG~~GtAlA~~la~~g--~~V~lw~r~~~~~~~i~~~~~n~~~l~~~~l~~~i~~t~dl~~al~--~ad~ii~ 76 (159)
T PF01210_consen 1 MKIAVIGAGSWGTALAALLADNG--HEVTLWGRDEEVVEEINETRENPKYLPGIKLPENIRATTDLEEALE--GADIIIL 76 (159)
T ss_dssp EEEEEE----HHCHHHHHHHHTC--EEEEEETSSHHHHHHHHHHSBBTTTECT-B-ETTEEEESSHHHHHT--TTSEEEE
T ss_pred CEEEEECCCHHHHHHHHHHHHCC--CEEEEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHH--HCCEEEE
T ss_conf 95999896999999999999779--9899994888999999971998765788434654003588999971--0839999
Q ss_pred ECCCCCHHHHHHHHHHHHHCCCEEEECCCHHH
Q ss_conf 65899989999999999857982998068366
Q T0622 69 AVPSASQVQKKVIIESLAKLHVEVLTIPNLDD 100 (138)
Q Consensus 69 a~~~~~~~~~~~i~~~~~~~~v~v~~iP~~~~ 100 (138)
+.|+......-+-+......+..+...+.-.+
T Consensus 77 avPs~~~~~~~~~l~~~l~~~~~iv~~~KGie 108 (159)
T PF01210_consen 77 AVPSQALREVLEQLKPYLKKGQIIVSATKGIE 108 (159)
T ss_dssp -S-GGGHHHHHHHHTTTHHTTSEEEE-----E
T ss_pred CCCHHHHHHHHHHHHHCCCCCCEEEEECCCCC
T ss_conf 26789999999986533688978999468766
No 13
>PF01488 Shikimate_DH: Shikimate / quinate 5-dehydrogenase; InterPro: IPR006151 This entry contains shikimate and quinate dehydrogenases, as well as glutamyl-tRNA reductases. Shikimate 5-dehydrogenase (1.1.1.25 from EC) catalyses the conversion of shikimate to 5-dehydroshikimate , . This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids . Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites, 3-dehydroquinate and dehydroshikimate. Glutamyl-tRNA reductase (1.2.1.70 from EC) catalyzes the first step of tetrapyrrole biosynthesis in plants, archaea and most bacteria. The dimeric enzyme has an unusual V-shaped architecture where each monomer consists of three domains linked by a long 'spinal' alpha-helix. The central catalytic domain specifically recognises the glutamate moiety of the substrate . ; GO: 0004764 shikimate 5-dehydrogenase activity, 0005737 cytoplasm; PDB: 1gpj_A 2d5c_A 2ev9_B 1wxd_A 2cy0_B 1nyt_A 1p74_A 1p77_A 2hk8_G 2hk9_B ....
Probab=92.49 E-value=0.1 Score=28.00 Aligned_cols=82 Identities=23% Similarity=0.343 Sum_probs=54.6
Q ss_pred CCCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCC---CCC--CEEECCHHHHHHHHHHCCCCEEEEECCCCCH
Q ss_conf 95179983376899999999718994489986078536485---028--8125078899999985499899996589998
Q T0622 1 KKKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKT---TMQ--GITIYRPKYLERLIKKHCISTVLLAVPSASQ 75 (138)
Q Consensus 1 ~krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~---~i~--g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~ 75 (138)
.++++|+|+|..|..++..+... +..-+-++..++.+... .+. ++.+...+++.+.+.+ .|.++-|+|....
T Consensus 12 ~k~vlviGaGg~a~~v~~~L~~~-g~~~i~I~nRt~~ka~~la~~~~~~~~~~~~~~~~~~~~~~--~DivI~aT~~~~~ 88 (135)
T PF01488_consen 12 GKRVLVIGAGGAARAVAAALAAL-GAKRITIVNRTPEKAEELAEEFGGKKIEVIPLEDLEELLQE--ADIVINATPAGMP 88 (135)
T ss_dssp TSEEEEE-----HHHHHHHHHHT-TSCEEEEEESSHHHHHHHHHHHTCCSEEEEEEGGHHHCHHG---SEEEE-SSSSST
T ss_pred CCEEEEECCCHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHCCCCCCCEEEHHHHHHHCCC--CCEEEECCCCCCC
T ss_conf 99899999829999999999986-99989999499999999999735466313338787733279--9999989989965
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999999
Q T0622 76 VQKKVIIESL 85 (138)
Q Consensus 76 ~~~~~i~~~~ 85 (138)
..-.+.+..+
T Consensus 89 ~i~~~~l~~~ 98 (135)
T PF01488_consen 89 IIEEEMLKSA 98 (135)
T ss_dssp SSTHHHHTTT
T ss_pred CCCHHHHHHH
T ss_conf 1398998677
No 14
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels). , , . Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases . Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding , but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved , , . It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilizes the RCK homodimer , , . Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue , , . RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 2hmv_A 2hmu_B 2hmt_A 2hms_D 2hmw_A 1lsu_A 3c85_A 3fwz_B 3eyw_A 1id1_A ....
Probab=91.63 E-value=0.27 Score=25.42 Aligned_cols=83 Identities=19% Similarity=0.310 Sum_probs=51.1
Q ss_pred EEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCC-CCCCEE-ECCH---HHHHHHHHHCCCCEEEEECCCCCHHHH
Q ss_conf 79983376899999999718994489986078536485-028812-5078---899999985499899996589998999
Q T0622 4 VLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKT-TMQGIT-IYRP---KYLERLIKKHCISTVLLAVPSASQVQK 78 (138)
Q Consensus 4 vlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~-~i~g~~-v~~~---~dl~~~i~~~~i~~iiia~~~~~~~~~ 78 (138)
++|+|+|+.|..+++.+++ . +..+-++|.++..... .-.+.+ ++|. .+..+-+.-..++.++++.+.. +.-
T Consensus 1 ivI~G~g~~~~~i~~~L~~-~-~~~vviv~~~~~~~~~~~~~~~~~i~gd~~~~~~l~~~~i~~a~~vii~~~~d--~~n 76 (116)
T PF02254_consen 1 IVICGYGRVGREIARELRE-G-GIPVVIVDKDPERIEELREEGVPVIYGDATDEEVLEEAGIEEADAVIILTDDD--EEN 76 (116)
T ss_dssp EEEE---HHHHHHHHHHHH-T-CEEEEEEESSHHHHHHHHHHSSEEEE--TTSHHHHHHTTGTTESEEEE-SSSH--HHH
T ss_pred EEEECCCHHHHHHHHHHHH-C-CCEEEEEECCHHHHHHHHCCCCEEEEECCCCHHHHHHCCCCCCCEEEEECCCH--HHH
T ss_conf 2998788899999999985-8-99899998888999986506834899426662249876988677799964987--899
Q ss_pred HHHHHHHHHCCC
Q ss_conf 999999985798
Q T0622 79 KVIIESLAKLHV 90 (138)
Q Consensus 79 ~~i~~~~~~~~v 90 (138)
..+...|...+-
T Consensus 77 ~~~~~~~r~~~~ 88 (116)
T PF02254_consen 77 LLIALTARSLNP 88 (116)
T ss_dssp HHHHHHHHHHTT
T ss_pred HHHHHHHHHHCC
T ss_conf 999999999789
No 15
>PF00743 FMO-like: Flavin-binding monooxygenase-like; InterPro: IPR000960 Flavin-containing monooxygenases (FMOs) constitute a family of xenobiotic-metabolising enzymes . Using an NADPH cofactor and FAD prosthetic group, these microsomal proteins catalyse the oxygenation of nucleophilic nitrogen, sulphur, phosphorous and selenium atoms in a range of structurally diverse compounds. FMOs have been implicated in the metabolism of a number of pharmaceuticals, pesticides and toxicants. In man, lack of hepatic FMO-catalysed trimethylamine metabolism results in trimethylaminuria (fish odour syndrome). Five mammalian forms of FMO are now known and have been designated FMO1-FMO5 , , , , . This is a recent nomenclature based on comparison of amino acid sequences, and has been introduced in an attempt to eliminate confusion inherent in multiple, laboratory-specific designations and tissue-based classifications . Following the determination of the complete nucleotide sequence of Saccharomyces cerevisiae (Baker's yeast) , a novel gene was found to encode a protein with similarity to mammalian monooygenases. ; GO: 0004499 flavin-containing monooxygenase activity, 0050660 FAD binding, 0050661 NADP binding; PDB: 1w4x_A 2gvc_E 1vqw_A 2gv8_B 2vq7_C 2vqb_C.
Probab=90.18 E-value=0.097 Score=28.16 Aligned_cols=28 Identities=43% Similarity=0.649 Sum_probs=12.7
Q ss_pred CCCEEEEECCHHHHHHHHHHHHCCCCEEE
Q ss_conf 95179983376899999999718994489
Q T0622 1 KKKVLIYGAGSAGLQLANMLRQGKEFHPI 29 (138)
Q Consensus 1 ~krvlIvGag~~a~~l~~~l~~~~~y~iv 29 (138)
+|+|+|||||.+|...++.+.+. ++.++
T Consensus 1 ~k~VaIIGAG~sGL~aak~l~~~-G~~~~ 28 (531)
T PF00743_consen 1 KKRVAIIGAGPSGLAAAKCLLEE-GLDPT 28 (531)
T ss_dssp --EEEEE-------HHHHHHHH----EEE
T ss_pred CCEEEEECCCHHHHHHHHHHHHC-CCCEE
T ss_conf 98899989649999999999878-99829
No 16
>PF04321 RmlD_sub_bind: RmlD substrate binding domain; InterPro: IPR005913 dTDP-4-dehydrorhamnose reductase (1.1.1.133 from EC) catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS molecules such as core antigen and O-antigen. dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH ; GO: 0008831 dTDP-4-dehydrorhamnose reductase activity, 0045226 extracellular polysaccharide biosynthetic process; PDB: 1n2s_A 1kbz_A 1kc1_A 1kc3_A 2ggs_A 1vl0_B.
Probab=89.43 E-value=0.56 Score=23.42 Aligned_cols=84 Identities=21% Similarity=0.305 Sum_probs=59.6
Q ss_pred CEEEEE-CCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCH------
Q ss_conf 179983-3768999999997189944899860785364850288125078899999985499899996589998------
Q T0622 3 KVLIYG-AGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQ------ 75 (138)
Q Consensus 3 rvlIvG-ag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~------ 75 (138)
++||+| .|..|..|.+.+.. .+|.++++- .. ...+.-.+.+.+++.....+.||-+......
T Consensus 2 kilI~Ga~G~lG~~l~~~l~~-~~~~v~~~~-r~---------~~d~~~~~~v~~~~~~~~pd~VIn~Aa~t~~d~~e~~ 70 (286)
T PF04321_consen 2 KILITGASGQLGRALARALEK-RGHEVIATS-RS---------QLDLTDPEAVEKLLEDVKPDVVINCAAYTNVDACESN 70 (286)
T ss_dssp EEEEE--------HHHHHCTT-TSEEEEE-S-TT---------C--TTSHHHHHHHHHHH--SEEEE------HHHHHHS
T ss_pred EEEEECCCCHHHHHHHHHHHH-CCCEEEEEC-CC---------CCCCCCHHHHHHHHHHCCCCEEEECHHHCCHHHHHCC
T ss_conf 899999999899999998644-798899946-76---------0379898999999996299989954011366555318
Q ss_pred ---------HHHHHHHHHHHHCCCEEEECCC
Q ss_conf ---------9999999999857982998068
Q T0622 76 ---------VQKKVIIESLAKLHVEVLTIPN 97 (138)
Q Consensus 76 ---------~~~~~i~~~~~~~~v~v~~iP~ 97 (138)
.....+.+.|...++++..+..
T Consensus 71 ~~~a~~vN~~~~~~la~~~~~~~~~li~iST 101 (286)
T PF04321_consen 71 PEEAYLVNVEAPKNLAEACKEHGARLIHIST 101 (286)
T ss_dssp HHHHHHHHTHHHHHHHHHHTTT--EEEEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf 7989988999999999999965990999533
No 17
>PF03807 F420_oxidored: NADP oxidoreductase coenzyme F420-dependent; InterPro: IPR004455 The function of F420-dependent NADP reductase is the transfer of electrons from reduced coenzyme F420 into an electron transport chain. It catalyses the reduction of F420 with NADP(+) and the reduction of NADP(+) with F420H(2).; GO: 0006118 electron transport; PDB: 3gt0_A 2ahr_E 2amf_A 2ag8_A 1yqg_A 2izz_B 2ger_E 2gr9_A 2gra_D 2rcy_C ....
Probab=88.57 E-value=0.11 Score=27.94 Aligned_cols=77 Identities=27% Similarity=0.269 Sum_probs=50.2
Q ss_pred CEEEEECCHHHHHHHHHHHHCC--CCEEEEEECCCHHHCCCC--CCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHH
Q ss_conf 1799833768999999997189--944899860785364850--288125078899999985499899996589998999
Q T0622 3 KVLIYGAGSAGLQLANMLRQGK--EFHPIAFIDDDRKKHKTT--MQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQK 78 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~--~y~ivGfiDd~~~~~g~~--i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~ 78 (138)
++.|+|+|..|..+++.+.+.. .+++.-..+.++++.... -.++.+... +..+.++ ..|.+++|.+ ++.+
T Consensus 1 kIgiIG~G~mg~al~~gl~~~~~~~~~i~i~~~~~~~~~~~l~~~~~~~~~~~-~~~~~~~--~aDvv~lav~---p~~~ 74 (96)
T PF03807_consen 1 KIGIIGAGNMGSALAKGLLESGFQPEEIIIVNSRSPEKAEELAKEYGVQIIAG-DNEEAVQ--EADVVFLAVK---PQQL 74 (96)
T ss_dssp EEEEB----HHHHHHHHHTTTTS-GGEEEEEE-SSHHHHHHHHHHCTTEEESS-SHHHHHH--HTSEEEE-S----HHHH
T ss_pred CEEEECCHHHHHHHHHHHHHCCCCHHHEEECCCCCHHHHHHHHHHHCCEEEEC-CHHHHHH--CCCEEEEEEC---HHHH
T ss_conf 99999952999999999998699878866225899799999999849807848-9899996--0999999978---9999
Q ss_pred HHHHHHH
Q ss_conf 9999999
Q T0622 79 KVIIESL 85 (138)
Q Consensus 79 ~~i~~~~ 85 (138)
..++..+
T Consensus 75 ~~v~~~~ 81 (96)
T PF03807_consen 75 ESVLEEL 81 (96)
T ss_dssp HHHHCCT
T ss_pred HHHHHHH
T ss_conf 9999986
No 18
>PF01946 Thi4: Thi4 family; InterPro: IPR002922 This family includes P32318 from SWISSPROT a putative thiamine biosynthetic enzyme . This enzyme is involved in the biosynthesis of the thiamine precursor thiazole, and is repressed by thiamine.; GO: 0009228 thiamin biosynthetic process; PDB: 2gjc_B 1rp0_B 2gmh_B 2gmj_A.
