Query 027584
Match_columns 221
No_of_seqs 160 out of 693
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 12:06:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027584.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027584hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1671 Ubiquinol cytochrome c 100.0 6.5E-34 1.4E-38 246.2 4.8 114 72-197 18-167 (210)
2 cd03470 Rieske_cytochrome_bc1 99.8 5.3E-20 1.2E-24 147.0 8.0 76 119-194 3-80 (126)
3 TIGR01416 Rieske_proteo ubiqui 99.8 1.2E-18 2.6E-23 145.7 8.4 79 117-195 41-127 (174)
4 COG0723 QcrA Rieske Fe-S prote 99.5 3.1E-14 6.6E-19 117.2 6.1 73 113-193 46-118 (177)
5 cd03476 Rieske_ArOX_small Smal 97.6 5.9E-05 1.3E-09 60.6 4.0 55 122-193 9-65 (126)
6 cd03478 Rieske_AIFL_N AIFL (ap 97.1 0.00098 2.1E-08 49.3 5.0 40 123-189 7-46 (95)
7 cd03477 Rieske_YhfW_C YhfW fam 97.0 0.0022 4.7E-08 48.6 6.0 43 124-192 7-49 (91)
8 cd03528 Rieske_RO_ferredoxin R 97.0 0.0021 4.5E-08 47.3 5.6 43 122-191 7-49 (98)
9 PF00355 Rieske: Rieske [2Fe-2 97.0 0.0029 6.4E-08 46.3 6.3 47 120-193 6-53 (97)
10 PF02921 UCR_TM: Ubiquinol cyt 96.9 1.3E-05 2.8E-10 58.6 -6.7 40 72-123 1-40 (64)
11 cd03469 Rieske_RO_Alpha_N Ries 96.8 0.0031 6.7E-08 47.7 5.6 47 119-191 4-51 (118)
12 cd03474 Rieske_T4moC Toluene-4 96.3 0.011 2.3E-07 44.7 5.5 43 123-192 8-50 (108)
13 cd03530 Rieske_NirD_small_Baci 96.1 0.016 3.5E-07 42.9 5.6 44 122-192 7-50 (98)
14 TIGR02694 arsenite_ox_S arseni 95.8 0.016 3.5E-07 47.0 4.7 55 122-193 12-68 (129)
15 cd03467 Rieske Rieske domain; 95.7 0.048 1E-06 40.2 6.7 43 123-191 8-50 (98)
16 cd04337 Rieske_RO_Alpha_Cao Ca 95.7 0.032 6.9E-07 44.5 5.9 52 114-192 16-67 (129)
17 cd03548 Rieske_RO_Alpha_OMO_CA 95.6 0.039 8.4E-07 44.1 6.1 52 113-193 13-64 (136)
18 PRK13474 cytochrome b6-f compl 95.4 0.029 6.3E-07 47.6 5.2 21 173-193 95-117 (178)
19 cd03479 Rieske_RO_Alpha_PhDO_l 95.4 0.042 9.1E-07 44.4 5.7 62 104-191 7-72 (144)
20 PRK09965 3-phenylpropionate di 95.3 0.027 5.9E-07 42.9 4.3 41 123-192 10-50 (106)
21 TIGR02377 MocE_fam_FeS Rieske 95.2 0.053 1.2E-06 41.1 5.5 44 122-192 8-51 (101)
22 cd03473 Rieske_CMP_Neu5Ac_hydr 94.7 0.064 1.4E-06 43.1 5.0 43 123-193 15-58 (107)
23 cd03531 Rieske_RO_Alpha_KSH Th 94.6 0.1 2.2E-06 40.6 5.8 46 119-190 5-50 (115)
24 cd03545 Rieske_RO_Alpha_OHBDO_ 94.3 0.15 3.3E-06 41.8 6.4 50 113-189 24-74 (150)
25 cd03538 Rieske_RO_Alpha_AntDO 93.9 0.2 4.4E-06 40.8 6.4 52 113-191 21-73 (146)
26 COG2146 {NirD} Ferredoxin subu 93.7 0.15 3.2E-06 39.8 5.1 41 122-189 11-52 (106)
27 cd03475 Rieske_SoxF_SoxL SoxF 93.3 0.054 1.2E-06 46.6 2.2 20 173-192 74-93 (171)
28 cd03529 Rieske_NirD Assimilato 93.3 0.3 6.5E-06 36.9 6.0 45 122-192 7-51 (103)
29 cd03472 Rieske_RO_Alpha_BPDO_l 93.3 0.24 5.3E-06 39.5 5.7 51 113-190 7-58 (128)
30 cd03535 Rieske_RO_Alpha_NDO Ri 93.2 0.32 6.9E-06 38.3 6.3 43 123-192 10-53 (123)
31 cd03471 Rieske_cytochrome_b6f 93.1 0.18 4E-06 41.2 4.9 16 177-192 49-64 (126)
32 TIGR02378 nirD_assim_sml nitri 92.7 0.42 9.2E-06 36.0 6.1 45 123-193 9-53 (105)
33 cd04338 Rieske_RO_Alpha_Tic55 92.7 0.3 6.6E-06 39.1 5.5 49 117-192 19-67 (134)
34 cd03536 Rieske_RO_Alpha_DTDO T 92.7 0.34 7.4E-06 38.1 5.7 43 123-192 8-51 (123)
35 cd03532 Rieske_RO_Alpha_VanA_D 92.4 0.45 9.8E-06 36.8 6.0 51 114-193 5-55 (116)
36 PRK09511 nirD nitrite reductas 92.3 0.46 9.9E-06 36.9 6.0 48 122-194 10-57 (108)
37 cd03480 Rieske_RO_Alpha_PaO Ri 92.1 0.39 8.6E-06 38.7 5.5 50 117-192 19-68 (138)
38 TIGR03171 soxL2 Rieske iron-su 90.8 0.15 3.2E-06 48.0 2.0 18 173-190 175-192 (321)
39 cd03541 Rieske_RO_Alpha_CMO Ri 89.9 0.98 2.1E-05 35.8 5.8 43 123-192 9-52 (118)
40 cd03539 Rieske_RO_Alpha_S5H Th 87.8 1.6 3.4E-05 34.9 5.7 41 123-189 8-49 (129)
41 cd03542 Rieske_RO_Alpha_HBDO R 84.5 2.8 6E-05 33.3 5.5 41 124-190 9-50 (123)
42 cd03537 Rieske_RO_Alpha_PrnD T 81.9 4.2 9.2E-05 32.6 5.6 43 122-192 10-52 (123)
43 PLN00095 chlorophyllide a oxyg 81.4 6.6 0.00014 38.1 7.6 51 113-189 70-121 (394)
44 PLN02281 chlorophyllide a oxyg 72.4 8.5 0.00018 38.6 5.8 54 113-193 218-271 (536)
45 TIGR03229 benzo_1_2_benA benzo 70.2 10 0.00022 36.6 5.7 52 113-191 37-89 (433)
46 PF08669 GCV_T_C: Glycine clea 69.0 7.5 0.00016 28.6 3.6 30 111-142 61-90 (95)
47 TIGR03228 anthran_1_2_A anthra 62.4 17 0.00037 35.2 5.6 52 113-191 37-89 (438)
48 PF08141 SspH: Small acid-solu 60.0 12 0.00027 27.2 3.2 19 128-146 13-31 (58)
49 TIGR02861 SASP_H small acid-so 60.0 11 0.00024 27.5 3.0 19 128-146 13-31 (58)
50 PLN02518 pheophorbide a oxygen 57.6 21 0.00047 35.5 5.5 54 114-193 89-142 (539)
51 PRK01625 sspH acid-soluble spo 54.6 16 0.00034 26.9 3.0 20 127-146 12-31 (59)
52 COG5649 Uncharacterized conser 54.6 5 0.00011 33.7 0.5 18 124-141 42-59 (132)
53 PRK03174 sspH acid-soluble spo 52.2 18 0.00039 26.6 3.0 19 128-146 13-31 (59)
54 PF14168 YjzC: YjzC-like prote 44.1 38 0.00083 24.8 3.6 31 103-133 5-37 (57)
55 COG1535 EntB Isochorismate hyd 36.5 16 0.00034 33.0 0.8 46 127-192 116-161 (218)
56 PF04194 PDCD2_C: Programmed c 35.7 27 0.00058 29.2 2.0 24 124-147 68-91 (164)
57 PRK07846 mycothione reductase; 34.2 15 0.00033 34.4 0.4 14 179-192 33-46 (451)
58 TIGR03452 mycothione_red mycot 33.6 15 0.00033 34.3 0.3 14 179-192 34-47 (452)
59 smart00026 EPEND Ependymins. E 33.0 77 0.0017 28.0 4.5 16 174-192 123-138 (191)
60 cd04470 S1_EF-P_repeat_1 S1_EF 30.9 70 0.0015 22.7 3.3 19 125-143 40-59 (61)
61 cd06815 PLPDE_III_AR_like_1 Ty 30.5 25 0.00054 32.0 1.1 17 175-191 148-164 (353)
62 PF01168 Ala_racemase_N: Alani 30.5 23 0.00051 29.1 0.9 15 175-189 142-156 (218)
63 cd06827 PLPDE_III_AR_proteobac 30.2 20 0.00044 33.0 0.5 15 175-189 146-160 (354)
64 PF13806 Rieske_2: Rieske-like 29.5 1.7E+02 0.0037 22.6 5.5 45 122-192 8-52 (104)
65 PF12913 SH3_6: SH3 domain of 28.0 44 0.00095 24.1 1.8 18 130-147 19-36 (54)
66 TIGR01438 TGR thioredoxin and 27.3 25 0.00054 33.5 0.5 15 177-191 43-57 (484)
67 COG4638 HcaE Phenylpropionate 27.2 1.6E+02 0.0034 26.7 5.6 32 113-145 26-57 (367)
68 COG1249 Lpd Pyruvate/2-oxoglut 25.7 24 0.00052 34.3 0.1 14 179-192 39-52 (454)
69 COG0231 Efp Translation elonga 25.4 1.4E+02 0.0031 24.5 4.5 20 124-143 106-126 (131)
70 KOG0192 Tyrosine kinase specif 25.3 26 0.00056 32.8 0.3 65 124-191 51-119 (362)
71 PF10172 DDA1: Det1 complexing 23.9 1.3E+02 0.0027 22.4 3.6 35 97-133 9-48 (65)
72 cd04463 S1_EF_like S1_EF_like: 23.1 95 0.0021 21.0 2.7 19 124-142 36-55 (55)
73 PRK03646 dadX alanine racemase 23.0 37 0.0008 31.4 0.8 15 175-189 148-162 (355)
74 PF09696 Ctf8: Ctf8; InterPro 21.5 93 0.002 25.1 2.7 54 116-185 58-111 (122)
75 cd06808 PLPDE_III Type III Pyr 21.3 35 0.00076 27.5 0.3 16 176-191 141-156 (211)
No 1
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=100.00 E-value=6.5e-34 Score=246.22 Aligned_cols=114 Identities=40% Similarity=0.715 Sum_probs=97.9
Q ss_pred cccCCCCCCchhhhhhhcCCCccccccCCCcccCCCCCCCCcceeEEEeccC----------------------------
Q 027584 72 RNEESLVPGVPATVAAVKNPTSKIVYDEYNHERYPPGDPSKRAFAYFVLTGG---------------------------- 123 (221)
Q Consensus 72 ~~~~~~~~~~p~~~~~~k~Pt~~~~y~~~~~~~~~~~~~~kr~f~y~~~~~~---------------------------- 123 (221)
.|++.+.|+++.|++. .++++...+++.|+.|+|+++|.+
T Consensus 18 ~~t~~~~p~~~~~~~~------------~~~~~~~~~~~~k~~~sy~~~g~~~~~~a~~ak~~v~~fi~smsAsadvlA~ 85 (210)
T KOG1671|consen 18 SHTDLMVPDFSDYRRE------------SVKDHQDTGEERKGFRSYLMVGAGAAGRAYAAKNLVTTFISSMSASADVLAM 85 (210)
T ss_pred ccccccCCCchhhhch------------hhhccccchhhhhceeeEEEecccceeehhhhhhhHHHHHHHhhhhhhhhhh
Confidence 3777777777776443 333334467778888899999853
Q ss_pred --------CCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCCCC
Q 027584 124 --------SIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQHHT 195 (221)
Q Consensus 124 --------~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~~~ 195 (221)
.||||++++|+||||||||+|||++||+.++.++.+.|+|||.|.+|+++|||||++||||||||||+++++
T Consensus 86 akiei~l~~IPeGk~~~~kwrGkpvfirhrt~~ei~~~r~V~~s~lrDPq~d~~rvk~~ewl~~igVCThLGCVp~~~AG 165 (210)
T KOG1671|consen 86 AKIEIKLSDIPEGKTVAFKWRGKPVFIRHRTKAEIEGERNVPQSTLRDPQDDVDRVKKPEWLVVIGVCTHLGCVPIANAG 165 (210)
T ss_pred eeeeeeeecCCCCCCcceeccCCceEEeeccccccccccccchhhccCchhhhhhccCcceEEEEeeecccccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred CC
Q 027584 196 IW 197 (221)
Q Consensus 196 ~~ 197 (221)
.+
T Consensus 166 d~ 167 (210)
T KOG1671|consen 166 DY 167 (210)
T ss_pred cc
Confidence 44
No 2
>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=99.81 E-value=5.3e-20 Score=146.96 Aligned_cols=76 Identities=51% Similarity=0.891 Sum_probs=67.6
Q ss_pred EeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcc--cccccCCCcEEEEEcccCCcCcccCCCC
Q 027584 119 VLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQ--DAERVKNPEWLVVVGVCTHLGFARDQHH 194 (221)
Q Consensus 119 ~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqs--d~~Rs~~PEwLVvIGICTHLGCIP~~~~ 194 (221)
.+..+.|+|||+++|+|+||||||+|||++||+++.+.+...+.||+. +..|+.+++|+++.++|||+||+|.+..
