Query psy9435
Match_columns 106
No_of_seqs 128 out of 608
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 19:16:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9435.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9435hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0449|consensus 99.8 2.8E-21 6.1E-26 146.7 5.3 67 39-105 34-102 (168)
2 PRK09487 sdhC succinate dehydr 99.8 2.2E-20 4.8E-25 135.2 4.4 57 48-104 3-64 (129)
3 PLN00127 succinate dehydrogena 99.8 2.4E-19 5.3E-24 136.8 4.9 62 43-104 41-112 (178)
4 PLN00130 succinate dehydrogena 99.7 1.6E-17 3.4E-22 129.2 6.1 59 47-105 118-181 (213)
5 TIGR02970 succ_dehyd_cytB succ 99.7 5.5E-17 1.2E-21 114.3 4.9 53 52-104 1-58 (120)
6 cd03499 SQR_TypeC_SdhC Succina 99.7 7.8E-17 1.7E-21 112.2 4.7 51 54-104 1-56 (117)
7 PLN00126 succinate dehydrogena 99.7 7.8E-17 1.7E-21 117.7 4.3 43 44-86 72-114 (129)
8 COG2009 SdhC Succinate dehydro 99.1 2.1E-10 4.5E-15 82.7 4.9 32 52-83 1-32 (132)
9 PLN00131 hypothetical protein; 98.9 5.5E-10 1.2E-14 86.6 3.5 29 50-78 1-29 (218)
10 PF01127 Sdh_cyt: Succinate de 98.9 6.5E-10 1.4E-14 75.7 2.5 55 50-104 1-62 (121)
11 cd03501 SQR_TypeA_SdhC_like Su 95.9 0.01 2.2E-07 39.9 3.3 36 70-105 2-42 (101)
12 TIGR02968 succ_dehyd_anc succi 95.5 0.028 6E-07 38.5 4.3 33 73-105 9-44 (105)
13 cd03494 SQR_TypeC_SdhD Succina 95.0 0.046 1E-06 37.7 4.3 33 73-105 3-38 (99)
14 cd03500 SQR_TypeA_SdhD_like Su 94.3 0.084 1.8E-06 35.9 4.2 33 72-104 5-43 (106)
15 cd03493 SQR_QFR_TM Succinate:q 93.8 0.036 7.7E-07 35.2 1.5 14 73-86 1-14 (98)
16 cd03495 SQR_TypeC_SdhD_like Su 74.4 7.1 0.00015 26.8 4.3 33 73-105 4-39 (100)
17 cd03497 SQR_TypeB_1_TM Succina 71.5 4.3 9.3E-05 31.2 2.9 35 71-105 6-46 (207)
18 cd00581 QFR_TypeB_TM Quinol:fu 63.0 8.4 0.00018 29.7 3.0 33 73-105 3-40 (206)
19 PRK14748 kdpF potassium-transp 61.5 10 0.00022 21.7 2.4 23 76-98 5-29 (29)
20 PRK13554 fumarate reductase cy 57.6 15 0.00032 29.4 3.6 40 66-105 19-63 (241)
21 PRK09488 sdhD succinate dehydr 56.3 25 0.00055 25.0 4.3 33 73-105 17-52 (115)
22 cd03526 SQR_QFR_TypeB_TM Succi 54.2 15 0.00033 28.2 3.1 33 73-105 3-40 (199)
23 cd03498 SQR_TypeB_2_TM Succina 53.8 12 0.00026 28.6 2.5 30 76-105 6-40 (209)
24 PRK13553 fumarate reductase cy 52.8 19 0.00042 29.4 3.6 40 66-105 19-63 (258)
25 PRK14750 kdpF potassium-transp 52.5 19 0.0004 20.7 2.5 23 76-98 5-29 (29)
26 COG2142 SdhD Succinate dehydro 52.1 31 0.00068 24.9 4.2 30 73-102 18-50 (117)
27 TIGR02046 sdhC_b558_fam succin 46.0 24 0.00052 27.3 3.1 34 72-105 6-44 (214)
28 cd03497 SQR_TypeB_1_TM Succina 44.6 26 0.00056 27.0 3.0 23 63-86 85-107 (207)
29 TIGR02115 potass_kdpF K+-trans 41.3 23 0.00049 19.7 1.7 21 79-99 3-25 (26)
30 PF09604 Potass_KdpF: F subuni 38.6 43 0.00092 18.3 2.5 20 79-98 4-25 (25)
31 TIGR02046 sdhC_b558_fam succin 33.3 66 0.0014 24.9 3.7 21 66-86 91-111 (214)
32 PF13172 PepSY_TM_1: PepSY-ass 25.3 1.1E+02 0.0024 16.9 2.9 16 71-86 5-20 (34)
33 PLN02920 pantothenate kinase 1 24.5 32 0.00069 29.8 0.6 30 75-104 188-219 (398)
34 PF13706 PepSY_TM_3: PepSY-ass 24.1 1.2E+02 0.0025 17.3 2.8 16 71-86 4-19 (37)
35 PRK14759 potassium-transportin 22.9 99 0.0021 17.6 2.3 20 79-98 8-29 (29)
36 PF03554 Herpes_UL73: UL73 vir 21.6 1.3E+02 0.0028 20.6 3.1 28 59-86 37-64 (82)
No 1
>KOG0449|consensus
Probab=99.83 E-value=2.8e-21 Score=146.68 Aligned_cols=67 Identities=43% Similarity=0.606 Sum_probs=60.0
Q ss_pred CCCccchhhhhhccCCCCCCCccccccchhhHHHHHHHHHHHHHHHHH--HHHHHhcCCCCHHHHhhhc
Q psy9435 39 VPSKEGHAVRNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYA--LGLAGVGLTTDINSVVPTY 105 (106)