Probab=88.29 E-value=0.32 Score=24.92 Aligned_cols=95 Identities=20% Similarity=0.307 Sum_probs=58.8
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECC----HHHHHHHHHHCCC------CEEEEECCC
Q ss_conf 179983376899999999718994489986078536485028812507----8899999985499------899996589
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYR----PKYLERLIKKHCI------STVLLAVPS 72 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~----~~dl~~~i~~~~i------~~iiia~~~ 72 (138)
-++|+|+|.+|...+..+.++ ++++ .+++.+....|....|-..+. .+....++++.++ +..+++
T Consensus 19 DVvIVGaG~aGL~AA~~la~~-g~kV-~viE~~~~~GGg~~~gG~~f~~~vv~~~a~~~L~Elgv~y~~~~~g~~v~--- 93 (230)
T PF01946_consen 19 DVVIVGAGPAGLAAAYYLARA-GLKV-LVIERRSSPGGGAWSGGMLFNKIVVREPADEFLDELGVRYEDEGDGVYVA--- 93 (230)
T ss_dssp SEEEE-------HHHHHHHHH-TS-E-EEEESSS---------------EEEETTTHHHHHHTT---EE-SSEEEES---
T ss_pred CEEEECCCHHHHHHHHHHHHC-CCEE-EEEECCCCCCCCCEECCCCCCCHHHHHHHHHHHHHCCCCCEECCCCEEEE---
T ss_conf 989999778899999999978-9959-99967998874404235325510101019999998399716406965985---
Q ss_pred CCHHHHHHHHHHHHHCCCEEEECCCHHHHH
Q ss_conf 998999999999985798299806836642
Q T0622 73 ASQVQKKVIIESLAKLHVEVLTIPNLDDLV 102 (138)
Q Consensus 73 ~~~~~~~~i~~~~~~~~v~v~~iP~~~~~~ 102 (138)
.+.+....+...+.+.|+++...-.+.+++
T Consensus 94 d~~e~~s~L~s~a~~aGvki~n~t~VeDli 123 (230)
T PF01946_consen 94 DSVEFTSTLASKALKAGVKIFNATRVEDLI 123 (230)
T ss_dssp -HHHHHHHHHHHHHTTTEEEECTEEEEE--
T ss_pred CHHHHHHHHHHHHHCCCCEEEEEEEEEEEE
T ss_conf 689999999998637898999952775657
No 19
>PF02826 2-Hacid_dh_C: D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; InterPro: IPR006140 A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related. All contain a glycine-rich region located in the central section of these enzymes, this region corresponds to the NAD-binding domain. The catalytic domain is described in IPR006139 from INTERPRO; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0048037 cofactor binding; PDB: 1gdh_B 1wwk_B 2dbr_B 2dbz_B 2dbq_A 2cuk_C 1yba_A 2p9c_B 2p9e_B 2p9g_A ....
Probab=87.45 E-value=0.59 Score=23.31 Aligned_cols=88 Identities=18% Similarity=0.301 Sum_probs=52.8
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHH---H
Q ss_conf 5179983376899999999718994489986078536485028812507889999998549989999658999899---9
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQ---K 78 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~---~ 78 (138)
+++.|+|.|..|..+++.+.. -+.++.++=-......+..-.+... .++.+++++ .|.|+++.|.+++.+ -
T Consensus 37 ktvgIvG~G~IG~~vA~~l~a-fG~~V~~~d~~~~~~~~~~~~~~~~---~~l~ell~~--aDiv~~~~plt~~T~~li~ 110 (178)
T PF02826_consen 37 KTVGIVGLGRIGRAVARRLKA-FGMKVIGYDRSPKPEEGADDLGVTY---VSLDELLAQ--ADIVSLHLPLTPETRGLIN 110 (178)
T ss_dssp SEEEEB-------HHHHHHHH-GT-EEEEECSSSHHHHHHHHTTEEE---SSHHHHHHH--TSEEEEESCSSTTTTTSBS
T ss_pred CEEEEEEECCCHHHHHHHHCC-CCCEEEEECCCCCHHHHHCCCCCEE---CCHHHHCCC--CCHHHHHCCCCCCCCCCCC
T ss_conf 989998478028999876413-9988999827777566402465401---366773011--3233300666323355115
Q ss_pred HHHHHHHHHCCCEEEECC
Q ss_conf 999999985798299806
Q T0622 79 KVIIESLAKLHVEVLTIP 96 (138)
Q Consensus 79 ~~i~~~~~~~~v~v~~iP 96 (138)
.+.+..+.. +.-+..+-
T Consensus 111 ~~~l~~mk~-ga~lIN~a 127 (178)
T PF02826_consen 111 AELLAKMKP-GAVLINVA 127 (178)
T ss_dssp HHHHHTS-T-TEEEEESS
T ss_pred HHHHHHHCC-CEEEECCC
T ss_conf 414102035-50787178
No 20
>PF03447 NAD_binding_3: Homoserine dehydrogenase, NAD binding domain; InterPro: IPR005106 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see . Homoserine dehydrogenase (1.1.1.3 from EC) catalyzes the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine , . Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116 from SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain . The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet. This entry represents the NAD(P)-binding domain of aspartate and homoserine dehydrogenase. Asparate dehydrogenase (1.4.1.21 from EC) is strictly specific for L-aspartate as substrate and catalyses the first step in NAD biosynthesis from aspartate. The enzyme has a higher affinity for NAD+ than NADP+ . Note that the C-terminus of the protein contributes a helix to this domain that is not covered by this model.; PDB: 2dc1_B 1h2h_A 1j5p_A 1ebu_D 1q7g_A 1tve_A 1ebf_B 3c8m_A 3do5_A 2ejw_B ....
Probab=86.61 E-value=0.34 Score=24.78 Aligned_cols=83 Identities=18% Similarity=0.233 Sum_probs=56.5
Q ss_pred ECCHHHHHHHHHHHHCC---CCEEEEEECCCHHHCCC---CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH
Q ss_conf 33768999999997189---94489986078536485---0288125078899999985499899996589998999999
Q T0622 8 GAGSAGLQLANMLRQGK---EFHPIAFIDDDRKKHKT---TMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKKVI 81 (138)
Q Consensus 8 Gag~~a~~l~~~l~~~~---~y~ivGfiDd~~~~~g~---~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i 81 (138)
|.|.-|..+++.+.+.+ +++++|+.|.+...... ......+. .++.+++....+|.++=+ .+.+...+.
T Consensus 1 G~G~VG~~~~~~l~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~~~~--~~~~~l~~~~~~dvvVE~---t~~~~~~~~ 75 (117)
T PF03447_consen 1 GCGNVGRGLLEQLQEKREEIDLRIVAVADRSALLSKDWKASLGDAAVV--DDLDELLEDPDIDVVVEC---TSSEAVAEY 75 (117)
T ss_dssp -------HHHHHHHHTHHHSEEEEEEEEESSEEE-TTHHHHHCHCCEE--SCHHHHHHHHS-SEEEE----S-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCCCCEE--CCHHHHHHCCCCCEEEEC---CCCHHHHHH
T ss_conf 927789999999976245676499999988874311112456787421--799999717899999999---996599999
Q ss_pred HHHHHHCCCEEEEC
Q ss_conf 99998579829980
Q T0622 82 IESLAKLHVEVLTI 95 (138)
Q Consensus 82 ~~~~~~~~v~v~~i 95 (138)
+..+.+.|+.+...
T Consensus 76 ~~~aL~~G~~VVt~ 89 (117)
T PF03447_consen 76 YPKALERGKHVVTA 89 (117)
T ss_dssp HHHHHHSSSEEEES
T ss_pred HHHHHHCCCEEEEE
T ss_conf 99999869969997
No 21
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325)
Probab=86.49 E-value=0.85 Score=22.29 Aligned_cols=82 Identities=17% Similarity=0.055 Sum_probs=56.4
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH
Q ss_conf 17998337689999999971899448998607853648502881250788999999854998999965899989999999
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKKVII 82 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i~ 82 (138)
.|||||.-+.-..-++.+.+..++....+ ..+...... ...++..+.+ .|.|++.+...++.....+-
T Consensus 1 svliVGG~~~~~~~~~~~~~~~G~~~~~h-g~~~~~~~~---------~~~l~~~i~~--aD~VI~~td~vsH~~~~~~k 68 (97)
T PF10087_consen 1 SVLIVGGRDDRERNYRRLLEKYGGKFIHH-GRDGGFEKK---------KSRLPSKIKR--ADLVIVFTDCVSHNAMWKAK 68 (97)
T ss_pred CEEEECCCHHHHHHHHHHHHHCCCEEEEE-ECCCCCCCH---------HHHHHHHCCC--CCEEEEECCCCCHHHHHHHH
T ss_conf 99999076042589999999869989999-558887514---------4656875589--99999980766979999999
Q ss_pred HHHHHCCCEEEECC
Q ss_conf 99985798299806
Q T0622 83 ESLAKLHVEVLTIP 96 (138)
Q Consensus 83 ~~~~~~~v~v~~iP 96 (138)
+.|...++++....
T Consensus 69 ~~ak~~~~p~~~~~ 82 (97)
T PF10087_consen 69 KEAKKYGIPIVFSR 82 (97)
T ss_pred HHHHHHCCCEEEEC
T ss_conf 99998399589988
No 22
>PF03721 UDPG_MGDP_dh_N: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; InterPro: IPR001732 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyze the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate , . The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin , which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation . In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence . GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyzes the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response , while in A. vinelandii it is essential for the encystment process . This entry represents the N-terminal NAD(+)-binding domain. Structural studies indicate that this domain forms an alpha-beta structure containing the six-stranded parallel beta sheet characteristic of the dinucleotide binding Rossman fold , .; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0006118 electron transport; PDB: 2q3e_L 2qg4_F 2o3j_A 3g79_A 1mfz_B 1muu_B 1mv8_D 1dli_A 1dlj_A 3gg2_A ....
Probab=86.25 E-value=0.58 Score=23.35 Aligned_cols=70 Identities=33% Similarity=0.474 Sum_probs=45.3
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCC-EEECCHHHHHHHHHHC-----------------CC
Q ss_conf 51799833768999999997189944899860785364850288-1250788999999854-----------------99
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQG-ITIYRPKYLERLIKKH-----------------CI 63 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g-~~v~~~~dl~~~i~~~-----------------~i 63 (138)
.+|.|+|.|..|.-++-.+.+. +|+++|+ |-|+.+...--.| .|++ -..+++++++. +.
T Consensus 1 mkI~ViG~GyvGl~~A~~lA~~-G~~Vig~-D~d~~~v~~l~~g~~p~~-Epgl~ell~~~~~~~~l~~t~d~~~~~~~a 77 (185)
T PF03721_consen 1 MKIAVIGLGYVGLPLAACLAEA-GHNVIGV-DIDEEKVEALNQGESPIY-EPGLEELLRKNVKSGRLRFTTDYSEAIADA 77 (185)
T ss_dssp -EEEEE-------HHHHHHHHH-TSEEEEE--S-HHHHHHHCSSS-SS---HHHHHHHHHHCC---EEEES-HHHHHHH-
T ss_pred CEEEEECCCHHHHHHHHHHHHC-CCEEEEE-ECCHHHHHHHHCCCCCCC-CCCHHHHHHHHCCCCCEEEECCHHHHHHHC
T ss_conf 9899989567689999999958-9979999-898899999878998624-654566544331467249987889987217
Q ss_pred CEEEEECCCCC
Q ss_conf 89999658999
Q T0622 64 STVLLAVPSAS 74 (138)
Q Consensus 64 ~~iiia~~~~~ 74 (138)
|.++|+.|...