T Consensus 3 ~vdl~~l~~G~~~~v~w~Gkpv~I~~rt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~CtH~gc~~~~~~ 80 (126)
T cd03470 3 EVDLSKIEEGQLITVEWRGKPVFIRRRTPEEIAEAKAVDLSLLDDPDPAANRVRSGKPEWLVVIGICTHLGCVPTYRA 80 (126)
T ss_pred EEEhhhCCCCCEEEEEECCeEEEEEECCHHHHhhhhhcchhhcCCccccccccccCCCcEEEEeCcCCCCCCeecccc
Confidence 344459999999999999999999999999999999988778887664 5689999999999999999999998764
No 3
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=99.76 E-value=1.2e-18 Score=145.70 Aligned_cols=79 Identities=48% Similarity=0.918 Sum_probs=69.5
Q ss_pred EEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccc--------cccCCCcEEEEEcccCCcCc
Q 027584 117 YFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDA--------ERVKNPEWLVVVGVCTHLGF 188 (221)
Q Consensus 117 y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~--------~Rs~~PEwLVvIGICTHLGC 188 (221)
.+.+..+.|+||+.++|+|+||||||+|||++||+.+.+++.+.|+||++.. .|+.+++|+++.++||||||
T Consensus 41 ~~~v~l~eL~pG~~~~v~~~GkpI~I~~~t~~~~~~~~~~~~~~l~Dp~~~~~~~~~~~~~r~~~~~~~a~~~~CtH~Gc 120 (174)
T TIGR01416 41 PTEVDVSKIQPGQQLTVEWRGKPVFIRRRTKKEIDALKALDLGALKDPNSEAQQPDYARVKRSGKPEWLVVIGICTHLGC 120 (174)
T ss_pred cEEEEHHHCCCCCeEEEEECCeEEEEEeCCHHHhhhhhccchhhcCCCcccccCcchhhhhhccCCcEEEEEeccCCCCC
Confidence 3555566999999999999999999999999999999999999999996542 46678999999999999999
Q ss_pred ccCCCCC
Q 027584 189 ARDQHHT 195 (221)
Q Consensus 189 IP~~~~~ 195 (221)
+|.+.+.
T Consensus 121 ~~~~~~~ 127 (174)
T TIGR01416 121 IPTYGPE 127 (174)
T ss_pred ccccccC
Confidence 9987643
No 4
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=99.50 E-value=3.1e-14 Score=117.24 Aligned_cols=73 Identities=36% Similarity=0.449 Sum_probs=59.9
Q ss_pred cceeEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 113 RAFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 113 r~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
-+.+-+.+....+.+++..+++|||+|+|+++|++.++.........++.+++ +||++++++||||||+|.+
T Consensus 46 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~a~~~iCtHlGC~~~~ 117 (177)
T COG0723 46 LAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRRTEYAGPKGGVTRDGDGGVGN--------KEIVAYSAICTHLGCTVPW 117 (177)
T ss_pred ccCCceeeeccCCccceEEEEecCCCCeeeEeecccccccccceecccCCCCC--------ccEEEEeeeccCCCCccCc
Confidence 44444555555779999999999999999999999777776655556666655 8999999999999999999
Q ss_pred C
Q 027584 193 H 193 (221)
Q Consensus 193 ~ 193 (221)
+
T Consensus 118 ~ 118 (177)
T COG0723 118 N 118 (177)
T ss_pred c
Confidence 5
No 5
>cd03476 Rieske_ArOX_small Small subunit of Arsenite oxidase (ArOX) family, Rieske domain; ArOX is a molybdenum/iron protein involved in the detoxification of arsenic, oxidizing it to arsenate. It consists of two subunits, a large subunit similar to members of the DMSO reductase family of molybdenum enzymes and a small subunit with a Rieske-type [2Fe-2S] cluster. The large subunit of ArOX contains the molybdenum site at which the oxidation of arsenite occurs. The small subunit contains a domain homologous to the Rieske domains of the cytochrome bc(1) and cytochrome b6f complexes as well as naphthalene 1,2-dioxygenase. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer.
Probab=97.63 E-value=5.9e-05 Score=60.65 Aligned_cols=55 Identities=16% Similarity=0.277 Sum_probs=42.9
Q ss_pred cCCCCCCCeEEEEECC--eeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 122 GGSIEPGSTVTVKWRG--KPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 122 ~~~IepGq~vtVkWRG--KPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
...|++|+.++++|.| ++|+|++..+...... ..+.++.++.++|||+||.....
T Consensus 9 ~~~l~~g~~~~~~~~~~~~~i~v~r~~~~~~~~~-----------------~~~g~~~A~~~~CpH~g~~L~~g 65 (126)
T cd03476 9 LSQLSPGQPVTFNYPDESSPCVLVKLGVPVPGGV-----------------GPDNDIVAFSALCTHMGCPLTYD 65 (126)
T ss_pred HHHCCCCCeEEEEcCCCCCcEEEEECCccccCcc-----------------ccCCEEEEEeCcCCCCCcccccc
Confidence 3489999999999998 8999999854432211 13579999999999999976553
No 6
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=97.11 E-value=0.00098 Score=49.31 Aligned_cols=40 Identities=20% Similarity=0.306 Sum_probs=35.5
Q ss_pred CCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcc
Q 027584 123 GSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFA 189 (221)
Q Consensus 123 ~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCI 189 (221)
..|++|+.+.++..|++|+|.+. +.++.++.++|||.||.
T Consensus 7 ~~l~~g~~~~~~~~~~~v~v~r~---------------------------~g~~~A~~~~CpH~g~~ 46 (95)
T cd03478 7 SDLGDGEMKEVDVGDGKVLLVRQ---------------------------GGEVHAIGAKCPHYGAP 46 (95)
T ss_pred hhCCCCCEEEEEeCCcEEEEEEE---------------------------CCEEEEEcCcCcCCCCc
Confidence 37899999999999999998873 46899999999999995
No 7
>cd03477 Rieske_YhfW_C YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea.
Probab=97.00 E-value=0.0022 Score=48.56 Aligned_cols=43 Identities=28% Similarity=0.417 Sum_probs=37.5
Q ss_pred CCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 124 SIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 124 ~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
.|+||+.+++...|++|.|.+- ...++.++..+|||+||....
T Consensus 7 dl~~g~~~~~~~~g~~v~v~r~--------------------------~~g~~~A~~~~CpH~g~~l~~ 49 (91)
T cd03477 7 DLAPGEGGVVNIGGKRLAVYRD--------------------------EDGVLHTVSATCTHLGCIVHW 49 (91)
T ss_pred hcCCCCeEEEEECCEEEEEEEC--------------------------CCCCEEEEcCcCCCCCCCCcc
Confidence 7899999999999999988764 256899999999999997754
No 8
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=96.98 E-value=0.0021 Score=47.32 Aligned_cols=43 Identities=21% Similarity=0.354 Sum_probs=37.1
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARD 191 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~ 191 (221)
...|++|+.+.++..|++|+|.|. +.++.++..+|+|.||.-.
T Consensus 7 ~~~l~~g~~~~~~~~g~~~~v~r~---------------------------~~~~~a~~~~CpH~g~~L~ 49 (98)
T cd03528 7 VDELPEGEPKRVDVGGRPIAVYRV---------------------------DGEFYATDDLCTHGDASLS 49 (98)
T ss_pred hhhcCCCCEEEEEECCeEEEEEEE---------------------------CCEEEEECCcCCCCCCCCC
Confidence 458999999999999999999875 2489999999999999653
No 9
>PF00355 Rieske: Rieske [2Fe-2S] domain; InterPro: IPR017941 There are multiple types of iron-sulphur clusters which are grouped into three main categories based on their atomic content: [2Fe-2S], [3Fe-4S], [4Fe-4S] (see PDOC00176 from PROSITEDOC), and other hybrid or mixed metal types. Two general types of [2Fe-2S] clusters are known and they differ in their coordinating residues. The ferredoxin-type [2Fe-2S] clusters are coordinated to the protein by four cysteine residues (see PDOC00175 from PROSITEDOC). The Rieske-type [2Fe-2S] cluster is coordinated to its protein by two cysteine residues and two histidine residues [, ]. The structure of several Rieske domains has been solved []. It contains three layers of antiparallel beta sheets forming two beta sandwiches. Both beta sandwiches share the central sheet 2. The metal-binding site is at the top of the beta sandwich formed by the sheets 2 and 3. The Fe1 iron of the Rieske cluster is coordinated by two cysteines while the other iron Fe2 is coordinated by two histidines. Two inorganic sulphide ions bridge the two iron ions forming a flat, rhombic cluster. Rieske-type iron-sulphur clusters are common to electron transfer chains of mitochondria and chloroplast and to non-haem iron oxygenase systems: The Rieske protein of the Ubiquinol-cytochrome c reductase (1.10.2.2 from EC) (also known as the bc1 complex or complex III), a complex of the electron transport chains of mitochondria and of some aerobic prokaryotes; it catalyses the oxidoreduction of ubiquinol and cytochrome c. The Rieske protein of chloroplastic plastoquinone-plastocyanin reductase (1.10.99.1 from EC) (also known as the b6f complex). It is functionally similar to the bc1 complex and catalyses the oxidoreduction of plastoquinol and cytochrome f. Bacterial naphthalene 1,2-dioxygenase subunit alpha, a component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol. Bacterial 3-phenylpropionate dioxygenase ferredoxin subunit. Bacterial toluene monoxygenase. Bacterial biphenyl dioxygenase. ; GO: 0016491 oxidoreductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 2XRX_A 2XR8_O 2XSH_G 2XSO_I 2YFI_C 2YFL_A 2YFJ_K 1G8J_D 1G8K_D 1NYK_B ....
