Query gi|254781042|ref|YP_003065455.1| succinate dehydrogenase hydrophobic membrane anchor [Candidatus Liberibacter asiaticus str. psy62] Match_columns 130 No_of_seqs 111 out of 586 Neff 6.7 Searched_HMMs 39220 Date Mon May 30 04:33:03 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781042.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02968 succ_dehyd_anc succi 100.0 2.3E-33 6E-38 213.5 14.0 105 18-122 1-105 (105) 2 COG2142 SdhD Succinate dehydro 100.0 1.2E-29 3E-34 192.0 11.8 116 10-125 2-117 (117) 3 cd03495 SQR_TypeC_SdhD_like Su 100.0 1.6E-29 4E-34 191.3 10.6 100 23-122 1-100 (100) 4 PRK09488 sdhD succinate dehydr 99.9 1.6E-25 4.2E-30 168.0 13.1 111 11-123 4-114 (115) 5 cd03494 SQR_TypeC_SdhD Succina 99.9 7.2E-24 1.8E-28 158.5 12.1 98 24-121 1-98 (99) 6 cd03500 SQR_TypeA_SdhD_like Su 99.5 1.2E-12 3E-17 93.5 13.4 101 22-122 2-105 (106) 7 pfam01127 Sdh_cyt Succinate de 99.5 4.9E-13 1.3E-17 95.7 9.7 92 4-96 2-99 (122) 8 cd03493 SQR_QFR_TM Succinate:q 99.2 1.2E-10 2.9E-15 81.9 10.2 88 26-113 1-92 (98) 9 pfam05328 CybS CybS. This fami 98.8 1.7E-08 4.3E-13 69.4 6.7 66 17-99 2-67 (107) 10 cd03496 SQR_TypeC_CybS SQR cat 98.7 6.7E-08 1.7E-12 65.9 7.0 62 19-97 1-62 (104) 11 cd03526 SQR_QFR_TypeB_TM Succi 98.6 5.6E-06 1.4E-10 54.7 15.2 103 19-121 86-194 (199) 12 TIGR02970 succ_dehyd_cytB succ 98.5 2.7E-06 6.8E-11 56.6 11.9 85 22-106 18-107 (123) 13 cd03501 SQR_TypeA_SdhC_like Su 98.4 5.8E-06 1.5E-10 54.6 10.9 90 23-112 2-94 (101) 14 cd03497 SQR_TypeB_1_TM Succina 98.3 4.4E-05 1.1E-09 49.6 14.0 103 20-122 86-205 (207) 15 PRK09487 sdhC succinate dehydr 98.3 4.8E-05 1.2E-09 49.3 12.9 74 26-99 28-104 (129) 16 pfam02967 consensus 98.1 0.00012 3E-09 47.0 12.8 113 8-122 107-222 (223) 17 cd03499 SQR_TypeC_SdhC Succina 98.1 1E-04 2.5E-09 47.5 11.8 77 26-102 20-98 (117) 18 KOG4097 consensus 98.0 1E-05 2.6E-10 53.2 5.8 66 20-102 66-132 (178) 19 cd00581 QFR_TypeB_TM Quinol:fu 98.0 0.00026 6.6E-09 45.1 11.8 117 9-127 87-205 (206) 20 PRK13554 fumarate reductase cy 97.8 0.00083 2.1E-08 42.1 12.0 118 8-128 111-228 (241) 21 cd03498 SQR_TypeB_2_TM Succina 97.6 0.0026 6.8E-08 39.2 12.6 91 25-115 93-196 (209) 22 PRK13553 fumarate reductase cy 97.5 0.003 7.7E-08 38.9 11.4 114 8-123 110-229 (252) 23 COG2009 SdhC Succinate dehydro 97.4 0.0055 1.4E-07 37.4 11.7 77 19-95 15-97 (132) 24 cd00546 QFR_TypeD_subunitC Qui 95.5 0.12 3.1E-06 29.5 8.3 65 19-83 15-82 (124) 25 PRK04987 fumarate reductase su 95.5 0.14 3.5E-06 29.3 8.4 65 19-83 18-85 (129) 26 pfam02300 Fumarate_red_C Fumar 95.2 0.18 4.6E-06 28.6 8.3 65 19-83 18-85 (128) 27 PRK13603 fumarate reductase su 94.4 0.31 7.9E-06 27.2 7.7 65 19-83 15-82 (126) 28 pfam02313 Fumarate_red_D Fumar 92.8 0.77 2E-05 24.9 7.9 54 46-99 43-98 (118) 29 PRK05470 fumarate reductase su 91.3 1.2 3E-05 23.9 9.2 54 46-99 43-97 (118) 30 cd00547 QFR_TypeD_subunitD Qui 89.0 1.8 4.6E-05 22.8 9.4 45 51-95 44-89 (115) 31 TIGR02046 sdhC_b558_fam succin 87.9 2.1 5.4E-05 22.4 13.7 102 21-126 103-230 (233) 32 COG3029 FrdC Fumarate reductas 87.2 1.8 4.6E-05 22.8 5.5 56 28-83 28-85 (129) 33 COG3080 FrdD Fumarate reductas 60.5 14 0.00035 17.7 3.9 69 30-99 24-97 (118) 34 KOG0449 consensus 59.9 14 0.00036 17.6 7.3 80 26-105 68-151 (168) 35 pfam00032 Cytochrom_B_C Cytoch 50.4 20 0.00051 16.7 3.8 63 29-94 30-92 (102) 36 smart00388 HisKA His Kinase A 44.1 7 0.00018 19.4 0.2 15 1-15 9-23 (66) 37 pfam00512 HisKA His Kinase A ( 41.9 8.2 0.00021 19.0 0.3 15 1-15 9-23 (66) 38 cd00290 cytochrome_b_C Cytochr 41.2 28 0.00072 15.9 4.7 62 29-94 81-142 (147) 39 cd00082 HisKA Histidine Kinase 39.9 9.3 0.00024 18.7 0.3 16 1-16 11-26 (65) 40 PRK09467 envZ osmolarity senso 30.0 20 0.0005 16.7 0.7 15 1-15 238-252 (437) 41 COG4781 Membrane domain of mem 29.2 44 0.0011 14.7 13.8 61 25-85 25-90 (340) 42 cd07229 Pat_TGL3_like Triacylg 29.0 27 0.00068 16.0 1.2 19 77-95 26-44 (391) 43 pfam05957 DUF883 Bacterial pro 28.3 46 0.0012 14.6 2.8 23 84-106 60-82 (94) 44 pfam11815 DUF3336 Domain of un 27.6 28 0.00073 15.8 1.1 23 75-97 96-118 (145) 45 cd07232 Pat_PLPL Patain-like p 27.6 33 0.00085 15.4 1.5 13 80-92 20-32 (407) 46 PRK10404 hypothetical protein; 27.2 48 0.0012 14.5 2.7 20 87-106 70-89 (101) 47 pfam08716 nsp7 nsp7 replicase. 26.2 39 0.001 15.0 1.6 30 68-97 51-80 (83) 48 PRK10604 sensor protein RstB; 26.2 27 0.0007 15.9 0.8 13 2-14 220-232 (433) 49 PRK11100 sensory histidine kin 25.1 29 0.00074 15.8 0.8 14 1-14 263-276 (475) 50 PRK09303 adaptive-response sen 24.8 26 0.00067 16.0 0.5 14 1-14 156-169 (378) 51 cd07206 Pat_TGL3-4-5_SDP1 Tria 23.9 36 0.00092 15.2 1.1 19 77-95 17-35 (298) 52 PRK10755 sensor protein BasS/P 23.5 28 0.00071 15.9 0.4 15 1-15 150-164 (355) 53 PRK13726 conjugal transfer pil 23.4 57 0.0015 14.1 2.1 31 28-58 10-40 (187) 54 KOG1277 consensus 22.8 59 0.0015 14.0 2.6 38 18-55 352-389 (593) 55 PRK11006 phoR phosphate regulo 21.8 38 0.00096 15.1 0.8 14 1-14 211-224 (431) 56 COG2215 ABC-type uncharacteriz 20.9 64 0.0016 13.8 3.6 33 16-48 122-154 (303) No 1 >TIGR02968 succ_dehyd_anc succinate dehydrogenase, hydrophobic membrane anchor protein; InterPro: IPR014312 In Escherichia coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase (a TCA cycle enzyme) are SdhC and SdhD. This entry is the SdhD, the hydrophobic membrane anchor protein. SdhC is apocytochrome b558, which also plays a role in anchoring the complex.. Probab=100.00 E-value=2.3e-33 Score=213.52 Aligned_cols=105 Identities=25% Similarity=0.445 Sum_probs=102.9 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH Q ss_conf 22108999999999999999999999999962899989999999462599999999999999998404889985127731 Q gi|254781042|r 18 AKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRL 97 (130) Q Consensus 18 a~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~ 97 (130) +|+|++||+.||+||++++||+++++.++...++.|||+|+++|++|++++++.+++++.++|||+|||+|+|||||+++ T Consensus 1 a~~G~~dw~~QR~TAv~~~~y~~~~~~~~~~~~~~~Y~~w~~~f~~~~~~~~~~l~l~~~~~HawiGm~~v~~DYv~~~~ 80 (105) T TIGR02968 1 ARSGLRDWLLQRVTAVVLALYTIFLIGFLLALPGATYEAWRALFAHPWMKIFTLLALLALLYHAWIGMRVVLEDYVKPEG 80 (105) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH T ss_conf 97429999999999999999999999999955899989999998664999999999999999738726765442236379 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999999999999999999999999 Q gi|254781042|r 98 LKIMFLFMNSCFVLLLIIFCLFSLL 122 (130) Q Consensus 98 ~k~~~~~~~~~~~~~~~~~~i~~i~ 122 (130) +|..++.++++++.++.+.++++++ T Consensus 81 lRl~l~~~~~~~l~~~~~~~~~~lw 105 (105) T TIGR02968 81 LRLVLQVLVILFLVAYAIWGAFILW 105 (105) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999999999999968 No 2 >COG2142 SdhD Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion] Probab=99.96 E-value=1.2e-29 Score=192.04 Aligned_cols=116 Identities=28% Similarity=0.420 Sum_probs=112.3 Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99830554221089999999999999999999999999628999899999994625999999999999999984048899 Q gi|254781042|r 10 GRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVII 89 (130) Q Consensus 10 ~~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~Ii 89 (130) .++|++|++|+|++||+.||+||++|.||++|+++......+.+|++|.++++||+++.++.+++.+.++|+++|+|+|+ T Consensus 2 ~~~~~s~~ar~G~~~~l~qRvTav~Lv~l~~~~l~~~l~~~~~~y~~~~~~~a~p~~~v~~lL~l~~~l~H~~~Glr~Ii 81 (117) T COG2142 2 MVARGSGSARYGSHDWLLQRVTAVILVLLVIWHLYFLLTWLNATYAAWVAFLANPFWKVFLLLLLVAALIHAWNGLRVII 81 (117) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 75446510002628899999999999999999999999807997999999996889999999999999999996169999 Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 851277318999999999999999999999999999 Q gi|254781042|r 90 EDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIA 125 (130) Q Consensus 90 eDYI~~~~~k~~~~~~~~~~~~~~~~~~i~~i~~i~ 125 (130) |||+|+++.|..++.++.+++.+..+.+++.