T Consensus 78 dv~~I~VpTP~ 88 (185)
T PF03721_consen 78 DVVFICVPTPL 88 (185)
T ss_dssp SEEEE-----B
T ss_pred CEEEEECCCCC
T ss_conf 67999659972
No 23
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=84.56 E-value=1.1 Score=21.72 Aligned_cols=105 Identities=12% Similarity=0.138 Sum_probs=64.7
Q ss_pred CCEEEEECCHHH-HHHHHHHHHC-CCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHH
Q ss_conf 517998337689-9999999718-99448998607853648502881250788999999854998999965899989999
Q T0622 2 KKVLIYGAGSAG-LQLANMLRQG-KEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKK 79 (138)
Q Consensus 2 krvlIvGag~~a-~~l~~~l~~~-~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~ 79 (138)
.++.++|+.+.- ..+++.+++. |+.+++|..+.--. --..+++.+.+.+.+.|.+++++.+...+..-
T Consensus 49 ~rifllG~~~~~~~~~~~~l~~~yP~l~i~G~~~g~f~----------~~e~~~i~~~I~~s~pdiv~vglG~PkQE~~~ 118 (172)
T PF03808_consen 49 KRIFLLGGSEEVLEKAAERLRARYPGLQIVGYYHGYFG----------PEEEEAIIEAINASGPDIVFVGLGSPKQEIFI 118 (172)
T ss_pred CEEEEECCCHHHHHHHHHHHHHHCCCCCEEEECCCCCC----------HHHHHHHHHHHHHCCCCEEEEECCCCHHHHHH
T ss_conf 83999909889999999999988899718852499999----------78999999999972969999988998789999
Q ss_pred HHHHHHHHCCCEEEECCCHHHHHCCCCCHHH--CCCCCHH
Q ss_conf 9999998579829980683664268745212--3557732
Q T0622 80 VIIESLAKLHVEVLTIPNLDDLVNGKLSIGQ--LKEVSID 117 (138)
Q Consensus 80 ~i~~~~~~~~v~v~~iP~~~~~~~~~~~~~~--lr~i~ie 117 (138)
.-.......++ +.-+=..++...|..+-.. ++.+.+|
T Consensus 119 ~~~~~~l~~~v-~i~vG~~~d~~aG~~~raP~w~~~~glE 157 (172)
T PF03808_consen 119 ARNRDRLPAGV-FIGVGAAFDFLAGKVKRAPKWMQKLGLE 157 (172)
T ss_pred HHHHHHCCCCE-EEEECCHHEECCCCCCCCCHHHHHHCCH
T ss_conf 99898779988-9995612033416847363999982845
No 24
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 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 includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 .; PDB: 2kg4_A 3cg6_B 2wal_A 2zkr_f 1s1i_G 2aif_A 2ale_A 1zwz_A 1e7k_B 2ozb_D ....
Probab=83.64 E-value=0.63 Score=23.12 Aligned_cols=60 Identities=22% Similarity=0.251 Sum_probs=49.2
Q ss_pred CCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCHHHHH
Q ss_conf 288125078899999985499899996589998999999999985798299806836642
Q T0622 43 MQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKKVIIESLAKLHVEVLTIPNLDDLV 102 (138)
Q Consensus 43 i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~iP~~~~~~ 102 (138)
-.|..+.|..+..+.+++..+..+++|.+..+......+...|...+|++..+++..++.
T Consensus 12 k~~~lv~G~~~v~k~i~~~~~~lvilA~D~~~~~~~~~i~~~c~~~~Ip~~~~~sk~~LG 71 (95)
T PF01248_consen 12 KAGKLVFGIKEVLKAIKKGKAKLVILASDCSPNTKKKHIPALCKEKNIPYVFVPSKEELG 71 (95)
T ss_dssp HCTEEE---HHHHHHHHHTCESEEEEETTTSSGGGTCTHHHHHHHTTEEEEEESTTTTHH
T ss_pred HCCCEEECHHHHHHHHHHCCCEEEEEECCCCCHHHCCCHHHHHHCCCCCEEECCCHHHHH
T ss_conf 659889875999999980997199996689921110025654216662679718999999
No 25
>PF05834 Lycopene_cycl: Lycopene cyclase protein; InterPro: IPR008671 This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare .; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0016117 carotenoid biosynthetic process
Probab=81.99 E-value=0.82 Score=22.39 Aligned_cols=34 Identities=38% Similarity=0.536 Sum_probs=25.8
Q ss_pred EEEEECCHHHHHHHHHHHH-CCCCEEEEEECCCHHH
Q ss_conf 7998337689999999971-8994489986078536
Q T0622 4 VLIYGAGSAGLQLANMLRQ-GKEFHPIAFIDDDRKK 38 (138)
Q Consensus 4 vlIvGag~~a~~l~~~l~~-~~~y~ivGfiDd~~~~ 38 (138)
++|+|+|-+|..+|..+.+ .++.++ .++|.++..
T Consensus 2 viIvGaG~AGl~lA~~L~~~~~gl~V-~lie~~~~~ 36 (374)
T PF05834_consen 2 VIIVGAGPAGLSLAARLARARPGLRV-LLIEPGPKP 36 (374)
T ss_pred EEEECCCHHHHHHHHHHHHCCCCCEE-EEECCCCCC
T ss_conf 89999769999999998632799879-998089655
No 26
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known . The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site . This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3e1y_D 1dt9_A 3e20_K 2vgn_A 2vgm_A 1x52_A 2qi2_A.
Probab=77.38 E-value=0.55 Score=23.48 Aligned_cols=57 Identities=14% Similarity=0.223 Sum_probs=46.3
Q ss_pred CCEEECCHHHHHHHHHHCCCCEEEEECCCCCH-----HH-------------HHHHHHHHHHCCCEEEECCCHHH
Q ss_conf 88125078899999985499899996589998-----99-------------99999999857982998068366
Q T0622 44 QGITIYRPKYLERLIKKHCISTVLLAVPSASQ-----VQ-------------KKVIIESLAKLHVEVLTIPNLDD 100 (138)
Q Consensus 44 ~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~-----~~-------------~~~i~~~~~~~~v~v~~iP~~~~ 100 (138)
.|..+||.++..+.+....|+.++++...... .. ...+++.+.+.|.+|.++|+-.+
T Consensus 19 ~g~~~yG~~eV~~Ale~GAV~~Llisd~l~~~~~~~r~~~~~~g~~~~~~~~~~~l~e~a~~~g~~V~iis~~~~ 93 (113)
T PF03465_consen 19 SGLAVYGIDEVMKALEMGAVETLLISDELFRSRDVERCKAPKCGEELEVVDLVEELIELAEQTGAKVEIISSEHE 93 (113)
T ss_dssp GCCEE---HHHHHHHHTT-EEEEEEECHHHTSCSHHHHH------------HHHHHHHHHHHT--EEEEE-TTS-
T ss_pred CCCEEECHHHHHHHHHHCCCCEEEEECCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCH
T ss_conf 990997189999999809978999946776501222156432100002478999999999974999999939984
No 27
>PF07991 IlvN: Acetohydroxy acid isomeroreductase, catalytic domain; InterPro: IPR013116 Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.; PDB: 1yrl_C 1yve_J 1qmg_C 3fr7_A 3fr8_A 1np3_A.
Probab=76.98 E-value=0.82 Score=22.41 Aligned_cols=90 Identities=18% Similarity=0.238 Sum_probs=58.6
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEE-EEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHH--
Q ss_conf 517998337689999999971899448-99860785364850288125078899999985499899996589998999--
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHP-IAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQK-- 78 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~i-vGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~-- 78 (138)
|++.|+|.|..|..-+..|+.+ ++++ ||.-....+.....-.|..++...+. ++ ..|.|++.+|+....++
T Consensus 5 k~IAViGYGsQG~ahAlNLrDS-Gv~V~vglr~gs~s~~kA~~~Gf~v~~~~eA---~~--~aDvv~~L~PD~~q~~vy~ 78 (165)
T PF07991_consen 5 KTIAVIGYGSQGHAHALNLRDS-GVDVIVGLREGSKSWEKAEADGFEVMSVAEA---VK--KADVVMILTPDEAQAEVYE 78 (165)
T ss_dssp -EEEEE----HHHHHHHHHHHH---EEEE---HHHHHHHHHHH---EST-HHHH---HC--T-SEEEE-S-HHHHHHHHH
T ss_pred CEEEEECCCHHHHHHHHHHHHC-CCCEEEEECCCCCCHHHHHHCCCEECCHHHH---HH--HCCEEEEECCHHHHHHHHH
T ss_conf 9899986671899999777747-9968999889995799999789956669998---74--4999999088478899999
Q ss_pred HHHHHHHHHCCCEEEECCCH
Q ss_conf 99999998579829980683
Q T0622 79 KVIIESLAKLHVEVLTIPNL 98 (138)
Q Consensus 79 ~~i~~~~~~~~v~v~~iP~~ 98 (138)
.++... ...|-.+.+...+
T Consensus 79 ~~I~p~-Lk~G~~L~faHGF 97 (165)
T PF07991_consen 79 EEIAPN-LKPGKTLAFAHGF 97 (165)
T ss_dssp HHHHHH-S-TT-EEEE----
T ss_pred HHHHHH-CCCCCEEEECCCC
T ss_conf 998865-6799889966876
No 28
>PF07992 Pyr_redox_2: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR013027 This entry describes both class I and class II oxidoreductases. FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase , , . Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently . Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) . Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase , thioredoxin reductase , mercuric reductase , lipoamide dehydrogenase , trypanothione reductase and NADH peroxidase have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication . ; PDB: 2tmd_A 1djq_A 1o95_B 1o94_A 1djn_A 1mok_C 2c3d_B 2c3c_B 1mo9_A 1xdi_B ....
Probab=76.76 E-value=0.8 Score=22.46 Aligned_cols=31 Identities=32% Similarity=0.542 Sum_probs=24.5
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf 179983376899999999718994489986078
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDD 35 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~ 35 (138)
+++|+|+|.+|..++..+.+. +++ +-+++.+
T Consensus 1 ~vvIIG~G~aGl~~a~~l~~~-~~~-v~vie~~ 31 (201)
T PF07992_consen 1 DVVIIGGGPAGLSAAYELLRL-GYK-VTVIERN 31 (201)
T ss_dssp EEEEE----HHHHHHHHHHHH-TSE-EEEEESS
T ss_pred CEEEECCCHHHHHHHHHHHHC-CCC-EEEEECC
T ss_conf 999999899999999999977-990-9999723
No 29
>PF02558 ApbA: Ketopantoate reductase PanE/ApbA; InterPro: IPR013332 ApbA, the ketopantoate reductase enzyme 1.1.1.169 from EC of Salmonella typhimurium is required for the synthesis of thiamine via the alternative pyrimidine biosynthetic pathway . Precursors to the pyrimidine moiety of thiamine are synthesized de novo by the purine biosynthetic pathway or the alternative pyrimidine biosynthetic (APB) pathway. The ApbA protein catalyzes the NADPH-specific reduction of ketopantoic acid to pantoic acid. This activity had previously been associated with the pantothenate biosynthetic gene panE . ApbA and PanE are allelic . ; PDB: 2ew2_A 3ego_A 2ofp_B 1yjq_A 1ks9_A 1yon_A 3g17_F 3hn2_D 2qyt_A 3ghy_A ....
Probab=76.74 E-value=0.86 Score=22.28 Aligned_cols=92 Identities=17% Similarity=0.244 Sum_probs=50.7
Q ss_pred EEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCHH---------HHHH-HHHHCCCCEEEEECCCC
Q ss_conf 7998337689999999971899448998607853648502881250788---------9999-99854998999965899
Q T0622 4 VLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRPK---------YLER-LIKKHCISTVLLAVPSA 73 (138)
Q Consensus 4 vlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~---------dl~~-~i~~~~i~~iiia~~~~ 73 (138)
++|+|+|..|..++..|.+ .++. |-|++.++....-.-.|..+.+.+ .... ......+|.+++|....
T Consensus 1 I~IiGaGaiG~~~a~~L~~-~g~~-V~l~~r~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~viv~vKa~ 78 (151)
T PF02558_consen 1 ILIIGAGAIGSLYAARLAK-AGHD-VTLLARSPRLEAIKENGLTIKSDDGDEIVRPPIVISDPAEDDGPFDLVIVAVKAY 78 (151)
T ss_dssp EEEE-------HHHHHHHH-CCCE-EEEE-SCHHHHHHHHEEEEEEESSEEEEECEEEECSSC-TTCCTESEEEE-SSGG
T ss_pred CEEECCCHHHHHHHHHHHH-CCCE-EEEEEECCHHHHHHHCEEEEEECCCCEEECCCCCCCCCCCCCCCCCEEEEEECCC
T ss_conf 9999969999999999997-8990-8999937288876123689996898188435300166201258988999995356
Q ss_pred CHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf 989999999999857982998068
Q T0622 74 SQVQKKVIIESLAKLHVEVLTIPN 97 (138)
Q Consensus 74 ~~~~~~~i~~~~~~~~v~v~~iP~ 97 (138)
.-+..-+.+..+......+..+-+
T Consensus 79 ~~~~al~~l~~~~~~~t~il~lqN 102 (151)
T PF02558_consen 79 QLEEALKALAPRLSPNTTILSLQN 102 (151)
T ss_dssp GHHHHHHHHGCGSETTCEEEEE--
T ss_pred CHHHHHHHHHHHCCCCCEEEEECC
T ss_conf 769999999864599999999638
No 30
>PF00044 Gp_dh_N: Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; InterPro: IPR000173 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain . The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme . GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis . The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself. GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins .; GO: 0004365 glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, 0051287 NAD binding, 0006096 glycolysis; PDB: 1znq_Q 1u8f_P 3gpd_R 1j0x_Q 1ihx_C 1ihy_D 1crw_R 1szj_R 1dss_G 4gpd_4 ....
