Query psy17358
Match_columns 202
No_of_seqs 216 out of 1954
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 20:15:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17358.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17358hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1671|consensus 100.0 3E-46 6.4E-51 298.3 5.3 196 3-202 14-210 (210)
2 TIGR01416 Rieske_proteo ubiqui 100.0 2.4E-39 5.3E-44 260.0 16.7 163 37-202 1-174 (174)
3 cd03470 Rieske_cytochrome_bc1 100.0 2.3E-34 4.9E-39 220.0 13.3 123 80-202 2-126 (126)
4 COG0723 QcrA Rieske Fe-S prote 100.0 6.4E-32 1.4E-36 217.6 9.1 159 33-202 6-166 (177)
5 PRK13474 cytochrome b6-f compl 100.0 3.2E-28 7E-33 196.2 14.9 137 32-198 8-159 (178)
6 cd03476 Rieske_ArOX_small Smal 99.9 9.8E-24 2.1E-28 161.3 10.3 102 83-202 8-115 (126)
7 TIGR03171 soxL2 Rieske iron-su 99.9 5.4E-24 1.2E-28 182.5 9.5 163 35-202 60-277 (321)
8 cd03528 Rieske_RO_ferredoxin R 99.9 9.8E-23 2.1E-27 148.4 9.4 90 83-199 6-96 (98)
9 cd03478 Rieske_AIFL_N AIFL (ap 99.9 8.1E-23 1.7E-27 148.5 8.9 89 83-198 5-94 (95)
10 TIGR02377 MocE_fam_FeS Rieske 99.9 1.9E-22 4E-27 148.5 9.4 91 82-198 6-97 (101)
11 PF00355 Rieske: Rieske [2Fe-2 99.9 2.4E-22 5.3E-27 146.0 9.7 87 83-196 7-97 (97)
12 cd03477 Rieske_YhfW_C YhfW fam 99.9 6E-22 1.3E-26 143.4 9.6 86 83-195 4-89 (91)
13 TIGR02694 arsenite_ox_S arseni 99.9 1.2E-21 2.5E-26 150.3 10.1 103 82-202 10-117 (129)
14 PRK09965 3-phenylpropionate di 99.9 9.7E-22 2.1E-26 145.8 9.3 89 83-199 8-98 (106)
15 cd03530 Rieske_NirD_small_Baci 99.9 1.8E-21 3.8E-26 142.1 9.6 92 83-202 6-98 (98)
16 cd03474 Rieske_T4moC Toluene-4 99.8 1E-20 2.2E-25 140.5 10.3 90 83-199 6-96 (108)
17 cd04337 Rieske_RO_Alpha_Cao Ca 99.8 1.6E-20 3.5E-25 144.1 10.7 108 66-199 5-117 (129)
18 cd03469 Rieske_RO_Alpha_N Ries 99.8 1.3E-20 2.8E-25 141.5 9.8 90 83-198 6-107 (118)
19 cd03471 Rieske_cytochrome_b6f 99.8 2.3E-20 5.1E-25 142.3 9.9 65 134-199 42-108 (126)
20 cd03475 Rieske_SoxF_SoxL SoxF 99.8 3.6E-20 7.8E-25 147.5 9.1 68 135-202 74-160 (171)
21 cd03467 Rieske Rieske domain; 99.8 7.7E-20 1.7E-24 133.2 10.2 89 83-197 6-95 (98)
22 cd03479 Rieske_RO_Alpha_PhDO_l 99.8 8.7E-20 1.9E-24 142.5 10.9 106 68-199 11-127 (144)
23 cd03531 Rieske_RO_Alpha_KSH Th 99.8 1.3E-19 2.8E-24 136.5 9.9 91 83-199 7-103 (115)
24 cd04338 Rieske_RO_Alpha_Tic55 99.8 4.5E-19 9.8E-24 136.9 10.2 92 82-199 22-122 (134)
25 COG2146 {NirD} Ferredoxin subu 99.8 3.7E-19 8.1E-24 132.2 9.4 92 82-201 9-103 (106)
26 PRK09511 nirD nitrite reductas 99.8 4.2E-19 9.1E-24 132.3 9.7 93 82-200 8-106 (108)
27 cd03532 Rieske_RO_Alpha_VanA_D 99.8 6.1E-19 1.3E-23 132.8 10.0 90 83-199 11-106 (116)
28 cd03529 Rieske_NirD Assimilato 99.8 6.6E-19 1.4E-23 129.9 9.0 89 83-198 6-100 (103)
29 TIGR02378 nirD_assim_sml nitri 99.8 6.4E-19 1.4E-23 130.2 8.8 90 82-198 6-101 (105)
30 cd03473 Rieske_CMP_Neu5Ac_hydr 99.8 3.8E-18 8.3E-23 126.0 8.6 88 83-197 13-104 (107)
31 cd03480 Rieske_RO_Alpha_PaO Ri 99.7 6.3E-18 1.4E-22 131.2 9.7 90 83-198 23-125 (138)
32 cd03548 Rieske_RO_Alpha_OMO_CA 99.7 1.3E-17 2.9E-22 128.9 10.2 89 83-198 20-119 (136)
33 cd03536 Rieske_RO_Alpha_DTDO T 99.7 2.8E-17 6.2E-22 125.0 10.2 91 83-199 6-111 (123)
34 PF13806 Rieske_2: Rieske-like 99.7 2.6E-17 5.5E-22 122.0 8.9 91 83-201 7-103 (104)
35 cd03472 Rieske_RO_Alpha_BPDO_l 99.7 4E-17 8.6E-22 125.2 9.9 80 78-183 8-90 (128)
36 cd03545 Rieske_RO_Alpha_OHBDO_ 99.7 1.3E-16 2.9E-21 125.4 10.7 96 77-198 24-139 (150)
37 cd03541 Rieske_RO_Alpha_CMO Ri 99.7 1.3E-16 2.8E-21 120.8 8.1 79 83-187 7-86 (118)
38 cd03542 Rieske_RO_Alpha_HBDO R 99.7 1.8E-16 4E-21 120.7 7.4 86 83-195 6-93 (123)
39 cd03537 Rieske_RO_Alpha_PrnD T 99.7 5.3E-16 1.1E-20 118.2 9.4 89 83-198 9-110 (123)
40 cd03535 Rieske_RO_Alpha_NDO Ri 99.7 7.7E-16 1.7E-20 117.1 10.2 75 83-183 8-84 (123)
41 cd03538 Rieske_RO_Alpha_AntDO 99.7 9.9E-16 2.2E-20 119.9 10.8 84 75-184 19-106 (146)
42 PLN02281 chlorophyllide a oxyg 99.6 1E-15 2.2E-20 140.3 10.9 90 83-198 226-319 (536)
43 cd03539 Rieske_RO_Alpha_S5H Th 99.6 1.1E-15 2.5E-20 117.2 9.4 88 83-196 6-116 (129)
44 PLN00095 chlorophyllide a oxyg 99.6 2.5E-15 5.4E-20 132.7 10.8 90 83-198 78-174 (394)
45 PF02921 UCR_TM: Ubiquinol cyt 99.5 3.7E-14 8E-19 95.9 4.1 64 7-73 1-64 (64)
46 PLN02518 pheophorbide a oxygen 99.4 3.3E-13 7.1E-18 125.1 9.1 90 83-198 96-201 (539)
47 TIGR03228 anthran_1_2_A anthra 99.4 1.8E-12 3.9E-17 117.6 10.0 74 83-182 44-119 (438)
48 TIGR03229 benzo_1_2_benA benzo 99.4 1.5E-12 3.3E-17 118.0 8.6 79 78-182 38-119 (433)
49 COG4638 HcaE Phenylpropionate 99.3 1.1E-11 2.3E-16 110.0 9.2 88 83-196 33-131 (367)
50 PF10399 UCR_Fe-S_N: Ubiquitin 98.3 1.2E-06 2.6E-11 53.9 3.8 36 33-71 6-41 (41)
51 PF08802 CytB6-F_Fe-S: Cytochr 94.0 0.12 2.6E-06 31.4 3.9 19 34-52 4-22 (39)
52 TIGR02811 formate_TAT formate 92.1 0.22 4.7E-06 33.8 3.5 16 34-49 7-22 (66)
53 PF10518 TAT_signal: TAT (twin 91.8 0.18 3.9E-06 27.8 2.3 16 35-50 1-16 (26)
54 TIGR01409 TAT_signal_seq Tat ( 86.9 0.61 1.3E-05 26.2 2.1 15 36-50 1-15 (29)
55 COG0473 LeuB Isocitrate/isopro 58.3 7.2 0.00016 34.8 2.1 34 148-181 252-287 (348)
56 PRK13747 putative mercury resi 48.3 5.4 0.00012 27.6 -0.2 9 160-168 24-32 (78)
57 PF11998 DUF3493: Protein of u 47.9 27 0.00059 24.2 3.2 18 38-55 20-37 (75)
58 PF05265 DUF723: Protein of un 45.0 15 0.00032 24.4 1.5 15 160-174 31-45 (60)
59 PRK09476 napG quinol dehydroge 43.5 37 0.0008 28.8 4.1 16 34-49 7-22 (254)
60 PF07897 DUF1675: Protein of u 42.9 8.6 0.00019 33.4 0.2 18 157-174 248-265 (284)
61 PRK09898 hypothetical protein; 42.8 15 0.00031 30.1 1.5 12 35-46 12-23 (208)
62 PF05052 MerE: MerE protein; 41.2 8 0.00017 26.6 -0.2 13 160-172 24-36 (75)
63 PF10080 DUF2318: Predicted me 40.3 1.5E+02 0.0032 21.7 8.9 62 134-201 27-90 (102)
64 PRK10882 hydrogenase 2 protein 39.2 19 0.0004 31.9 1.7 12 36-47 1-12 (328)
65 PF00642 zf-CCCH: Zinc finger 37.1 15 0.00033 19.9 0.5 8 2-9 19-26 (27)
66 PRK10468 hydrogenase 2 small s 37.0 21 0.00045 32.2 1.6 20 34-53 11-30 (371)
67 PRK14993 tetrathionate reducta 36.3 39 0.00085 28.5 3.2 12 35-46 2-13 (244)
68 TIGR00391 hydA hydrogenase (Ni 35.4 20 0.00044 32.2 1.4 20 34-53 13-32 (365)
69 PF00301 Rubredoxin: Rubredoxi 34.3 44 0.00095 20.9 2.4 29 161-189 1-31 (47)
70 PF12666 PrgI: PrgI family pro 32.4 81 0.0017 22.0 3.9 29 15-52 5-33 (93)
71 COG0375 HybF Zn finger protein 31.3 25 0.00054 26.4 1.0 18 160-177 85-104 (115)
72 PRK00420 hypothetical protein; 29.8 41 0.0009 25.1 2.0 34 141-176 22-56 (112)
73 PF02891 zf-MIZ: MIZ/SP-RING z 28.6 13 0.00029 23.4 -0.7 28 138-166 14-46 (50)
74 TIGR01412 tat_substr_1 Tat-tra 28.1 49 0.0011 30.3 2.5 11 34-44 6-16 (414)
75 COG1773 Rubredoxin [Energy pro 27.8 74 0.0016 20.7 2.7 31 160-190 2-34 (55)
76 PF07282 OrfB_Zn_ribbon: Putat 26.9 60 0.0013 21.3 2.3 32 141-173 27-58 (69)
77 PRK08997 isocitrate dehydrogen 26.4 47 0.001 29.5 2.1 35 147-181 242-276 (334)
78 PRK06451 isocitrate dehydrogen 26.1 43 0.00094 30.7 1.8 33 149-181 314-346 (412)
79 PRK08572 rps17p 30S ribosomal 25.3 24 0.00052 26.2 0.0 16 164-180 19-34 (108)
80 PF09740 DUF2043: Uncharacteri 25.2 29 0.00063 25.9 0.5 19 160-178 86-106 (110)
81 PRK14990 anaerobic dimethyl su 25.1 68 0.0015 31.6 3.2 11 35-45 13-23 (814)
82 TIGR02088 LEU3_arch isopropylm 24.6 42 0.00091 29.7 1.5 34 148-181 235-268 (322)
83 COG3765 WzzB Chain length dete 23.9 1.7E+02 0.0037 26.2 5.0 37 11-50 291-327 (347)
84 PRK15488 thiosulfate reductase 23.5 57 0.0012 31.9 2.3 12 35-46 2-13 (759)
85 PF15061 DUF4538: Domain of un 23.3 56 0.0012 21.5 1.5 14 79-92 44-57 (58)
86 TIGR03630 arch_S17P archaeal r 22.5 28 0.00061 25.6 -0.0 17 163-180 16-32 (102)
87 PRK07474 sulfur oxidation prot 22.1 61 0.0013 25.6 1.8 15 35-49 7-21 (154)
88 TIGR03396 PC_PLC phospholipase 22.0 60 0.0013 31.8 2.0 15 36-50 1-15 (690)
89 TIGR00397 mauM_napG MauM/NapG 21.9 1.3E+02 0.0028 24.8 3.8 12 36-47 2-13 (213)
90 PF07250 Glyoxal_oxid_N: Glyox 21.7 64 0.0014 27.3 1.9 21 160-180 40-61 (243)
91 PRK15102 trimethylamine N-oxid 21.7 41 0.00088 33.3 0.9 14 36-49 1-14 (825)
92 PF12318 FAD-SLDH: Membrane bo 20.9 1.1E+02 0.0023 24.4 3.0 8 35-42 1-8 (168)
93 PRK02888 nitrous-oxide reducta 20.3 62 0.0013 31.3 1.7 15 166-180 176-193 (635)
94 PRK07362 isocitrate dehydrogen 20.3 71 0.0015 29.8 2.0 34 148-181 377-410 (474)
95 KOG0100|consensus 20.2 1.2E+02 0.0025 28.3 3.3 31 168-201 486-518 (663)
No 1
>KOG1671|consensus
Probab=100.00 E-value=3e-46 Score=298.35 Aligned_cols=196 Identities=70% Similarity=1.182 Sum_probs=179.4
Q ss_pred ccccccCCCCCCCCccccccCCCCCCCCCccCCccc-hhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcChhhhhcccce
Q psy17358 3 QVRFAHTDIKVPDFSHYRRDSVKDPGVNARETEEAR-KAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASADVLAMAKIE 81 (202)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R-R~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~~~~~~~~~~~ 81 (202)
|.---|||+.+|||+.||++.++| .++....| |-|.|..+|+.+++.+.+|..++..|+.+|...++..+.+.++
T Consensus 14 ~l~~~~t~~~~p~~~~~~~~~~~~----~~~~~~~~k~~~sy~~~g~~~~~~a~~ak~~v~~fi~smsAsadvlA~akie 89 (210)
T KOG1671|consen 14 GLGSSHTDLMVPDFSDYRRESVKD----HQDTGEERKGFRSYLMVGAGAAGRAYAAKNLVTTFISSMSASADVLAMAKIE 89 (210)
T ss_pred ccccccccccCCCchhhhchhhhc----cccchhhhhceeeEEEecccceeehhhhhhhHHHHHHHhhhhhhhhhheeee
Confidence 344459999999999999999877 22233444 5558999998888888888888999999999999999999999
Q ss_pred eeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCE
Q psy17358 82 VKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGG 161 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~ 161 (202)
++++++|||..++|+|+|+|+||.+|+..||+..+.|+...++||+.++.|.++.+|+++.++||||||.+.|+.+++++
T Consensus 90 i~l~~IPeGk~~~~kwrGkpvfirhrt~~ei~~~r~V~~s~lrDPq~d~~rvk~~ewl~~igVCThLGCVp~~~AGd~gg 169 (210)
T KOG1671|consen 90 IKLSDIPEGKTVAFKWRGKPVFIRHRTKAEIEGERNVPQSTLRDPQDDVDRVKKPEWLVVIGVCTHLGCVPIANAGDYGG 169 (210)
T ss_pred eeeecCCCCCCcceeccCCceEEeeccccccccccccchhhccCchhhhhhccCcceEEEEeeeccccccccccccccCc
Confidence 99999999999999999999999999999999999999999999998888999999999999999999999999999999
Q ss_pred EEcCCCCeEECCCCccccCCCCCCCccceEEEeCCcEEEEC
Q psy17358 162 YYCPCHGSHYDASGRIRKGPAPLNLEVPKYEFPEPGLLVVG 202 (202)
Q Consensus 162 ~~CPcHGs~FD~~G~vi~GPA~~~L~~~p~~i~~~~~~~ig 202 (202)
|+||||||+||..||+..||||.+|+++.|.+.++++++||
T Consensus 170 ~~CPCHGSHYdasGRIrkGPAPlnlevP~y~F~~~d~vivg 210 (210)
T KOG1671|consen 170 YYCPCHGSHYDASGRIRKGPAPLNLEVPTYEFTSEDKVIVG 210 (210)
T ss_pred eecccccccccccCceecCCCCCccCCCceecccCceEecC
Confidence 99999999999999999999999999999999988888887
No 2
>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=100.00 E-value=2.4e-39 Score=260.03 Aligned_cols=163 Identities=47% Similarity=0.942 Sum_probs=141.7
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcChhhhhc-ccceeeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhh
Q psy17358 37 ARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASADVLAM-AKIEVKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKE 115 (202)
Q Consensus 37 ~RR~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~~~~~~~-~~~~v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~ 115 (202)
+||+||++++++.+.++++ .++.|++.++.|.++..+. +.++|++++|++|+.+.+.|+|++++|++++++|+...
