Query T0604 3NLC, Vibrio parahaemolyticus, 549 residues
Match_columns 549
No_of_seqs 329 out of 2758
Neff 7.3
Searched_HMMs 11830
Date Mon Jul 5 09:36:49 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0604.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0604.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03486 HI0933_like: HI0933-l 100.0 0 0 332.5 12.9 380 109-536 2-408 (409)
2 PF01134 GIDA: Glucose inhibit 100.0 5.2E-39 4.4E-43 259.7 9.0 343 109-539 1-389 (392)
3 PF00890 FAD_binding_2: FAD bi 99.8 7.3E-18 6.2E-22 127.0 14.3 168 109-279 1-206 (421)
4 PF01266 DAO: FAD dependent ox 99.7 4.9E-17 4.1E-21 121.9 11.2 177 109-289 1-212 (358)
5 PF01946 Thi4: Thi4 family; I 99.6 1.4E-15 1.2E-19 112.7 8.8 140 105-278 15-166 (230)
6 PF01494 FAD_binding_3: FAD bi 99.5 2.1E-14 1.8E-18 105.3 10.9 158 109-275 3-170 (356)
7 PF00743 FMO-like: Flavin-bind 99.4 6.1E-13 5.1E-17 96.2 9.4 139 107-276 1-149 (531)
8 PF05834 Lycopene_cycl: Lycope 99.3 8.7E-12 7.3E-16 88.9 9.0 141 109-279 1-144 (374)
9 PF04820 Trp_halogenase: Trypt 99.2 2.8E-11 2.3E-15 85.8 9.3 167 109-276 1-210 (454)
10 PF07992 Pyr_redox_2: Pyridine 99.2 3.6E-11 3.1E-15 85.0 7.4 106 109-275 1-107 (201)
11 PF01593 Amino_oxidase: Flavin 99.1 4.7E-10 4E-14 78.0 11.8 50 224-274 213-262 (449)
12 PF00732 GMC_oxred_N: GMC oxid 98.9 3.6E-10 3E-14 78.8 4.9 36 109-144 2-38 (298)
13 PF00070 Pyr_redox: Pyridine n 98.6 9.1E-08 7.7E-12 63.7 9.5 80 109-261 1-81 (81)
14 PF06039 Mqo: Malate:quinone o 98.6 4E-06 3.4E-10 53.4 16.5 187 108-299 4-265 (488)
15 PF06100 Strep_67kDa_ant: Stre 98.2 1.7E-05 1.4E-09 49.5 11.4 59 216-274 203-271 (500)
16 PF00743 FMO-like: Flavin-bind 97.6 8E-05 6.8E-09 45.2 6.4 37 105-141 181-217 (531)
17 PF00996 GDI: GDP dissociation 97.2 0.0017 1.4E-07 36.9 10.0 53 221-274 233-286 (438)
18 PF03721 UDPG_MGDP_dh_N: UDP-g 95.9 0.0019 1.6E-07 36.6 2.8 33 108-140 1-33 (185)
19 PF01262 AlaDh_PNT_C: Alanine 95.8 0.003 2.5E-07 35.4 3.6 39 105-143 18-56 (168)
20 PF02558 ApbA: Ketopantoate re 95.4 0.0048 4.1E-07 34.1 3.5 32 110-141 1-32 (151)
21 PF01210 NAD_Gly3P_dh_N: NAD-d 95.4 0.0037 3.1E-07 34.8 2.7 34 108-141 1-34 (159)
22 PF02737 3HCDH_N: 3-hydroxyacy 94.9 0.0077 6.5E-07 32.8 3.1 33 109-141 1-33 (180)
23 PF01488 Shikimate_DH: Shikima 94.4 0.021 1.8E-06 30.0 4.4 35 106-140 11-46 (135)
24 PF00670 AdoHcyase_NAD: S-aden 91.2 0.052 4.4E-06 27.6 2.6 34 107-140 23-56 (162)
25 PF00899 ThiF: ThiF family; I 90.6 0.12 9.8E-06 25.4 4.0 33 107-139 2-35 (135)
26 PF00056 Ldh_1_N: lactate/mala 88.8 0.22 1.9E-05 23.7 4.3 32 109-140 2-36 (142)
27 PF00208 ELFV_dehydrog: Glutam 87.9 0.26 2.2E-05 23.2 4.1 31 106-136 31-61 (244)
28 PF03446 NAD_binding_2: NAD bi 87.1 0.16 1.4E-05 24.5 2.7 35 108-142 2-36 (163)
29 PF03435 Saccharop_dh: Sacchar 86.5 0.57 4.8E-05 21.1 5.2 33 110-142 1-35 (386)
30 PF00289 CPSase_L_chain: Carba 86.5 0.23 1.9E-05 23.6 3.2 35 106-140 1-35 (110)
31 PF02254 TrkA_N: TrkA-N domain 85.8 0.4 3.4E-05 22.0 4.2 32 110-142 1-33 (116)
32 PF03949 Malic_M: Malic enzyme 84.9 0.22 1.8E-05 23.7 2.5 34 107-140 25-69 (255)
33 PF10727 Rossmann-like: Rossma 82.1 0.35 2.9E-05 22.4 2.5 35 104-138 7-41 (127)
34 PF02826 2-Hacid_dh_C: D-isome 81.8 0.8 6.8E-05 20.1 4.3 42 102-143 31-72 (178)
35 PF07991 IlvN: Acetohydroxy ac 80.1 0.6 5.1E-05 20.9 3.2 32 107-138 4-35 (165)
36 PF01564 Spermine_synth: Sperm 75.1 0.79 6.7E-05 20.2 2.7 39 104-142 74-112 (246)
37 PF04016 DUF364: Domain of unk 74.8 1.2 0.0001 19.0 3.6 36 104-143 109-145 (232)
38 PF05185 PRMT5: PRMT5 arginine 70.0 1.6 0.00014 18.2 3.3 36 107-142 187-226 (447)
39 PF05728 UPF0227: Uncharacteri 69.6 2.1 0.00018 17.5 4.0 28 109-136 60-87 (187)
40 PF00106 adh_short: short chai 67.7 1.6 0.00013 18.3 2.8 31 108-138 1-32 (167)
41 PF03853 YjeF_N: YjeF-related 63.7 2.7 0.00023 16.8 3.7 27 110-136 33-62 (173)
42 PF10100 DUF2338: Uncharacteri 60.8 3.1 0.00026 16.5 3.2 31 108-138 2-33 (429)
43 PF03807 F420_oxidored: NADP o 57.8 2.7 0.00022 16.9 2.5 32 109-140 1-36 (96)
44 PF09140 MipZ: ATPase MipZ; I 55.7 3.7 0.00032 15.9 3.1 30 109-138 1-37 (261)
45 PF07942 N2227: N2227-like pro 52.2 4.3 0.00036 15.6 4.0 12 396-407 180-191 (270)
46 PF05368 NmrA: NmrA-like famil 51.8 4.3 0.00037 15.6 4.0 31 110-140 1-32 (233)
47 PF01973 MAF_flag10: Protein o 43.2 2.9 0.00024 16.7 0.8 19 267-285 26-44 (170)
48 PF11814 DUF3335: Domain of un 42.0 6.1 0.00052 14.6 3.1 21 114-136 73-93 (227)
49 PF01408 GFO_IDH_MocA: Oxidore 38.3 7 0.00059 14.2 3.4 33 109-141 2-37 (120)
50 PF01034 Syndecan: Syndecan do 36.6 3 0.00025 16.6 0.0 10 507-516 301-310 (327)
51 PF00398 RrnaAD: Ribosomal RNA 35.5 7.8 0.00066 14.0 2.6 34 107-142 31-64 (262)
52 PF04321 RmlD_sub_bind: RmlD s 30.1 8.4 0.00071 13.7 1.4 31 109-139 2-33 (286)
53 PF05577 Peptidase_S28: Serine 29.3 9.8 0.00083 13.3 3.0 25 107-131 112-136 (433)
54 PF08886 GshA: Glutamate-cyste 27.9 10 0.00088 13.2 3.1 45 223-271 97-141 (404)
55 PF04445 DUF548: Protein of un 27.6 11 0.00089 13.1 1.6 21 267-288 77-97 (234)
56 PF00291 PALP: Pyridoxal-phosp 27.5 11 0.00089 13.1 3.8 32 107-138 55-86 (297)
57 PF02374 ArsA_ATPase: Anion-tr 27.0 11 0.00091 13.1 4.0 32 110-141 4-40 (305)
58 PF02882 THF_DHG_CYH_C: Tetrah 26.9 11 0.00091 13.1 3.5 33 107-139 36-69 (160)
59 PF03833 PolC_DP2: DNA polymer 26.5 11 0.00093 13.0 2.2 47 485-531 591-645 (900)
60 PF08659 KR: KR domain; Inter 26.4 11 0.00093 13.0 3.2 30 110-139 3-34 (181)
61 PF01784 NIF3: NIF3 (NGG1p int 25.3 12 0.00097 12.9 2.0 15 335-349 165-179 (241)
62 PF01370 Epimerase: NAD depend 23.3 13 0.0011 12.6 4.2 32 110-141 1-34 (238)
63 PF12381 Peptidase_C3G: Tungro 23.2 13 0.0011 12.6 1.7 36 492-529 183-221 (231)
64 PF06690 DUF1188: Protein of u 22.1 13 0.0011 12.5 2.4 28 109-137 44-71 (252)
65 PF07156 Prenylcys_lyase: Pren 22.0 13 0.0011 12.5 4.8 51 220-274 128-184 (368)
No 1
>PF03486 HI0933_like: HI0933-like protein; InterPro: IPR004792 This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases.; PDB: 2gqf_A 2i0z_A.
Probab=100.00 E-value=0 Score=332.49 Aligned_cols=380 Identities=21% Similarity=0.286 Sum_probs=255.1
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCC---CCCCCCHHHHHHHHH
Q ss_conf 66898798799999999996599089983588832110100012435423602345541355---652124045532200
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGG---AGTFSDGKLYSQVKD 185 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~gg---ag~fsdgkl~t~~~~ 185 (549)
+|+||||||||||||+.|++.|.+|+||||++.++.+... .+.++||.+|.......+... ++.|....+
T Consensus 2 dviIIGgGaAGl~AAi~aa~~G~~V~ilEk~~~~GkKil~-tG~GrCNiTN~~~~~~~~~~~~~~~~~f~~~~l------ 74 (409)
T PF03486_consen 2 DVIIIGGGAAGLMAAITAARNGLSVIILEKNPKLGKKILI-TGNGRCNITNLNVSPEEFFSEYPRNPKFLKSAL------ 74 (409)
T ss_dssp SEEEE-------CCCHHHHH----EEEE--------HHHH---------B-SSS-HHHCCHT----TTTTHHHH------
T ss_pred CEEEECCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC-CCCCCCCCCCCCCCHHHHHHHCCCCHHHHHHHH------
T ss_conf 3999997799999999997389948999688654555546-799877656677898999763356717689999------
Q ss_pred HCCCHHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEECCCCEEE
Q ss_conf 02117899999996689510013676410001279999999999996698899813433204058758999986784897
Q T0604 186 PNFYGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNGEEIK 265 (549)
Q Consensus 186 ~~~~~~~vl~~~~~~Ga~~~i~~~~kph~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~~g~~i~ 265 (549)
..+...++++||.+.|++..+...+++|+.|+++..|+++|++++.+.|++++++++|++|..+++++.+|.+.++.++.
T Consensus 75 ~~f~~~d~~~ff~~~Gi~~~~e~~gr~fP~s~ka~~Vi~~L~~~l~~~gV~i~~~~~v~~i~~~~~~~f~v~~~~~~~~~ 154 (409)
T PF03486_consen 75 KRFSPKDTIAFFEELGIPTKEEEDGRVFPVSDKASDVIDALLKELKRLGVEIHFGSKVTSIEKKDDGVFGVKTEDGKTIR 154 (409)
T ss_dssp HHS-HHHHHHHHHH----EEE-----EEETT--HHHHHHHHHHHHHH---EEE-S--EEEEEC-SS-EEEEEE-TTEEEE
T ss_pred HHCCHHHHHHHHHHCCCEEEECCCCEECCCCCCHHHHHHHHHHHHHHCCCEEECCCEEEEEEECCCCEEEEEECCCCEEE
T ss_conf 83899999999996698257666986379989999999999999998898997277777999759926999978996850
Q ss_pred ECEEEEECCC-------CHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHH--HHHHCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf 0568993188-------7679999999669711148745686430354554--087636544666677665247876588
Q T0604 266 SRHVVLAVGH-------SARDTFEMLHERGVYMEAKPFSVGFRIEHKQSMI--DEARFGPNAGHPILGAADYKLVHHCKN 336 (549)
Q Consensus 266 ad~VVlAtGh-------sard~~~~l~~~Gi~~~~k~~a~G~rie~~~~~i--d~~q~g~~~~~~~l~~a~ykl~~~~~~ 336 (549)
|+.||+|||+ |..++|.+++++|+++.+..++. +.+.....++ ..++ + ..+.... +.. +
T Consensus 155 a~~vIlAtGG~s~p~~Gs~g~gy~~a~~lGh~i~~~~PaL-~~l~~~~~~~~~~~l~-----G-~~~~~~~--~~~---~ 222 (409)
T PF03486_consen 155 ADKVILATGGKSYPKTGSDGSGYKLAKSLGHTIIPPYPAL-VPLKTKEPWLWFKKLS-----G-VSLKAVA--ILL---D 222 (409)
T ss_dssp ESEEEE------STT--------HHHHH--------EEES-------GHHHHCCCC---------EEEEEE--EEE----
T ss_pred CCEEEECCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEE-CCEEECCCHHHHHHCC-----C-CCEEEEE--EEE---C
T ss_conf 9949998898654556899358999997599635786710-8876055111233338-----9-8000047--872---4
Q ss_pred CCEEEEEEECCCCEEEEEECCCCEEEECCCCHHHCCCCCC------CCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 9632688616786688731578637878831111266666------7347985034567777631025776999999996
Q T0604 337 GRTVYSFCMCPGGTVVAATSEEGRVVTNGMSQYSRAERNA------NSAIVVGISPEVDYPGDPLAGIRFQRELESNAYK 410 (549)
Q Consensus 337 g~~v~tfcmcpgG~vv~~~s~~g~~~~nGmS~~~r~~~~a------n~al~v~i~~~~~~~~~~l~g~~~q~~lE~~a~~ 410 (549)
+....+. .|.++.+.++- +|....+ -|.++ +....+.+++-+..+.+. +...|.+.