Probab=75.06 E-value=0.87 Score=22.25 Aligned_cols=90 Identities=17% Similarity=0.114 Sum_probs=54.2
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEEEEEECCC--HH----------HCCCC------------CCCEEEC--CHHHHHH
Q ss_conf 179983376899999999718994489986078--53----------64850------------2881250--7889999
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDD--RK----------KHKTT------------MQGITIY--RPKYLER 56 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~--~~----------~~g~~------------i~g~~v~--~~~dl~~ 56 (138)
+|.|-|.|+-|+.+++.+..++++++||+-|-. ++ .+|+. ++|.++. ...+..+
T Consensus 2 kVgINGfGRIGR~v~R~~~~~~~~evVaInd~~~~~~~~a~llkyDsvhG~~~~~v~~~~~~l~v~g~~I~v~~~~dp~~ 81 (151)
T PF00044_consen 2 KVGINGFGRIGRLVFRAALKRPDIEVVAINDLSPDPEYLAYLLKYDSVHGRFPGEVEVEDDGLIVNGKEIRVFSERDPAE 81 (151)
T ss_dssp EEEEB-------HHHHHHHTHSSEEEEEEEESSSSHHHHHHHHHEESTTCCGSSHEEEESSEEEETTEEEEEEHTSSGGG
T ss_pred EEEEECCCHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHCCCCCCCCEEECCCCCCCEEEECCCEEEEECCCCHHH
T ss_conf 79896886899999998613554389998445532167887751122333010012444326885572588602288102
Q ss_pred HH-HHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf 99-8549989999658999899999999998579829980
Q T0622 57 LI-KKHCISTVLLAVPSASQVQKKVIIESLAKLHVEVLTI 95 (138)
Q Consensus 57 ~i-~~~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~i 95 (138)
+- .++++|.|+=+++.....+..+ .-.+.|++-.++
T Consensus 82 lpW~~~gVDiVvecTG~f~~~~~~~---~hl~~GaKkVii 118 (151)
T PF00044_consen 82 LPWGELGVDIVVECTGKFTTRENAS---KHLKAGAKKVII 118 (151)
T ss_dssp S-TTTTT-SEEEE---TT-SHHHHC---HHHHCT-EEEEE
T ss_pred CCHHHHCCCEEEECCCCCCCCCCHH---HHHHCCCCEEEE
T ss_conf 0276625788994897860103166---686264888999
No 31
>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=74.66 E-value=2.2 Score=19.71 Aligned_cols=77 Identities=17% Similarity=0.188 Sum_probs=56.8
Q ss_pred HHHCCCCEEEEEECCCHHHCCCCCCCEEECCH-------HHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 97189944899860785364850288125078-------89999998549989999658999899999999998579829
Q T0622 20 LRQGKEFHPIAFIDDDRKKHKTTMQGITIYRP-------KYLERLIKKHCISTVLLAVPSASQVQKKVIIESLAKLHVEV 92 (138)
Q Consensus 20 l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~-------~dl~~~i~~~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v 92 (138)
..+..+.++.+|+..+..+.|--..|.|-+-. .....+.....||.|+|.-+..+.+++.++...|...-+.+
T Consensus 164 ~~k~~gi~t~AFI~g~~~~rGPl~~GLpTLE~HR~~~~~~~a~~L~~~g~iD~V~IGd~~~s~~el~~l~~~~~~~~~~L 243 (357)
T PF05913_consen 164 WFKEYGIRTAAFIPGDEAKRGPLFEGLPTLEMHRGLPPLAQAKHLFATGLIDDVIIGDPYASEEELEQLSQYFNKNIITL 243 (357)
T ss_dssp HHHH---EEEEE---SS--B-------BSSGGGTTS-HHHHHHHHCCSTT--EEE---B---HHHHHH---HHHCSCEEE
T ss_pred HHHHCCCCEEEEEECCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHCCCEEE
T ss_conf 99976996799972786556875589772398679999999999997189998998899799999999998640585368
Q ss_pred EECC
Q ss_conf 9806
Q T0622 93 LTIP 96 (138)
Q Consensus 93 ~~iP 96 (138)
.+-+
T Consensus 244 ~v~~ 247 (357)
T PF05913_consen 244 RVEL 247 (357)
T ss_dssp EE--
T ss_pred EEEE
T ss_conf 8640
No 32
>PF00899 ThiF: ThiF family; InterPro: IPR000594 Ubiquitin-activating enzyme (E1 enzyme) , activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin- conjugating enzymes (E2). The family of ubiquitin-activating enzymes shares in its catalytic domain significant similarity with a large family of NAD/FAD-binding proteins. This domain is based on the common NAD/FAD-binding fold and finds members of several families, including UBA ubiquitin activating enzymes; the hesA/moeB/thiF family; NADH peroxidases; the LDH family; sarcosin oxidase; phytoene dehydrogenases; alanine dehydrogenases; hydroxyacyl-CoA dehydrogenases and many other NAD/FAD dependent dehydrogenases and oxidases.; GO: 0003824 catalytic activity; PDB: 1jwa_B 1jwb_B 1jw9_B 1zfn_A 1zud_1 1zkm_A 3h9g_A 3h9q_C 3h5r_C 3h5n_C ....
Probab=74.25 E-value=2.3 Score=19.65 Aligned_cols=89 Identities=25% Similarity=0.360 Sum_probs=51.7
Q ss_pred CCCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCC---HHHCCCCCC-----------------------CEEECC----
Q ss_conf 95179983376899999999718994489986078---536485028-----------------------812507----
Q T0622 1 KKKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDD---RKKHKTTMQ-----------------------GITIYR---- 50 (138)
Q Consensus 1 ~krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~---~~~~g~~i~-----------------------g~~v~~---- 50 (138)
+.+++|+|+|..|-.+++.+.+. +..=.-++|++ ++..++... +..+-.
T Consensus 2 ~~~v~iiG~GglGs~ia~~L~~~-Gv~~i~ivD~d~v~~~Nl~rq~~~~~~diG~~Ka~~~~~~l~~~np~~~i~~~~~~ 80 (135)
T PF00899_consen 2 KSKVLIIGAGGLGSEIAKNLARS-GVGEITIVDDDIVEESNLNRQFLFNEEDIGKNKAEALAERLKRINPDVKIEAIPKN 80 (135)
T ss_dssp T-EEEEES-S----HHHHHHHH-----EEEEEESSB--GGGGGT-TTS-GGGTTSBHHHHHHHHHHHHSTTSEEEEEESH
T ss_pred CCEEEEECCCHHHHHHHHHHHHC-CCCCEEEECCEEEEEECCCCCCCCCHHHCCCCCHHHHHHHHHHHCCCEEEEEEECC
T ss_conf 88899988788999999999980-97636852890887755776546874553865378988878875076289999446
Q ss_pred --HHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEE
Q ss_conf --88999999854998999965899989999999999857982998
Q T0622 51 --PKYLERLIKKHCISTVLLAVPSASQVQKKVIIESLAKLHVEVLT 94 (138)
Q Consensus 51 --~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~ 94 (138)
.+.+.++. .+.|.++.|..+ .+....+-+.|...++.+..
T Consensus 81 i~~~~~~~~~--~~~d~Vv~~~d~--~~~~~~l~~~~~~~~~~~i~ 122 (135)
T PF00899_consen 81 IDEENIDELL--KNFDLVVDCVDN--FEARKLLNEYCRKHGIPFID 122 (135)
T ss_dssp CSHHHHHHHH--CTSSEEEEESSS--HHHHHHHHHHHHHTT-EEEE
T ss_pred CCHHHHHHHH--CCCCEEEECCCC--HHHHHHHHHHHHHCCCCEEE
T ss_conf 7566787652--369799986899--99999999999987998999
No 33
>PF10100 DUF2338: Uncharacterized protein conserved in bacteria (DUF2338)
Probab=73.65 E-value=1.3 Score=21.11 Aligned_cols=31 Identities=29% Similarity=0.522 Sum_probs=23.8
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf 51799833768999999997189944899860
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFID 33 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiD 33 (138)
.||||+|+|..|.++|..+....+.+ +|+..
T Consensus 2 ~~vLilGtGP~aiQLAv~~k~~~~~~-vgi~g 32 (429)
T PF10100_consen 2 NRVLILGTGPVAIQLAVDLKKHGDCK-VGIAG 32 (429)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCCCE-EEECC
T ss_conf 84599637769999999998535745-64305
No 34
>PF03949 Malic_M: Malic enzyme, NAD binding domain; InterPro: IPR012302 Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate , a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis . There are 3 forms of the enzyme : an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form . Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase ; and the hypothetical Saccharomyces cerevisiae protein YKL029c. Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity . The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate-or divalent metal ion-binding in the active site . Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme , although it is absent in the sequences from some species. There are three well conserved regions in the enzyme sequences. Two of them seem to be involved in the binding NAD or NADP. The significance of the third one, located in the central part of the enzymes, is not yet known.; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding; PDB: 1llq_A 1o0s_B 1gq2_L 2aw5_B 1pjl_D 1gz4_C 1pj2_C 1efk_D 1do8_A 1efl_C ....
Probab=70.05 E-value=2.8 Score=19.05 Aligned_cols=85 Identities=19% Similarity=0.291 Sum_probs=45.0
Q ss_pred CCEEEEECCHHHHHHHHHHHHC------------CCCE---EEEEECCCHHHCC----CCCCC-EEECCHHHHHHHHHHC
Q ss_conf 5179983376899999999718------------9944---8998607853648----50288-1250788999999854
Q T0622 2 KKVLIYGAGSAGLQLANMLRQG------------KEFH---PIAFIDDDRKKHK----TTMQG-ITIYRPKYLERLIKKH 61 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~------------~~y~---ivGfiDd~~~~~g----~~i~g-~~v~~~~dl~~~i~~~ 61 (138)
.|++++|||.+|..+++.+..- .++. -.|++.++..... .+.+. .+..+..+|.+.++.-
T Consensus 26 ~riv~~GAGsAg~gia~~l~~~~~~~G~s~eeA~~~i~~~D~~Glv~~~r~~l~~~~~~fa~~~~~~~~~~~L~e~v~~~ 105 (255)
T PF03949_consen 26 QRIVFFGAGSAGIGIADLLVDAMVTEGLSEEEARKRIWLVDSKGLVTKDRDDLNPHKKPFARDTNPEKGWGSLEEAVKGV 105 (255)
T ss_dssp -EEEEE-------HHHHHHHHHHHC----HHHHHTTEEE----EEEBTTTSSCSHHHHCCHBSSSTTT--SSHHHHHHHH
T ss_pred CEEEEECCCHHHHHHHHHHHHHHHHCCCCHHHHHCCEEEECCCCEEECCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHCC
T ss_conf 57999898889999999999999861588566518099984757587899765299998726477554547899998436
Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf 99899996589998999999999985
Q T0622 62 CISTVLLAVPSASQVQKKVIIESLAK 87 (138)
Q Consensus 62 ~i~~iiia~~~~~~~~~~~i~~~~~~ 87 (138)
+.+.++=+. ..+.-..++++....+
T Consensus 106 kPtvLIG~S-~~~g~Fteevv~~Ma~ 130 (255)
T PF03949_consen 106 KPTVLIGLS-GQPGAFTEEVVRAMAK 130 (255)
T ss_dssp --SEEEEES-S----S-HHHHHHHHH
T ss_pred CCCEEEEEC-CCCCCCCHHHHHHHHH
T ss_conf 996899847-9999889999999871
No 35
>PF01370 Epimerase: NAD dependent epimerase/dehydratase family; InterPro: IPR001509 This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions .; GO: 0003824 catalytic activity, 0050662 coenzyme binding, 0044237 cellular metabolic process; PDB: 1eq2_F 2cnb_A 1gy8_C 2c20_B 3enk_A 1a9y_A 1lrk_A 1kvr_A 1lrj_A 1lrl_A ....
Probab=70.04 E-value=2.8 Score=19.05 Aligned_cols=96 Identities=18% Similarity=0.196 Sum_probs=59.7
Q ss_pred EEEEEC-CHHHHHHHHHHHHCCCCEEE-EEECCCHHHCC-C-----CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCC-
Q ss_conf 799833-76899999999718994489-98607853648-5-----028812507889999998549989999658999-
Q T0622 4 VLIYGA-GSAGLQLANMLRQGKEFHPI-AFIDDDRKKHK-T-----TMQGITIYRPKYLERLIKKHCISTVLLAVPSAS- 74 (138)
Q Consensus 4 vlIvGa-g~~a~~l~~~l~~~~~y~iv-GfiDd~~~~~g-~-----~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~- 74 (138)
|||.|+ |-.|..+++.+.+.+ +.++ ++.-....... . .+....+...+.+.+.++..++|.|+.+.....
T Consensus 1 IlI~Ga~G~iG~~l~~~l~~~g-~~v~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~d~vi~~a~~~~~ 79 (238)
T PF01370_consen 1 ILITGATGFIGSALVRALLERG-HEVIDALSRRESKASLCEERLNVEFIEGDLRDPDAIEDALKGAKPDVVIHLAGPSGV 79 (238)
T ss_dssp EEEE-----HHHHHHHHHHHHT-SEEEEEESSSSTGGGHHHHHHTEEEEESETTSHHHHHHHHHHHTESEEEEECSSHSH
T ss_pred EEEECCCCHHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHCCCCCCCEEEECCCCCCC
T ss_conf 8998368789999999999779-864222212334444333212589864011232010100013476264301344334
Q ss_pred ------H--------HHHHHHHHHHHHCCC-EEEECCCHHH
Q ss_conf ------8--------999999999985798-2998068366
Q T0622 75 ------Q--------VQKKVIIESLAKLHV-EVLTIPNLDD 100 (138)
Q Consensus 75 ------~--------~~~~~i~~~~~~~~v-~v~~iP~~~~ 100 (138)
. .....+++.|.+.++ ++..+.+...
T Consensus 80 ~~~~~~~~~~~~~n~~~~~~ll~~~~~~~~~~~i~~sS~~v 120 (238)
T PF01370_consen 80 PKSSDDPEDTYESNVEGTRNLLEAAREAGVKRFIFVSSTGV 120 (238)
T ss_dssp HHHHHSHHHHHHHHTHHHHHHHHHHHHHTTSEEEEEEEGGG
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 54321112222222222222211112357521222111002
No 36
>PF00732 GMC_oxred_N: GMC oxidoreductase; InterPro: IPR000172 The glucose-methanol-choline (GMC) oxidoreductases are FAD flavoproteins oxidoreductases , . These enzymes include a variety of proteins; choline dehydrogenase (CHD), methanol oxidase (MOX) and cellobiose dehydrogenase (1.1.99.18 from EC) which share a number of regions of sequence similarities. One of these regions, located in the N-terminal section, corresponds to the FAD ADP- binding domain. The function of the other conserved domains is not yet known.; GO: 0016614 oxidoreductase activity, acting on CH-OH group of donors, 0050660 FAD binding; PDB: 2jbv_B 1gpe_A 1gal_A 1cf3_A 1ijh_A 3b3r_A 2gew_A 1cc2_A 1b4v_A 1n4v_A ....