Probab=96.96 E-value=0.0029 Score=46.31 Aligned_cols=47 Identities=23% Similarity=0.374 Sum_probs=38.3
Q ss_pred eccCCCCC-CCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 120 LTGGSIEP-GSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 120 ~~~~~Iep-Gq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
.....|++ |....++..+++|+|++. +.++.++..+|||+||.....
T Consensus 6 ~~~~el~~~~~~~~~~~~~~~v~~~~~---------------------------~g~~~A~~~~CpH~g~~l~~~ 53 (97)
T PF00355_consen 6 CRSSELPEPGDVKRVDVGGKLVLVRRS---------------------------DGEIYAFSNRCPHQGCPLSEG 53 (97)
T ss_dssp EEGGGSHSTTEEEEEEETTEEEEEEET---------------------------TTEEEEEESB-TTTSBBGGCS
T ss_pred eEHHHCCCCCCEEEEEcCCcEEEEEeC---------------------------CCCEEEEEccCCccceeEcce
Confidence 33458888 999999998888887754 789999999999999998776
No 10
>PF02921 UCR_TM: Ubiquinol cytochrome reductase transmembrane region; InterPro: IPR004192 The ubiquinol cytochrome c reductase (cytochrome bc1) complex is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis. The bc1 complex contains 11 subunits, 3 respiratory subunits (cytochrome B, cytochrome C1, Rieske protein), 2 core proteins and 6 low-molecular weight proteins. Each subunit of the cytochrome bc1 complex provides a single helix (this domain) to make up the transmembrane region of the complex.; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1NU1_E 1L0L_E 1BCC_E 1SQB_E 1SQQ_E 1SQP_E 1PPJ_E 2A06_R 1BE3_E 1BGY_E ....
Probab=96.87 E-value=1.3e-05 Score=58.61 Aligned_cols=40 Identities=33% Similarity=0.585 Sum_probs=28.0
Q ss_pred cccCCCCCCchhhhhhhcCCCccccccCCCcccCCCCCCCCcceeEEEeccC
Q 027584 72 RNEESLVPGVPATVAAVKNPTSKIVYDEYNHERYPPGDPSKRAFAYFVLTGG 123 (221)
Q Consensus 72 ~~~~~~~~~~p~~~~~~k~Pt~~~~y~~~~~~~~~~~~~~kr~f~y~~~~~~ 123 (221)
+|+|+++|||..|++.. |+. +.++++++||+|+||++|++
T Consensus 1 Ahtdi~~PdF~~Yr~~~--~~~----------~~~~~~~~rr~fsY~~~g~~ 40 (64)
T PF02921_consen 1 AHTDIKVPDFSDYRRKS--PSK----------RSRESDDSRRAFSYFMVGGG 40 (64)
T ss_dssp -GGGTS----TTTBSGG--TTS-----------SHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCchhhcccc--ccc----------ccCCCCcccceeeehhhhhH
Confidence 59999999999996655 543 36778899999999999864
No 11
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=96.82 E-value=0.0031 Score=47.73 Aligned_cols=47 Identities=28% Similarity=0.422 Sum_probs=38.5
Q ss_pred EeccCCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccC
Q 027584 119 VLTGGSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARD 191 (221)
Q Consensus 119 ~~~~~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~ 191 (221)
+.....|+ +|+.+.+++.|++|+|.|.. +.++.++..+|+|+||.-.
T Consensus 4 v~~~~el~~~g~~~~~~~~~~~i~v~r~~--------------------------~g~~~a~~n~CpH~g~~L~ 51 (118)
T cd03469 4 VGHSSELPEPGDYVTLELGGEPLVLVRDR--------------------------DGEVRAFHNVCPHRGARLC 51 (118)
T ss_pred eEEHHHCCCCCCEEEEEECCccEEEEECC--------------------------CCCEEEEEEeCCCCCCEee
Confidence 33345898 99999999999999998741 4679999999999999443
No 12
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=96.29 E-value=0.011 Score=44.75 Aligned_cols=43 Identities=19% Similarity=0.297 Sum_probs=36.4
Q ss_pred CCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 123 GSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 123 ~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
..|++|+.+.++..|++++|+++. +.++.++..+|+|.|| |+.
T Consensus 8 ~~l~~g~~~~~~~~~~~~~~~~~~--------------------------~g~~~A~~n~CpH~g~-~L~ 50 (108)
T cd03474 8 DDVWEGEMELVDVDGEEVLLVAPE--------------------------GGEFRAFQGICPHQEI-PLA 50 (108)
T ss_pred hccCCCceEEEEECCeEEEEEEcc--------------------------CCeEEEEcCcCCCCCC-Ccc
Confidence 489999999999999988887761 4679999999999997 454
No 13
>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
Probab=96.11 E-value=0.016 Score=42.93 Aligned_cols=44 Identities=20% Similarity=0.228 Sum_probs=37.2
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
...|++|+.+.++-.|++|+|.|. .+.++.++..+|+|.|| |+.
T Consensus 7 ~~~l~~~~~~~~~~~g~~i~l~r~--------------------------~~g~~~A~~~~CpH~g~-~L~ 50 (98)
T cd03530 7 LEDIPPRGARKVQTGGGEIAVFRT--------------------------ADDEVFALENRCPHKGG-PLS 50 (98)
T ss_pred HHHCCCCCcEEEEECCEEEEEEEe--------------------------CCCCEEEEcCcCCCCCC-Ccc
Confidence 458999999999999999999876 14679999999999998 654
No 14
>TIGR02694 arsenite_ox_S arsenite oxidase, small subunit. This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7.
Probab=95.78 E-value=0.016 Score=47.04 Aligned_cols=55 Identities=11% Similarity=0.222 Sum_probs=40.6
Q ss_pred cCCCCCCCeEEEEECC--eeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 122 GGSIEPGSTVTVKWRG--KPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 122 ~~~IepGq~vtVkWRG--KPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
...|++|+++.|...+ .++||++...... ... ..+.+++++..+|||+||.....
T Consensus 12 ~~dl~~g~~~~~~~~~~~~~~~v~~~~~~~~--------~~~---------~~~G~~~A~~~~CpH~g~~L~~~ 68 (129)
T TIGR02694 12 ISELKLNEPLDFNYPDASSPGVLLKLGTPVE--------GGV---------GPDGDIVAFSTLCTHMGCPVSYS 68 (129)
T ss_pred HHHCCCCCCEEEecCCCCCCEEEEecCCccc--------Ccc---------ccCCEEEEEeCcCCCCCcccccc
Confidence 3489999999999986 4899988532210 111 12679999999999999988654
No 15
>cd03467 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.
Probab=95.72 E-value=0.048 Score=40.17 Aligned_cols=43 Identities=30% Similarity=0.487 Sum_probs=36.5
Q ss_pred CCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccC
Q 027584 123 GSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARD 191 (221)
Q Consensus 123 ~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~ 191 (221)
..|++|..+.++.-|+.|+|.++ .+.++.++.++|+|.||...
T Consensus 8 ~~~~~~~~~~~~~~~~~~~v~~~--------------------------~~~~~~a~~~~CpH~g~~l~ 50 (98)
T cd03467 8 SELPPGGGRVVVVGGGPVVVVRR--------------------------EGGEVYALSNRCTHQGCPLS 50 (98)
T ss_pred cccCCCceEEEEECCeEEEEEEe--------------------------CCCEEEEEcCcCCCCCccCC
Confidence 36889999999999999999886 13589999999999999443
No 16
>cd04337 Rieske_RO_Alpha_Cao Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the plastid-envelope inner and thylakoid membranes, that catalyzes the conversion of chlorophyllide a to chlorophyllide b. CAO is found not only in plants but also in chlorophytes and prochlorophytes. This domain represents the N-terminal rieske domain of the oxygenase alpha subunit. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Cao is closely related to several other plant RO's including Tic 55, a 55 kDa protein associated with protein transport through the inner
Probab=95.66 E-value=0.032 Score=44.50 Aligned_cols=52 Identities=17% Similarity=0.185 Sum_probs=41.4
Q ss_pred ceeEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 114 AFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 114 ~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
.+-|.+.-...|++|+.++++.-|++++|.|. .+.++.++..+|+|.|| |+.
T Consensus 16 ~~W~~v~~~~el~~g~~~~~~v~g~~l~l~r~--------------------------~~g~v~A~~n~CpH~g~-~L~ 67 (129)
T cd04337 16 NFWYPVEFSKDLKMDTMVPFELFGQPWVLFRD--------------------------EDGTPGCIRDECAHRAC-PLS 67 (129)
T ss_pred CccEEEEEHHHCCCCCeEEEEECCcEEEEEEC--------------------------CCCcEEEEeCcCCCCcC-Ccc
Confidence 33445555568999999999999999988875 15679999999999999 444
No 17
>cd03548 Rieske_RO_Alpha_OMO_CARDO Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the
Probab=95.57 E-value=0.039 Score=44.12 Aligned_cols=52 Identities=17% Similarity=0.354 Sum_probs=40.8
Q ss_pred cceeEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 113 RAFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 113 r~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
+.|.++.. ...|++|+.++|+..|++|+|+|. +.++.++..+|+|.|+ |+.
T Consensus 13 ~~W~~v~~-~~el~~g~~~~~~~~g~~i~l~r~---------------------------~g~v~A~~n~CpHrg~-~L~ 63 (136)
T cd03548 13 NHWYPALF-SHELEEGEPKGIQLCGEPILLRRV---------------------------DGKVYALKDRCLHRGV-PLS 63 (136)
T ss_pred cCcEEEEE-HHHCCCCCeEEEEECCcEEEEEec---------------------------CCEEEEEeCcCcCCCC-ccc
Confidence 44544443 458999999999999999998764 5678999999999997 554
Q ss_pred C
Q 027584 193 H 193 (221)
Q Consensus 193 ~ 193 (221)
.
T Consensus 64 ~ 64 (136)
T cd03548 64 K 64 (136)
T ss_pred c
Confidence 3
No 18
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=95.43 E-value=0.029 Score=47.57 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=16.0
Q ss_pred CCcE--EEEEcccCCcCcccCCC
Q 027584 173 NPEW--LVVVGVCTHLGFARDQH 193 (221)
Q Consensus 173 ~PEw--LVvIGICTHLGCIP~~~ 193 (221)
+.++ +.+.++||||||...+.