T Consensus 1 ~RR~fl~~~~~~~~~~~~~---~~~~p~v~~~~P~~~~~a~~~~~~v~l~eL~pG~~~~v~~~GkpI~I~~~t~~~~~~~ 77 (174)
T TIGR01416 1 TRRDFLYAATGAVGAVGAA---AAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTVEWRGKPVFIRRRTKKEIDAL 77 (174)
T ss_pred ChHHHHHHHHHHHHHHHHH---HHHHHHHheeCcchhccccCCcEEEEHHHCCCCCeEEEEECCeEEEEEeCCHHHhhhh
Confidence 6999999999866544433 4567888888999887776 67899999999999999999999999999999999998
Q ss_pred hhchhcccCCCccc--------cccccCCceEEEeccccCCCcccCcccCC--CCEEEcCCCCeEECCCCccccCCCCCC
Q psy17358 116 QAVAISTLRDPQAD--------SERVKDPKWLVLIGVCTHLGCVPVANAGD--FGGYYCPCHGSHYDASGRIRKGPAPLN 185 (202)
Q Consensus 116 ~~v~~~~l~dp~~~--------~~r~~~g~~~a~s~~CtHlGc~l~~~~~~--~~~~~CPcHGs~FD~~G~vi~GPA~~~ 185 (202)
.++....++||... .+|+.+++|+|++++|||+||++.|.... ++.|+||||||+||++|+++.|||+++
T Consensus 78 ~~~~~~~l~Dp~~~~~~~~~~~~~r~~~~~~~a~~~~CtH~Gc~~~~~~~~~~~~~~~CPcHgs~Fd~~G~~~~gpa~~~ 157 (174)
T TIGR01416 78 KALDLGALKDPNSEAQQPDYARVKRSGKPEWLVVIGICTHLGCIPTYGPEEGDKGGFFCPCHGSHYDTAGRVRKGPAPLN 157 (174)
T ss_pred hccchhhcCCCcccccCcchhhhhhccCCcEEEEEeccCCCCCccccccCCCCCCEEEeCCCCCEECCCCcEecCCCCCC
Confidence 88887888888432 45666899999999999999999886432 368999999999999999999999999
Q ss_pred CccceEEEeCCcEEEEC
Q psy17358 186 LEVPKYEFPEPGLLVVG 202 (202)
Q Consensus 186 L~~~p~~i~~~~~~~ig 202 (202)
|++||+++++|++|+||
T Consensus 158 L~~~~~~~~~~~~~~ig 174 (174)
T TIGR01416 158 LPVPPYKFLSDTTILIG 174 (174)
T ss_pred CCCCCEEEcCCCEEEeC
Confidence 99999999999999998
No 3
>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=100.00 E-value=2.3e-34 Score=220.04 Aligned_cols=123 Identities=61% Similarity=1.205 Sum_probs=111.5
Q ss_pred ceeeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCcc--ccccccCCceEEEeccccCCCcccCcccC
Q psy17358 80 IEVKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQA--DSERVKDPKWLVLIGVCTHLGCVPVANAG 157 (202)
Q Consensus 80 ~~v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~--~~~r~~~g~~~a~s~~CtHlGc~l~~~~~ 157 (202)
+++++++|++|+.+++.|+|+||+|++++++||+...+.....+.+|+. ..+|..+++|+|++++|||+||.+.++..
T Consensus 2 ~~vdl~~l~~G~~~~v~w~Gkpv~I~~rt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~CtH~gc~~~~~~~ 81 (126)
T cd03470 2 VEVDLSKIEEGQLITVEWRGKPVFIRRRTPEEIAEAKAVDLSLLDDPDPAANRVRSGKPEWLVVIGICTHLGCVPTYRAG 81 (126)
T ss_pred EEEEhhhCCCCCEEEEEECCeEEEEEECCHHHHhhhhhcchhhcCCccccccccccCCCcEEEEeCcCCCCCCeeccccC
Confidence 5789999999999999999999999999999999988776666665543 36788899999999999999999998865
Q ss_pred CCCEEEcCCCCeEECCCCccccCCCCCCCccceEEEeCCcEEEEC
Q psy17358 158 DFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEFPEPGLLVVG 202 (202)
Q Consensus 158 ~~~~~~CPcHGs~FD~~G~vi~GPA~~~L~~~p~~i~~~~~~~ig 202 (202)
+.+.|+||||||+||++|+++.|||+++|++||+++++++.|+||
T Consensus 82 ~~~~~~CPcHgs~Fdl~G~~~~gPa~~~L~~~p~~~~~~~~l~ig 126 (126)
T cd03470 82 DYGGFFCPCHGSHYDASGRIRKGPAPLNLEVPPYKFLSDTTIVIG 126 (126)
T ss_pred CCCEEEecCcCCEECCCCeEecCCCCCCCCeeeEEEecCCEEEeC
Confidence 568999999999999999999999999999999999998999998
No 4
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=99.97 E-value=6.4e-32 Score=217.59 Aligned_cols=159 Identities=36% Similarity=0.603 Sum_probs=124.4
Q ss_pred cCCccchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcChhh-hhcccceeeccCCCCCceEEEEEcCeeEEEEeCCHHH
Q psy17358 33 ETEEARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASADV-LAMAKIEVKLADIPEGRNVTFKWRGKPLFIRHRAAAE 111 (202)
Q Consensus 33 ~~~~~RR~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~~~~-~~~~~~~v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~ 111 (202)
....+||+||..+++..+..+ +..++.++...+.|.++. .+.+.++++...+.+++...+.|+++|+++.++++.+
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~---~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~ 82 (177)
T COG0723 6 ATGLSRRDFLVLLTTGVGAVG---AGAALYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRRTEYA 82 (177)
T ss_pred cccccHHHhhhhhhccccccc---eeeeeeehhhcccCcccccccCCceeeeccCCccceEEEEecCCCCeeeEeecccc
Confidence 357889999998887664333 223566777777776655 5667788888888999999999999999988776544
Q ss_pred HHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcc-cCCCCEEEcCCCCeEECCCCccccCCCCCCCccce
Q psy17358 112 IAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVAN-AGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPK 190 (202)
Q Consensus 112 i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~-~~~~~~~~CPcHGs~FD~~G~vi~GPA~~~L~~~p 190 (202)
+.+........+.+ ...+|+|++++||||||.+.|+ ..+.++|+||||||+||.+|+|+.|||++||++++
T Consensus 83 ~~~~~~~~~~~~~~--------~~~~~~a~~~iCtHlGC~~~~~~~~~~~~~~CPCHGS~yd~~g~vv~GPA~~~L~~~~ 154 (177)
T COG0723 83 GPKGGVTRDGDGGV--------GNKEIVAYSAICTHLGCTVPWNNAGAEGGFFCPCHGSRYDPDGGVVKGPAPRPLPIPP 154 (177)
T ss_pred cccccceecccCCC--------CCccEEEEeeeccCCCCccCcccCCCCCeEEccCCCCeEcCCCCeeCCCCCCCcCCce
Confidence 44443333333333 2368999999999999999995 44459999999999999999999999999999999
Q ss_pred EEEeCCcEEEEC
Q psy17358 191 YEFPEPGLLVVG 202 (202)
Q Consensus 191 ~~i~~~~~~~ig 202 (202)
+++++|+.+.+|
T Consensus 155 ~~~~~d~~~~~~ 166 (177)
T COG0723 155 LEYDSDKLYLIG 166 (177)
T ss_pred EEEeCCceEEEE
Confidence 999988877764
No 5
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=99.96 E-value=3.2e-28 Score=196.20 Aligned_cols=137 Identities=28% Similarity=0.544 Sum_probs=103.5
Q ss_pred ccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcChhhhhccc--------ceeeccCC----CCCceEEEE-Ec
Q psy17358 32 RETEEARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASADVLAMAK--------IEVKLADI----PEGRNVTFK-WR 98 (202)
Q Consensus 32 ~~~~~~RR~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~~~~~~~~~--------~~v~~~~l----~~g~~~~~~-~~ 98 (202)
+..+.+||+||..++++.+.++++ ..+.|+++.+.|.+...+... .+|.++++ ++|+...+. +.
T Consensus 8 ~~~d~~RR~FL~~~~~~~gg~~a~---~~~~P~v~~~~Pp~~~~~~g~~~a~d~~G~~I~~s~~~~~~~~g~~~~v~~~~ 84 (178)
T PRK13474 8 DVPSMGRRQFMNLLTFGTVTGVAL---GALYPVVKYFIPPSAGGAGGGTTAKDELGNDIPASQFLATHPAGDRSLVQGLK 84 (178)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHH---HHHHHhhheeCChhHccCCCcceeecccCCeeehhhccccCCCCCcEEEEEcC
Confidence 345689999999988755443322 356788888877766533321 23456666 678777776 56
Q ss_pred CeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCce--EEEeccccCCCcccCcccCCCCEEEcCCCCeEECCCCc
Q psy17358 99 GKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKW--LVLIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDASGR 176 (202)
Q Consensus 99 g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~--~a~s~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~ 176 (202)
|++.+++. ..+|++ ||++++|||+||++.|+..+ +.|.||||||+||.+|+
T Consensus 85 g~~~~lv~--------------------------~~~g~~~~~a~~~~CtH~gc~l~~~~~~-~~~~CP~Hgs~Fd~tG~ 137 (178)
T PRK13474 85 GDPTYLVV--------------------------EEDGTIASYGINAVCTHLGCVVPWNSGE-NKFQCPCHGSQYDATGK 137 (178)
T ss_pred CCeEEEEE--------------------------eCCCEEEEEEecCCCCCCCCccccccCC-CEEEecCcCCEECCCCC
Confidence 76633332 147888 67799999999999998765 69999999999999999
Q ss_pred cccCCCCCCCccceEEEeCCcE
Q psy17358 177 IRKGPAPLNLEVPKYEFPEPGL 198 (202)
Q Consensus 177 vi~GPA~~~L~~~p~~i~~~~~ 198 (202)
++.||++++|+.|++++++|.+
T Consensus 138 ~~~gPa~~~L~~y~v~v~~g~v 159 (178)
T PRK13474 138 VVRGPAPLSLALVHVTVEDDKV 159 (178)
T ss_pred CccCCCCCCCCeEeEEEECCEE
Confidence 9999999999999999987654
No 6
>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=99.90 E-value=9.8e-24 Score=161.33 Aligned_cols=102 Identities=25% Similarity=0.507 Sum_probs=83.9
Q ss_pred eccCCCCCceEEEEEcC--eeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCC
Q psy17358 83 KLADIPEGRNVTFKWRG--KPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFG 160 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g--~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~ 160 (202)
++++|++|+.+.+.+.+ .++++++..++.. -.+..+++++|++++|||+||+|.++. +.+
T Consensus 8 ~~~~l~~g~~~~~~~~~~~~~i~v~r~~~~~~-----------------~~~~~~g~~~A~~~~CpH~g~~L~~g~-~~~ 69 (126)
T cd03476 8 NLSQLSPGQPVTFNYPDESSPCVLVKLGVPVP-----------------GGVGPDNDIVAFSALCTHMGCPLTYDP-SNK 69 (126)
T ss_pred eHHHCCCCCeEEEEcCCCCCcEEEEECCcccc-----------------CccccCCEEEEEeCcCCCCCccccccc-cCC
Confidence 78999999999999987 7888776421100 001246899999999999999999866 558
Q ss_pred EEEcCCCCeEECC--CCccccCCCCCCCccceEEEe--CCcEEEEC
Q psy17358 161 GYYCPCHGSHYDA--SGRIRKGPAPLNLEVPKYEFP--EPGLLVVG 202 (202)
Q Consensus 161 ~~~CPcHGs~FD~--~G~vi~GPA~~~L~~~p~~i~--~~~~~~ig 202 (202)
.|.||||||+||+ +|+++.||+..+|++||++++ +|.++++|
T Consensus 70 ~v~CP~Hg~~Fdl~tgG~~~~gPa~~~L~~ypv~ve~~~g~V~~~~ 115 (126)
T cd03476 70 TFVCPCHFSQFDPARGGQMVSGQATQNLPQIVLEYDEASGDIYAVG 115 (126)
T ss_pred EEEccCcCCEEeCCCCCeEEcCCCCCCCCeEEEEEECCCCEEEEEE
Confidence 9999999999999 479999999999999999998 77787775
No 7
>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=99.90 E-value=5.4e-24 Score=182.49 Aligned_cols=163 Identities=21% Similarity=0.346 Sum_probs=102.1
Q ss_pred CccchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcChhhhhc----------ccceeeccCCCCCceEEE--EEc--Ce
Q psy17358 35 EEARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASADVLAM----------AKIEVKLADIPEGRNVTF--KWR--GK 100 (202)
Q Consensus 35 ~~~RR~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~~~~~~~----------~~~~v~~~~l~~g~~~~~--~~~--g~ 100 (202)
.++||+||..+++..+.+ +++ .+.+++..+.|.+...+. ....|++++|++|+...+ ++. +.
T Consensus 60 D~~RR~fL~~al~gAga~-a~~---~avPlv~~l~PP~~a~atG~pk~La~D~~GnPIKASdL~vnSp~~~lfeyPl~gd 135 (321)
T TIGR03171 60 DEGRRKFLKGLIFGIAAA-AVV---GIIPGLRVLVPPTVAAASGFPKSLLVDSSGNPIKASSIPVNSPIITIFEYPMTGE 135 (321)
T ss_pred CccHHHHHHHHHHHHHHH-Hhh---hhhhheecccCchhhhccCCCceEEecCCCCeeeHHHccCCCcccccccCcCCCC
Confidence 578999999888766542 222 244888888886654432 123577889999887753 332 33
Q ss_pred eEEEEeCCHHHHHhhhhchhcccCCCccc-cccc-----cCCceEEEeccccCCCcccCc---cc---------------
Q psy17358 101 PLFIRHRAAAEIAKEQAVAISTLRDPQAD-SERV-----KDPKWLVLIGVCTHLGCVPVA---NA--------------- 156 (202)
Q Consensus 101 pv~i~~~~~~~i~~~~~v~~~~l~dp~~~-~~r~-----~~g~~~a~s~~CtHlGc~l~~---~~--------------- 156 (202)
|-++.+......... ++....++-|+.+ .|+. +++.++|||++|||+||++.+ .+
T Consensus 136 P~fLIklgka~~~~v-~i~p~~v~~~~~g~~y~~pgGVGp~~~IVAyS~IC~H~GC~~~~~~~Ypp~~~~~~~~~~~~~~ 214 (321)
T TIGR03171 136 PNFLLNLGDSSGKPV-EIPPTKVVVPQTGKTYTFPGGVGPNKSIVAYSAICQHLGCTPPYIHFYPPNYVNPSQLTAPEPD 214 (321)
T ss_pred cHHHHHhhhhcCCce-ecCccccccCCCCcceeccCCcCCCCCEEEEecccCcCCCCcchhhccCccccccccccccccc
Confidence 333221110000000 1122222222221 1222 368999999999999998833 20
Q ss_pred ----------CC---CCEEEcCCCCeEECC-C-CccccCCCCCCCccceEEEeCC--cEEEEC
Q psy17358 157 ----------GD---FGGYYCPCHGSHYDA-S-GRIRKGPAPLNLEVPKYEFPEP--GLLVVG 202 (202)
Q Consensus 157 ----------~~---~~~~~CPcHGs~FD~-~-G~vi~GPA~~~L~~~p~~i~~~--~~~~ig 202 (202)
.+ .+.|.||||||+||+ + |+++.|||+++|++++++++++ .++.+|
T Consensus 215 ~~~~~~~~~~~~~~~~~~~~CPCHgS~FD~~~gg~Vv~GPA~rpLp~i~l~~d~~~~~l~AvG 277 (321)
T TIGR03171 215 QLTAQALLAAKQANVPALIHCDCHGSTYDPYHGAAVLTGPTVRPLPAVILEWDSSTDYLYAIG 277 (321)
T ss_pred ccchhhhhhhhccCCCCeEECCCCCCEECCCCCCceeCCCCCCCCCcceEEEeCCCCeEEEEe
Confidence 01 138999999999999 4 5899999999999999999854 366655
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=99.88 E-value=9.8e-23 Score=148.44 Aligned_cols=90 Identities=21% Similarity=0.370 Sum_probs=79.7
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
.+++|++|+.+.+.+.+.++++.+ .+++++|++++|||+||+|.++..+.+.+
T Consensus 6 ~~~~l~~g~~~~~~~~g~~~~v~r---------------------------~~~~~~a~~~~CpH~g~~L~~g~~~~~~i 58 (98)
T cd03528 6 AVDELPEGEPKRVDVGGRPIAVYR---------------------------VDGEFYATDDLCTHGDASLSEGYVEGGVI 58 (98)
T ss_pred EhhhcCCCCEEEEEECCeEEEEEE---------------------------ECCEEEEECCcCCCCCCCCCCCeEeCCEE
Confidence 678999999999999999998764 25699999999999999998876555899
Q ss_pred EcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEE
Q psy17358 163 YCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLL 199 (202)
Q Consensus 163 ~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~ 199 (202)
.||||||+||+ +|+++.+|+..+|+.||+++++|.++
T Consensus 59 ~Cp~Hg~~fd~~~G~~~~~p~~~~L~~~~v~~~~g~v~ 96 (98)
T cd03528 59 ECPLHGGRFDLRTGKALSLPATEPLKTYPVKVEDGDVY 96 (98)
T ss_pred EeCCcCCEEECCCCcccCCCCCCCcceEeEEEECCEEE
Confidence 99999999999 99999999999999999999866543
No 9
>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=99.88 E-value=8.1e-23 Score=148.47 Aligned_cols=89 Identities=19% Similarity=0.334 Sum_probs=79.7
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
.+++|++|+.+.+.+.+.++++.+ .+|+++|++++|||+||+|.++..+.+.+
T Consensus 5 ~~~~l~~g~~~~~~~~~~~v~v~r---------------------------~~g~~~A~~~~CpH~g~~L~~g~~~~~~i 57 (95)
T cd03478 5 RLSDLGDGEMKEVDVGDGKVLLVR---------------------------QGGEVHAIGAKCPHYGAPLAKGVLTDGRI 57 (95)
T ss_pred ehhhCCCCCEEEEEeCCcEEEEEE---------------------------ECCEEEEEcCcCcCCCCccCCCeEeCCEE
Confidence 678999999999999999988764 26899999999999999999876555899
Q ss_pred EcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcE
Q psy17358 163 YCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGL 198 (202)
Q Consensus 163 ~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~ 198 (202)
.||||||+||+ +|+++.+|+..+|++||+++++|.+
T Consensus 58 ~CP~Hg~~Fdl~tG~~~~~p~~~~l~~~~v~~~~g~i 94 (95)
T cd03478 58 RCPWHGACFNLRTGDIEDAPALDSLPCYEVEVEDGRV 94 (95)
T ss_pred EcCCCCCEEECCCCcCcCCCccCCcceEEEEEECCEE
Confidence 99999999998 9999999998999999999987654
No 10
>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=99.88 E-value=1.9e-22 Score=148.52 Aligned_cols=91 Identities=20% Similarity=0.267 Sum_probs=80.2
Q ss_pred eeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCE
Q psy17358 82 VKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGG 161 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~ 161 (202)
.++++|++|+.+.+.+.+.++++.+ ..+|+++|+++.|||+|++|..+..+.+.
