Query 028579
Match_columns 207
No_of_seqs 67 out of 69
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 13:43:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028579.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028579hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07298 NnrU: NnrU protein; 97.7 3.9E-05 8.5E-10 63.4 3.6 53 146-198 1-55 (191)
2 cd03500 SQR_TypeA_SdhD_like Su 89.1 3.8 8.3E-05 30.0 7.9 93 98-196 8-100 (106)
3 PF10242 L_HGMIC_fpl: Lipoma H 66.2 6.7 0.00015 31.9 3.1 32 83-115 137-168 (181)
4 TIGR02968 succ_dehyd_anc succi 61.4 26 0.00057 25.8 5.2 70 127-197 32-101 (105)
5 PRK13628 serine/threonine tran 56.5 47 0.001 30.5 7.0 58 98-167 14-74 (402)
6 COG4094 Predicted membrane pro 55.4 7.4 0.00016 34.6 1.7 18 145-162 2-19 (219)
7 TIGR01583 formate-DH-gamm form 54.0 33 0.00071 27.9 5.1 67 93-164 104-171 (204)
8 PF11446 DUF2897: Protein of u 52.9 8.2 0.00018 27.3 1.3 27 146-172 5-31 (55)
9 PF01127 Sdh_cyt: Succinate de 51.7 50 0.0011 23.7 5.2 49 124-174 48-96 (121)
10 PRK10179 formate dehydrogenase 51.3 19 0.00041 30.0 3.4 67 91-163 107-174 (217)
11 cd03494 SQR_TypeC_SdhD Succina 49.3 1.1E+02 0.0024 22.9 7.3 69 129-201 28-96 (99)
12 PRK11283 gltP glutamate/aspart 47.3 83 0.0018 29.2 7.2 55 100-166 8-73 (437)
13 PF01292 Ni_hydr_CYTB: Prokary 47.0 20 0.00043 27.1 2.6 72 97-170 100-173 (182)
14 cd03493 SQR_QFR_TM Succinate:q 46.7 78 0.0017 21.1 5.3 50 124-174 23-72 (98)
15 PF00375 SDF: Sodium:dicarboxy 44.8 58 0.0013 28.9 5.6 79 102-194 3-86 (390)
16 PF01146 Caveolin: Caveolin; 43.4 22 0.00048 29.4 2.6 24 176-199 70-93 (148)
17 PF09685 Tic20: Tic20-like pro 41.0 1.3E+02 0.0028 21.3 6.8 60 96-159 1-63 (109)
18 PF11190 DUF2976: Protein of u 40.1 54 0.0012 25.2 4.1 57 123-180 6-63 (87)
19 TIGR02125 CytB-hydogenase Ni/F 40.0 49 0.0011 26.1 4.0 67 97-164 115-189 (211)
20 PF00033 Cytochrom_B_N: Cytoch 37.9 50 0.0011 24.7 3.6 71 96-167 104-176 (188)
21 KOG4026 Uncharacterized conser 35.9 30 0.00066 30.5 2.4 34 84-118 142-175 (207)
22 COG3736 VirB8 Type IV secretor 34.6 25 0.00055 31.1 1.8 36 92-129 33-84 (239)
23 PRK10639 formate dehydrogenase 34.5 33 0.00072 28.2 2.3 65 93-164 107-173 (211)
24 PRK14749 hypothetical protein; 33.9 21 0.00045 23.4 0.9 20 105-124 3-26 (30)
25 PRK13027 C4-dicarboxylate tran 33.7 1.4E+02 0.0029 27.7 6.3 64 101-176 9-76 (421)
26 PF12555 TPPK_C: Thiamine pyro 33.7 44 0.00096 22.9 2.5 41 94-137 5-45 (53)
27 PF03839 Sec62: Translocation 33.2 45 0.00097 29.2 3.0 32 90-121 99-131 (224)
28 PRK01663 C4-dicarboxylate tran 33.1 1.7E+02 0.0037 27.2 6.9 64 103-180 12-78 (428)
29 PF04024 PspC: PspC domain; I 33.1 54 0.0012 23.1 2.9 28 173-200 27-54 (61)
30 PRK12369 putative transporter; 29.6 1E+02 0.0022 27.7 4.7 75 96-173 7-91 (326)
31 PF06472 ABC_membrane_2: ABC t 28.5 1E+02 0.0023 26.1 4.4 77 96-175 19-96 (281)
32 PF08173 YbgT_YccB: Membrane b 28.5 42 0.0009 21.4 1.5 21 105-125 3-27 (28)
33 PRK13872 conjugal transfer pro 27.4 61 0.0013 27.0 2.8 29 163-193 23-56 (228)
34 PF09900 DUF2127: Predicted me 27.2 68 0.0015 25.5 2.9 51 120-170 43-97 (141)
35 PF11137 DUF2909: Protein of u 27.2 1.5E+02 0.0032 21.6 4.4 32 152-183 12-45 (63)
36 KOG4193 G protein-coupled rece 27.2 70 0.0015 31.5 3.5 80 102-184 434-523 (610)
37 PRK10621 hypothetical protein; 26.9 66 0.0014 26.9 2.9 36 168-205 226-261 (266)
38 TIGR01299 synapt_SV2 synaptic 26.9 1.6E+02 0.0034 29.3 5.8 23 175-197 331-353 (742)
39 PF00854 PTR2: POT family; In 25.8 1E+02 0.0023 26.1 3.9 37 98-134 71-107 (372)
40 cd03501 SQR_TypeA_SdhC_like Su 25.8 2.5E+02 0.0055 20.1 5.7 64 129-193 32-96 (101)
