Query         gi|254781041|ref|YP_003065454.1| succinate dehydrogenase protein, cytochrome b subunit [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 129
No_of_seqs    106 out of 995
Neff          6.8 
Searched_HMMs 39220
Date          Mon May 30 03:30:55 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781041.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02970 succ_dehyd_cytB succ 100.0       0       0  273.6  14.7  119    6-124     1-122 (123)
  2 PRK09487 sdhC succinate dehydr 100.0 3.8E-44       0  260.4  15.2  124    2-125     3-127 (129)
  3 cd03499 SQR_TypeC_SdhC Succina 100.0 1.1E-42       0  252.5  13.9  117    8-124     1-117 (117)
  4 KOG0449 consensus              100.0 2.1E-35 5.4E-40  212.7   7.6  122    2-123    43-166 (168)
  5 pfam01127 Sdh_cyt Succinate de 100.0 1.1E-32 2.8E-37  197.9  14.3  118    4-121     1-121 (122)
  6 COG2009 SdhC Succinate dehydro 100.0 2.2E-27 5.6E-32  168.9  14.0  122    6-127     1-127 (132)
  7 cd03501 SQR_TypeA_SdhC_like Su  99.8 1.4E-18 3.5E-23  120.9  11.8   98   23-121     1-98  (101)
  8 cd03493 SQR_QFR_TM Succinate:q  99.7 1.2E-16 3.1E-21  110.2  10.1   97   27-123     1-97  (98)
  9 cd03500 SQR_TypeA_SdhD_like Su  99.0 6.1E-09 1.6E-13   68.2  12.0   78   23-100     2-80  (106)
 10 COG2142 SdhD Succinate dehydro  98.5 2.1E-06 5.3E-11   54.4  11.0   76   26-103    17-92  (117)
 11 TIGR02968 succ_dehyd_anc succi  98.2 4.4E-05 1.1E-09   47.1  12.1   79   26-106     8-86  (105)
 12 cd03497 SQR_TypeB_1_TM Succina  98.2 0.00015 3.7E-09   44.3  13.7  109   12-121    80-199 (207)
 13 cd03498 SQR_TypeB_2_TM Succina  97.9  0.0012   3E-08   39.3  13.8  101   19-120    86-196 (209)
 14 cd03494 SQR_TypeC_SdhD Succina  97.8   0.001 2.6E-08   39.6  12.0   70   27-98      3-72  (99)
 15 PRK09488 sdhD succinate dehydr  97.7  0.0012 3.2E-08   39.2  12.1   72   25-98     15-86  (115)
 16 cd03495 SQR_TypeC_SdhD_like Su  97.7 0.00054 1.4E-08   41.2   9.2   76   26-103     3-78  (100)
 17 cd03526 SQR_QFR_TypeB_TM Succi  97.6  0.0023 5.8E-08   37.8  11.3   93    6-100    74-168 (199)
 18 cd03498 SQR_TypeB_2_TM Succina  97.0   0.024 6.1E-07   32.2  11.5   96   30-125     6-111 (209)
 19 cd03526 SQR_QFR_TypeB_TM Succi  95.4    0.18 4.6E-06   27.4  11.7   67   28-94      4-72  (199)
 20 cd03497 SQR_TypeB_1_TM Succina  95.2     0.2 5.1E-06   27.1  11.5   66   27-92      8-76  (207)
 21 cd00581 QFR_TypeB_TM Quinol:fu  94.7    0.19 4.8E-06   27.3   7.2   62   30-91      6-76  (206)
 22 TIGR02046 sdhC_b558_fam succin  94.3    0.36 9.3E-06   25.7  13.8  112    4-117    87-217 (233)
 23 PRK13554 fumarate reductase cy  93.1    0.59 1.5E-05   24.6   9.2   90    6-95      5-105 (241)
 24 cd00546 QFR_TypeD_subunitC Qui  93.0    0.59 1.5E-05   24.6   7.2   90   24-113    20-114 (124)
 25 pfam02967 consensus             89.8     1.4 3.5E-05   22.6   8.7   78   17-94     13-100 (223)
 26 PRK13553 fumarate reductase cy  88.7     1.7 4.3E-05   22.1   8.9   78   18-95     17-104 (252)
 27 COG3029 FrdC Fumarate reductas  88.2     1.8 4.6E-05   21.9   6.2   83    1-85      1-84  (129)
 28 pfam02313 Fumarate_red_D Fumar  87.9     1.9 4.8E-05   21.8   8.2   46   54-99     48-93  (118)
 29 PRK13603 fumarate reductase su  81.6     3.8 9.7E-05   20.2   7.3   89   25-113    21-114 (126)
 30 PRK04987 fumarate reductase su  79.6     4.5 0.00011   19.8  12.5   91   24-114    23-118 (129)
 31 cd00547 QFR_TypeD_subunitD Qui  79.3     4.6 0.00012   19.7   8.5   44   54-97     44-87  (115)
 32 pfam02300 Fumarate_red_C Fumar  79.1     4.6 0.00012   19.7  12.1  106    7-114     8-118 (128)
 33 PRK05470 fumarate reductase su  57.2      14 0.00037   17.0   9.8   47   52-98     46-92  (118)
 34 PRK13867 type IV secretion sys  35.6      15 0.00037   17.0   0.7   28    3-33      7-36  (63)
 35 pfam02941 FeThRed_A Ferredoxin  32.0      16 0.00042   16.7   0.5   11    6-16     41-51  (67)
 36 pfam10573 UPF0561 Uncharacteri  26.1      34 0.00086   15.0   1.3   17    5-21     58-74  (126)
 37 TIGR00947 2A73 inorganic carbo  24.0      25 0.00063   15.7   0.2   23   15-37      7-29  (467)
 38 pfam00584 SecE SecE/Sec61-gamm  23.4      54  0.0014   13.8   4.5   41   83-128     8-48  (56)
 39 PRK05740 secE preprotein trans  23.2      55  0.0014   13.8   9.5   47   77-128    68-114 (124)

No 1  
>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=100.00  E-value=0  Score=273.57  Aligned_cols=119  Identities=33%  Similarity=0.627  Sum_probs=117.2

Q ss_pred             CCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH--HHHHHH-HCCCHHHHHHHHHHHHHHH
Q ss_conf             4989997735102666599999999999999999999999999985163035--546753-0683169999999999999
Q gi|254781041|r    6 NNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTL--SSLRCY-MDGSVFEVCLFLYTWAVIH   82 (129)
Q Consensus         6 ~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~--~~~~~~-~~~~~~k~~~~~~~~~~~y   82 (129)
                      ++||+|||||+||+|+||++||+|||||+++++++++++|++..+..+||+|  +.+++. ++++++|++.+++.++++|
T Consensus         1 ~~RP~sphL~~yr~p~~a~~SIlHRitG~~Lf~~l~~~~w~L~~~l~s~~~f~~~~~~~~l~~~~~~kl~l~~~~~a~~y   80 (123)
T TIGR02970         1 KQRPLSPHLQIYRFPITAILSILHRITGVLLFFGLPFLLWLLSLSLSSPESFLNATVQALLLSSPLGKLILFGLLWALLY   80 (123)
T ss_pred             CCCCCCCCCCEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998998642201523677779999999999999999999999850788999999999897317999999999999999