T Consensus 223 ~~~~~~~----~GellfT~~Gi-----SGp~vl~-lS~~~~~~l~~~~~~~i~id~~P~~~~~~-----l~~~l~~~--- 284 (409)
T PF03486_consen 223 GKKKAEE----TGELLFTHYGI-----SGPAVLQ-LSRYAARALNKKKGVEISIDFLPDLSEEE-----LEELLQRR--- 284 (409)
T ss_dssp ---EEEE----EEEEE-----------E-EHHHH-HCCCHHHHHH--TTEEEEEES-TTS-HHH-----HHHHHHHH---
T ss_pred CCCCEEE----ECCEEEECCCC-----CHHHHHH-HHHHHHHHHHHCCCCEEEEECCCCCCHHH-----HHHHHHHH---
T ss_conf 7773568----50779987872-----5799999-99999999974899379998489999999-----99999999---
Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC-CCCEEECCHHHHCHHHHHHHHHHHHHHCCCCC---CCCCCCCEEEEE
Q ss_conf 27876541343588884455421013443000-57604526254031899999999988612220---552467837981
Q T0604 411 LGGENYDAPAQKIGDFLKGRDPSQLGDVEPSF-TPGIKLTDLSKALPPFAVEAIREAIPAFDRKI---KGFASEDGLLTG 486 (549)
Q Consensus 411 ~gg~~~~~p~Q~~~dfl~~~~s~~~~~~~~s~-~~~~~~~~L~~~lP~~v~~~l~~~l~~f~~~~---~Gf~~~ea~l~G 486 (549)
......+.+.+.+..++..|....+-. ...+ .+....++ +++.....|.+.|+.|...+ .||..++++.||
T Consensus 285 ~~~~~~~~~~~~l~~~lp~rl~~~ll~-~~~i~~~~~~~~~----l~~~~~~~L~~~lk~~~~~i~g~~~~~~A~VT~GG 359 (409)
T PF03486_consen 285 KETNPKKTLKNLLSGLLPKRLAQALLK-KAGIQDPDKKVAE----LSKKERNKLAETLKSFPLEITGTRGFKEAQVTAGG 359 (409)
T ss_dssp HCCSTTSBHCCCCTTTS-HHHHHHHHH-HTT------BGGG------HHHHHHHHHHHHHEEEEE-----GGC-SEEE--
T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCHHH----CCHHHHHHHHHHHHCCEEEECCCCCCCEEEEECCC
T ss_conf 886815469998777757999999999-8289774430212----18789999999984787670344787668997784
Q ss_pred EEECEECCEEECCCCCCCCCCCCCCEEECCC---CCHHHH--HHHHHHHHHHHHH
Q ss_conf 0011026624204887430268985420123---533578--9999999999999
Q T0604 487 VETRTSSPVCIKRGKDFQSVNLKGFYPAGEG---AGYAGG--ILSAGIDGIKVAE 536 (549)
Q Consensus 487 VEtr~ssPvri~r~~tleS~~i~GLY~~GEg---aGyagG--I~saa~~G~~~a~ 536 (549)
|++++++| +|||||.+||||||||- .|..|| +.+|+.+|..|+.
T Consensus 360 V~~~ei~~------~TmESk~~~gLyf~GEvLDvdg~~GGYNLq~AwssG~~Ag~ 408 (409)
T PF03486_consen 360 VDLKEINP------KTMESKLVPGLYFAGEVLDVDGPCGGYNLQWAWSSGYLAGK 408 (409)
T ss_dssp --GGGB-T------TT-BBSS----EE----SS-B------HHHHHHHHHHHHH-
T ss_pred CCHHHCCH------HHHHHCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf 24777098------78863258993571048870217776499999998798746
No 2
>PF01134 GIDA: Glucose inhibited division protein A; InterPro: IPR002218 Bacterial glucose inhibited division protein A (gene gidA) is a protein of 70 Kd whose function is not yet known and whose sequence is highly conserved. It is evolutionary related to yeast hypothetical protein YGL236C, Caenorhabditis elegans hypothetical protein F52H3.2 and a Bacillus subtilis protein called gid (and which is different from B. subtilis gidA).; GO: 0050660 FAD binding, 0008033 tRNA processing; PDB: 2cul_A 3g5q_A 3g5r_A 3g5s_A 2zxi_A 2zxh_A 3cp8_D 3ces_C 3cp2_A.
Probab=100.00 E-value=5.2e-39 Score=259.68 Aligned_cols=343 Identities=21% Similarity=0.267 Sum_probs=224.9
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEE-ECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHC
Q ss_conf 6689879879999999999659908998-358883211010001243542360234554135565212404553220002
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIV-ERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVKDPN 187 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~Vl-Erg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~~~~ 187 (549)
.|+|||||+||+.||+.+|+.|++|+|+ ++.+.. ....||+.++..+.|+. ...+....
T Consensus 1 DViVVGgG~AG~eAA~aaAr~G~~v~Li~~~~~~i---------------g~m~Cnpsigg~akG~L-----~rEidaLg 60 (392)
T PF01134_consen 1 DVIVVGGGHAGCEAALAAARMGAKVLLITHNTDTI---------------GEMSCNPSIGGIAKGHL-----VREIDALG 60 (392)
T ss_dssp CEEEE-------HHHHHHHH----EEEEES-GGGT---------------T--SSSSEE-------H-----HHHHHH--
T ss_pred CEEEECCCHHHHHHHHHHHHCCCCEEEEECCCCCC---------------CCCCCCCCCCCCCHHHH-----HHHHHHHC
T ss_conf 98999887599999999997899789996566764---------------55565521267645789-----99999730
Q ss_pred CCHHHHHHHHHHCCCCCCCCCCCCC------CEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEECCC
Q ss_conf 1178999999966895100136764------1000127999999999999669889981343320405875899998678
Q T0604 188 FYGRKVITEFVEAGAPEEILYVSKP------HIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNG 261 (549)
Q Consensus 188 ~~~~~vl~~~~~~Ga~~~i~~~~kp------h~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~~g 261 (549)
..+.+.-...+...+++...|- ....| ...+-..|++.+++...--.++.+|++|..++++++||.+.+|
T Consensus 61 ---G~m~~~aD~~~iq~r~lN~skGpAv~a~raqvD-r~~y~~~~~~~L~~~~nl~i~~~~V~~l~~~~~~v~gV~~~~G 136 (392)
T PF01134_consen 61 ---GLMGRAADKTGIQFRMLNRSKGPAVWALRAQVD-RELYSREMREMLENHPNLEIIQGEVTDLIVENGKVKGVVTEDG 136 (392)
T ss_dssp ----HHHHHHHHCEEEEEEESTT---TT-EEEEEE--HHHHHHHHHHHHHTSTTEEEEES-EEE-EBSSSBBEEEEE---
T ss_pred ---CHHHHHHHHHCEEEEECCCCCCCCCCCHHHHHH-HHHHHHHHHHHHHCCCCCEEEEEECCCEEECCCEEEEEECCCC
T ss_conf ---799998776320100004676885432386754-9999999999997599959998201012316982899992899
Q ss_pred CEEEECEEEEECCC---------------------CHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf 48970568993188---------------------767999999966971114874568643035455408763654466
Q T0604 262 EEIKSRHVVLAVGH---------------------SARDTFEMLHERGVYMEAKPFSVGFRIEHKQSMIDEARFGPNAGH 320 (549)
Q Consensus 262 ~~i~ad~VVlAtGh---------------------sard~~~~l~~~Gi~~~~k~~a~G~rie~~~~~id~~q~g~~~~~ 320 (549)
.++.++.||+|||. ++....+.|.++|..+ ..|.+|+.+......||.+..-...++
T Consensus 137 ~~i~a~~vIlaTGtfl~g~i~ig~~~~~~Gr~~~~~s~~Ls~~L~~~g~~~--~r~ktgtppri~~~SId~s~~~~q~~~ 214 (392)
T PF01134_consen 137 ETIEAKAVILATGTFLNGCIHIGLRCYSGGRRGELTSDGLSESLKELGFEL--GRFKTGTPPRIDKDSIDFSKLEEQSGD 214 (392)
T ss_dssp -BEEEEEEEE----TB-EEEE----EE----TTS--BCHHHHHHHHTT-TC--EEEEEE---EEEGGGS-GCCSEEE---
T ss_pred CEEECCEEEEECCCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCC--EEEECCCCCEECCCCCCHHHHHHCCCC
T ss_conf 886289899917877468379811024568865432368999998669730--554057673122687576776620479
Q ss_pred CCCCCCCCEEEEECCCCCEEEEEEECCCC------EEEEEECCCCEEEECCCCHHHCCCCCCCCEEEEEECCCC-CCCCC
Q ss_conf 66776652478765889632688616786------688731578637878831111266666734798503456-77776
Q T0604 321 PILGAADYKLVHHCKNGRTVYSFCMCPGG------TVVAATSEEGRVVTNGMSQYSRAERNANSAIVVGISPEV-DYPGD 393 (549)
Q Consensus 321 ~~l~~a~ykl~~~~~~g~~v~tfcmcpgG------~vv~~~s~~g~~~~nGmS~~~r~~~~an~al~v~i~~~~-~~~~~ 393 (549)
....+++| -.||-- ++.....++ +.. +.-..+.+. ++...
T Consensus 215 ~~~~~fs~---------------~~~~~~~~q~~~~~~~t~~~~----------~~~--------i~~~~~~s~~~~~g~ 261 (392)
T PF01134_consen 215 DPPEPFSY---------------LNCPMNKEQYPCFITYTNEAT----------HEI--------IRDNLHRSPHLFEGC 261 (392)
T ss_dssp -S-B-SSS---------------SCCCCCHHHHHEEEEEHHHHH----------HHH--------HHHCGGG-T-T-TT-
T ss_pred CCCCCCCC---------------CCCCCCHHHHHHHHHHHHHHH----------HHH--------HHHHHHCCHHHHCCH
T ss_conf 99999887---------------999897889999999987987----------999--------874011185664330
Q ss_pred -CCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC-CCCEEECCHHHHCHHHHHHHHHHHHHHCC
Q ss_conf -3102577699999999627876541343588884455421013443000-57604526254031899999999988612
Q T0604 394 -PLAGIRFQRELESNAYKLGGENYDAPAQKIGDFLKGRDPSQLGDVEPSF-TPGIKLTDLSKALPPFAVEAIREAIPAFD 471 (549)
Q Consensus 394 -~l~g~~~q~~lE~~a~~~gg~~~~~p~Q~~~dfl~~~~s~~~~~~~~s~-~~~~~~~~L~~~lP~~v~~~l~~~l~~f~ 471 (549)
.-.|.+||++||.|..++..+.++.. ||+. ..+ ...+++.+++++||..+|..+.++
T Consensus 262 ie~~gpRycpsie~K~v~f~~~~~h~v------~Lep----------E~~~~~~~y~~G~stslp~~~Q~~~~r~----- 320 (392)
T PF01134_consen 262 IEGIGPRYCPSIEDKPVRFPDKPRHQV------FLEP----------EGLDTNEYYPNGFSTSLPWDVQKRIFRS----- 320 (392)
T ss_dssp CHHHHHTT-CTTCHHHHCSTSSSSEEE------EEEE-----------S----EEEEE---SSS-HHHHHHHHTT-----
T ss_pred HHHHHCCCCCHHHCCCCCCCCCCCEEE------EEEC----------CCCCCCEEEECCCCCCCCHHHHHHHHHH-----
T ss_conf 231203465145338766799897699------9924----------8887865981462134898999999971-----
Q ss_pred CCCCCCCCCCEEE--EEEEECEECCEEECCCCCCCCCCCCCCEEECCC---CCH----HHHHHHHHHHHHHHHHHHH
Q ss_conf 2205524678379--810011026624204887430268985420123---533----5789999999999999999
Q T0604 472 RKIKGFASEDGLL--TGVETRTSSPVCIKRGKDFQSVNLKGFYPAGEG---AGY----AGGILSAGIDGIKVAEAVA 539 (549)
Q Consensus 472 ~~~~Gf~~~ea~l--~GVEtr~ssPvri~r~~tleS~~i~GLY~~GEg---aGy----agGI~saa~~G~~~a~~i~ 539 (549)
|||+.+++.+. |+||+++++|.++. .|||+|.++|||+||+. .|| |+|| ++|+|+|..+-
T Consensus 321 --IpGLEna~i~r~gy~~eyd~i~p~~L~--~tLe~k~~~~Lf~AGQInGt~GYeEAaaqGl----~AGiNaa~~~~ 389 (392)
T PF01134_consen 321 --IPGLENAEIVRPGYAHEYDYIDPPQLL--PTLETKKIPGLFFAGQINGTEGYEEAAAQGL----IAGINAARKLQ 389 (392)
T ss_dssp ------TT--EEE---EEEEEEE-GGGB---TTSBBSSCBTEEE----------HHHHH-----------HHHHHHT
T ss_pred --CHHHHCCCEECCCCEEEEEEECHHHCC--CCEEECCCCCEEECCCCCCCHHHHHHHHHHH----HHHHHHHHHHC
T ss_conf --431321820046614641048722504--6027479998598113678438999999899----99999999962
No 3
>PF00890 FAD_binding_2: FAD binding domain of the Pfam family.; InterPro: IPR003953 In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate (1.3.99.1 from EC): fumarate reductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh) is used in aerobic growth. Both complexes consist of two main components: a membrane-extrinsic component composed of a FAD-binding flavoprotein and an iron-sulphur protein; and an hydrophobic component composed of a membrane anchor protein and/or a cytochrome B. In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (1.3.5.1 from EC) is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphur protein. The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is covalently bound to a histidine residue which is located in the N-terminal section of the protein . The sequence around that histidine is well conserved in Frd and Sdh from various bacterial and eukaryotic species . This family includes members that bind FAD such as the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. ; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 1zp0_A 1zoy_A 1nek_A 1nen_A 2acz_A 1chu_A 1knr_A 1knp_A 2e5v_B 1y0p_A ....
Probab=99.77 E-value=7.3e-18 Score=127.02 Aligned_cols=168 Identities=27% Similarity=0.360 Sum_probs=110.0
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCC-CCCCC--------CCC-HHHHHHHHCCCCCCCCCHH
Q ss_conf 6689879879999999999659908998358883211010001-24354--------236-0234554135565212404
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFG-FWRKR--------TLN-PESNVQFGEGGAGTFSDGK 178 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~-~~~~~--------~~~-~~~n~~~g~ggag~fsdgk 178 (549)
.|||||+|.|||.||+.+++.|.+|+|+|++...++......+ ++..+ ..+ ++..........+...+..