Q Consensus 39 ~~~~~~~~~~~~r~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~~~--~~l~sl~~p~~f~~~~~~~ 105 (106)
++.++.++++|+|++||+||||+||+||+||++||+|||||++|++++ +|...+...++++.+++.+
T Consensus 34 ~~~~e~~~~~~~r~~RPlSPHLTIYqpQLt~~LS~~hRiSG~~la~gv~~~G~~~l~~~g~~~~~v~~~ 102 (168)
T KOG0449|consen 34 TEIKERQLLKNQRSNRPLSPHLTIYQPQLTWMLSIFHRISGVVLAGGVWLVGVSGLLGMGDITATVSKV 102 (168)
T ss_pred cccchHHHhhhhhcCCCCCCceeeechhHHHHHHHHHhhhhheehhhHHHHHHHHHhcCcchHHHHHHH
Confidence 566777899999999999999999999999999999999999999987 5556888899999988754
No 2
>PRK09487 sdhC succinate dehydrogenase cytochrome b556 large membrane subunit; Provisional
Probab=99.81 E-value=2.2e-20 Score=135.21 Aligned_cols=57 Identities=25% Similarity=0.326 Sum_probs=49.6
Q ss_pred hhhccCCCCCCCccccccchhhHHHHHHHHHHHHHHHHH----HHHH-HhcCCCCHHHHhhh
Q psy9435 48 RNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYA----LGLA-GVGLTTDINSVVPT 104 (106)
Q Consensus 48 ~~~r~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~~~----~~l~-sl~~p~~f~~~~~~ 104 (106)
+|++++||+||||+|||+|+||++||+||+||++|++++ |++. ++.+||+|+.+.+.
T Consensus 3 ~~~~~~RPlsphL~iyr~~~t~~~SIlHRiSGv~L~~~~~~~~~~l~~~~~~p~~f~~~~~~ 64 (129)
T PRK09487 3 RNVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQAAAI 64 (129)
T ss_pred ccccCCCCCCCCcceeccchhHHHHHHHHhHhHHHHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence 456678999999999999999999999999999998876 5554 67789999998764
No 3
>PLN00127 succinate dehydrogenase (ubiquinone) cytochrome b subunit; Provisional
Probab=99.77 E-value=2.4e-19 Score=136.78 Aligned_cols=62 Identities=35% Similarity=0.402 Sum_probs=53.6
Q ss_pred cchhhhhhccCCCCCCCc-------cccccchhhHHHHHHHHHHHHHHHHH--HH-HHHhcCCCCHHHHhhh
Q psy9435 43 EGHAVRNERLGRPLSPHL-------TIYKLQITSVLSITHRGTGVALTAYA--LG-LAGVGLTTDINSVVPT 104 (106)
Q Consensus 43 ~~~~~~~~r~~RPvSPhL-------~iYr~~lt~i~SIlHRiTGv~L~~~~--~~-l~sl~~p~~f~~~~~~ 104 (106)
++++.++++++||+|||| +|||||+||++||+|||||++|++++ ++ +..+.+||+|+.+.+.
T Consensus 41 ~~~~~~~~~~~RPlSPHL~~~~~~~tiYk~pltai~SIlHRITGv~L~~g~~~~~l~~l~~~~e~f~~~~~~ 112 (178)
T PLN00127 41 TPKNHRMLLEKRPLSPDVMDIDGKSTHYKFPVVALSSITNRVTGCVLSGGAAGGGVLALVGGSEAVPATMEG 112 (178)
T ss_pred CChhhHHHhcCCCCCcccccccCCCcEEeccchhhhhHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHH
Confidence 468899999999999999 99999999999999999999999988 33 3455679999887653
No 4
>PLN00130 succinate dehydrogenase (SDH3); Provisional
Probab=99.70 E-value=1.6e-17 Score=129.24 Aligned_cols=59 Identities=34% Similarity=0.353 Sum_probs=50.5
Q ss_pred hhhhccCCCCCCCccccccchhhHHHHHHHHHHHHHHHHH--HHHHHh---cCCCCHHHHhhhc
Q psy9435 47 VRNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYA--LGLAGV---GLTTDINSVVPTY 105 (106)
Q Consensus 47 ~~~~r~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~~~--~~l~sl---~~p~~f~~~~~~~ 105 (106)
+.+.|.+||+||||+|||||+||++||+|||||++|++++ ++++.+ ..+-+|+.|.+++
T Consensus 118 ~~~~RlnRPlSPHLqIYrpQLTs~lSI~HRITGvaLsg~ly~f~la~lK~G~i~~t~~~FyQf~ 181 (213)
T PLN00130 118 EPKIKSFRPLSPHLSVYQPQMNSMLSIFNRISGVYLTGVTFAGYLLYLKMGMICLTYPSFYQVL 181 (213)
T ss_pred hhhccCCCCCCCccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHhccccccchhHHHHH
Confidence 7778999999999999999999999999999999999998 555666 4466777776654
No 5
>TIGR02970 succ_dehyd_cytB succinate dehydrogenase, cytochrome b556 subunit. 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 family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) 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 TIGR02046).