Probab=68.27 E-value=1.6 Score=20.68 Aligned_cols=26 Identities=27% Similarity=0.497 Sum_probs=22.4
Q ss_pred EEEEECCHHHHHHHHHHHHCCCCEEE
Q ss_conf 79983376899999999718994489
Q T0622 4 VLIYGAGSAGLQLANMLRQGKEFHPI 29 (138)
Q Consensus 4 vlIvGag~~a~~l~~~l~~~~~y~iv 29 (138)
++|||+|.+|-.+|..|..++.++|+
T Consensus 3 ~IIVGsG~~G~v~A~rLa~~g~~~Vl 28 (298)
T PF00732_consen 3 VIIVGSGAGGGVVASRLAEAGGYSVL 28 (298)
T ss_dssp EEEE-------HHHHHHTTSTTS-EE
T ss_pred EEEECCCHHHHHHHHHHHHCCCCEEE
T ss_conf 99989788999999999768897699
No 37
>PF03446 NAD_binding_2: NAD binding domain of 6-phosphogluconate dehydrogenase; InterPro: IPR006115 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) , . Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved . The protein is a homodimer in which the monomers act independently : each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet . NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket . This family represents the NAD binding domain of 6-phosphogluconate dehydrogenase which adopts a Rossman fold. The C-terminal domain is described in IPR006114 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0006098 pentose-phosphate shunt; PDB: 1vpd_A 1yb4_A 1wp4_C 2cvz_C 2uyy_C 1pgj_B 2p4q_A 1pgp_A 1pgq_A 1pgo_A ....
Probab=67.00 E-value=3.3 Score=18.66 Aligned_cols=93 Identities=17% Similarity=0.270 Sum_probs=56.9
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCC-CC---------------EEEC--C-HHHHHHHHHH--
Q ss_conf 517998337689999999971899448998607853648502-88---------------1250--7-8899999985--
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTM-QG---------------ITIY--R-PKYLERLIKK-- 60 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i-~g---------------~~v~--~-~~dl~~~i~~-- 60 (138)
+++-++|.|..|..+++.+.++ +|.+.+ +|.++++..... .| +.+. . .+...+++..
T Consensus 2 ~~Ig~IGlG~MG~~~a~~L~~~-g~~V~v-~dr~~~~~~~~~~~g~~~~~s~~e~~~~~d~vi~~v~~~~av~~v~~~~~ 79 (163)
T PF03446_consen 2 MKIGFIGLGNMGSAMARNLARA-GHEVTV-YDRSPEKAEALAEEGATVADSPAELAEQADVVILCVPDDAAVEEVLFGEE 79 (163)
T ss_dssp BEEEEB-------HHHHHHHH--CSEEEE---SSHHHHHHHHHHTEEEESSHHHHHHHBSEEEE-SSSHHHHHHHHHH--
T ss_pred CEEEEEEHHHHHHHHHHHHHHC-CCEEEE-EECCHHHHHHHHHHCCEEECCHHHHHHHCCHHEEECCCHHHHHHHHHCCC
T ss_conf 8899981599899999999845-997999-90978899999973356631588898734012542487788998873334
Q ss_pred -----CCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEECC
Q ss_conf -----499899996589998999999999985798299806
Q T0622 61 -----HCISTVLLAVPSASQVQKKVIIESLAKLHVEVLTIP 96 (138)
Q Consensus 61 -----~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~iP 96 (138)
..-..+++-..+.+++...++...+.+.|+.+.-.|
T Consensus 80 gi~~~l~~g~iiid~sT~~p~~~~~~~~~~~~~g~~~vdap 120 (163)
T PF03446_consen 80 GILSGLRKGKIIIDMSTISPSTSRELAERLAEKGIRYVDAP 120 (163)
T ss_dssp -HGGGS----EEEE-S---HHHHHHHHHHHHHTT-EEEE--
T ss_pred CCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 60016878988998378747777889999875044444237
No 38
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR013027 from INTERPRO. It is found in both class I and class II oxidoreductases. FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase , , . Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently . Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) . Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase , thioredoxin reductase , mercuric reductase , lipoamide dehydrogenase , trypanothione reductase and NADH peroxidase have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication . ; GO: 0016491 oxidoreductase activity, 0050660 FAD binding; PDB: 2v3a_A 2v3b_A 2yvj_A 2gr0_A 2gr2_A 2gqw_A 2yvf_A 2gr1_A 1f3p_A 1d7y_A ....
Probab=65.15 E-value=3.6 Score=18.44 Aligned_cols=25 Identities=32% Similarity=0.453 Sum_probs=20.0
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEE
Q ss_conf 17998337689999999971899448
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHP 28 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~i 28 (138)
+++|+|+|..|..+|..+.+. +.++
T Consensus 1 ~vvViGgG~~g~E~A~~l~~~-g~~V 25 (81)
T PF00070_consen 1 RVVVIGGGYIGLELAEELARL-GKEV 25 (81)
T ss_dssp EEEEE-E-HHHHHHHHHHHHT-SSEE
T ss_pred CEEEECCCHHHHHHHHHHHHH-CCEE
T ss_conf 999999699999999999863-9889
No 39
>PF00106 adh_short: short chain dehydrogenase alcohol dehydrogenase superfamily signature glucose/ribitol dehydrogenase family signature; InterPro: IPR002198 The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases. As the first member of this family to be characterised was Drosophila alcohol dehydrogenase, this family used to be called , , 'insect-type', or 'short-chain' alcohol dehydrogenases. Most member of this family are proteins of about 250 to 300 amino acid residues. Most dehydrogenases possess at least 2 domains , the first binding the coenzyme, often NAD, and the second binding the substrate. This latter domain determines the substrate specificity and contains amino acids involved in catalysis. Little sequence similarity has been found in the coenzyme binding domain although there is a large degree of structural similarity, and it has therefore been suggested that the structure of dehydrogenases has arisen through gene fusion of a common ancestral coenzyme nucleotide sequence with various substrate specific domains .; GO: 0016491 oxidoreductase activity, 0008152 metabolic process; PDB: 2q2w_D 2q2q_A 2q2v_B 1wmb_B 1x1t_A 2ag5_A 2rh4_A 3csd_B 1x7g_A 1x7h_A ....
Probab=65.05 E-value=3.6 Score=18.43 Aligned_cols=72 Identities=18% Similarity=0.182 Sum_probs=47.9
Q ss_pred CCEEEEECCH-HHHHHHHHHHHCCCCEEEEEECCC--HHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHH
Q ss_conf 5179983376-899999999718994489986078--5364850288125078899999985499899996589998999
Q T0622 2 KKVLIYGAGS-AGLQLANMLRQGKEFHPIAFIDDD--RKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQK 78 (138)
Q Consensus 2 krvlIvGag~-~a~~l~~~l~~~~~y~ivGfiDd~--~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~ 78 (138)
|.++|.|++. .|..+++.+.+. +...+.+.+.+ ... .+++.+-+...+....++......++.+
T Consensus 1 k~vlItGa~~giG~~ia~~l~~~-g~~~vi~~~r~~~~~~------------~~~~~~~l~~~~~~~~~~~~D~~~~~~i 67 (167)
T PF00106_consen 1 KTVLITGASGGIGRAIARELAER-GASVVILTSRNSLEEE------------LEELIAELPASGGEIEYIQCDISDPESI 67 (167)
T ss_dssp -EEEEESTTSSTT-HHHHHHHHT-TTEEEEEEESSHCHHH------------HHHHHHHHHHHTSEEEEEEEETTSHHHH
T ss_pred CEEEEECCCCHHHHHHHHHHHHC-CCCEEECCCCCCCCCC------------CCCCCCCCCCCCCCEEEEEECCCCCCCC
T ss_conf 99999799829999999999984-9905403311223311------------1222222222233101454213322011
Q ss_pred HHHHHHHH
Q ss_conf 99999998
Q T0622 79 KVIIESLA 86 (138)
Q Consensus 79 ~~i~~~~~ 86 (138)
+++++.+.
T Consensus 68 ~~~~~~~~ 75 (167)
T PF00106_consen 68 KALIEEVS 75 (167)
T ss_dssp HHHHHHHH
T ss_pred CCCCCCCC
T ss_conf 12222222
No 40
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.
Probab=64.07 E-value=3.7 Score=18.31 Aligned_cols=66 Identities=20% Similarity=0.228 Sum_probs=50.2
Q ss_pred CCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf 899448998607853648502881250788999999854998999965899989999999999857982998068
Q T0622 23 GKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKKVIIESLAKLHVEVLTIPN 97 (138)
Q Consensus 23 ~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~iP~ 97 (138)
..+|+|.-+--+++...+... +.|...+++++++.+.++.|. ...-.+++-..|...++.+.++|+
T Consensus 60 ~~G~~V~Y~~~~d~~~~~s~~--------~~L~~~~~~~~~~~~~~~~P~-d~rl~~~l~~~~~~~~i~~~~~~~ 125 (224)
T PF04244_consen 60 QKGFRVHYIELDDPENTGSFT--------DALARLLKEHGIDRLHVQEPG-DYRLEQRLKELAESLGIPLEVLED 125 (224)
T ss_pred HCCCEEEEEECCCCCCCCCHH--------HHHHHHHHHHCCCEEEEECCC-CHHHHHHHHHHHHHCCCCEEEECC
T ss_conf 689869999678865535599--------999999998199779997787-599999999999865987699579
No 41
>PF02423 OCD_Mu_crystall: Ornithine cyclodeaminase/mu-crystallin family; InterPro: IPR003462 This family contains the bacterial Ornithine cyclodeaminase enzyme, which catalyses the deamination of ornithine to proline . This family also contains mu-crystallin the major component of the eye lens in several Australian marsupials, mRNA for this protein has also been found in human retina .; PDB: 3hdj_B 1u7h_A 1x7d_B 1vll_B 1omo_B 2i99_B.
Probab=63.31 E-value=3.3 Score=18.63 Aligned_cols=71 Identities=14% Similarity=0.275 Sum_probs=50.5
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCC---CC--CCEEECCHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 5179983376899999999718994489986078536485---02--8812507889999998549989999658999
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKT---TM--QGITIYRPKYLERLIKKHCISTVLLAVPSAS 74 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~---~i--~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~ 74 (138)
+++.|+|+|..|..-++++..-..++=|-+++.++.+.-. .+ .|+.+-..++.++.++. .|.|+.|.++..
T Consensus 129 ~~l~iiGaG~QA~~~l~a~~~~~~i~~v~v~~r~~~~~~~~~~~~~~~~~~v~~~~s~~~av~~--aDvI~taT~s~~ 204 (313)
T PF02423_consen 129 RTLAIIGAGVQARAHLRALAAVRPIEEVRVYSRSPERAEAFAARLSRLGVDVEAVDSVEEAVRG--ADVIVTATPSTE 204 (313)
T ss_dssp -EEEEE----HHHHHHHHHHHHS--SEEEE--SSHHHHHHHHHHHCC---EEEEESSHHHHHCC--SSEEEE----SS
T ss_pred CEEEEECCCHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHCCCCCEEEECCHHHHHHC--CCEEEEEECCCC
T ss_conf 7799988878999999999986897589997698789999999763046643881899999844--999999404899
No 42
>PF01494 FAD_binding_3: FAD binding domain; InterPro: IPR002938 Monooxygenases incorporate one hydroxyl group into substrates and are found in many metabolic pathways. In this reaction, two atoms of dioxygen are reduced to one hydroxyl group and one H_2O molecule by the concomitant oxidation of NAD(P)H . P-hydroxybenzoate hydroxylase from Pseudomonas fluorescens contains this sequence motif (present in in flavoprotein hydroxylases) with a putative dual function in FAD and NADPH binding .; GO: 0004497 monooxygenase activity, 0006118 electron transport, 0006725 aromatic compound metabolic process; PDB: 3gmc_B 3gmb_A 3cgv_A 2c4c_A 2bry_B 2bra_B 3fmw_A 2qa2_A 2qa1_A 1foh_C ....
Probab=62.12 E-value=3.3 Score=18.63 Aligned_cols=34 Identities=32% Similarity=0.497 Sum_probs=26.3
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHH
Q ss_conf 517998337689999999971899448998607853
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRK 37 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~ 37 (138)
-+|+|+|+|-+|..++..|.+. +++ |-+++.++.
T Consensus 2 ~dViIvGgG~aGl~~A~~L~~~-G~~-v~viE~~~~ 35 (356)
T PF01494_consen 2 YDVIIVGGGPAGLALALALARA-GIR-VLVIERRPS 35 (356)
T ss_dssp EEEEEE-------HHHHHHHHC-TCE-EEEEESSSS
T ss_pred CEEEEECCCHHHHHHHHHHHHC-CCE-EEEEECCCC
T ss_conf 6699989899999999999976-995-789711247
No 43
>PF02737 3HCDH_N: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; InterPro: IPR006176 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain . There are two major regions of similarity in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process; PDB: 3hdh_C 1f14_A 1il0_B 3had_B 1f0y_A 1lso_B 1f12_A 1f17_A 1lsj_B 1m76_A ....
Probab=58.63 E-value=4.7 Score=17.72 Aligned_cols=34 Identities=26% Similarity=0.504 Sum_probs=26.7
Q ss_pred CEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHH
Q ss_conf 179983376899999999718994489986078536
Q T0622 3 KVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKK 38 (138)
Q Consensus 3 rvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~ 38 (138)
+|.|+|+|-.|..++..+.+. +|. |-++|.++..
T Consensus 1 kV~ViGaG~mG~~iA~~~a~~-G~~-V~l~d~~~~~ 34 (180)
T PF02737_consen 1 KVAVIGAGTMGRGIAALFARA-GHE-VVLYDPDPEA 34 (180)
T ss_dssp EEEEE-------HHHHHHHHT--SE-EEEE-SSHHH
T ss_pred CEEEECCCHHHHHHHHHHHHC-CCE-EEEEECCHHH
T ss_conf 989995688999999999837-990-8999899999
No 44
>PF00551 Formyl_trans_N: Formyl transferase; InterPro: IPR002376 A number of formyl transferases belong to this group. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. Formyltetrahydrofolate dehydrogenase produces formate from formyl- tetrahydrofolate. This is the N-terminal domain of these enzymes and is found upstream of the C-terminal domain (IPR005793 from INTERPRO). The trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase catalyses the second, third and fifth steps in de novo purine biosynthesis. The glycinamide ribonucleotide transformylase belongs to this group.; GO: 0016742 hydroxymethyl-, formyl- and related transferase activity, 0009058 biosynthetic process; PDB: 1s3i_A 2cfi_A 2bw0_A 2bln_B 1z7e_E 1yrw_A 1fmt_A 2fmt_B 1zgh_A 3dcj_A ....