41 PF12273 RCR: Chitin synthesis 25.3 43 0.00093 25.7 1.4 15 103-117 2-16 (130)
42 PF06682 DUF1183: Protein of u 24.8 90 0.002 28.7 3.6 25 100-124 155-179 (318)
43 TIGR02185 Trep_Strep conserved 24.5 1.6E+02 0.0034 24.3 4.7 17 126-142 142-158 (189)
44 TIGR03745 conj_TIGR03745 integ 23.2 1.5E+02 0.0033 23.8 4.1 58 123-181 22-80 (104)
45 TIGR02970 succ_dehyd_cytB succ 22.8 1.8E+02 0.0039 22.1 4.3 49 121-170 41-89 (120)
46 PF10864 DUF2663: Protein of u 22.4 1.2E+02 0.0027 24.9 3.6 40 130-171 45-84 (130)
47 PRK09039 hypothetical protein; 22.1 86 0.0019 28.2 2.9 25 131-159 18-42 (343)
48 PF11877 DUF3397: Protein of u 21.9 3.1E+02 0.0066 20.9 5.5 38 161-205 76-116 (116)
49 PF15383 TMEM237: Transmembran 21.7 2.5E+02 0.0053 25.0 5.5 67 124-205 122-196 (253)
50 PF09605 Trep_Strep: Hypotheti 21.5 1.5E+02 0.0032 24.4 3.9 58 96-155 102-167 (186)
51 PRK15006 thiosulfate reductase 21.5 65 0.0014 27.9 1.9 73 89-169 172-248 (261)
52 PF05425 CopD: Copper resistan 21.4 3.3E+02 0.0071 19.8 6.3 49 102-159 8-62 (105)
53 cd03499 SQR_TypeC_SdhC Succina 21.3 3.5E+02 0.0076 20.1 5.8 80 98-184 22-108 (117)
54 TIGR00771 DcuC c4-dicarboxylat 21.0 1.5E+02 0.0033 26.9 4.3 51 105-155 256-306 (388)
55 PF00209 SNF: Sodium:neurotran 21.0 5.6E+02 0.012 23.6 7.9 67 126-193 405-475 (523)
56 PF09600 Cyd_oper_YbgE: Cyd op 20.9 3.8E+02 0.0082 20.3 6.7 58 109-182 8-65 (82)
57 PF00586 AIRS: AIR synthase re 20.8 50 0.0011 23.3 1.0 10 87-96 1-10 (96)
No 1
>PF07298 NnrU: NnrU protein; InterPro: IPR009915 This family consists of several plant and bacterial NnrU proteins. NnrU is thought to be involved in the reduction of nitric oxide. The exact function of NnrU is unclear. It is thought however that NnrU and perhaps NnrT are required for expression of both nirK and nor [].
Probab=97.67 E-value=3.9e-05 Score=63.41 Aligned_cols=53 Identities=26% Similarity=0.278 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHhccc--ccccchhhhhhhhhhhHHHHhhcchhHHHHHHHHHHH
Q 028579 146 VMLVLILIFATVHSGL--ASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVSSNL 198 (207)
Q Consensus 146 VML~LlliFAi~HSGl--AsLR~~gEk~IGaRayRVlFA~vSLPLAv~~IvYFi~ 198 (207)
++++.++.|+..||.. ..+|++.++.+|+|.||.+|+++|+..-+.+|.++-.
T Consensus 1 ~li~~l~lF~~~Hs~~~~p~~R~~l~~~lG~~~y~~~ysllSl~~l~lii~~~~~ 55 (191)
T PF07298_consen 1 LLILGLALFLGQHSVPARPGLRARLIARLGERGYRGLYSLLSLAGLVLIIWGYRS 55 (191)
T ss_pred CHHHHHHHHHHHHhhhccHhhhHHHHHHcCchhhHHHHHHHHHHHHHHHHHHHHh
Confidence 3667888999999995 7899999999999999999999999988877776643
No 2
>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=89.05 E-value=3.8 Score=29.95 Aligned_cols=93 Identities=15% Similarity=0.053 Sum_probs=54.4
Q ss_pred ccchhHHHHHHHHHHHHHHhhheeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhhhhh
Q 028579 98 QKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAY 177 (207)
Q Consensus 98 Qk~~SW~yF~~iLgvVL~~L~v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGaRay 177 (207)
|++++++.+-.+..-+....+..+. -+.+|=+..+.+++.- +..+.+++..+..+-+...+|.--|+.+-.+.+
T Consensus 8 qRiTgv~L~~~l~~hi~~~~~~~~~-----~~~~~~~~~~~~~~p~-~~i~~~lll~~~~~H~~~Glr~il~Dy~~~~~~ 81 (106)
T cd03500 8 QRITGVFLVFLLAGHFWVQHMDNGG-----DVIDFAFVANRLASPL-WKVWDLLLLVLALLHGGNGLRNILLDYVRRPRL 81 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-----CccCHHHHHHHHcChH-HHHHHHHHHHHHHHHHHHhHHHHHHHHccCchH
Confidence 5666666555444433333333222 3344555555555333 444556667777777899999999999877777
Q ss_pred HHHHhhcchhHHHHHHHHH
Q 028579 178 RVLFAGVSLPLAVSTIVSS 196 (207)
Q Consensus 178 RVlFA~vSLPLAv~~IvYF 196 (207)
|..+-.+..=.++.++++.