T Consensus 1 DVlVVG~G~AGl~AA~~Aae~G~~Vilvek~~~~gg~~~~~~g~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~ 80 (421)
T PF00890_consen 1 DVLVVGGGLAGLAAALAAAEAGAKVILVEKGPELGGNSAFSGGGFDAAGTKPQKEAGIGDSPEEFFEDWMKASGGRADPD 80 (421)
T ss_dssp SEEEE-------HHHHHHHHCST-EEEEESSSGGGSGGGG---EEB-SSSHHHHHSTSTCHHHHHHHHHHHHTTT-S-HH
T ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCEECCCHHHHCCCCCCCHHHHHHHHHHHCCCCCCHH
T ss_conf 98999987999999999986699899998467567763235897321387666302335309999999986415667899
Q ss_pred HHHHHHHHCCCHHHHHHHHHHCCCCCCCC---------CCCC--C---C-E------ECCHHHHHHHHHHHHHHHCC-CE
Q ss_conf 55322000211789999999668951001---------3676--4---1-0------00127999999999999669-88
Q T0604 179 LYSQVKDPNFYGRKVITEFVEAGAPEEIL---------YVSK--P---H-I------GTFKLVTMIEKMRATIIELG-GE 236 (549)
Q Consensus 179 l~t~~~~~~~~~~~vl~~~~~~Ga~~~i~---------~~~k--p---h-~------gtd~~~~vv~~L~~~l~~~G-~~ 236 (549)
+.....+ ...+.++|+.++|.+.... .... + + . .......++..|.+.+++.| ++
T Consensus 81 l~~~~~~---~~~~~~~wl~~~g~~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~~~~~g~v~ 157 (421)
T PF00890_consen 81 LVRAFVE---NSGEAIDWLEDWGVPFSKTADGPFDPTEFGGHSPPRTPHSMGDPGDSPWGGGKGVVDALREAAEDAGNVD 157 (421)
T ss_dssp HHHHHHH---HHHHHHHHHHH----B-BGG---BSEEE----CSEEEEB-STTG-------HHHHHHHHHHHHHHTTTEE
T ss_pred HHHHHHH---HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf 9997532---2699999999858875423322223323577433236412454432234217899999999997489879
Q ss_pred EEEECCCCCCEECCCEEEEEEEC---CCC--EEEEC-EEEEECCCCHHH
Q ss_conf 99813433204058758999986---784--89705-689931887679
Q T0604 237 IRFSTRVDDLHMEDGQITGVTLS---NGE--EIKSR-HVVLAVGHSARD 279 (549)
Q Consensus 237 i~~~t~V~~i~~~~g~v~gV~t~---~g~--~i~ad-~VVlAtGhsard 279 (549)
|++++.+++|+.++++|+||+.. ++. ++.|+ .||||||.-+++
T Consensus 158 i~~~t~~~~Li~d~g~V~Gv~~~~~~~g~~~~i~A~k~VVlAtGGf~~N 206 (421)
T PF00890_consen 158 ILYNTRATDLITDDGRVTGVVAENPRDGRYVRIKAKKAVVLATGGFGGN 206 (421)
T ss_dssp EEESEEEEE--BCTTBB---EEEESTTTCEEEEEES-EEEE-----CC-
T ss_pred EEECCCHHHEEEECCEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCC
T ss_conf 9939892310986899999999976499589999755899757765645
No 4
>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=99.70 E-value=4.9e-17 Score=121.86 Aligned_cols=177 Identities=28% Similarity=0.389 Sum_probs=110.8
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCC---CCC-------HHHHHHH-----HCCCCCC
Q ss_conf 668987987999999999965990899835888321101000124354---236-------0234554-----1355652
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKR---TLN-------PESNVQF-----GEGGAGT 173 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~---~~~-------~~~n~~~-----g~ggag~ 173 (549)
.|+|||||++|+.+|+.|+++|++|+|||++...++.+....+++... ..+ ..+.... ..+....
T Consensus 1 Dv~IIGaGi~Gl~~A~~La~~G~~V~lle~~~~~~gaS~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~ 80 (358)
T PF01266_consen 1 DVIIIGAGIAGLSTAYELARRGYRVLLLERGDPGSGASGRNGGLLHPGLGAERDPRLLKLARESIDLWRELAEEYGIPVG 80 (358)
T ss_dssp EEEEE-------HHHHHHHHSS-EEEEEESSSTTSSCTTTSEEEE-CSSSSHSSCHHHHHHHHHHHHHHHHHHHTTTTCB
T ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEE
T ss_conf 99999966999999999997799699996542367765534212445543323332322203478999999886296411
Q ss_pred C-CCHHHHHHHHHH-CCCHHHHHHHHHHCCCCCCCC------------------CCCCCCEECCHHHHHHHHHHHHHHHC
Q ss_conf 1-240455322000-211789999999668951001------------------36764100012799999999999966
Q T0604 174 F-SDGKLYSQVKDP-NFYGRKVITEFVEAGAPEEIL------------------YVSKPHIGTFKLVTMIEKMRATIIEL 233 (549)
Q Consensus 174 f-sdgkl~t~~~~~-~~~~~~vl~~~~~~Ga~~~i~------------------~~~kph~gtd~~~~vv~~L~~~l~~~ 233 (549)
| -.+.+.....+. ....+...+....+|.+.+.+ ....+..++.....+++.|.+.+++.
T Consensus 81 ~~~~g~l~~~~~~~~~~~~~~~~~~~~~~g~~~~~l~~~~~~~~~p~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~ 160 (358)
T PF01266_consen 81 FRRTGVLYLASDEDDLESLRRLAARLRRAGLPIELLSADELRELFPALSPRVHGGLYYPDAGVIDPRRLAQALAREAEAL 160 (358)
T ss_dssp BEECCHEEEESSHHHHHHHHHHHHHHHCTTETEEEESHHHHHHHSTTS-TTTCEEEEETTEEEEEHHHHHHHHHHHHHH-
T ss_pred CCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 14454687527778755577664310002443112549999753886433311222215764110667788889999860
Q ss_pred CCEEEEECCCCCCEECCCEEEEEEECCCCEEEECEEEEECCCCHHHHHHHHHHCCC
Q ss_conf 98899813433204058758999986784897056899318876799999996697
Q T0604 234 GGEIRFSTRVDDLHMEDGQITGVTLSNGEEIKSRHVVLAVGHSARDTFEMLHERGV 289 (549)
Q Consensus 234 G~~i~~~t~V~~i~~~~g~v~gV~t~~g~~i~ad~VVlAtGhsard~~~~l~~~Gi 289 (549)
|++++++++|++|..+++++++|+|.+|+ +.++.||+|+|..+.. ++...|.
T Consensus 161 G~~~~~~~~V~~i~~~~~~~~~v~t~~g~-i~a~~vV~aaG~~~~~---l~~~~g~ 212 (358)
T PF01266_consen 161 GVEIRTGTEVTSIEREGGGVRGVRTSDGE-IRADKVVNAAGAWSRQ---LLKDLGL 212 (358)
T ss_dssp --EEEESEEEEEEEBCCTEBE-EEEEETE-EEEEEEEE--GGCHHH---HHHCTTT
T ss_pred CCEEEEEEEEEEEEECCCCCCCCCCCCCC-CCCCEEEEECCCCHHH---HHHCCCC
T ss_conf 44151113676652037764332233333-4332289926833455---4110344
No 5
>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=99.60 E-value=1.4e-15 Score=112.66 Aligned_cols=140 Identities=24% Similarity=0.275 Sum_probs=99.0
Q ss_pred CCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf 76776689879879999999999659908998358883211010001243542360234554135565212404553220
Q T0604 105 NLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVK 184 (549)
Q Consensus 105 ~~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~ 184 (549)
.....|+|||||||||.||+.|++.|++|+|||+...+|+..+ ..+.+ |+... +.
T Consensus 15 ~~~~DVvIVGaG~aGL~AA~~la~~g~kV~viE~~~~~GGg~~------~gG~~---------------f~~~v----v~ 69 (230)
T PF01946_consen 15 YAEVDVVIVGAGPAGLAAAYYLARAGLKVLVIERRSSPGGGAW------SGGML---------------FNKIV----VR 69 (230)
T ss_dssp CTEESEEEE-------HHHHHHHHHTS-EEEEESSS------------------------------------EE----EE
T ss_pred HCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCE------ECCCC---------------CCCHH----HH
T ss_conf 3558989999778899999999978995999967998874404------23532---------------55101----01
Q ss_pred HHCCCHHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECC-CEEEEEEECCC--
Q ss_conf 002117899999996689510013676410001279999999999996698899813433204058-75899998678--
Q T0604 185 DPNFYGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMED-GQITGVTLSNG-- 261 (549)
Q Consensus 185 ~~~~~~~~vl~~~~~~Ga~~~i~~~~kph~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~-g~v~gV~t~~g-- 261 (549)
. . ..+++.++|.+.+.... +...-........|...+.+.|+++...+.|+|+..++ +++.||+++..
T Consensus 70 ~---~---a~~~L~Elgv~y~~~~~---g~~v~d~~e~~s~L~s~a~~aGvki~n~t~VeDli~r~g~RV~GVV~nw~~v 140 (230)
T PF01946_consen 70 E---P---ADEFLDELGVRYEDEGD---GVYVADSVEFTSTLASKALKAGVKIFNATRVEDLITREGDRVAGVVTNWTPV 140 (230)
T ss_dssp T---T---THHHHHHTT---EE-SS---EEEES-HHHHHHHHHHHHHTTTEEEECTEEEEE--B-----B---EEEEHHH
T ss_pred H---H---HHHHHHHCCCCCEECCC---CEEEECHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCCCEEEEEEEEEEE
T ss_conf 0---1---99999983997164069---6598568999999999863789899995277565772478189999930140
Q ss_pred ---------CEEEECEEEEECCCCHH
Q ss_conf ---------48970568993188767
Q T0604 262 ---------EEIKSRHVVLAVGHSAR 278 (549)
Q Consensus 262 ---------~~i~ad~VVlAtGhsar 278 (549)
.++.++.||-||||.|-
T Consensus 141 ~~~g~hvDP~~I~ak~VIDaTGHda~ 166 (230)
T PF01946_consen 141 EMAGLHVDPLTIEAKVVIDATGHDAP 166 (230)
T ss_dssp HT---T---EE-EEEEEEE-------
T ss_pred HHHHCCCCCCEEEEEEEEECCCCCCH
T ss_conf 34425678101777799978789638
No 6
>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=99.55 E-value=2.1e-14 Score=105.28 Aligned_cols=158 Identities=23% Similarity=0.273 Sum_probs=87.1
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC-CCCC-HHHHHHHHHH
Q ss_conf 6689879879999999999659908998358883211010001243542360234554135565-2124-0455322000
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAG-TFSD-GKLYSQVKDP 186 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~ggag-~fsd-gkl~t~~~~~ 186 (549)
+|+|||||||||++|+.|+++|++|+||||.+......+. ..+.+.....+...|.. .+.. +.........
T Consensus 3 dViIvGgG~aGl~~A~~L~~~G~~v~viE~~~~~~~~~~~-------~~l~~~~~~~l~~~Gl~~~~~~~~~~~~~~~~~ 75 (356)
T PF01494_consen 3 DVIIVGGGPAGLALALALARAGIRVLVIERRPSPRPRGRG-------IGLSPNALRLLDQLGLLDEIEAEGSPSKIMRQF 75 (356)
T ss_dssp EEEEE-------HHHHHHHHCTCEEEEEESSSSHHHS-----------EEEHHHHHHHHHTT-HHHHHCTSCEEEEEEEE
T ss_pred EEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEE-------ECCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEE
T ss_conf 6999898999999999999769957897112475412111-------001333322112321188887543023320244
Q ss_pred CCCHHHHHHHH---HHCCCCCCCC-CCCCCCEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEE--CC
Q ss_conf 21178999999---9668951001-367641000127999999999999669889981343320405875899998--67
Q T0604 187 NFYGRKVITEF---VEAGAPEEIL-YVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTL--SN 260 (549)
Q Consensus 187 ~~~~~~vl~~~---~~~Ga~~~i~-~~~kph~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t--~~ 260 (549)
.... +.... .......+.. ....+.........+.+.|++.+++.|++++++++|+++..+++.+..+.. .+
T Consensus 76 ~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~l~~~L~~~~~~~~~~i~~~~~v~~~~~~~~~v~~~~~~~~~ 153 (356)
T PF01494_consen 76 FYGG--FSDIEIWGGDPFIREDLEIDTKGPYGLVIPRAELDRILRDHAESAGATIRFGHRVVSIEQDEDGVTVTVRDGED 153 (356)
T ss_dssp EEEE--HCTTEEEEEESEEEEECCHHCCSTEEEEE-HHHHHHHHHHHHHHSTEEEECSEEEEEEEECSSCEEEEEEEEET
T ss_pred ECCC--CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCEEEEEEEECC
T ss_conf 2244--32111111112100001346788716887789998876421243201455533511221111211689985059
Q ss_pred CC--EEEECEEEEECCC
Q ss_conf 84--8970568993188
Q T0604 261 GE--EIKSRHVVLAVGH 275 (549)
Q Consensus 261 g~--~i~ad~VVlAtGh 275 (549)
|+ +++||.||.|+|.
T Consensus 154 g~~~~i~adlvVgADG~ 170 (356)
T PF01494_consen 154 GEEETIRADLVVGADGA 170 (356)
T ss_dssp TEEEEEEEEEEEE----
T ss_pred CCEEEEEEEEEEECCCC
T ss_conf 97799996268730558
No 7
>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=99.40 E-value=6.1e-13 Score=96.18 Aligned_cols=139 Identities=27% Similarity=0.415 Sum_probs=85.4
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf 77668987987999999999965990899835888321101000124354236023455413556521240455322000
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVKDP 186 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~~~ 186 (549)
.+||+|||||++||.+|..|.+.|+++++||+.+++|+ .|+... +. ..+.+..+..-..++-
T Consensus 1 ~k~VaIIGAG~sGL~aak~l~~~G~~~~~fE~~~~iGG-------~W~~~~-~~------~~g~~~~Y~~~~~n~~---- 62 (531)
T PF00743_consen 1 KKRVAIIGAGPSGLAAAKCLLEEGLDPTCFEKSSDIGG-------TWRYNE-NP------EPGRASVYPSLVTNTS---- 62 (531)
T ss_dssp --EEEEE-------HHHHHHHH---EEEEE-SSS------------TTT--------------B-SS-TTTBSSS-----
T ss_pred CCEEEEECCCHHHHHHHHHHHHCCCCEEEEECCCCCCC-------CCCCCC-CC------CCCCCCCCCCCEECCC----
T ss_conf 98899989649999999999878998299974899556-------784188-16------9997468578157969----
Q ss_pred CCCHHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCC--EEEEECCCCCCEECC-----CEEEEEEEC
Q ss_conf 2117899999996689510013676410001279999999999996698--899813433204058-----758999986
Q T0604 187 NFYGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGG--EIRFSTRVDDLHMED-----GQITGVTLS 259 (549)
Q Consensus 187 ~~~~~~vl~~~~~~Ga~~~i~~~~kph~gtd~~~~vv~~L~~~l~~~G~--~i~~~t~V~~i~~~~-----g~v~gV~t~ 259 (549)
... ..|..+-.|. .+...| ....+.+.|+.++++.+. .|+|+|+|+++...+ +++. |++.
T Consensus 63 k~~-----~~fsdfP~p~--~~p~f~-----~~~ei~~Yl~~ya~~f~L~~~Irf~t~V~~v~~~~d~~~~g~W~-V~~~ 129 (531)
T PF00743_consen 63 KEM-----MCFSDFPFPE--DYPNFP-----SHSEILDYLESYAEHFGLRKHIRFNTEVVSVEKDEDFSETGKWR-VTTR 129 (531)
T ss_dssp CCC-----CHCTTC-HHC--CS-SS------BHHHHHHHHHHHHCCTCCGGGEETSEEEEEEEEECCTTTCCEEE-EEET
T ss_pred HHH-----HCCCCCCCCC--CCCCCC-----CHHHHHHHHHHHHHHCCCCCEEECCCEEEEEEECCCCCCCCCEE-EEEC
T ss_conf 899-----7267899999--788895-----99999999999999829971469280998810367656799289-9984
Q ss_pred CCC---EEEECEEEEECCCC
Q ss_conf 784---89705689931887
Q T0604 260 NGE---EIKSRHVVLAVGHS 276 (549)
Q Consensus 260 ~g~---~i~ad~VVlAtGhs 276 (549)
++. +..+|+||+|+||-
T Consensus 130 ~~g~~~~~~fd~VvvatG~~ 149 (531)
T PF00743_consen 130 DDGKEETEVFDAVVVATGHF 149 (531)
T ss_dssp TTTEEEEEEESEEEE-----
T ss_pred CCCEEEEEEECEEEEEECCC
T ss_conf 79889999949899998589
No 8
>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=99.27 E-value=8.7e-12 Score=88.93 Aligned_cols=141 Identities=23% Similarity=0.317 Sum_probs=87.2
Q ss_pred CEEEECCCHHHHHHHHHH--HHCCCEEEEEECCCCCC-CCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf 668987987999999999--96599089983588832-110100012435423602345541355652124045532200
Q T0604 109 RPIVIGFGPCGLFAGLVL--AQMGFNPIIVERGKEVR-ERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVKD 185 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~L--a~~G~~V~VlErg~~vg-~r~~~~~~~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~~ 185 (549)
.|||||||||||..|+.| ++.|.+|+|+|+.+... .+.. +..+|.......+.. +..+...