Probab=99.67 E-value=5.5e-17 Score=114.35 Aligned_cols=53 Identities=42% Similarity=0.533 Sum_probs=45.2
Q ss_pred cCCCCCCCccccccchhhHHHHHHHHHHHHHHHHH----HHHH-HhcCCCCHHHHhhh
Q psy9435 52 LGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYA----LGLA-GVGLTTDINSVVPT 104 (106)
Q Consensus 52 ~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~~~----~~l~-sl~~p~~f~~~~~~ 104 (106)
++||+||||++||+|+++++||+|||||++|++++ +++. ...+|++|+.+.+.
T Consensus 1 ~~RP~sphl~~yr~~~~~~~silhRiTGv~l~~~~~~~~~~l~~~~~~~~~~~~~~~~ 58 (120)
T TIGR02970 1 KQRPLSPHLQIYRFPITAILSILHRITGVLLFFGLPFLLWWLSLSLSSPESFATVHAL 58 (120)
T ss_pred CCCCCCCCcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 46999999999999999999999999999999876 4343 45678999887664
No 6
>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=99.66 E-value=7.8e-17 Score=112.19 Aligned_cols=51 Identities=49% Similarity=0.613 Sum_probs=44.2
Q ss_pred CCCCCCccccccchhhHHHHHHHHHHHHHHHHH----HHH-HHhcCCCCHHHHhhh
Q psy9435 54 RPLSPHLTIYKLQITSVLSITHRGTGVALTAYA----LGL-AGVGLTTDINSVVPT 104 (106)
Q Consensus 54 RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~~~----~~l-~sl~~p~~f~~~~~~ 104 (106)
||+|||+++||||++|++||+||+||++|++++ +++ .+..+|++|+.+.+.
T Consensus 1 rP~sphl~iY~~~~~~~~Si~hRiSGv~L~~~~~~~~~~~~~~~~~~~~y~~~~~~ 56 (117)
T cd03499 1 RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLLWWLLASLSSPESFESVSAL 56 (117)
T ss_pred CCCCCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 899999999999999999999999999999988 333 345579999988764
No 7
>PLN00126 succinate dehydrogenase, cytochrome b subunit family; Provisional
Probab=99.66 E-value=7.8e-17 Score=117.70 Aligned_cols=43 Identities=40% Similarity=0.546 Sum_probs=40.2
Q ss_pred chhhhhhccCCCCCCCccccccchhhHHHHHHHHHHHHHHHHH
Q psy9435 44 GHAVRNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYA 86 (106)
Q Consensus 44 ~~~~~~~r~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~~~ 86 (106)
+....++|++||+||||+|||||+||++||+|||||++|++++
T Consensus 72 s~~L~~qRlnRPLSPHLqIYRpQLT~~lSI~HRITGvaLs~~i 114 (129)
T PLN00126 72 SRPLSAPVANRPLSPHLPLKKPQLSATFSISHRIFGAALGAAI 114 (129)
T ss_pred ccccchhhcCCCCCCccccccccchhhhhHHHHHHHHHHHHHH
Confidence 3567889999999999999999999999999999999999887
No 8
>COG2009 SdhC Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion]
Probab=99.06 E-value=2.1e-10 Score=82.72 Aligned_cols=32 Identities=53% Similarity=0.748 Sum_probs=30.4
Q ss_pred cCCCCCCCccccccchhhHHHHHHHHHHHHHH
Q psy9435 52 LGRPLSPHLTIYKLQITSVLSITHRGTGVALT 83 (106)
Q Consensus 52 ~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~ 83 (106)
.+||++||+++||+++++.+||+||+||+++.