T Consensus 95 ~g~~~~~a~~~~CtH~gc~l~~~ 117 (178)
T PRK13474 95 DGTIASYGINAVCTHLGCVVPWN 117 (178)
T ss_pred CCEEEEEEecCCCCCCCCccccc
Confidence 4556 56789999999987654
No 19
>cd03479 Rieske_RO_Alpha_PhDO_like Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form th
Probab=95.36 E-value=0.042 Score=44.40 Aligned_cols=62 Identities=21% Similarity=0.267 Sum_probs=44.9
Q ss_pred cCCCCCCCCccee---EEEeccCCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEE
Q 027584 104 RYPPGDPSKRAFA---YFVLTGGSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVV 179 (221)
Q Consensus 104 ~~~~~~~~kr~f~---y~~~~~~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVv 179 (221)
|.-+|.|.-+-|. |.+.....|+ +|+.+.++--|++|+|.|. .+.++.++
T Consensus 7 ~~~~~~~~~~~~~~~W~~v~~~~eL~~~g~~~~~~~~g~~i~v~r~--------------------------~~G~v~A~ 60 (144)
T cd03479 7 RVGPGTPMGELLRRYWQPVALSSELTEDGQPVRVRLLGEDLVAFRD--------------------------TSGRVGLL 60 (144)
T ss_pred ecCCCCchhhHhhCceEEEEEHHHCCCCCCEEEEEECCcEEEEEEe--------------------------CCCCEEEE
Confidence 4555666443333 3333445899 7999999999999988775 15679999
Q ss_pred EcccCCcCcccC
Q 027584 180 VGVCTHLGFARD 191 (221)
Q Consensus 180 IGICTHLGCIP~ 191 (221)
..+|+|.||.=.
T Consensus 61 ~n~CpHrG~~L~ 72 (144)
T cd03479 61 DEHCPHRGASLV 72 (144)
T ss_pred cCcCCCCCCccc
Confidence 999999999543
No 20
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=95.35 E-value=0.027 Score=42.92 Aligned_cols=41 Identities=12% Similarity=0.176 Sum_probs=34.3
Q ss_pred CCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 123 GSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 123 ~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
..|++|+.+.|+.. ++|+|.+. +.++.++-.+|+|+|| |+.
T Consensus 10 ~~l~~g~~~~~~~~-~~i~v~~~---------------------------~g~~~A~~~~CpH~g~-~L~ 50 (106)
T PRK09965 10 ADLPEGEALRVDTS-PVIALFNV---------------------------GGEFYAIDDRCSHGNA-SLS 50 (106)
T ss_pred HHcCCCCeEEEeCC-CeEEEEEE---------------------------CCEEEEEeCcCCCCCC-CCC
Confidence 48999999988876 78877764 4689999999999999 764
No 21
>TIGR02377 MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE subfamily. This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H].
Probab=95.20 E-value=0.053 Score=41.08 Aligned_cols=44 Identities=18% Similarity=0.269 Sum_probs=37.2
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
...|++|+.+.++-.|++|+|.|. .+.+++++...|+|+|| |+.
T Consensus 8 ~~dl~~g~~~~~~~~g~~i~l~r~--------------------------~~g~~~A~~~~CpH~g~-~L~ 51 (101)
T TIGR02377 8 ADDIGREDVARFDHGGRTFAIYRT--------------------------PDDQYYATDGLCTHEYA-HLA 51 (101)
T ss_pred HHHcCCCCEEEEEECCeEEEEEEe--------------------------CCCEEEEEcCcCCCCCC-CCC
Confidence 348999999999999999999774 14679999999999999 665
No 22
>cd03473 Rieske_CMP_Neu5Ac_hydrolase_N Cytidine monophosphate-N-acetylneuraminic acid (CMP Neu5Ac) hydroxylase family, N-terminal Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. CMP Neu5Ac hydroxylase is the key enzyme for the synthesis of N-glycolylneuraminic acid (NeuGc) from N-acetylneuraminic acid (Neu5Ac), NeuGc and Neu5Ac are members of a family of cell surface sugars called sialic acids. All mammals except humans have both NeuGc variants on their cell surfaces. In humans, the gene encoding CMP Neu5Ac hydroxylase has a mutation within its coding region that abolishes NeuGc production.
Probab=94.70 E-value=0.064 Score=43.14 Aligned_cols=43 Identities=19% Similarity=0.200 Sum_probs=37.7
Q ss_pred CCCCCCCeEEEEE-CCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 123 GSIEPGSTVTVKW-RGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 123 ~~IepGq~vtVkW-RGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
..|+||++..|++ .|+.|.|.+. +.+|+.+-.+|||.|+ |+..
T Consensus 15 ~eL~~G~~~~v~v~~g~~I~V~~~---------------------------~G~~~A~~n~CpH~g~-pL~~ 58 (107)
T cd03473 15 ANLKEGINFFRNKEDGKKYIIYKS---------------------------KSELKACKNQCKHQGG-LFIK 58 (107)
T ss_pred hcCCCCceEEEEecCCcEEEEEEE---------------------------CCEEEEEcCCCCCCCc-cccC
Confidence 3899999999999 9999999875 5689999999999999 6543
No 23
>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.
Probab=94.59 E-value=0.1 Score=40.57 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=38.0
Q ss_pred EeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCccc
Q 027584 119 VLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFAR 190 (221)
Q Consensus 119 ~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP 190 (221)
+.-...|++|+.++++=-|++|+|.|. .+.++.++-.+|+|.|+.=
T Consensus 5 v~~~~dl~~g~~~~~~~~g~~i~l~r~--------------------------~~g~~~a~~n~CpH~ga~L 50 (115)
T cd03531 5 LGLARDFRDGKPHGVEAFGTKLVVFAD--------------------------SDGALNVLDAYCRHMGGDL 50 (115)
T ss_pred EEEHHHCCCCCeEEEEECCeEEEEEEC--------------------------CCCCEEEEcCcCCCCCCCC
Confidence 333458999999999999999999874 2578999999999999943
No 24
>cd03545 Rieske_RO_Alpha_OHBDO_like Rieske non-heme iron oxygenase (RO) family, Ortho-halobenzoate-1,2-dioxygenase (OHBDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of OHBDO, salicylate 5-hydroxylase (S5H), terephthalate 1,2-dioxygenase system (TERDOS) and similar proteins. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OHBDO converts 2-chlorobenzoate (2-CBA) to catechol as well as 2,4-dCBA and 2,5-dCBA to 4-chlorocatechol, as part of the chlorobenzoate degradation pathway. Although ortho-substituted chlorobe
Probab=94.28 E-value=0.15 Score=41.79 Aligned_cols=50 Identities=22% Similarity=0.358 Sum_probs=38.7
Q ss_pred cceeEEEeccCCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcc
Q 027584 113 RAFAYFVLTGGSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFA 189 (221)
Q Consensus 113 r~f~y~~~~~~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCI 189 (221)
+.|.++... ..|+ +|+.++++..|++|+|.|.. +.++.++-.+|+|.|+.
T Consensus 24 ~~W~~v~~~-~el~~~g~~~~~~i~g~~iiv~r~~--------------------------~g~v~A~~n~CpHrg~~ 74 (150)
T cd03545 24 KTWSYVGLE-AEIPNAGDFKSTFVGDTPVVVTRAE--------------------------DGSLHAWVNRCAHRGAL 74 (150)
T ss_pred CceEEEEEH-HHCCCCCCEEEEEECCceEEEEECC--------------------------CCCEEEEcccCcCCCCE
Confidence 344444433 3787 69999999999999887751 45788999999999995
No 25
>cd03538 Rieske_RO_Alpha_AntDO Rieske non-heme iron oxygenase (RO) family, Anthranilate 1,2-dioxygenase (AntDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. AntDO converts anthranilate to catechol, a naturally occurring compound formed through tryptophan degradation and an important intermediate in the metabolism of many N-heterocyclic compounds such as indole, o-nitrobenzoate, carbazole, and quinaldine.
Probab=93.90 E-value=0.2 Score=40.78 Aligned_cols=52 Identities=25% Similarity=0.409 Sum_probs=41.2
Q ss_pred cceeEEEeccCCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccC
Q 027584 113 RAFAYFVLTGGSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARD 191 (221)
Q Consensus 113 r~f~y~~~~~~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~ 191 (221)
+.|.++... ..|+ +|+.++++--|+||+|.|.. +.++.++..+|+|.|+.-.
T Consensus 21 ~~W~~v~~~-~elp~~G~~~~~~i~g~~i~v~r~~--------------------------~g~v~A~~n~CpHrg~~L~ 73 (146)
T cd03538 21 NAWIYVGHE-SQVPNPGDYITTRIGDQPVVMVRHT--------------------------DGSVHVLYNRCPHKGTKIV 73 (146)
T ss_pred cCCEEEEEH-HHCCCCCCEEEEEECCeeEEEEECC--------------------------CCCEEEEeccCcCCCCEee
Confidence 556655543 3787 79999999999999988751 4689999999999999764
No 26
>COG2146 {NirD} Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only]
Probab=93.74 E-value=0.15 Score=39.85 Aligned_cols=41 Identities=22% Similarity=0.343 Sum_probs=35.9
Q ss_pred cCCCCCCCeEEEEECC-eeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcc
Q 027584 122 GGSIEPGSTVTVKWRG-KPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFA 189 (221)
Q Consensus 122 ~~~IepGq~vtVkWRG-KPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCI 189 (221)
...|+||..+.|.+.+ +++++++. +.+++.+..+|+|.||-
T Consensus 11 ~~dl~~~~~~~v~~~~~~~~~~~~~---------------------------~g~v~A~~n~CpH~~~~ 52 (106)
T COG2146 11 VDDLPEGGGVRVLVGGGRFALVVRA---------------------------DGEVFAIDNRCPHAGAP 52 (106)
T ss_pred hHhcCCCCceEEEecCCEEEEEEec---------------------------CCEEEEEeCcCCCCCCc
Confidence 4589999999999966 88888776 68999999999999995
No 27
>cd03475 Rieske_SoxF_SoxL SoxF and SoxL family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. SoxF is a subunit of the terminal oxidase supercomplex SoxM in the plasma membrane of Sulfolobus acidocaldarius that combines features of a cytochrome bc(1) complex and a cytochrome. The Rieske domain of SoxF has a 12 residue insertion which is not found in eukaryotic and bacterial Rieske proteins and is thought to influence the redox properties of the iron-sulfur cluster. SoxL is a Rieske protein which may be part of an archaeal bc-complex homologue whose physiological function is still unknown. SoxL has two features not seen in other Rieske proteins; (i) a significantly greater distance between the two cluster-binding sites and (ii) an unexpected Pro - Asp substitution at one of the cluster binding sites. SoxF and SoxL are found in archaea and in bacteria.
Probab=93.32 E-value=0.054 Score=46.63 Aligned_cols=20 Identities=25% Similarity=0.526 Sum_probs=18.0
Q ss_pred CCcEEEEEcccCCcCcccCC
Q 027584 173 NPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 173 ~PEwLVvIGICTHLGCIP~~ 192 (221)
+.++.++.++||||||.+.+
T Consensus 74 ~g~IvA~S~iCpHlGc~l~~ 93 (171)
T cd03475 74 NKSIVAFSAICQHLGCQPPP 93 (171)
T ss_pred CCEEEEEeCcCCCCCCcccc
Confidence 68999999999999998764
No 28
>cd03529 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.
Probab=93.32 E-value=0.3 Score=36.86 Aligned_cols=45 Identities=20% Similarity=0.088 Sum_probs=36.9
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
...|++|+.+.++=.|++|+|.+- .+.++..+-..|+|.|+-+..
