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!