+++++ T Consensus 82 ~DYi~~~~~r~~l~~~~~~~~v~~~~~g~~~l~~v~ 117 (117) T COG2142 82 EDYIKPEKLRLALQILLVLALVLTGVYGTFVLWGVA 117 (117) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECC T ss_conf 999733989999999999999999999898215339 No 3 >cd03495 SQR_TypeC_SdhD_like Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is Probab=99.96 E-value=1.6e-29 Score=191.32 Aligned_cols=100 Identities=30% Similarity=0.487 Sum_probs=97.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH Q ss_conf 99999999999999999999999996289998999999946259999999999999999840488998512773189999 Q gi|254781042|r 23 GHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMF 102 (130) Q Consensus 23 ~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~~k~~~ 102 (130) +||+.||+||++++|+++|+++.+.+..+.||+++.+|+++|+|++++.++++++++|+++|+|+|+|||||+++.|+.+ T Consensus 1 ~HW~~QRitAi~lipL~~wfi~~~~~~~~~~y~~v~~~~~~p~~~il~~l~i~~~~~H~~lG~qvIIEDYIh~~~~k~~~ 80 (100) T cd03495 1 HHWWAQRVTAVALVPLVLWFVFSVALLLGASYAEVVAWLAHPFNAILLILTLVSAFYHARLGMQVVIEDYVHSEGLRLAL 80 (100) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHH T ss_conf 94699999999999999999999998749999999999979299999999999999999708846410234784399999 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999 Q gi|254781042|r 103 LFMNSCFVLLLIIFCLFSLL 122 (130) Q Consensus 103 ~~~~~~~~~~~~~~~i~~i~ 122 (130) +.+++++++++++.+++++. T Consensus 81 i~~~~~~~~~~~~~~i~ail 100 (100) T cd03495 81 IIAVKLFAIATAAAGIFAIL 100 (100) T ss_pred HHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999999999969 No 4 >PRK09488 sdhD succinate dehydrogenase cytochrome b556 small membrane subunit; Provisional Probab=99.93 E-value=1.6e-25 Score=168.02 Aligned_cols=111 Identities=23% Similarity=0.442 Sum_probs=104.3 Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98305542210899999999999999999999999996289998999999946259999999999999999840488998 Q gi|254781042|r 11 RVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIE 90 (130) Q Consensus 11 ~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~Iie 90 (130) ++-++| |||.+||+.||+||+++..|+++++.++...++.|||+|+++|+++++|+++.+++++.+.|+|+|+|+|.+ T Consensus 4 ~vts~~--rsGl~DWl~QRvsAvim~~Y~~~l~~f~~~~~~~~y~~W~~~F~~~~mkift~l~~lsl~~HAWIGlw~V~t 81 (115) T PRK09488 4 NASALG--RNGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWRGFFASAFTKVFTLLALFSILIHAWIGMWQVLT 81 (115) T ss_pred CCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 012556--764999999999999999999999999997799999999999856899999999999999999975766578 Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 512773189999999999999999999999999 Q gi|254781042|r 91 DYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLK 123 (130) Q Consensus 91 DYI~~~~~k~~~~~~~~~~~~~~~~~~i~~i~~ 123 (130) ||+|+..+|..++.......+++.++++..++. T Consensus 82 DYik~~~lR~~lq~~~~l~l~~y~~wgi~IlWG 114 (115) T PRK09488 82 DYVKPLALRLMLQLVIVVALVVYVIYGFVVVWG 114 (115) T ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 653649999999999999999999999963116 No 5 >cd03494 SQR_TypeC_SdhD Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the high potential quinine, ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. SdhD and SdhC are the two transmembrane proteins of bacterial SQRs. They contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD an Probab=99.91 E-value=7.2e-24 Score=158.50 Aligned_cols=98 Identities=19% Similarity=0.356 Sum_probs=93.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 99999999999999999999999962899989999999462599999999999999998404889985127731899999 Q gi|254781042|r 24 HFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMFL 103 (130) Q Consensus 24 hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~~k~~~~ 103 (130) ||+.||+||+++.+|+++++.++...++.||++|+++|++|++|+++.+++++.+.|+|+|+|+|.|||+|+.++|..++ T Consensus 1 DWl~QRvTAvil~~Y~~~l~~~~~~~~~~~y~~W~~~f~~~~~ki~t~l~~~sl~~HAWIGlw~V~tDYi~~~~lR~~l~ 80 (99) T cd03494 1 DWLVQRVTAVIMALYTIFLVGFLLASPPLTYEAWSGLFSSLWMKIFTLLALLALLLHAWIGLWDILTDYVKPAGLRLLLQ 80 (99) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH T ss_conf 91999999999999999999999986999999999999748999999999999999999968876787258099999999 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999 Q gi|254781042|r 104 FMNSCFVLLLIIFCLFSL 121 (130) Q Consensus 104 ~~~~~~~~~~~~~~i~~i 121 (130) ........++.++++..+ T Consensus 81 ~~~~l~l~~y~~w~~~il 98 (99) T cd03494 81 VLIILVLFGYLIWGIQIL 98 (99) T ss_pred HHHHHHHHHHHHHHHHEE T ss_conf 999999999999998401 No 6 >cd03500 SQR_TypeA_SdhD_like Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase D (SdhD)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial Probab=99.49 E-value=1.2e-12 Score=93.46 Aligned_cols=101 Identities=15% Similarity=0.076 Sum_probs=89.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--HC-CCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 89999999999999999999999999--62-8999899999994625999999999999999984048899851277318 Q gi|254781042|r 22 TGHFIKQRFTAIANIPFIIFFIAFFI--KY-GDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLL 98 (130) Q Consensus 22 ~~hW~~QRiSAi~L~~l~i~~i~~~~--~~-~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~~ 98 (130) ...|.+||+|++.|+++....++..- .. ++.||+.+.+..++|..++...+++....+|+-.|+++|++||..+++. T Consensus 2 ~~~W~~~RiSGv~Lv~ll~~H~~~~h~~~~~~~i~f~~V~~r~~~P~w~~~d~llL~lal~HG~NGlR~il~Dy~~~~~~ 81 (106) T cd03500 2 SLAWLFQRITGVFLVFLLAGHFWVQHMDNGGDVIDFAFVANRLASPLWKVWDLLLLVLALLHGGNGLRNILLDYVRRPRL 81 (106) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHH T ss_conf 29999999999999999999999999616676466999999876959999999999999998241178979987368228 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999 Q gi|254781042|r 99 KIMFLFMNSCFVLLLIIFCLFSLL 122 (130) Q Consensus 99 k~~~~~~~~~~~~~~~~~~i~~i~ 122 (130) |+.+.......+.+..+.+.+.++ T Consensus 82 r~~~~~~l~~~~~~~~v~Gt~vi~ 105 (106) T cd03500 82 RRAVKGLLYVAGLLLIVLGTYVIF 105 (106) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999999999999999997544511 No 7 >pfam01127 Sdh_cyt Succinate dehydrogenase/Fumarate reductase transmembrane subunit. This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes. Probab=99.46 E-value=4.9e-13 Score=95.65 Aligned_cols=92 Identities=21% Similarity=0.181 Sum_probs=77.7 Q ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHCCCCCHHHH-HHHHHCCHHHHHHHHHHHHH Q ss_conf 03334899830554221089999999999999999999999-----9996289998999-99994625999999999999 Q gi|254781042|r 4 DMRSSLGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIA-----FFIKYGDAPYEQI-VSVLSNVAVASIMGLGTISI 77 (130) Q Consensus 4 ~~~t~~~~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~-----~~~~~~~~~y~~~-~~~~~~~~~~il~~l~~~~~ 77 (130) +.++|+++.++....+.++.+|+.||+|++++.++ .+++. ......+.+|+++ .+++++|..++...+...+. T Consensus 2 ~~~rp~sphl~i~~~~~~~~~si~hRiTGv~l~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 80 (122) T pfam01127 2 RKNRPLSPHLGLYRAHLGTILSILHRITGVALAVL-LIHLLLWLLLLALLLGPDSYARVVVAWLSSPFKLILLLLLLLAL 80 (122) T ss_pred CCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999756156523579879999999999999-99999999999875794789999999871299999999999999 Q ss_pred HHHHHHHHHHHHHHHCCCH Q ss_conf 9999840488998512773 Q gi|254781042|r 78 SVHMQLGMQVIIEDYIHYR 96 (130) Q Consensus 78 ~~Ha~lGl~~IieDYI~~~ 96 (130) ++|+..|+|++++|.-... T Consensus 81 ~yH~~~GiRhli~D~g~g~ 99 (122) T pfam01127 81 FYHAANGLRHLIWDVGKGL 99 (122) T ss_pred HHHHHHHHHHHHHHCCCCC T ss_conf 9999867999999722366 No 8 >cd03493 SQR_QFR_TM Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQRs may reduce either high or low potential quinones while QFRs oxidize only low potential quinols. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit(s) containing the electron donor/acceptor (quinol or quinone). The reversible reduction of Probab=99.23 E-value=1.2e-10 Score=81.90 Aligned_cols=88 Identities=22% Similarity=0.263 Sum_probs=73.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHH--HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--HHHHHH Q ss_conf 999999999999999999999962899989--9999994625999999999999999984048899851277--318999 Q gi|254781042|r 26 IKQRFTAIANIPFIIFFIAFFIKYGDAPYE--QIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHY--RLLKIM 101 (130) Q Consensus 26 ~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~--~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~--~~~k~~ 101 (130) +.