T Consensus 7 ~~~l~~g~~~~~~~~g~~i~l~r~--------------------------~~g~~~A~~~~CpH~g~~ll~ 51 (103)
T cd03529 7 LDDLPPGSGVAALVGDTQIAIFRL--------------------------PGREVYAVQNMDPHSRANVLS 51 (103)
T ss_pred HHHCCCCCcEEEEECCEEEEEEEe--------------------------CCCeEEEEeCcCCCCCCcccC
Confidence 348999999999999999988765 123899999999999986543
No 29
>cd03472 Rieske_RO_Alpha_BPDO_like Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is i
Probab=93.27 E-value=0.24 Score=39.51 Aligned_cols=51 Identities=24% Similarity=0.363 Sum_probs=37.1
Q ss_pred cceeEEEeccCCCCC-CCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCccc
Q 027584 113 RAFAYFVLTGGSIEP-GSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFAR 190 (221)
Q Consensus 113 r~f~y~~~~~~~Iep-Gq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP 190 (221)
+.|.++... ..|++ |..++++..|+||+|.+. .+.++.++-.+|+|.||.=
T Consensus 7 ~~W~~v~~~-~el~~~g~~~~~~~~~~~i~l~r~--------------------------~~g~i~A~~n~C~Hrg~~L 58 (128)
T cd03472 7 RSWLLLGHE-THIPKAGDYLTTYMGEDPVIVVRQ--------------------------KDGSIRVFLNQCRHRGMRI 58 (128)
T ss_pred CCCeEeEEH-HHCCCCCCEEEEEECCceEEEEEC--------------------------CCCCEEEEhhhCcCCCCee
Confidence 344443333 36875 777888899999988874 1467899999999999943
No 30
>cd03535 Rieske_RO_Alpha_NDO Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. NDO is a three-component RO system consisting of a reductase, a ferredoxin, and a hetero-hexameric alpha-beta subunit oxygenase component. NDO catalyzes the oxidation of naphthalene to cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-dihydrodiol) with the consumption of O2 and NAD(P)H. NDO has a relaxed substrate specificity and can oxidize almost 1
Probab=93.23 E-value=0.32 Score=38.27 Aligned_cols=43 Identities=19% Similarity=0.258 Sum_probs=35.0
Q ss_pred CCCCC-CCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 123 GSIEP-GSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 123 ~~Iep-Gq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
..|++ |..++++..|++|+|.|.. +.++.++..+|+|.|+ |+.
T Consensus 10 ~el~~~g~~~~~~~~~~~iiv~r~~--------------------------~g~~~A~~n~CpHrg~-~L~ 53 (123)
T cd03535 10 SEIPNAGDYVVRYIGDDSFIVCRDE--------------------------DGEIRAMFNSCRHRGM-QVC 53 (123)
T ss_pred HHCCCCCCEEEEEECCeEEEEEECC--------------------------CCCEEEEcccCccCCC-Eee
Confidence 47876 7888888999999998751 4678999999999998 554
No 31
>cd03471 Rieske_cytochrome_b6f Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, PetM, and PetN. Rieske ISP, one of the large subunits of the cytochrome bc-type complexes, is involved in respiratory and photosynthetic electron transfer. The core of the chloroplast b6f complex is similar to the analogous respiratory cytochrome bc(1) complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=93.10 E-value=0.18 Score=41.19 Aligned_cols=16 Identities=38% Similarity=0.542 Sum_probs=13.7
Q ss_pred EEEEcccCCcCcccCC
Q 027584 177 LVVVGVCTHLGFARDQ 192 (221)
Q Consensus 177 LVvIGICTHLGCIP~~ 192 (221)
+.+.++|||+||....
T Consensus 49 ~A~~~~CpH~G~~l~~ 64 (126)
T cd03471 49 YGINAVCTHLGCVVPW 64 (126)
T ss_pred EEecCCCcCCCCCcCc
Confidence 6889999999997654
No 32
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=92.71 E-value=0.42 Score=35.96 Aligned_cols=45 Identities=16% Similarity=0.140 Sum_probs=38.2
Q ss_pred CCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 123 GSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 123 ~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
..|++|+.+.++=.|++|.|.+. .+.++.++-..|+|.|+.|+..
T Consensus 9 ~el~~g~~~~~~v~g~~l~v~r~--------------------------~~~~~~a~~~~CpH~g~~~L~~ 53 (105)
T TIGR02378 9 DDIPEETGVCVLLGDTQIAIFRV--------------------------PGDQVFAIQNMCPHKRAFVLSR 53 (105)
T ss_pred HHCCCCCcEEEEECCEEEEEEEe--------------------------CCCcEEEEeCcCCCCCCccccc
Confidence 48999999999999999988864 1467999999999998888764
No 33
>cd04338 Rieske_RO_Alpha_Tic55 Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport through the plant inner chloroplast membrane. This domain represents the N-terminal Rieske domain of the Tic55 oxygenase alpha subunit. Tic55 is closely related to the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO), Ptc52, and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis.
Probab=92.68 E-value=0.3 Score=39.08 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=39.6
Q ss_pred EEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 117 YFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 117 y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
|.+.-...|++|+.++++.-|++|+|.|. .+.++.++-.+|+|.|+ |+.
T Consensus 19 ~~v~~~~el~~~~~~~~~v~g~~ivl~r~--------------------------~~G~v~A~~n~CpHrga-~L~ 67 (134)
T cd04338 19 YPLYLLKDVPTDAPLGLSVYDEPFVLFRD--------------------------QNGQLRCLEDRCPHRLA-KLS 67 (134)
T ss_pred EEEEEHHHCCCCCCEEEEECCceEEEEEc--------------------------CCCCEEEEcCcCCCCcC-ccc
Confidence 34444559999999999999999999875 15689999999999998 544
No 34
>cd03536 Rieske_RO_Alpha_DTDO This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit (DitA) of diterpenoid dioxygenase (DTDO). DTDO is a novel aromatic-ring-hydroxylating dioxygenase found in Pseudomonas and other proteobacteria that degrades dehydroabietic acid (DhA). Specifically, DitA hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. The ditA1 and ditA2 genes encode the alpha and beta subunits of the oxygenase component of DTDO while the ditA3 gene encodes the ferredoxin component of DTDO. The organization of the genes encoding the various diterpenoid dioxygenase components, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual iron-sulfur cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.
Probab=92.66 E-value=0.34 Score=38.09 Aligned_cols=43 Identities=28% Similarity=0.429 Sum_probs=34.6
Q ss_pred CCCCC-CCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 123 GSIEP-GSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 123 ~~Iep-Gq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
..|++ |..++++-.|++|+|.|. .+.++.++..+|+|.|+ |+.
T Consensus 8 ~el~~~g~~~~~~~~~~~i~v~r~--------------------------~~g~v~A~~n~CpH~g~-~L~ 51 (123)
T cd03536 8 SEIPNKGDFMVRDMGSDSVIVARD--------------------------KDGEIHVSLNVCPHRGM-RIS 51 (123)
T ss_pred HHCCCCCCEEEEEECCceEEEEEC--------------------------CCCCEEEEeeeCCCCCC-Ccc
Confidence 36777 778888899999988875 14688999999999998 543
No 35
>cd03532 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degrad
Probab=92.38 E-value=0.45 Score=36.78 Aligned_cols=51 Identities=14% Similarity=0.205 Sum_probs=38.6
Q ss_pred ceeEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 114 AFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 114 ~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
.|.++.. ...|+ |+.++++--|++|+|.|. .+.++.++-.+|+|.|+ |+..
T Consensus 5 ~W~~v~~-~~el~-~~~~~~~~~g~~i~l~r~--------------------------~~g~~~a~~n~CpH~g~-~L~~ 55 (116)
T cd03532 5 AWYVAAW-ADELG-DKPLARTLLGEPVVLYRT--------------------------QDGRVAALEDRCPHRSA-PLSK 55 (116)
T ss_pred cEEEEEE-HHHcC-CCcEEEEECCceEEEEEC--------------------------CCCCEEEeCCcCCCCCC-CccC
Confidence 3444433 34787 999999999999999874 14678999999999999 5543
No 36
>PRK09511 nirD nitrite reductase small subunit; Provisional
Probab=92.33 E-value=0.46 Score=36.92 Aligned_cols=48 Identities=15% Similarity=0.094 Sum_probs=39.9
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCCC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQHH 194 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~~ 194 (221)
...|++|+.+.|+-.|+.|.|.|-. .+.+++.+-..|||-|+.|+...
T Consensus 10 ~~dl~~g~~~~v~v~g~~i~l~~~~-------------------------~~g~~~A~~n~CpH~~~~~L~~G 57 (108)
T PRK09511 10 IDDILPGTGVCALVGDEQVAIFRPY-------------------------HDEQVFAISNIDPFFQASVLSRG 57 (108)
T ss_pred HhHcCCCceEEEEECCEEEEEEEEC-------------------------CCCEEEEEeCcCCCCCCcccCCc
Confidence 3489999999999999999988620 15689999999999999887654
No 37
>cd03480 Rieske_RO_Alpha_PaO Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO) and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PaO expression increases upon physical wounding of plant leaves and is thought to catalyze a key step in chlorophyll degradation. The
Probab=92.08 E-value=0.39 Score=38.69 Aligned_cols=50 Identities=16% Similarity=0.251 Sum_probs=39.7
Q ss_pred EEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 117 YFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 117 y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
|.+.-...|++|+.++++-.|++|+|.|.. .+.++.++..+|+|.|+ |+.
T Consensus 19 ~~v~~~~el~~g~~~~~~~~g~~i~v~r~~-------------------------~dG~~~A~~n~CpHrga-~L~ 68 (138)
T cd03480 19 YPVAYVEDLDPSRPTPFTLLGRDLVIWWDR-------------------------NSQQWRAFDDQCPHRLA-PLS 68 (138)
T ss_pred EEEEEHHHCCCCCcEEEEECCeeEEEEEEC-------------------------CCCEEEEEcCCCcCCcC-ccc
Confidence 334445589999999999999999998740 15789999999999998 444
No 38
>TIGR03171 soxL2 Rieske iron-sulfur protein SoxL2. This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system.
Probab=90.77 E-value=0.15 Score=47.98 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=15.5
Q ss_pred CCcEEEEEcccCCcCccc
Q 027584 173 NPEWLVVVGVCTHLGFAR 190 (221)
Q Consensus 173 ~PEwLVvIGICTHLGCIP 190 (221)
+..+....+|||||||.|
T Consensus 175 ~~~IVAyS~IC~H~GC~~ 192 (321)
T TIGR03171 175 NKSIVAYSAICQHLGCTP 192 (321)
T ss_pred CCCEEEEecccCcCCCCc
Confidence 466778899999999977
No 39
>cd03541 Rieske_RO_Alpha_CMO Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. CMO is a novel RO found in certain plants which catalyzes the first step in betaine synthesis. CMO is not found in animals or bacteria. In these organisms, the first step in betaine synthesis is catalyzed by either the membrane-bound choline dehydrogenase (CDH) or the soluble choline oxidase (COX).
Probab=89.95 E-value=0.98 Score=35.82 Aligned_cols=43 Identities=16% Similarity=0.127 Sum_probs=34.3
Q ss_pred CCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 123 GSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 123 ~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
..|+ +|..++++.-|+||+|.|.. +.++.++-.+|+|.|+ |+.