T Consensus 82 r~~~~~~~~~~~~~~~~~g 100 (106)
T cd03500 82 RRAVKGLLYVAGLLLIVLG 100 (106)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7776655544444444443
No 3
>PF10242 L_HGMIC_fpl: Lipoma HMGIC fusion partner-like protein; InterPro: IPR019372 This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains. In certain instances, as in LHFPL5, mutations cause deafness in humans [] or hypospadias []. LHFPL1 is transcribed in six liver tumour cell lines [].
Probab=66.24 E-value=6.7 Score=31.90 Aligned_cols=32 Identities=31% Similarity=0.605 Sum_probs=26.6
Q ss_pred CccccccccceecCcccchhHHHHHHHHHHHHH
Q 028579 83 ATLAGEDSAAFDLKNQKLTSWVYFSVILGVVLF 115 (207)
Q Consensus 83 p~LVGEDsAvF~l~~Qk~~SW~yF~~iLgvVL~ 115 (207)
-.+=||||..|++++= --.|.|..+++|++..
T Consensus 137 ~~~CG~~s~~y~~g~C-~~gwa~~la~~~~~~~ 168 (181)
T PF10242_consen 137 RQLCGPDSDPYKLGDC-SLGWAYYLAIIGVADA 168 (181)
T ss_pred HhhhcCCCCceeCCCC-CCChHHHHHHHHHHHH
Confidence 3577999999999975 6689999999999633
No 4
>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=61.42 E-value=26 Score=25.84 Aligned_cols=70 Identities=10% Similarity=0.157 Sum_probs=45.3
Q ss_pred CchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhhhhhHHHHhhcchhHHHHHHHHHH
Q 028579 127 GYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVSSN 197 (207)
Q Consensus 127 G~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGaRayRVlFA~vSLPLAv~~IvYFi 197 (207)
+-+.+|-+..+-++... .-.+..++.+++.+-+...+|.--|..+.....|..--..-.=.++...+|.+
T Consensus 32 ~~~~~y~~~~~~~~~~~-~~i~~~l~~~~~~~H~~~Glr~ii~Dy~~~~~~r~~l~~~~~~~~~~~~~~~~ 101 (105)
T TIGR02968 32 LPGLTYEAWRALFAHPW-MKIFTLLALLALLYHAWIGMRVVLEDYVKPEGLRLVLQVLIILFLVAYLIWGA 101 (105)
T ss_pred cCCCCHHHHHHHHhChH-HHHHHHHHHHHHHHHHHHhHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445655555555444 45555666777777789999999999998888887655544444444444443
No 5
>PRK13628 serine/threonine transporter SstT; Provisional
Probab=56.51 E-value=47 Score=30.50 Aligned_cols=58 Identities=22% Similarity=0.403 Sum_probs=44.3
Q ss_pred ccchhHHHHHHHHHHHHHHhh---heeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccch
Q 028579 98 QKLTSWVYFSVILGVVLFLLQ---LLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDM 167 (207)
Q Consensus 98 Qk~~SW~yF~~iLgvVL~~L~---v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~ 167 (207)
.++.-|+.-+.++|+++.... ..|+.| .|+-|++.+. |+..-++|.-+=+|.+++++.
T Consensus 14 ~~l~~~ilig~vlGi~~G~~~~~~~~~l~~---iG~iFl~llk---------miV~PLVf~sIv~gI~~l~~~ 74 (402)
T PRK13628 14 GSLVKQILIGLVLGILLALLSPPAAEAVGL---LGTLFVGALK---------AVAPILVFVLVMASIANHKKG 74 (402)
T ss_pred ccHHHHHHHHHHHHHHHHHhhHHHHHHHhc---cHHHHHHHHH---------HHHHHHHHHHHHHHHHhCccc
Confidence 456678888899999888754 256666 8999998764 566777888888899998764
No 6
>COG4094 Predicted membrane protein [Function unknown]
Probab=55.43 E-value=7.4 Score=34.62 Aligned_cols=18 Identities=17% Similarity=0.438 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHhcccc
Q 028579 145 VVMLVLILIFATVHSGLA 162 (207)
Q Consensus 145 ~VML~LlliFAi~HSGlA 162 (207)
.+|++.+++|...||+-+
T Consensus 2 ~~lvl~l~lFl~~Hsv~~ 19 (219)
T COG4094 2 LILVLGLVLFLGLHSVRV 19 (219)
T ss_pred hHHHHHHHHHHHHhcccc
Confidence 578899999999999976
No 7
>TIGR01583 formate-DH-gamm formate dehydrogenase, gamma subunit. NiFe-hydrogenase and thiosulfate reductase contain homologous gamma subunits, and these can be found scoring in the noise of this model.
Probab=54.02 E-value=33 Score=27.90 Aligned_cols=67 Identities=15% Similarity=0.208 Sum_probs=39.5
Q ss_pred eecCcccchhHHHHHHHHHHHHHHhhheeee-CCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccc
Q 028579 93 FDLKNQKLTSWVYFSVILGVVLFLLQLLWID-NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASL 164 (207)
Q Consensus 93 F~l~~Qk~~SW~yF~~iLgvVL~~L~v~WId-psTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsL 164 (207)
||. .||+.-|+.+.+.+..++..+...=.+ |..+++..-.+. ...=| ..+..++++|.++|-.+|..