||+|+++++++.+++++.+....+.+++ ++.+++++|+.+++..++..+.++|+..|+|++++||.++ .+.++. T Consensus 1 ~~~Ritgv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~H~~~Gir~~~~D~~~~~~~~~~~~ 80 (98) T cd03493 1 ILHRITGVALLLFLPLHLLGLLALLGGPYAFAEVVAFLSSPLGKLLYLLLLLALLYHALNGIRHLIWDYGKGLELKLRKA 80 (98) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCHHHHHH T ss_conf 92113779999999999999999806989999999999269999999999999999974072677442011466899999 Q ss_pred HHHHHHHHHHHH Q ss_conf 999999999999 Q gi|254781042|r 102 FLFMNSCFVLLL 113 (130) Q Consensus 102 ~~~~~~~~~~~~ 113 (130) ........+... T Consensus 81 ~~~~~~~~~~~~ 92 (98) T cd03493 81 LGYAVLALSVLL 92 (98) T ss_pred HHHHHHHHHHHH T ss_conf 999999999999 No 9 >pfam05328 CybS CybS. This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularized tumours in the head and neck. Probab=98.79 E-value=1.7e-08 Score=69.38 Aligned_cols=66 Identities=21% Similarity=0.321 Sum_probs=54.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 42210899999999999999999999999996289998999999946259999999999999999840488998512773 Q gi|254781042|r 17 SAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYR 96 (130) Q Consensus 17 sa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~ 96 (130) +..+|+.||.++|+-|+.|+|+++.-. +....+.+...++..+...|...|.|.+|.||++.+ T Consensus 2 ~~~~gS~HW~~ER~~sv~LlpL~~~~~-----------------~~~~~~p~~D~~La~~l~~H~h~Gf~s~I~DYip~r 64 (107) T pfam05328 2 NKSHGSYHWTFERILAVGLLPLTPAPF-----------------LAGSPSPVMDAILAAALLLHCHWGFQSCIIDYIPKR 64 (107) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHH-----------------HHCCCCHHHHHHHHHHHHHHHHHCCCEEEECCCCHH T ss_conf 976655102999999999998889999-----------------807997589999999999998855154786015745 Q ss_pred HHH Q ss_conf 189 Q gi|254781042|r 97 LLK 99 (130) Q Consensus 97 ~~k 99 (130) ... T Consensus 65 ~~g 67 (107) T pfam05328 65 VYG 67 (107) T ss_pred HCC T ss_conf 416 No 10 >cd03496 SQR_TypeC_CybS SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homolog of the bacterial SdhD subunit. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of Probab=98.68 E-value=6.7e-08 Score=65.87 Aligned_cols=62 Identities=18% Similarity=0.272 Sum_probs=49.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH Q ss_conf 2108999999999999999999999999962899989999999462599999999999999998404889985127731 Q gi|254781042|r 19 KDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRL 97 (130) Q Consensus 19 ~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~ 97 (130) .||+.||.++|+-|+.|+|+++--. +..-.+.....++..+...|...|.|.+|.||++.+. T Consensus 1 ~~gSyHW~~ER~~sv~LlpL~~~~~-----------------~~~~~~pv~D~~La~~l~~H~h~Gf~s~I~DYip~r~ 62 (104) T cd03496 1 LHGSYHWTFERILAVSLLPLTPAAF-----------------FAPGLSPVMDAALAAALLLHSHWGFESCIIDYVPKRV 62 (104) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH-----------------HCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCHHH T ss_conf 9974010999999999998889999-----------------7488648799999999999988540446761047221 No 11 >cd03526 SQR_QFR_TypeB_TM Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Type B proteins contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside in the transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor/acc Probab=98.61 E-value=5.6e-06 Score=54.73 Aligned_cols=103 Identities=10% Similarity=0.066 Sum_probs=76.1 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-- Q ss_conf 21089999999999999999999999999628----999899999994625999999999999999984048899851-- Q gi|254781042|r 19 KDGTGHFIKQRFTAIANIPFIIFFIAFFIKYG----DAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDY-- 92 (130) Q Consensus 19 ~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~----~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY-- 92 (130) |..+--|..||+|+++++....|.++.+...+ ..+|+...+-+++|+...+-++.+++..+|...|++...--. T Consensus 86 ~~~t~~~~~Qr~TG~il~~fi~~Hl~~~~~~~~~~~~~~~~~~~~~f~~p~~~~~Ylv~l~a~~~H~~~Glws~~vtWGw 165 (199) T cd03526 86 HGDTTLWWIQAMTGFAMLFFGSVHLYIMMTQAQPDRTIGFVMSSNRMSSEWMWPLYIVLLFAVELHGSVGLYSFAVTWGW 165 (199) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 54069999999999999999999999999623578877789999999474399999999999999999879999999853 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 27731899999999999999999999999 Q gi|254781042|r 93 IHYRLLKIMFLFMNSCFVLLLIIFCLFSL 121 (130) Q Consensus 93 I~~~~~k~~~~~~~~~~~~~~~~~~i~~i 121 (130) +.++..+..-....+.-..+..++.+..+ T Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~~~~~lgl 194 (199) T cd03526 166 FDGETPDKSRANLKKLKTLMSAFLSVLGL 194 (199) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 56886288999999999999999999999 No 12 >TIGR02970 succ_dehyd_cytB succinate dehydrogenase, cytochrome b556 subunit; InterPro: IPR014314 In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase (a TCA cycle enzyme) are SdhC and SdhD. This entry is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see IPR014312 from INTERPRO) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see IPR011138 from INTERPRO).. Probab=98.54 E-value=2.7e-06 Score=56.61 Aligned_cols=85 Identities=14% Similarity=0.007 Sum_probs=72.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCCCH--HHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 89999999999999999999999999--6289998--999999-946259999999999999999840488998512773 Q gi|254781042|r 22 TGHFIKQRFTAIANIPFIIFFIAFFI--KYGDAPY--EQIVSV-LSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYR 96 (130) Q Consensus 22 ~~hW~~QRiSAi~L~~l~i~~i~~~~--~~~~~~y--~~~~~~-~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~ 96 (130) .--++.+|+|+++|...+..+++-+. ..++++| +..+++ +++|+.|+.....+-+.+||..-|+|+.+-|==.++ T Consensus 18 a~~SIlHRitG~~Lf~~l~~~~w~L~~~l~s~~~f~~~~~~~~l~~~~~~kl~l~~~~~a~~yH~~~GIRHL~~D~G~G~ 97 (123) T TIGR02970 18 AILSILHRITGVLLFFGLPFLLWLLSLSLSSPESFLNATVQALLLSSPLGKLILFGLLWALLYHLLAGIRHLLWDLGYGL 97 (123) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 67777999999999999999999999985078899999999989731799999999999999999988999998728886 Q ss_pred HHHHHHHHHH Q ss_conf 1899999999 Q gi|254781042|r 97 LLKIMFLFMN 106 (130) Q Consensus 97 ~~k~~~~~~~ 106 (130) ..|..-.... T Consensus 98 ~~~~~~~~a~ 107 (123) T TIGR02970 98 ELKSARISAW 107 (123) T ss_pred CHHHHHHHHH T ss_conf 5567888999 No 13 >cd03501 SQR_TypeA_SdhC_like Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacteria Probab=98.41 E-value=5.8e-06 Score=54.63 Aligned_cols=90 Identities=9% Similarity=0.160 Sum_probs=70.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CHHHH Q ss_conf 99999999999999999999999996--2899989999999462599999999999999998404889985127-73189 Q gi|254781042|r 23 GHFIKQRFTAIANIPFIIFFIAFFIK--YGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIH-YRLLK 99 (130) Q Consensus 23 ~hW~~QRiSAi~L~~l~i~~i~~~~~--~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~-~~~~k 99 (130) -.|..+|+|++.+..+.+..++.... .++..||+..+..++|..++.....+.+..+|+-.|++.+.-|.=. .++.+ T Consensus 2 wA~~lHRiTGv~l~~fL~~Hi~~ls~~~~~p~~y~~~~~~~~~p~~~~~e~gLv~a~~fHa~NGiRiil~Df~~~g~~~q 81 (101) T cd03501 2 WAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVFHALNGIRLILVDFGSGGPRYQ 81 (101) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89999999999999999999999999844999999999997182799999999999999974039999999830447889 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999999 Q gi|254781042|r 100 IMFLFMNSCFVLL 112 (130) Q Consensus 100 ~~~~~~~~~~~~~ 112 (130) +.+....-....+ T Consensus 82 k~l~~~v~~l~~v 94 (101) T cd03501 82 RQLFYIVLVLTVV 94 (101) T ss_pred HHHHHHHHHHHHH T ss_conf 9999999999999 No 14 >cd03497 SQR_TypeB_1_TM Succinate:quinone oxidoreductase (SQR) Type B subfamily 1, transmembrane subunit; composed of proteins similar to Bacillus subtilis SQR. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside on the transmembrane subunit. The transmembrane subunit of Bacillus subtilis SQR is also called Sdh cytochrome b558 subunit. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, Probab=98.34 E-value=4.4e-05 Score=49.55 Aligned_cols=103 Identities=13% Similarity=0.164 Sum_probs=80.7 Q ss_pred CHHHH--HHHHHHHHHHHHHHHHHHHHHHHH-------------CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 10899--999999999999999999999996-------------289998999999946259999999999999999840 Q gi|254781042|r 20 DGTGH--FIKQRFTAIANIPFIIFFIAFFIK-------------YGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLG 84 (130) Q Consensus 20 ~G~~h--W~~QRiSAi~L~~l~i~~i~~~~~-------------~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lG 84 (130) ++.+. +..||+|+++++...+|.++.+-. ..+.+|+..++-+++|+...+-++.+++..+|..-| T Consensus 86 ~~~rNw~~~~qr~TGii~l~FIi~Hv~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~Yii~~la~~fHlanG 165 (207) T cd03497 86 DYFRNWMYTLQRITGIILLVFIAWHVWHTRFAEALGHVDIQTPEAGEANLSAMRNALASPLMLIFYIIGVLAAVFHFANG 165 (207) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 41401999999999999999999999999998860654446676213589999999608099999999999999999988 Q ss_pred HHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 48899851--277318999999999999999999999999 Q gi|254781042|r 85 MQVIIEDY--IHYRLLKIMFLFMNSCFVLLLIIFCLFSLL 122 (130) Q Consensus 85 l~~IieDY--I~~~~~k~~~~~~~~~~~~~~~~~~i~~i~ 122 (130) +|+-..+- ..+++.++...........++.+.++-+++ T Consensus 166 lwSf~~twGit~sprsq~~~~~v~~~v~v~l~~~g~~ai~ 205 (207) T cd03497 166 LWTFLITWGITVSPRSQRVSTYVCLLVFVVVSFMGVAAIW 205 (207) T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999833068999999999999999999999999998 No 15 >PRK09487 sdhC succinate dehydrogenase cytochrome b556 large membrane subunit; Provisional Probab=98.26 E-value=4.8e-05 Score=49.30 Aligned_cols=74 Identities=15% Similarity=0.211 Sum_probs=61.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH--CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CHHHH Q ss_conf 99999999999999999999996--2899989999999462599999999999999998404889985127-73189 Q gi|254781042|r 26 IKQRFTAIANIPFIIFFIAFFIK--YGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIH-YRLLK 99 (130) Q Consensus 26 ~~QRiSAi~L~~l~i~~i~~~~~--~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~-~~~~k 99 (130) +.+|+|++++....+.+++.+.. ..+.+|+...+.++++..++....+..+.+||..-|+++.+-|.=+ .+.++ T Consensus 28 IlHRiSGv~lf~~~~~~~~~l~~sl~s~~~f~~~~~~~~~~~~k~il~~~~~al~yH~~~GIRHL~~D~G~~~e~l~ 104 (129) T PRK09487 28 ILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQAAAIMDSFFVKFIMWGILTALAYHIVVGIRHLLMDFGYLEETLE 104 (129) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 99999999999999999999999954968799999999779999999999999999999868999998020031279 No 16 >pfam02967 consensus Probab=98.14 E-value=0.00012 Score=47.01 Aligned_cols=113 Identities=12% Similarity=0.048 Sum_probs=84.9 Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 48998305542210899999999999999999999999996289-99899999994625999999999999999984048 Q gi|254781042|r 8 SLGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGD-APYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQ 86 (130) Q Consensus 8 ~~~~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~-~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~ 86 (130) =++..+.+. |..|.-|+.|.+|+.+++++....++.....++ .+-+.=.+.+.++....+-.++++..-+|+-+|+. T Consensus 107 ~~~h~~~m~--H~DT~lW~~Q~~Tgf~lffl~~vHL~~i~~~~~~I~~~~Sa~Rv~~~~~~~fYl~LL~~V~lH~~IGlY 184 (223) T pfam02967 107 LRAHKQRMK--HKDTTLWWWQAVTGFALFFLASVHLFTILTNPETIGPHLSAERIYHGNMWLLYLLLLPAVELHAGIGLY 184 (223) T ss_pred HHHHHHHCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 999983578--887602899999999999999999999971802078367789995787199999999999999887676 Q ss_pred HHHHHHC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8998512--77318999999999999999999999999 Q gi|254781042|r 87 VIIEDYI--HYRLLKIMFLFMNSCFVLLLIIFCLFSLL 122 (130) Q Consensus 87 ~IieDYI--~~~~~k~~~~~~~~~~~~~~~~~~i~~i~ 122 (130) -+.--+- .++..|..+....+........+++.+++ T Consensus 185 Rl~VKWG~~~~~~~r~~l~~~k~~l~~~fi~lGl~sL~ 222 (223) T pfam02967 185 RLAVKWGWIEGLENRKRLRKVKKVLSVVFIVLGLLSLL 222 (223) T ss_pred HHEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 32013441247104899999999999999999999972 No 17 >cd03499 SQR_TypeC_SdhC Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. The two-electron oxidation of succinate in the flavoprotein a Probab=98.11 E-value=1e-04 Score=47.47 Aligned_cols=77 Identities=17% Similarity=0.168 Sum_probs=64.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH--HCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH Q ss_conf 9999999999999999999999--6289998999999946259999999999999999840488998512773189999 Q gi|254781042|r 26 IKQRFTAIANIPFIIFFIAFFI--KYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMF 102 (130) Q Consensus 26 ~~QRiSAi~L~~l~i~~i~~~~--~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~~k~~~ 102 (130) +.+|+|++++......+.+.+. ...+.+|+...+.++++..+........+..||..-|+++.+-|.-+....|..- T Consensus 20 I~HRiSGv~l~~~~~~~~~~l~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~yH~~~GiRHL~wD~g~g~~~~~~~ 98 (117) T cd03499 20 ILHRITGVALFLGLPLLLWWLLASLSSPESFESVSALLGSWLGKLVLFGLTWALFYHLLNGIRHLIWDLGKGLELKTVY 98 (117) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH T ss_conf 9999999999999999999999980287789999999615799999999999999999866899999811356499999 No 18 >KOG4097 consensus Probab=98.05 E-value=1e-05 Score=53.21 Aligned_cols=66 Identities=17% Similarity=0.375 Sum_probs=54.6 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 10899999999999999999999999996289998999999946-25999999999999999984048899851277318 Q gi|254781042|r 20 DGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSN-VAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLL 98 (130) Q Consensus 20 ~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~-~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~~~~~ 98 (130) +|+.||.++|+-++.++|+..- .++.. |++......+-+....|...|.+.++.||+++... T Consensus 66 ~~Syhw~~ERi~s~~llpl~pa-----------------a~~~~~p~s~~mDa~La~~l~~h~hwGf~scViDYi~~~v~ 128 (178) T KOG4097 66 AGSYHWTVERIVSVGLLPLLPA-----------------AYLTTGPISPAMDASLAVALLLHCHWGFESCVIDYIRPRVY 128 (178) T ss_pred CCCHHHHHHHHHHHHHHHHHHH-----------------HHHCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHH T ss_conf 5321124999999998876458-----------------88648987088999999999987440301578763072000 Q ss_pred HHHH Q ss_conf 9999 Q gi|254781042|r 99 KIMF 102 (130) Q Consensus 99 k~~~ 102 (130) +..- T Consensus 129 g~~~ 132 (178) T KOG4097 129 GVLH 132 (178) T ss_pred CHHH T ss_conf 1248 No 19 >cd00581 QFR_TypeB_TM Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and rhodoquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside in the transmembrane subunit. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The Probab=97.98 E-value=0.00026 Score=45.09 Aligned_cols=117 Identities=8% Similarity=0.003 Sum_probs=83.8 Q ss_pred HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8998305542210899999999999999999999999996289-998999999946259999999999999999840488 Q gi|254781042|r 9 LGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGD-APYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQV 87 (130) Q Consensus 9 ~~~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~-~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~ 87 (130) ++..+.+. |..|.-|+.|.+|+.+++++....++.....++ .+-+.-.+.+.+.....+-.+++...-.|+-+|+.- T Consensus 87 ~~h~~~m~--H~DT~lW~~Q~~TGf~lffl~~iHL~~i~t~~~~I~~~~Sa~Rv~~~~~~~fYl~LL~~VelH~~IGlYR 164 (206) T cd00581 87 RRHMQLMK--HGDTSLWWIQAVTGFVLFFLASAHLYEMLTNPEIIGPHTSAYRVVHGGWWLLYLALLPAVELHGGIGLYR 164 (206) T ss_pred HHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 99984477--8876018999999999999999999999748511374021899975771999999999999998654441 Q ss_pred HHHHHCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9985127-731899999999999999999999999999964 Q gi|254781042|r 88 IIEDYIH-YRLLKIMFLFMNSCFVLLLIIFCLFSLLKIAIL 127 (130) Q Consensus 88 IieDYI~-~~~~k~~~~~~~~~~~~~~~~~~i~~i~~i~l~ 127 (130) +.