T Consensus 1 DviIvGaG~AGl~lA~~L~~~~~gl~V~lie~~~~~~~~~~~-tW~~~~~~~~~l~~~---------------v~~~W~~ 64 (374)
T PF05834_consen 1 DVIIVGAGPAGLSLAARLARARPGLRVLLIEPGPKPPWPNNR-TWCFWEPDLGPLDPL---------------VSHRWSD 64 (374)
T ss_pred CEEEECCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCC-EEEECCCCCHHHHHH---------------HHHCCCC
T ss_conf 989999769999999998632799879998089655666684-797346752205789---------------8615686
Q ss_pred HCCCHHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEECCCCEEE
Q ss_conf 02117899999996689510013676410001279999999999996698899813433204058758999986784897
Q T0604 186 PNFYGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNGEEIK 265 (549)
Q Consensus 186 ~~~~~~~vl~~~~~~Ga~~~i~~~~kph~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~~g~~i~ 265 (549)
... .+......... +++ .......+.+.+.+++. .++.++++.+|+++...++.+ .|++.+|+++.
T Consensus 65 ~~v----------~~~~~~~~~~~-~~Y-~~i~~~~f~~~l~~~~~-~~~~~~~~~~V~~v~~~~~~~-~v~~~~G~~l~ 130 (374)
T PF05834_consen 65 WRV----------YFPDGRRILHD-YPY-KMIDSADFYEHLLERLE-ANGVIFLEARVSSVEPDGDHS-VVTLADGRTLR 130 (374)
T ss_pred CEE----------EECCCCEEECC-CCC-EEEEHHHHHHHHHHHHC-CCCEEEECCEEEEEECCCCCC-EEEECCCCEEE
T ss_conf 089----------90899535426-786-25709999999998704-265499927799965057642-03406997898
Q ss_pred ECEEEEECCCCHHH
Q ss_conf 05689931887679
Q T0604 266 SRHVVLAVGHSARD 279 (549)
Q Consensus 266 ad~VVlAtGhsard 279 (549)
|+.||.|.|++...
T Consensus 131 A~~ViDarg~~~~~ 144 (374)
T PF05834_consen 131 ARLVIDARGPSPPP 144 (374)
T ss_pred EEEEEECCCCCCCC
T ss_conf 78999898877556
No 9
>PF04820 Trp_halogenase: Tryptophan halogenase; InterPro: IPR006905 Tryptophan halogenase catalyses the chlorination of tryptophan to form 7-chlorotryptophan. This is the first step in the biosynthesis of pyrrolnitrin, an antibiotic with broad-spectrum anti-fungal activity. Tryptophan halogenase is NADH-dependent .; PDB: 2wet_D 2wes_B 2weu_A 2oal_B 2o9z_A 2e4g_B 2oam_A 2oa1_A 2apg_A 2ard_A ....
Probab=99.22 E-value=2.8e-11 Score=85.77 Aligned_cols=167 Identities=21% Similarity=0.204 Sum_probs=89.0
Q ss_pred CEEEECCCHHHHHHHHHHHHCC---CEEEEEECCCCC----CCCCCCC-CCCCC-CCCC----CHHHHHHHHCCC-----
Q ss_conf 6689879879999999999659---908998358883----2110100-01243-5423----602345541355-----
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMG---FNPIIVERGKEV----RERTKDT-FGFWR-KRTL----NPESNVQFGEGG----- 170 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G---~~V~VlErg~~v----g~r~~~~-~~~~~-~~~~----~~~~n~~~g~gg----- 170 (549)
+|||||+|+||.++|..|++.+ ++|+|+|+..-+ |+.+.+. ..+.+ .++- -..++..+-.|.
T Consensus 1 ~i~ivGgG~ag~~~A~~l~~~~~~~~~v~lves~~~~~~~vGe~t~p~~~~~~~~~gi~e~~~~~~~~at~k~g~~f~~W 80 (454)
T PF04820_consen 1 DIVIVGGGTAGWMAAAALAKALPGQISVTLVESPDIPTIGVGESTIPSIRHFLRRLGIDEAEFMRATDATFKLGIRFENW 80 (454)
T ss_dssp EEEEE-------HHHHHHHHHCCCSSEEEEEE-SSS-------B--THHHHCCCC----HHHHCHHCT-EEE-EEEEESS
T ss_pred CEEEECCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHCCEEECEEEECCC
T ss_conf 98999886999999999997357885699982689999882754307799999984988399999819833474896234
Q ss_pred -------CCCCCC-H-----------HHHHHHHH-HCCCHHHHHHH-HHH--CCCCCCCC-CCCCCCEECCHHHHHHHHH
Q ss_conf -------652124-0-----------45532200-02117899999-996--68951001-3676410001279999999
Q T0604 171 -------AGTFSD-G-----------KLYSQVKD-PNFYGRKVITE-FVE--AGAPEEIL-YVSKPHIGTFKLVTMIEKM 226 (549)
Q Consensus 171 -------ag~fsd-g-----------kl~t~~~~-~~~~~~~vl~~-~~~--~Ga~~~i~-~~~kph~gtd~~~~vv~~L 226 (549)
-..|.. + .+..+... ........+.. ... ..++.... .....+--......+-+.|
T Consensus 81 ~~~~~~y~hpF~~~~~~~~~~~~~~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yayhlDR~~Fd~~L 160 (454)
T PF04820_consen 81 SEKGESYFHPFGSYGPGIDGVDFHHYWLRARARGFAGPFDDYSLSAVAACAGKFAPPPEDFLGPFNYAYHLDRAKFDRFL 160 (454)
T ss_dssp SSC--EEEEESS----BETTEBHHHHHHHHHHTSCCSHHHHHHHCHHHHHHTTBTSB-TTHTBTSS-EEB--HHHHHHHH
T ss_pred CCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEHHHHHHHH
T ss_conf 67996289657777878877773799998640477799799879999998259999875556788747996599999999
Q ss_pred HHHHHHCCCEEEEECCCCCCEEC-CCEEEEEEECCCCEEEECEEEEECCCC
Q ss_conf 99999669889981343320405-875899998678489705689931887
Q T0604 227 RATIIELGGEIRFSTRVDDLHME-DGQITGVTLSNGEEIKSRHVVLAVGHS 276 (549)
Q Consensus 227 ~~~l~~~G~~i~~~t~V~~i~~~-~g~v~gV~t~~g~~i~ad~VVlAtGhs 276 (549)
++.+.+.|++++.+ +|+++..+ +|.+.+|.+.+|+++++|.+|-|+|..
T Consensus 161 ~~~A~~~GV~~~eg-~V~~v~~~~~G~i~~v~~~~g~~i~ad~~IDaSG~~ 210 (454)
T PF04820_consen 161 RDHARERGVEVIEG-TVVDVELDEDGDIASVRLEDGREIEADFFIDASGFR 210 (454)
T ss_dssp HHHHHHC--EEEES--EEEEEE-----EEEEEES---EEE-SEEEE-----
T ss_pred HHHHHHCCCEEEEC-EEEEEEECCCCCEEEEEECCCCEEEEEEEEECCCCC
T ss_conf 99999789989969-798999879986789995899799964899898863
No 10
>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=99.16 E-value=3.6e-11 Score=85.02 Aligned_cols=106 Identities=25% Similarity=0.376 Sum_probs=72.1
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHCC
Q ss_conf 66898798799999999996599089983588832110100012435423602345541355652124045532200021
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVKDPNF 188 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~~~~~ 188 (549)
+|+|||||||||.+|..|++.|++++|+|+.... ..++.... .
T Consensus 1 ~vvIIG~G~aGl~~a~~l~~~~~~v~vie~~~~~-------~~~~~~~~----~-------------------------- 43 (201)
T PF07992_consen 1 DVVIIGGGPAGLSAAYELLRLGYKVTVIERNPGG-------GGYNRSQI----P-------------------------- 43 (201)
T ss_dssp EEEEE----HHHHHHHHHHHHTSEEEEEESSSSS-------STTTCSGH----H--------------------------
T ss_pred CEEEECCCHHHHHHHHHHHHCCCCEEEEECCCCC-------CEEEECCC----E--------------------------
T ss_conf 9999998999999999999779909999723532-------00000011----0--------------------------
Q ss_pred CHHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEECCCC-EEEEC
Q ss_conf 17899999996689510013676410001279999999999996698899813433204058758999986784-89705
Q T0604 189 YGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNGE-EIKSR 267 (549)
Q Consensus 189 ~~~~vl~~~~~~Ga~~~i~~~~kph~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~~g~-~i~ad 267 (549)
........ ....+.........+.+++++.+.+|.++..++..+ ++.+++ ++.+|
T Consensus 44 --~~~~~~~~-------------------~~~~~~~~~~~~~~~~~i~~~~~~~v~~i~~~~~~v---~~~~g~~~~~~d 99 (201)
T PF07992_consen 44 --NFFLWPDS-------------------NLYELSRELLEQLKQYGIEVIQNGEVVSIDPEGKRV---TLKDGKGTIKYD 99 (201)
T ss_dssp --HHHHHHHH-------------------HHHHHHHHHHHHHHHHHHEEEHSHHEEEEETTTTEE---EEEESEEEEEEE
T ss_pred --EECCCCCC-------------------CCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC---CCCCCEEEEECC
T ss_conf --00023432-------------------112221001233331254200024432000111111---222210144110
Q ss_pred EEEEECCC
Q ss_conf 68993188
Q T0604 268 HVVLAVGH 275 (549)
Q Consensus 268 ~VVlAtGh 275 (549)
.+|+|+|.
T Consensus 100 ~lvlAtG~ 107 (201)
T PF07992_consen 100 YLVLATGS 107 (201)
T ss_dssp EEEE--TC
T ss_pred EEEEECCC
T ss_conf 59982056
No 11
>PF01593 Amino_oxidase: Flavin containing amine oxidoreductase This is a subset of the Pfam family; InterPro: IPR002937 This entry consists of various amine oxidases, including maize polyamine oxidase (PAO) , L-amino acid oxidases (LAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. In vertebrates MAO plays an important role in regulating the intracellular levels of amines via their oxidation; these include various neurotransmitters, neurotoxins and trace amines . In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium . PAOs in plants, bacteria and protozoa oxidise spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines . Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2ive_B 2ivd_A 1sez_A 1yvv_A 2vvl_G 2vvm_A 2yr6_A 2yr5_B 2yr4_B 1o5w_D ....
Probab=99.12 E-value=4.7e-10 Score=78.03 Aligned_cols=50 Identities=36% Similarity=0.552 Sum_probs=42.7
Q ss_pred HHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEECCCCEEEECEEEEECC
Q ss_conf 999999996698899813433204058758999986784897056899318
Q T0604 224 EKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNGEEIKSRHVVLAVG 274 (549)
Q Consensus 224 ~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~~g~~i~ad~VVlAtG 274 (549)
..+...++..|++|+++++|+.|..++++++ |++.+|+++++|.||+|+.
T Consensus 213 ~~~~~~~~~~g~~i~~~~~V~~I~~~~~~v~-v~~~~g~~~~ad~VI~a~p 262 (449)
T PF01593_consen 213 LALALALEELGGKIRLNTPVTSIETEDDKVT-VVTEDGETIEADYVISAVP 262 (449)
T ss_dssp HHHHHHHHHCGGCEETSEEEEEEEEESSCEE-EEEETSSEEEESEEEE-S-
T ss_pred HHHHHHHHCCCCEEECCCCCEEEEECCCCCC-CCCCCCEEEEEEEEEECCC
T ss_conf 9999987302867975886289883144321-1124211564003674487
No 12
>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=98.93 E-value=3.6e-10 Score=78.78 Aligned_cols=36 Identities=25% Similarity=0.456 Sum_probs=32.5
Q ss_pred CEEEECCCHHHHHHHHHHHHCC-CEEEEEECCCCCCC
Q ss_conf 6689879879999999999659-90899835888321
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMG-FNPIIVERGKEVRE 144 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G-~~V~VlErg~~vg~ 144 (549)
.+||||+|++|...|..|++.| ++|+|||+|+....
T Consensus 2 D~IIVGsG~~G~v~A~rLa~~g~~~VlvLEaG~~~~~ 38 (298)
T PF00732_consen 2 DVIIVGSGAGGGVVASRLAEAGGYSVLVLEAGPRYSP 38 (298)
T ss_dssp EEEEE-------HHHHHHTTSTTS-EEEEE----GTT
T ss_pred CEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCC
T ss_conf 9999897889999999997688976999960587776
No 13
>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=98.64 E-value=9.1e-08 Score=63.70 Aligned_cols=80 Identities=29% Similarity=0.376 Sum_probs=63.6
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHCC
Q ss_conf 66898798799999999996599089983588832110100012435423602345541355652124045532200021
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVKDPNF 188 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg~r~~~~~~~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~~~~~ 188 (549)
||+|||+|+.|+.+|..|++.|.+|+|++|.+.+.. . +
T Consensus 1 ~vvViGgG~~g~E~A~~l~~~g~~Vtlv~~~~~~~~-~-----------~------------------------------ 38 (81)
T PF00070_consen 1 RVVVIGGGYIGLELAEELARLGKEVTLVERSDRLLP-G-----------L------------------------------ 38 (81)
T ss_dssp EEEEE-E-HHHHHHHHHHHHTSSEEEEEESSSSSST-T-----------S------------------------------
T ss_pred CEEEECCCHHHHHHHHHHHHHCCEEEEEEECCCHHH-H-----------C------------------------------
T ss_conf 999999699999999999863988999997783134-0-----------8------------------------------
Q ss_pred CHHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEEC-CC
Q ss_conf 17899999996689510013676410001279999999999996698899813433204058758999986-78
Q T0604 189 YGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLS-NG 261 (549)
Q Consensus 189 ~~~~vl~~~~~~Ga~~~i~~~~kph~gtd~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~-~g 261 (549)
-+.+.+.+.+.+++.|+++++++.++.+..+++.++ |+++ ||
T Consensus 39 ------------------------------~~~~~~~~~~~l~~~gV~~~~~~~v~~i~~~~~~~~-V~~~~d~ 81 (81)
T PF00070_consen 39 ------------------------------DPEIAKYLQDKLEENGVEIHTNAEVTEIEGDEDGVY-VTLKKDG 81 (81)
T ss_dssp ------------------------------SHHHHHHHHHHHHHTTEEEEESEEEEEEEECTTEEE-EEEE---
T ss_pred ------------------------------CHHHHHHHHHHHHHCCCEEEECCEEEEEEEECCEEE-EEEEECC
T ss_conf ------------------------------999999999999978999993999999999799899-9997678
No 14
>PF06039 Mqo: Malate:quinone oxidoreductase (Mqo); InterPro: IPR006231 The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase . ; GO: 0008924 malate dehydrogenase (acceptor) activity, 0006099 tricarboxylic acid cycle
Probab=98.58 E-value=4e-06 Score=53.38 Aligned_cols=187 Identities=14% Similarity=0.175 Sum_probs=99.1
Q ss_pred CCEEEECCCHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf 7668987987999999999965--9908998358883211010001-243542360234554135565212404553220
Q T0604 108 ERPIVIGFGPCGLFAGLVLAQM--GFNPIIVERGKEVRERTKDTFG-FWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVK 184 (549)
Q Consensus 108 ~rVVVVGaGpAGL~AAl~La~~--G~~V~VlErg~~vg~r~~~~~~-~~~~~~~~~~~n~~~g~ggag~fsdgkl~t~~~ 184 (549)
-.||+||||..|-+.++.|.+. -.++.|+||-+.++.-.....+ -+..+.-+.+.|+..... .|..+-.|- ..+.