T Consensus 1 ~~r~~~~~l~~~~~~~~~~~silHRitGv~l~ 32 (132)
T COG2009 1 RKRPVSPHLQIYRPPITMYASILHRISGVILA 32 (132)
T ss_pred CCCCCCCccceeecchHHHHHHHHHhHHHHHH
Confidence 36999999999999999999999999999995
No 9
>PLN00131 hypothetical protein; Provisional
Probab=98.95 E-value=5.5e-10 Score=86.63 Aligned_cols=29 Identities=52% Similarity=0.707 Sum_probs=27.2
Q ss_pred hccCCCCCCCccccccchhhHHHHHHHHH
Q psy9435 50 ERLGRPLSPHLTIYKLQITSVLSITHRGT 78 (106)
Q Consensus 50 ~r~~RPvSPhL~iYr~~lt~i~SIlHRiT 78 (106)
|+.+||+||||+||++|+||++||+|||-
T Consensus 1 m~inRPvSPHL~IYkPQlTw~~Si~hRif 29 (218)
T PLN00131 1 MHILRPLSPHLPIYKPQLTSAFPIFRRCF 29 (218)
T ss_pred CCCCCCCCCCccccchhhhhhHHHHHHHH
Confidence 46789999999999999999999999986
No 10
>PF01127 Sdh_cyt: Succinate dehydrogenase/Fumarate reductase transmembrane subunit; InterPro: IPR000701 This entry includes the transmembrane subunit from both succinate dehydrogenase and fumarate reductase complexes. Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalysed by the related complex II of the respiratory chain (succinate dehydrogenase) []. Three protein subunits contain the fumarate reductase complex. Subunit A contains the site of fumarate reduction and a covalently bound flavin adenine dinucleotide prosthetic group. Subunit B contains three iron-sulphur centres. The menaquinol-oxidizing subunit C consists of five membrane-spanning, primarily helical segments and binds two haem b molecules []. Succinate dehydrogenase (SDH) is a membrane-bound complex of two main components: a membrane-extrinsic component composed of an FAD-binding flavoprotein and an iron-sulphur protein, and a hydrophobic component composed of a cytochrome b and a membrane anchor protein. The cytochrome b component is a mono-haem transmembrane protein [, , ] belonging to a family that includes: Cytochrome b-556 from bacterial SDH (gene sdhC). Cytochrome b560 from the mammalian mitochondrial SDH complex, which is encoded in the mitochondrial genome of some algae and in the plant Marchantia polymorpha. Cytochrome b from yeast mitochondrial SDH complex (gene SDH3 or CYB3). Protein cyt-1 from Caenorhabditis elegans. These cytochromes are proteins of about 130 residues that comprise three transmembrane regions. There are two conserved histidines which may be involved in binding the haem group.; GO: 0016627 oxidoreductase activity, acting on the CH-CH group of donors; PDB: 2WDQ_H 1NEN_D 2WP9_L 2WDV_H 2ACZ_D 2WS3_L 2WU2_H 2WDR_D 2WU5_H 1NEK_D ....
Probab=98.91 E-value=6.5e-10 Score=75.73 Aligned_cols=55 Identities=31% Similarity=0.315 Sum_probs=38.7
Q ss_pred hccCCCCCCCccccccchhhHHHHHHHHHHHHHHH-HH----HHHH--HhcCCCCHHHHhhh
Q psy9435 50 ERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTA-YA----LGLA--GVGLTTDINSVVPT 104 (106)
Q Consensus 50 ~r~~RPvSPhL~iYr~~lt~i~SIlHRiTGv~L~~-~~----~~l~--sl~~p~~f~~~~~~ 104 (106)
||.+||++||.++||++..+..+++||+||++|.+ .+ +.+. ....+++|+.+.+.
T Consensus 1 ~~~~r~~~p~~~~~~~~~~~~~~~~qRiTgi~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (121)
T PF01127_consen 1 MRSNRPRSPHRGIYRFHSGTWAWILQRITGIILLLLFLHLHIWFLLSALGGGPISYDEVVAF 62 (121)
T ss_dssp --ST--BHHCTTTST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHHHHHHHHH
T ss_pred CCCCCCCCcccceecCCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCHhhHHHHHHH
Confidence 68899999999999999999999999999999998 33 1122 23457788887654
No 11
>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=95.86 E-value=0.01 Score=39.87 Aligned_cols=36 Identities=33% Similarity=0.353 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHH----HHHH-HhcCCCCHHHHhhhc
Q psy9435 70 VLSITHRGTGVALTAYA----LGLA-GVGLTTDINSVVPTY 105 (106)
Q Consensus 70 i~SIlHRiTGv~L~~~~----~~l~-sl~~p~~f~~~~~~~ 105 (106)
.+-++||+||+++.+.+ +.+. ...++++|+.+.+.+
T Consensus 2 ~~~~lhRitGi~L~~fl~~hl~~~~~~~~~~~~y~~~~~~~ 42 (101)
T cd03501 2 WAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATY 42 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 35689999999998876 3333 344688888886643
No 12
>TIGR02968 succ_dehyd_anc succinate dehydrogenase, hydrophobic membrane anchor protein. 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 family is the SdhD, the hydrophobic membrane anchor protein. SdhC is apocytochrome b558, which also plays a role in anchoring the complex.