Probab=58.29 E-value=4.7 Score=17.68 Aligned_cols=69 Identities=19% Similarity=0.292 Sum_probs=45.9
Q ss_pred CCEEEE--ECCHHHHHHHHHHHHCC-CCEEEEEECCCHHHCCCC---CCCEEE-------CC-----HHHHHHHHHHCCC
Q ss_conf 517998--33768999999997189-944899860785364850---288125-------07-----8899999985499
Q T0622 2 KKVLIY--GAGSAGLQLANMLRQGK-EFHPIAFIDDDRKKHKTT---MQGITI-------YR-----PKYLERLIKKHCI 63 (138)
Q Consensus 2 krvlIv--Gag~~a~~l~~~l~~~~-~y~ivGfiDd~~~~~g~~---i~g~~v-------~~-----~~dl~~~i~~~~i 63 (138)
.|++++ |.|..+..+++++..+. ...+++++...+...+.. -.+++. +. .+++.+.+++.++
T Consensus 1 mrI~~~~Sg~~~~~~~~l~~l~~~~~~~~iv~Vvt~~~~~~~~~~a~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 80 (181)
T PF00551_consen 1 MRIAFFGSGSGSNLQALLEALKAGGLEAEIVLVVTNPDKARGRKRAIRNGIPAQVIQEKNFQPRSLNDPELLEWLKELNP 80 (181)
T ss_dssp -EEEEEE----HHHHHHHHHHHHTTSEEEEEEEEESSTTEHHHHHHHHHCHCEEECCGGGSSSHHHHHHHHHHHHHHTT-
T ss_pred CEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCC
T ss_conf 97999976997799999999985899977999997885422202466379998996514799846611889999997699
Q ss_pred CEEEEEC
Q ss_conf 8999965
Q T0622 64 STVLLAV 70 (138)
Q Consensus 64 ~~iiia~ 70 (138)
|.++++.
T Consensus 81 Dliv~~~ 87 (181)
T PF00551_consen 81 DLIVVAG 87 (181)
T ss_dssp SEEEESS
T ss_pred CEEEHHH
T ss_conf 8689544
No 45
>PF00056 Ldh_1_N: lactate/malate dehydrogenase, NAD binding domain Prosite entry for lactate dehydrogenase Prosite entry for malate dehydrogenase; InterPro: IPR001236 L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis . L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate . The enzyme participates in the citric acid cycle.; GO: 0016491 oxidoreductase activity, 0006100 tricarboxylic acid cycle intermediate metabolic process; PDB: 3fi9_A 4mdh_B 5mdh_B 3d5t_D 1b8p_A 1b8u_A 1b8v_A 1wze_A 2cvq_A 1bmd_A ....
Probab=55.25 E-value=5.3 Score=17.37 Aligned_cols=66 Identities=21% Similarity=0.193 Sum_probs=38.8
Q ss_pred CEEEEECC-HHHHHHHHHHHHCCCCEEEEEECCCHHHC-CC--------CCCCEEECCHHHHHHHHHHCCCCEEEEEC
Q ss_conf 17998337-68999999997189944899860785364-85--------02881250788999999854998999965
Q T0622 3 KVLIYGAG-SAGLQLANMLRQGKEFHPIAFIDDDRKKH-KT--------TMQGITIYRPKYLERLIKKHCISTVLLAV 70 (138)
Q Consensus 3 rvlIvGag-~~a~~l~~~l~~~~~y~ivGfiDd~~~~~-g~--------~i~g~~v~~~~dl~~~i~~~~i~~iiia~ 70 (138)
++.|+|+| .-|..++..+...+-..=+.++|.++.+. |. ......+.-..+ ....-.+.|.++++-
T Consensus 2 KV~IiGagg~VG~~~a~~l~~~~~~~el~L~D~~~~~~~g~a~Dl~~~~~~~~~~~~~~~~--~~~~~~~adivvita 77 (142)
T PF00056_consen 2 KVAIIGAGGNVGSALAYSLALKGIADELVLIDINEEKAKGEALDLSDASAFLNSNVIITGG--DYEDLKDADIVVITA 77 (142)
T ss_dssp EEEEE-----HHHHHHHHHHHTTTSSEEEEE-SSHHHHHHHHHHHHTHHTTSEEEEEEEST--HGGGGTTESEEEEE-
T ss_pred EEEEECCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHCCCCCCCCEEECCC--CHHHHCCCCEEEEEE
T ss_conf 8999998789999999999718877669994488777560417888678746576563246--278857998899950
No 46
>PF01266 DAO: FAD dependent oxidoreductase; InterPro: IPR006076 This entry includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase (1.1.99.5 from EC), Sarcosine oxidase beta subunit (1.5.3.1 from EC), D-alanine oxidase (1.4.99.1 from EC), D-aspartate oxidase (1.4.3.1 from EC). D-amino acid oxidase (1.4.3.3 from EC) (DAMOX or DAO) is an FAD flavoenzyme that catalyzes the oxidation of neutral and basic D-amino acids into their corresponding keto acids. DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase (1.4.3.1 from EC) (DASOX) is an enzyme, structurally related to DAO, which catalyzes the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown to be important for the enzyme's catalytic activity.; GO: 0016491 oxidoreductase activity; PDB: 1y56_B 2rgh_A 2rgo_A 3da1_A 2qcu_B 2r4e_B 2r45_A 2r46_B 2r4j_B 3dme_B ....
Probab=53.82 E-value=4.2 Score=17.98 Aligned_cols=91 Identities=18% Similarity=0.252 Sum_probs=51.4
Q ss_pred EEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCC--CEEECC----------------HHHHHHHHHHCCC--
Q ss_conf 79983376899999999718994489986078536485028--812507----------------8899999985499--
Q T0622 4 VLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQ--GITIYR----------------PKYLERLIKKHCI-- 63 (138)
Q Consensus 4 vlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~--g~~v~~----------------~~dl~~~i~~~~i-- 63 (138)
|+|||+|-.|...|..+.+ .+|+|+ +++.+..-.+.+-. |.--.+ .+.+.++..+++.
T Consensus 2 v~IIGaGi~Gl~~A~~La~-~G~~V~-lle~~~~~~gaS~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~ 79 (358)
T PF01266_consen 2 VIIIGAGIAGLSTAYELAR-RGYRVL-LLERGDPGSGASGRNGGLLHPGLGAERDPRLLKLARESIDLWRELAEEYGIPV 79 (358)
T ss_dssp EEEE-------HHHHHHHH-SS-EEE-EEESSSTTSSCTTTSEEEE-CSSSSHSSCHHHHHHHHHHHHHHHHHHHTTTTC
T ss_pred EEEECCCHHHHHHHHHHHH-CCCEEE-EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf 9999966999999999997-799699-99654236776553421244554332333232220347899999988629641
Q ss_pred -----CEEEEECCCCCHHHHHHHHHHHHHCCCEEEECC
Q ss_conf -----899996589998999999999985798299806
Q T0622 64 -----STVLLAVPSASQVQKKVIIESLAKLHVEVLTIP 96 (138)
Q Consensus 64 -----~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~iP 96 (138)
..+.++.+....+.+.+....+...+..+..+.
T Consensus 80 ~~~~~g~l~~~~~~~~~~~~~~~~~~~~~~g~~~~~l~ 117 (358)
T PF01266_consen 80 GFRRTGVLYLASDEDDLESLRRLAARLRRAGLPIELLS 117 (358)
T ss_dssp BBEECCHEEEESSHHHHHHHHHHHHHHHCTTETEEEES
T ss_pred ECCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 11445468752777875557766431000244311254
No 47
>PF04412 DUF521: Protein of unknown function (DUF521); InterPro: IPR007506 This is a group of hypothetical proteins.
Probab=53.17 E-value=5.7 Score=17.16 Aligned_cols=75 Identities=15% Similarity=0.132 Sum_probs=52.8
Q ss_pred HHHHHHHHHCCC---CEEEEEECCCHHHCCCCC---CCEEECCHHHHHHHHHHC------CCCEEEEECCCCCHHHHHHH
Q ss_conf 999999971899---448998607853648502---881250788999999854------99899996589998999999
Q T0622 14 LQLANMLRQGKE---FHPIAFIDDDRKKHKTTM---QGITIYRPKYLERLIKKH------CISTVLLAVPSASQVQKKVI 81 (138)
Q Consensus 14 ~~l~~~l~~~~~---y~ivGfiDd~~~~~g~~i---~g~~v~~~~dl~~~i~~~------~i~~iiia~~~~~~~~~~~i 81 (138)
++|-.++..+.. |+++|+--+.+... ... ......+.+|+.+...+. .+|.|.+-.|..+-+++.++
T Consensus 230 KalgAA~atsga~~m~Hv~GvTPEa~~~~-~~~~~~~e~i~i~~~dl~~~~~~l~~~~~~~~DlV~lGcPH~S~~E~~~l 308 (400)
T PF04412_consen 230 KALGAAMATSGAVAMYHVEGVTPEAPTLE-AAFGGKAEKITITRADLEAVWEELNNAGDEEVDLVALGCPHASLEELREL 308 (400)
T ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCCCC-HHCCCCCEEEEECHHHHHHHHHHHCCCCCCCCCEEEECCCCCCHHHHHHH
T ss_conf 99878776306600599857788987631-12058750899679999999997243788877879978999999999999
Q ss_pred HHHHHHCC
Q ss_conf 99998579
Q T0622 82 IESLAKLH 89 (138)
Q Consensus 82 ~~~~~~~~ 89 (138)
.+.|...+
T Consensus 309 a~ll~gr~ 316 (400)
T PF04412_consen 309 AELLEGRK 316 (400)
T ss_pred HHHHHCCC
T ss_conf 99983789
No 48
>PF04016 DUF364: Domain of unknown function (DUF364); InterPro: IPR007161 This is a family of bacterial and archaeal proteins of unknown function.
Probab=52.21 E-value=5.9 Score=17.06 Aligned_cols=86 Identities=15% Similarity=0.152 Sum_probs=55.9
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH
Q ss_conf 51799833768999999997189944899860785364850288125078899999985499899996589998999999
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAVPSASQVQKKVI 81 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i 81 (138)
++|.+||.=.. +++.++... .-+-++|-++...+..-.+. +.+.-+.++.+ .|.++++-.+.-+.-+.++
T Consensus 113 ~kV~vVG~~~P---~v~~l~~~g--~~~~v~e~~~~~~~~~~~~~---~~~~~~~~l~~--~D~v~iTGsTlvN~Tl~~l 182 (232)
T PF04016_consen 113 KKVAVVGYFQP---IVKRLRERG--AELRVLERNPENIGPQEGDL---PDEAAEELLPW--ADVVLITGSTLVNGTLDRL 182 (232)
T ss_pred CEEEEECCCCH---HHHHHHHCC--CCEEEEECCCCCCCCCCCCC---CHHHHHHHHCC--CCEEEEEECCEECCCHHHH
T ss_conf 98999917718---899998639--95799978875456666787---72677776344--8889999673022899999
Q ss_pred HHHHHHCCCEEEECCC
Q ss_conf 9999857982998068
Q T0622 82 IESLAKLHVEVLTIPN 97 (138)
Q Consensus 82 ~~~~~~~~v~v~~iP~ 97 (138)
+..|.....-+..=|+
T Consensus 183 L~~~~~~~~vvl~GpS 198 (232)
T PF04016_consen 183 LALAKRAAPVVLYGPS 198 (232)
T ss_pred HHHCCCCCEEEEECCC
T ss_conf 9738668859999377
No 49
>PF07075 DUF1343: Protein of unknown function (DUF1343); InterPro: IPR008302 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=48.88 E-value=6.7 Score=16.74 Aligned_cols=117 Identities=15% Similarity=0.270 Sum_probs=69.2
Q ss_pred ECCHHHHHHHHHHHHCCCCEEEEEECCCH---------HHCCCC---CCCEEECCH---H--HHHHHHHHCCCCEEEEEC
Q ss_conf 33768999999997189944899860785---------364850---288125078---8--999999854998999965
Q T0622 8 GAGSAGLQLANMLRQGKEFHPIAFIDDDR---------KKHKTT---MQGITIYRP---K--YLERLIKKHCISTVLLAV 70 (138)
Q Consensus 8 Gag~~a~~l~~~l~~~~~y~ivGfiDd~~---------~~~g~~---i~g~~v~~~---~--dl~~~i~~~~i~~iiia~ 70 (138)
|.+..+.+.+..|.+.++.+++.++...- ...+.. --|+||++. . -..+.++ ++|.+++-+
T Consensus 9 ~v~~~~~~~~d~L~~~~gv~l~~lF~PEHG~rG~~~ag~~v~~~~D~~tglpV~SLYG~~~~Pt~~~L~--~iDvlvfDi 86 (362)
T PF07075_consen 9 GVDRDGRHLIDVLLRAPGVNLVALFGPEHGFRGDAQAGEKVSDSVDPRTGLPVYSLYGKTRKPTPEMLK--GIDVLVFDI 86 (362)
T ss_pred CCCCCCCCHHHHHHHCCCCCEEEEECCCCCCCCCHHCCCCCCCCCCCCCCCEEEECCCCCCCCCHHHHH--CCCEEEEEC
T ss_conf 237888669999976769877898078767630240288678875888999489798998998999980--899999946
Q ss_pred CCCCHHH------HHHHHHHHHHCCCEEEECCCHHHHHCCCCCHHHCCCCCHHHCCCCCCCCC
Q ss_conf 8999899------99999999857982998068366426874521235577320377987675
Q T0622 71 PSASQVQ------KKVIIESLAKLHVEVLTIPNLDDLVNGKLSIGQLKEVSIDDLLGRVAVTP 127 (138)
Q Consensus 71 ~~~~~~~------~~~i~~~~~~~~v~v~~iP~~~~~~~~~~~~~~lr~i~ieDLL~R~~v~l 127 (138)
.+.-... +....+.|.++++++.++=+..=+. |..--..+-+-..+-+-|+.|+.+
T Consensus 87 QDVG~RfYTYi~Tm~~~MeAaa~~g~~~iVLDRPNPl~-G~~veGp~l~~~~~SFvG~~~iP~ 148 (362)
T PF07075_consen 87 QDVGARFYTYISTMGYAMEAAAENGKEFIVLDRPNPLG-GRYVEGPVLDPEFRSFVGMYPIPV 148 (362)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCC-CCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 35661476899999999999997099499983889889-987766786810036457765532
No 50
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics , . One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose . This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA , . This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes . It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; PDB: 1ipa_A 1gz0_H.