T Consensus 104 yN~-~Qk~~y~~i~~~~~~~~~TGl~m~~~~~~~~~~~~~~~~~---~~~~H-~~~a~l~~~~vi~Hiy~a~~ 171 (204)
T TIGR01583 104 YNA-GQKSWYWILVLGGFLMIITGIFMWFLDFPSTAFSIELLRI---SALIH-NFSAIILAVGFIVHIYMAVF 171 (204)
T ss_pred CCh-HHHHHHHHHHHHHHHHHHHHHHHHHHHcccccCCHHHHHH---HHHHH-HHHHHHHHHHHHHHHHHHHh
Confidence 554 478999988776666666554332001 222333333333 23345 45556778889999999876
No 8
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=52.94 E-value=8.2 Score=27.34 Aligned_cols=27 Identities=11% Similarity=0.356 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhcccccccchhhhhh
Q 028579 146 VMLVLILIFATVHSGLASLRDMGEKVI 172 (207)
Q Consensus 146 VML~LlliFAi~HSGlAsLR~~gEk~I 172 (207)
+.++++++|+++=|++|.||..|--++
T Consensus 5 ~wlIIviVlgvIigNia~LK~sAk~K~ 31 (55)
T PF11446_consen 5 PWLIIVIVLGVIIGNIAALKYSAKMKF 31 (55)
T ss_pred hhHHHHHHHHHHHhHHHHHHHhcccCC
Confidence 557888999999999999999887443
No 9
>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=51.69 E-value=50 Score=23.72 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=32.1
Q ss_pred CCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhh
Q 028579 124 NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGA 174 (207)
Q Consensus 124 psTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGa 174 (207)
...+-+.+|-+..+..++ .-...+.+++++++.+-+.-.+|.-.|+ +|-
T Consensus 48 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~H~~~Gir~il~D-~g~ 96 (121)
T PF01127_consen 48 ALGGGPISYDEVVAFFSS-PFWAILYFLLLVAFFFHALNGIRHILED-WGI 96 (121)
T ss_dssp HCCSSHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT
T ss_pred hhcCCHhhHHHHHHHhCC-HHHHHHHHHHHHHHHHHHHhhHHHHHHH-hcc
Confidence 344556677777666665 4233443666777775578889999998 453
No 10
>PRK10179 formate dehydrogenase-N subunit gamma; Provisional
Probab=51.28 E-value=19 Score=30.03 Aligned_cols=67 Identities=15% Similarity=0.216 Sum_probs=39.6
Q ss_pred cceecCcccchhHHHHHHHHHHHHHHhhheeee-CCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhccccc
Q 028579 91 AAFDLKNQKLTSWVYFSVILGVVLFLLQLLWID-NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLAS 163 (207)
Q Consensus 91 AvF~l~~Qk~~SW~yF~~iLgvVL~~L~v~WId-psTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAs 163 (207)
..||-+ ||+.-|..+.+++..++..|. +|.. ..+.++..- +.-..-=| ..+..++++|.++|--+|.
T Consensus 107 gk~N~~-QKl~y~~i~~~~~~~i~TGl~-l~~~~~~~~~~~~~---~r~a~~iH-~~~a~l~~~fiivHiY~a~ 174 (217)
T PRK10179 107 GKYNAG-QKMMFWSIMSMIFVLLVTGVI-IWRPYFAQYFPMQV---VRYSLLIH-AAAGIILIHAILIHMYMAF 174 (217)
T ss_pred cccCHH-HHHHHHHHHHHHHHHHHHHHH-HHHHhhhhhCCHHH---HHHHHHHH-HHHHHHHHHHHHHHHHHHh
Confidence 347766 889999877777666666655 4521 122222222 22122345 4444667888999998874
No 11
>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=49.31 E-value=1.1e+02 Score=22.92 Aligned_cols=69 Identities=13% Similarity=0.105 Sum_probs=46.5
Q ss_pred hhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhhhhhHHHHhhcchhHHHHHHHHHHHHHH
Q 028579 129 GKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVSSNLLIQ 201 (207)
Q Consensus 129 G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGaRayRVlFA~vSLPLAv~~IvYFi~~~~ 201 (207)
|.+|-+..+-+++.- .-++.+++..+..|-....+|.--|..|.+..-|...-.. .+++++.|.+-.++
T Consensus 28 ~~~y~~~~~~~~~p~-~~i~~~l~~~~~~~H~~~Glr~vi~DYv~~~~lr~~l~~~---~~~~l~~~~~~~~~ 96 (99)
T cd03494 28 PLTYEAWSGLFSSLW-MKIFTLLALLALLLHAWIGLWDILTDYVKPAGLRLLLQVL---IILVLFGYLIWGIQ 96 (99)
T ss_pred CCCHHHHHHHHhCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH---HHHHHHHHHHHHHH
Confidence 455655555555433 4555567778888889999999999999888777765433 34556666655544
No 12
>PRK11283 gltP glutamate/aspartate:proton symporter; Provisional
Probab=47.27 E-value=83 Score=29.22 Aligned_cols=55 Identities=24% Similarity=0.415 Sum_probs=40.6
Q ss_pred chhHHHHHHHHHHHHHHhhh-----------eeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccc
Q 028579 100 LTSWVYFSVILGVVLFLLQL-----------LWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRD 166 (207)
Q Consensus 100 ~~SW~yF~~iLgvVL~~L~v-----------~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~ 166 (207)
+..|+..+.++|+++....- .|+.| .|+-|+..+ -|+.+=++|.-+=+|.+++.+
T Consensus 8 l~~~IliglvlGi~~G~~~~~~~~~~~~~~~~~l~~---~G~iFl~lL---------km~VvPLVf~Sii~gI~~l~~ 73 (437)