Q ss_pred             HHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999989999985212335899999999999999999999999
Q gi|254781041|r   83 HMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWI  124 (129)
Q Consensus        83 H~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~~~~  124 (129)
                      |++||||||+||+|+|+|+++++++++++++++++.++..|+
T Consensus        81 H~~~GIRHL~~D~G~G~~~~~~~~~a~~v~~~~~vl~~~~~~  122 (123)
T TIGR02970        81 HLLAGIRHLLWDLGYGLELKSARISAWVVLVLSLVLTVLAGI  122 (123)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999889999987288865567888999999999999999984


No 2  
>PRK09487 sdhC succinate dehydrogenase cytochrome b556 large membrane subunit; Provisional
Probab=100.00  E-value=3.8e-44  Score=260.43  Aligned_cols=124  Identities=19%  Similarity=0.344  Sum_probs=119.4

Q ss_pred             CCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             62004989997735102666599999999999999999999999999985163035546753068316999999999999
Q gi|254781041|r    2 SSIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVI   81 (129)
Q Consensus         2 ~~m~~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~   81 (129)
                      +|||+|||+|||||+||+|+||++||+||+||+++++++++..|++..+..+||+|+.++..++++++|++.++..++++
T Consensus         3 ~~m~~~RPls~~L~~~r~pitai~SIlHRiSGv~lf~~~~~~~~~l~~sl~s~~~f~~~~~~~~~~~~k~il~~~~~al~   82 (129)
T PRK09487          3 RNVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQAAAIMDSFFVKFIMWGILTALA   82 (129)
T ss_pred             CCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             53457999998853035439999999999999999999999999999995496879999999977999999999999999


Q ss_pred             HHHHHHHHHHHHHCCH-HCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999989999985212-3358999999999999999999999999
Q gi|254781041|r   82 HHMLGGIRYLIWDVSL-CLDKKIATQMAKINIIASILTVLIVWII  125 (129)
Q Consensus        82 yH~~nGiRHL~wD~g~-g~~~~~~~~s~~~vl~~sil~~~~~~~i  125 (129)
                      ||++||+|||+||+|+ |+++++++.+++++++++++.+++.|+.
T Consensus        83 yH~~~GIRHL~~D~G~~~e~l~~~~~sa~iv~~l~~vltvl~~i~  127 (129)
T PRK09487         83 YHIVVGIRHLLMDFGYLEETLEAGKRSAKVSFVITVVLSLLAGVL  127 (129)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999986899999802003127998899999999999999999999


No 3  
>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=100.00  E-value=1.1e-42  Score=252.52  Aligned_cols=117  Identities=35%  Similarity=0.666  Sum_probs=114.8

Q ss_pred             CCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89997735102666599999999999999999999999999985163035546753068316999999999999999998
Q gi|254781041|r    8 RPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGG   87 (129)
Q Consensus         8 RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nG   87 (129)
                      ||+|||||+||+|+||++||+||+||++++++++++.+++.....+||.|+.++...+++++|++++++++++.||++||
T Consensus         1 RP~sPhL~iyk~~~ta~~SI~HRiSGv~l~~~~~~~~~~l~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~yH~~~G   80 (117)
T cd03499           1 RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLLWWLLASLSSPESFESVSALLGSWLGKLVLFGLTWALFYHLLNG   80 (117)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99897433045169999999999999999999999999999980287789999999615799999999999999999866


Q ss_pred             HHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999985212335899999999999999999999999
Q gi|254781041|r   88 IRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWI  124 (129)
Q Consensus        88 iRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~~~~  124 (129)
                      +||++||+|+|+|+|++|++|+++++++++.++++|+
T Consensus        81 iRHL~wD~g~g~~~~~~~~s~~~v~~~s~~~t~~~~~  117 (117)
T cd03499          81 IRHLIWDLGKGLELKTVYKSGYAVLVLSVVLTVLLGI  117 (117)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             8999998113564999999999999999999999979


No 4  
>KOG0449 consensus
Probab=100.00  E-value=2.1e-35  Score=212.66  Aligned_cols=122  Identities=28%  Similarity=0.329  Sum_probs=96.8

Q ss_pred             CCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHCCCHHHHHHHH-HCCCHHHHHHHHHHHH
Q ss_conf             6200498999773510266659999999999999999999999-9999985163035546753-0683169999999999
Q gi|254781041|r    2 SSIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVV-FWFFCIANGEHTLSSLRCY-MDGSVFEVCLFLYTWA   79 (129)
Q Consensus         2 ~~m~~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~-~~l~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~~~   79 (129)
                      +|++.|||+||||+||+||+||..||+|||||+++..+..++. ..+......++.++.+... ++....-.+|+.++++
T Consensus        43 ~~~r~~RPlSPHLTIYqpQLt~~LS~~hRiSG~~la~gv~~~G~~~l~~~g~~~~~v~~~~~~~~~~~~~~~~K~~iayp  122 (168)
T KOG0449          43 KNQRSNRPLSPHLTIYQPQLTWMLSIFHRISGVVLAGGVWLVGVSGLLGMGDITATVSKVYQLKLPTAVQWPAKFSIAYP  122 (168)
T ss_pred             HHHHCCCCCCCCEEEECHHHHHHHHHHHHHHHHEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             66652899998530634128999999875513001446999888998457516888888897316456775689999999


Q ss_pred             HHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998999998521233589999999999999999999999
Q gi|254781041|r   80 VIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVW  123 (129)
Q Consensus        80 ~~yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~~~  123 (129)
                      +.||..||||||+||.|++++++++|++||++++++++++..+.
T Consensus       123 ~a~Ht~ngiRHLiwd~~k~L~i~~vY~tGy~v~alt~vls~~l~  166 (168)
T KOG0449         123 FAYHTGNGIRHLIWDLGKELTIKGVYKTGYAVLALTVVLSAYLA  166 (168)
T ss_pred             HHHHHHCCHHHHHHHHCCCCCCCCEEEECHHHHHHHHHHHHHHH
T ss_conf             99997153233445531455300111201168999999999996


No 5  
>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=100.00  E-value=1.1e-32  Score=197.85  Aligned_cols=118  Identities=30%  Similarity=0.531  Sum_probs=104.3

Q ss_pred             CCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHCCCHHHHH-HHHHCCCHHHHHHHHHHHHH
Q ss_conf             00498999773510266659999999999999999999999999998--5163035546-75306831699999999999
Q gi|254781041|r    4 IKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCI--ANGEHTLSSL-RCYMDGSVFEVCLFLYTWAV   80 (129)
Q Consensus         4 m~~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~--~~~~~~~~~~-~~~~~~~~~k~~~~~~~~~~   80 (129)
                      |++|||+|||+|+||+|.++..||+||+||++++++...+..|+...  ...+++|+.+ ...+++++.++.++++.+++
T Consensus         1 ~~~~rp~sphl~i~~~~~~~~~si~hRiTGv~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   80 (122)
T pfam01127         1 MRKNRPLSPHLGLYRAHLGTILSILHRITGVALAVLLIHLLLWLLLLALLLGPDSYARVVVAWLSSPFKLILLLLLLLAL   80 (122)
T ss_pred             CCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999975615652357987999999999999999999999999875794789999999871299999999999999


Q ss_pred             HHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999989999985212335899999999999999999999
Q gi|254781041|r   81 IHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLI  121 (129)
Q Consensus        81 ~yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~  121 (129)
                      .||+.||+||++||+|+|+|+|+.+++++++++.+++.++.
T Consensus        81 ~yH~~~GiRhli~D~g~g~~~~~~~~~~~~v~~~~~~~~~~  121 (122)
T pfam01127        81 FYHAANGLRHLIWDVGKGLELKTARKTGLLVLALSLVLTLL  121 (122)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998679999997223665999999999999999999988