Probab=48.72 E-value=5.3 Score=17.39 Aligned_cols=49 Identities=14% Similarity=0.112 Sum_probs=36.0
Q ss_pred ECCHHHHHHHHHHC-CCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf 50788999999854-998999965899989999999999857982998068
Q T0622 48 IYRPKYLERLIKKH-CISTVLLAVPSASQVQKKVIIESLAKLHVEVLTIPN 97 (138)
Q Consensus 48 v~~~~dl~~~i~~~-~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~iP~ 97 (138)
|+|.--+.+.++.. .+..++++.. .......+++..+...++++..++.
T Consensus 2 i~G~~~V~eaL~~~~~i~~l~~~~~-~~~~~~~~i~~~~~~~~i~v~~v~~ 51 (76)
T PF08032_consen 2 IEGIHAVEEALKSGPRIEKLYVTEG-RQDPRIEEILKLAKKNGIPVEEVSK 51 (76)
T ss_dssp E---HHHHHHHHH-GGEEEEEEE------CCTHHHHHHHHH---EEEEE-H
T ss_pred EEEHHHHHHHHCCCCCCCEEEEECC-CCCHHHHHHHHHHHHCCCEEEECCH
T ss_conf 8874899999808999209999869-7561589999999986998999399
No 51
>PF02670 DXP_reductoisom: 1-deoxy-D-xylulose 5-phosphate reductoisomerase; InterPro: IPR013512 1-deoxy-D-xylulose 5-phosphate reductoisomerase synthesizes 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate in a single step by intramolecular rearrangement and reduction and is responsible for terpenoid biosynthesis in some organisms . In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the non-mevalonate pathway for isoprenoid biosynthesis.; PDB: 2jcy_A 2jd0_B 2jd1_B 2jcv_A 2c82_B 2jcz_B 2jd2_A 2jcx_B 1r0l_B 1r0k_A ....
Probab=44.16 E-value=7.9 Score=16.29 Aligned_cols=52 Identities=21% Similarity=0.356 Sum_probs=32.1
Q ss_pred EEEEECC-HHHHHHHHHHHHCC-CCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEE
Q ss_conf 7998337-68999999997189-944899860785364850288125078899999985499899996
Q T0622 4 VLIYGAG-SAGLQLANMLRQGK-EFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLA 69 (138)
Q Consensus 4 vlIvGag-~~a~~l~~~l~~~~-~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia 69 (138)
+.|+|++ .-|.+-.+-+++.+ .|+++|+--. +.+ +.+.+.+++++...+.++
T Consensus 1 I~ILGsTGSIG~qtLdVi~~~~d~f~v~~Lsa~------~n~--------~~L~~q~~~f~p~~v~v~ 54 (129)
T PF02670_consen 1 IAILGSTGSIGTQTLDVIRRHPDRFEVVALSAG------SNI--------ELLAEQAREFKPKYVVVA 54 (129)
T ss_dssp EEEE--------HHHHHHHHTTTTEEEEEEEES------S-H--------HHHHHHHHHCT-SEEEES
T ss_pred CEEECCCCHHHHHHHHHHHHCCCCEEEEEEECC------CCH--------HHHHHHHHHHCCCEEEEE
T ss_conf 989745854889999999969874599999858------889--------999999999699989990
No 52
>PF09445 Methyltransf_15: RNA cap guanine-N2 methyltransferase; PDB: 3gdh_B 3egi_C.
Probab=40.43 E-value=4.7 Score=17.72 Aligned_cols=88 Identities=23% Similarity=0.345 Sum_probs=50.6
Q ss_pred EECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCH--------HHHHHHHHHCC----CCEEEEECCCCC
Q ss_conf 833768999999997189944899860785364850288125078--------89999998549----989999658999
Q T0622 7 YGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRP--------KYLERLIKKHC----ISTVLLAVPSAS 74 (138)
Q Consensus 7 vGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~--------~dl~~~i~~~~----i~~iiia~~~~~ 74 (138)
.|+|-.+.++|+. +.-|-.+|-||.+.-..-++..+||. .|..++.++.. .|.|+++.|.-.
T Consensus 8 cG~GGN~I~FA~~------~~~ViaiDidp~~l~~a~~Na~vYGV~~~I~~i~gD~~~~~~~~~~~~~~D~vf~sPPWGG 81 (163)
T PF09445_consen 8 CGVGGNTIQFAKT------FDRVIAIDIDPERLECAKHNAEVYGVADNIDFICGDFFELLKKLKFEKIFDVVFLSPPWGG 81 (163)
T ss_dssp ------HHHHHH---------EEEEE-S-HHHHHHHHHHHHH---GGGEEEEE--HHHHGGGB------SEEEE------
T ss_pred CCCCHHHHHHHHH------CCEEEEEECCHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHCCCCCCEEEEEECCCCCC
T ss_conf 7666749999974------9979999899999999998678608887579997959999874155554279998999999
Q ss_pred HH----------------HHHHHHHHHHHCCCE-EEECCCHHH
Q ss_conf 89----------------999999999857982-998068366
Q T0622 75 QV----------------QKKVIIESLAKLHVE-VLTIPNLDD 100 (138)
Q Consensus 75 ~~----------------~~~~i~~~~~~~~v~-v~~iP~~~~ 100 (138)
+. .+.+++..+....-+ +..+|+-.+
T Consensus 82 p~Y~~~~~fdL~~~~~p~~~~~l~~~~~~~t~ni~lfLPRn~d 124 (163)
T PF09445_consen 82 PSYSKQDVFDLENSMQPYNLEKLLKLASKITPNIVLFLPRNSD 124 (163)
T ss_dssp -GGGGSSSB-TTTSSS-----HHHHHHHHH-S-EEEEEETTB-
T ss_pred CCCCCCCCCCHHHHCCCCCHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf 6655322027866049964999999998636858999489899
No 53
>PF00290 Trp_syntA: Tryptophan synthase alpha chain; InterPro: IPR002028 Tryptophan synthase (4.2.1.20 from EC) catalyzes the last step in the biosynthesis of tryptophan , : L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H_2O It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the 2 subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 from INTERPRO is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) , . The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism. ; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process; PDB: 1tjr_B 1rd5_B 1ujp_A 1wxj_A 2ekc_B 1geq_A 2dzw_A 1wdw_G 2dzs_B 2e09_B ....
Probab=34.00 E-value=11 Score=15.30 Aligned_cols=39 Identities=18% Similarity=0.264 Sum_probs=22.5
Q ss_pred EECCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHH
Q ss_conf 250788999999854998999965899989999999999
Q T0622 47 TIYRPKYLERLIKKHCISTVLLAVPSASQVQKKVIIESL 85 (138)
Q Consensus 47 ~v~~~~dl~~~i~~~~i~~iiia~~~~~~~~~~~i~~~~ 85 (138)
|.-..+++.+.+++++++-|.+..|.++.+++..+...+
T Consensus 124 P~EE~~~~~~~~~~~gl~~I~lvaPtT~~~Ri~~i~~~a 162 (259)
T PF00290_consen 124 PPEEAEELREACRKHGLDLIFLVAPTTPDERIKKIAKHA 162 (259)
T ss_dssp BGGGHHHHHHHHHHTT-EEBEEE-TTS-HHHHHHHHHH-
T ss_pred CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHC
T ss_conf 988899999999986996899979999999999999768
No 54
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain has an alpha/beta fold that is a common motif found in several different cobalamin-binding proteins. Proteins containing this domain include: methionine synthase; the small subunit of glutamate mutase ; the alpha and beta subunits of methylmalonyl-CoA mutase; and mono- and tri-methylamine corrinoid proteins (MMCP and TCP, respectively) . In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) . The core structure of the cobalamin domain consists of 5 parallel beta-sheets, surrounded by 4-5 alpha helices in three layers, alpha/beta/alpha . The fold of the domain resembles that of the nucleotide-binding proteins (a Rossman fold). Upon binding B12, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. ; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1be1_A 1id8_A 1fmf_A 1ccw_C 1i9c_A 1cb7_A 1b1a_A 2i2x_B 1y80_A 3bul_A ....
Probab=33.82 E-value=12 Score=15.28 Aligned_cols=68 Identities=13% Similarity=0.130 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEEC-CCCCHHHHHHHHHHHHHCCC
Q ss_conf 89999999971899448998607853648502881250788999999854998999965-89998999999999985798
Q T0622 12 AGLQLANMLRQGKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLAV-PSASQVQKKVIIESLAKLHV 90 (138)
Q Consensus 12 ~a~~l~~~l~~~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia~-~~~~~~~~~~i~~~~~~~~v 90 (138)
.|...+.+..+..+|.+. ++|.+... +++.+.+++.+.+.+.++. .........++++.+++..-
T Consensus 15 lgl~~la~~l~~~G~~v~-~l~~~~~~-------------~~~~~~~~~~~pd~v~iS~~~~~~~~~~~~l~~~~k~~~p 80 (121)
T PF02310_consen 15 LGLLYLAAYLREAGFEVD-ILDANASM-------------EDLVAAIRAERPDVVGISVTYTPQIEDAKRLAREIKRRNP 80 (121)
T ss_dssp ---HHHHHHHHHGT-EEE-EE-CCE-H-------------HHHHHHHHHHTESEEEEEESSCTCCCHHHHHHHHHHC-GT
T ss_pred HHHHHHHHHHHHCCCEEE-EECCCCCH-------------HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf 999999999987899699-97998998-------------9999999975998999984786849999999999981696
Q ss_pred EEE
Q ss_conf 299
Q T0622 91 EVL 93 (138)
Q Consensus 91 ~v~ 93 (138)
+++
T Consensus 81 ~~~ 83 (121)
T PF02310_consen 81 DIK 83 (121)
T ss_dssp TSE
T ss_pred CCE
T ss_conf 987
No 55
>PF05049 IIGP: Interferon-inducible GTPase (IIGP); InterPro: IPR007743 Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defense. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing .; PDB: 1tpz_A 1tq6_A 1tq2_A 1tqd_A 1tq4_A.
Probab=31.72 E-value=12 Score=15.06 Aligned_cols=95 Identities=8% Similarity=0.112 Sum_probs=58.7
Q ss_pred CEEEEECCHHH-HHHHHHHHH----CCCCEEEEEECCCH--------HHCCCCCCCEEECCH-----HHHHHHHHHCCCC
Q ss_conf 17998337689-999999971----89944899860785--------364850288125078-----8999999854998
Q T0622 3 KVLIYGAGSAG-LQLANMLRQ----GKEFHPIAFIDDDR--------KKHKTTMQGITIYRP-----KYLERLIKKHCIS 64 (138)
Q Consensus 3 rvlIvGag~~a-~~l~~~l~~----~~~y~ivGfiDd~~--------~~~g~~i~g~~v~~~-----~dl~~~i~~~~i~ 64 (138)
++.|+|...+| -.++++++- +++--.+|.+.... ....-.+-.+|=.|+ ++..+.+.-+..|
T Consensus 37 ~iav~G~sGsGKSSfINalRgl~~ed~~aA~tGv~etT~~~~~Y~~p~~pnv~lwDlPG~Gt~~f~~~~Yl~~~~~~~yD 116 (376)
T PF05049_consen 37 NIAVTGESGSGKSSFINALRGLGHEDPGAAPTGVVETTMEPTRYPHPKFPNVVLWDLPGIGTANFPPEDYLEEVKFYEYD 116 (376)
T ss_dssp EEEEE-------HHHHHHH---------------HSCCTS-EEEE-SS-TTEEEEE-------S--HHHHHHHTTGGG-S
T ss_pred EEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCCCCCCCHHHHHHHCCCCCCC
T ss_conf 89996589986569999975658777777888870568985112789988887985899987888868999980743288
Q ss_pred EEEEECCCCCHHHHHHHHHHHHHCCCEEEECCC
Q ss_conf 999965899989999999999857982998068
Q T0622 65 TVLLAVPSASQVQKKVIIESLAKLHVEVLTIPN 97 (138)
Q Consensus 65 ~iiia~~~~~~~~~~~i~~~~~~~~v~v~~iP~ 97 (138)
..++-.+.-..+.--.+...|...+.+++++=.
T Consensus 117 ~fIiiss~rf~~ndv~lak~~~~~~k~~yfVRS 149 (376)
T PF05049_consen 117 FFIIISSDRFTENDVALAKEIQRMGKKFYFVRS 149 (376)
T ss_dssp EEEEEESSS--HHHHHHHHHHHHTT-EEEEEE-
T ss_pred EEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 899985896423069999999984997799841
No 56
>PF08915 tRNA-Thr_ED: Archaea-specific editing domain of threonyl-tRNA synthetase; InterPro: IPR015011 Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet . ; PDB: 1y2q_A 2hl1_A 2hkz_A 2hl2_A 2hl0_A.