--+-- ++..|..+....+........+++.++.+...- T Consensus 165 l~VKWG~~~~~~R~~lrk~~~~~~~~fl~lGl~tL~a~~~i 205 (206) T cd00581 165 LAVKWGWFASESRKRLRRIKNVLSAFFLVLGLLTLLAYIKI 205 (206) T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 13446413644569999999999999999999999999953 No 20 >PRK13554 fumarate reductase cytochrome b-556 subunit; Provisional Probab=97.80 E-value=0.00083 Score=42.12 Aligned_cols=118 Identities=9% Similarity=0.072 Sum_probs=83.6 Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 48998305542210899999999999999999999999996289998999999946259999999999999999840488 Q gi|254781042|r 8 SLGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQV 87 (130) Q Consensus 8 ~~~~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~ 87 (130) =++..+.+. |..|.-|+.|=+|+.+++++....++..+..++.+-+.=.+.+.+.....+-.+++...-.|+-+|+-- T Consensus 111 ~~~h~~~m~--H~DT~LW~~Q~~TGf~lffl~~vHL~~ilt~p~I~~~~SA~Rv~~~~~w~fYl~LL~~VelHa~IGlYR 188 (241) T PRK13554 111 LRSHMGSIK--HKDTHAWFWQLITGFILFFLVPVHLFTMILNPEIGPHLSAERVYHDNAWLLYALLLPAVVIHAMIGLYR 188 (241) T ss_pred HHHHHHHCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHE T ss_conf 999984578--888720899999999999999989988650799881051899964760999999999999997764311 Q ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99851277318999999999999999999999999999642 Q gi|254781042|r 88 IIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIAILG 128 (130) Q Consensus 88 IieDYI~~~~~k~~~~~~~~~~~~~~~~~~i~~i~~i~l~g 128 (130) +.-.+=-.++ |..+....+........+++.++.+-.+-| T Consensus 189 l~VKWG~~~~-R~~lrk~~~~ltv~fivlGllsL~af~~iG 228 (241) T PRK13554 189 VAVKWGLTTN-RSGLRKVAKVLIIYLLCLGTLSLVSYIFIG 228 (241) T ss_pred EEEEEEEECC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 4534100035-799999999999999999999999999956 No 21 >cd03498 SQR_TypeB_2_TM Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. C. glutamicum SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside in the transmembrane subunit. The transmembrane subunit of members of this subfamily is also called Sdh cytochrome b558 subunit based on the Bacillus subtilis protein. The structural arrangem Probab=97.64 E-value=0.0026 Score=39.21 Aligned_cols=91 Identities=13% Similarity=0.198 Sum_probs=72.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCC------------CCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999628------------999899999994625999999999999999984048899851 Q gi|254781042|r 25 FIKQRFTAIANIPFIIFFIAFFIKYG------------DAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDY 92 (130) Q Consensus 25 W~~QRiSAi~L~~l~i~~i~~~~~~~------------~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY 92 (130) -..||+|+++++...+|.+..+-.-. ...|+.+.+-|++|+...+-.+.+++..+|-+-|.|...... T Consensus 93 sr~M~~tG~ill~Fiv~Hl~~f~~~~~~~~~~~~~~~~~d~y~~v~~~F~~p~~~~~Yvvam~~L~~HL~HG~~Sa~qTl 172 (209) T cd03498 93 SRTMIWSGLIILLFIILHLLDFTFGVVGPVSPPMGVGRGDVYELLVASFQQPWIAALYVLAMVALGLHLSHGFWSAFQTL 172 (209) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999999999999985121155446666650159999999951649999999999999999998999999982 Q ss_pred -CCCHHHHHHHHHHHHHHHHHHHH Q ss_conf -27731899999999999999999 Q gi|254781042|r 93 -IHYRLLKIMFLFMNSCFVLLLII 115 (130) Q Consensus 93 -I~~~~~k~~~~~~~~~~~~~~~~ 115 (130) +.+++.+.....+...+..++++ T Consensus 173 G~~~~~~~~~~~~i~~~~a~~i~~ 196 (209) T cd03498 173 GLNNPRYRPALKAVGRVVAILIAG 196 (209) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 799813589999999999999999 No 22 >PRK13553 fumarate reductase cytochrome b-556 subunit; Provisional Probab=97.51 E-value=0.003 Score=38.88 Aligned_cols=114 Identities=10% Similarity=0.079 Sum_probs=75.5 Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 48998305542210899999999999999999999999996289-99899999994625999999999999999984048 Q gi|254781042|r 8 SLGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGD-APYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQ 86 (130) Q Consensus 8 ~~~~~rglgsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~-~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~ 86 (130) =++..+.+. |..|.-|+.|=+|+.+++++....++.+...++ .+-..=.+.+.+.....+-.+++...-.|+-+|+- T Consensus 110 ~~~h~~~m~--H~DT~LW~~Q~~TGf~lffl~svHL~~ilt~p~~Igp~~SA~Rv~~~~~w~fYl~LL~~VelHa~IGlY 187 (252) T PRK13553 110 FRTHKKLMK--HGDTSLWWIQAFTGFAMFFLASIHLFVMLTNPEKIGPDGSSDRVVSQNMWLLYIVLLFAVELHGSIGLY 187 (252) T ss_pred HHHHHHHCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 999983578--888720899999999999999989998763824269641378883577199999999999999776542 Q ss_pred HHHHHHCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89985127-----73189999999999999999999999999 Q gi|254781042|r 87 VIIEDYIH-----YRLLKIMFLFMNSCFVLLLIIFCLFSLLK 123 (130) Q Consensus 87 ~IieDYI~-----~~~~k~~~~~~~~~~~~~~~~~~i~~i~~ 123 (130) -+.--+-- .+..|..+....+........+++.++.. T Consensus 188 Rl~VKWG~~~~~~~~~~R~~l~k~k~~l~v~fivlGl~sL~a 229 (252) T PRK13553 188 RLAIKWGWFEGKNIKESRKKLKKVKWAMSVFFIVLGLLTLAA 229 (252) T ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 024454423677737679999999999999999999999999 No 23 >COG2009 SdhC Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion] Probab=97.41 E-value=0.0055 Score=37.36 Aligned_cols=77 Identities=12% Similarity=0.066 Sum_probs=52.1 Q ss_pred CCHHHHHHHHHHHHHHHHH-HHHHHHHH-HHHCCCCCHHHHHH----HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2108999999999999999-99999999-99628999899999----994625999999999999999984048899851 Q gi|254781042|r 19 KDGTGHFIKQRFTAIANIP-FIIFFIAF-FIKYGDAPYEQIVS----VLSNVAVASIMGLGTISISVHMQLGMQVIIEDY 92 (130) Q Consensus 19 ~~G~~hW~~QRiSAi~L~~-l~i~~i~~-~~~~~~~~y~~~~~----~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY 92 (130) +.+..-+..||+|++++.. +..-++.. .......++++..+ -..+++.++.......+.++|+..|++..+-|+ T Consensus 15 ~~~~~~silHRitGv~l~~Fl~~hil~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~H~~nGIR~l~~d~ 94 (132) T COG2009 15 PITMYASILHRISGVILAFFLFVHILLASSWLAGSASFNAAFEFYHALLGSFIVKLVLLGLVLALLYHGLNGIRHLLWDF 94 (132) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77999999999799999999999999999998888757999999996367679999999999999999998799999997 Q ss_pred CCC Q ss_conf 277 Q gi|254781042|r 93 IHY 95 (130) Q Consensus 93 I~~ 95 (130) =.. T Consensus 95 g~~ 97 (132) T COG2009 95 GYG 97 (132) T ss_pred HCC T ss_conf 411 No 24 >cd00546 QFR_TypeD_subunitC Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits. Probab=95.55 E-value=0.12 Score=29.54 Aligned_cols=65 Identities=17% Similarity=0.210 Sum_probs=52.0 Q ss_pred CCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 210899-999999999999999999999996289--99899999994625999999999999999984 Q gi|254781042|r 19 KDGTGH-FIKQRFTAIANIPFIIFFIAFFIKYGD--APYEQIVSVLSNVAVASIMGLGTISISVHMQL 83 (130) Q Consensus 19 ~~G~~h-W~~QRiSAi~L~~l~i~~i~~~~~~~~--~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~l 83 (130) |++-.. ...--.|++-...+.+.+++-...+.+ .+++.|.+|.+||+.-++.++.+.++++|+.- T Consensus 15 k~~FYr~YMlRE~T~v~~~~f~lvLl~Gl~~L~~g~~aw~~f~~flqnP~vv~lniiaL~a~L~Ha~T 82 (124) T cd00546 15 KLDFYRFYMLREATAVPTVWFSLVLLYGLFALGSGPESWAGFVSFLQNPIVVLLNIIALAAALLHAKT 82 (124) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 58489999998883799999999999999998069899999999983859999999999999999999 No 25 >PRK04987 fumarate reductase subunit C; Provisional Probab=95.49 E-value=0.14 Score=29.29 Aligned_cols=65 Identities=18% Similarity=0.172 Sum_probs=51.9 Q ss_pred CCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 2108999-99999999999999999999996289--99899999994625999999999999999984 Q gi|254781042|r 19 KDGTGHF-IKQRFTAIANIPFIIFFIAFFIKYGD--APYEQIVSVLSNVAVASIMGLGTISISVHMQL 83 (130) Q Consensus 19 ~~G~~hW-~~QRiSAi~L~~l~i~~i~~~~~~~~--~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~l 83 (130) |++-..| ..--.|++-...+.+.+++-...+.+ .+++.|.+|.+||+.-++.++.+.++++|+.