Probab=95.47 E-value=0.028 Score=38.53 Aligned_cols=33 Identities=15% Similarity=0.110 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHH-HHHH--HhcCCCCHHHHhhhc
Q psy9435 73 ITHRGTGVALTAYA-LGLA--GVGLTTDINSVVPTY 105 (106)
Q Consensus 73 IlHRiTGv~L~~~~-~~l~--sl~~p~~f~~~~~~~ 105 (106)
++||+||++|...+ |++. ....+++|+.+.+.+
T Consensus 9 ~~~RiSgv~L~~l~~~~~~~~~~~~~~~y~~~~~~~ 44 (105)
T TIGR02968 9 LLQRVTAVVLALYTIFLIGFLLALPGLTYEAWRALF 44 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 57999999998877 4443 333466898887643
No 13
>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=95.02 E-value=0.046 Score=37.74 Aligned_cols=33 Identities=12% Similarity=0.143 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHH-HHHH--HhcCCCCHHHHhhhc
Q psy9435 73 ITHRGTGVALTAYA-LGLA--GVGLTTDINSVVPTY 105 (106)
Q Consensus 73 IlHRiTGv~L~~~~-~~l~--sl~~p~~f~~~~~~~ 105 (106)
++||+||++|...+ +.+. ...+++||+...+.+
T Consensus 3 ~~qRiSav~L~~l~~~~v~~~~~~~~~~y~~~~~~~ 38 (99)
T cd03494 3 LVQRVTAVIMALYTIFLVGFLLASPPLTYEAWSGLF 38 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 47999999999887 3332 344689999988754
No 14
>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=94.35 E-value=0.084 Score=35.88 Aligned_cols=33 Identities=24% Similarity=0.064 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHH-HHH---HH-h-cCCCCHHHHhhh
Q psy9435 72 SITHRGTGVALTAYA-LGL---AG-V-GLTTDINSVVPT 104 (106)
Q Consensus 72 SIlHRiTGv~L~~~~-~~l---~s-l-~~p~~f~~~~~~ 104 (106)
=++||+||++|.+.+ +-+ .. . ..+++|+...+.
T Consensus 5 w~~qRiTgv~L~~~l~~hi~~~~~~~~~~~~~~~~~~~~ 43 (106)
T cd03500 5 WLFQRITGVFLVFLLAGHFWVQHMDNGGDVIDFAFVANR 43 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCccCHHHHHHH
Confidence 378999999999887 222 22 2 268899987764
No 15
>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=93.82 E-value=0.036 Score=35.24 Aligned_cols=14 Identities=57% Similarity=0.695 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHH
Q psy9435 73 ITHRGTGVALTAYA 86 (106)
Q Consensus 73 IlHRiTGv~L~~~~ 86 (106)
++||+||++|.+.+
T Consensus 1 ~~~Ritgv~l~~~~ 14 (98)
T cd03493 1 ILHRITGVALLLFL 14 (98)
T ss_pred CeehhhHHHHHHHH
Confidence 47999999999887
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=74.41 E-value=7.1 Score=26.80 Aligned_cols=33 Identities=27% Similarity=0.148 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHH-HHHHHh--cCCCCHHHHhhhc
Q psy9435 73 ITHRGTGVALTAYA-LGLAGV--GLTTDINSVVPTY 105 (106)
Q Consensus 73 IlHRiTGv~L~~~~-~~l~sl--~~p~~f~~~~~~~ 105 (106)
+.+|+||++|.... |.+..+ ..+.||++..+.+
T Consensus 4 ~~qRvTav~L~~l~~~~v~~~~~~~~~~y~~~~~~~ 39 (100)
T cd03495 4 WAQRVTAVALVPLVLWFVFSVALLLGASYAEVVAWL 39 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 36899999999877 433322 3467888877653
No 17
>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=71.47 E-value=4.3 Score=31.25 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=26.6
Q ss_pred HHHHHHHHHHH-HHHHH----HH-HHHhcCCCCHHHHhhhc
Q psy9435 71 LSITHRGTGVA-LTAYA----LG-LAGVGLTTDINSVVPTY 105 (106)
Q Consensus 71 ~SIlHRiTGv~-L~~~~----~~-l~sl~~p~~f~~~~~~~ 105 (106)
..-+|-+||++ |.+.+ .+ +..+.+||.|++|.+.+
T Consensus 6 ~~~~~slTGl~pL~lFl~~Hl~gN~~i~~g~~afn~ya~~l 46 (207)
T cd03497 6 IRRLHSLLGVVPIGLFLIEHLLTNSSAASGPEGFNAAVNFM 46 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 45689999999 88776 22 34667899999998753
No 18
>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=63.01 E-value=8.4 Score=29.73 Aligned_cols=33 Identities=15% Similarity=0.072 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHH----HH-HHHhcCCCCHHHHhhhc
Q psy9435 73 ITHRGTGVALTAYA----LG-LAGVGLTTDINSVVPTY 105 (106)
Q Consensus 73 IlHRiTGv~L~~~~----~~-l~sl~~p~~f~~~~~~~ 105 (106)
.+|=+||++|.+.+ .+ +..+.+||.|++|.+.+
T Consensus 3 ~~~slTGliL~lFl~~Hm~gNl~i~~G~eafn~ya~~L 40 (206)
T cd00581 3 FLQSATGLFLALFMWAHMLFVSSILLGKEAMYWVARFF 40 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 47889999988776 22 34777899999997643
No 19
>PRK14748 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=61.53 E-value=10 Score=21.72 Aligned_cols=23 Identities=17% Similarity=-0.048 Sum_probs=16.9
Q ss_pred HHHHHHHHHHH--HHHHHhcCCCCH
Q psy9435 76 RGTGVALTAYA--LGLAGVGLTTDI 98 (106)
Q Consensus 76 RiTGv~L~~~~--~~l~sl~~p~~f 98 (106)