T Consensus 9 ~el~~~g~~~~~~~~g~~i~v~r~~--------------------------dg~v~A~~n~C~Hrg~-~L~ 52 (118)
T cd03541 9 DQVKEKNQYFTGRLGNVEYVVCRDG--------------------------NGKLHAFHNVCTHRAS-ILA 52 (118)
T ss_pred HHCCCCCCeEEEEECCeEEEEEECC--------------------------CCCEEEEeCCCCCCcC-Ccc
Confidence 3566 47788999999999998751 4578899999999999 443
No 40
>cd03539 Rieske_RO_Alpha_S5H This alignment model represents the N-terminal rieske iron-sulfur domain of the oxygenase alpha subunit (NagG) of salicylate 5-hydroxylase (S5H). S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits.
Probab=87.83 E-value=1.6 Score=34.94 Aligned_cols=41 Identities=27% Similarity=0.413 Sum_probs=34.1
Q ss_pred CCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcc
Q 027584 123 GSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFA 189 (221)
Q Consensus 123 ~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCI 189 (221)
..|+ +|..++++..|++|+|.|.. +.++.++..+|+|.|..
T Consensus 8 ~~l~~~g~~~~~~~~~~~v~v~r~~--------------------------dg~v~A~~n~C~Hrg~~ 49 (129)
T cd03539 8 AEIPNPGDFKRTLIGERSVIMTRDP--------------------------DGGINVVENVCAHRGMR 49 (129)
T ss_pred HHCCCCCCEEEEEECCcEEEEEECC--------------------------CCCEEEEeccCcCCCCE
Confidence 3676 69999999999999887752 45789999999999974
No 41
>cd03542 Rieske_RO_Alpha_HBDO Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. HBDO catalyzes the double hydroxylation of 2-halobenzoates with concomitant release of halogenide and carbon dioxide, yielding catechol.
Probab=84.50 E-value=2.8 Score=33.33 Aligned_cols=41 Identities=24% Similarity=0.360 Sum_probs=33.2
Q ss_pred CCCC-CCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCccc
Q 027584 124 SIEP-GSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFAR 190 (221)
Q Consensus 124 ~Iep-Gq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP 190 (221)
.|++ |..++++-.|+||+|.|.. +.++.++-.+|+|.|+.=
T Consensus 9 elp~~g~~~~~~~~~~~i~l~r~~--------------------------~g~v~A~~n~C~Hrg~~L 50 (123)
T cd03542 9 QIPNNNDYFTTTIGRQPVVITRDK--------------------------DGELNAFINACSHRGAML 50 (123)
T ss_pred HCCCCCCEEEEEECCcEEEEEECC--------------------------CCCEEEEcccCcCCCCcc
Confidence 6776 7788888899999888752 457889999999999944
No 42
>cd03537 Rieske_RO_Alpha_PrnD This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit of aminopyrrolnitrin oxygenase (PrnD). PrnD is a novel Rieske N-oxygenase that catalyzes the final step in the pyrrolnitrin biosynthetic pathway, the oxidation of the amino group in aminopyrrolnitrin to a nitro group, forming the antibiotic pyrrolnitrin. The biosynthesis of pyrrolnitrin is one of the best examples of enzyme-catalyzed arylamine oxidation. Although arylamine oxygenases are widely distributed within the microbial world and used in a variety of metabolic reactions, PrnD represents one of only two known examples of arylamine oxygenases or N-oxygenases involved in arylnitro group formation, the other being AurF involved in aureothin biosynthesis.
Probab=81.95 E-value=4.2 Score=32.58 Aligned_cols=43 Identities=19% Similarity=0.320 Sum_probs=33.7
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
...|+ ++.+.++.-|++++|.|. .+.++.++-.+|+|.|+ |+.
T Consensus 10 ~~~l~-~~~~~~~~~g~~ivl~r~--------------------------~~g~v~a~~n~CpHrg~-~Ls 52 (123)
T cd03537 10 SDDLK-DKPTELTLFGRPCVAWRG--------------------------ATGRAVVMDRHCSHLGA-NLA 52 (123)
T ss_pred HHHcC-CCcEEEEECCeEEEEEEc--------------------------cCCEEEEEcCCCCCCCC-Ccc
Confidence 34675 677899999999988774 14678999999999998 443
No 43
>PLN00095 chlorophyllide a oxygenase; Provisional
Probab=81.42 E-value=6.6 Score=38.11 Aligned_cols=51 Identities=16% Similarity=0.201 Sum_probs=40.0
Q ss_pred cceeEEEeccCCC-CCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcc
Q 027584 113 RAFAYFVLTGGSI-EPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFA 189 (221)
Q Consensus 113 r~f~y~~~~~~~I-epGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCI 189 (221)
+.+-|.+.-...| ++|+.+.++=-|+||+|.+. .+.+|.++-.+|+|.||.
T Consensus 70 r~~WypVa~ssdL~~~g~~~~f~L~GepIVL~Rd--------------------------~dGqv~Af~N~CPHRGap 121 (394)
T PLN00095 70 RAHWFPVAFAAGLRDEDALIAFDLFNVPWVLFRD--------------------------ADGEAGCIKDECAHRACP 121 (394)
T ss_pred hcCeEEEEEHHHCCCCCceEEEEECCEEEEEEEC--------------------------CCCCEEEEeccCCCCCCc
Confidence 3344444445589 88999999999999988864 146799999999999993
No 44
>PLN02281 chlorophyllide a oxygenase
Probab=72.42 E-value=8.5 Score=38.64 Aligned_cols=54 Identities=19% Similarity=0.203 Sum_probs=41.8
Q ss_pred cceeEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 113 RAFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 113 r~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
+.+-|.+.-...|++|+.+.++.-|+||+|.|. .+.++.++-.+|.|-|| |+.
T Consensus 218 rn~Wy~Va~s~EL~~g~~~~v~llG~~IVL~R~--------------------------~dG~v~A~~D~CPHRga-PLs 270 (536)
T PLN02281 218 KNFWYPVAFTADLKHDTMVPIECFEQPWVIFRG--------------------------EDGKPGCVRNTCAHRAC-PLD 270 (536)
T ss_pred hcccEEEEEHHHCCCCCeEEEEECCEEEEEEEC--------------------------CCCeEEEEeCcCcCCCC-ccc
Confidence 334455555568999999999999999988764 25678899999999998 554
Q ss_pred C
Q 027584 193 H 193 (221)
Q Consensus 193 ~ 193 (221)
.
T Consensus 271 ~ 271 (536)
T PLN02281 271 L 271 (536)
T ss_pred c
Confidence 3
No 45
>TIGR03229 benzo_1_2_benA benzoate 1,2-dioxygenase, large subunit. Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family all act on benzoate, but may have additional activities on various benozate analogs. This model describes the large subunit. Between the trusted and noise cutoffs are similar enzymes, likely to act on benzoate but perhaps best identified according to some other activity, such as 2-chlorobenzoate 1,2-dioxygenase (1.14.12.13).
Probab=70.19 E-value=10 Score=36.58 Aligned_cols=52 Identities=23% Similarity=0.373 Sum_probs=40.1
Q ss_pred cceeEEEeccCCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccC
Q 027584 113 RAFAYFVLTGGSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARD 191 (221)
Q Consensus 113 r~f~y~~~~~~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~ 191 (221)
+.+.|+... +.|+ +|..+++.--|+||+|.|- .+.++-++..+|+|-|+.-.
T Consensus 37 ~~W~~v~~~-selp~~gd~~t~~~~~~~vvv~R~--------------------------~dG~i~af~N~C~HRga~L~ 89 (433)
T TIGR03229 37 GNWIYLAHE-SQIPNNNDYYTTYMGRQPIFIARN--------------------------KDGELNAFINACSHRGAMLC 89 (433)
T ss_pred hCCEEEEEH-HHCCCCCCeEEEEECCeEEEEEEC--------------------------CCCcEEEEeCcCCCCCCCcc
Confidence 556666644 3776 5788999999999988764 25688899999999998544
No 46
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=69.03 E-value=7.5 Score=28.58 Aligned_cols=30 Identities=37% Similarity=0.461 Sum_probs=23.5
Q ss_pred CCcceeEEEeccCCCCCCCeEEEEECCeeEEE
Q 027584 111 SKRAFAYFVLTGGSIEPGSTVTVKWRGKPVFI 142 (221)
Q Consensus 111 ~kr~f~y~~~~~~~IepGq~vtVkWRGKPVFI 142 (221)
..-+++||... ..++|+.++|+|+|+++=+
T Consensus 61 ~~Iala~v~~~--~~~~g~~l~v~~~g~~~~a 90 (95)
T PF08669_consen 61 KNIALAYVDRE--YAEPGTELEVEIRGKRVPA 90 (95)
T ss_dssp EEEEEEEEEGG--GGSTTSEEEEEETTEEEEE
T ss_pred ceEEEEEECHH--HcCCCCEEEEEECCEEEEE
Confidence 33567777655 7899999999999999743
No 47
>TIGR03228 anthran_1_2_A anthranilate 1,2-dioxygenase, large subunit. Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the large subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase large subunit, among the larger set of ring-hydroxylating dioxygenases.
Probab=62.40 E-value=17 Score=35.19 Aligned_cols=52 Identities=21% Similarity=0.360 Sum_probs=41.0
Q ss_pred cceeEEEeccCCCC-CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccC
Q 027584 113 RAFAYFVLTGGSIE-PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARD 191 (221)
Q Consensus 113 r~f~y~~~~~~~Ie-pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~ 191 (221)
+.+.|+.-.. .|+ ||.-+++..-|+||+|.|- .+.++-++..+|+|-|+.-.
T Consensus 37 ~~W~~v~h~s-elp~~GDy~t~~ig~~pviv~R~--------------------------~dG~i~a~~N~C~HRGa~L~ 89 (438)
T TIGR03228 37 KNWIYACHES-ELPNNHDFVTVRAGRQPMIVTRD--------------------------GKGELHALVNACQHRGATLT 89 (438)
T ss_pred hCCEEEEEHH-HCCCCCCeEEEEECCeEEEEEEC--------------------------CCCCEEEEcccCCCCCCccc
Confidence 6677776553 675 4999999999999998764 25678899999999998554
No 48
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=60.01 E-value=12 Score=27.22 Aligned_cols=19 Identities=26% Similarity=0.557 Sum_probs=16.9
Q ss_pred CCeEEEEECCeeEEEEeCC
Q 027584 128 GSTVTVKWRGKPVFIRRRT 146 (221)
Q Consensus 128 Gq~vtVkWRGKPVFI~rRT 146 (221)
..++.|...|+||||-|-.
T Consensus 13 ~~~i~V~y~G~pV~Ie~vd 31 (58)
T PF08141_consen 13 PDMIEVTYNGVPVWIEHVD 31 (58)
T ss_pred CceEEEEECCEEEEEEEEc
Confidence 4788999999999999875
No 49
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=59.97 E-value=11 Score=27.48 Aligned_cols=19 Identities=26% Similarity=0.630 Sum_probs=17.0
Q ss_pred CCeEEEEECCeeEEEEeCC
Q 027584 128 GSTVTVKWRGKPVFIRRRT 146 (221)
Q Consensus 128 Gq~vtVkWRGKPVFI~rRT 146 (221)
..++.|...|.||||-|-.