- T Consensus 18 k~~FYr~YMlRE~T~v~~~~f~lvLl~Gl~~L~~g~~aw~~fv~flqnPivvilniiaLaa~L~Ha~T 85 (129) T PRK04987 18 KLPFYRFYMLREATAVPAVWFSLVLIYGLFALKSGPEAWAGFVSFLQNPVVVILNIITLAAALLHTKT 85 (129) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 48489999999985799999999999999998069889999999984859999999999999999999 No 26 >pfam02300 Fumarate_red_C Fumarate reductase subunit C. Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 15kD hydrophobic subunit C. Probab=95.22 E-value=0.18 Score=28.58 Aligned_cols=65 Identities=17% Similarity=0.178 Sum_probs=51.5 Q ss_pred CCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCC--CCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 2108999-9999999999999999999999628--999899999994625999999999999999984 Q gi|254781042|r 19 KDGTGHF-IKQRFTAIANIPFIIFFIAFFIKYG--DAPYEQIVSVLSNVAVASIMGLGTISISVHMQL 83 (130) Q Consensus 19 ~~G~~hW-~~QRiSAi~L~~l~i~~i~~~~~~~--~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~l 83 (130) |++-..+ ..---|++-...+.+.+++-...+. +.+++.|.+|.+||+.-++.++.+.++++|+.- T Consensus 18 k~~FYr~YMlRE~T~v~~~~f~lvLl~Gl~~L~~G~~aw~~f~~flqnP~vv~lniiaL~a~L~Ha~T 85 (128) T pfam02300 18 KLDFYRFYMLREGTAVPTVWFSLVLLYGLFALSQGPEAWNGFVSFLQNPVVVILNIIALAAALLHTKT 85 (128) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 58489999998883799999999999999998068889999999983859999999999999999999 No 27 >PRK13603 fumarate reductase subunit C; Provisional Probab=94.38 E-value=0.31 Score=27.22 Aligned_cols=65 Identities=12% Similarity=0.182 Sum_probs=48.9 Q ss_pred CCHHHHHHHHH-HHHHHHHHHHHHHHHHHHH--CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 21089999999-9999999999999999996--28999899999994625999999999999999984 Q gi|254781042|r 19 KDGTGHFIKQR-FTAIANIPFIIFFIAFFIK--YGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQL 83 (130) Q Consensus 19 ~~G~~hW~~QR-iSAi~L~~l~i~~i~~~~~--~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~l 83 (130) |++-+.|-+-| -|++-...+.+.+++-... .++.+.+.|.+|.+||..-++.++.+.++++|+.- T Consensus 15 k~~FY~~YMlRE~T~vp~vwF~l~L~~Gl~~L~~g~~aw~~fl~flqNPivv~lNiiaL~a~L~Ha~T 82 (126) T PRK13603 15 RRRSYLRFMLREISCIFVAWFVLYLMLVLRAVGAGGNSYQRFLDFSANPVVVVLNVVALSFLLLHAVT 82 (126) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 58449999997762799999999999999997059889999999971967899999999999998999 No 28 >pfam02313 Fumarate_red_D Fumarate reductase subunit D. Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D. Probab=92.75 E-value=0.77 Score=24.91 Aligned_cols=54 Identities=17% Similarity=0.098 Sum_probs=44.2 Q ss_pred HHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCC-HHHH Q ss_conf 99628999899999994625999999999999999984048899851-277-3189 Q gi|254781042|r 46 FIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDY-IHY-RLLK 99 (130) Q Consensus 46 ~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY-I~~-~~~k 99 (130) ++..+..|||.+.+|-.+++.+.+....++.-+||+-=-+..-.-|- +|. +..| T Consensus 43 ~~~~~a~~y~~i~aFa~s~iG~l~ll~~i~lplWh~~HRihhglHDlkih~g~~~~ 98 (118) T pfam02313 43 LIDAEALSYDRIIAFAQSWIGKLFLLVLIILPLWHAMHRIHHGLHDLKIHRGPAGK 98 (118) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEECCCCCC T ss_conf 67854258999999997089999999999999999999999877641012156744 No 29 >PRK05470 fumarate reductase subunit D; Provisional Probab=91.27 E-value=1.2 Score=23.89 Aligned_cols=54 Identities=15% Similarity=0.071 Sum_probs=44.1 Q ss_pred HHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCHHHH Q ss_conf 99628999899999994625999999999999999984048899851-2773189 Q gi|254781042|r 46 FIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDY-IHYRLLK 99 (130) Q Consensus 46 ~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY-I~~~~~k 99 (130) ++..+..||+.+.+|-++++.+......++.-+||+.=-+.+-.-|- +|.+..| T Consensus 43 ~~~~~a~~y~~i~aFa~~~iGkl~ll~~i~lplWh~~HRihHglHDlkih~~~g~ 97 (118) T PRK05470 43 LFPGDALSYERVLAFAQSFIGKLFLLLMIVLPLWHGLHRIHHGMHDLKIHVPAGK 97 (118) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCH T ss_conf 5777633699999999706899999999999999999999987766300024402 No 30 >cd00547 QFR_TypeD_subunitD Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits. Probab=88.98 E-value=1.8 Score=22.77 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=40.0 Q ss_pred CCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCC Q ss_conf 999899999994625999999999999999984048899851-277 Q gi|254781042|r 51 DAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDY-IHY 95 (130) Q Consensus 51 ~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY-I~~ 95 (130) ..|||.+.+|-++++.+.+....++.-+||+-=-+..-..|- +|. T Consensus 44 a~sy~~i~aFa~s~iGkl~ll~~i~lplWh~~HRihhglHDlkih~ 89 (115) T cd00547 44 ALSYDRIIAFAQSWIGKLFLLVLIILPMWHAMHRIHHGLHDLKIHH 89 (115) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 4799999999960899999999999999999999998766514101 No 31 >TIGR02046 sdhC_b558_fam succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; InterPro: IPR011138 This family contains succinate dehydrogenase subunit C of Bacillus subtilis, designated cytochrome b-558, and related sequences that include a fumarate reductase subunit C. This family is only weakly similar to the main group of succinate dehydrogenase cytochrome b subunits described by IPR000701 from INTERPRO, so that some members score above the gathering threshold and some do not .. Probab=87.94 E-value=2.1 Score=22.36 Aligned_cols=102 Identities=21% Similarity=0.207 Sum_probs=72.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---------C----C--------HHHHHHHHHCCHHHHHHHHHHHHHHH Q ss_conf 0899999999999999999999999996289---------9----9--------89999999462599999999999999 Q gi|254781042|r 21 GTGHFIKQRFTAIANIPFIIFFIAFFIKYGD---------A----P--------YEQIVSVLSNVAVASIMGLGTISISV 79 (130) Q Consensus 21 G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~---------~----~--------y~~~~~~~~~~~~~il~~l~~~~~~~ 79 (130) -+---..||.|+++.+....|.++.+-.... . | |+.++.-|++|....+-++.+++..+ T Consensus 103 ~~~~s~~m~~~GIi~l~Fi~~H~~~f~~~~~~~~~~~~~~a~~~~DGfdhP~~~y~~~v~~Fs~p~~~~~YiVa~l~L~f 182 (233) T TIGR02046 103 ASWASRTMLVTGIIVLLFIGLHLLDFTLGAQLAEAFEMGVAKFRIDGFDHPADIYEMVVLTFSSPIVLSIYIVAMLALGF 182 (233) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 14898899998799999999999999999874677778888867787666068999999986071688999999999999 Q ss_pred HHHHHHHHHHHHH-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9984048899851-----2773189999999999999999999999999996 Q gi|254781042|r 80 HMQLGMQVIIEDY-----IHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIAI 126 (130) Q Consensus 80 Ha~lGl~~IieDY-----I~~~~~k~~~~~~~~~~~~~~~~~~i~~i~~i~l 126 (130) |-.-|+|..+.=- .++.++|..+ +.++.++.+.-...-+++.+ T Consensus 183 H~~HG~wSa~qTLG~n~t~~~~~ik~~s----~v~al~i~~Gf~~vpl~~~~ 230 (233) T TIGR02046 183 HLSHGLWSAAQTLGLNSTIRSQRIKAVS----NVVALVIFIGFAAVPLKFLL 230 (233) T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999981798800678889999----99999999999999999998 No 32 >COG3029 FrdC Fumarate reductase subunit C [Energy production and conversion] Probab=87.22 E-value=1.8 Score=22.76 Aligned_cols=56 Identities=18% Similarity=0.186 Sum_probs=43.3 Q ss_pred HHHHHHHHHHHHHHHHHHHH--HCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999--628999899999994625999999999999999984 Q gi|254781042|r 28 QRFTAIANIPFIIFFIAFFI--KYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQL 83 (130) Q Consensus 28 QRiSAi~L~~l~i~~i~~~~--~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~l 83 (130) .-.|++-..-..+.+++-.. ...+.+++.+.+|.+||..-++.++.+.++++|+.- T Consensus 28 RE~T~ip~vwF~l~L~~gl~al~~gp~~~~~fldFl~NPvVv~lNlitL~a~LlHt~T 85 (129) T COG3029 28 REATAIPAVWFSLELIYGLFALGSGPEAWQGFLDFLANPVVVILNLITLAAALLHTVT 85 (129) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCEEEEEHHHHHHHHHHHHHH T ss_conf 8730589999999999999997059567888999854985875169999999999999 No 33 >COG3080 FrdD Fumarate reductase subunit D [Energy production and conversion] Probab=60.49 E-value=14 Score=17.68 Aligned_cols=69 Identities=13% Similarity=0.163 Sum_probs=44.2 Q ss_pred HHHHHHHHHHHHHHHHHH---HCCCCCH-HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCHHHH Q ss_conf 999999999999999999---6289998-99999994625999999999999999984048899851-2773189 Q gi|254781042|r 30 FTAIANIPFIIFFIAFFI---KYGDAPY-EQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDY-IHYRLLK 99 (130) Q Consensus 30 iSAi~L~~l~i~~i~~~~---~~~~~~y-~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDY-I~~~~~k 99 (130) +||++ .