No 6  
>COG2009 SdhC Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion]
Probab=99.95  E-value=2.2e-27  Score=168.87  Aligned_cols=122  Identities=31%  Similarity=0.509  Sum_probs=103.4

Q ss_pred             CCCCCCCCCCEECCCHHHHHHHHHHHHHHHHH--HHHHHHHH--HHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             49899977351026665999999999999999--99999999--999985163035546753068316999999999999
Q gi|254781041|r    6 NNRPLSPHLQIYRLIPTMFVSIVHRITGSVVY--LGTPVVVF--WFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVI   81 (129)
Q Consensus         6 ~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~--~~~~~~~~--~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~   81 (129)
                      ++||.|||+|+||+|+++..|++||+||+++.  ....++..  |+.....+++.++.+.....+++.++.++++.+++.
T Consensus         1 ~~r~~~~~l~~~~~~~~~~~silHRitGv~l~~Fl~~hil~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~   80 (132)
T COG2009           1 RKRPVSPHLQIYRPPITMYASILHRISGVILAFFLFVHILLASSWLAGSASFNAAFEFYHALLGSFIVKLVLLGLVLALL   80 (132)
T ss_pred             CCCCCCCCCCEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             99887875141206779999999997999999999999999999988887579999999963676799999999999999


Q ss_pred             HHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf             9999989999985212335899999999999999999-999999975
Q gi|254781041|r   82 HHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILT-VLIVWIIKD  127 (129)
Q Consensus        82 yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~-~~~~~~i~~  127 (129)
                      ||.+||+||++||+|++++.+....+++.....+.+. ++..|.+..
T Consensus        81 ~H~~nGIR~l~~d~g~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~  127 (132)
T COG2009          81 YHGLNGIRHLLWDFGYGLELKGVGYTGAALVFFSAVTLTLLLWVIVW  127 (132)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998799999997411153202156899999999999999999999


No 7  
>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=99.79  E-value=1.4e-18  Score=120.89  Aligned_cols=98  Identities=22%  Similarity=0.349  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCHH
Q ss_conf             99999999999999999999999999985163035546753068316999999999999999998999998521233589
Q gi|254781041|r   23 MFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKK  102 (129)
Q Consensus        23 ~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~~~  102 (129)
                      |+++++||+||+++++.+++..+.+.....+||.|+.+.+..+++++|+.++++..+..||.+||+|+++.|+|.+- .+
T Consensus         1 mwA~~lHRiTGv~l~~fL~~Hi~~ls~~~~~p~~y~~~~~~~~~p~~~~~e~gLv~a~~fHa~NGiRiil~Df~~~g-~~   79 (101)
T cd03501           1 MWAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVFHALNGIRLILVDFGSGG-PR   79 (101)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HH
T ss_conf             98999999999999999999999999984499999999999718279999999999999997403999999983044-78


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999
Q gi|254781041|r  103 IATQMAKINIIASILTVLI  121 (129)
Q Consensus       103 ~~~~s~~~vl~~sil~~~~  121 (129)
                      ..|...|++++++++..+.
T Consensus        80 ~qk~l~~~v~~l~~v~~i~   98 (101)
T cd03501          80 YQRQLFYIVLVLTVVLIVA   98 (101)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999960


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=99.70  E-value=1.2e-16  Score=110.22  Aligned_cols=97  Identities=25%  Similarity=0.459  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCHHHHHH
Q ss_conf             99999999999999999999999851630355467530683169999999999999999989999985212335899999
Q gi|254781041|r   27 IVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQ  106 (129)
Q Consensus        27 I~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~~~~~~~  106 (129)
                      ++||+||+++.+..+.+.+++.....+++.++.....++++..+.+..+..+++.||..||+||++||+|++.+.+..+.
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             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254781041|r  107 MAKINIIASILTVLIVW  123 (129)
Q Consensus       107 s~~~vl~~sil~~~~~~  123 (129)
                      +++++.+++++.++..+
T Consensus        81 ~~~~~~~~~~~~~~~~~   97 (98)
T cd03493          81 LGYAVLALSVLLTVLLL   97 (98)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999997


No 9  
>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=99.04  E-value=6.1e-09  Score=68.19  Aligned_cols=78  Identities=14%  Similarity=0.136  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCC
Q ss_conf             999999999999999999999999999851630-355467530683169999999999999999989999985212335
Q gi|254781041|r   23 MFVSIVHRITGSVVYLGTPVVVFWFFCIANGEH-TLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLD  100 (129)
Q Consensus        23 ~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~  100 (129)
                      +....+||+||+.+.+.+....+.......+++ .|+.+..-+++|..|...++..+.-.||-.||+|..+-|...+-.
T Consensus         2 ~~~W~~~RiSGv~Lv~ll~~H~~~~h~~~~~~~i~f~~V~~r~~~P~w~~~d~llL~lal~HG~NGlR~il~Dy~~~~~   80 (106)
T cd03500           2 SLAWLFQRITGVFLVFLLAGHFWVQHMDNGGDVIDFAFVANRLASPLWKVWDLLLLVLALLHGGNGLRNILLDYVRRPR   80 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCH
T ss_conf             2999999999999999999999999961667646699999987695999999999999999824117897998736822


No 10 
>COG2142 SdhD Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion]
Probab=98.52  E-value=2.1e-06  Score=54.36  Aligned_cols=76  Identities=17%  Similarity=0.275  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCHHH
Q ss_conf             999999999999999999999999851630355467530683169999999999999999989999985212335899
Q gi|254781041|r   26 SIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKI  103 (129)
Q Consensus        26 SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~~~~  103 (129)
                      ..+-|+||+++.+....+.+..  ....+..|+.....+.+++.|....+..++..||..||.|+.+-|+-+++..+.
T Consensus        17 ~l~qRvTav~Lv~l~~~~l~~~--l~~~~~~y~~~~~~~a~p~~~v~~lL~l~~~l~H~~~Glr~Ii~DYi~~~~~r~   92 (117)
T COG2142          17 WLLQRVTAVILVLLVIWHLYFL--LTWLNATYAAWVAFLANPFWKVFLLLLLVAALIHAWNGLRVIIEDYIKPEKLRL   92 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH--HHCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999--980799799999999688999999999999999999616999999973398999


No 11 
>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=98.23  E-value=4.4e-05  Score=47.10  Aligned_cols=79  Identities=20%  Similarity=0.207  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCHHHHH
Q ss_conf             99999999999999999999999985163035546753068316999999999999999998999998521233589999
Q gi|254781041|r   26 SIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIAT  105 (129)
Q Consensus        26 SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~~~~~~  105 (129)
                      .+.-|+|++++....+.+..  ......+.+|+..++.++++..|+.......+..+|.-=|+|..+.|+=+..-++-.-
T Consensus         8 w~~QR~TAv~~~~y~~~~~~--~~~~~~~~~Y~~w~~~f~~~~~~~~~~l~l~~~~~HawiGm~~v~~DYv~~~~lRl~l   85 (105)
T TIGR02968         8 WLLQRVTAVVLALYTIFLIG--FLLALPGATYEAWRALFAHPWMKIFTLLALLALLYHAWIGMRVVLEDYVKPEGLRLVL   85 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHH--HHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             99999999999999999999--9995589998999999866499999999999999973872676544223637999999