T Consensus 4 ~DVvlIGgGImsaTL~~~L~~l~p~~~I~i~Erl~~~A~eSS~~wNNAGTGHaa~cElNYTpe~~-dGsi~i~KA-~~In 81 (488)
T PF06039_consen 4 YDVVLIGGGIMSATLGTLLKELEPSWSIAIFERLDSVALESSNGWNNAGTGHAALCELNYTPEKA-DGSIDISKA-VKIN 81 (488)
T ss_pred CCEEEECCHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHCCCCCCCCCCCHHHHHHCCCCCCCC-CCCCCHHHH-HHHH
T ss_conf 12899896088999999999709987389998057523330687655533011444305886778-984327888-9999
Q ss_pred HH-----------------------------------CCCHHHHHHHHHHCC---CCCCCCCCC----------------
Q ss_conf 00-----------------------------------211789999999668---951001367----------------
Q T0604 185 DP-----------------------------------NFYGRKVITEFVEAG---APEEILYVS---------------- 210 (549)
Q Consensus 185 ~~-----------------------------------~~~~~~vl~~~~~~G---a~~~i~~~~---------------- 210 (549)
.. ...+.++-+.+..+. ....+.+..
T Consensus 82 e~FeiSrqfWa~lv~~g~l~~p~~FI~~~pHmsfv~Ge~nv~fLkkRy~~l~~~~lF~~me~sed~~~i~~w~PL~m~gR 161 (488)
T PF06039_consen 82 EQFEISRQFWAYLVEKGILPDPESFINPVPHMSFVWGEENVDFLKKRYEALKEHPLFPGMEFSEDPAQIAEWAPLVMEGR 161 (488)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHCCCCCCCCEECCCHHHHHHHCCEEECCC
T ss_conf 99999999999998678878868853579816999884878999999999743878787586569899974167701797
Q ss_pred ---------CCCEECCH-HHHHHHHHHHHHHHC-CCEEEEECCCCCCEECCCEEEEEEEC-----CCCEEEECEEEEECC
Q ss_conf ---------64100012-799999999999966-98899813433204058758999986-----784897056899318
Q T0604 211 ---------KPHIGTFK-LVTMIEKMRATIIEL-GGEIRFSTRVDDLHMEDGQITGVTLS-----NGEEIKSRHVVLAVG 274 (549)
Q Consensus 211 ---------kph~gtd~-~~~vv~~L~~~l~~~-G~~i~~~t~V~~i~~~~g~v~gV~t~-----~g~~i~ad~VVlAtG 274 (549)
+.-.|||. ...+.+.|.+.+++. +.+++++++|++|...++.-..|.+. +..++.++.|++..|
T Consensus 162 ~~~e~vAat~~~~GTDVnfG~LTr~l~~~l~~~~~~~l~~~~eV~~i~r~~dg~w~v~~~~~~~~~~~~~~a~FVfvGAG 241 (488)
T PF06039_consen 162 DPDEPVAATRMEEGTDVNFGALTRQLVEYLQKQPGFELHLNHEVTDIKRNGDGSWTVKVKDLKTGNKRTVRAKFVFVGAG 241 (488)
T ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEECCEEEEEEECCCCCEEEEEEECCCCCEEEEECCEEEECCC
T ss_conf 97886678806887657689999999999985559269843443020005788469998744789758998388998977
Q ss_pred CCHHHHHHHHHHCCCCC--CCCCCCCC
Q ss_conf 87679999999669711--14874568
Q T0604 275 HSARDTFEMLHERGVYM--EAKPFSVG 299 (549)
Q Consensus 275 hsard~~~~l~~~Gi~~--~~k~~a~G 299 (549)
+. ...+|++.||+- .-.-|.++
T Consensus 242 G~---sL~Llqksgi~e~~~yggfPVs 265 (488)
T PF06039_consen 242 GG---SLPLLQKSGIPEGKGYGGFPVS 265 (488)
T ss_pred HH---HHHHHHHCCCCHHCCCCCCCCC
T ss_conf 78---8999998599530274778736
No 15
>PF06100 Strep_67kDa_ant: Streptococcal 67 kDa myosin-cross-reactive antigen like family ; InterPro: IPR010354 Members of this family are thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis .
Probab=98.16 E-value=1.7e-05 Score=49.51 Aligned_cols=59 Identities=22% Similarity=0.369 Sum_probs=41.6
Q ss_pred CCHHHHHHHHHHHHHHHCCCEEEEECCCCCCEECC--C--EEEEEEE-CCCC--EE---EECEEEEECC
Q ss_conf 01279999999999996698899813433204058--7--5899998-6784--89---7056899318
Q T0604 216 TFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMED--G--QITGVTL-SNGE--EI---KSRHVVLAVG 274 (549)
Q Consensus 216 td~~~~vv~~L~~~l~~~G~~i~~~t~V~~i~~~~--g--~v~gV~t-~~g~--~i---~ad~VVlAtG 274 (549)
.++-..++.-|...+++.||.++|+++|+||..+. + .++.+++ .+|. .+ +-|.|++..|
T Consensus 203 YNQyESiilPl~~~L~~~GV~F~~~t~Vtdi~~~~~~~~~~~~~i~~~~~g~~~~i~l~~~DlVfvTnG 271 (500)
T PF06100_consen 203 YNQYESIILPLIKYLKSQGVDFQFNTRVTDIDFDPTGDQKVATRIHLTQDGKEETIDLGEDDLVFVTNG 271 (500)
T ss_pred CCCHHHHHHHHHHHHHHCCCEEECCCEEEEEEEEECCCCEEEEEEEEECCCCEEEEECCCCCEEEEECC
T ss_conf 453325899999999988987978988999998715898267999997389655787289988999688
No 16
>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=97.55 E-value=8e-05 Score=45.22 Aligned_cols=37 Identities=19% Similarity=0.216 Sum_probs=32.6
Q ss_pred CCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf 7677668987987999999999965990899835888
Q T0604 105 NLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKE 141 (549)
Q Consensus 105 ~~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~ 141 (549)
-..+||+|||+|.+|.-.|..|++.+.+|.+.-|...
T Consensus 181 ~~GKrVvVVG~G~Sa~DIa~ela~~a~~v~l~~R~~~ 217 (531)
T PF00743_consen 181 FKGKRVVVVGSGNSAIDIAPELAKVAKKVTLSQRSGT 217 (531)
T ss_dssp GTT-EEEEE---HHHHHCHHHHHHCSSCEEEEECS--
T ss_pred CCCCEEEEECCCCCHHHHHHHHHHHCCEEEEEEECCC
T ss_conf 7999899984376799999999855782799993654
No 17
>PF00996 GDI: GDP dissociation inhibitor; InterPro: IPR002005 Rab proteins constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic , ; C-terminal geranylgeranylation is crucial for their membrane association and function. This post-translational modification is catalysed by Rab geranylgeranyl transferase (Rab-GGTase), a multi-subunit enzyme that contains a catalytic heterodimer and an accessory component, termed Rab escort protein (REP)-1 . REP-1 presents newly- synthesised Rab proteins to the catalytic component, and forms a stable complex with the prenylated proteins following the transfer reaction. The mechanism of REP-1-mediated membrane association of Rab5 is similar to that mediated by Rab GDP dissociation inhibitor (GDI). REP-1 and Rab GDI also share other functional properties, including the ability to inhibit the release of GDP and to remove Rab proteins from membranes. The crystal structure of the bovine alpha-isoform of Rab GDI has been determined to a resolution of 1.81A . The protein is composed of two main structural units: a large complex multi-sheet domain I, and a smaller alpha-helical domain II. The structural organisation of domain I is closely related to FAD-containing monooxygenases and oxidases . Conserved regions common to GDI and the choroideraemia gene product, which delivers Rab to catalytic subunits of Rab geranylgeranyltransferase II, are clustered on one face of the domain . The two most conserved regions form a compact structure at the apex of the molecule; site-directed mutagenesis has shown these regions to play a critical role in the binding of Rab proteins .; GO: 0043087 regulation of GTPase activity; PDB: 1vg9_E 1vg0_A 1ltx_R 3cph_H 2bcg_G 1ukv_G 3cpi_H 3cpj_G 1gnd_A 1lv0_A ....
Probab=97.23 E-value=0.0017 Score=36.90 Aligned_cols=53 Identities=25% Similarity=0.413 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHCCCEEEEECCCCCCEE-CCCEEEEEEECCCCEEEECEEEEECC
Q ss_conf 9999999999966988998134332040-58758999986784897056899318
Q T0604 221 TMIEKMRATIIELGGEIRFSTRVDDLHM-EDGQITGVTLSNGEEIKSRHVVLAVG 274 (549)
Q Consensus 221 ~vv~~L~~~l~~~G~~i~~~t~V~~i~~-~~g~v~gV~t~~g~~i~ad~VVlAtG 274 (549)
.+-+.+-+.+.=.|+.+..++.+.++.. +++++.+|.. +|+++.|+.||....
T Consensus 233 ELpQ~FcRlsAV~GGtYmLn~~i~~i~~d~~~k~~~V~s-~ge~~~~k~vV~dps 286 (438)
T PF00996_consen 233 ELPQGFCRLSAVYGGTYMLNKPIDEIVYDENGKVVGVKS-GGETIKAKKVVGDPS 286 (438)
T ss_dssp -HHHHHHHHHHH----EESS--ECBEEBETT--BEEEBE----EEBESEEEEEGG
T ss_pred HHHHHHHHHHHHCCCEEEECCCCHHHEECCCCCEEEEEC-CCEEEEECEEEECCC
T ss_conf 054789998875287899478631304415872899971-995998098998930
No 18
>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=95.90 E-value=0.0019 Score=36.62 Aligned_cols=33 Identities=36% Similarity=0.426 Sum_probs=30.3
Q ss_pred CCEEEECCCHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 766898798799999999996599089983588
Q T0604 108 ERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGK 140 (549)
Q Consensus 108 ~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~ 140 (549)
.+|.|||.|.-||.+|..||+.|++|+.+|.++
T Consensus 1 mkI~ViG~GyvGl~~A~~lA~~G~~Vig~D~d~ 33 (185)
T PF03721_consen 1 MKIAVIGLGYVGLPLAACLAEAGHNVIGVDIDE 33 (185)
T ss_dssp -EEEEE-------HHHHHHHHHTSEEEEE-S-H
T ss_pred CEEEEECCCHHHHHHHHHHHHCCCEEEEEECCH
T ss_conf 989998956768999999995899799998988
No 19
>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=95.83 E-value=0.003 Score=35.37 Aligned_cols=39 Identities=23% Similarity=0.242 Sum_probs=33.5
Q ss_pred CCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCC
Q ss_conf 767766898798799999999996599089983588832
Q T0604 105 NLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVR 143 (549)
Q Consensus 105 ~~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg 143 (549)
-.+.+|+|+|+|.+|+.|+..|.+.|.+|+++|......
T Consensus 18 v~pakvvViGaG~vG~~A~~~a~~LGa~v~~~D~~~~~~ 56 (168)
T PF01262_consen 18 VPPAKVVVIGAGVVGLGAAETAKGLGAEVVVPDVRPERL 56 (168)
T ss_dssp B---EEEEE-------HHHHHHHH---EEEEEESSHHHH
T ss_pred CCCEEEEEECCCHHHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf 788699997987899999999987799799703798999
No 20
>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=95.44 E-value=0.0048 Score=34.08 Aligned_cols=32 Identities=25% Similarity=0.439 Sum_probs=30.1
Q ss_pred EEEECCCHHHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf 68987987999999999965990899835888
Q T0604 110 PIVIGFGPCGLFAGLVLAQMGFNPIIVERGKE 141 (549)
Q Consensus 110 VVVVGaGpAGL~AAl~La~~G~~V~VlErg~~ 141 (549)
|.|||+|.-|.+-|..|++.|.+|.++.|.+.
T Consensus 1 I~IiGaGaiG~~~a~~L~~~g~~V~l~~r~~~ 32 (151)
T PF02558_consen 1 ILIIGAGAIGSLYAARLAKAGHDVTLLARSPR 32 (151)
T ss_dssp EEEE-------HHHHHHHHCCCEEEEE-SCHH
T ss_pred CEEECCCHHHHHHHHHHHHCCCEEEEEEECCH
T ss_conf 99999699999999999978990899993728
No 21
>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=95.37 E-value=0.0037 Score=34.82 Aligned_cols=34 Identities=29% Similarity=0.364 Sum_probs=30.8
Q ss_pred CCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf 7668987987999999999965990899835888
Q T0604 108 ERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKE 141 (549)
Q Consensus 108 ~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~ 141 (549)
.+|.|+|||..|...|..|++.|++|.++.|.+.
T Consensus 1 mkI~ViGaG~~GtAlA~~la~~g~~V~lw~r~~~ 34 (159)
T PF01210_consen 1 MKIAVIGAGSWGTALAALLADNGHEVTLWGRDEE 34 (159)
T ss_dssp EEEEEE----HHCHHHHHHHHTCEEEEEETSSHH
T ss_pred CEEEEECCCHHHHHHHHHHHHCCCEEEEEECCHH
T ss_conf 9599989699999999999977998999948889
No 22
>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=94.88 E-value=0.0077 Score=32.80 Aligned_cols=33 Identities=24% Similarity=0.381 Sum_probs=30.0
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf 668987987999999999965990899835888
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKE 141 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~ 141 (549)
+|.|||+|.-|---|..++.+|++|+++|+.+.
T Consensus 1 kV~ViGaG~mG~~iA~~~a~~G~~V~l~d~~~~ 33 (180)
T PF02737_consen 1 KVAVIGAGTMGRGIAALFARAGHEVVLYDPDPE 33 (180)
T ss_dssp EEEEE-------HHHHHHHHT-SEEEEE-SSHH
T ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEECCHH
T ss_conf 989995688999999999837990899989999
No 23
>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=94.37 E-value=0.021 Score=30.03 Aligned_cols=35 Identities=31% Similarity=0.369 Sum_probs=31.0
Q ss_pred CCCCEEEECCCHHHHHHHHHHHHCCCE-EEEEECCC
Q ss_conf 677668987987999999999965990-89983588
Q T0604 106 LTERPIVIGFGPCGLFAGLVLAQMGFN-PIIVERGK 140 (549)
Q Consensus 106 ~~~rVVVVGaGpAGL~AAl~La~~G~~-V~VlErg~ 140 (549)
..++|+|||+|-+|-.++..|+..|++ ++|+-|..