T Consensus 6 ~~~~dl~~g~~~~~~~~g~~i~l~r--------------------------~~~g~~~A~~~~CpH~g~~L~~G~~~~~~ 59 (101)
T TIGR02377 6 CDADDIGREDVARFDHGGRTFAIYR--------------------------TPDDQYYATDGLCTHEYAHLADGLVMDTT 59 (101)
T ss_pred EEHHHcCCCCEEEEEECCeEEEEEE--------------------------eCCCEEEEEcCcCCCCCCCCCCCEEcCCE
Confidence 3788999999999999999988764 24789999999999999999877655589
Q ss_pred EEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcE
Q psy17358 162 YYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGL 198 (202)
Q Consensus 162 ~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~ 198 (202)
+.||||||+||+ ||+++.+|+..+|++||+++++|.+
T Consensus 60 i~CP~Hg~~Fdl~tG~~~~~p~~~~l~~y~v~v~~g~v 97 (101)
T TIGR02377 60 VECPKHAGCFDYRTGEALNPPVCVNLKTYPVKVVDGAV 97 (101)
T ss_pred EECCccCCEEECCCCcccCCCccCCcceEeEEEECCEE
Confidence 999999999998 9999999998999999999986654
No 11
>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=99.88 E-value=2.4e-22 Score=145.96 Aligned_cols=87 Identities=29% Similarity=0.548 Sum_probs=74.3
Q ss_pred eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCccc--CCC
Q psy17358 83 KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANA--GDF 159 (202)
Q Consensus 83 ~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~--~~~ 159 (202)
..++|++ |....+.+.+..+++.+ .+|+++|++++|||+||+|.++. .+.
T Consensus 7 ~~~el~~~~~~~~~~~~~~~v~~~~---------------------------~~g~~~A~~~~CpH~g~~l~~~~~~~~~ 59 (97)
T PF00355_consen 7 RSSELPEPGDVKRVDVGGKLVLVRR---------------------------SDGEIYAFSNRCPHQGCPLSEGPFSEDG 59 (97)
T ss_dssp EGGGSHSTTEEEEEEETTEEEEEEE---------------------------TTTEEEEEESB-TTTSBBGGCSSEETTT
T ss_pred EHHHCCCCCCEEEEEcCCcEEEEEe---------------------------CCCCEEEEEccCCccceeEcceeccccc
Confidence 6788988 88888888555665542 48999999999999999999983 444
Q ss_pred CEEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCC
Q psy17358 160 GGYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEP 196 (202)
Q Consensus 160 ~~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~ 196 (202)
+.+.||||||+||+ ||+++.+|+..+|+.||+++++|
T Consensus 60 ~~i~Cp~Hg~~Fd~~tG~~~~~p~~~~l~~~~v~ve~~ 97 (97)
T PF00355_consen 60 GVIVCPCHGWRFDLDTGECVGGPAPRPLPLYPVKVEGD 97 (97)
T ss_dssp TEEEETTTTEEEETTTSBEEESTTCSBSTEEEEEEETT
T ss_pred CEEEeCCcCCEEeCCCceEecCCCCCCcCCCCeEEeCC
Confidence 79999999999999 69999999999999999999875
No 12
>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=99.87 E-value=6e-22 Score=143.40 Aligned_cols=86 Identities=28% Similarity=0.534 Sum_probs=76.7
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
.+++|++|+.+.+.+.+.+++|.+ ..+|+++|++++|||+||.|.++..+ +.|
T Consensus 4 ~~~dl~~g~~~~~~~~g~~v~v~r--------------------------~~~g~~~A~~~~CpH~g~~l~~g~~~-~~i 56 (91)
T cd03477 4 DIEDLAPGEGGVVNIGGKRLAVYR--------------------------DEDGVLHTVSATCTHLGCIVHWNDAE-KSW 56 (91)
T ss_pred chhhcCCCCeEEEEECCEEEEEEE--------------------------CCCCCEEEEcCcCCCCCCCCcccCCC-CEE
Confidence 467899999999999999988764 35799999999999999999987654 799
Q ss_pred EcCCCCeEECCCCccccCCCCCCCccceEEEeC
Q psy17358 163 YCPCHGSHYDASGRIRKGPAPLNLEVPKYEFPE 195 (202)
Q Consensus 163 ~CPcHGs~FD~~G~vi~GPA~~~L~~~p~~i~~ 195 (202)
.||||||+||.+|+++.+|+.++|++|+++-.+
T Consensus 57 ~CP~Hg~~Fd~~G~~~~~Pa~~~l~~y~v~~~~ 89 (91)
T cd03477 57 DCPCHGSRFSYDGEVIEGPAVSGLKPADDAPID 89 (91)
T ss_pred ECCCCCCEECCCCcEeeCCCCCCCCeeEeeccc
Confidence 999999999999999999999999999998654
No 13
>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=99.86 E-value=1.2e-21 Score=150.32 Aligned_cols=103 Identities=21% Similarity=0.413 Sum_probs=81.1
Q ss_pred eeccCCCCCceEEEEEcC--eeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCC
Q psy17358 82 VKLADIPEGRNVTFKWRG--KPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDF 159 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g--~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~ 159 (202)
.++++|++|+++.+.+.+ .++++++... |..+.. ..+|+++|++++|||+||+|.|... .
T Consensus 10 ~~~~dl~~g~~~~~~~~~~~~~~~v~~~~~----------------~~~~~~-~~~G~~~A~~~~CpH~g~~L~~~~~-~ 71 (129)
T TIGR02694 10 ANISELKLNEPLDFNYPDASSPGVLLKLGT----------------PVEGGV-GPDGDIVAFSTLCTHMGCPVSYSAD-N 71 (129)
T ss_pred EeHHHCCCCCCEEEecCCCCCCEEEEecCC----------------cccCcc-ccCCEEEEEeCcCCCCCcccccccC-C
Confidence 478999999999999865 3666665210 000111 1479999999999999999998754 4
Q ss_pred CEEEcCCCCeEECC-C-CccccCCCCCCCccceEEEeC-CcEEEEC
Q psy17358 160 GGYYCPCHGSHYDA-S-GRIRKGPAPLNLEVPKYEFPE-PGLLVVG 202 (202)
Q Consensus 160 ~~~~CPcHGs~FD~-~-G~vi~GPA~~~L~~~p~~i~~-~~~~~ig 202 (202)
..|.||||||+||+ | |+++.+|+.++|++||+++++ |.++.+|
T Consensus 72 ~~i~CP~Hga~Fdl~tgG~~~~gP~~~~L~~y~v~v~~~G~V~~~~ 117 (129)
T TIGR02694 72 KTFNCPCHFSVFDPEKGGQQVWGQATQNLPQIVLRVADNGDIFAEG 117 (129)
T ss_pred CEEEcCCCCCEECCCCCCcEECCCCCCCCCeeEEEEECCCeEEEEe
Confidence 89999999999999 5 699999999999999999975 6676654
No 14
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=99.86 E-value=9.7e-22 Score=145.85 Aligned_cols=89 Identities=16% Similarity=0.217 Sum_probs=75.6
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCC-CE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDF-GG 161 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~-~~ 161 (202)
.+++|++|+.+.+.+. .++++.+ .+|+++|++++|||+||+|+.+..++ +.
T Consensus 8 ~~~~l~~g~~~~~~~~-~~i~v~~---------------------------~~g~~~A~~~~CpH~g~~L~~G~~~~~~~ 59 (106)
T PRK09965 8 PVADLPEGEALRVDTS-PVIALFN---------------------------VGGEFYAIDDRCSHGNASLSEGYLEDDAT 59 (106)
T ss_pred eHHHcCCCCeEEEeCC-CeEEEEE---------------------------ECCEEEEEeCcCCCCCCCCCceEECCCCE
Confidence 6789999999888876 6666653 37899999999999999997654444 68
Q ss_pred EEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEE
Q psy17358 162 YYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLL 199 (202)
Q Consensus 162 ~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~ 199 (202)
+.||||||+||+ ||+++.+|+..+|++|++++++|.++
T Consensus 60 i~Cp~Hg~~Fd~~tG~~~~~p~~~~l~~y~v~v~~g~v~ 98 (106)
T PRK09965 60 VECPLHAASFCLRTGKALCLPATDPLRTYPVHVEGGDIF 98 (106)
T ss_pred EEcCCCCCEEEcCCCCeeCCCCCCCcceEeEEEECCEEE
Confidence 999999999999 99999999999999999999866543
No 15
>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=99.86 E-value=1.8e-21 Score=142.10 Aligned_cols=92 Identities=21% Similarity=0.265 Sum_probs=79.0
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
.+++|++|+.+.+.+.+.+++|.+ ..+|+++|+++.|||+||+|.++..+.+.+
T Consensus 6 ~~~~l~~~~~~~~~~~g~~i~l~r--------------------------~~~g~~~A~~~~CpH~g~~L~~g~~~~~~i 59 (98)
T cd03530 6 ALEDIPPRGARKVQTGGGEIAVFR--------------------------TADDEVFALENRCPHKGGPLSEGIVHGEYV 59 (98)
T ss_pred EHHHCCCCCcEEEEECCEEEEEEE--------------------------eCCCCEEEEcCcCCCCCCCccCCEEcCCEE
Confidence 678899999999999999988764 246899999999999999999877666899
Q ss_pred EcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEEEEC
Q psy17358 163 YCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLLVVG 202 (202)
Q Consensus 163 ~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~~ig 202 (202)
.||||||+||+ +|++. +|+..+|+.||+++++ +.|.|+
T Consensus 60 ~Cp~Hg~~Fdl~~G~~~-~p~~~~l~~y~v~v~~-g~v~v~ 98 (98)
T cd03530 60 TCPLHNWVIDLETGEAQ-GPDEGCVRTFPVKVED-GRVYLG 98 (98)
T ss_pred ECCCCCCEEECCCCCCC-CCCCCccceEeEEEEC-CEEEEC
Confidence 99999999999 89875 6777899999999975 456654
No 16
>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=99.84 E-value=1e-20 Score=140.46 Aligned_cols=90 Identities=20% Similarity=0.265 Sum_probs=77.0
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
.+++|++|+.+.+.+.+.+++++++ .+|+++|++++|||+||+|.++..+++.+
T Consensus 6 ~~~~l~~g~~~~~~~~~~~~~~~~~--------------------------~~g~~~A~~n~CpH~g~~L~~g~~~g~~i 59 (108)
T cd03474 6 SLDDVWEGEMELVDVDGEEVLLVAP--------------------------EGGEFRAFQGICPHQEIPLAEGGFDGGVL 59 (108)
T ss_pred ehhccCCCceEEEEECCeEEEEEEc--------------------------cCCeEEEEcCcCCCCCCCcccCcccCCEE
Confidence 6789999999999998877766542 47899999999999999999877666799
Q ss_pred EcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEE
Q psy17358 163 YCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLL 199 (202)
Q Consensus 163 ~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~ 199 (202)
.||||||+||+ +|+++ +|+..+|+.||+++++|.++
T Consensus 60 ~CP~Hg~~Fdl~~G~~~-~~~~~~L~~~~v~v~~g~v~ 96 (108)
T cd03474 60 TCRAHLWQFDADTGEGL-NPRDCRLARYPVKVEGGDIL 96 (108)
T ss_pred EeCCcCCEEECCCcccc-CCCCCccceEeEEEECCEEE
Confidence 99999999999 77776 58889999999999866543
No 17
>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=99.84 E-value=1.6e-20 Score=144.15 Aligned_cols=108 Identities=20% Similarity=0.209 Sum_probs=89.4
Q ss_pred ccCCcChhhhhccccee-eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEecc
Q psy17358 66 SSMAASADVLAMAKIEV-KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGV 144 (202)
Q Consensus 66 ~~~~p~~~~~~~~~~~v-~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~ 144 (202)
++-.+.+..+......+ .+++|++|+.+.+.+.|.++++++ ..+|+++|+++.
T Consensus 5 ~~~~~~~~~~~~~W~~v~~~~el~~g~~~~~~v~g~~l~l~r--------------------------~~~g~v~A~~n~ 58 (129)
T cd04337 5 GSSLELEPGLRNFWYPVEFSKDLKMDTMVPFELFGQPWVLFR--------------------------DEDGTPGCIRDE 58 (129)
T ss_pred ccCccccchhhCccEEEEEHHHCCCCCeEEEEECCcEEEEEE--------------------------CCCCcEEEEeCc
Confidence 44445555665555555 778999999999999999987764 357999999999
Q ss_pred ccCCCcccCcccCCCCEEEcCCCCeEECCCCccccCCCC----CCCccceEEEeCCcEE
Q psy17358 145 CTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAP----LNLEVPKYEFPEPGLL 199 (202)
Q Consensus 145 CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GPA~----~~L~~~p~~i~~~~~~ 199 (202)
|||+|++|..+..+.+.+.||+|||+||.+|+++..|+. .+|+.||+++++|.++
T Consensus 59 CpH~g~~L~~G~~~~~~i~CP~Hgw~Fd~tG~~~~~P~~~~~~~~l~~y~v~v~~g~V~ 117 (129)
T cd04337 59 CAHRACPLSLGKVIEGRIQCPYHGWEYDGDGECTKMPSTKCLNVGIAALPCMEQDGMIW 117 (129)
T ss_pred CCCCcCCcccCcEeCCEEEeCCCCCEECCCCCEEeCCcCCCccCCcceEeEEEECCEEE
Confidence 999999999877666899999999999999999998865 3899999999877653
No 18
>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=99.84 E-value=1.3e-20 Score=141.48 Aligned_cols=90 Identities=27% Similarity=0.439 Sum_probs=79.1
Q ss_pred eccCCC-CCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccC-CCC
Q psy17358 83 KLADIP-EGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAG-DFG 160 (202)
Q Consensus 83 ~~~~l~-~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~-~~~ 160 (202)
.+++|+ +|+.+.+.+.+.++++.+ ..+|+++|++++|||+||+|.++.. +.+
T Consensus 6 ~~~el~~~g~~~~~~~~~~~i~v~r--------------------------~~~g~~~a~~n~CpH~g~~L~~g~~~~~~ 59 (118)
T cd03469 6 HSSELPEPGDYVTLELGGEPLVLVR--------------------------DRDGEVRAFHNVCPHRGARLCEGRGGNAG 59 (118)
T ss_pred EHHHCCCCCCEEEEEECCccEEEEE--------------------------CCCCCEEEEEEeCCCCCCEeeeccCCCCC
Confidence 568898 999999999999988764 3479999999999999999998876 668
Q ss_pred EEEcCCCCeEECCCCccccCCCCC----------CCccceEEEeCCcE
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPAPL----------NLEVPKYEFPEPGL 198 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA~~----------~L~~~p~~i~~~~~ 198 (202)
.+.||||||+||.+|+++.+|+.. .|+.||+++++|.+
T Consensus 60 ~i~Cp~Hg~~Fd~~G~~~~~P~~~~~~~~~~~~~~L~~~~v~~~~g~v 107 (118)
T cd03469 60 RLVCPYHGWTYDLDGKLVGVPREEGFPGFDKEKLGLRTVPVEEWGGLI 107 (118)
T ss_pred EEECCCCCCEECCCCcEEeCCcccccCCCCHHHCCCeEEEEEEECCEE
Confidence 999999999999999999999764 49999999987654
No 19
>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=99.83 E-value=2.3e-20 Score=142.26 Aligned_cols=65 Identities=42% Similarity=0.849 Sum_probs=57.9
Q ss_pred cCCce--EEEeccccCCCcccCcccCCCCEEEcCCCCeEECCCCccccCCCCCCCccceEEEeCCcEE
Q psy17358 134 KDPKW--LVLIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEFPEPGLL 199 (202)
Q Consensus 134 ~~g~~--~a~s~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GPA~~~L~~~p~~i~~~~~~ 199 (202)
.+|++ +|++++|||+||++.+...+ +.+.||||||+||.+|+++.+|++.+|++|++++++|.++
T Consensus 42 ~dg~i~~~A~~~~CpH~G~~l~~~~~~-~~i~CP~Hg~~Fd~tG~~~~gPa~~~L~~y~V~vedg~I~ 108 (126)
T cd03471 42 EDKTIANYGINAVCTHLGCVVPWNAAE-NKFKCPCHGSQYDATGKVVRGPAPLSLALVHATVDDDKVV 108 (126)
T ss_pred CCCeEEEEEecCCCcCCCCCcCccCCC-CEEEcCCCCCEECCCCCEecCCCCCCCceEeEEEECCEEE
Confidence 36766 89999999999999887654 7999999999999999999999999999999999876543
No 20
>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=99.82 E-value=3.6e-20 Score=147.47 Aligned_cols=68 Identities=35% Similarity=0.661 Sum_probs=57.7
Q ss_pred CCceEEEeccccCCCcccCcc---------------cCCCCEEEcCCCCeEECC-CC-ccccCCCCCCCccceEEEeC--
Q psy17358 135 DPKWLVLIGVCTHLGCVPVAN---------------AGDFGGYYCPCHGSHYDA-SG-RIRKGPAPLNLEVPKYEFPE-- 195 (202)
Q Consensus 135 ~g~~~a~s~~CtHlGc~l~~~---------------~~~~~~~~CPcHGs~FD~-~G-~vi~GPA~~~L~~~p~~i~~-- 195 (202)
+++++|++++|||+||++.+. ..+.+.|.||||||+||+ +| .++.|||+++|+++++++++
T Consensus 74 ~g~IvA~S~iCpHlGc~l~~~~~y~~~~~~~~~~~g~~~~~~i~CPcHgS~FD~~tGg~v~~GPA~~pLp~~~L~~d~~~ 153 (171)
T cd03475 74 NKSIVAFSAICQHLGCQPPPIVSYPSYYPPDKAPGLASKGAVIHCCCHGSTYDPYKGGVVLTGPAPRPLPAVILEYDSST 153 (171)
T ss_pred CCEEEEEeCcCCCCCCcccccccccccccccccccccccCCEEEcCCCCCEEeCCCCCeEcCCCCCCCcCEeEEEEeCCC
Confidence 689999999999999988741 123489999999999999 56 78999999999999999985
Q ss_pred CcEEEEC
Q psy17358 196 PGLLVVG 202 (202)
Q Consensus 196 ~~~~~ig 202 (202)
|.++.||
T Consensus 154 d~iyAvG 160 (171)
T cd03475 154 DDLYAVG 160 (171)
T ss_pred CcEEEEe
Confidence 5566665
No 21
>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=99.82 E-value=7.7e-20 Score=133.22 Aligned_cols=89 Identities=30% Similarity=0.590 Sum_probs=78.2
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
..++|++|....+...++.++|.+ ..+++++|+++.|||+||+|.+...+.+.+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~v~~--------------------------~~~~~~~a~~~~CpH~g~~l~~~~~~~~~i 59 (98)
T cd03467 6 ALSELPPGGGRVVVVGGGPVVVVR--------------------------REGGEVYALSNRCTHQGCPLSEGEGEDGCI 59 (98)
T ss_pred eccccCCCceEEEEECCeEEEEEE--------------------------eCCCEEEEEcCcCCCCCccCCcCccCCCEE
Confidence 457788999999999888887764 246899999999999999999876556899
Q ss_pred EcCCCCeEECC-CCccccCCCCCCCccceEEEeCCc
Q psy17358 163 YCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPG 197 (202)
Q Consensus 163 ~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~ 197 (202)
.||||||+||+ +|+++.+|+..+|+.||++++++.