T PRK11283 8 LAWQILIALVLGILLGAYLHYHSDSRDWLVSNLLSP---AGDIFIHLI---------KMIVVPIVISTLIVGIAGVGD 73 (437)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccchhhHHHHHHhh---hHHHHHHHH---------HHHHHHHHHHHHHHHHHhccc
Confidence 45678899999999887542 25555 788888865 467777777777788888864
No 13
>PF01292 Ni_hydr_CYTB: Prokaryotic cytochrome b561; InterPro: IPR011577 Cytochrome b561 is an integral membrane and electron transport protein, that binds two haem groups non-covalently. This domain is also found in a number of nickel-dependent hydrogenase subunits which are also B-type cytochromes that interact with quinones and anchor the hydrogenase to the membrane. Members of the 'eukaryotic cytochrome b561' family can be found in IPR004877 from INTERPRO.; GO: 0009055 electron carrier activity, 0016021 integral to membrane
Probab=47.04 E-value=20 Score=27.15 Aligned_cols=72 Identities=21% Similarity=0.298 Sum_probs=42.6
Q ss_pred cccchhHHHHHHHHHHHHHHhhheeeeCCCCchh--hHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhh
Q 028579 97 NQKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGK--AFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEK 170 (207)
Q Consensus 97 ~Qk~~SW~yF~~iLgvVL~~L~v~WIdpsTG~G~--~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk 170 (207)
-||..-|+.+...+..++..+...+ ...+|++- ...+.......=|++.+..++ .|.++|-.+|-......|
T Consensus 100 ~~~~~~~~~~~~~~~~~iTG~~~~~-~~~~~~~~~~~~~~~~~~~~~vH~~~a~~~i-~~i~~Hv~~a~~~~~~~~ 173 (182)
T PF01292_consen 100 GQKIVHWVLYLLLLLLPITGLLLWF-ASAEGFPLFAASPGGAQIARSVHFFLAWLLI-AFIILHVYAALFHHFRWR 173 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-hhcccCccccccchHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhhhHH
Confidence 3667778888777777776655443 32333322 112222223334656665555 999999998877766543
No 14
>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=46.66 E-value=78 Score=21.10 Aligned_cols=50 Identities=22% Similarity=0.164 Sum_probs=31.5
Q ss_pred CCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhh
Q 028579 124 NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGA 174 (207)
Q Consensus 124 psTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGa 174 (207)
-..+.+.++ +.+...-++.-...+.+++.++..+-+..-+|.-.|...-.
T Consensus 23 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~H~~~Gir~i~~D~~~~ 72 (98)
T cd03493 23 ALLGGPYAF-AEVVAFLSSPLGKLLYLLLLLALLYHALNGIRHLIWDYGKG 72 (98)
T ss_pred HHhcCHHHH-HHHHHHHhCHHHHHHHHHHHHHHHHHHHHhHHHHHHHcccc
Confidence 344555555 44444444453555566677777777888899888877643
No 15
>PF00375 SDF: Sodium:dicarboxylate symporter family; InterPro: IPR001991 It has been shown [] that integral membrane proteins that mediate the uptake of a wide variety of molecules with the concomitant uptake of sodium ions (sodium symporters) can be grouped, on the basis of sequence and functional similarities into a number of distinct families. One of these families [] is known as the sodium:dicarboxylate symporter family (SDF). Such re-uptake of neurotransmitters from the synapses, is thought to be an important mechanism for terminating their action, by removing these chemicals from the synaptic cleft, and transporting them into presynaptic nerve terminals, and surrounding neuroglia. this removal is also believed to prevent them accumulating to the point of reaching neurotoxic [, ]. The structure of these transporter proteins has been variously reported to contain from 8 to 10 transmembrane (TM) regions, although 10 now seems to be the accepted value. Members of the family include: several mammalian excitatory amino acid transporters, and a number of bacterial transporters. They vary with regars to their dependence on transport of sodium, and other ions.; GO: 0017153 sodium:dicarboxylate symporter activity, 0006835 dicarboxylic acid transport, 0016020 membrane; PDB: 3V8G_B 1XFH_A 3KBC_B 2NWX_B 3V8F_B 2NWL_B 2NWW_A.
Probab=44.83 E-value=58 Score=28.91 Aligned_cols=79 Identities=32% Similarity=0.479 Sum_probs=44.6
Q ss_pred hHHHHHHHHHHHHHHh-----hheeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhhhh
Q 028579 102 SWVYFSVILGVVLFLL-----QLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARA 176 (207)
Q Consensus 102 SW~yF~~iLgvVL~~L-----~v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGaRa 176 (207)
-|+..+.++|+++..+ ..-|+. =.|+-|++.+ -|+.+-++|.-+=+|.+++|+ .+..|.-.