T Consensus 13 ~~~i~V~Y~G~pV~Ie~vd 31 (58)
T TIGR02861 13 PEMINVTYKGVPVYIEHVD 31 (58)
T ss_pred ccceEEEECCEEEEEEEEc
Confidence 5788999999999999985
No 50
>PLN02518 pheophorbide a oxygenase
Probab=57.63 E-value=21 Score=35.54 Aligned_cols=54 Identities=15% Similarity=0.247 Sum_probs=41.0
Q ss_pred ceeEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCCC
Q 027584 114 AFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQH 193 (221)
Q Consensus 114 ~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~~ 193 (221)
.+-|.+.-...|++|+.+.++--|+||+|.|- ..+.+|.++-.+|+|.|+ |+..
T Consensus 89 ~~Wy~Va~~~dL~~g~p~~~~llG~~lVl~Rd-------------------------~~~G~~~A~~d~CPHRga-pLS~ 142 (539)
T PLN02518 89 DHWYPVSLVEDLDPSVPTPFQLLGRDLVLWKD-------------------------PNQGEWVAFDDKCPHRLA-PLSE 142 (539)
T ss_pred hhCEEEEEHHHCCCCCeEEEEECCEEEEEEEE-------------------------CCCCeEEEEcccCcCcCC-Cccc
Confidence 33455555568999999999999999998863 014678899999999998 5553
No 51
>PRK01625 sspH acid-soluble spore protein H; Provisional
Probab=54.64 E-value=16 Score=26.94 Aligned_cols=20 Identities=30% Similarity=0.591 Sum_probs=17.5
Q ss_pred CCCeEEEEECCeeEEEEeCC
Q 027584 127 PGSTVTVKWRGKPVFIRRRT 146 (221)
Q Consensus 127 pGq~vtVkWRGKPVFI~rRT 146 (221)
-..++.|...|.||||-|-.
T Consensus 12 S~~~i~V~Y~G~pV~Iq~vd 31 (59)
T PRK01625 12 SSSRIDVTYEGVPVWIESCD 31 (59)
T ss_pred CCcceEEEECCEEEEEEEEc
Confidence 35789999999999999985
No 52
>COG5649 Uncharacterized conserved protein [Function unknown]
Probab=54.60 E-value=5 Score=33.66 Aligned_cols=18 Identities=50% Similarity=1.034 Sum_probs=15.5
Q ss_pred CCCCCCeEEEEECCeeEE
Q 027584 124 SIEPGSTVTVKWRGKPVF 141 (221)
Q Consensus 124 ~IepGq~vtVkWRGKPVF 141 (221)
.--||-.-.|||||-|||
T Consensus 42 eA~P~v~e~vKWrg~Pvw 59 (132)
T COG5649 42 EAVPGVHEAVKWRGSPVW 59 (132)
T ss_pred HhCcChhheeeecCcccc
Confidence 445788899999999999
No 53
>PRK03174 sspH acid-soluble spore protein H; Provisional
Probab=52.21 E-value=18 Score=26.63 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=17.0
Q ss_pred CCeEEEEECCeeEEEEeCC
Q 027584 128 GSTVTVKWRGKPVFIRRRT 146 (221)
Q Consensus 128 Gq~vtVkWRGKPVFI~rRT 146 (221)
..++.|..+|.||||-|-.
T Consensus 13 p~~i~VtY~G~pV~Ie~vd 31 (59)
T PRK03174 13 PDMANVTYNGVPIYIQHVD 31 (59)
T ss_pred ccceEEEECCEEEEEEEEc
Confidence 5789999999999999875
No 54
>PF14168 YjzC: YjzC-like protein
Probab=44.07 E-value=38 Score=24.75 Aligned_cols=31 Identities=19% Similarity=0.461 Sum_probs=23.9
Q ss_pred ccCCCCCCCCcceeEEEec--cCCCCCCCeEEE
Q 027584 103 ERYPPGDPSKRAFAYFVLT--GGSIEPGSTVTV 133 (221)
Q Consensus 103 ~~~~~~~~~kr~f~y~~~~--~~~IepGq~vtV 133 (221)
..|.+|+.+....+|+++| |+.|+-++.|++
T Consensus 5 ~~fkpG~kapn~G~Y~EvG~~G~~v~~p~~v~l 37 (57)
T PF14168_consen 5 TQFKPGQKAPNNGTYVEVGERGGHVNNPKEVKL 37 (57)
T ss_pred cccCCCCcCCCCceEEEECCCCCccCCCcEEEe
Confidence 3688999999999999998 555666666554
No 55
>COG1535 EntB Isochorismate hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=36.49 E-value=16 Score=33.03 Aligned_cols=46 Identities=28% Similarity=0.377 Sum_probs=29.8
Q ss_pred CCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 127 PGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 127 pGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
++..+-+||| -=-.+||+=+.. -|...-+=||+.||-+|+||.-+.
T Consensus 116 ~~D~vL~kwr---YsAF~~s~Llq~-----------------lr~~grdQLIItGVyaHigcl~TA 161 (218)
T COG1535 116 ADDTVLTKWR---YSAFHRSPLLQM-----------------LREKGRDQLIITGVYAHIGCLTTA 161 (218)
T ss_pred CCceEEeeee---hhhhhcChHHHH-----------------HHHcCCCcEEEeehhhhhhhhhhH
Confidence 3567888888 223355442211 233455679999999999998764
No 56
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=35.69 E-value=27 Score=29.15 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=20.6
Q ss_pred CCCCCCeEEEEECCeeEEEEeCCH
Q 027584 124 SIEPGSTVTVKWRGKPVFIRRRTE 147 (221)
Q Consensus 124 ~IepGq~vtVkWRGKPVFI~rRT~ 147 (221)
+..|.|.++..|.|+|+|+--...
T Consensus 68 ~~~P~QvlRY~~gG~PLw~s~~~~ 91 (164)
T PF04194_consen 68 SRNPEQVLRYCRGGKPLWISSTPI 91 (164)
T ss_pred hcCCCeEEEECCCCeEEEecCCCC
Confidence 568999999999999999976543
No 57
>PRK07846 mycothione reductase; Reviewed
Probab=34.16 E-value=15 Score=34.39 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=12.0
Q ss_pred EEcccCCcCcccCC
Q 027584 179 VVGVCTHLGFARDQ 192 (221)
Q Consensus 179 vIGICTHLGCIP~~ 192 (221)
+=|.|.+-||||+-
T Consensus 33 ~GGtC~n~GCiPsK 46 (451)
T PRK07846 33 FGGTCLNVGCIPTK 46 (451)
T ss_pred CCCcccCcCcchhH
Confidence 46999999999964
No 58
>TIGR03452 mycothione_red mycothione reductase. Mycothiol, a glutathione analog in Mycobacterium tuberculosis and related species, can form a disulfide-linked dimer called mycothione. This enzyme can reduce mycothione to regenerate two mycothiol molecules. The enzyme shows some sequence similarity to glutathione-disulfide reductase, trypanothione-disulfide reductase, and dihydrolipoamide dehydrogenase. The characterized protein from M. tuberculosis, a homodimer, has FAD as a cofactor, one per monomer, and uses NADPH as a substrate.
Probab=33.56 E-value=15 Score=34.32 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=12.0
Q ss_pred EEcccCCcCcccCC
Q 027584 179 VVGVCTHLGFARDQ 192 (221)
Q Consensus 179 vIGICTHLGCIP~~ 192 (221)
+=|.|.+-||||+-
T Consensus 34 ~GGtC~n~GCiPsK 47 (452)
T TIGR03452 34 FGGTCLNVGCIPTK 47 (452)
T ss_pred CCCeeeccCccchH
Confidence 46999999999964
No 59
>smart00026 EPEND Ependymins. Ependymins are the predominant proteins in the cerebrospinal fluid (CSF) of teleost fish. They have been implicated in the neurochemistry of memory and neuronal regeneration. They are glycoproteins of about 200 amino acids that can bind calcium. Four cysteines are conserved that probably form disulfide bonds.
Probab=33.01 E-value=77 Score=27.99 Aligned_cols=16 Identities=13% Similarity=0.050 Sum_probs=12.5
Q ss_pred CcEEEEEcccCCcCcccCC
Q 027584 174 PEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 174 PEwLVvIGICTHLGCIP~~ 192 (221)
.+|.+.. |+.||||+.
T Consensus 123 g~y~~~~---T~~gCiPVs 138 (191)
T smart00026 123 GHYSLST---TSCGCLPLS 138 (191)
T ss_pred ccEEEEE---ecCCEEEEE
Confidence 5677665 999999975
No 60
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=30.87 E-value=70 Score=22.74 Aligned_cols=19 Identities=21% Similarity=0.546 Sum_probs=15.1
Q ss_pred CCCCCeEE-EEECCeeEEEE
Q 027584 125 IEPGSTVT-VKWRGKPVFIR 143 (221)
Q Consensus 125 IepGq~vt-VkWRGKPVFI~ 143 (221)
|.+|..++ +.|.|+||-|.
T Consensus 40 L~e~~~v~v~~~~~~~i~v~ 59 (61)
T cd04470 40 LKEGMEVIVLFYNGEPIGVE 59 (61)
T ss_pred CcCCCEEEEEEECCEEEEEE
Confidence 77888777 45999999873
No 61
>cd06815 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=30.54 E-value=25 Score=32.04 Aligned_cols=17 Identities=29% Similarity=0.387 Sum_probs=14.2
Q ss_pred cEEEEEcccCCcCcccC
Q 027584 175 EWLVVVGVCTHLGFARD 191 (221)
Q Consensus 175 EwLVvIGICTHLGCIP~ 191 (221)
..+-+.|+|||++|...
T Consensus 148 ~~l~~~Gi~tH~~~~~~ 164 (353)
T cd06815 148 PGIELVGIGTNLGCYGG 164 (353)
T ss_pred CCcEEEecccCccccCC
Confidence 45889999999999754
No 62
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel. This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alanine racemase activity.; PDB: 3KW3_A 1B54_A 1CT5_A 2ODO_B 2RJG_A 3B8V_D 2RJH_D 3B8T_D 3B8W_B 3B8U_A ....
Probab=30.46 E-value=23 Score=29.09 Aligned_cols=15 Identities=33% Similarity=0.414 Sum_probs=13.5
Q ss_pred cEEEEEcccCCcCcc
Q 027584 175 EWLVVVGVCTHLGFA 189 (221)
Q Consensus 175 EwLVvIGICTHLGCI 189 (221)
..+-+.|++||+||.
T Consensus 142 ~~l~l~Gl~th~~~~ 156 (218)
T PF01168_consen 142 PNLRLEGLMTHFAHA 156 (218)
T ss_dssp TTEEEEEEEEBGSST
T ss_pred CCceEeeEecccccc
Confidence 448999999999999
No 63
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=30.22 E-value=20 Score=32.99 Aligned_cols=15 Identities=20% Similarity=0.226 Sum_probs=13.2
Q ss_pred cEEEEEcccCCcCcc
Q 027584 175 EWLVVVGVCTHLGFA 189 (221)
Q Consensus 175 EwLVvIGICTHLGCI 189 (221)
..+-+.|++||+||.
T Consensus 146 ~~l~l~Gi~tH~a~a 160 (354)
T cd06827 146 PNVASIVLMTHFACA 160 (354)
T ss_pred CCceEEEEEeeccCC
Confidence 458899999999995
No 64
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=29.45 E-value=1.7e+02 Score=22.60 Aligned_cols=45 Identities=18% Similarity=0.263 Sum_probs=35.8
Q ss_pred cCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCcCcccCC
Q 027584 122 GGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHLGFARDQ 192 (221)
Q Consensus 122 ~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHLGCIP~~ 192 (221)
...|++|+.+.+.=.|+.|.|.|- .+.+++.+-..|+|.+=-|+.