T Consensus 60 ~Cp~H~~~f~~~~G~~~~~p~~~~l~~~~v~~~~~~ 95 (98)
T cd03467 60 VCPCHGSRFDLRTGEVVSGPAPRPLPKYPVKVEGDG 95 (98)
T ss_pred EeCCCCCEEeCCCccCcCCCCCCCcCEEEEEEeCCc
Confidence 99999999999 999999999999999999998533
No 22
>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=99.82 E-value=8.7e-20 Score=142.50 Aligned_cols=106 Identities=17% Similarity=0.161 Sum_probs=86.4
Q ss_pred CCcChhhhhccccee-eccCCC-CCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccc
Q psy17358 68 MAASADVLAMAKIEV-KLADIP-EGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVC 145 (202)
Q Consensus 68 ~~p~~~~~~~~~~~v-~~~~l~-~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~C 145 (202)
-.|-..++......+ .+++|+ +|+.+.+.+.|.+++|.+ ..+|+++|++++|
T Consensus 11 ~~~~~~~~~~~W~~v~~~~eL~~~g~~~~~~~~g~~i~v~r--------------------------~~~G~v~A~~n~C 64 (144)
T cd03479 11 GTPMGELLRRYWQPVALSSELTEDGQPVRVRLLGEDLVAFR--------------------------DTSGRVGLLDEHC 64 (144)
T ss_pred CCchhhHhhCceEEEEEHHHCCCCCCEEEEEECCcEEEEEE--------------------------eCCCCEEEEcCcC
Confidence 345555666555544 788999 699999999998887754 3578999999999
Q ss_pred cCCCcccCcccCCCCEEEcCCCCeEECCCCccccCCCCC---------CCccceEEEeCCcEE
Q psy17358 146 THLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPL---------NLEVPKYEFPEPGLL 199 (202)
Q Consensus 146 tHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GPA~~---------~L~~~p~~i~~~~~~ 199 (202)
||+||+|.++..+.+.+.||||||+||.+|+++..|+.. .|..|++++.+|.++
T Consensus 65 pHrG~~L~~G~~~~~~i~CP~Hgw~F~~~G~~~~~P~~~~~~~~~~~~~l~~~~v~~~~G~I~ 127 (144)
T cd03479 65 PHRGASLVFGRVEECGLRCCYHGWKFDVDGQCLEMPSEPPDSQLKQKVRQPAYPVRERGGLVW 127 (144)
T ss_pred CCCCCcccCCcccCCEEEccCCCcEECCCCCEEECCCCccccCCccccCcceEeEEEECCEEE
Confidence 999999999876668999999999999999999988532 689999999776543
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=99.81 E-value=1.3e-19 Score=136.45 Aligned_cols=91 Identities=19% Similarity=0.167 Sum_probs=79.3
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
.+++|++|+.+.+.+.|.+++|.+ ..+|+++|++++|||+|++|..+..+.+.+
T Consensus 7 ~~~dl~~g~~~~~~~~g~~i~l~r--------------------------~~~g~~~a~~n~CpH~ga~L~~G~~~~~~i 60 (115)
T cd03531 7 LARDFRDGKPHGVEAFGTKLVVFA--------------------------DSDGALNVLDAYCRHMGGDLSQGTVKGDEI 60 (115)
T ss_pred EHHHCCCCCeEEEEECCeEEEEEE--------------------------CCCCCEEEEcCcCCCCCCCCccCcccCCEE
Confidence 578899999999999999988764 358999999999999999999887777899
Q ss_pred EcCCCCeEECCCCccccCCC------CCCCccceEEEeCCcEE
Q psy17358 163 YCPCHGSHYDASGRIRKGPA------PLNLEVPKYEFPEPGLL 199 (202)
Q Consensus 163 ~CPcHGs~FD~~G~vi~GPA------~~~L~~~p~~i~~~~~~ 199 (202)
.||+|||+||.+|+++..|+ ...|+.||+++++|.++
T Consensus 61 ~CP~Hg~~fd~~G~~~~~p~~~~~p~~~~l~~ypv~~~~g~v~ 103 (115)
T cd03531 61 ACPFHDWRWGGDGRCKAIPYARRVPPLARTRAWPTLERNGQLF 103 (115)
T ss_pred ECCCCCCEECCCCCEEECCcccCCCcccccceEeEEEECCEEE
Confidence 99999999999999998764 45799999999876553
No 24
>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=99.79 E-value=4.5e-19 Score=136.92 Aligned_cols=92 Identities=15% Similarity=0.164 Sum_probs=79.3
Q ss_pred eeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCE
Q psy17358 82 VKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGG 161 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~ 161 (202)
..+++|++|+.+.+.+.|.+++|.+ ..+|+++|+.++|||.|++|..+..+.+.
T Consensus 22 ~~~~el~~~~~~~~~v~g~~ivl~r--------------------------~~~G~v~A~~n~CpHrga~L~~G~~~~~~ 75 (134)
T cd04338 22 YLLKDVPTDAPLGLSVYDEPFVLFR--------------------------DQNGQLRCLEDRCPHRLAKLSEGQLIDGK 75 (134)
T ss_pred EEHHHCCCCCCEEEEECCceEEEEE--------------------------cCCCCEEEEcCcCCCCcCcccCCeecCCE
Confidence 4789999999999999999998764 35799999999999999999987766689
Q ss_pred EEcCCCCeEECCCCccccCCC---------CCCCccceEEEeCCcEE
Q psy17358 162 YYCPCHGSHYDASGRIRKGPA---------PLNLEVPKYEFPEPGLL 199 (202)
Q Consensus 162 ~~CPcHGs~FD~~G~vi~GPA---------~~~L~~~p~~i~~~~~~ 199 (202)
+.||+|||+||.+|+++..|. ...|++||+++.+|.++
T Consensus 76 i~CP~Hgw~Fd~~G~~~~~P~~~~~~~~~~~~~l~~y~v~~~~G~V~ 122 (134)
T cd04338 76 LECLYHGWQFGGEGKCVKIPQLPADAKIPKNACVKSYEVRDSQGVVW 122 (134)
T ss_pred EEccCCCCEECCCCCEEECCCCCccCCCCcccCcceEeEEEECCEEE
Confidence 999999999999999998763 25699999999876554
No 25
>COG2146 {NirD} Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only]
Probab=99.79 E-value=3.7e-19 Score=132.21 Aligned_cols=92 Identities=23% Similarity=0.353 Sum_probs=75.4
Q ss_pred eeccCCCCCceEEEEEcC-eeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCC
Q psy17358 82 VKLADIPEGRNVTFKWRG-KPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFG 160 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g-~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~ 160 (202)
..+++|+++..+.+.+.+ ..+++++ .+|++||+.+.|||.||+++.+..++.
T Consensus 9 c~~~dl~~~~~~~v~~~~~~~~~~~~---------------------------~~g~v~A~~n~CpH~~~~l~~g~v~~~ 61 (106)
T COG2146 9 CKVDDLPEGGGVRVLVGGGRFALVVR---------------------------ADGEVFAIDNRCPHAGAPLSRGLVEGD 61 (106)
T ss_pred EehHhcCCCCceEEEecCCEEEEEEe---------------------------cCCEEEEEeCcCCCCCCcccccEeCCC
Confidence 478999999999998844 4454432 589999999999999999888766543
Q ss_pred -EEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEEEE
Q psy17358 161 -GYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLLVV 201 (202)
Q Consensus 161 -~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~~i 201 (202)
.+.||||+|+||+ ||+++.+|+...|++||+++++| .+.|
T Consensus 62 ~~i~Cp~H~a~Fdl~tG~~~~~p~~~~l~~y~vrve~g-~v~v 103 (106)
T COG2146 62 ETVVCPLHGARFDLRTGECLEPPAGKTLKTYPVRVEGG-RVFV 103 (106)
T ss_pred CEEECCccCCEEEcCCCceecCCCCCceeEEeEEEECC-EEEE
Confidence 6999999999999 99999999755599999999855 4443
No 26
>PRK09511 nirD nitrite reductase small subunit; Provisional
Probab=99.79 E-value=4.2e-19 Score=132.33 Aligned_cols=93 Identities=10% Similarity=0.044 Sum_probs=76.0
Q ss_pred eeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcc-cCcccC-C-
Q psy17358 82 VKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCV-PVANAG-D- 158 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~-l~~~~~-~- 158 (202)
..+++|++|+.+.+...++.|+|.+. ..+|+|||+++.|||.|++ |+.+.. +
T Consensus 8 ~~~~dl~~g~~~~v~v~g~~i~l~~~-------------------------~~~g~~~A~~n~CpH~~~~~L~~G~~~~~ 62 (108)
T PRK09511 8 CKIDDILPGTGVCALVGDEQVAIFRP-------------------------YHDEQVFAISNIDPFFQASVLSRGLIAEH 62 (108)
T ss_pred eEHhHcCCCceEEEEECCEEEEEEEE-------------------------CCCCEEEEEeCcCCCCCCcccCCceEccC
Confidence 37899999999999999998887641 1378999999999999996 776533 1
Q ss_pred C--CEEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEEE
Q psy17358 159 F--GGYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLLV 200 (202)
Q Consensus 159 ~--~~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~~ 200 (202)
. ..+.||+|||+||+ ||+++..|+ .+|++||+++++|.+++
T Consensus 63 ~g~~~V~CP~H~~~Fdl~TG~~~~~~~-~~l~typV~ve~g~V~v 106 (108)
T PRK09511 63 QGELWVASPLKKQRFRLSDGLCMEDEQ-FSVKHYDARVKDGVVQL 106 (108)
T ss_pred CCeEEEECCCCCCEEECCCcccCCCCC-ccEeeEeEEEECCEEEE
Confidence 1 24999999999999 999997665 79999999998766543
No 27
>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=99.79 E-value=6.1e-19 Score=132.80 Aligned_cols=90 Identities=17% Similarity=0.261 Sum_probs=77.1
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
..++|+ |+.+.+.+.|.+++|.+ ..+|+++|++++|||+|++|..+..+.+.+
T Consensus 11 ~~~el~-~~~~~~~~~g~~i~l~r--------------------------~~~g~~~a~~n~CpH~g~~L~~G~~~~~~i 63 (116)
T cd03532 11 WADELG-DKPLARTLLGEPVVLYR--------------------------TQDGRVAALEDRCPHRSAPLSKGSVEGGGL 63 (116)
T ss_pred EHHHcC-CCcEEEEECCceEEEEE--------------------------CCCCCEEEeCCcCCCCCCCccCCcccCCEE
Confidence 667888 88888888888888764 357999999999999999999877666899
Q ss_pred EcCCCCeEECCCCccccCCCC------CCCccceEEEeCCcEE
Q psy17358 163 YCPCHGSHYDASGRIRKGPAP------LNLEVPKYEFPEPGLL 199 (202)
Q Consensus 163 ~CPcHGs~FD~~G~vi~GPA~------~~L~~~p~~i~~~~~~ 199 (202)
.||+|||+||.+|+++..|+. .+|+.||+++++|.++
T Consensus 64 ~Cp~Hg~~fd~~G~~~~~p~~~~~~~~~~l~~~~v~~~~g~v~ 106 (116)
T cd03532 64 VCGYHGLEFDSDGRCVHMPGQERVPAKACVRSYPVVERDALIW 106 (116)
T ss_pred EeCCCCcEEcCCCCEEeCCCCCCCCCccccccCCEEEECCEEE
Confidence 999999999999999998864 3799999999866543
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=99.78 E-value=6.6e-19 Score=129.87 Aligned_cols=89 Identities=12% Similarity=0.102 Sum_probs=73.7
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcc-cCcccC----
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCV-PVANAG---- 157 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~-l~~~~~---- 157 (202)
.+++|++|+.+.+...|.++++.+ ..+|+++|+.+.|||+|++ +..+..
T Consensus 6 ~~~~l~~g~~~~~~~~g~~i~l~r--------------------------~~~g~~~A~~~~CpH~g~~ll~~G~~~~~~ 59 (103)
T cd03529 6 ALDDLPPGSGVAALVGDTQIAIFR--------------------------LPGREVYAVQNMDPHSRANVLSRGIVGDIG 59 (103)
T ss_pred EHHHCCCCCcEEEEECCEEEEEEE--------------------------eCCCeEEEEeCcCCCCCCcccCCceEcccC
Confidence 678999999999999999988764 2456999999999999997 543321
Q ss_pred CCCEEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcE
Q psy17358 158 DFGGYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGL 198 (202)
Q Consensus 158 ~~~~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~ 198 (202)
+...+.||+|||+||+ ||+++.+|+ .+|+.||+++++|.+
T Consensus 60 ~~~~i~Cp~Hg~~Fdl~tG~~~~~p~-~~l~~y~v~~~~g~v 100 (103)
T cd03529 60 GEPVVASPLYKQHFSLKTGRCLEDED-VSVATFPVRVEDGEV 100 (103)
T ss_pred CCeEEECCCCCCEEEcCCCCccCCCC-ccEeeEeEEEECCEE
Confidence 1248999999999998 999999886 589999999986554
No 29
>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=99.78 E-value=6.4e-19 Score=130.24 Aligned_cols=90 Identities=17% Similarity=0.236 Sum_probs=74.2
Q ss_pred eeccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCC-CcccCcccCCCC
Q psy17358 82 VKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHL-GCVPVANAGDFG 160 (202)
Q Consensus 82 v~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHl-Gc~l~~~~~~~~ 160 (202)
..+++|++|+.+.+.+.|.+++|.+ ..+++++|+.+.|||+ ++++..+..+..
T Consensus 6 ~~~~el~~g~~~~~~v~g~~l~v~r--------------------------~~~~~~~a~~~~CpH~g~~~L~~g~~~~~ 59 (105)
T TIGR02378 6 CAIDDIPEETGVCVLLGDTQIAIFR--------------------------VPGDQVFAIQNMCPHKRAFVLSRGIVGDA 59 (105)
T ss_pred EEHHHCCCCCcEEEEECCEEEEEEE--------------------------eCCCcEEEEeCcCCCCCCccccceEEccC
Confidence 3678999999999999999998764 2367899999999999 777876533223
Q ss_pred ----EEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcE
Q psy17358 161 ----GYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGL 198 (202)
Q Consensus 161 ----~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~ 198 (202)
.+.||+|||+||+ +|+++.+|. .+|++||+++++|.+
T Consensus 60 ~~~~~i~Cp~Hg~~Fdl~tG~~~~~~~-~~L~~y~v~v~~g~v 101 (105)
T TIGR02378 60 QGELWVACPLHKRNFRLEDGRCLEDDS-GSVRTYEVRVEDGRV 101 (105)
T ss_pred CCcEEEECCcCCCEEEcCCccccCCCC-ccEeeEeEEEECCEE
Confidence 3999999999999 999998774 699999999986554
No 30
>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=99.75 E-value=3.8e-18 Score=126.01 Aligned_cols=88 Identities=20% Similarity=0.260 Sum_probs=75.3
Q ss_pred eccCCCCCceEEEEE-cCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcc--cCCC
Q psy17358 83 KLADIPEGRNVTFKW-RGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVAN--AGDF 159 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~-~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~--~~~~ 159 (202)
++.+|++|..+.+.+ .|+.|+|++ .+|+|||+.+.|||+|++|..+ ..+.