T Consensus 3 ~~ilia~vlGi~~G~~~~~~~~~~~l~---~~G~lfi~ll---------~~~v~PLVf~sii~gi~~l~~--~~~~g~i~ 68 (390)
T PF00375_consen 3 LQILIAIVLGILLGLIDFSPEAAQWLS---FPGDLFIRLL---------KMLVLPLVFSSIISGIASLGD--AKKLGRIG 68 (390)
T ss_dssp HHHHHHHHHHHHHHHHTTHHHHHHHTH---HHHHHHHHHH---------HHHHHHHHHHHHHHHCHSHT---TTSHHHHH
T ss_pred HHHHHHHHHHHHHHhHHhhHHHHHHHH---HHHHHHHHHH---------HHHHHHHHHHHHHhhccCCcc--ccccccHH
Confidence 4777888888888883 223333 2466666554 455555566666688999985 44445444
Q ss_pred hHHHHhhcchhHHHHHHH
Q 028579 177 YRVLFAGVSLPLAVSTIV 194 (207)
Q Consensus 177 yRVlFA~vSLPLAv~~Iv 194 (207)
.|.++-.+..-+....+.
T Consensus 69 ~~~i~~~~~~t~~A~~ig 86 (390)
T PF00375_consen 69 GRTILYFLLTTLLAAAIG 86 (390)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 554444333333333333
No 16
>PF01146 Caveolin: Caveolin; InterPro: IPR001612 Caveolins [, , ] are a family of integral membrane proteins which are the principal components of caveolae membranes. Cavoleae are flask-shaped plasma membrane invaginations whose exact cellular function is not yet clear. Caveolins may act as scaffolding proteins within caveolar membranes by compartmentalizing and concentrating signalling molecules. Various classes of signalling molecules, including G-protein subunits, receptor and non-receptor tyrosine kinases, endothelial nitric oxide synthase (eNOS), and small GTPases, bind Cav-1 through its 'caveolin-scaffolding domain'. Currently, three different forms of caveolins are known: caveolin-1 (or VIP21), caveolin-2 and caveolin-3 (or M-caveolin). Caveolins are proteins of about 20 Kd, they form high molecular mass homo-oligomers. Structurally they seem to have N-terminal and C-terminal hydrophilic segments and a long central transmembrane domain that probably forms a hairpin in the membrane. Both extremities are known to face the cytoplasm. Caveolae are enriched with cholesterol and Cav-1 is one of the few proteins that binds cholesterol tightly and specifically.
Probab=43.42 E-value=22 Score=29.36 Aligned_cols=24 Identities=29% Similarity=0.303 Sum_probs=21.2
Q ss_pred hhHHHHhhcchhHHHHHHHHHHHH
Q 028579 176 AYRVLFAGVSLPLAVSTIVSSNLL 199 (207)
Q Consensus 176 ayRVlFA~vSLPLAv~~IvYFi~~ 199 (207)
-||++=+++++|+|+++-++|-++
T Consensus 70 ~Yr~Ls~ilaiP~A~~~Gi~FA~l 93 (148)
T PF01146_consen 70 CYRILSLILAIPLAFLWGILFACL 93 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999888654
No 17
>PF09685 Tic20: Tic20-like protein; InterPro: IPR019109 This entry represents a group of uncharacterised conserved proteins including a chloroplast protein import component called Tic20. Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. Tic20 is a core member of the Tic complex and is deeply embedded in the inner envelope membrane. It is thought to function as a protein conducting component of the Tic complex [].
Probab=41.00 E-value=1.3e+02 Score=21.27 Aligned_cols=60 Identities=17% Similarity=0.354 Sum_probs=28.8
Q ss_pred CcccchhHHHHH---HHHHHHHHHhhheeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhc
Q 028579 96 KNQKLTSWVYFS---VILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHS 159 (207)
Q Consensus 96 ~~Qk~~SW~yF~---~iLgvVL~~L~v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HS 159 (207)
||++.....|++ ..++.+..+.. |+-.... .+|++.-..-+-.-+++++...++..+...
T Consensus 1 ~er~~a~l~~ls~~~~~~~~i~pli~--~~~~k~~--~~~vr~ha~qal~~~i~~~i~~~i~~~l~~ 63 (109)
T PF09685_consen 1 EERTWAALAYLSFFSPFLGFIGPLIV--WIVKKDK--SPFVRFHAKQALNFQITFLIISIILFILSF 63 (109)
T ss_pred CcHHHHHHHHHHHHhHHHHHHHHHHH--HHHcCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666667765 34444443333 3333222 567776655443323444444444444333
No 18
>PF11190 DUF2976: Protein of unknown function (DUF2976); InterPro: IPR021356 Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition.