Q ss_pred             H
Q ss_conf             9
Q gi|254781041|r  106 Q  106 (129)
Q Consensus       106 ~  106 (129)
                      .
T Consensus        86 ~   86 (105)
T TIGR02968        86 Q   86 (105)
T ss_pred             H
T ss_conf             9


No 12 
>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=98.17  E-value=0.00015  Score=44.27  Aligned_cols=109  Identities=13%  Similarity=0.245  Sum_probs=84.8

Q ss_pred             CCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHH---------CCCHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             77351026665999999999999999999999999999--851---------6303554675306831699999999999
Q gi|254781041|r   12 PHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFC--IAN---------GEHTLSSLRCYMDGSVFEVCLFLYTWAV   80 (129)
Q Consensus        12 phL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~--~~~---------~~~~~~~~~~~~~~~~~k~~~~~~~~~~   80 (129)
                      |+-..|+..-+ +.+.+-|+||+++.+++....+-+-.  ...         .++.|+...+.+++++...+=.....+.
T Consensus        80 ~n~~~y~~~rN-w~~~~qr~TGii~l~FIi~Hv~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~Yii~~la~  158 (207)
T cd03497          80 SNTGRYDYFRN-WMYTLQRITGIILLVFIAWHVWHTRFAEALGHVDIQTPEAGEANLSAMRNALASPLMLIFYIIGVLAA  158 (207)
T ss_pred             CCCCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             66676641401-99999999999999999999999999886065444667621358999999960809999999999999


Q ss_pred             HHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999989999985212335899999999999999999999
Q gi|254781041|r   81 IHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLI  121 (129)
Q Consensus        81 ~yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~  121 (129)
                      .+|+.||+-=...+.|.-.+.++.+...++.....++++..
T Consensus       159 ~fHlanGlwSf~~twGit~sprsq~~~~~v~~~v~v~l~~~  199 (207)
T cd03497         159 VFHFANGLWTFLITWGITVSPRSQRVSTYVCLLVFVVVSFM  199 (207)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999889999999833068999999999999999999999


No 13 
>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=97.87  E-value=0.0012  Score=39.30  Aligned_cols=101  Identities=13%  Similarity=0.059  Sum_probs=71.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----------CCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66659999999999999999999999999998516----------30355467530683169999999999999999989
Q gi|254781041|r   19 LIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANG----------EHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGI   88 (129)
Q Consensus        19 ~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~----------~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGi   88 (129)
                      .+-+.+.|-+-|+||+++..++.....-+-.....          .|.|+.....+++++...+=.....++.+|+.+|+
T Consensus        86 ~~~~s~asr~M~~tG~ill~Fiv~Hl~~f~~~~~~~~~~~~~~~~~d~y~~v~~~F~~p~~~~~Yvvam~~L~~HL~HG~  165 (209)
T cd03498          86 KKLASLASRTMIWSGLIILLFIILHLLDFTFGVVGPVSPPMGVGRGDVYELLVASFQQPWIAALYVLAMVALGLHLSHGF  165 (209)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             65456999999999999999999999998512115544666665015999999995164999999999999999999899


Q ss_pred             HHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998521233589999999999999999999
Q gi|254781041|r   89 RYLIWDVSLCLDKKIATQMAKINIIASILTVL  120 (129)
Q Consensus        89 RHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~  120 (129)
                      .-...+.|.. +.+..+....+....++++.+
T Consensus       166 ~Sa~qTlG~~-~~~~~~~~~~i~~~~a~~i~~  196 (209)
T cd03498         166 WSAFQTLGLN-NPRYRPALKAVGRVVAILIAG  196 (209)
T ss_pred             HHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999982799-813589999999999999999


No 14 
>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=97.76  E-value=0.001  Score=39.63  Aligned_cols=70  Identities=19%  Similarity=0.199  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             999999999999999999999998516303554675306831699999999999999999899999852123
Q gi|254781041|r   27 IVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLC   98 (129)
Q Consensus        27 I~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g   98 (129)
                      ...|+|++++......+...+  ...+|-+|+..+.+++++..|........+..+|.-=|+|+...|+=+.
T Consensus         3 l~QRvTAvil~~Y~~~l~~~~--~~~~~~~y~~W~~~f~~~~~ki~t~l~~~sl~~HAWIGlw~V~tDYi~~   72 (99)
T cd03494           3 LVQRVTAVIMALYTIFLVGFL--LASPPLTYEAWSGLFSSLWMKIFTLLALLALLLHAWIGLWDILTDYVKP   72 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             999999999999999999999--9869999999999997489999999999999999999688767872580


No 15 
>PRK09488 sdhD succinate dehydrogenase cytochrome b556 small membrane subunit; Provisional
Probab=97.74  E-value=0.0012  Score=39.19  Aligned_cols=72  Identities=21%  Similarity=0.192  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             99999999999999999999999998516303554675306831699999999999999999899999852123
Q gi|254781041|r   25 VSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLC   98 (129)
Q Consensus        25 ~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g   98 (129)
                      -.+..|+|++++......+...  .....|-+|+..+.++++...|+.-.....++.+|..=|+|+...|+=+.
T Consensus        15 DWl~QRvsAvim~~Y~~~l~~f--~~~~~~~~y~~W~~~F~~~~mkift~l~~lsl~~HAWIGlw~V~tDYik~   86 (115)
T PRK09488         15 DFILVRATAIVLTLYIIYMVGF--FATSGELTYEVWRGFFASAFTKVFTLLALFSILIHAWIGMWQVLTDYVKP   86 (115)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             9999999999999999999999--99779999999999985689999999999999999997576657865364


No 16 
>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=97.66  E-value=0.00054  Score=41.19  Aligned_cols=76  Identities=13%  Similarity=0.054  Sum_probs=60.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCHHH
Q ss_conf             999999999999999999999999851630355467530683169999999999999999989999985212335899
Q gi|254781041|r   26 SIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKI  103 (129)
Q Consensus        26 SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~~~~  103 (129)
                      .+..|+|++++....+.+.+.+.  ....++|+.+.+.+++++...........-.||+-.|++..+-|+=.+...|.
T Consensus         3 W~~QRitAi~lipL~~wfi~~~~--~~~~~~y~~v~~~~~~p~~~il~~l~i~~~~~H~~lG~qvIIEDYIh~~~~k~   78 (100)
T cd03495           3 WWAQRVTAVALVPLVLWFVFSVA--LLLGASYAEVVAWLAHPFNAILLILTLVSAFYHARLGMQVVIEDYVHSEGLRL   78 (100)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH--HHCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHH
T ss_conf             69999999999999999999999--87499999999999792999999999999999997088464102347843999


No 17 
>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=97.57  E-value=0.0023  Score=37.76  Aligned_cols=93  Identities=11%  Similarity=0.010  Sum_probs=67.1