T Consensus 13 ~l~eL~~G~~~~v~v~~g~~I~V~~---------------------------~~G~~~A~~n~CpH~g~pL~~g~g~~~g 65 (107)
T cd03473 13 EVANLKEGINFFRNKEDGKKYIIYK---------------------------SKSELKACKNQCKHQGGLFIKDIEDLDG 65 (107)
T ss_pred HHhcCCCCceEEEEecCCcEEEEEE---------------------------ECCEEEEEcCCCCCCCccccCCcceEeC
Confidence 458899999999999 999988865 3789999999999999998863 3455
Q ss_pred CEEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCc
Q psy17358 160 GGYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPG 197 (202)
Q Consensus 160 ~~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~ 197 (202)
+.+.||+|+|+||+ ||+++..|+..+-+.+-+++..++
T Consensus 66 ~~V~CP~Hg~~FDLrTG~~~~~p~~~~~~~~~~~~~~~~ 104 (107)
T cd03473 66 RTVRCTKHNWKLDVSTMKYVNPPDSFCQDELVVEYDEDG 104 (107)
T ss_pred CEEEeCCCCCEEEcCCCCCccCCcccccceeEEEEcccC
Confidence 78999999999999 999999998888877777776544
No 31
>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=99.75 E-value=6.3e-18 Score=131.16 Aligned_cols=90 Identities=21% Similarity=0.317 Sum_probs=76.5
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCcccccccc-CCceEEEeccccCCCcccCcccC-CCC
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVK-DPKWLVLIGVCTHLGCVPVANAG-DFG 160 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~-~g~~~a~s~~CtHlGc~l~~~~~-~~~ 160 (202)
.+++|++|+.+.+.+.|.+++|.+ .. +|+++|+.++|||.|++|..+.. ..+
T Consensus 23 ~~~el~~g~~~~~~~~g~~i~v~r--------------------------~~~dG~~~A~~n~CpHrga~L~~G~~~~~~ 76 (138)
T cd03480 23 YVEDLDPSRPTPFTLLGRDLVIWW--------------------------DRNSQQWRAFDDQCPHRLAPLSEGRIDEEG 76 (138)
T ss_pred EHHHCCCCCcEEEEECCeeEEEEE--------------------------ECCCCEEEEEcCCCcCCcCccccceEcCCC
Confidence 678999999999999999998764 23 89999999999999999987654 236
Q ss_pred EEEcCCCCeEECCCCccccCCC-----------CCCCccceEEEeCCcE
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPA-----------PLNLEVPKYEFPEPGL 198 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA-----------~~~L~~~p~~i~~~~~ 198 (202)
.+.||+|||+||.+|+++..|. ...|..||+++.+|.+
T Consensus 77 ~i~CP~Hgw~Fd~tG~~~~~P~~~~~g~~~~~~~~~l~~ypv~v~~g~V 125 (138)
T cd03480 77 CLECPYHGWSFDGSGSCQRIPQAAEGGKAHTSPRACVASLPTAVRQGLL 125 (138)
T ss_pred EEEeCCCCCEECCCCCEEECCCCccccccCCCcccccceEeEEEECCEE
Confidence 8999999999999999998763 3679999999976654
No 32
>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=99.74 E-value=1.3e-17 Score=128.95 Aligned_cols=89 Identities=22% Similarity=0.296 Sum_probs=75.0
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCccc--CCCC
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANA--GDFG 160 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~--~~~~ 160 (202)
..++|++|+.+.+.+.|.+++|.+ .+|+++|+.+.|||.|++|..+. .+.+
T Consensus 20 ~~~el~~g~~~~~~~~g~~i~l~r---------------------------~~g~v~A~~n~CpHrg~~L~~g~~~~~~~ 72 (136)
T cd03548 20 FSHELEEGEPKGIQLCGEPILLRR---------------------------VDGKVYALKDRCLHRGVPLSKKPECFTKG 72 (136)
T ss_pred EHHHCCCCCeEEEEECCcEEEEEe---------------------------cCCEEEEEeCcCcCCCCccccCcccccCC
Confidence 678899999999999999988754 37899999999999999998753 3447
Q ss_pred EEEcCCCCeEECC-CCccccC---CC-----CCCCccceEEEeCCcE
Q psy17358 161 GYYCPCHGSHYDA-SGRIRKG---PA-----PLNLEVPKYEFPEPGL 198 (202)
Q Consensus 161 ~~~CPcHGs~FD~-~G~vi~G---PA-----~~~L~~~p~~i~~~~~ 198 (202)
.+.||+|||+||+ +|+++.. |. ...|+.||+++.+|.+
T Consensus 73 ~i~Cp~Hgw~Fdl~tG~~~~~~~~p~~~~~~~~~L~~ypv~~~~g~V 119 (136)
T cd03548 73 TITCWYHGWTYRLDDGKLVTILANPDDPLIGRTGLKTYPVEEAKGMI 119 (136)
T ss_pred EEEecCCccEEeCCCccEEEcccCCCccccccCCCceEeEEEECCEE
Confidence 9999999999998 9999863 32 3579999999976654
No 33
>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=99.73 E-value=2.8e-17 Score=125.05 Aligned_cols=91 Identities=20% Similarity=0.303 Sum_probs=72.9
Q ss_pred eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCC-CC
Q psy17358 83 KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGD-FG 160 (202)
Q Consensus 83 ~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~-~~ 160 (202)
.+++|++ |..+.+...+.++++++ ..+|+++|+.++|||.|++|.+.... ..
T Consensus 6 ~~~el~~~g~~~~~~~~~~~i~v~r--------------------------~~~g~v~A~~n~CpH~g~~L~~~~~~~~~ 59 (123)
T cd03536 6 HESEIPNKGDFMVRDMGSDSVIVAR--------------------------DKDGEIHVSLNVCPHRGMRISTTDGGNTQ 59 (123)
T ss_pred EHHHCCCCCCEEEEEECCceEEEEE--------------------------CCCCCEEEEeeeCCCCCCCcccccCCCcC
Confidence 5678887 55566578888887764 35799999999999999999875542 25
Q ss_pred EEEcCCCCeEECCCCccccCCCC-------------CCCccceEEEeCCcEE
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPAP-------------LNLEVPKYEFPEPGLL 199 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA~-------------~~L~~~p~~i~~~~~~ 199 (202)
.+.||+|||+||.+|+++..|.. .+|.+|++++.+|-++
T Consensus 60 ~i~Cp~Hgw~fd~~G~~~~~p~~~~~~~~~~~~~~~~~L~~~~v~~~~g~If 111 (123)
T cd03536 60 IHVCIYHGWAFRPNGDFIGAPVEKECMHGKMRTKAELGLHKARVTLYGGLIF 111 (123)
T ss_pred EEECCcCCCEECCCCcEEECCccccccccCCCCHHHCCCcceeEEEECCEEE
Confidence 79999999999999999988863 5689999999776554
No 34
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=99.72 E-value=2.6e-17 Score=121.95 Aligned_cols=91 Identities=18% Similarity=0.267 Sum_probs=78.2
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccC-CCcccCcccCCC--
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTH-LGCVPVANAGDF-- 159 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtH-lGc~l~~~~~~~-- 159 (202)
.+++|++|+.+.+.+.|+.|.|.+. .++++||+++.||| .+-+++.+..+.
T Consensus 7 ~~~~L~~~~~~~~~v~g~~Ialf~~--------------------------~~~~vyAi~n~Cph~~~~~Ls~G~i~~~~ 60 (104)
T PF13806_consen 7 PLDDLPPGEGRAVEVDGRQIALFRV--------------------------RDGEVYAIDNRCPHSQAGPLSDGLIGDGN 60 (104)
T ss_dssp ETTTSCTTSEEEEEETTEEEEEEEE--------------------------STTEEEEEESBETTTTSSCGCGSEEEECT
T ss_pred cHHHCCCCCcEEEEECCeEEEEEEe--------------------------CCCCEEEEeccCCccCCcccceeEEccCC
Confidence 7899999999999999999988752 47999999999999 789998765332
Q ss_pred --CEEEcCCCCeEECC-CCccccCCCCCCCccceEEEeCCcEEEE
Q psy17358 160 --GGYYCPCHGSHYDA-SGRIRKGPAPLNLEVPKYEFPEPGLLVV 201 (202)
Q Consensus 160 --~~~~CPcHGs~FD~-~G~vi~GPA~~~L~~~p~~i~~~~~~~i 201 (202)
..+.||+|+++||+ ||+++..|. .+|++||+++++| .|+|
T Consensus 61 g~~~V~CPlH~~~f~L~tG~~~~~~~-~~l~~ypvrv~~g-~V~V 103 (104)
T PF13806_consen 61 GEPCVACPLHKWRFDLRTGECLEDPD-VSLRTYPVRVEDG-QVYV 103 (104)
T ss_dssp TEEEEEETTTTEEEETTTTEESSECS-EBSBEEEEEECTT-EEEE
T ss_pred CCEEEECCCCCCeEECCCcCcCCCCC-CcEEeEEEEEECC-EEEE
Confidence 38999999999999 999999776 9999999999855 4544
No 35
>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=99.72 E-value=4e-17 Score=125.16 Aligned_cols=80 Identities=23% Similarity=0.404 Sum_probs=64.0
Q ss_pred cccee-eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcc
Q psy17358 78 AKIEV-KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVAN 155 (202)
Q Consensus 78 ~~~~v-~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~ 155 (202)
+.+.+ .+++|++ |..+++.+.+.++++++ ..+|+++|+.++|||.|++|.++
T Consensus 8 ~W~~v~~~~el~~~g~~~~~~~~~~~i~l~r--------------------------~~~g~i~A~~n~C~Hrg~~L~~g 61 (128)
T cd03472 8 SWLLLGHETHIPKAGDYLTTYMGEDPVIVVR--------------------------QKDGSIRVFLNQCRHRGMRICRS 61 (128)
T ss_pred CCeEeEEHHHCCCCCCEEEEEECCceEEEEE--------------------------CCCCCEEEEhhhCcCCCCeeecc
Confidence 33334 6788886 55566778888887764 35899999999999999999876
Q ss_pred cC-CCCEEEcCCCCeEECCCCccccCCCC
Q psy17358 156 AG-DFGGYYCPCHGSHYDASGRIRKGPAP 183 (202)
Q Consensus 156 ~~-~~~~~~CPcHGs~FD~~G~vi~GPA~ 183 (202)
.. +.+.+.||||||+||.+|+++..|+.
T Consensus 62 ~~g~~~~i~CP~Hgw~fd~~G~~~~~P~~ 90 (128)
T cd03472 62 DAGNAKAFTCTYHGWAYDTAGNLVNVPFE 90 (128)
T ss_pred CCCCcCEEECCcCCeEECCCcCEEeccCc
Confidence 43 33589999999999999999999974
No 36
>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=99.70 E-value=1.3e-16 Score=125.41 Aligned_cols=96 Identities=22% Similarity=0.281 Sum_probs=76.6
Q ss_pred ccccee-eccCCC-CCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCc
Q psy17358 77 MAKIEV-KLADIP-EGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVA 154 (202)
Q Consensus 77 ~~~~~v-~~~~l~-~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~ 154 (202)
...+.+ ..++|+ +|..+++.+.+.+++|.+ ..+|+++|+.++|||.|++|..
T Consensus 24 ~~W~~v~~~~el~~~g~~~~~~i~g~~iiv~r--------------------------~~~g~v~A~~n~CpHrg~~L~~ 77 (150)
T cd03545 24 KTWSYVGLEAEIPNAGDFKSTFVGDTPVVVTR--------------------------AEDGSLHAWVNRCAHRGALVCR 77 (150)
T ss_pred CceEEEEEHHHCCCCCCEEEEEECCceEEEEE--------------------------CCCCCEEEEcccCcCCCCEecc
Confidence 344444 678898 589889999999988764 2479999999999999999987
Q ss_pred cc-CCCCEEEcCCCCeEECCCCccccCCCC-----------------CCCccceEEEeCCcE
Q psy17358 155 NA-GDFGGYYCPCHGSHYDASGRIRKGPAP-----------------LNLEVPKYEFPEPGL 198 (202)
Q Consensus 155 ~~-~~~~~~~CPcHGs~FD~~G~vi~GPA~-----------------~~L~~~p~~i~~~~~ 198 (202)
+. ++.+.+.||+|||+||++|+++..|+. ..|..+++++.++-+
T Consensus 78 g~~g~~~~i~CP~Hgw~Fdl~G~~~~ip~~~~~~~~~~~~~~~~~~~~~L~~~~v~~~~g~i 139 (150)
T cd03545 78 ERRGNDGSLTCVYHQWAYDLKGNLKGVPFRRGLKGQGGMPKDFDMKQHGLEKLRVETVGGLV 139 (150)
T ss_pred cccCCCCEEECCCCCCEECCCCCEEECccccccccccccccCcCHHHCCCcceeEeEECCEE
Confidence 53 345789999999999999999998752 368888888865433
No 37
>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=99.68 E-value=1.3e-16 Score=120.77 Aligned_cols=79 Identities=19% Similarity=0.336 Sum_probs=65.8
Q ss_pred eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCE
Q psy17358 83 KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGG 161 (202)
Q Consensus 83 ~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~ 161 (202)
..++|++ |..+++.+.+.++++.+ ..+|+++|+.++|||.|++|.++..+.+.
T Consensus 7 ~~~el~~~g~~~~~~~~g~~i~v~r--------------------------~~dg~v~A~~n~C~Hrg~~L~~g~~~~~~ 60 (118)
T cd03541 7 YSDQVKEKNQYFTGRLGNVEYVVCR--------------------------DGNGKLHAFHNVCTHRASILACGSGKKSC 60 (118)
T ss_pred EHHHCCCCCCeEEEEECCeEEEEEE--------------------------CCCCCEEEEeCCCCCCcCCccCCccccCE
Confidence 4567775 55668888899998764 35789999999999999999987776689
Q ss_pred EEcCCCCeEECCCCccccCCCCCCCc
Q psy17358 162 YYCPCHGSHYDASGRIRKGPAPLNLE 187 (202)
Q Consensus 162 ~~CPcHGs~FD~~G~vi~GPA~~~L~ 187 (202)
|.||+|||+||.+|+++..|....++
T Consensus 61 i~CP~Hgw~f~l~G~l~~~P~~~~~~ 86 (118)
T cd03541 61 FVCPYHGWVYGLDGSLTKATQATGIQ 86 (118)
T ss_pred EEeCCCCCEEcCCCeEEeCCCccccc
Confidence 99999999999999999998655443
No 38
>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=99.66 E-value=1.8e-16 Score=120.71 Aligned_cols=86 Identities=23% Similarity=0.388 Sum_probs=68.1
Q ss_pred eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCccc-CCCC
Q psy17358 83 KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANA-GDFG 160 (202)
Q Consensus 83 ~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~-~~~~ 160 (202)
.+++|++ |..+.++..+.+++|.+ ..+|+++|++++|||+|+++..+. ++.+
T Consensus 6 ~~~elp~~g~~~~~~~~~~~i~l~r--------------------------~~~g~v~A~~n~C~Hrg~~L~~g~~~~~~ 59 (123)
T cd03542 6 HESQIPNNNDYFTTTIGRQPVVITR--------------------------DKDGELNAFINACSHRGAMLCRRKQGNKG 59 (123)
T ss_pred EHHHCCCCCCEEEEEECCcEEEEEE--------------------------CCCCCEEEEcccCcCCCCccccccccCCC
Confidence 5688886 55677788888887764 357999999999999999998753 3446
Q ss_pred EEEcCCCCeEECCCCccccCCCCCCCccceEEEeC
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEFPE 195 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA~~~L~~~p~~i~~ 195 (202)
.|.||+|||+||.+|+++..| ...+..||..++.