Probab=24.72 E-value=14 Score=14.70 Aligned_cols=71 Identities=21% Similarity=0.185 Sum_probs=42.0
Q ss_pred EEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHHCCCCEEEEE----------CCCCCHHHHHHHHHHHHHCCCEEEECC
Q ss_conf 4899860785364850288125078899999985499899996----------589998999999999985798299806
Q T0622 27 HPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKKHCISTVLLA----------VPSASQVQKKVIIESLAKLHVEVLTIP 96 (138)
Q Consensus 27 ~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~~~i~~iiia----------~~~~~~~~~~~i~~~~~~~~v~v~~iP 96 (138)
-+|.|+.-...... ...++.--..+++..++.+.+++.|++= .|..+.+.++++.+.+...|.+|+..|
T Consensus 36 ~LvvF~~VE~~D~~-~p~~vv~~av~eI~~~a~kv~~~~vvlYPYAHLSs~La~P~~A~~vL~~le~~L~~~g~eV~rAP 114 (137)
T PF08915_consen 36 ALVVFIAVEKGDEE-NPEGVVEKAVEEIKWVAKKVKAKRVVLYPYAHLSSDLASPDVAQEVLKELEERLKSEGYEVKRAP 114 (137)
T ss_dssp EEEEEEE-BGGGGG--HHHHHHHHHHHHHHHHHHTT-SEEEEEE-GCC-SSB--HHHHHHHHHHHH---TT---B-----
T ss_pred EEEEEEEECCCCCC-CHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf 48999986468878-88899999999999999862987899946200157668948999999999999964895499816
Q ss_pred CH
Q ss_conf 83
Q T0622 97 NL 98 (138)
Q Consensus 97 ~~ 98 (138)
-.
T Consensus 115 FG 116 (137)
T PF08915_consen 115 FG 116 (137)
T ss_dssp --
T ss_pred CC
T ss_conf 62
No 57
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyzes the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyzes N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand . ; PDB: 1pii_A 1jcm_P 1jul_A 2c3z_A 1lbf_A 1a53_A 1igs_A 1juk_A 1lbl_A 1vc4_B ....
Probab=22.32 E-value=18 Score=14.01 Aligned_cols=58 Identities=22% Similarity=0.212 Sum_probs=42.7
Q ss_pred CEEECCHH---HHH--HHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEE-CCCHHHHH
Q ss_conf 81250788---999--999854998999965899989999999999857982998-06836642
Q T0622 45 GITIYRPK---YLE--RLIKKHCISTVLLAVPSASQVQKKVIIESLAKLHVEVLT-IPNLDDLV 102 (138)
Q Consensus 45 g~~v~~~~---dl~--~~i~~~~i~~iiia~~~~~~~~~~~i~~~~~~~~v~v~~-iP~~~~~~ 102 (138)
.+|++-.+ +-. ...+..+.|.|++-....+.+.+.++++.|..+|..+.+ +.+..|+-
T Consensus 110 ~~PvLrKDFIid~~QI~eA~~~GADavLLI~~~L~~~~l~~l~~~a~~lGle~LVEVh~~~El~ 173 (255)
T PF00218_consen 110 SLPVLRKDFIIDPYQIYEARAAGADAVLLIAAILSDEQLKELLELAHSLGLEALVEVHNEEELE 173 (255)
T ss_dssp SS-EEEES---SHHHHHHHHHTT-SEEEEECCCS-HHHHHHHHHHHHTTT-EEEEE-SSHHHHH
T ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCEEEEEHHHCCHHHHHHHHHHHHHCCCCEEEEECCHHHHH
T ss_conf 7876241220869999999985999886048648999999999999984992699859999999
No 58
>PF00670 AdoHcyase_NAD: S-adenosyl-L-homocysteine hydrolase, NAD binding domain; InterPro: IPR015878 S-adenosyl-L-homocysteine hydrolase (3.3.1.1 from EC) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. AdoHcyase is an ubiquitous enzyme which binds and requires NAD^+ as a cofactor. AdoHcyase is a highly conserved protein of about 430 to 470 amino acids. This entry represents the glycine-rich region in the central part of AdoHcyase, which is thought to be involved in NAD-binding.; PDB: 3gvp_D 1v8b_D 3ce6_A 2zj0_D 2zj1_C 2ziz_A 3dhy_B 1ky5_A 2h5l_A 1xwf_C ....
Probab=22.06 E-value=17 Score=14.23 Aligned_cols=51 Identities=22% Similarity=0.269 Sum_probs=36.2
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHCC-CCCCCEEECCHHHH
Q ss_conf 517998337689999999971899448998607853648-50288125078899
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKHK-TTMQGITIYRPKYL 54 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~g-~~i~g~~v~~~~dl 54 (138)
|+++++|.|.-|+-+|..++.-. --|=+.+-||-+.- ....|..|..+++.
T Consensus 24 k~vvV~GYG~~GkGvA~~lrg~G--a~V~VtEvDPi~aleA~mdGf~V~~~~ea 75 (162)
T PF00670_consen 24 KNVVVIGYGWCGKGVAQRLRGLG--ARVIVTEVDPIRALEAAMDGFEVMPMEEA 75 (162)
T ss_dssp -EEEEE---------HHHHHH-----EEEEE-SSHHHHHHHHH---EEE-HHHH
T ss_pred CEEEEECCCCCCHHHHHHHHHCC--CEEEEEECCHHHHHHHHHCCCCCCCHHHH
T ss_conf 78999778733599999997393--98999979989999867178744659998
No 59
>PF01262 AlaDh_PNT_C: Alanine dehydrogenase/PNT, C-terminal domain; InterPro: IPR007698 Alanine dehydrogenases () and pyridine nucleotide transhydrogenase () have been shown to share regions of similarity . Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. Pyridine nucleotide transhydrogenase catalyzes the reduction of NADP^+ to NADPH with the concomitant oxidation of NADH to NAD^+. This enzyme is located in the plasma membrane of prokaryotes and in the inner membrane of the mitochondria of eukaryotes. The transhydrogenation between NADH and NADP is coupled with the translocation of a proton across the membrane. In prokaryotes the enzyme is composed of two different subunits, an alpha chain (gene pntA) and a beta chain (gene pntB), while in eukaryotes it is a single chain protein. The sequence of alanine dehydrogenase from several bacterial species are related with those of the alpha subunit of bacterial pyridine nucleotide transhydrogenase and of the N-terminal half of the eukaryotic enzyme. The two most conserved regions correspond respectively to the N-terminal extremity of these proteins and to a central glycine-rich region which is part of the NAD(H)-binding site. This is a C-terminal domain of alanine dehydrogenases (1.4.1.1 from EC). This domain is also found in the lysine 2-oxoglutarate reductases. ; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2vhx_F 2vhz_B 2voe_F 2vhw_B 2vhy_B 2voj_A 2vhv_B 1pjb_A 1say_A 1pjc_A ....
Probab=21.33 E-value=19 Score=13.88 Aligned_cols=64 Identities=19% Similarity=0.217 Sum_probs=38.1
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHC--CCCCCC--EEE---------------------CCHHHHHH
Q ss_conf 51799833768999999997189944899860785364--850288--125---------------------07889999
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFIDDDRKKH--KTTMQG--ITI---------------------YRPKYLER 56 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiDd~~~~~--g~~i~g--~~v---------------------~~~~dl~~ 56 (138)
.+++|+|+|..|..-++.+..- +.+++.+ |.++... .....+ +.+ -..+.+.+
T Consensus 21 akvvViGaG~vG~~A~~~a~~L-Ga~v~~~-D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (168)
T PF01262_consen 21 AKVVVIGAGVVGLGAAETAKGL-GAEVVVP-DVRPERLEQVESLGAKFVDTDYEEDEEREDYAKEEFYEFPESYESNFAE 98 (168)
T ss_dssp -EEEEE-------HHHHHHHH----EEEEE-ESSHHHHHHHHHHTTEECEETTTTTTTSB--CHHHSHHHEEHHHHHHHH
T ss_pred EEEEEECCCHHHHHHHHHHHHC-CCEEEEE-CCCHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 6999979878999999999877-9979970-3798999764234685578563013444453333236676236997987
Q ss_pred HHHHCCCCEEEEE
Q ss_conf 9985499899996
Q T0622 57 LIKKHCISTVLLA 69 (138)
Q Consensus 57 ~i~~~~i~~iiia 69 (138)
.++. .|.+|.+
T Consensus 99 ~i~~--~DivI~~ 109 (168)
T PF01262_consen 99 FIAE--ADIVIGA 109 (168)
T ss_dssp HHHH---SEEEEH
T ss_pred HHCC--CCEEEEE
T ss_conf 7635--9899995
No 60
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation . This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light . The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain . Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore , . Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm . This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 1u3d_A 1u3c_A 1dnp_B 2e0i_D 1qnf_A 1tez_A 1owp_A 1own_A 1owm_A 1owl_A ....
Probab=20.78 E-value=20 Score=13.81 Aligned_cols=47 Identities=17% Similarity=0.185 Sum_probs=36.8
Q ss_pred HHHHHHHHHCCCCEEEEECCCCCHH--HHHHHHHHHHHCCCEEEECCCH
Q ss_conf 8999999854998999965899989--9999999998579829980683
Q T0622 52 KYLERLIKKHCISTVLLAVPSASQV--QKKVIIESLAKLHVEVLTIPNL 98 (138)
Q Consensus 52 ~dl~~~i~~~~i~~iiia~~~~~~~--~~~~i~~~~~~~~v~v~~iP~~ 98 (138)
+-+.+++++++++.|+........+ .-.++.+.|.+.|+.+....+-
T Consensus 78 ~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~~ 126 (166)
T PF00875_consen 78 DVLPELAKEYGITAVYFNREYEPYERQRDQAVRKRLKKQGIKVHQFDDH 126 (166)
T ss_dssp HHHHHHHHHCTESEEEEE---SHHHHHHHHHHHHHHHH-TSEEEEE--S
T ss_pred HHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf 9999999995999899955779899999999999988769779998881
No 61
>PF00208 ELFV_dehydrog: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; InterPro: IPR006096 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: 2bma_F 1b3b_B 1b26_C 2tmg_B 1bvu_F 1gtm_A 1euz_A 1nr1_E 1l1f_A 1nqt_C ....
Probab=20.62 E-value=20 Score=13.79 Aligned_cols=31 Identities=32% Similarity=0.351 Sum_probs=26.8
Q ss_pred CCEEEEECCHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf 51799833768999999997189944899860
Q T0622 2 KKVLIYGAGSAGLQLANMLRQGKEFHPIAFID 33 (138)
Q Consensus 2 krvlIvGag~~a~~l~~~l~~~~~y~ivGfiD 33 (138)
++++|-|.|..|..+++.+.+. +.+++++-|
T Consensus 33 ~~vaiqG~GnVG~~~a~~l~~~-Gakvv~vsD 63 (244)
T PF00208_consen 33 KRVAIQGFGNVGSNAARKLAEL-GAKVVAVSD 63 (244)
T ss_dssp -EEEEE----HHHHHHHHHHHC-T-EEEEE--
T ss_pred CEEEEECCCHHHHHHHHHHHHC-CCEEEEEEC
T ss_conf 8899989778999999999987-998999985
No 62
>PF09822 ABC_transp_aux: ABC-type uncharacterized transport system
Probab=20.01 E-value=21 Score=13.71 Aligned_cols=117 Identities=13% Similarity=0.142 Sum_probs=62.6
Q ss_pred HHHHHHHHH--CCCCEEEEEECCCHHHCCCCCCCEEECCHHHHHHHHHH---------------CCCCEEEEECCCC--C
Q ss_conf 999999971--89944899860785364850288125078899999985---------------4998999965899--9
Q T0622 14 LQLANMLRQ--GKEFHPIAFIDDDRKKHKTTMQGITIYRPKYLERLIKK---------------HCISTVLLAVPSA--S 74 (138)
Q Consensus 14 ~~l~~~l~~--~~~y~ivGfiDd~~~~~g~~i~g~~v~~~~dl~~~i~~---------------~~i~~iiia~~~~--~ 74 (138)
..+.+++.+ ++.-..+||+...+........+..--+...+.+.+++ .+++.++|+.|.. +
T Consensus 132 ~~lt~aI~~v~~~~~~~i~~l~ghge~~~~~~~~~~~~~~~~~~~~L~~~y~V~~l~l~~~~IP~d~d~Lvi~~P~~~ls 211 (271)
T PF09822_consen 132 YELTSAIKKVTRPEKPKIYFLTGHGERGMGSFDNDGGTSLSTLVNALEQNYEVEELNLSDEEIPEDADVLVIAGPQKDLS 211 (271)
T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCCCCEEEEECCCCCCC
T ss_conf 99999999974124756999778864333211246765699999999760268853676123566788999969998899
Q ss_pred HHHHHHHHHHHHHCCCEEEECCCHHHHH-CCCCCHHHCCCCCHHHCCCCCCCCCCHHH
Q ss_conf 8999999999985798299806836642-68745212355773203779876758688
Q T0622 75 QVQKKVIIESLAKLHVEVLTIPNLDDLV-NGKLSIGQLKEVSIDDLLGRVAVTPQAEL 131 (138)
Q Consensus 75 ~~~~~~i~~~~~~~~v~v~~iP~~~~~~-~~~~~~~~lr~i~ieDLL~R~~v~ld~~~ 131 (138)
..++..+-+.+.. |=++.++-+..... .+.......+.-.+++||..-=+.++...
T Consensus 212 ~~e~~~ld~yl~~-GG~~l~~~dp~~~~~~~~~~~~~~~~~~L~~lL~~~Gi~~~~~~ 268 (271)
T PF09822_consen 212 EEELYALDQYLMN-GGKLLILLDPFSVDPQGSPAGMGQPDSNLNDLLEHYGIRLNPDL 268 (271)
T ss_pred HHHHHHHHHHHHC-CCEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHCCEECCCE
T ss_conf 9999999999986-99799997775445443444445432488999998297758688
Done!