|..+..+.... ..+..+. |...++..||..+.+..++++.-+||+---+.+=..|- +|.+..| T Consensus 24 vsAii-aPV~iLl~GillPlG~~d~~~lse~llaf~~s~Igkl~llvl~vlplw~a~HRihHgmhdlk~h~pag~ 97 (118) T COG3080 24 VSAII-APVLILLVGILLPLGLFDADALSERLLAFAQSPIGKLFLLVLIVLPLWCALHRIHHGMHDLKIHVPAGK 97 (118) T ss_pred EHHHH-HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEEE T ss_conf 11799-989999999982036668056679999999747999999999999998899888642432245202101 No 34 >KOG0449 consensus Probab=59.86 E-value=14 Score=17.62 Aligned_cols=80 Identities=10% Similarity=-0.080 Sum_probs=47.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHH----HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 99999999999999999999996289998999999946259999----99999999999984048899851277318999 Q gi|254781042|r 26 IKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASI----MGLGTISISVHMQLGMQVIIEDYIHYRLLKIM 101 (130) Q Consensus 26 ~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il----~~l~~~~~~~Ha~lGl~~IieDYI~~~~~k~~ 101 (130) ..+|+|+++|..-+..+-+.-+...+.....+..+.+....... -........+|.+.|+++.+=|==+.-++|.+ T Consensus 68 ~~hRiSG~~la~gv~~~G~~~l~~~g~~~~~v~~~~~~~~~~~~~~~~K~~iayp~a~Ht~ngiRHLiwd~~k~L~i~~v 147 (168) T KOG0449 68 IFHRISGVVLAGGVWLVGVSGLLGMGDITATVSKVYQLKLPTAVQWPAKFSIAYPFAYHTGNGIRHLIWDLGKELTIKGV 147 (168) T ss_pred HHHHHHHHEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCE T ss_conf 98755130014469998889984575168888888973164567756899999999999715323344553145530011 Q ss_pred HHHH Q ss_conf 9999 Q gi|254781042|r 102 FLFM 105 (130) Q Consensus 102 ~~~~ 105 (130) -... T Consensus 148 Y~tG 151 (168) T KOG0449 148 YKTG 151 (168) T ss_pred EEEC T ss_conf 1201 No 35 >pfam00032 Cytochrom_B_C Cytochrome b(C-terminal)/b6/petD. Probab=50.38 E-value=20 Score=16.70 Aligned_cols=63 Identities=11% Similarity=0.093 Sum_probs=45.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999999962899989999999462599999999999999998404889985127 Q gi|254781042|r 29 RFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIH 94 (130) Q Consensus 29 RiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~ 94 (130) +..+++.....+..++.+.- .|....+.--..|.++....+++...+.=+|+|.+.+-|-|+- T Consensus 30 K~~Gv~~~~~si~il~~lP~---l~~s~~rs~~~rp~~~~~f~~fv~~fi~LtwlG~~p~e~p~~~ 92 (102) T pfam00032 30 KLGGVIAMVLSILILFLLPF---LDRSKVRSLRFRPLSKILFWIFVVNFLLLTWLGGQPVEYPYIL 92 (102) T ss_pred HHHHHHHHHHHHHHHHHHHC---CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH T ss_conf 77889999999999877050---1666502332131899999999999999999437988047999 No 36 >smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases. Probab=44.06 E-value=7 Score=19.36 Aligned_cols=15 Identities=27% Similarity=0.707 Sum_probs=11.9 Q ss_pred CCCCHHHHHHHHHHC Q ss_conf 986033348998305 Q gi|254781042|r 1 MDFDMRSSLGRVRGM 15 (130) Q Consensus 1 m~~~~~t~~~~~rgl 15 (130) |.||+|||++.+++. T Consensus 9 isHelrtPL~~i~~~ 23 (66) T smart00388 9 LSHELRTPLTAIRGY 23 (66) T ss_pred HHHHHHCHHHHHHHH T ss_conf 769870818889999 No 37 >pfam00512 HisKA His Kinase A (phosphoacceptor) domain. dimerization and phosphoacceptor domain of histidine kinases. Probab=41.88 E-value=8.2 Score=18.97 Aligned_cols=15 Identities=27% Similarity=0.707 Sum_probs=11.6 Q ss_pred CCCCHHHHHHHHHHC Q ss_conf 986033348998305 Q gi|254781042|r 1 MDFDMRSSLGRVRGM 15 (130) Q Consensus 1 m~~~~~t~~~~~rgl 15 (130) +.||+|||+..++|. T Consensus 9 isHelrtPL~~i~~~ 23 (66) T pfam00512 9 LSHELRTPLTAIRGY 23 (66) T ss_pred HHHHHCCHHHHHHHH T ss_conf 729871848888748 No 38 >cd00290 cytochrome_b_C Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms. Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites. The C-terminal domain is involved in forming the ubiquinol/ubiquinone binding sites, but not the heme binding sites. The N-terminal portion of cytochrome b, which contains both heme binding sites, is described in a separate CD. Probab=41.23 E-value=28 Score=15.86 Aligned_cols=62 Identities=10% Similarity=-0.034 Sum_probs=39.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999999962899989999999462599999999999999998404889985127 Q gi|254781042|r 29 RFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIH 94 (130) Q Consensus 29 RiSAi~L~~l~i~~i~~~~~~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lGl~~IieDYI~ 94 (130) +.-+++.....+..++.+....... .+. -.+|..+....+++...+.=.|+|.+.+-+.|+- T Consensus 81 KlgGViam~~si~iL~~lP~l~~~~---~~s-~~~p~~~~~fw~fv~~f~~LtwlG~~pve~Py~~ 142 (147) T cd00290 81 KLLGVLAMAASILSLFLVPFLENSN---KRS-QFRPLRPTAFWVFLAGTLVLGWLGIQPVEYPFSL 142 (147) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCC---CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH T ss_conf 8899999999999999987642477---664-0276999999999999999998168888421888 No 39 >cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes. Probab=39.89 E-value=9.3 Score=18.66 Aligned_cols=16 Identities=25% Similarity=0.536 Sum_probs=12.9 Q ss_pred CCCCHHHHHHHHHHCC Q ss_conf 9860333489983055 Q gi|254781042|r 1 MDFDMRSSLGRVRGMG 16 (130) Q Consensus 1 m~~~~~t~~~~~rglg 16 (130) +.||+|||++.+++.. T Consensus 11 iaHelrtPL~~i~~~~ 26 (65) T cd00082 11 VSHELRTPLTAIRGAL 26 (65) T ss_pred HHHHHCCHHHHHHCCH T ss_conf 7298704888886014 No 40 >PRK09467 envZ osmolarity sensor protein; Provisional Probab=29.97 E-value=20 Score=16.75 Aligned_cols=15 Identities=33% Similarity=0.587 Sum_probs=12.4 Q ss_pred CCCCHHHHHHHHHHC Q ss_conf 986033348998305 Q gi|254781042|r 1 MDFDMRSSLGRVRGM 15 (130) Q Consensus 1 m~~~~~t~~~~~rgl 15 (130) ..||.|||+.+.|+. T Consensus 238 vSHeLRTPLT~irl~ 252 (437) T PRK09467 238 VSHDLRTPLTRIRLA 252 (437) T ss_pred HHHHHCCHHHHHHHH T ss_conf 344432789999999 No 41 >COG4781 Membrane domain of membrane-anchored glycerophosphoryl diester phosphodiesterase [Energy production and conversion] Probab=29.24 E-value=44 Score=14.70 Aligned_cols=61 Identities=15% Similarity=0.338 Sum_probs=42.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---CCCCCHHHHHHHHHCCHHHHHHHHHH--HHHHHHHHHHH Q ss_conf 999999999999999999999996---28999899999994625999999999--99999998404 Q gi|254781042|r 25 FIKQRFTAIANIPFIIFFIAFFIK---YGDAPYEQIVSVLSNVAVASIMGLGT--ISISVHMQLGM 85 (130) Q Consensus 25 W~~QRiSAi~L~~l~i~~i~~~~~---~~~~~y~~~~~~~~~~~~~il~~l~~--~~~~~Ha~lGl 85 (130) -+.|=+-+.+..|+..|+..+... .+..|||.|.+.++||+-.+++..++ ++.+.|-..|. T Consensus 25 ~lf~ii~~~v~~p~l~~~f~fiL~VtG~~~is~nN~~~ils~p~~vl~Ll~~l~ll~~~vY~efg~ 90 (340) T COG4781 25 LLFQIIVEFVIVPFLSWLFSFILDVTGQPFISYNNVGEILSHPPLVLLLLALLFLLLLLVYLEFGL 90 (340) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999998639861217379999748589999999999999999999999 No 42 >cd07229 Pat_TGL3_like Triacylglycerol lipase 3. Triacylglycerol lipase 3 (TGL3) are responsible for all the TAG lipase activity of the lipid particle. Triacylglycerol (TAG) lipases are also necessary for the mobilization of TAG stored in lipid particles. TGL3 contains the consensus sequence motif GXSXG, which is found in lipolytic enzymes. This family includes Tgl3p from Saccharomyces cerevisiae. Probab=28.98 E-value=27 Score=15.99 Aligned_cols=19 Identities=26% Similarity=0.495 Sum_probs=13.1 Q ss_pred HHHHHHHHHHHHHHHHCCC Q ss_conf 9999984048899851277 Q gi|254781042|r 77 ISVHMQLGMQVIIEDYIHY 95 (130) Q Consensus 77 ~~~Ha~lGl~~IieDYI~~ 95 (130) .+-|++.|....||||+.. T Consensus 26 Ly~~~~~GTK~LIe~Yi~e 44 (391) T cd07229 26 LFTRAYAGTKLLIEEYITE 44 (391) T ss_pred HHHHCCCCCHHHHHHHHHH T ss_conf 8866004708999999999 No 43 >pfam05957 DUF883 Bacterial protein of unknown function (DUF883). This family consists of several hypothetical bacterial proteins of unknown function. Probab=28.32 E-value=46 Score=14.61 Aligned_cols=23 Identities=13% Similarity=0.160 Sum_probs=16.3 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 04889985127731899999999 Q gi|254781042|r 84 GMQVIIEDYIHYRLLKIMFLFMN 106 (130) Q Consensus 84 Gl~~IieDYI~~~~~k~~~~~~~ 106 (130) ..