T Consensus 8 ~~~L~~~~~~~~~v~g~~Ialf~~--------------------------~~~~vyAi~n~Cph~~~~~Ls 52 (104)
T PF13806_consen 8 LDDLPPGEGRAVEVDGRQIALFRV--------------------------RDGEVYAIDNRCPHSQAGPLS 52 (104)
T ss_dssp TTTSCTTSEEEEEETTEEEEEEEE--------------------------STTEEEEEESBETTTTSSCGC
T ss_pred HHHCCCCCcEEEEECCeEEEEEEe--------------------------CCCCEEEEeccCCccCCcccc
Confidence 358999999999999999999875 256889999999995333433
No 65
>PF12913 SH3_6: SH3 domain of the SH3b1 type; PDB: 3M1U_B.
Probab=28.00 E-value=44 Score=24.06 Aligned_cols=18 Identities=22% Similarity=0.418 Sum_probs=12.1
Q ss_pred eEEEEECCeeEEEEeCCH
Q 027584 130 TVTVKWRGKPVFIRRRTE 147 (221)
Q Consensus 130 ~vtVkWRGKPVFI~rRT~ 147 (221)
+-+..|-|.||+|.|.+.
T Consensus 19 Q~s~l~~gtPv~i~H~S~ 36 (54)
T PF12913_consen 19 QNSALHPGTPVYILHTSR 36 (54)
T ss_dssp EEEEE-TT-EEEEEEE-T
T ss_pred hhcccCCCCCEEEEEECC
Confidence 456778899999999854
No 66
>TIGR01438 TGR thioredoxin and glutathione reductase selenoprotein. This homodimeric, FAD-containing member of the pyridine nucleotide disulfide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-term arm of the protein is proposed to allow broad substrate specificity.
Probab=27.30 E-value=25 Score=33.55 Aligned_cols=15 Identities=20% Similarity=0.479 Sum_probs=12.8
Q ss_pred EEEEcccCCcCcccC
Q 027584 177 LVVVGVCTHLGFARD 191 (221)
Q Consensus 177 LVvIGICTHLGCIP~ 191 (221)
+.+=|.|.|-||||+
T Consensus 43 ~~~GGtc~n~GCiPs 57 (484)
T TIGR01438 43 WGIGGTCVNVGCIPK 57 (484)
T ss_pred eeccccccccCcCch
Confidence 357899999999994
No 67
>COG4638 HcaE Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]
Probab=27.23 E-value=1.6e+02 Score=26.73 Aligned_cols=32 Identities=16% Similarity=0.344 Sum_probs=24.5
Q ss_pred cceeEEEeccCCCCCCCeEEEEECCeeEEEEeC
Q 027584 113 RAFAYFVLTGGSIEPGSTVTVKWRGKPVFIRRR 145 (221)
Q Consensus 113 r~f~y~~~~~~~IepGq~vtVkWRGKPVFI~rR 145 (221)
+.+.|+ .-...|++++-+++.==|++|.|.|-
T Consensus 26 ~~Wy~v-~~~~el~~~~~~~~~i~g~~lvi~R~ 57 (367)
T COG4638 26 KHWYVV-AHSSELPKPDPLTVRIGGEPLVVVRD 57 (367)
T ss_pred hCEEEE-ccHHHCCCCCceeEEEcCeEEEEEEC
Confidence 444444 43458999999999999999988765
No 68
>COG1249 Lpd Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]
Probab=25.66 E-value=24 Score=34.27 Aligned_cols=14 Identities=21% Similarity=0.582 Sum_probs=11.8
Q ss_pred EEcccCCcCcccCC
Q 027584 179 VVGVCTHLGFARDQ 192 (221)
Q Consensus 179 vIGICTHLGCIP~~ 192 (221)
+=|.|.+-||||+.
T Consensus 39 lGGtCln~GCIPsK 52 (454)
T COG1249 39 LGGTCLNVGCIPSK 52 (454)
T ss_pred cCceEEeeCccccH
Confidence 45899999999963
No 69
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=25.35 E-value=1.4e+02 Score=24.46 Aligned_cols=20 Identities=25% Similarity=0.576 Sum_probs=17.6
Q ss_pred CCCCCCeEEE-EECCeeEEEE
Q 027584 124 SIEPGSTVTV-KWRGKPVFIR 143 (221)
Q Consensus 124 ~IepGq~vtV-kWRGKPVFI~ 143 (221)
-|.||..+.| .|.|+|+-|.
T Consensus 106 ~l~eg~~v~v~~~~g~~i~v~ 126 (131)
T COG0231 106 FLKEGMEVEVLLYNGEPIAVE 126 (131)
T ss_pred hcCCCCEEEEEEECCEEEEEE
Confidence 7899998888 9999999775
No 70
>KOG0192 consensus Tyrosine kinase specific for activated (GTP-bound) p21cdc42Hs [Signal transduction mechanisms]
Probab=25.35 E-value=26 Score=32.83 Aligned_cols=65 Identities=22% Similarity=0.310 Sum_probs=38.3
Q ss_pred CCCCCCeEEEEECCee-EEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCCc---CcccC
Q 027584 124 SIEPGSTVTVKWRGKP-VFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTHL---GFARD 191 (221)
Q Consensus 124 ~IepGq~vtVkWRGKP-VFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTHL---GCIP~ 191 (221)
.--.|+.....|||+- |.|......+..... ...++.--.--.|..+|+++-++|+||-- -||-.
T Consensus 51 ~G~~g~V~~~~~~g~~~vavK~~~~~~~~~~~---~~~f~~E~~il~~l~HpNIV~f~G~~~~~~~~~~iVt 119 (362)
T KOG0192|consen 51 SGSFGTVYKGKWRGTDVVAVKIISDPDFDDES---RKAFRREASLLSRLRHPNIVQFYGACTSPPGSLCIVT 119 (362)
T ss_pred cCCceeEEEEEeCCceeEEEEEecchhcChHH---HHHHHHHHHHHHhCCCCCeeeEEEEEcCCCCceEEEE
Confidence 4456888899999999 877776654422111 00000000000245589999999999954 45553
No 71
>PF10172 DDA1: Det1 complexing ubiquitin ligase; InterPro: IPR018276 This entry represents DDA1 (DET1- and DDB1-associated protein 1) ubiquitin ligase, which binds strongly with Det1 (De-etiolated 1) and DDB1 (Damaged DNA binding protein 1 associated 1). Together DDA1, DDB1 and Det1 form the DDD core complex, which recruits a specific UBE2E enzyme to form specific DDD-E2 complexes []. Component of the DDD-E2 complexes which may provide a platform for interaction with cul4a and WD repeat proteins. These proteins may be involved in ubiquitination and subsequent proteasomal degradation of target proteins.
Probab=23.87 E-value=1.3e+02 Score=22.38 Aligned_cols=35 Identities=29% Similarity=0.565 Sum_probs=24.4
Q ss_pred ccCCCcccCCCCCC----CCcceeEEEeccCCCC-CCCeEEE
Q 027584 97 YDEYNHERYPPGDP----SKRAFAYFVLTGGSIE-PGSTVTV 133 (221)
Q Consensus 97 y~~~~~~~~~~~~~----~kr~f~y~~~~~~~Ie-pGq~vtV 133 (221)
|+..||.++...++ .++.-+|+.+ ...+ ++|.|+.
T Consensus 9 ~~~~NFS~~~~~~~~~~~~~~~~vYl~t--~t~Pp~~QvI~t 48 (65)
T PF10172_consen 9 YNRGNFSRYSPSSPSSSSPKRPSVYLPT--DTDPPPEQVIVT 48 (65)
T ss_pred cCcccccccCccccccccCCCceEEeeC--CCCCCcccEEee
Confidence 67788887776554 4688899998 3777 4555544
No 72
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=23.14 E-value=95 Score=20.97 Aligned_cols=19 Identities=42% Similarity=0.550 Sum_probs=14.4
Q ss_pred CCCCCCeEEE-EECCeeEEE
Q 027584 124 SIEPGSTVTV-KWRGKPVFI 142 (221)
Q Consensus 124 ~IepGq~vtV-kWRGKPVFI 142 (221)
-|.+|+.+.| .|.|+||.|
T Consensus 36 ~l~eg~~v~v~~~~g~~i~~ 55 (55)
T cd04463 36 SFEPGEVVLVDTRTGQYVGV 55 (55)
T ss_pred hCCCCCEEEEEEECCEEEeC
Confidence 4678887774 699999854
No 73
>PRK03646 dadX alanine racemase; Reviewed
Probab=22.98 E-value=37 Score=31.37 Aligned_cols=15 Identities=13% Similarity=0.065 Sum_probs=13.0
Q ss_pred cEEEEEcccCCcCcc
Q 027584 175 EWLVVVGVCTHLGFA 189 (221)
Q Consensus 175 EwLVvIGICTHLGCI 189 (221)
..+-+.|++|||+|.
T Consensus 148 ~~l~~~Gi~sH~a~a 162 (355)
T PRK03646 148 GNVGEMTLMSHFARA 162 (355)
T ss_pred CCCEEEEEEcCCCCC
Confidence 457789999999996
No 74
>PF09696 Ctf8: Ctf8; InterPro: IPR018607 Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Probab=21.45 E-value=93 Score=25.09 Aligned_cols=54 Identities=19% Similarity=0.250 Sum_probs=32.1
Q ss_pred eEEEeccCCCCCCCeEEEEECCeeEEEEeCCHHHHHHhhcCCCCCCCCCcccccccCCCcEEEEEcccCC
Q 027584 116 AYFVLTGGSIEPGSTVTVKWRGKPVFIRRRTEEDIKLANSVDLGSLRDPQQDAERVKNPEWLVVVGVCTH 185 (221)
Q Consensus 116 ~y~~~~~~~IepGq~vtVkWRGKPVFI~rRT~eeI~~l~~vd~~~LrDPqsd~~Rs~~PEwLVvIGICTH 185 (221)
.||.+|-.-+=.|+.+..+ ||+.|++|.... |...+.......+-+-+++|++|
T Consensus 58 ~~L~IG~~q~L~Gkv~kL~---kPLaVLrk~~~~-------------~~~~~~~~~~~~~e~evv~II~~ 111 (122)
T PF09696_consen 58 VTLYIGKHQRLEGKVVKLK---KPLAVLRKRKSN-------------DDSSDDSEEESSTEYEVVDIIRY 111 (122)
T ss_pred EEEEECCCEEEEEEEeccC---CCEEEEEEcccC-------------cccccccCCCCCeEEEEEEeeee
Confidence 3444553455567777775 999999997654 21222222335566667777765
No 75
>cd06808 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these p
Probab=21.34 E-value=35 Score=27.49 Aligned_cols=16 Identities=44% Similarity=0.679 Sum_probs=13.3
Q ss_pred EEEEEcccCCcCcccC
Q 027584 176 WLVVVGVCTHLGFARD 191 (221)
Q Consensus 176 wLVvIGICTHLGCIP~ 191 (221)
.+-+.|++||+||...
T Consensus 141 ~l~l~Gl~~H~~~~~~ 156 (211)
T cd06808 141 HLRLVGLHTHFGSADE 156 (211)
T ss_pred CCcEEEEEEecCCCCC
Confidence 4778899999999654
Done!