T Consensus 60 ~i~CP~Hg~~Fd~~G~~~~~p-~~~~~~y~~~~~~ 93 (123)
T cd03542 60 TFTCPFHGWTFSNTGKLLKVK-DPKTAGYPEGFNC 93 (123)
T ss_pred EEECcCCCCEecCCccEEECC-cccccCcCcccCh
Confidence 899999999999999999655 4556667766543
No 39
>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=99.66 E-value=5.3e-16 Score=118.19 Aligned_cols=89 Identities=18% Similarity=0.213 Sum_probs=72.2
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
..++|+ ++.+.+++.|.++++.+ ..+|+++|+.++|||+|++|+.+..+++.+
T Consensus 9 ~~~~l~-~~~~~~~~~g~~ivl~r--------------------------~~~g~v~a~~n~CpHrg~~Ls~G~v~~~~l 61 (123)
T cd03537 9 RSDDLK-DKPTELTLFGRPCVAWR--------------------------GATGRAVVMDRHCSHLGANLADGRVKDGCI 61 (123)
T ss_pred EHHHcC-CCcEEEEECCeEEEEEE--------------------------ccCCEEEEEcCCCCCCCCCccCCEEeCCEE
Confidence 456664 56778888898887754 357899999999999999999877666899
Q ss_pred EcCCCCeEECCCCccccCCC-------------CCCCccceEEEeCCcE
Q psy17358 163 YCPCHGSHYDASGRIRKGPA-------------PLNLEVPKYEFPEPGL 198 (202)
Q Consensus 163 ~CPcHGs~FD~~G~vi~GPA-------------~~~L~~~p~~i~~~~~ 198 (202)
.||+|||+||.+|+++..|. ...|..||++..+|-+
T Consensus 62 ~CpyHGw~Fd~~G~~~~iP~~~~~~~~~~~~p~~~~~~~~pv~e~~G~V 110 (123)
T cd03537 62 QCPFHHWRYDEQGQCVHIPGHSTAVRRLEPVPRGARQPTLVTAERYGYV 110 (123)
T ss_pred ECCCCCCEECCCCCEEECCCCcccccccccCCcccccccEeEEEECCEE
Confidence 99999999999999987763 2468899999866533
No 40
>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=99.66 E-value=7.7e-16 Score=117.14 Aligned_cols=75 Identities=23% Similarity=0.396 Sum_probs=61.4
Q ss_pred eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCC-CC
Q psy17358 83 KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGD-FG 160 (202)
Q Consensus 83 ~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~-~~ 160 (202)
.+++|++ |..+.+.+.+.+++|++ ..+|+++|+.++|||.|++|..+..+ .+
T Consensus 8 ~~~el~~~g~~~~~~~~~~~iiv~r--------------------------~~~g~~~A~~n~CpHrg~~L~~g~~~~~~ 61 (123)
T cd03535 8 HESEIPNAGDYVVRYIGDDSFIVCR--------------------------DEDGEIRAMFNSCRHRGMQVCRAEMGNTS 61 (123)
T ss_pred EHHHCCCCCCEEEEEECCeEEEEEE--------------------------CCCCCEEEEcccCccCCCEeeccccCCCC
Confidence 6788887 55555667778887764 24799999999999999999876543 26
Q ss_pred EEEcCCCCeEECCCCccccCCCC
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPAP 183 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA~ 183 (202)
.+.||+|||+||.||+++..|+.
T Consensus 62 ~i~Cp~Hgw~Fd~tG~~~~~p~~ 84 (123)
T cd03535 62 HFRCPYHGWTYRNTGRLVGVPAQ 84 (123)
T ss_pred EEECCcCCCEECCCcCEeeCCCc
Confidence 89999999999999999998853
No 41
>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=99.65 E-value=9.9e-16 Score=119.91 Aligned_cols=84 Identities=24% Similarity=0.371 Sum_probs=67.6
Q ss_pred hhccccee-eccCCC-CCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCccc
Q psy17358 75 LAMAKIEV-KLADIP-EGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVP 152 (202)
Q Consensus 75 ~~~~~~~v-~~~~l~-~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l 152 (202)
+..+...+ .+++|+ +|+.+.+.+.|.+|+|++ ..+|+++|+.++|||.|++|
T Consensus 19 ~~~~W~~v~~~~elp~~G~~~~~~i~g~~i~v~r--------------------------~~~g~v~A~~n~CpHrg~~L 72 (146)
T cd03538 19 FGNAWIYVGHESQVPNPGDYITTRIGDQPVVMVR--------------------------HTDGSVHVLYNRCPHKGTKI 72 (146)
T ss_pred hhcCCEEEEEHHHCCCCCCEEEEEECCeeEEEEE--------------------------CCCCCEEEEeccCcCCCCEe
Confidence 33344444 678898 789999999999998764 35799999999999999999
Q ss_pred Cccc-C-CCCEEEcCCCCeEECCCCccccCCCCC
Q psy17358 153 VANA-G-DFGGYYCPCHGSHYDASGRIRKGPAPL 184 (202)
Q Consensus 153 ~~~~-~-~~~~~~CPcHGs~FD~~G~vi~GPA~~ 184 (202)
.+.. + +.+.+.||+|||+||.+|+++..|+.+
T Consensus 73 ~~~~~g~~~~~i~CP~Hgw~Fd~~G~~~~~p~~~ 106 (146)
T cd03538 73 VSDGCGNTGKFFRCPYHAWSFKTDGSLLAIPLKK 106 (146)
T ss_pred ecccccccCCEEECCCCCCEECCCCCEEECCchh
Confidence 7543 2 235799999999999999999998643
No 42
>PLN02281 chlorophyllide a oxygenase
Probab=99.64 E-value=1e-15 Score=140.30 Aligned_cols=90 Identities=23% Similarity=0.304 Sum_probs=72.0
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCEE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGGY 162 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~~ 162 (202)
..++|++|..+.+.+.|.++++ +|..+|+++|+.++|||.|++|+.+..+.+.+
T Consensus 226 ~s~EL~~g~~~~v~llG~~IVL--------------------------~R~~dG~v~A~~D~CPHRgaPLs~G~v~g~~L 279 (536)
T PLN02281 226 FTADLKHDTMVPIECFEQPWVI--------------------------FRGEDGKPGCVRNTCAHRACPLDLGTVNEGRI 279 (536)
T ss_pred EHHHCCCCCeEEEEECCEEEEE--------------------------EECCCCeEEEEeCcCcCCCCccccceeeCCEE
Confidence 4455555666666666666554 35568999999999999999999887777899
Q ss_pred EcCCCCeEECCCCccccCCCC----CCCccceEEEeCCcE
Q psy17358 163 YCPCHGSHYDASGRIRKGPAP----LNLEVPKYEFPEPGL 198 (202)
Q Consensus 163 ~CPcHGs~FD~~G~vi~GPA~----~~L~~~p~~i~~~~~ 198 (202)
.||+|||+||.+|+++..|.. ..|..||+++.+|-+
T Consensus 280 ~CPYHGW~FD~dG~cv~iP~~~~~~~~l~sYPV~e~~GlV 319 (536)
T PLN02281 280 QCPYHGWEYSTDGECKKMPSTKLLKVKIKSLPCLEQEGMI 319 (536)
T ss_pred EeCCCCCEECCCCCEeeCCCCccccCCcceEeEEEECCEE
Confidence 999999999999999999864 458899999976544
No 43
>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=99.64 E-value=1.1e-15 Score=117.23 Aligned_cols=88 Identities=22% Similarity=0.277 Sum_probs=70.6
Q ss_pred eccCCC-CCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCccc-CCCC
Q psy17358 83 KLADIP-EGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANA-GDFG 160 (202)
Q Consensus 83 ~~~~l~-~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~-~~~~ 160 (202)
..++|+ +|...++.+.+.+|++.+ ..+|+++|+.|+|||.|.+|..+. ++.+
T Consensus 6 ~~~~l~~~g~~~~~~~~~~~v~v~r--------------------------~~dg~v~A~~n~C~Hrg~~L~~g~~~~~~ 59 (129)
T cd03539 6 LEAEIPNPGDFKRTLIGERSVIMTR--------------------------DPDGGINVVENVCAHRGMRFCRERNGNAK 59 (129)
T ss_pred EHHHCCCCCCEEEEEECCcEEEEEE--------------------------CCCCCEEEEeccCcCCCCEeeeeccCccC
Confidence 457787 588888888888887754 357999999999999999998754 3436
Q ss_pred EEEcCCCCeEECCCCccccCCCC---------------------CCCccceEEEeCC
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPAP---------------------LNLEVPKYEFPEP 196 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA~---------------------~~L~~~p~~i~~~ 196 (202)
.+.||+|||+||.+|+++.-|.. ..|..++++..++
T Consensus 60 ~l~CPyHgw~fdl~G~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~v~~~~g 116 (129)
T cd03539 60 DFVCPYHQWNYSLKGDLQGVPFRRGVKKDGKVNGGMPKDFKTKDHGLTKLKVATRGG 116 (129)
T ss_pred EEECCCCCCEECCCCCEeeccccccccccccccccccCCcChHHCCCceeeEeEECC
Confidence 89999999999999999987642 4577888877644
No 44
>PLN00095 chlorophyllide a oxygenase; Provisional
Probab=99.62 E-value=2.5e-15 Score=132.73 Aligned_cols=90 Identities=19% Similarity=0.214 Sum_probs=76.7
Q ss_pred eccCC-CCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCCCE
Q psy17358 83 KLADI-PEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDFGG 161 (202)
Q Consensus 83 ~~~~l-~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~~~ 161 (202)
.+++| ++|+...+.+.|.+++|.+ +.+|+++|+.+.|||.||+|+.+..+.+.
T Consensus 78 ~ssdL~~~g~~~~f~L~GepIVL~R--------------------------d~dGqv~Af~N~CPHRGapLSeG~v~~g~ 131 (394)
T PLN00095 78 FAAGLRDEDALIAFDLFNVPWVLFR--------------------------DADGEAGCIKDECAHRACPLSLGKLVDGK 131 (394)
T ss_pred EHHHCCCCCceEEEEECCEEEEEEE--------------------------CCCCCEEEEeccCCCCCCccccCcccCCE
Confidence 67888 6788898999999987764 35789999999999999999988776789
Q ss_pred EEcCCCCeEECCCCccccCCCCCC------CccceEEEeCCcE
Q psy17358 162 YYCPCHGSHYDASGRIRKGPAPLN------LEVPKYEFPEPGL 198 (202)
Q Consensus 162 ~~CPcHGs~FD~~G~vi~GPA~~~------L~~~p~~i~~~~~ 198 (202)
+.||+|||+||.+|+++.-|.... +..||+++.+|.+
T Consensus 132 L~CPYHGW~FD~~G~C~~iP~~~~~~~~~~v~tYPV~e~dGlV 174 (394)
T PLN00095 132 AQCPYHGWEYETGGECAKMPSCKKFLKGVFADAAPVIERDGFI 174 (394)
T ss_pred EEecCCCcEECCCCCEeeCCCccccccccccceEEEEEECCEE
Confidence 999999999999999999886432 5799999986654
No 45
>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=99.47 E-value=3.7e-14 Score=95.91 Aligned_cols=64 Identities=59% Similarity=0.970 Sum_probs=53.5
Q ss_pred ccCCCCCCCCccccccCCCCCCCCCccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcChh
Q psy17358 7 AHTDIKVPDFSHYRRDSVKDPGVNARETEEARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASAD 73 (202)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~RR~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~~~ 73 (202)
|||||++|||++||++. |.+..++...+||.|-|.++|..+++++.+|..++..|+..|.+.+|
T Consensus 1 Ahtdi~~PdF~~Yr~~~---~~~~~~~~~~~rr~fsY~~~g~~~~~~a~~AK~~V~~fv~~mSaSAD 64 (64)
T PF02921_consen 1 AHTDIKVPDFSDYRRKS---PSKRSRESDDSRRAFSYFMVGGGGVASAYAAKSTVQDFVSSMSASAD 64 (64)
T ss_dssp -GGGTS----TTTBSGG---TTS-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSHH
T ss_pred CCCCCCCCCchhhcccc---cccccCCCCcccceeeehhhhhHHHHHHHHHHHHHHHHHHhcCccCC
Confidence 79999999999999988 88888788899999999999999999999999999999999988765
No 46
>PLN02518 pheophorbide a oxygenase
Probab=99.44 E-value=3.3e-13 Score=125.06 Aligned_cols=90 Identities=18% Similarity=0.252 Sum_probs=70.8
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccc-cCCceEEEeccccCCCcccCcccCC-CC
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERV-KDPKWLVLIGVCTHLGCVPVANAGD-FG 160 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~-~~g~~~a~s~~CtHlGc~l~~~~~~-~~ 160 (202)
.+++|++|+...+.+.|++++|. |+ .+|+++|+.++|||.|++|+.+..+ .+
T Consensus 96 ~~~dL~~g~p~~~~llG~~lVl~--------------------------Rd~~~G~~~A~~d~CPHRgapLS~G~v~~~g 149 (539)
T PLN02518 96 LVEDLDPSVPTPFQLLGRDLVLW--------------------------KDPNQGEWVAFDDKCPHRLAPLSEGRIDENG 149 (539)
T ss_pred EHHHCCCCCeEEEEECCEEEEEE--------------------------EECCCCeEEEEcccCcCcCCCcccceecCCC
Confidence 45667667777777777777664 44 5899999999999999999987653 47
Q ss_pred EEEcCCCCeEECCCCccccCCC--------------CCCCccceEEEeCCcE
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPA--------------PLNLEVPKYEFPEPGL 198 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA--------------~~~L~~~p~~i~~~~~ 198 (202)
.+.||+|||+||.+|+++.-|. ...+..||+++.+|-+
T Consensus 150 ~L~CpYHGW~Fd~~G~c~~IP~~~~~~~~~~~~~~~~a~v~sypv~e~~GlI 201 (539)
T PLN02518 150 HLQCSYHGWSFDGCGSCTRIPQAAPEGPEARAVKSPRACAIKFPTMVSQGLL 201 (539)
T ss_pred EEEcCCCCCEEcCCCCeeecccccccccccccccCcccccceEeEEEECCEE
Confidence 8999999999999999987552 1248899999976543
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=99.38 E-value=1.8e-12 Score=117.58 Aligned_cols=74 Identities=23% Similarity=0.456 Sum_probs=63.3
Q ss_pred eccCCC-CCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCc-ccCCCC
Q psy17358 83 KLADIP-EGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVA-NAGDFG 160 (202)
Q Consensus 83 ~~~~l~-~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~-~~~~~~ 160 (202)
..++|+ +|+-+++.+.+.||+|++ ..+|+++|+.|+|+|.|+.|.. ..++.+
T Consensus 44 h~selp~~GDy~t~~ig~~pviv~R--------------------------~~dG~i~a~~N~C~HRGa~L~~~~~Gn~~ 97 (438)
T TIGR03228 44 HESELPNNHDFVTVRAGRQPMIVTR--------------------------DGKGELHALVNACQHRGATLTRVGKGNQS 97 (438)
T ss_pred EHHHCCCCCCeEEEEECCeEEEEEE--------------------------CCCCCEEEEcccCCCCCCccccCCccccC
Confidence 567787 488899989999998763 4689999999999999999986 455557
Q ss_pred EEEcCCCCeEECCCCccccCCC
Q psy17358 161 GYYCPCHGSHYDASGRIRKGPA 182 (202)
Q Consensus 161 ~~~CPcHGs~FD~~G~vi~GPA 182 (202)
.|.||+|||.||.+|+++.-|.
T Consensus 98 ~~~CPYHgW~y~~dG~L~~vp~ 119 (438)
T TIGR03228 98 TFTCPFHAWCYKSDGRLVKVKA 119 (438)
T ss_pred EEEcCCCCCcccCCCceeecCc
Confidence 8999999999999999998764
No 48
>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=99.37 E-value=1.5e-12 Score=117.99 Aligned_cols=79 Identities=28% Similarity=0.480 Sum_probs=64.6
Q ss_pred cccee-eccCCCC-CceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcc
Q psy17358 78 AKIEV-KLADIPE-GRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVAN 155 (202)
Q Consensus 78 ~~~~v-~~~~l~~-g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~ 155 (202)
..+.+ ..++|++ |..+++.+.+.||+|++ ..+|+++|+.|+|+|.|+.|...
T Consensus 38 ~W~~v~~~selp~~gd~~t~~~~~~~vvv~R--------------------------~~dG~i~af~N~C~HRga~L~~~ 91 (433)
T TIGR03229 38 NWIYLAHESQIPNNNDYYTTYMGRQPIFIAR--------------------------NKDGELNAFINACSHRGAMLCRH 91 (433)
T ss_pred CCEEEEEHHHCCCCCCeEEEEECCeEEEEEE--------------------------CCCCcEEEEeCcCCCCCCCcccc
Confidence 33434 6788984 56677888899998864 36899999999999999999875
Q ss_pred c-CCCCEEEcCCCCeEECCCCccccCCC
Q psy17358 156 A-GDFGGYYCPCHGSHYDASGRIRKGPA 182 (202)
Q Consensus 156 ~-~~~~~~~CPcHGs~FD~~G~vi~GPA 182 (202)
. ++.+.|.||+|||+||.+|+++..|.
T Consensus 92 ~~g~~~~~~CPyHgW~f~~~G~l~~vP~ 119 (433)
T TIGR03229 92 KRGNKTTYTCPFHGWTFNNSGKLLKVKD 119 (433)
T ss_pred cccCCCEEEcCCCCCEecCCcceEeCCC
Confidence 3 44479999999999999999998876
No 49
>COG4638 HcaE Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]
Probab=99.29 E-value=1.1e-11 Score=109.99 Aligned_cols=88 Identities=31% Similarity=0.436 Sum_probs=73.6
Q ss_pred eccCCCCCceEEEEEcCeeEEEEeCCHHHHHhhhhchhcccCCCccccccccCCceEEEeccccCCCcccCcccCCC-CE
Q psy17358 83 KLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCTHLGCVPVANAGDF-GG 161 (202)
Q Consensus 83 ~~~~l~~g~~~~~~~~g~pv~i~~~~~~~i~~~~~v~~~~l~dp~~~~~r~~~g~~~a~s~~CtHlGc~l~~~~~~~-~~ 161 (202)
..++|+.+..+++...|++++|. |+.+|+++|+.++|+|.|..|+.+.... +.