-|+|+++.+.+ +...+|.-+|.|
T Consensus 5 vi~G~ilv~lLlgYLvyALi~aE~F 29 (29)
T PRK14748 5 VITGVLLVFLLLGYLVYALINAEAF 29 (29)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcccC
Confidence 37888888776 555678878776
No 20
>PRK13554 fumarate reductase cytochrome b-556 subunit; Provisional
Probab=57.63 E-value=15 Score=29.41 Aligned_cols=40 Identities=13% Similarity=-0.006 Sum_probs=30.9
Q ss_pred chhhHHHHHHHHHHHHHHHHH----HH-HHHhcCCCCHHHHhhhc
Q psy9435 66 QITSVLSITHRGTGVALTAYA----LG-LAGVGLTTDINSVVPTY 105 (106)
Q Consensus 66 ~lt~i~SIlHRiTGv~L~~~~----~~-l~sl~~p~~f~~~~~~~ 105 (106)
+.++.+--+|=+||++|.+.+ ++ +..+.+||.|+.+.+.+
T Consensus 19 ~~~a~~d~lmslTGl~L~lFL~~Hm~~N~sil~G~eafN~~a~fl 63 (241)
T PRK13554 19 PWSAKADKLQSATGIMLGCFLLLHMHFESSILLGKEAFYHVVQFL 63 (241)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 456888889999999988776 22 24777899999987754
No 21
>PRK09488 sdhD succinate dehydrogenase cytochrome b556 small membrane subunit; Provisional
Probab=56.29 E-value=25 Score=25.01 Aligned_cols=33 Identities=18% Similarity=0.089 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHH-HHHHHh--cCCCCHHHHhhhc
Q psy9435 73 ITHRGTGVALTAYA-LGLAGV--GLTTDINSVVPTY 105 (106)
Q Consensus 73 IlHRiTGv~L~~~~-~~l~sl--~~p~~f~~~~~~~ 105 (106)
+.+|+|+++|.... |.+..+ ..+.||+...+.|
T Consensus 17 ~~QRvTAv~l~~l~~~~v~~~~~~~g~~y~~~~~~f 52 (115)
T PRK09488 17 ILVRATAIVLTLYIIYMVGFFATSGELTYEVWRGFF 52 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 45899999998877 444322 2356888877654
No 22
>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=54.19 E-value=15 Score=28.16 Aligned_cols=33 Identities=15% Similarity=0.059 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHH----HH-HHHhcCCCCHHHHhhhc
Q psy9435 73 ITHRGTGVALTAYA----LG-LAGVGLTTDINSVVPTY 105 (106)
Q Consensus 73 IlHRiTGv~L~~~~----~~-l~sl~~p~~f~~~~~~~ 105 (106)
.+|=+||++|.+.+ ++ +..+.+||.|++|.+.+
T Consensus 3 ~lmalTGl~L~lFl~~Hm~gNl~i~~g~~afn~ya~~l 40 (199)
T cd03526 3 WLQSATGLFLGLFMIGHLFFNSTILLGDNVMNWVAKKF 40 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 46778999988776 22 34667899999987753
No 23
>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=53.80 E-value=12 Score=28.57 Aligned_cols=30 Identities=23% Similarity=0.140 Sum_probs=22.5
Q ss_pred HHHHHHHHHHH----HH-HHHhcCCCCHHHHhhhc
Q psy9435 76 RGTGVALTAYA----LG-LAGVGLTTDINSVVPTY 105 (106)
Q Consensus 76 RiTGv~L~~~~----~~-l~sl~~p~~f~~~~~~~ 105 (106)
=+||.+|.+.+ ++ +..+.+||.|++|.+.+
T Consensus 6 a~TGl~L~lFl~~Hm~gNl~i~~g~~afn~ya~~l 40 (209)
T cd03498 6 ALTGLFLVLFLLVHLLGNLKIFFGPEAFNAYAEFL 40 (209)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 36999998776 22 34777899999998754
No 24
>PRK13553 fumarate reductase cytochrome b-556 subunit; Provisional
Probab=52.78 E-value=19 Score=29.42 Aligned_cols=40 Identities=15% Similarity=0.193 Sum_probs=30.9
Q ss_pred chhhHHHHHHHHHHHHHHHHH---HHH--HHhcCCCCHHHHhhhc
Q psy9435 66 QITSVLSITHRGTGVALTAYA---LGL--AGVGLTTDINSVVPTY 105 (106)
Q Consensus 66 ~lt~i~SIlHRiTGv~L~~~~---~~l--~sl~~p~~f~~~~~~~ 105 (106)
..++.+-.+|=+||++|++.+ ..+ ..+.+||.|+...+++
T Consensus 19 r~~a~lD~~qSltGviLglFl~~Hm~~~ssil~G~~afn~va~f~ 63 (258)
T PRK13553 19 RIPAKLDFLQSATGLFLGLFMWAHMFFVSTILISDDAMYKVAKFF 63 (258)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHH
Confidence 456888889999999988877 223 3777899999877654
No 25
>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=52.46 E-value=19 Score=20.66 Aligned_cols=23 Identities=13% Similarity=-0.050 Sum_probs=16.2
Q ss_pred HHHHHHHHHHH--HHHHHhcCCCCH
Q psy9435 76 RGTGVALTAYA--LGLAGVGLTTDI 98 (106)
Q Consensus 76 RiTGv~L~~~~--~~l~sl~~p~~f 98 (106)
=|+|+++.+.+ +.+.++.-+|+|
T Consensus 5 vi~g~llv~lLl~YLvYAL~naE~F 29 (29)
T PRK14750 5 IVCGALLVLLLLGYLVYALFNAEDF 29 (29)
T ss_pred HHHHHHHHHHHHHHHHHHHcCcccC
Confidence 36788887766 555678777765
No 26
>COG2142 SdhD Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion]
Probab=52.12 E-value=31 Score=24.90 Aligned_cols=30 Identities=20% Similarity=0.112 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHH-HHHH-HhcC-CCCHHHHh
Q psy9435 73 ITHRGTGVALTAYA-LGLA-GVGL-TTDINSVV 102 (106)
Q Consensus 73 IlHRiTGv~L~~~~-~~l~-sl~~-p~~f~~~~ 102 (106)
++.|+||++|.+.. |.++ .+.. ..+|+...