Q ss_pred             CCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             4989997735102666599999999999999999999999999985--16303554675306831699999999999999
Q gi|254781041|r    6 NNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIA--NGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHH   83 (129)
Q Consensus         6 ~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~--~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH   83 (129)
                      +.||..-|-+ |+ .-..+.+-+-|+||++++++.....+-.....  ..++.++...+.+.++..-.+-.....+..+|
T Consensus        74 ~a~~~~~~~~-~~-~~~t~~~~~Qr~TG~il~~fi~~Hl~~~~~~~~~~~~~~~~~~~~~f~~p~~~~~Ylv~l~a~~~H  151 (199)
T cd03526          74 QALTFKTHKD-LM-HGDTTLWWIQAMTGFAMLFFGSVHLYIMMTQAQPDRTIGFVMSSNRMSSEWMWPLYIVLLFAVELH  151 (199)
T ss_pred             HHHHHHHHHH-CC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             8753316775-05-540699999999999999999999999996235788777899999994743999999999999999


Q ss_pred             HHHHHHHHHHHCCHHCC
Q ss_conf             99989999985212335
Q gi|254781041|r   84 MLGGIRYLIWDVSLCLD  100 (129)
Q Consensus        84 ~~nGiRHL~wD~g~g~~  100 (129)
                      ..||+-=+....|.-..
T Consensus       152 ~~~Glws~~vtWGw~~~  168 (199)
T cd03526         152 GSVGLYSFAVTWGWFDG  168 (199)
T ss_pred             HHHHHHHHHHHHHCCCC
T ss_conf             99879999999853568


No 18 
>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=96.96  E-value=0.024  Score=32.19  Aligned_cols=96  Identities=13%  Similarity=0.165  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CHHCCH-
Q ss_conf             9999999999999999999985163035546753068--31699999999999999999899999852-----123358-
Q gi|254781041|r   30 RITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDG--SVFEVCLFLYTWAVIHHMLGGIRYLIWDV-----SLCLDK-  101 (129)
Q Consensus        30 RitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~~~k~~~~~~~~~~~yH~~nGiRHL~wD~-----g~g~~~-  101 (129)
                      =+||.++.+++......=.....+||.|+.....+++  ++......++..++..|...|++--.-.-     .|..+. 
T Consensus         6 A~TGl~l~~Flv~Hl~gNl~~~~G~eafN~ya~~L~~~~~ll~i~~~~Ll~~~~~Hi~~ai~l~~~nr~ar~~~Y~~~~~   85 (209)
T cd03498           6 ALTGLFLVLFLLVHLLGNLKIFFGPEAFNAYAEFLHTLNPLLWIARLVLLVAAVLHIVFGLQLTIRNRAARPVRYAVKNR   85 (209)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             69999999999999999999972999999999998407729999999999999999999999998845447876400167


Q ss_pred             --HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --999999999999999999999999
Q gi|254781041|r  102 --KIATQMAKINIIASILTVLIVWII  125 (129)
Q Consensus       102 --~~~~~s~~~vl~~sil~~~~~~~i  125 (129)
                        ++...+....+...++..+++|=+
T Consensus        86 ~~~~s~asr~M~~tG~ill~Fiv~Hl  111 (209)
T cd03498          86 KKLASLASRTMIWSGLIILLFIILHL  111 (209)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             65456999999999999999999999


No 19 
>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=95.39  E-value=0.18  Score=27.40  Aligned_cols=67  Identities=15%  Similarity=0.054  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999998516303554675306831--69999999999999999989999985
Q gi|254781041|r   28 VHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSV--FEVCLFLYTWAVIHHMLGGIRYLIWD   94 (129)
Q Consensus        28 ~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~k~~~~~~~~~~~yH~~nGiRHL~wD   94 (129)
                      ++=+||+++..++......-.....|||.|+....++++..  .......+..++.+|..-|+|-..-+
T Consensus         4 ~qSlTGl~L~lFl~~Hm~~N~~i~~g~e~fn~~a~~l~~~p~l~~~~~~~i~~~~l~H~~~a~~~~~~~   72 (199)
T cd03526           4 LQSATGLFLGLFMIGHLFFNSTILLGDNVMNWVAKKFELLPIVVSFLAAFIFAVFIAHAFLGVRKFPIY   72 (199)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998999999999999999999999199999999999865759999999999999999999999998997


No 20 
>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=95.24  E-value=0.2  Score=27.12  Aligned_cols=66  Identities=17%  Similarity=0.140  Sum_probs=52.2

Q ss_pred             HHHHHHHHH-HHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC-CHHHHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999-9999999999999985163035546753068-3169999-9999999999999899999
Q gi|254781041|r   27 IVHRITGSV-VYLGTPVVVFWFFCIANGEHTLSSLRCYMDG-SVFEVCL-FLYTWAVIHHMLGGIRYLI   92 (129)
Q Consensus        27 I~HRitGi~-l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~k~~~-~~~~~~~~yH~~nGiRHL~   92 (129)
                      =+|-.+|++ +.+++......=..+..|+|.|+....++++ +..+.++ +++..|+.+|..-|+.-..
T Consensus         8 rlhSL~GvipvglFLi~Hl~~Nl~a~~G~e~FN~~a~fm~slP~l~~ie~~~i~lpll~Hai~Gi~i~~   76 (207)
T cd03497           8 RLHSLLGVVPIGLFLIEHLLTNSSAASGPEGFNAAVNFMHSLPGLLLIEIFGIFLPLLFHAIYGIYIAF   76 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999981989999999998859619999999999999999999999999


No 21 
>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=94.70  E-value=0.19  Score=27.28  Aligned_cols=62  Identities=15%  Similarity=0.125  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHC---------CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999998516303554675306---------83169999999999999999989999
Q gi|254781041|r   30 RITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMD---------GSVFEVCLFLYTWAVIHHMLGGIRYL   91 (129)
Q Consensus        30 RitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---------~~~~k~~~~~~~~~~~yH~~nGiRHL   91 (129)
                      -+||+++..++........+...|||.++.+..+++         .++.+++.......+..|..-..|.+
T Consensus         6 s~TGl~LalFm~~Hm~fvSSILlg~~a~~~va~f~E~~~~~~~g~p~v~~~~~~~I~~~f~~Ha~lA~RK~   76 (206)
T cd00581           6 SATGLFLALFMWAHMLFVSSILLGKEAMYWVARFFEGAFFFGHGYPWVVSVVAAIVFALFVAHAFLALRKF   76 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             88899999999999999999971899999999998510302788448999999999999999999999866


No 22 
>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=94.26  E-value=0.36  Score=25.73  Aligned_cols=112  Identities=15%  Similarity=0.097  Sum_probs=78.1

Q ss_pred             CCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-------------------CHHHHHHHHH
Q ss_conf             004989997735102666599999999999999999999999999985163-------------------0355467530
Q gi|254781041|r    4 IKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGE-------------------HTLSSLRCYM   64 (129)
Q Consensus         4 m~~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~-------------------~~~~~~~~~~   64 (129)
                      .|+-||.+ =-..=|++ +.++|-+-|.||++...++....+-+......+                   |.|+.+...+
T Consensus        87 ~~~ar~~~-Y~~~~~~~-~~~~s~~m~~~GIi~l~Fi~~H~~~f~~~~~~~~~~~~~~a~~~~DGfdhP~~~y~~~v~~F  164 (233)
T TIGR02046        87 KRAARPVR-YAHKSRAK-ASWASRTMLVTGIIVLLFIGLHLLDFTLGAQLAEAFEMGVAKFRIDGFDHPADIYEMVVLTF  164 (233)
T ss_pred             HHCCCCCC-CCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             86027888-53257001-14898899998799999999999999999874677778888867787666068999999986