T Consensus 33 ~~~el~~~~~~~~~i~g~~lvi~--------------------------R~~dg~~~al~d~C~HRga~Ls~g~~~~~~~ 86 (367)
T COG4638 33 HSSELPKPDPLTVRIGGEPLVVV--------------------------RDKDGQVHALADVCPHRGARLSEGRVGGKGR 86 (367)
T ss_pred cHHHCCCCCceeEEEcCeEEEEE--------------------------ECCCCCEEEEeccCCCCCchhccccCCCCce
Confidence 46788888888898899998775 4579999999999999999999887655 79
Q ss_pred EEcCCCCeEECCCCccccCCC-----C-----CCCccceEEEeCC
Q psy17358 162 YYCPCHGSHYDASGRIRKGPA-----P-----LNLEVPKYEFPEP 196 (202)
Q Consensus 162 ~~CPcHGs~FD~~G~vi~GPA-----~-----~~L~~~p~~i~~~ 196 (202)
+.||+|||+||.+|+++.-|+ . ..|..+|++.-.|
T Consensus 87 l~CpyHgW~y~~~G~~~~ip~~~~~~~~~~~~~~l~~~~~~~~~G 131 (367)
T COG4638 87 LTCPYHGWTYDLDGRLRGVPARGYPLDFDKSEHGLKRYPVEERYG 131 (367)
T ss_pred EecCCCceEECCCCcEecCCccccCCCCCHhhCCccccceEEEcc
Confidence 999999999999999998772 1 2477788887654
No 50
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=98.27 E-value=1.2e-06 Score=53.95 Aligned_cols=36 Identities=28% Similarity=0.380 Sum_probs=26.5
Q ss_pred cCCccchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCcC
Q psy17358 33 ETEEARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAAS 71 (202)
Q Consensus 33 ~~~~~RR~fl~i~tG~~~~~g~~~A~~l~~~~~~~~~p~ 71 (202)
..+.+||+||+++|++.+.+|++ .+++||+.+++|.
T Consensus 6 ~~~~~RRdFL~~at~~~gavG~~---~~a~Pfv~s~~Ps 41 (41)
T PF10399_consen 6 PVDPTRRDFLTIATSAVGAVGAA---AAAWPFVSSMNPS 41 (41)
T ss_dssp ----HHHHHHHHHHHHHHHHHHH---HHHHHHHHTTSS-
T ss_pred CCCchHHHHHHHHHHHHHHHHHH---HHHHHHHhccCCC
Confidence 34789999999999988777755 4678999999884
No 51
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=93.97 E-value=0.12 Score=31.36 Aligned_cols=19 Identities=11% Similarity=0.254 Sum_probs=14.2
Q ss_pred CCccchhHHHHHHHHHHHH
Q psy17358 34 TEEARKAFSYVVAAGTAIG 52 (202)
Q Consensus 34 ~~~~RR~fl~i~tG~~~~~ 52 (202)
+.++||+||..++++++.+
T Consensus 4 Pdm~RR~lmN~ll~Gava~ 22 (39)
T PF08802_consen 4 PDMSRRQLMNLLLGGAVAV 22 (39)
T ss_dssp --HHHHHHHHHHHHHHHHH
T ss_pred CChhHHHHHHHHHHhhHHH
Confidence 4689999999999877544
No 52
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=92.11 E-value=0.22 Score=33.78 Aligned_cols=16 Identities=13% Similarity=0.316 Sum_probs=11.9
Q ss_pred CCccchhHHHHHHHHH
Q psy17358 34 TEEARKAFSYVVAAGT 49 (202)
Q Consensus 34 ~~~~RR~fl~i~tG~~ 49 (202)
...+||+||..+.+++
T Consensus 7 ~~~sRR~Flk~lg~~a 22 (66)
T TIGR02811 7 ADPSRRDLLKGLGVGA 22 (66)
T ss_pred CCccHHHHHHHHHHHH
Confidence 4679999999765533
No 53
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=91.78 E-value=0.18 Score=27.79 Aligned_cols=16 Identities=31% Similarity=0.229 Sum_probs=12.2
Q ss_pred CccchhHHHHHHHHHH
Q psy17358 35 EEARKAFSYVVAAGTA 50 (202)
Q Consensus 35 ~~~RR~fl~i~tG~~~ 50 (202)
+++||+||....+...
T Consensus 1 ~~sRR~fLk~~~a~~a 16 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAAA 16 (26)
T ss_pred CCcHHHHHHHHHHHHH
Confidence 3789999998776553
No 54
>TIGR01409 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence. Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors.
Probab=86.88 E-value=0.61 Score=26.19 Aligned_cols=15 Identities=33% Similarity=0.260 Sum_probs=11.2
Q ss_pred ccchhHHHHHHHHHH
Q psy17358 36 EARKAFSYVVAAGTA 50 (202)
Q Consensus 36 ~~RR~fl~i~tG~~~ 50 (202)
++||+||..++...+
T Consensus 1 ~sRR~Flk~~~~~~a 15 (29)
T TIGR01409 1 LSRRDFLKGAAAAGA 15 (29)
T ss_pred CchhhhHHHHHHHHH
Confidence 479999998865443
No 55
>COG0473 LeuB Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]
Probab=58.30 E-value=7.2 Score=34.76 Aligned_cols=34 Identities=41% Similarity=0.615 Sum_probs=25.9
Q ss_pred CCcccCcccCCC--CEEEcCCCCeEECCCCccccCC
Q psy17358 148 LGCVPVANAGDF--GGYYCPCHGSHYDASGRIRKGP 181 (202)
Q Consensus 148 lGc~l~~~~~~~--~~~~CPcHGs~FD~~G~vi~GP 181 (202)
+|-.++-|-++. ..++=|+|||-.|..|+-+..|
T Consensus 252 lGl~PSAnig~~~~~~lfEPvHGSAPDIAGkgiANP 287 (348)
T COG0473 252 LGLAPSANLGDERGPALFEPVHGSAPDIAGKGIANP 287 (348)
T ss_pred cccCccCccCCCCCCceeecCCCCcccccCCCccCh
Confidence 444555554443 6789999999999999988877
No 56
>PRK13747 putative mercury resistance protein; Provisional
Probab=48.33 E-value=5.4 Score=27.59 Aligned_cols=9 Identities=44% Similarity=1.017 Sum_probs=7.3
Q ss_pred CEEEcCCCC
Q psy17358 160 GGYYCPCHG 168 (202)
Q Consensus 160 ~~~~CPcHG 168 (202)
..+.||||-
T Consensus 24 AvLTCPCHL 32 (78)
T PRK13747 24 AVLTCPCHL 32 (78)
T ss_pred HHhcCcchH
Confidence 468999995
No 57
>PF11998 DUF3493: Protein of unknown function (DUF3493); InterPro: IPR021883 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length.
Probab=47.91 E-value=27 Score=24.21 Aligned_cols=18 Identities=22% Similarity=0.239 Sum_probs=14.7
Q ss_pred chhHHHHHHHHHHHHHHH
Q psy17358 38 RKAFSYVVAAGTAIGGAY 55 (202)
Q Consensus 38 RR~fl~i~tG~~~~~g~~ 55 (202)
=|.|+|.+-++++..|+.
T Consensus 20 lR~f~y~a~~aSa~iG~~ 37 (75)
T PF11998_consen 20 LRRFFYGAFGASAGIGLF 37 (75)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 488999999999877644
No 58
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=44.98 E-value=15 Score=24.40 Aligned_cols=15 Identities=27% Similarity=0.452 Sum_probs=12.8
Q ss_pred CEEEcCCCCeEECCC
Q psy17358 160 GGYYCPCHGSHYDAS 174 (202)
Q Consensus 160 ~~~~CPcHGs~FD~~ 174 (202)
-++.||-||.....+
T Consensus 31 vtI~CP~HG~~~~s~ 45 (60)
T PF05265_consen 31 VTIRCPKHGNFTCST 45 (60)
T ss_pred eEEECCCCCcEEecc
Confidence 689999999988764
No 59
>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional
Probab=43.53 E-value=37 Score=28.83 Aligned_cols=16 Identities=19% Similarity=0.264 Sum_probs=12.0
Q ss_pred CCccchhHHHHHHHHH
Q psy17358 34 TEEARKAFSYVVAAGT 49 (202)
Q Consensus 34 ~~~~RR~fl~i~tG~~ 49 (202)
..++||.||..+++..
T Consensus 7 ~~~~rr~f~~~~~~~~ 22 (254)
T PRK09476 7 PQNGRRRFLRDVVRTA 22 (254)
T ss_pred CCccHHHHHHHHHHHH
Confidence 4789999997766544
No 60
>PF07897 DUF1675: Protein of unknown function (DUF1675); InterPro: IPR012463 The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Q9SFV5 from SWISSPROT) is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=42.92 E-value=8.6 Score=33.39 Aligned_cols=18 Identities=33% Similarity=0.687 Sum_probs=14.5
Q ss_pred CCCCEEEcCCCCeEECCC
Q psy17358 157 GDFGGYYCPCHGSHYDAS 174 (202)
Q Consensus 157 ~~~~~~~CPcHGs~FD~~ 174 (202)
.+.-.|+|-|||+.|.+.
T Consensus 248 ~~~v~i~c~chg~~~~~~ 265 (284)
T PF07897_consen 248 GEEVRIVCVCHGSFLSPA 265 (284)
T ss_pred CCeEEEEEEecCCCCCHH
Confidence 334689999999999874
No 61
>PRK09898 hypothetical protein; Provisional
Probab=42.77 E-value=15 Score=30.11 Aligned_cols=12 Identities=17% Similarity=0.149 Sum_probs=10.0
Q ss_pred CccchhHHHHHH
Q psy17358 35 EEARKAFSYVVA 46 (202)
Q Consensus 35 ~~~RR~fl~i~t 46 (202)
.++||+||..+.
T Consensus 12 ~~~RR~flk~~~ 23 (208)
T PRK09898 12 GLTRLEFLRISG 23 (208)
T ss_pred chhHHHHHHhhc
Confidence 489999999865
No 62
>PF05052 MerE: MerE protein; InterPro: IPR007746 The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon often located on plasmids or transposons [, ]. It has been suggested that MerE is a broad mercury transporter mediating transport across the bacterial membrane [].
Probab=41.16 E-value=8 Score=26.64 Aligned_cols=13 Identities=31% Similarity=0.623 Sum_probs=8.7
Q ss_pred CEEEcCCCCeEEC
Q psy17358 160 GGYYCPCHGSHYD 172 (202)
Q Consensus 160 ~~~~CPcHGs~FD 172 (202)
-.+.||||--.-.
T Consensus 24 A~lTCPCHLpil~ 36 (75)
T PF05052_consen 24 ALLTCPCHLPILA 36 (75)
T ss_pred HHhhCcchHHHHH
Confidence 3578999964433
No 63
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=40.34 E-value=1.5e+02 Score=21.75 Aligned_cols=62 Identities=19% Similarity=0.383 Sum_probs=38.2
Q ss_pred cCCceEEEeccccCCCcccCcccCCCCEEEcCCCCeEECC--CCccccCCCCCCCccceEEEeCCcEEEE
Q psy17358 134 KDPKWLVLIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDA--SGRIRKGPAPLNLEVPKYEFPEPGLLVV 201 (202)
Q Consensus 134 ~~g~~~a~s~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~--~G~vi~GPA~~~L~~~p~~i~~~~~~~i 201 (202)
.+|.+.+..+.|- =|...-...+++.++|--=|-+|.. =|..-.|=-|-|| ++++++++ |+|
T Consensus 27 ~dg~~~va~daCe--iC~~~GY~q~g~~lvC~~C~~~~~~~~ig~~~GGCNP~P~---~~~~~~~~-I~I 90 (102)
T PF10080_consen 27 PDGSYRVAFDACE--ICGPKGYYQEGDQLVCKNCGVRFNLPTIGGKSGGCNPIPL---PYTVDGGN-III 90 (102)
T ss_pred CCCCEEEEEEecc--ccCCCceEEECCEEEEecCCCEEehhhcccccCCCCccCC---ceEecCCe-EEE
Confidence 4688888887773 3322222234589999999999998 3533333122333 88886554 444
No 64
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=39.18 E-value=19 Score=31.95 Aligned_cols=12 Identities=25% Similarity=0.315 Sum_probs=9.4
Q ss_pred ccchhHHHHHHH
Q psy17358 36 EARKAFSYVVAA 47 (202)
Q Consensus 36 ~~RR~fl~i~tG 47 (202)
++||.||..+.+
T Consensus 1 ~~RR~fl~~~~~ 12 (328)
T PRK10882 1 MNRRNFLKAASA 12 (328)
T ss_pred CCHHHHHHHHHH
Confidence 479999997644
No 65
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=37.13 E-value=15 Score=19.93 Aligned_cols=8 Identities=50% Similarity=0.945 Sum_probs=6.7
Q ss_pred CccccccC
Q psy17358 2 NQVRFAHT 9 (202)
Q Consensus 2 ~~~~~~~~ 9 (202)
++|+|+|.
T Consensus 19 ~~C~f~H~ 26 (27)
T PF00642_consen 19 DKCRFAHG 26 (27)
T ss_dssp GGSSSBSS
T ss_pred CCcCccCC
Confidence 58999996
No 66
>PRK10468 hydrogenase 2 small subunit; Provisional
Probab=37.03 E-value=21 Score=32.24 Aligned_cols=20 Identities=30% Similarity=0.238 Sum_probs=15.8
Q ss_pred CCccchhHHHHHHHHHHHHH
Q psy17358 34 TEEARKAFSYVVAAGTAIGG 53 (202)
Q Consensus 34 ~~~~RR~fl~i~tG~~~~~g 53 (202)
..++||+||+.+++.++.+|
T Consensus 11 ~g~sRR~Flk~~~~~~a~~g 30 (371)
T PRK10468 11 HGINRRDFMKLCAALAATMG 30 (371)
T ss_pred CCCcHHHHHHHHHHHHHHhC
Confidence 47899999999988765443
No 67
>PRK14993 tetrathionate reductase subunit B; Provisional
Probab=36.34 E-value=39 Score=28.47 Aligned_cols=12 Identities=8% Similarity=0.368 Sum_probs=9.5
Q ss_pred CccchhHHHHHH
Q psy17358 35 EEARKAFSYVVA 46 (202)
Q Consensus 35 ~~~RR~fl~i~t 46 (202)
+.+||.||..+.
T Consensus 2 ~~~RR~flk~~~ 13 (244)
T PRK14993 2 DSSKRQFLQQLG 13 (244)
T ss_pred CccHHHHHHHHH
Confidence 478999998655
No 68
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA). Called (hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase reactions performing different specific functions in different species eg (EC 1.12.2.1) in Desulfovibrio gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC 1.18.99.1) in E.coli and a number of other species and (EC 1.12.99.-) in the archea.
Probab=35.42 E-value=20 Score=32.22 Aligned_cols=20 Identities=25% Similarity=0.187 Sum_probs=15.4
Q ss_pred CCccchhHHHHHHHHHHHHH
Q psy17358 34 TEEARKAFSYVVAAGTAIGG 53 (202)
Q Consensus 34 ~~~~RR~fl~i~tG~~~~~g 53 (202)
..++||+||+.++..+..+|
T Consensus 13 ~g~sRR~FlK~~~~~~a~~~ 32 (365)
T TIGR00391 13 QGINRRDFLKLCAALATTLG 32 (365)
T ss_pred cCCCHHHHHHHHHHHHHHhc
Confidence 47899999999887665443
No 69
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=34.29 E-value=44 Score=20.94 Aligned_cols=29 Identities=34% Similarity=0.626 Sum_probs=19.8
Q ss_pred EEEcCCCCeEECC-CCccccC-CCCCCCccc
Q psy17358 161 GYYCPCHGSHYDA-SGRIRKG-PAPLNLEVP 189 (202)
Q Consensus 161 ~~~CPcHGs~FD~-~G~vi~G-PA~~~L~~~ 189 (202)
.|.|+-=|+.||. .|....| |+..+...+
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~L 31 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDL 31 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHC
Confidence 3789999999999 8988777 443444433
No 70
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=32.35 E-value=81 Score=22.03 Aligned_cols=29 Identities=10% Similarity=0.046 Sum_probs=19.8
Q ss_pred CCccccccCCCCCCCCCccCCccchhHHHHHHHHHHHH
Q psy17358 15 DFSHYRRDSVKDPGVNARETEEARKAFSYVVAAGTAIG 52 (202)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~RR~fl~i~tG~~~~~ 52 (202)
|+++|..+.+ .+.+-|++++.+.|+...+
T Consensus 5 di~~~e~ki~---------~GlT~RQl~~l~~~~~~~~ 33 (93)
T PF12666_consen 5 DISKYEEKIF---------FGLTLRQLICLAIGALVGV 33 (93)
T ss_pred chhhccchhc---------cCCCHHHHHHHHHHHHHHH
Confidence 5666654443 3679999999888766443
No 71
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=31.32 E-value=25 Score=26.44 Aligned_cols=18 Identities=28% Similarity=0.623 Sum_probs=14.0
Q ss_pred CEEEcC-CCCeEECC-CCcc
Q psy17358 160 GGYYCP-CHGSHYDA-SGRI 177 (202)
Q Consensus 160 ~~~~CP-cHGs~FD~-~G~v 177 (202)
..+.|| ||+-.++. +|+-
T Consensus 85 ~~~~CP~C~s~~~~i~~G~e 104 (115)
T COG0375 85 LDYRCPKCGSINLRIIGGDE 104 (115)
T ss_pred heeECCCCCCCceEEecCCe
Confidence 345599 99999998 7754
No 72
>PRK00420 hypothetical protein; Validated
Probab=29.80 E-value=41 Score=25.11 Aligned_cols=34 Identities=29% Similarity=0.408 Sum_probs=25.2
Q ss_pred EeccccCCCcccCcccCCCCEEEcCCCCeEECC-CCc
Q psy17358 141 LIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDA-SGR 176 (202)
Q Consensus 141 ~s~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~-~G~ 176 (202)
.+..||-=|.++-.. ..+..+||-||..+.. +++
T Consensus 22 l~~~CP~Cg~pLf~l--k~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 22 LSKHCPVCGLPLFEL--KDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred ccCCCCCCCCcceec--CCCceECCCCCCeeeeccHH
Confidence 568899977776432 2367999999999887 543
No 73
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=28.57 E-value=13 Score=23.40 Aligned_cols=28 Identities=29% Similarity=0.439 Sum_probs=10.9
Q ss_pred eEEEeccccCCCcc-c----CcccCCCCEEEcCC
Q psy17358 138 WLVLIGVCTHLGCV-P----VANAGDFGGYYCPC 166 (202)
Q Consensus 138 ~~a~s~~CtHlGc~-l----~~~~~~~~~~~CPc 166 (202)
+=|-+..|.|+.|- + ..+. +.+.|.||.