T Consensus 11 ~~k~vlviGaGg~a~~v~~~L~~~g~~~i~I~nRt~ 46 (135)
T PF01488_consen 11 KGKRVLVIGAGGAARAVAAALAALGAKRITIVNRTP 46 (135)
T ss_dssp TTSEEEEE-----HHHHHHHHHHTTSCEEEEEESSH
T ss_pred CCCEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCH
T ss_conf 799899999829999999999986999899994999
No 24
>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=91.16 E-value=0.052 Score=27.60 Aligned_cols=34 Identities=29% Similarity=0.456 Sum_probs=31.6
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 7766898798799999999996599089983588
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGK 140 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~ 140 (549)
.++|+|+|-|..|=-+|..|...|.+|+|.|..+
T Consensus 23 Gk~vvV~GYG~~GkGvA~~lrg~Ga~V~VtEvDP 56 (162)
T PF00670_consen 23 GKNVVVIGYGWCGKGVAQRLRGLGARVIVTEVDP 56 (162)
T ss_dssp --EEEEE---------HHHHHH---EEEEE-SSH
T ss_pred CCEEEEECCCCCCHHHHHHHHHCCCEEEEEECCH
T ss_conf 8789997787335999999973939899997998
No 25
>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=90.61 E-value=0.12 Score=25.42 Aligned_cols=33 Identities=27% Similarity=0.357 Sum_probs=28.6
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCCE-EEEEECC
Q ss_conf 77668987987999999999965990-8998358
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGFN-PIIVERG 139 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~~-V~VlErg 139 (549)
..+|+|||+|.-|...|..|++.|+. .++++..
T Consensus 2 ~~~v~iiG~GglGs~ia~~L~~~Gv~~i~ivD~d 35 (135)
T PF00899_consen 2 KSKVLIIGAGGLGSEIAKNLARSGVGEITIVDDD 35 (135)
T ss_dssp T-EEEEES-S----HHHHHHHH----EEEEEESS
T ss_pred CCEEEEECCCHHHHHHHHHHHHCCCCCEEEECCE
T ss_conf 8889998878899999999998097636852890
No 26
>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=88.84 E-value=0.22 Score=23.67 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=28.7
Q ss_pred CEEEECCC-HHHHHHHHHHHHCCC--EEEEEECCC
Q ss_conf 66898798-799999999996599--089983588
Q T0604 109 RPIVIGFG-PCGLFAGLVLAQMGF--NPIIVERGK 140 (549)
Q Consensus 109 rVVVVGaG-pAGL~AAl~La~~G~--~V~VlErg~ 140 (549)
||.|||+| .-|..+|+.|+..|+ +..|+++.+
T Consensus 2 KV~IiGagg~VG~~~a~~l~~~~~~~el~L~D~~~ 36 (142)
T PF00056_consen 2 KVAIIGAGGNVGSALAYSLALKGIADELVLIDINE 36 (142)
T ss_dssp EEEEE-----HHHHHHHHHHHTTTSSEEEEE-SSH
T ss_pred EEEEECCCHHHHHHHHHHHHCCCCCCEEEEECCCC
T ss_conf 89999987899999999997188776699944887
No 27
>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=87.92 E-value=0.26 Score=23.24 Aligned_cols=31 Identities=32% Similarity=0.441 Sum_probs=28.7
Q ss_pred CCCCEEEECCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 6776689879879999999999659908998
Q T0604 106 LTERPIVIGFGPCGLFAGLVLAQMGFNPIIV 136 (549)
Q Consensus 106 ~~~rVVVVGaGpAGL~AAl~La~~G~~V~Vl 136 (549)
..+||+|-|.|-.|..+|..|.+.|.+|+.+
T Consensus 31 ~g~~vaiqG~GnVG~~~a~~l~~~Gakvv~v 61 (244)
T PF00208_consen 31 KGKRVAIQGFGNVGSNAARKLAELGAKVVAV 61 (244)
T ss_dssp CC-EEEEE----HHHHHHHHHHHCT-EEEEE
T ss_pred CCCEEEEECCCHHHHHHHHHHHHCCCEEEEE
T ss_conf 6988999897789999999999879989999
No 28
>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=87.10 E-value=0.16 Score=24.51 Aligned_cols=35 Identities=26% Similarity=0.306 Sum_probs=31.7
Q ss_pred CCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCC
Q ss_conf 76689879879999999999659908998358883
Q T0604 108 ERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEV 142 (549)
Q Consensus 108 ~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~v 142 (549)
.+|-+||.|--|.--|..|+++|++|.+++|.+..
T Consensus 2 ~~Ig~IGlG~MG~~~a~~L~~~g~~V~v~dr~~~~ 36 (163)
T PF03446_consen 2 MKIGFIGLGNMGSAMARNLARAGHEVTVYDRSPEK 36 (163)
T ss_dssp BEEEEB-------HHHHHHHH-CSEEEE--SSHHH
T ss_pred CEEEEEEHHHHHHHHHHHHHHCCCEEEEEECCHHH
T ss_conf 88999815998999999998459979999097889
No 29
>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=86.53 E-value=0.57 Score=21.09 Aligned_cols=33 Identities=27% Similarity=0.319 Sum_probs=28.8
Q ss_pred EEEECCCHHHHHHHHHHHHCCC--EEEEEECCCCC
Q ss_conf 6898798799999999996599--08998358883
Q T0604 110 PIVIGFGPCGLFAGLVLAQMGF--NPIIVERGKEV 142 (549)
Q Consensus 110 VVVVGaGpAGL~AAl~La~~G~--~V~VlErg~~v 142 (549)
|+|+|+|..|-.++..|++++- +++|..|...-
T Consensus 1 IlvlG~G~vG~~v~~~L~~~~~~~~v~va~r~~~~ 35 (386)
T PF03435_consen 1 ILVLGAGFVGRAVARYLARRGDVSRVTVADRNPEK 35 (386)
T ss_dssp EEEE----THHHHHHHHHCCCCE-EEEEEESSHHH
T ss_pred CEEECCCHHHHHHHHHHHHCCCCCEEEEEECCHHH
T ss_conf 99996839999999999838787538999899999
No 30
>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=86.50 E-value=0.23 Score=23.56 Aligned_cols=35 Identities=11% Similarity=0.249 Sum_probs=30.9
Q ss_pred CCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 67766898798799999999996599089983588
Q T0604 106 LTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGK 140 (549)
Q Consensus 106 ~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~ 140 (549)
|-+||+|+|.|+.+.-+...+.+.|++++++--.+
T Consensus 1 ~~kkvLIanrG~ia~r~~r~~~e~gi~tv~v~s~~ 35 (110)
T PF00289_consen 1 MIKKVLIANRGEIAVRIIRALRELGIETVAVNSNP 35 (110)
T ss_dssp SSSEEEES--HHHHHHHHHHHHHHSSEEEEEESGG
T ss_pred CCCEEEEECCCHHHHHHHHHHHHCCCEEEEECCHH
T ss_conf 98679998988999999999998699478982858
No 31
>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=85.79 E-value=0.4 Score=22.01 Aligned_cols=32 Identities=25% Similarity=0.385 Sum_probs=28.3
Q ss_pred EEEECCCHHHHHHHHHHHHCCC-EEEEEECCCCC
Q ss_conf 6898798799999999996599-08998358883
Q T0604 110 PIVIGFGPCGLFAGLVLAQMGF-NPIIVERGKEV 142 (549)
Q Consensus 110 VVVVGaGpAGL~AAl~La~~G~-~V~VlErg~~v 142 (549)
|+|+|.|..|...+-.|.+ +. +++++|+.+..
T Consensus 1 ivI~G~g~~~~~i~~~L~~-~~~~vviv~~~~~~ 33 (116)
T PF02254_consen 1 IVICGYGRVGREIARELRE-GGIPVVIVDKDPER 33 (116)
T ss_dssp EEEE---HHHHHHHHHHHH-TCEEEEEEESSHHH
T ss_pred EEEECCCHHHHHHHHHHHH-CCCEEEEEECCHHH
T ss_conf 2998788899999999985-89989999888899
No 32
>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=84.95 E-value=0.22 Score=23.70 Aligned_cols=34 Identities=21% Similarity=0.362 Sum_probs=28.2
Q ss_pred CCCEEEECCCHHHHHHHHHHHHC----CC-------EEEEEECCC
Q ss_conf 77668987987999999999965----99-------089983588
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQM----GF-------NPIIVERGK 140 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~----G~-------~V~VlErg~ 140 (549)
..|++++|||-||+-.|-.|... |+ ++.++++..
T Consensus 25 d~riv~~GAGsAg~gia~~l~~~~~~~G~s~eeA~~~i~~~D~~G 69 (255)
T PF03949_consen 25 DQRIVFFGAGSAGIGIADLLVDAMVTEGLSEEEARKRIWLVDSKG 69 (255)
T ss_dssp G-EEEEE-------HHHHHHHHHHHC----HHHHHTTEEE----E
T ss_pred HCEEEEECCCHHHHHHHHHHHHHHHHCCCCHHHHHCCEEEECCCC
T ss_conf 357999898889999999999999861588566518099984757
No 33
>PF10727 Rossmann-like: Rossmann-like domain; PDB: 3dfu_A 3c24_B.
Probab=82.06 E-value=0.35 Score=22.43 Aligned_cols=35 Identities=26% Similarity=0.195 Sum_probs=30.5
Q ss_pred CCCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf 77677668987987999999999965990899835
Q T0604 104 ENLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVER 138 (549)
Q Consensus 104 ~~~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlEr 138 (549)
++..-+|.|||+|-.|-..|..|.+.|+.|.-+..
T Consensus 7 ~~~rl~IgiIGaGrVG~~La~~l~~aG~~v~~v~s 41 (127)
T PF10727_consen 7 RPARLRIGIIGAGRVGTALARALARAGHPVVGVYS 41 (127)
T ss_dssp -----EEEEEE-----SHHHHHHHHSSSEEEE-SS
T ss_pred CCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEEE
T ss_conf 77763699988898999999999978996999996
No 34
>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=81.76 E-value=0.8 Score=20.15 Aligned_cols=42 Identities=19% Similarity=0.217 Sum_probs=35.4
Q ss_pred CCCCCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCC
Q ss_conf 887767766898798799999999996599089983588832
Q T0604 102 APENLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVR 143 (549)
Q Consensus 102 ~~~~~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~vg 143 (549)
+..-..++|.|||.|.-|...|-.|.-.|.+|+.+++.....
T Consensus 31 ~~~l~gktvgIvG~G~IG~~vA~~l~afG~~V~~~d~~~~~~ 72 (178)
T PF02826_consen 31 GRELRGKTVGIVGLGRIGRAVARRLKAFGMKVIGYDRSPKPE 72 (178)
T ss_dssp SS-GGGSEEEEB-------HHHHHHHHGT-EEEEECSSSHHH
T ss_pred CCCCCCCEEEEEEECCCHHHHHHHHCCCCCEEEEECCCCCHH
T ss_conf 746789989998478028999876413998899982777756
No 35
>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=80.12 E-value=0.6 Score=20.91 Aligned_cols=32 Identities=31% Similarity=0.416 Sum_probs=29.3
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf 77668987987999999999965990899835
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGFNPIIVER 138 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~~V~VlEr 138 (549)
.++|.|||-|--|..-|+-|...|++|+|=.|
T Consensus 4 ~k~IAViGYGsQG~ahAlNLrDSGv~V~vglr 35 (165)
T PF07991_consen 4 GKTIAVIGYGSQGHAHALNLRDSGVDVIVGLR 35 (165)
T ss_dssp --EEEEE----HHHHHHHHHHHH--EEEE---
T ss_pred CCEEEEECCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf 99899986671899999777747996899988
No 36
>PF01564 Spermine_synth: Spermine/spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (), spermine synthase () and putrescine N-methyltransferase () . The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain . The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) . ; GO: 0003824 catalytic activity; PDB: 1iy9_B 1jq3_D 1inl_B 2cmh_A 2cmg_A 3bwb_A 3bwc_A 2i7c_B 2pt9_B 2pss_C ....
Probab=75.10 E-value=0.79 Score=20.17 Aligned_cols=39 Identities=26% Similarity=0.199 Sum_probs=26.0
Q ss_pred CCCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCC
Q ss_conf 776776689879879999999999659908998358883
Q T0604 104 ENLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEV 142 (549)
Q Consensus 104 ~~~~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~v 142 (549)
.+.+++|+|||+|-.|+...+.-.....+++++|-.+.+
T Consensus 74 ~~~p~~VLiiGgG~G~~~~~ll~~~~~~~v~~VEiDp~V 112 (246)
T PF01564_consen 74 HPNPKRVLIIGGGDGGTARELLKHPPVEQVTVVEIDPEV 112 (246)
T ss_dssp SSS--EEEEE----HHHHHHHTTSTTTSEEEEEES-HHH
T ss_pred CCCCCCEEEEECCCHHHHHHHHHCCCCEEEEEEECCHHH
T ss_conf 987687899967805999999645994069999657789
No 37
>PF04016 DUF364: Domain of unknown function (DUF364); InterPro: IPR007161 This is a family of bacterial and archaeal proteins of unknown function.
Probab=74.77 E-value=1.2 Score=18.99 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=20.6
Q ss_pred CCCCCCEEEECC-CHHHHHHHHHHHHCCCEEEEEECCCCCC
Q ss_conf 776776689879-8799999999996599089983588832
Q T0604 104 ENLTERPIVIGF-GPCGLFAGLVLAQMGFNPIIVERGKEVR 143 (549)
Q Consensus 104 ~~~~~rVVVVGa-GpAGL~AAl~La~~G~~V~VlErg~~vg 143 (549)
....+||++||. .| +.. .|.+.|.++.|+|+++...
T Consensus 109 ~~~~~kV~vVG~~~P--~v~--~l~~~g~~~~v~e~~~~~~ 145 (232)
T PF04016_consen 109 IYPGKKVAVVGYFQP--IVK--RLRERGAELRVLERNPENI 145 (232)
T ss_pred CCCCCEEEEECCCCH--HHH--HHHHCCCCEEEEECCCCCC
T ss_conf 479998999917718--899--9986399579997887545
No 38
>PF05185 PRMT5: PRMT5 arginine-N-methyltransferase; InterPro: IPR007857 The human homologue of Saccharomyces cerevisiae Skb1 (Shk1 kinase-binding protein 1) is a protein methyltransferase . These proteins seem to play a role in Jak signalling.; GO: 0008168 methyltransferase activity, 0005737 cytoplasm; PDB: 3b3j_A 3b3f_C 3b3g_B 2v7e_A 2v74_F.
Probab=70.03 E-value=1.6 Score=18.23 Aligned_cols=36 Identities=22% Similarity=0.169 Sum_probs=19.6
Q ss_pred CCCEEEECCCHHHHH--HHHHHHHCC--CEEEEEECCCCC
Q ss_conf 776689879879999--999999659--908998358883
Q T0604 107 TERPIVIGFGPCGLF--AGLVLAQMG--FNPIIVERGKEV 142 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~--AAl~La~~G--~~V~VlErg~~v 142 (549)
.+.|++||||-..|. |+-++++.| .+|..+|+++..