T Consensus 18 l~qRvTav~Lv~l~~~~l~~~l~~~~~~y~~~~ 50 (117)
T COG2142 18 LLQRVTAVILVLLVIWHLYFLLTWLNATYAAWV 50 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 67999999999887 4444 2222 55555544
No 27
>TIGR02046 sdhC_b558_fam succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family. This family consists of the succinate dehydrogenase subunit C of Bacillus subtilis, designated cytochrome b-558, and related sequences that include a fumarate reductase subunit C. This subfamily is only weakly similar to the main group of succinate dehydrogenase cytochrome b subunits described by Pfam model pfam01127.
Probab=46.02 E-value=24 Score=27.29 Aligned_cols=34 Identities=18% Similarity=0.189 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHH----HH-HHHhcCCCCHHHHhhhc
Q psy9435 72 SITHRGTGVALTAYA----LG-LAGVGLTTDINSVVPTY 105 (106)
Q Consensus 72 SIlHRiTGv~L~~~~----~~-l~sl~~p~~f~~~~~~~ 105 (106)
-++|=+||+++.+.+ .+ +..+.+||.|+.|.+.+
T Consensus 6 K~lmalTGl~l~~Fl~~Hm~gNl~~~~g~~afn~ya~~L 44 (214)
T TIGR02046 6 KVVMALTGLVLLLFLVVHMVGNLFALFGAEAFNAAAHFL 44 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 356778999998766 22 34677899999997753
No 28
>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=44.64 E-value=26 Score=26.96 Aligned_cols=23 Identities=22% Similarity=0.330 Sum_probs=18.2
Q ss_pred cccchhhHHHHHHHHHHHHHHHHH
Q psy9435 63 YKLQITSVLSITHRGTGVALTAYA 86 (106)
Q Consensus 63 Yr~~lt~i~SIlHRiTGv~L~~~~ 86 (106)
|+.. ....|-++|+||+++.+.+
T Consensus 85 y~~~-~~~a~~~mritG~ill~Fl 107 (207)
T cd03497 85 YDYF-RNWMYTLQRITGIILLVFI 107 (207)
T ss_pred Cccc-chHHHHHHHHHHHHHHHHH
Confidence 4433 4578999999999998877
No 29
>TIGR02115 potass_kdpF K+-transporting ATPase, KdpF subunit. This model describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (TIGR00680). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.
Probab=41.34 E-value=23 Score=19.70 Aligned_cols=21 Identities=5% Similarity=-0.179 Sum_probs=15.0
Q ss_pred HHHHHHHH--HHHHHhcCCCCHH
Q psy9435 79 GVALTAYA--LGLAGVGLTTDIN 99 (106)
Q Consensus 79 Gv~L~~~~--~~l~sl~~p~~f~ 99 (106)
|.++++++ +.+.++.-||.|.
T Consensus 3 ~~~l~~~L~~YL~~aLl~PErF~ 25 (26)
T TIGR02115 3 LLVLAVGLFIYLFYALLRPERFX 25 (26)
T ss_pred HHHHHHHHHHHHHHHHhCHHhcC
Confidence 55565555 6677888899885
No 30
>PF09604 Potass_KdpF: F subunit of K+-transporting ATPase (Potass_KdpF); InterPro: IPR011726 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the F subunit (KdpF) of a P-type K+-translocating ATPase (Kdp). KdpF is a very small integral membrane peptide. The kdpABC operon of Escherichia coli codes for the high affinity K+-translocating Kdp complex []. KdpF is found upstream of the KdpA subunit (IPR004623 from INTERPRO). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. More information about this protein can be found at Protein of the Month: ATP Synthases [].
Probab=38.63 E-value=43 Score=18.33 Aligned_cols=20 Identities=5% Similarity=-0.107 Sum_probs=12.8
Q ss_pred HHHHHHHH--HHHHHhcCCCCH
Q psy9435 79 GVALTAYA--LGLAGVGLTTDI 98 (106)
Q Consensus 79 Gv~L~~~~--~~l~sl~~p~~f 98 (106)
|.++++++ +.+.++.-||.|
T Consensus 4 ~~~v~~~L~~YL~~aLl~PErF 25 (25)
T PF09604_consen 4 GGIVAVALFVYLFYALLRPERF 25 (25)
T ss_pred HHHHHHHHHHHHHHHHhCcccC
Confidence 34444444 666788889876
No 31
>TIGR02046 sdhC_b558_fam succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family. This family consists of the succinate dehydrogenase subunit C of Bacillus subtilis, designated cytochrome b-558, and related sequences that include a fumarate reductase subunit C. This subfamily is only weakly similar to the main group of succinate dehydrogenase cytochrome b subunits described by Pfam model pfam01127.