T Consensus 14 ~P~Rg~~C~H~~CFDl~~fl~~~~-~~~~W~CPi 46 (50)
T PF02891_consen 14 IPVRGKNCKHLQCFDLESFLESNQ-RTPKWKCPI 46 (50)
T ss_dssp SEEEETT--SS--EEHHHHHHHHH-HS---B-TT
T ss_pred eCccCCcCcccceECHHHHHHHhh-ccCCeECcC
Confidence 34678899999992 1 1112 236799984
No 74
>TIGR01412 tat_substr_1 Tat-translocated enzyme. This model represents a small family of proteins with a typical Tat (twin-arginine translocation) signal sequence, suggesting that the family is exported in a folded state, perhaps with a bound redox cofactor. Members of this family show homology to Dyp, a dye-decolorizing peroxidase from Geotrichum candidum that lacks any typical heme-binding site.
Probab=28.07 E-value=49 Score=30.34 Aligned_cols=11 Identities=9% Similarity=0.247 Sum_probs=9.6
Q ss_pred CCccchhHHHH
Q psy17358 34 TEEARKAFSYV 44 (202)
Q Consensus 34 ~~~~RR~fl~i 44 (202)
.+++||+||+.
T Consensus 6 ~~~~rr~~~~~ 16 (414)
T TIGR01412 6 QQPSRRTLLKT 16 (414)
T ss_pred CCccHHHHHHh
Confidence 48999999977
No 75
>COG1773 Rubredoxin [Energy production and conversion]
Probab=27.83 E-value=74 Score=20.72 Aligned_cols=31 Identities=26% Similarity=0.380 Sum_probs=23.0
Q ss_pred CEEEcCCCCeEECC-CCccccC-CCCCCCccce
Q psy17358 160 GGYYCPCHGSHYDA-SGRIRKG-PAPLNLEVPK 190 (202)
Q Consensus 160 ~~~~CPcHGs~FD~-~G~vi~G-PA~~~L~~~p 190 (202)
..|.|.-=|+.||. -|....| ++..+.+-+|
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlP 34 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLP 34 (55)
T ss_pred CceEecCCceEeccccCCccCCCCCCCchhhCC
Confidence 46899999999999 8988887 4444444444
No 76
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=26.86 E-value=60 Score=21.27 Aligned_cols=32 Identities=19% Similarity=0.248 Sum_probs=23.7
Q ss_pred EeccccCCCcccCcccCCCCEEEcCCCCeEECC
Q psy17358 141 LIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDA 173 (202)
Q Consensus 141 ~s~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~ 173 (202)
.|..|++=|-.... ......|.||--|..+|.
T Consensus 27 TSq~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCccccccc-ccccceEEcCCCCCEECc
Confidence 58889887776654 233489999977777886
No 77
>PRK08997 isocitrate dehydrogenase; Provisional
Probab=26.43 E-value=47 Score=29.53 Aligned_cols=35 Identities=34% Similarity=0.481 Sum_probs=25.4
Q ss_pred CCCcccCcccCCCCEEEcCCCCeEECCCCccccCC
Q psy17358 147 HLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGP 181 (202)
Q Consensus 147 HlGc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GP 181 (202)
=+|..++-|-++...++=|.|||--|..|+-+..|
T Consensus 242 glGl~psanig~~~a~FEp~HGSAPdIAGk~iANP 276 (334)
T PRK08997 242 GLGMAPGANIGRDAAIFEAVHGSAPDIAGKNLANP 276 (334)
T ss_pred CCCcCcceeECCCceEEECCCCchhhhCCCCccCc
Confidence 34444444444335778899999999999988877
No 78
>PRK06451 isocitrate dehydrogenase; Validated
Probab=26.12 E-value=43 Score=30.66 Aligned_cols=33 Identities=33% Similarity=0.537 Sum_probs=24.7
Q ss_pred CcccCcccCCCCEEEcCCCCeEECCCCccccCC
Q psy17358 149 GCVPVANAGDFGGYYCPCHGSHYDASGRIRKGP 181 (202)
Q Consensus 149 Gc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GP 181 (202)
|..++-|-++...++=|+|||..|..|+-+..|
T Consensus 314 Gl~pSanig~~~alFEpvHGSAPdiAGk~iANP 346 (412)
T PRK06451 314 GMLGGANIGDTGGMFEAIHGTAPKYAGKNVANP 346 (412)
T ss_pred hhcceeeeCCCCceeECCCCCccccCCCCCcCc
Confidence 444444444445788999999999999988777
No 79
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=25.30 E-value=24 Score=26.24 Aligned_cols=16 Identities=38% Similarity=0.968 Sum_probs=9.6
Q ss_pred cCCCCeEECCCCccccC
Q psy17358 164 CPCHGSHYDASGRIRKG 180 (202)
Q Consensus 164 CPcHGs~FD~~G~vi~G 180 (202)
||+||.. -..|+.+.|
T Consensus 19 cP~~g~l-~irgk~l~G 34 (108)
T PRK08572 19 CPFHGTL-PVRGQVLEG 34 (108)
T ss_pred CCCccee-eeeeEEEEE
Confidence 9999932 225555554
No 80
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=25.20 E-value=29 Score=25.87 Aligned_cols=19 Identities=26% Similarity=0.419 Sum_probs=13.9
Q ss_pred CEEEcCCCCeEECC--CCccc
Q psy17358 160 GGYYCPCHGSHYDA--SGRIR 178 (202)
Q Consensus 160 ~~~~CPcHGs~FD~--~G~vi 178 (202)
..+.||+||=.-+- .|..+
T Consensus 86 D~~kCPfHG~IIpRD~~G~Pi 106 (110)
T PF09740_consen 86 DRKKCPFHGKIIPRDDEGNPI 106 (110)
T ss_pred CcccCCCCCcccCCCCCCCCC
Confidence 57799999988776 45443
No 81
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=25.08 E-value=68 Score=31.61 Aligned_cols=11 Identities=18% Similarity=0.292 Sum_probs=9.6
Q ss_pred CccchhHHHHH
Q psy17358 35 EEARKAFSYVV 45 (202)
Q Consensus 35 ~~~RR~fl~i~ 45 (202)
+++||+||+.+
T Consensus 13 ~~sRR~FLk~~ 23 (814)
T PRK14990 13 EVSRRGLVKTT 23 (814)
T ss_pred CccHHHHHHHH
Confidence 78999999964
No 82
>TIGR02088 LEU3_arch isopropylmalate/isohomocitrate dehydrogenases. This family is closely related to both the LeuB genes found in TIGR00169 and the mitochondrial eukaryotic isocitrate dehydratases found in TIGR00175. All of these are included within the broader subfamily model, pfam00180.
Probab=24.63 E-value=42 Score=29.66 Aligned_cols=34 Identities=41% Similarity=0.631 Sum_probs=24.4
Q ss_pred CCcccCcccCCCCEEEcCCCCeEECCCCccccCC
Q psy17358 148 LGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGP 181 (202)
Q Consensus 148 lGc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GP 181 (202)
+|..++-|-++...++=|.|||.||..|+-+..|
T Consensus 235 lGl~pSanig~~~a~fep~hGsa~diaG~~~aNp 268 (322)
T TIGR02088 235 LGLAPSANIGDRKALFEPVHGSAPDIAGKGIANP 268 (322)
T ss_pred CCCCceeEEcCCceEEecCCCChhHhCCCCCCCh
Confidence 4444444444346788999999999999877666
No 83
>COG3765 WzzB Chain length determinant protein [Cell envelope biogenesis, outer membrane]
Probab=23.86 E-value=1.7e+02 Score=26.23 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=24.7
Q ss_pred CCCCCCccccccCCCCCCCCCccCCccchhHHHHHHHHHH
Q psy17358 11 IKVPDFSHYRRDSVKDPGVNARETEEARKAFSYVVAAGTA 50 (202)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~RR~fl~i~tG~~~ 50 (202)
+.-.+|+.|| +-..|..|.. +..-||.++-++.+.-|
T Consensus 291 v~d~~~~~yR--Yl~~P~~Pvk-rd~PrrA~ilil~~LiG 327 (347)
T COG3765 291 VLDERFSTYR--YLQKPTLPVK-RDSPRRAIILILGALIG 327 (347)
T ss_pred CcccceeEEE--ecCCCCCCCc-CCCcchHHHHHHHHHHH
Confidence 3447899998 7777776642 13458888777665554
No 84
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=23.51 E-value=57 Score=31.85 Aligned_cols=12 Identities=17% Similarity=0.160 Sum_probs=9.7
Q ss_pred CccchhHHHHHH
Q psy17358 35 EEARKAFSYVVA 46 (202)
Q Consensus 35 ~~~RR~fl~i~t 46 (202)
.++||+||+.+.
T Consensus 2 ~~sRR~Flk~~~ 13 (759)
T PRK15488 2 SLSRRDFLKGAG 13 (759)
T ss_pred CccHHHHHHHHH
Confidence 589999999654
No 85
>PF15061 DUF4538: Domain of unknown function (DUF4538)
Probab=23.30 E-value=56 Score=21.51 Aligned_cols=14 Identities=21% Similarity=0.370 Sum_probs=8.4
Q ss_pred cceeeccCCCCCce
Q psy17358 79 KIEVKLADIPEGRN 92 (202)
Q Consensus 79 ~~~v~~~~l~~g~~ 92 (202)
|-.+..+|++++..
T Consensus 44 R~gI~qedvQP~gl 57 (58)
T PF15061_consen 44 RAGIKQEDVQPGGL 57 (58)
T ss_pred HhcccHhhcCCCCC
Confidence 44466677776543
No 86
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=22.47 E-value=28 Score=25.58 Aligned_cols=17 Identities=41% Similarity=0.915 Sum_probs=10.2
Q ss_pred EcCCCCeEECCCCccccC
Q psy17358 163 YCPCHGSHYDASGRIRKG 180 (202)
Q Consensus 163 ~CPcHGs~FD~~G~vi~G 180 (202)
.||+||. --..|+.+.|
T Consensus 16 ~cpf~g~-l~irgk~l~G 32 (102)
T TIGR03630 16 KCPFHGH-LKVRGQILEG 32 (102)
T ss_pred CCCccce-eeeeeEEEEE
Confidence 4999992 1225665555
No 87
>PRK07474 sulfur oxidation protein SoxY; Provisional
Probab=22.08 E-value=61 Score=25.57 Aligned_cols=15 Identities=7% Similarity=-0.051 Sum_probs=11.5
Q ss_pred CccchhHHHHHHHHH
Q psy17358 35 EEARKAFSYVVAAGT 49 (202)
Q Consensus 35 ~~~RR~fl~i~tG~~ 49 (202)
..+||.||..++++.
T Consensus 7 ~~~rr~~l~~~~~~~ 21 (154)
T PRK07474 7 ALSRRQALALGGGAL 21 (154)
T ss_pred CcCHHHHHHHHHHHH
Confidence 589999998866543
No 88
>TIGR03396 PC_PLC phospholipase C, phosphocholine-specific, Pseudomonas-type. Members of this protein family are bacterial, phosphatidylcholine-hydrolyzing phospholipase C enzymes, with a characteristic domain architecture as found in hemolytyic (PlcH) and nonhemolytic (PlcN) secreted enzymes of Pseudomonas aeruginosa. PlcH hydrolyzes phosphatidylcholine to diacylglycerol and phosphocholine, but unlike PlcN can also hydrolyze sphingomyelin to ceramide ((N-acylsphingosine)) and phosphocholine. Members of this family share the twin-arginine signal sequence for Sec-independent transport across the plasma membrane. PlcH is secreted as a heterodimer with a small chaperone, PlcR, encoded immediately downstream.
Probab=21.98 E-value=60 Score=31.77 Aligned_cols=15 Identities=40% Similarity=0.510 Sum_probs=11.2
Q ss_pred ccchhHHHHHHHHHH
Q psy17358 36 EARKAFSYVVAAGTA 50 (202)
Q Consensus 36 ~~RR~fl~i~tG~~~ 50 (202)
.+||+||..+++.++
T Consensus 1 ~~RR~fl~~~a~~~~ 15 (690)
T TIGR03396 1 ISRRDFLKLAAAGGA 15 (690)
T ss_pred CCHHHHHHHHHHHHH
Confidence 479999988766443
No 89
>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein. MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar.
Probab=21.85 E-value=1.3e+02 Score=24.76 Aligned_cols=12 Identities=17% Similarity=-0.045 Sum_probs=8.4
Q ss_pred ccchhHHHHHHH
Q psy17358 36 EARKAFSYVVAA 47 (202)
Q Consensus 36 ~~RR~fl~i~tG 47 (202)
.+||+||.-+..
T Consensus 2 ~~rr~~~~~~~~ 13 (213)
T TIGR00397 2 PERRDAFADAAR 13 (213)
T ss_pred ccHHHHHHHHHH
Confidence 589999964443
No 90
>PF07250 Glyoxal_oxid_N: Glyoxal oxidase N-terminus; InterPro: IPR009880 This entry represents the N terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyses the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium [].
Probab=21.72 E-value=64 Score=27.32 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=17.1
Q ss_pred CEEEcCCCCeEECC-CCccccC
Q psy17358 160 GGYYCPCHGSHYDA-SGRIRKG 180 (202)
Q Consensus 160 ~~~~CPcHGs~FD~-~G~vi~G 180 (202)
..+.|+.|.+.||+ ++++..-
T Consensus 40 ~~~d~~a~s~~yD~~tn~~rpl 61 (243)
T PF07250_consen 40 LKFDGPAHSVEYDPNTNTFRPL 61 (243)
T ss_pred cccCceEEEEEEecCCCcEEec
Confidence 57899999999999 8876543
No 91
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=21.67 E-value=41 Score=33.31 Aligned_cols=14 Identities=14% Similarity=0.176 Sum_probs=10.4
Q ss_pred ccchhHHHHHHHHH
Q psy17358 36 EARKAFSYVVAAGT 49 (202)
Q Consensus 36 ~~RR~fl~i~tG~~ 49 (202)
++||+||+.+.+++
T Consensus 1 ~sRR~flk~~~~~~ 14 (825)
T PRK15102 1 ASRRRFLKGLGGLS 14 (825)
T ss_pred CCHHHHHHHHHHHH
Confidence 48999999655544
No 92
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=20.93 E-value=1.1e+02 Score=24.41 Aligned_cols=8 Identities=13% Similarity=0.177 Sum_probs=6.8
Q ss_pred CccchhHH
Q psy17358 35 EEARKAFS 42 (202)
Q Consensus 35 ~~~RR~fl 42 (202)
+.+||+||
T Consensus 1 g~sRR~~L 8 (168)
T PF12318_consen 1 GLSRRRLL 8 (168)
T ss_pred CCcHHHHH
Confidence 36899999
No 93
>PRK02888 nitrous-oxide reductase; Validated
Probab=20.31 E-value=62 Score=31.33 Aligned_cols=15 Identities=20% Similarity=0.266 Sum_probs=11.5
Q ss_pred CCCeEEC--C-CCccccC
Q psy17358 166 CHGSHYD--A-SGRIRKG 180 (202)
Q Consensus 166 cHGs~FD--~-~G~vi~G 180 (202)
-||++|. + |+-|+.+
T Consensus 176 ~Hg~~~~~~p~t~yv~~~ 193 (635)
T PRK02888 176 IHGLRPQKIPRTGYVFCN 193 (635)
T ss_pred ccccCccccCCccEEEeC
Confidence 5899998 3 7877765
No 94
>PRK07362 isocitrate dehydrogenase; Validated
Probab=20.30 E-value=71 Score=29.78 Aligned_cols=34 Identities=35% Similarity=0.512 Sum_probs=25.5
Q ss_pred CCcccCcccCCCCEEEcCCCCeEECCCCccccCC
Q psy17358 148 LGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGP 181 (202)
Q Consensus 148 lGc~l~~~~~~~~~~~CPcHGs~FD~~G~vi~GP 181 (202)
+|..++-|-++...++=|+|||.-|..|+-+..|
T Consensus 377 lGlaPSANiG~~~a~FEpvHGSAPdIAGk~iANP 410 (474)
T PRK07362 377 LGMAPGANIGDNAAIFEATHGTAPKHAGLDRINP 410 (474)
T ss_pred ccccceeeeCCCceeeecCCCCchhhcCCCCcCc
Confidence 3444444444446889999999999999988877
No 95
>KOG0100|consensus
Probab=20.17 E-value=1.2e+02 Score=28.28 Aligned_cols=31 Identities=29% Similarity=0.455 Sum_probs=23.5
Q ss_pred CeEECCCCccccCCCCCCCccceEEEe--CCcEEEE
Q psy17358 168 GSHYDASGRIRKGPAPLNLEVPKYEFP--EPGLLVV 201 (202)
Q Consensus 168 Gs~FD~~G~vi~GPA~~~L~~~p~~i~--~~~~~~i 201 (202)
-+.||++|-+ |||+..++..+.++ .+++|.|
T Consensus 486 LGkFdltGip---PAPRGvpqIEVtFevDangiL~V 518 (663)
T KOG0100|consen 486 LGKFDLTGIP---PAPRGVPQIEVTFEVDANGILQV 518 (663)
T ss_pred cccccccCCC---CCCCCCccEEEEEEEccCceEEE
Confidence 3689999954 99999999988775 3456654
Done!