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             68316999999999999999998999998521233589999999999999999
Q gi|254781041|r   65 DGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASIL  117 (129)
Q Consensus        65 ~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil  117 (129)
                      +++.....=..+..++.+|+-+|+-=.+.-.|.+.+.-..+..+...+...++
T Consensus       165 s~p~~~~~YiVa~l~L~fH~~HG~wSa~qTLG~n~t~~~~~ik~~s~v~al~i  217 (233)
T TIGR02046       165 SSPIVLSIYIVAMLALGFHLSHGLWSAAQTLGLNSTIRSQRIKAVSNVVALVI  217 (233)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             07168899999999999999999999999817988006788899999999999


No 23 
>PRK13554 fumarate reductase cytochrome b-556 subunit; Provisional
Probab=93.13  E-value=0.59  Score=24.59  Aligned_cols=90  Identities=12%  Similarity=0.056  Sum_probs=69.5

Q ss_pred             CCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC-----------CHHHHHHH
Q ss_conf             4989997735102666599999999999999999999999999985163035546753068-----------31699999
Q gi|254781041|r    6 NNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDG-----------SVFEVCLF   74 (129)
Q Consensus         6 ~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-----------~~~k~~~~   74 (129)
                      ..-|..-|-...--|.++..-...-+||+++..++........+...|+|.++.+..+++.           ++.+++-.
T Consensus         5 ~~~~~~~~~~~~g~~w~A~lD~~QS~TG~~LalFm~~HM~fvSSILlg~~a~~~Va~f~E~~~~~~~G~g~p~v~s~~~~   84 (241)
T PRK13554          5 TRVHTAVNTGPFGHPWSAKADKLQSATGIMLGCFLLLHMHFESSILLGKEAFYHVVQFLEGGMFSSTGHGFPIVTKVFSV   84 (241)
T ss_pred             CCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             00451021787899860789999987889999999999998999752898999999998442776269887026889999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999899999852
Q gi|254781041|r   75 LYTWAVIHHMLGGIRYLIWDV   95 (129)
Q Consensus        75 ~~~~~~~yH~~nGiRHL~wD~   95 (129)
                      +....+.-|.+-..|.+=..+
T Consensus        85 ~I~~lf~vHa~lA~RKfP~~~  105 (241)
T PRK13554         85 FMLLVVIVHAAVALRRFPAQL  105 (241)
T ss_pred             HHHHHHHHHHHHHHHHCCCCH
T ss_conf             999999999999986678058


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=93.03  E-value=0.59  Score=24.58  Aligned_cols=90  Identities=8%  Similarity=0.099  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHHC---CHH
Q ss_conf             99999999999999999999999999851630355467530683169999999999999999989999--9852---123
Q gi|254781041|r   24 FVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYL--IWDV---SLC   98 (129)
Q Consensus        24 ~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL--~wD~---g~g   98 (129)
                      ..-.++-.|.+....+...+.+++.++..|||+++.+..+..+++.-+.-.....+-.||...=..-.  .++.   |+-
T Consensus        20 r~YMlRE~T~v~~~~f~lvLl~Gl~~L~~g~~aw~~f~~flqnP~vv~lniiaL~a~L~Ha~TwF~~~Pk~m~i~v~g~~   99 (124)
T cd00546          20 RFYMLREATAVPTVWFSLVLLYGLFALGSGPESWAGFVSFLQNPIVVLLNIIALAAALLHAKTWFEMAPKVMNIIVKGER   99 (124)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCHHEEEEECCEE
T ss_conf             99999888379999999999999999806989999999998385999999999999999999999974230042178867


Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             358999999999999
Q gi|254781041|r   99 LDKKIATQMAKINII  113 (129)
Q Consensus        99 ~~~~~~~~s~~~vl~  113 (129)
                      .+.+...+..|.+.+
T Consensus       100 ~~~~~iv~~~wa~~~  114 (124)
T cd00546         100 VPPEAITKALWAVTA  114 (124)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             878999999999999


No 25 
>pfam02967 consensus
Probab=89.80  E-value=1.4  Score=22.56  Aligned_cols=78  Identities=12%  Similarity=0.079  Sum_probs=53.1

Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC----------CHHHHHHHHHHHHHHHHHHH
Q ss_conf             02666599999999999999999999999999985163035546753068----------31699999999999999999
Q gi|254781041|r   17 YRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDG----------SVFEVCLFLYTWAVIHHMLG   86 (129)
Q Consensus        17 yk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~----------~~~k~~~~~~~~~~~yH~~n   86 (129)
                      -|...++..-...-+||+++..++........+...|||.++.+..+++.          ++.+++..+....+.-|.+-
T Consensus        13 kksr~~A~lD~~Qs~TGl~LalFm~~Hm~fvSSILlg~~a~~~va~f~E~~~~~~~gG~p~v~s~~a~~i~~lf~~Ha~l   92 (223)
T pfam02967        13 KKSRWPAKLDFLQSLTGLFLALFLWAHMLFVSSILLGKEAMYWVAKFFEGSFFSSEGGYPWVTSIIAAVIFALFLAHAFL   92 (223)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             85676288999998789999999999999999985089899999999855676327995246899999999999999999


Q ss_pred             HHHHHHHH
Q ss_conf             89999985
Q gi|254781041|r   87 GIRYLIWD   94 (129)
Q Consensus        87 GiRHL~wD   94 (129)
                      ..|.+=-.
T Consensus        93 A~RKfP~~  100 (223)
T pfam02967        93 AMRKFPAN  100 (223)
T ss_pred             HHHHCCCC
T ss_conf             99766815


No 26 
>PRK13553 fumarate reductase cytochrome b-556 subunit; Provisional
Probab=88.69  E-value=1.7  Score=22.10  Aligned_cols=78  Identities=10%  Similarity=0.089  Sum_probs=61.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC----------CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2666599999999999999999999999999985163035546753068----------316999999999999999998
Q gi|254781041|r   18 RLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDG----------SVFEVCLFLYTWAVIHHMLGG   87 (129)
Q Consensus        18 k~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~----------~~~k~~~~~~~~~~~yH~~nG   87 (129)
                      |-+.++..-...-+||++|..++........+...|||.++.+..+++.          ++.+++..+....+.-|.+-.
T Consensus        17 ksr~~A~lD~~Qs~TGl~LalFm~~Hm~fvSSILlg~~a~~~Va~f~E~~~~~~~gG~p~v~s~~a~~I~~lf~vHa~lA   96 (252)
T PRK13553         17 KSRIPAKLDFLQSATGLFLGLFMWAHMFFVSTILISDEAMYKVAKFFEGSFIFDKPGEPALVSFVAAGVIVIFVVHAFLA   96 (252)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78864899999988899999999999999999850898999999997200240479851236999999999999999999


Q ss_pred             HHHHHHHC
Q ss_conf             99999852
Q gi|254781041|r   88 IRYLIWDV   95 (129)
Q Consensus        88 iRHL~wD~   95 (129)
                      .|.+=..+
T Consensus        97 ~RKfP~~~  104 (252)
T PRK13553         97 MRKFPINY  104 (252)
T ss_pred             HHHCCCCH
T ss_conf             97668058


No 27 
>COG3029 FrdC Fumarate reductase subunit C [Energy production and conversion]
Probab=88.22  E-value=1.8  Score=21.92  Aligned_cols=83  Identities=13%  Similarity=0.229  Sum_probs=56.3