T Consensus 187 ~~vVldVGaGrGpL~~~a~~A~a~~~~a~kVyAVEkN~~A 226 (447)
T PF05185_consen 187 DKVVLDVGAGRGPLSMFALQAGARAGRAVKVYAVEKNPNA 226 (447)
T ss_dssp T-EEEEE------HHHHHHH---------EEEEE-SSTHH
T ss_pred CEEEEEECCCCCHHHHHHHHHHCCCCCCEEEEEECCCHHH
T ss_conf 8499998997659999999861523542599998799878
No 39
>PF05728 UPF0227: Uncharacterised protein family (UPF0227); InterPro: IPR008886 Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes in that they contain a domain distantly related to IPR000073 from INTERPRO.
Probab=69.55 E-value=2.1 Score=17.53 Aligned_cols=28 Identities=18% Similarity=0.476 Sum_probs=24.5
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 6689879879999999999659908998
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIV 136 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~Vl 136 (549)
.+++||+...|++|++...+.+.+.+|+
T Consensus 60 ~~~LiGSSLGG~~A~~LA~~~~~~aVLi 87 (187)
T PF05728_consen 60 NVVLIGSSLGGYYATYLAERYGIKAVLI 87 (187)
T ss_pred CEEEEEECHHHHHHHHHHHHHCCCEEEE
T ss_conf 7189997869999999999849997999
No 40
>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=67.67 E-value=1.6 Score=18.33 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=22.7
Q ss_pred CCEEEECCCHH-HHHHHHHHHHCCCEEEEEEC
Q ss_conf 76689879879-99999999965990899835
Q T0604 108 ERPIVIGFGPC-GLFAGLVLAQMGFNPIIVER 138 (549)
Q Consensus 108 ~rVVVVGaGpA-GL~AAl~La~~G~~V~VlEr 138 (549)
+.|+|+||+.. |...|..|+++|..++++-.
T Consensus 1 k~vlItGa~~giG~~ia~~l~~~g~~~vi~~~ 32 (167)
T PF00106_consen 1 KTVLITGASGGIGRAIARELAERGASVVILTS 32 (167)
T ss_dssp -EEEEESTTSSTT-HHHHHHHHTTTEEEEEEE
T ss_pred CEEEEECCCCHHHHHHHHHHHHCCCCEEECCC
T ss_conf 99999799829999999999984990540331
No 41
>PF03853 YjeF_N: YjeF-related protein N-terminus; InterPro: IPR004443 The C-terminal region of yjeF from Escherichia coli shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Saccharomyces cerevisiae YKL151C and Bacillus subtilis yxkO match the yjeF C-terminal domain but lack this region. The proteins in this group are of unknown function.; PDB: 3d3k_B 3d3j_A 2dg2_F 2o8n_A 1jzt_A 2ax3_A.
Probab=63.67 E-value=2.7 Score=16.80 Aligned_cols=27 Identities=33% Similarity=0.448 Sum_probs=22.0
Q ss_pred EEEECC---CHHHHHHHHHHHHCCCEEEEE
Q ss_conf 689879---879999999999659908998
Q T0604 110 PIVIGF---GPCGLFAGLVLAQMGFNPIIV 136 (549)
Q Consensus 110 VVVVGa---GpAGL~AAl~La~~G~~V~Vl 136 (549)
+|++|. |-=|+.+|..|+++|++|.|+
T Consensus 33 ~vl~G~GNNGGDglv~AR~L~~~G~~V~v~ 62 (173)
T PF03853_consen 33 LVLCGPGNNGGDGLVAARHLAQRGYKVTVF 62 (173)
T ss_dssp EEEE----------HHHHHHHHTTSEEEEE
T ss_pred EEEECCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf 999899987699999999999879933999
No 42
>PF10100 DUF2338: Uncharacterized protein conserved in bacteria (DUF2338)
Probab=60.80 E-value=3.1 Score=16.49 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=26.7
Q ss_pred CCEEEECCCHHHHHHHHHHHHCCC-EEEEEEC
Q ss_conf 766898798799999999996599-0899835
Q T0604 108 ERPIVIGFGPCGLFAGLVLAQMGF-NPIIVER 138 (549)
Q Consensus 108 ~rVVVVGaGpAGL~AAl~La~~G~-~V~VlEr 138 (549)
.+|+|+|.||+-+-.|..|...|- +|-+.-|
T Consensus 2 ~~vLilGtGP~aiQLAv~~k~~~~~~vgi~gR 33 (429)
T PF10100_consen 2 NRVLILGTGPVAIQLAVDLKKHGDCKVGIAGR 33 (429)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCCCEEEECCC
T ss_conf 84599637769999999998535745643057
No 43
>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=57.75 E-value=2.7 Score=16.88 Aligned_cols=32 Identities=31% Similarity=0.294 Sum_probs=27.2
Q ss_pred CEEEECCCHHHHHHHHHHHHCC---CEEEEE-ECCC
Q ss_conf 6689879879999999999659---908998-3588
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMG---FNPIIV-ERGK 140 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G---~~V~Vl-Erg~ 140 (549)
+|.|||+|--|..-+..|.+.| .++++. .|.+
T Consensus 1 kIgiIG~G~mg~al~~gl~~~~~~~~~i~i~~~~~~ 36 (96)
T PF03807_consen 1 KIGIIGAGNMGSALAKGLLESGFQPEEIIIVNSRSP 36 (96)
T ss_dssp EEEEB----HHHHHHHHHTTTTS-GGEEEEEE-SSH
T ss_pred CEEEECCHHHHHHHHHHHHHCCCCHHHEEECCCCCH
T ss_conf 999999529999999999986998788662258997
No 44
>PF09140 MipZ: ATPase MipZ; InterPro: IPR015223 MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication . It is responsible for the temporal and spatial regulation of FtsZ ring formation .
Probab=55.69 E-value=3.7 Score=15.94 Aligned_cols=30 Identities=27% Similarity=0.403 Sum_probs=22.6
Q ss_pred CEEEECCCHHH-------HHHHHHHHHCCCEEEEEEC
Q ss_conf 66898798799-------9999999965990899835
Q T0604 109 RPIVIGFGPCG-------LFAGLVLAQMGFNPIIVER 138 (549)
Q Consensus 109 rVVVVGaGpAG-------L~AAl~La~~G~~V~VlEr 138 (549)
+||+||.|-.| +-.|+.|++.|++|-+++-
T Consensus 1 hii~v~s~KGG~GKSTva~~la~aL~~~G~~Vg~lD~ 37 (261)
T PF09140_consen 1 HIIVVGSEKGGVGKSTVAVHLAVALARMGHRVGLLDL 37 (261)
T ss_pred CEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf 9899945888866888999999999977984889834
No 45
>PF07942 N2227: N2227-like protein; InterPro: IPR012901 This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (P53934 from SWISSPROT). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions .
Probab=52.17 E-value=4.3 Score=15.59 Aligned_cols=12 Identities=8% Similarity=0.014 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHH
Q ss_conf 025776999999
Q T0604 396 AGIRFQRELESN 407 (549)
Q Consensus 396 ~g~~~q~~lE~~ 407 (549)
-.++|-+.|.+.
T Consensus 180 Nii~Yi~tI~~l 191 (270)
T PF07942_consen 180 NIIDYIETIYNL 191 (270)
T ss_pred HHHHHHHHHHHH
T ss_conf 899999999998
No 46
>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=51.82 E-value=4.3 Score=15.55 Aligned_cols=31 Identities=23% Similarity=0.190 Sum_probs=28.1
Q ss_pred EEEECC-CHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 689879-8799999999996599089983588
Q T0604 110 PIVIGF-GPCGLFAGLVLAQMGFNPIIVERGK 140 (549)
Q Consensus 110 VVVVGa-GpAGL~AAl~La~~G~~V~VlErg~ 140 (549)
|+|+|| |--|-..+-.|.+.|++|.++=|.+
T Consensus 1 I~V~GaTG~~G~~v~~~L~~~g~~V~~l~R~~ 32 (233)
T PF05368_consen 1 ILVTGATGNVGRAVVRALLARGHEVRALVRNP 32 (233)
T ss_dssp EEEES----HHHHHHHHHHHTGGEEEEEESSG
T ss_pred CEEECCCCHHHHHHHHHHHHCCCCCEEEECCC
T ss_conf 98999886799999999983899848998035
No 47
>PF01973 MAF_flag10: Protein of unknown function DUF115; InterPro: IPR002826 The prokaryotic proteins in this family have no known function.
Probab=43.21 E-value=2.9 Score=16.66 Aligned_cols=19 Identities=21% Similarity=0.340 Sum_probs=8.8
Q ss_pred CEEEEECCCCHHHHHHHHH
Q ss_conf 5689931887679999999
Q T0604 267 RHVVLAVGHSARDTFEMLH 285 (549)
Q Consensus 267 d~VVlAtGhsard~~~~l~ 285 (549)
.++|++.|.|-.+..++|+
T Consensus 26 ~~~IvgaGPSL~~~i~~lk 44 (170)
T PF01973_consen 26 PAFIVGAGPSLDKNIEWLK 44 (170)
T ss_pred EEEEECCCCCHHHHHHHHH
T ss_conf 7999925878899999998
No 48
>PF11814 DUF3335: Domain of unknown function (DUF3335)
Probab=41.95 E-value=6.1 Score=14.60 Aligned_cols=21 Identities=43% Similarity=0.732 Sum_probs=13.7
Q ss_pred CCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 79879999999999659908998
Q T0604 114 GFGPCGLFAGLVLAQMGFNPIIV 136 (549)
Q Consensus 114 GaGpAGL~AAl~La~~G~~V~Vl 136 (549)
|.+|-|| |+.++++|++|-|+
T Consensus 73 GC~P~GL--AlAA~~rG~~v~v~ 93 (227)
T PF11814_consen 73 GCGPYGL--ALAAARRGFKVEVW 93 (227)
T ss_pred CCCHHHH--HHHHHHCCCCEEEE
T ss_conf 8478899--99999869946999
No 49
>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=38.26 E-value=7 Score=14.24 Aligned_cols=33 Identities=27% Similarity=0.327 Sum_probs=25.1
Q ss_pred CEEEECCCHHHHHHHHHHHHC--CCEEE-EEECCCC
Q ss_conf 668987987999999999965--99089-9835888
Q T0604 109 RPIVIGFGPCGLFAGLVLAQM--GFNPI-IVERGKE 141 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~--G~~V~-VlErg~~ 141 (549)
||.|||+|..|-.-...+.+. +++++ ++++...
T Consensus 2 rv~iIG~G~~~~~~~~~~~~~~~~~~v~av~d~~~~ 37 (120)
T PF01408_consen 2 RVGIIGAGRIGKRHLRALRRSPPGVEVVAVVDPDPE 37 (120)
T ss_dssp EEEEECE-THHHHHHHHHHHTTTTEEEEEEESSSHH
T ss_pred EEEEECCCHHHHHHHHHHHHCCCCCEEEEEECCCHH
T ss_conf 899993839999999999964999389999879999
No 50
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans, which are involved in the organization of cytoskeleton and/or actin microfilaments, have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions , . Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length and whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion , . ; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1ejq_B 1ybo_C 1ejp_A 1oby_Q.
Probab=36.61 E-value=3 Score=16.57 Aligned_cols=10 Identities=30% Similarity=0.415 Sum_probs=3.8
Q ss_pred CCCCCEEECC
Q ss_conf 6898542012
Q T0604 507 NLKGFYPAGE 516 (549)
Q Consensus 507 ~i~GLY~~GE 516 (549)
+=.|=|.-+|
T Consensus 301 kdegsy~l~e 310 (327)
T PF01034_consen 301 KDEGSYALDE 310 (327)
T ss_dssp ----------
T ss_pred CCCCCCCCCC
T ss_conf 7887246997
No 51
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In yeast, and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB . The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast (MTF1, ) and human (h-mtTFB) mitochondrial transcription factors, which are nuclear encoded. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity . ; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 1yub_A 1qaq_A 1qan_A 1qao_A 2erc_A 1qam_A 2h1r_A 1zq9_B 1qyr_A 3fut_B ....
Probab=35.46 E-value=7.8 Score=13.96 Aligned_cols=34 Identities=24% Similarity=0.326 Sum_probs=28.0
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCC
Q ss_conf 776689879879999999999659908998358883
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEV 142 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~~V~VlErg~~v 142 (549)
...|+=||+|+..|+.++ ++.+.+|+++|..+..
T Consensus 31 ~~~VlEiGpG~G~LT~~L--~~~~~~v~aiE~D~~l 64 (262)
T PF00398_consen 31 GDTVLEIGPGPGALTREL--LKRGKRVVAIEIDPRL 64 (262)
T ss_dssp TEEEEEE-----THHHHH--HHHSSEEEEEESSHHH
T ss_pred CCEEEEECCCCCHHHHHH--HHHHCCCEEEECHHHH
T ss_conf 988999789888899999--9842766789871647
No 52
>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=30.07 E-value=8.4 Score=13.74 Aligned_cols=31 Identities=23% Similarity=0.338 Sum_probs=27.2
Q ss_pred CEEEEC-CCHHHHHHHHHHHHCCCEEEEEECC
Q ss_conf 668987-9879999999999659908998358
Q T0604 109 RPIVIG-FGPCGLFAGLVLAQMGFNPIIVERG 139 (549)
Q Consensus 109 rVVVVG-aGpAGL~AAl~La~~G~~V~VlErg 139 (549)
||+|+| .|.-|-..+-.|.+.|+.|+.+.|.
T Consensus 2 kilI~Ga~G~lG~~l~~~l~~~~~~v~~~~r~ 33 (286)
T PF04321_consen 2 KILITGASGQLGRALARALEKRGHEVIATSRS 33 (286)
T ss_dssp EEEEE--------HHHHHCTTTSEEEEE-STT
T ss_pred EEEEECCCCHHHHHHHHHHHHCCCEEEEECCC
T ss_conf 89999999989999999864479889994676
No 53
>PF05577 Peptidase_S28: Serine carboxypeptidase S28; InterPro: IPR008758 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S28 (clan SC). The predicted active site residues for members of this family and family S10 occur in the same order in the sequence: S, D, H. These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase , , , .; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis
Probab=29.33 E-value=9.8 Score=13.33 Aligned_cols=25 Identities=20% Similarity=0.118 Sum_probs=20.5
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCC
Q ss_conf 7766898798799999999996599
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGF 131 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~ 131 (549)
..+||++|++-+|+.||+.=.+.-.
T Consensus 112 ~~p~i~~GGSY~G~LaAW~R~kYP~ 136 (433)
T PF05577_consen 112 NSPWIVFGGSYPGMLAAWFRLKYPH 136 (433)
T ss_pred CCCEEEECCCCHHHHHHHHHHHCCC
T ss_conf 9998998786264899999975887
No 54
>PF08886 GshA: Glutamate-cysteine ligase; InterPro: IPR011718 This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria . It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Probab=27.88 E-value=10 Score=13.17 Aligned_cols=45 Identities=18% Similarity=0.314 Sum_probs=25.5
Q ss_pred HHHHHHHHHHCCCEEEEECCCCCCEECCCEEEEEEECCCCEEEECEEEE
Q ss_conf 9999999996698899813433204058758999986784897056899
Q T0604 223 IEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNGEEIKSRHVVL 271 (549)
Q Consensus 223 v~~L~~~l~~~G~~i~~~t~V~~i~~~~g~v~gV~t~~g~~i~ad~VVl 271 (549)
+..|++-+...|-+++.++--.+|.. .+.+++.+|+++....++-
T Consensus 97 v~~L~~I~~~AG~~VriGsl~~~i~e----p~~~~l~~G~~l~lepl~r 141 (404)
T PF08886_consen 97 VAALKRILRQAGFNVRIGSLDPEITE----PTELTLPNGDTLTLEPLVR 141 (404)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCCCC----CEEEECCCCCEEEEEEEEE
T ss_conf 99999999975955896377713378----7477769998798875673
No 55
>PF04445 DUF548: Protein of unknown function (DUF548); InterPro: IPR007536 This is a protein of unknown function found in proteobacteria. In Salmonella typhimurium, expression of this protein is regulated by heat shock .; PDB: 2r6z_A 2oyr_A 2pgx_A 2pkw_A.