-.-.+||||.++.+.+.+..- T Consensus 60 ~~~~~~d~yV~~~Pw~svgiAag 82 (94) T pfam05957 60 DAADAADDYVHENPWQAVGIAAG 82 (94) T ss_pred HHHHHHHHHHHHCCHHHHHHHHH T ss_conf 99998999998792999999999 No 44 >pfam11815 DUF3336 Domain of unknown function (DUF3336). This family of proteins are functionally uncharacterized. This family is found in bacteria and eukaryotes. This presumed domain is typically between 143 to 227 amino acids in length. Probab=27.64 E-value=28 Score=15.83 Aligned_cols=23 Identities=26% Similarity=0.421 Sum_probs=18.0 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHH Q ss_conf 99999998404889985127731 Q gi|254781042|r 75 ISISVHMQLGMQVIIEDYIHYRL 97 (130) Q Consensus 75 ~~~~~Ha~lGl~~IieDYI~~~~ 97 (130) ...+-|+..|...+||||+..-. T Consensus 96 ~~LY~~s~~GTK~lIeeYi~Ev~ 118 (145) T pfam11815 96 PRLYRHSYVGTKKLIEEYIDEVV 118 (145) T ss_pred HHHHHHCCCCCHHHHHHHHHHHH T ss_conf 88862501154899999999999 No 45 >cd07232 Pat_PLPL Patain-like phospholipase. Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants and fungi. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates. Probab=27.61 E-value=33 Score=15.44 Aligned_cols=13 Identities=23% Similarity=0.600 Sum_probs=4.4 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9984048899851 Q gi|254781042|r 80 HMQLGMQVIIEDY 92 (130) Q Consensus 80 Ha~lGl~~IieDY 92 (130) |+..|....|||| T Consensus 20 ~~~~GTK~lIe~Y 32 (407) T cd07232 20 ETYYGTKNLVEEY 32 (407) T ss_pred HHHCCCHHHHHHH T ss_conf 7433728999999 No 46 >PRK10404 hypothetical protein; Provisional Probab=27.24 E-value=48 Score=14.49 Aligned_cols=20 Identities=15% Similarity=0.117 Sum_probs=14.6 Q ss_pred HHHHHHCCCHHHHHHHHHHH Q ss_conf 89985127731899999999 Q gi|254781042|r 87 VIIEDYIHYRLLKIMFLFMN 106 (130) Q Consensus 87 ~IieDYI~~~~~k~~~~~~~ 106 (130) .--+||||.++-+.+-+..- T Consensus 70 ~~aD~YVhdnPW~aVGiaA~ 89 (101) T PRK10404 70 YRADDYVHEKPWQGIGVGAA 89 (101) T ss_pred HHHHHHHHCCCCHHHHHHHH T ss_conf 98999998497299999999 No 47 >pfam08716 nsp7 nsp7 replicase. nsp7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure. It forms a hexadecameric supercomplex with nsp7 that adopts a hollow cylinder-like structure. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase. Probab=26.24 E-value=39 Score=15.00 Aligned_cols=30 Identities=17% Similarity=0.386 Sum_probs=23.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHH Q ss_conf 999999999999998404889985127731 Q gi|254781042|r 68 SIMGLGTISISVHMQLGMQVIIEDYIHYRL 97 (130) Q Consensus 68 il~~l~~~~~~~Ha~lGl~~IieDYI~~~~ 97 (130) -++.++.+....|+-.|+....|||..+.. T Consensus 51 ~ll~Ll~~llS~~~~~dl~~l~d~~~~~~s 80 (83) T pfam08716 51 KLLSLLAVLLSKHGAVDLEELCDDYLDNST 80 (83) T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHCCCC T ss_conf 999999999805445898999999854553 No 48 >PRK10604 sensor protein RstB; Provisional Probab=26.16 E-value=27 Score=15.92 Aligned_cols=13 Identities=31% Similarity=0.503 Sum_probs=8.0 Q ss_pred CCCHHHHHHHHHH Q ss_conf 8603334899830 Q gi|254781042|r 2 DFDMRSSLGRVRG 14 (130) Q Consensus 2 ~~~~~t~~~~~rg 14 (130) +|++|||+.+.|+ T Consensus 220 SHELRTPLt~i~~ 232 (433) T PRK10604 220 AHELRTPLVRLRY 232 (433) T ss_pred CHHHCCHHHHHHH T ss_conf 2443168999999 No 49 >PRK11100 sensory histidine kinase CreC; Provisional Probab=25.15 E-value=29 Score=15.77 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=10.1 Q ss_pred CCCCHHHHHHHHHH Q ss_conf 98603334899830 Q gi|254781042|r 1 MDFDMRSSLGRVRG 14 (130) Q Consensus 1 m~~~~~t~~~~~rg 14 (130) +.|++|||+...+| T Consensus 263 vSHELRTPLt~I~g 276 (475) T PRK11100 263 LTHELKSPLAAIRG 276 (475) T ss_pred CHHHHHHHHHHHHH T ss_conf 40865117999999 No 50 >PRK09303 adaptive-response sensory kinase; Validated Probab=24.79 E-value=26 Score=16.04 Aligned_cols=14 Identities=21% Similarity=0.342 Sum_probs=12.2 Q ss_pred CCCCHHHHHHHHHH Q ss_conf 98603334899830 Q gi|254781042|r 1 MDFDMRSSLGRVRG 14 (130) Q Consensus 1 m~~~~~t~~~~~rg 14 (130) |+|++|||+..++| T Consensus 156 vSHELRTPLTaI~g 169 (378) T PRK09303 156 LAHDLRTPLTAASL 169 (378) T ss_pred HHHHHCHHHHHHHH T ss_conf 36761531999999 No 51 >cd07206 Pat_TGL3-4-5_SDP1 Triacylglycerol lipase 3, 4, and 5 and Sugar-Dependent 1 lipase. Triacylglycerol lipases are involved in triacylglycerol mobilization and degradation; they are found in lipid particles. TGL4 is 30% homologus to TGL3, whereas TGL5 is 26% homologus to TGL3. Sugar-Dependent 1 (SDP1) lipase has a patatin-like acyl-hydrolase domain that initiates the breakdown of storage oil in germinating Arabidopsis seeds. This family includes subfamilies of proteins: TGL3, TGL4, TGL5, and SDP1. Probab=23.94 E-value=36 Score=15.24 Aligned_cols=19 Identities=37% Similarity=0.607 Sum_probs=13.2 Q ss_pred HHHHHHHHHHHHHHHHCCC Q ss_conf 9999984048899851277 Q gi|254781042|r 77 ISVHMQLGMQVIIEDYIHY 95 (130) Q Consensus 77 ~~~Ha~lGl~~IieDYI~~ 95 (130) .+-|+..|....||||+.. T Consensus 17 LY~~~~~GTK~LIe~Yi~e 35 (298) T cd07206 17 LYRHAYFGTKHLIEDYIEE 35 (298) T ss_pred HHHHCCCCHHHHHHHHHHH T ss_conf 8765124618999999999 No 52 >PRK10755 sensor protein BasS/PmrB; Provisional Probab=23.48 E-value=28 Score=15.90 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=12.3 Q ss_pred CCCCHHHHHHHHHHC Q ss_conf 986033348998305 Q gi|254781042|r 1 MDFDMRSSLGRVRGM 15 (130) Q Consensus 1 m~~~~~t~~~~~rgl 15 (130) +.|++|||+...||- T Consensus 150 ~SHELRTPLt~I~~~ 164 (355) T PRK10755 150 VAHELRTPLAGVRLH 164 (355) T ss_pred HHHHHCCHHHHHHHH T ss_conf 577740389999999 No 53 >PRK13726 conjugal transfer pilus assembly protein TraE; Provisional Probab=23.44 E-value=57 Score=14.07 Aligned_cols=31 Identities=16% Similarity=0.021 Sum_probs=23.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 9999999999999999999962899989999 Q gi|254781042|r 28 QRFTAIANIPFIIFFIAFFIKYGDAPYEQIV 58 (130) Q Consensus 28 QRiSAi~L~~l~i~~i~~~~~~~~~~y~~~~ 58 (130) +|+.|++++.+...++.++....-.....++ T Consensus 10 ~~~~~~~~~~l~~~~~~sl~~nv~~~~~~~~ 40 (187) T PRK13726 10 SRVMAIAFIFLSVLIVLSLSVNVIQGVNNYR 40 (187) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 4029999999999999999999999887887 No 54 >KOG1277 consensus Probab=22.81 E-value=59 Score=14.00 Aligned_cols=38 Identities=24% Similarity=0.361 Sum_probs=25.9 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH Q ss_conf 22108999999999999999999999999962899989 Q gi|254781042|r 18 AKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYE 55 (130) Q Consensus 18 a~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~~~~~~y~ 55 (130) ++.|-+||+.|-+-...|+|-......++++....-|. T Consensus 352 ~r~gG~~Wik~m~lta~Lfp~~~~~t~~~~N~vai~y~ 389 (593) T KOG1277 352 ARLGGRRWIKNMLLTASLFPVPVFGTAFLLNTVAIAYG 389 (593) T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 13244779999988741322789999999999999824 No 55 >PRK11006 phoR phosphate regulon sensor protein; Provisional Probab=21.81 E-value=38 Score=15.13 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=12.4 Q ss_pred CCCCHHHHHHHHHH Q ss_conf 98603334899830 Q gi|254781042|r 1 MDFDMRSSLGRVRG 14 (130) Q Consensus 1 m~~~~~t~~~~~rg 14 (130) |.|++|||+...+| T Consensus 211 vSHELRTPLT~I~G 224 (431) T PRK11006 211 VSHELRTPLTVLQG 224 (431) T ss_pred CCHHHHHHHHHHHH T ss_conf 20866177999999 No 56 >COG2215 ABC-type uncharacterized transport system, permease component [General function prediction only] Probab=20.93 E-value=64 Score=13.77 Aligned_cols=33 Identities=6% Similarity=-0.049 Sum_probs=26.0 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 542210899999999999999999999999996 Q gi|254781042|r 16 GSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIK 48 (130) Q Consensus 16 gsa~~G~~hW~~QRiSAi~L~~l~i~~i~~~~~ 48 (130) -|...-..+|++|++|.++++.+..|.++.-.. T Consensus 122 ~s~~~~~s~~~lE~~S~~Lli~~G~w~~~r~lr 154 (303) T COG2215 122 SSITFALSEPWLELISFLLLILLGLWLLWRTLR 154 (303) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 466776515899999999999999999999998 Done!