Q ss_pred             CCCCCC-CCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             962004-9899977351026665999999999999999999999999999851630355467530683169999999999
Q gi|254781041|r    1 MSSIKN-NRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWA   79 (129)
Q Consensus         1 m~~m~~-~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~   79 (129)
                      |+++|. -||+-|.=  +|-..--..-.+--+|.+-...+...+.+++.+...+|++++.+.++..+++.-+.-.....+
T Consensus         1 ~skrk~Yvrpm~~tW--Wkkl~fYr~yMlRE~T~ip~vwF~l~L~~gl~al~~gp~~~~~fldFl~NPvVv~lNlitL~a   78 (129)
T COG3029           1 TSKRKPYVRPMTRTW--WKKLPFYRFYMLREATAIPAVWFSLELIYGLFALGSGPEAWQGFLDFLANPVVVILNLITLAA   78 (129)
T ss_pred             CCCCCCCCCCCCHHH--HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCEEEEEHHHHHHH
T ss_conf             997661006341678--860837999999873058999999999999999705956788899985498587516999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254781041|r   80 VIHHML   85 (129)
Q Consensus        80 ~~yH~~   85 (129)
                      ..+|..
T Consensus        79 ~LlHt~   84 (129)
T COG3029          79 ALLHTV   84 (129)
T ss_pred             HHHHHH
T ss_conf             999999


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=87.92  E-value=1.9  Score=21.82  Aligned_cols=46  Identities=9%  Similarity=0.142  Sum_probs=41.1

Q ss_pred             CCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHC
Q ss_conf             3035546753068316999999999999999998999998521233
Q gi|254781041|r   54 EHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCL   99 (129)
Q Consensus        54 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~   99 (129)
                      ..+|+.+..+..++++|++......-...|-+--+.|-+=|++..-
T Consensus        48 a~~y~~i~aFa~s~iG~l~ll~~i~lplWh~~HRihhglHDlkih~   93 (118)
T pfam02313        48 ALSYDRIIAFAQSWIGKLFLLVLIILPLWHAMHRIHHGLHDLKIHR   93 (118)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEC
T ss_conf             2589999999970899999999999999999999998776410121


No 29 
>PRK13603 fumarate reductase subunit C; Provisional
Probab=81.56  E-value=3.8  Score=20.15  Aligned_cols=89  Identities=7%  Similarity=-0.032  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHC---CHHC
Q ss_conf             99999999999999999999999998516303554675306831699999999999999999899--999852---1233
Q gi|254781041|r   25 VSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIR--YLIWDV---SLCL   99 (129)
Q Consensus        25 ~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiR--HL~wD~---g~g~   99 (129)
                      .-.+--.|.+-...+...+.+++.+...|||+++.+.++..+++.-++-.....+-.||.-.=.-  -=.++.   |.-.
T Consensus        21 ~YMlRE~T~vp~vwF~l~L~~Gl~~L~~g~~aw~~fl~flqNPivv~lNiiaL~a~L~Ha~TwF~maPkam~I~vk~e~l  100 (126)
T PRK13603         21 RFMLREISCIFVAWFVLYLMLVLRAVGAGGNSYQRFLDFSANPVVVVLNVVALSFLLLHAVTWFGSAPRAMVIQVRGRRV  100 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf             99997762799999999999999997059889999999971967899999999999998999998663304753658288


Q ss_pred             CHHHHHHHHHHHHH
Q ss_conf             58999999999999
Q gi|254781041|r  100 DKKIATQMAKINII  113 (129)
Q Consensus       100 ~~~~~~~s~~~vl~  113 (129)
                      +.+...+.-|.+.+
T Consensus       101 ~~~~iv~~~wa~t~  114 (126)
T PRK13603        101 PARAVLAGHYAAWL  114 (126)
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             70577888999999


No 30 
>PRK04987 fumarate reductase subunit C; Provisional
Probab=79.56  E-value=4.5  Score=19.77  Aligned_cols=91  Identities=8%  Similarity=0.073  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHH---CCHH
Q ss_conf             99999999999999999999999999851630355467530683169999999999999999989999--985---2123
Q gi|254781041|r   24 FVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYL--IWD---VSLC   98 (129)
Q Consensus        24 ~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL--~wD---~g~g   98 (129)
                      ..-.+.-.|++....+...+.+++.+...|||+++.+..+..+++.-+.-.....+-.||...=..-.  .+.   -|..
T Consensus        23 r~YMlRE~T~v~~~~f~lvLl~Gl~~L~~g~~aw~~fv~flqnPivvilniiaLaa~L~Ha~TwF~~~Pk~m~i~v~~~~  102 (129)
T PRK04987         23 RFYMLREATAVPAVWFSLVLIYGLFALKSGPEAWAGFVSFLQNPVVVILNIITLAAALLHTKTWFEMAPKVMNIIVKDEK  102 (129)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999998579999999999999999806988999999998485999999999999999999999985577546726861


Q ss_pred             CCHHHHHHHHHHHHHH
Q ss_conf             3589999999999999
Q gi|254781041|r   99 LDKKIATQMAKINIIA  114 (129)
Q Consensus        99 ~~~~~~~~s~~~vl~~  114 (129)
                      .+.+...+.-|.+.+.
T Consensus       103 l~~~~i~~~~wa~~~~  118 (129)
T PRK04987        103 MGPEPIIKALWAVTAV  118 (129)
T ss_pred             CCHHHHHHHHHHHHHH
T ss_conf             7849999999999999


No 31 
>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=79.32  E-value=4.6  Score=19.73  Aligned_cols=44  Identities=9%  Similarity=0.172  Sum_probs=40.4

Q ss_pred             CCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             30355467530683169999999999999999989999985212
Q gi|254781041|r   54 EHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSL   97 (129)
Q Consensus        54 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~   97 (129)
                      ..+|+.+..+..++++|++......-...|-+--++|-+=|++.
T Consensus        44 a~sy~~i~aFa~s~iGkl~ll~~i~lplWh~~HRihhglHDlki   87 (115)
T cd00547          44 ALSYDRIIAFAQSWIGKLFLLVLIILPMWHAMHRIHHGLHDLKI   87 (115)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             47999999999608999999999999999999999987665141


No 32 
>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=79.10  E-value=4.6  Score=19.69  Aligned_cols=106  Identities=9%  Similarity=0.070  Sum_probs=71.6

Q ss_pred             CCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             98999773510266659999999999999999999999999998516303554675306831699999999999999999
Q gi|254781041|r    7 NRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLG   86 (129)
Q Consensus         7 ~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~n   86 (129)
                      -||+.|+=-.  -..-=..-.+.-.|.+....+...+.+++.++..|||+++.+..+..+++.-+.-.....+-.||...
T Consensus         8 vR~m~~~WW~--k~~FYr~YMlRE~T~v~~~~f~lvLl~Gl~~L~~G~~aw~~f~~flqnP~vv~lniiaL~a~L~Ha~T   85 (128)
T pfam02300         8 VREMKPTWWK--KLDFYRFYMLREGTAVPTVWFSLVLLYGLFALSQGPEAWNGFVSFLQNPVVVILNIIALAAALLHTKT   85 (128)
T ss_pred             CCCCCCCHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             4889964665--58489999998883799999999999999998068889999999983859999999999999999999