Probab=27.57 E-value=11 Score=13.13 Aligned_cols=21 Identities=29% Similarity=0.340 Sum_probs=12.4
Q ss_pred CEEEEECCCCHHHHHHHHHHCC
Q ss_conf 5689931887679999999669
Q T0604 267 RHVVLAVGHSARDTFEMLHERG 288 (549)
Q Consensus 267 d~VVlAtGhsard~~~~l~~~G 288 (549)
+.|+-||.+-+||.|-+. ..|
T Consensus 77 ~~VlDaTaGLG~DA~vlA-~lG 97 (234)
T PF04445_consen 77 PSVLDATAGLGRDAFVLA-SLG 97 (234)
T ss_dssp --EEETT-----HHHHHH-H--
T ss_pred CEEEECCCCCCHHHHHHH-CCC
T ss_conf 979988886637999998-048
No 56
>PF00291 PALP: Pyridoxal-phosphate dependent enzyme; InterPro: IPR001926 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . Pyridoxal-5'-phosphate-dependent enzymes (B6 enzymes) catalyze manifold reactions in the metabolism of amino acids. Most of these enzymes can be assigned to one of three different families of homologous proteins, the alpha, beta and gamma families. The alpha and gamma family might be distantly related with one another, but are clearly not homologous with the beta family. The beta family includes L- and D-serine dehydratase, threonine dehydratase, the beta subunit of tryptophan synthase, threonine synthase and cysteine synthase. These enzymes catalyze beta-replacement or beta-elimination reactions . Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts . The 3D structure of the beta-subunit of tryptophan synthase has been solved. The subunit has two domains that are approximately the same size and similar to each other in folding pattern. Each has a core containing a four-stranded parallel beta-sheet with three helices on its inner side and one on the outer side. The cofactor is bound at the interface between the domains .; GO: 0003824 catalytic activity, 0030170 pyridoxal phosphate binding, 0008152 metabolic process; PDB: 2pqm_B 3bm5_B 1d6s_B 1oas_B 1fcj_A 1y7l_A 1ve1_A 2ecq_A 2efy_B 2eco_A ....
Probab=27.54 E-value=11 Score=13.13 Aligned_cols=32 Identities=19% Similarity=0.151 Sum_probs=27.4
Q ss_pred CCCEEEECCCHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf 77668987987999999999965990899835
Q T0604 107 TERPIVIGFGPCGLFAGLVLAQMGFNPIIVER 138 (549)
Q Consensus 107 ~~rVVVVGaGpAGL~AAl~La~~G~~V~VlEr 138 (549)
...|+.-.+|-.|...|+.+++.|++++++=.
T Consensus 55 ~~~v~~~ssGN~g~a~A~~a~~~G~~~~i~~p 86 (297)
T PF00291_consen 55 GTTVVEASSGNHGRALAAAAARLGIKCTIVVP 86 (297)
T ss_dssp HEEEEEECTSHHHHHHHHHHHH-TEEEEEEEE
T ss_pred CCEEEEECCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf 84499727328899999999982984168753
No 57
>PF02374 ArsA_ATPase: Anion-transporting ATPase; InterPro: IPR003348 This ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell. In Escherichia coli an anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. This ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance . The ArsA and ArsB proteins form a membrane-bound pump that functions as an oxyanion-translocating ATPase. The ArsC protein is an arsenate reductase that reduces arsenate to arsenite, which is subsequently pumped out of the cell .; GO: 0005524 ATP binding, 0006820 anion transport, 0016020 membrane; PDB: 1f48_A 1ii0_A 1ihu_A 1ii9_B 2ph1_A.
Probab=27.03 E-value=11 Score=13.07 Aligned_cols=32 Identities=25% Similarity=0.294 Sum_probs=23.1
Q ss_pred EEEECCCHHHH-----HHHHHHHHCCCEEEEEECCCC
Q ss_conf 68987987999-----999999965990899835888
Q T0604 110 PIVIGFGPCGL-----FAGLVLAQMGFNPIIVERGKE 141 (549)
Q Consensus 110 VVVVGaGpAGL-----~AAl~La~~G~~V~VlErg~~ 141 (549)
+++.|-|-.|= ..|+.+|++|.+|+|+.-.+.
T Consensus 4 i~~~GKGGVGKTT~aaA~A~~~A~~G~~tLlvStDpa 40 (305)
T PF02374_consen 4 IFFGGKGGVGKTTVAAATALALARRGKRTLLVSTDPA 40 (305)
T ss_dssp EEEE-------HHHHHHHHHHHHH----EEEEESSTT
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf 9993788874489999999999837996599836974
No 58
>PF02882 THF_DHG_CYH_C: Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain; InterPro: IPR000672 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (), methenyl-THF cyclohydrolase () and formyl-THF synthetase () , . The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase ; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein , . Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site , and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds.; GO: 0003824 catalytic activity, 0009396 folic acid and derivative biosynthetic process; PDB: 1dig_B 1a4i_B 1dib_B 1dia_B 2c2y_A 2c2x_A 1ee9_A 1edz_A 1b0a_A.
Probab=26.86 E-value=11 Score=13.05 Aligned_cols=33 Identities=12% Similarity=0.173 Sum_probs=17.9
Q ss_pred CCCEEEECC-CHHHHHHHHHHHHCCCEEEEEECC
Q ss_conf 776689879-879999999999659908998358
Q T0604 107 TERPIVIGF-GPCGLFAGLVLAQMGFNPIIVERG 139 (549)
Q Consensus 107 ~~rVVVVGa-GpAGL~AAl~La~~G~~V~VlErg 139 (549)
.++|+|||. +..|--.|..|.++|..|++....
T Consensus 36 Gk~vvVvGrS~~VG~Pla~lL~~~~atVt~~hs~ 69 (160)
T PF02882_consen 36 GKKVVVVGRSNIVGKPLAMLLLNKNATVTVCHSK 69 (160)
T ss_dssp --EEEEE---ST---HHHHHHHCTT-EEEEE-SS
T ss_pred CCEEEEECCCCCHHHHHHHHHHHCCCEEEEECCC
T ss_conf 9999998997334899999998789989983789
No 59
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.
Probab=26.50 E-value=11 Score=13.01 Aligned_cols=47 Identities=23% Similarity=0.360 Sum_probs=29.7
Q ss_pred EEEEECEECCEEECC----C----CCCCCCCCCCCEEECCCCCHHHHHHHHHHHH
Q ss_conf 810011026624204----8----8743026898542012353357899999999
Q T0604 485 TGVETRTSSPVCIKR----G----KDFQSVNLKGFYPAGEGAGYAGGILSAGIDG 531 (549)
Q Consensus 485 ~GVEtr~ssPvri~r----~----~tleS~~i~GLY~~GEgaGyagGI~saa~~G 531 (549)
.|++.|.-.|+||-- - +--+++.+.+|||+|+.-|-..-|..|+--|
T Consensus 591 s~~~ir~raptrIG~RmGRPEKa~~RkMkPpvh~LFPIG~aGG~~R~i~~Aa~~~ 645 (900)
T PF03833_consen 591 SGFKIRPRAPTRIGARMGRPEKAKPRKMKPPVHVLFPIGEAGGSRRDIQKAAKKG 645 (900)
T ss_pred CCCEEECCCCCEEECCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHCC
T ss_conf 8957602686324424689875654657999754053556674022399998627
No 60
>PF08659 KR: KR domain; InterPro: IPR013968 This domain is found in bacterial polyketide synthases that catalyse the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. ; PDB: 2vz9_A 2vz8_B 2z5l_A 2fr1_A 2fr0_A.
Probab=26.39 E-value=11 Score=13.00 Aligned_cols=30 Identities=27% Similarity=0.416 Sum_probs=23.2
Q ss_pred EEEEC-CCHHHHHHHHHHHHCCCE-EEEEECC
Q ss_conf 68987-987999999999965990-8998358
Q T0604 110 PIVIG-FGPCGLFAGLVLAQMGFN-PIIVERG 139 (549)
Q Consensus 110 VVVVG-aGpAGL~AAl~La~~G~~-V~VlErg 139 (549)
++|+| .|.-|+..|-.|+++|.+ ++++-|.
T Consensus 3 ylItGG~GglG~~~a~~L~~~g~~~lvl~~r~ 34 (181)
T PF08659_consen 3 YLITGGLGGLGLSLARWLAERGARHLVLLGRS 34 (181)
T ss_dssp EEEE--------HHHHHHHH----EEEEEE--
T ss_pred EEEECCCCHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf 99979972999999999998499999997899
No 61
>PF01784 NIF3: NIF3 (NGG1p interacting factor 3); InterPro: IPR002678 This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown .; PDB: 2nyd_B 1nmp_E 1nmo_E 2yyb_A 2fyw_B 2gx8_C.
Probab=25.34 E-value=12 Score=12.88 Aligned_cols=15 Identities=20% Similarity=0.532 Sum_probs=9.1
Q ss_pred CCCCEEEEEEECCCC
Q ss_conf 889632688616786
Q T0604 335 KNGRTVYSFCMCPGG 349 (549)
Q Consensus 335 ~~g~~v~tfcmcpgG 349 (549)
.....+...++|+|+
T Consensus 165 ~~~~~v~kVai~~Gs 179 (241)
T PF01784_consen 165 DPDKPVKKVAICGGS 179 (241)
T ss_dssp GTTSEEECEEE----
T ss_pred CCCCCCCEEEEEECC
T ss_conf 987725879999377
No 62
>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=23.34 E-value=13 Score=12.64 Aligned_cols=32 Identities=22% Similarity=0.242 Sum_probs=26.0
Q ss_pred EEEEC-CCHHHHHHHHHHHHCCCEEE-EEECCCC
Q ss_conf 68987-98799999999996599089-9835888
Q T0604 110 PIVIG-FGPCGLFAGLVLAQMGFNPI-IVERGKE 141 (549)
Q Consensus 110 VVVVG-aGpAGL~AAl~La~~G~~V~-VlErg~~ 141 (549)
|+|+| .|.-|-..+..|.+.|..|+ .+=|...
T Consensus 1 IlI~Ga~G~iG~~l~~~l~~~g~~v~~~~~~~~~ 34 (238)
T PF01370_consen 1 ILITGATGFIGSALVRALLERGHEVIDALSRRES 34 (238)
T ss_dssp EEEE-----HHHHHHHHHHHHTSEEEEEESSSST
T ss_pred EEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 8998368789999999999779864222212334
No 63
>PF12381 Peptidase_C3G: Tungro spherical virus-type peptidase
Probab=23.19 E-value=13 Score=12.62 Aligned_cols=36 Identities=28% Similarity=0.442 Sum_probs=26.1
Q ss_pred ECCEEECCCCCCCCCCCCCCEEECC---CCCHHHHHHHHHH
Q ss_conf 2662420488743026898542012---3533578999999
Q T0604 492 SSPVCIKRGKDFQSVNLKGFYPAGE---GAGYAGGILSAGI 529 (549)
Q Consensus 492 ssPvri~r~~tleS~~i~GLY~~GE---gaGyagGI~saa~ 529 (549)
=+|+ .|.++..-++|-|+..+|- |-|||.-|++..+
T Consensus 183 Gs~i--~~~~t~~~RKIvGiHVAG~~~~~~gYAe~itQEDL 221 (231)
T PF12381_consen 183 GSPI--VRNNTQMVRKIVGIHVAGSANHAMGYAESITQEDL 221 (231)
T ss_pred CCEE--EECCHHHHHHHHEEEECCCCCCCCEEHHHHHHHHH
T ss_conf 6606--77145664343245612555545231204119999
No 64
>PF06690 DUF1188: Protein of unknown function (DUF1188); InterPro: IPR009573 This family consists of several hypothetical archaeal proteins of around 260 residues in length, which seem to be specific to Methanobacterium, Methanococcus and Methanopyrus species. The function of this family is unknown.
Probab=22.10 E-value=13 Score=12.49 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=16.3
Q ss_pred CEEEECCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf 66898798799999999996599089983
Q T0604 109 RPIVIGFGPCGLFAGLVLAQMGFNPIIVE 137 (549)
Q Consensus 109 rVVVVGaGpAGL~AAl~La~~G~~V~VlE 137 (549)
+++|+|+=..|-+.|..|.+.- +|+|++
T Consensus 44 ~~lIfGaYltG~~iA~~L~k~~-eV~vvD 71 (252)
T PF06690_consen 44 QALIFGAYLTGAYIAETLDKDC-EVTVVD 71 (252)
T ss_pred EEEEEEEEEEHHHHHHHHHCCC-EEEEEC
T ss_conf 3799976430078999751675-199980
No 65
>PF07156 Prenylcys_lyase: Prenylcysteine lyase; InterPro: IPR010795 This entry represents a conserved region found in a group of prenylcysteine lyases (1.8.3.5 from EC) that are approximately 500 residues long. Prenylcysteine lyase is a FAD-dependent thioether oxidase that degrades a variety of prenylcysteines, producing free cysteine, an isoprenoid aldehyde and hydrogen peroxide as products of the reaction . It has been noted that this enzyme has considerable homology with ClP55, a 55 kDa protein that is associated with chloride ion pumps .
Probab=22.03 E-value=13 Score=12.48 Aligned_cols=51 Identities=22% Similarity=0.279 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHCCCEEEEECCCCCCE-E-CCCE-EEEEEECC--CCEEEE-CEEEEECC
Q ss_conf 9999999999996698899813433204-0-5875-89999867--848970-56899318
Q T0604 220 VTMIEKMRATIIELGGEIRFSTRVDDLH-M-EDGQ-ITGVTLSN--GEEIKS-RHVVLAVG 274 (549)
Q Consensus 220 ~~vv~~L~~~l~~~G~~i~~~t~V~~i~-~-~~g~-v~gV~t~~--g~~i~a-d~VVlAtG 274 (549)
.++.+.|.+ +-+.++ .+++|++|. . .++. +..+...+ +...++ |.||+|+-
T Consensus 128 ~qI~~~ll~---~S~a~v-Ln~~VtsI~~~~~~~~~~y~v~~~~~~~~~~~~fD~VVIAtP 184 (368)
T PF07156_consen 128 WQIFEGLLN---ASKANV-LNTTVTSITSRSGNGYSLYTVTYKSTSGTESEFFDIVVIATP 184 (368)
T ss_pred HHHHHHHHH---HCCCCE-ECCEEEEEEECCCCCCEEEEEEEECCCCCCCCCCCEEEECCC
T ss_conf 999999999---715817-445457854126898415899984588875665778998777
Done!