Probab=33.27 E-value=66 Score=24.88 Aligned_cols=21 Identities=29% Similarity=0.184 Sum_probs=17.5
Q ss_pred chhhHHHHHHHHHHHHHHHHH
Q psy9435 66 QITSVLSITHRGTGVALTAYA 86 (106)
Q Consensus 66 ~lt~i~SIlHRiTGv~L~~~~ 86 (106)
+-....|-+.|+||+++.+.+
T Consensus 91 ~~~t~a~~~m~~tG~ill~Fi 111 (214)
T TIGR02046 91 PGVSWASRTMRVTGIIVLIFI 111 (214)
T ss_pred CcccHHHHHHHHHHHHHHHHH
Confidence 445688999999999998776
No 32
>PF13172 PepSY_TM_1: PepSY-associated TM helix
Probab=25.34 E-value=1.1e+02 Score=16.87 Aligned_cols=16 Identities=19% Similarity=0.250 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHH
Q psy9435 71 LSITHRGTGVALTAYA 86 (106)
Q Consensus 71 ~SIlHRiTGv~L~~~~ 86 (106)
..-+||..|+..++.+
T Consensus 5 ~~~~H~~~g~~~~~~l 20 (34)
T PF13172_consen 5 WRKIHRWLGLIAAIFL 20 (34)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3457999999988876
No 33
>PLN02920 pantothenate kinase 1
Probab=24.46 E-value=32 Score=29.79 Aligned_cols=30 Identities=13% Similarity=0.210 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHH-HHHH-HhcCCCCHHHHhhh
Q psy9435 75 HRGTGVALTAYA-LGLA-GVGLTTDINSVVPT 104 (106)
Q Consensus 75 HRiTGv~L~~~~-~~l~-sl~~p~~f~~~~~~ 104 (106)
.||+|..++++. |+|+ -|....+|++++++
T Consensus 188 ~RVgGTsIGGGT~~GL~~LLtg~~sfdEll~l 219 (398)
T PLN02920 188 ERVSGTSVGGGTFWGLGKLLTKCKSFDELLEL 219 (398)
T ss_pred EEEcccccchHhHHHHHHHHcCCCCHHHHHHH
Confidence 699999999988 9997 55568999998764
No 34
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=24.09 E-value=1.2e+02 Score=17.29 Aligned_cols=16 Identities=31% Similarity=0.291 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHH
Q psy9435 71 LSITHRGTGVALTAYA 86 (106)
Q Consensus 71 ~SIlHRiTGv~L~~~~ 86 (106)
+-.+||-.|++.++.+
T Consensus 4 ~~~~H~W~Gl~~g~~l 19 (37)
T PF13706_consen 4 LRKLHRWLGLILGLLL 19 (37)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3467999999998876
No 35
>PRK14759 potassium-transporting ATPase subunit F; Provisional
Probab=22.86 E-value=99 Score=17.63 Aligned_cols=20 Identities=5% Similarity=-0.247 Sum_probs=12.8
Q ss_pred HHHHHHHH--HHHHHhcCCCCH
Q psy9435 79 GVALTAYA--LGLAGVGLTTDI 98 (106)
Q Consensus 79 Gv~L~~~~--~~l~sl~~p~~f 98 (106)
|.+.++++ +.+.++.-||.|
T Consensus 8 ~~~va~~L~vYL~~ALlrPErF 29 (29)
T PRK14759 8 AGAVSLGLLIYLTYALLRPERF 29 (29)
T ss_pred HHHHHHHHHHHHHHHHhCcccC
Confidence 44444444 666788888876
No 36
>PF03554 Herpes_UL73: UL73 viral envelope glycoprotein ; InterPro: IPR005211 This entry represents a conserved region found in a number of viral proteins: BLRF1, U46, 53, and UL73, collectively known as glycoprotein N. These UL73-like envelope glycoproteins, which associate in a high molecular mass complex with their counterpart protein gM, induce neutralizing antibody responses in the host. These glycoproteins are highly polymorphic, particularly in the N-terminal region [].; GO: 0019031 viral envelope
Probab=21.60 E-value=1.3e+02 Score=20.61 Aligned_cols=28 Identities=21% Similarity=0.037 Sum_probs=24.8
Q ss_pred CccccccchhhHHHHHHHHHHHHHHHHH
Q psy9435 59 HLTIYKLQITSVLSITHRGTGVALTAYA 86 (106)
Q Consensus 59 hL~iYr~~lt~i~SIlHRiTGv~L~~~~ 86 (106)
|=..|++.+.+..|||.=+-++++.++.
T Consensus 37 ~adtY~~sl~SFsSIW~iiN~~il~~A~ 64 (82)
T PF03554_consen 37 SADTYEPSLSSFSSIWAIINVVILLCAF 64 (82)
T ss_pred ccCEeeeeehHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999887765
Done!