Q ss_pred             HHHHH--HHH---CCHHCCHHHHHHHHHHHHHH
Q ss_conf             89999--985---21233589999999999999
Q gi|254781041|r   87 GIRYL--IWD---VSLCLDKKIATQMAKINIIA  114 (129)
Q Consensus        87 GiRHL--~wD---~g~g~~~~~~~~s~~~vl~~  114 (129)
                      =..-.  .++   -|...+.+...+..|.+.+.
T Consensus        86 wF~~~Pk~m~i~v~g~~l~~~~iv~~~wa~~~~  118 (128)
T pfam02300        86 WFSLAPKAMNIIVKGERLPPEVIVKGLWAATAV  118 (128)
T ss_pred             HHHHCHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             998741641122379038769999999999999


No 33 
>PRK05470 fumarate reductase subunit D; Provisional
Probab=57.16  E-value=14  Score=17.00  Aligned_cols=47  Identities=13%  Similarity=0.149  Sum_probs=41.8

Q ss_pred             HCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             16303554675306831699999999999999999899999852123
Q gi|254781041|r   52 NGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLC   98 (129)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g   98 (129)
                      .+..+|+.+..+..++++|++.+........|-+--+-|-+=|++.-
T Consensus        46 ~~a~~y~~i~aFa~~~iGkl~ll~~i~lplWh~~HRihHglHDlkih   92 (118)
T PRK05470         46 GDALSYERVLAFAQSFIGKLFLLLMIVLPLWHGLHRIHHGMHDLKIH   92 (118)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             76336999999997068999999999999999999999877663000


No 34 
>PRK13867 type IV secretion system chaperone VirE1; Provisional
Probab=35.62  E-value=15  Score=16.97  Aligned_cols=28  Identities=32%  Similarity=0.310  Sum_probs=16.6

Q ss_pred             CCCCCCCCCCCCCEECCCHH--HHHHHHHHHHH
Q ss_conf             20049899977351026665--99999999999
Q gi|254781041|r    3 SIKNNRPLSPHLQIYRLIPT--MFVSIVHRITG   33 (129)
Q Consensus         3 ~m~~~RPlsphL~iyk~~~t--~~~SI~HRitG   33 (129)
                      |.++|||+||-   -|||--  --+|..||--|
T Consensus         7 nankn~pv~~~---e~p~~~h~ee~s~~~~~ng   36 (63)
T PRK13867          7 NANKNRPVSPI---ERPEEIHIEEMSGSHPSNG   36 (63)
T ss_pred             CCCCCCCCCCC---CCHHHHHHHHHCCCCCCCC
T ss_conf             25778765775---4647877988523568898


No 35 
>pfam02941 FeThRed_A Ferredoxin thioredoxin reductase variable alpha chain.
Probab=31.99  E-value=16  Score=16.71  Aligned_cols=11  Identities=36%  Similarity=0.751  Sum_probs=8.9

Q ss_pred             CCCCCCCCCCE
Q ss_conf             49899977351
Q gi|254781041|r    6 NNRPLSPHLQI   16 (129)
Q Consensus         6 ~~RPlsphL~i   16 (129)
                      +.||+||+|.+
T Consensus        41 kGr~ISanlP~   51 (67)
T pfam02941        41 KGRPISANLPF   51 (67)
T ss_pred             CCCEECCCCCE
T ss_conf             69695699879


No 36 
>pfam10573 UPF0561 Uncharacterized protein family UPF0561. This family of proteins has no known function.
Probab=26.11  E-value=34  Score=14.99  Aligned_cols=17  Identities=35%  Similarity=0.585  Sum_probs=14.2

Q ss_pred             CCCCCCCCCCCEECCCH
Q ss_conf             04989997735102666
Q gi|254781041|r    5 KNNRPLSPHLQIYRLIP   21 (129)
Q Consensus         5 ~~~RPlsphL~iyk~~~   21 (129)
                      +.+||--|.+|+|.|+-
T Consensus        58 ~~~r~rkpd~qVY~Pr~   74 (126)
T pfam10573        58 TPRRPRRPDLQVYHPRH   74 (126)
T ss_pred             CCCCCCCCCCEEECCCC
T ss_conf             98888897531544442


No 37 
>TIGR00947 2A73 inorganic carbon transporter; InterPro: IPR006007    One pathway for the assimilation of ammonia and glutamate biosynthesis involves glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate.  2 L-glutamate + NADP+ = L-glutamine + 2-oxoglutarate + NADPH + H+  This family includes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including Escherichia coli.   Many photosynthetic organisms including cyanobacteria can concentrate CO_2/HCO_3^- against a greater than ten-fold concentration gradient. In cyanobacteria, the CO_2 concentrating mechanism involves: CO_2 conversion to HCO_3^- energy-dependent HCO_3^- transport, and  carbonic anhydrase-catalyzed formation of CO_2 from HCO_3^- in the carboxysomes. The gene believed to encode the transporter, possibly a Na^+:HCO_3^- symporter, is designated ictB or ORF467 in Synechococcus sp. strain PCC 7942. The protein is 467 amino acyl residues long and possesses 10 putative transmembrane alpha-helical spanners. .
Probab=23.95  E-value=25  Score=15.74  Aligned_cols=23  Identities=26%  Similarity=0.205  Sum_probs=19.6

Q ss_pred             CEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             51026665999999999999999
Q gi|254781041|r   15 QIYRLIPTMFVSIVHRITGSVVY   37 (129)
Q Consensus        15 ~iyk~~~t~~~SI~HRitGi~l~   37 (129)
                      .-|+||--.-.|.+||.-|-.-+
T Consensus         7 ~~y~PQ~WG~~S~LHRL~G~~~~   29 (467)
T TIGR00947         7 AGYSPQEWGRSSVLHRLVGSLRA   29 (467)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             77787433652046777632788


No 38 
>pfam00584 SecE SecE/Sec61-gamma subunits of protein translocation complex. SecE is part of the SecYEG complex in bacteria which translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha translocates protein from the cytoplasm to the ER. Archaea have a similar complex.
Probab=23.38  E-value=54  Score=13.85  Aligned_cols=41  Identities=12%  Similarity=0.478  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999899999852123358999999999999999999999999752
Q gi|254781041|r   83 HMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWIIKDI  128 (129)
Q Consensus        83 H~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~~~~i~~~  128 (129)
                      ..-+.+|...|-     +.++...+..++++.+++.++++|.+..+
T Consensus         8 ~v~~ElkkV~WP-----tr~e~~~~t~~Vi~~~~i~~~~~~~vD~~   48 (56)
T pfam00584         8 EVKAELKKVVWP-----TRKETLKTTVVVLIFVLVMALFLWLVDLV   48 (56)
T ss_pred             HHHHHHHHCCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999997836598-----97999869999999999999999999999


No 39 
>PRK05740 secE preprotein translocase subunit SecE; Reviewed
Probab=23.25  E-value=55  Score=13.83  Aligned_cols=47  Identities=23%  Similarity=0.432  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999899999852123358999999999999999999999999752
Q gi|254781041|r   77 TWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWIIKDI  128 (129)
Q Consensus        77 ~~~~~yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~~~~~i~~~  128 (129)
                      .+.|.-..-..+|...|-.     .++...+..++++..++.++++|.+-.+
T Consensus        68 ~~~f~~e~~~E~rKVvWPt-----r~Et~~~T~iV~~~vii~~l~lw~~D~~  114 (124)
T PRK05740         68 FFAFAKESRTEVRKVVWPT-----RQETLQTTLIVIAVVIVMALILWGLDSI  114 (124)
T ss_pred             HHHHHHHHHHHHHHCCCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999573998-----6998879999999999999999999999


Done!