Probab=40.13 E-value=54 Score=25.18 Aligned_cols=57 Identities=19% Similarity=0.304 Sum_probs=38.8
Q ss_pred eCCCCchhhHHHHHhccCCChHHHHHHHHH-HHHHHhcccccccchhhhhhhhhhhHHH
Q 028579 123 DNSTGYGKAFIDSVSSLSDSHEVVMLVLIL-IFATVHSGLASLRDMGEKVIGARAYRVL 180 (207)
Q Consensus 123 dpsTG~G~~Fidavssls~Sh~~VML~Lll-iFAi~HSGlAsLR~~gEk~IGaRayRVl 180 (207)
+|++|=|+++++.+.....+- ++.++|++ .+|..--.-+++-...|-.=|..-|.=+
T Consensus 6 ~Ps~g~~~~~~~~i~~y~~d~-~~l~gLv~~a~afi~Va~~~i~~y~eir~gK~~W~~f 63 (87)
T PF11190_consen 6 PPSSGGGGGIMETIKGYAKDG-VLLLGLVLAAAAFIVVAKAAISTYNEIRDGKKTWGDF 63 (87)
T ss_pred CCCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccHHHh
Confidence 799999999999999988776 55556655 4444444444555555555577777644
No 19
>TIGR02125 CytB-hydogenase Ni/Fe-hydrogenase, b-type cytochrome subunit. This model describes a family of cytochrome b proteins which appear to be specific for nickel-iron hydrogenase complexes. Every genome which contains a member of this family posesses a Ni/Fe hydrogenase according to Genome Properties (GenProp0177), and most are gene clustered with other hydrogenase components. Some Ni/Fe hydrogenase-containing species lack a member of this family but contain other CytB homologs (pfam01292) which may substitute for it.
Probab=39.96 E-value=49 Score=26.07 Aligned_cols=67 Identities=22% Similarity=0.238 Sum_probs=39.3
Q ss_pred cccchhHHHHHHHHHHHHHHhhheeeeC-CCCchhhHHHHHh-------ccCCChHHHHHHHHHHHHHHhcccccc
Q 028579 97 NQKLTSWVYFSVILGVVLFLLQLLWIDN-STGYGKAFIDSVS-------SLSDSHEVVMLVLILIFATVHSGLASL 164 (207)
Q Consensus 97 ~Qk~~SW~yF~~iLgvVL~~L~v~WIdp-sTG~G~~Fidavs-------sls~Sh~~VML~LlliFAi~HSGlAsL 164 (207)
-||+.-|+.+..++..++..+...+-++ ..|+.-.+.+.+. .+..=|+ ++..+++.|.++|-.+|-.
T Consensus 115 ~~k~~~~~l~~~~~~~~lTG~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~iH~-~~a~~l~~~i~~Hi~~a~~ 189 (211)
T TIGR02125 115 LQFVAYFGFIVLILFMILTGLALYYYHNGLGGLLPSLFGWVEPLFGGLANVRFIHH-LGMWAFVIFVPVHVYMAVR 189 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHhCChHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence 4678888877777777777766544222 2333322222211 0122364 5556777999999998764
No 20
>PF00033 Cytochrom_B_N: Cytochrome b(N-terminal)/b6/petB; InterPro: IPR016174 This entry represents a haem-binding domain with a 4-helical bundle structure that is found in transmembrane di-haem cytochromes. The domain contains four transmembrane helices in an up-and-down bundle, and binds two haem groups in between the helices; three of the four haem-binding residues is conserved between family members. Proteins containing this domain include: N-terminal domain of mitochondrial cytochrome b subunit, in which the domain contains an extra transmembrane linker helix that is absent in plant and cyanobacteria subunits []. Cytochrome b6 subunit of the cytochrome b6f complex, which provides the electronic connection between the photosystems I and II reaction centres of oxygenic photosynthesis, and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis []. Cytochrome gamma subunit of formate dehydrogenase-N (Fdn-N), which acts as a major component of Escherichia coli nitrate respiration []. ; GO: 0022904 respiratory electron transport chain, 0016020 membrane; PDB: 1KQG_C 1KQF_C.
Probab=37.90 E-value=50 Score=24.72 Aligned_cols=71 Identities=17% Similarity=0.144 Sum_probs=38.7
Q ss_pred CcccchhHHHHHHHHHHHHHHhhh--eeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccch
Q 028579 96 KNQKLTSWVYFSVILGVVLFLLQL--LWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDM 167 (207)
Q Consensus 96 ~~Qk~~SW~yF~~iLgvVL~~L~v--~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~ 167 (207)
.-||..-|+.+..++...+..+.. .+.-+-.+....-.+..+-...-|++.+ .+++.|.++|-.+|.....
T Consensus 104 ~~~~~~~~~l~~~~~~~~iTG~~~~~~~~~~~~~~~~~~~~~~~~~~~iH~~~~-~ll~~~i~~Hi~~a~~~~~ 176 (188)
T PF00033_consen 104 PLQKLVYWALYLLLLLMAITGLIMLWFFWWPLPPWLLPPPGLAEWARLIHFILA-YLLLAFIIIHIYAAIFHHF 176 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC-----TTTTGGGS-HHHH-HHHHHHHHHHH-HHHHHHHHHHHHHHHHBT-
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccchhhcCChHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhh
Confidence 346677777666666666666655 1111222222333344444456675555 4555899999888776554
No 21
>KOG4026 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.88 E-value=30 Score=30.51 Aligned_cols=34 Identities=21% Similarity=0.609 Sum_probs=29.2
Q ss_pred ccccccccceecCcccchhHHHHHHHHHHHHHHhh
Q 028579 84 TLAGEDSAAFDLKNQKLTSWVYFSVILGVVLFLLQ 118 (207)
Q Consensus 84 ~LVGEDsAvF~l~~Qk~~SW~yF~~iLgvVL~~L~ 118 (207)
..=||++-.|++++=++ .|.|..+|+|++++.+-
T Consensus 142 ~~CG~~a~ky~lG~CsI-gWaY~lAIig~~daliL 175 (207)
T KOG4026|consen 142 RMCGAKAGKYYLGDCSI-GWAYYLAIIGILDALIL 175 (207)
T ss_pred HHhccccCCccCccccc-cHHHHHHHHHHHHHHHH
Confidence 46799999999999855 69999999999987654
No 22
>COG3736 VirB8 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]
Probab=34.57 E-value=25 Score=31.15 Aligned_cols=36 Identities=22% Similarity=0.310 Sum_probs=22.1
Q ss_pred ceecCcccchhHHHHHHHHHHHHHHh----------------hheeeeCCCCch
Q 028579 92 AFDLKNQKLTSWVYFSVILGVVLFLL----------------QLLWIDNSTGYG 129 (207)
Q Consensus 92 vF~l~~Qk~~SW~yF~~iLgvVL~~L----------------~v~WIdpsTG~G 129 (207)
++.++.+. +|++-.+++..++.++ |++|+|++||--
T Consensus 33 ~~~~~r~r--~~~~~va~~~~~l~v~~~~~Ia~llPLK~~epy~v~vd~~tg~~ 84 (239)
T COG3736 33 VIKLERSR--RLAWRVAILFTLLAVAAVIAIAILLPLKKTEPYVVRVDNNTGNV 84 (239)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhhccccccccEEEEEcCCCceE
Confidence 34455554 6766555444433322 789999999853
No 23
>PRK10639 formate dehydrogenase-O subunit gamma; Provisional
Probab=34.46 E-value=33 Score=28.18 Aligned_cols=65 Identities=15% Similarity=0.258 Sum_probs=36.6
Q ss_pred eecCcccchhHHHHHHHHHHHHHHhhheeeeC--CCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccc
Q 028579 93 FDLKNQKLTSWVYFSVILGVVLFLLQLLWIDN--STGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASL 164 (207)
Q Consensus 93 F~l~~Qk~~SW~yF~~iLgvVL~~L~v~WIdp--sTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsL 164 (207)
||- .||+.-|..+.+.+..++..+. .|- | ...++....+. ...=|++.+ .++++|.++|--+|-.
T Consensus 107 yN~-~qk~~y~~~~~~~~~~~iTGl~-l~~-p~~~~~~~~~~~~~---~~~~H~~~a-~~~i~~iivHiy~a~~ 173 (211)
T PRK10639 107 YNF-GQKCVFWAAIIFLVLLLVSGVI-IWR-PYFAPAFSIPVIRF---ALMLHSFAA-VALIVVIMVHIYAALW 173 (211)
T ss_pred cCH-HHHHHHHHHHHHHHHHHHHHHH-HHH-HhhcccCChHHHHH---HHHHHHHHH-HHHHHHHHHHHHHHhc
Confidence 554 3899999888777666666654 331 1 01122221221 234464555 4555688999988754
No 24
>PRK14749 hypothetical protein; Provisional
Probab=33.93 E-value=21 Score=23.39 Aligned_cols=20 Identities=35% Similarity=0.806 Sum_probs=14.6
Q ss_pred HHHHHHHHH----HHHhhheeeeC
Q 028579 105 YFSVILGVV----LFLLQLLWIDN 124 (207)
Q Consensus 105 yF~~iLgvV----L~~L~v~WIdp 124 (207)
||+=|||+- ++++|.+|+++
T Consensus 3 YfaWiLG~~lAc~f~ilna~w~E~ 26 (30)
T PRK14749 3 YLLWFVGILLMCSLSTLVLVWLDP 26 (30)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677777665 46889999874
No 25
>PRK13027 C4-dicarboxylate transporter DctA; Reviewed
Probab=33.70 E-value=1.4e+02 Score=27.72 Aligned_cols=64 Identities=28% Similarity=0.368 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHHHHHHhhh---eeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccc-hhhhhhhhhh
Q 028579 101 TSWVYFSVILGVVLFLLQL---LWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRD-MGEKVIGARA 176 (207)
Q Consensus 101 ~SW~yF~~iLgvVL~~L~v---~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~-~gEk~IGaRa 176 (207)
.-++.-+.++|+++.++.- -|++| .|+-|+..+ -|+.+-++|.-+=+|.+++.+ +-=.+||-|.
T Consensus 9 ~~~i~igl~lGi~~G~~~~~~~~~l~~---iG~iFl~lL---------km~VvPlVf~sii~gI~~l~~~~~~grig~~~ 76 (421)
T PRK13027 9 FGQVVIALVLGVALGAFFPHFAESLKP---LGDGFIKLI---------KMLIGPIVFCVVVSGIAGAGDLKKVGRVGLKA 76 (421)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh---hHHHHHHHH---------HHHHHHHHHHHHHHHHHhCccchhcchhHHHH
Confidence 3456667777777765432 35544 899999875 467777888888889999843 2224455554
No 26
>PF12555 TPPK_C: Thiamine pyrophosphokinase C terminal; InterPro: IPR022215 This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyses the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme.
Probab=33.68 E-value=44 Score=22.92 Aligned_cols=41 Identities=20% Similarity=0.493 Sum_probs=32.5
Q ss_pred ecCcccchhHHHHHHHHHHHHHHhhheeeeCCCCchhhHHHHHh
Q 028579 94 DLKNQKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGKAFIDSVS 137 (207)
Q Consensus 94 ~l~~Qk~~SW~yF~~iLgvVL~~L~v~WIdpsTG~G~~Fidavs 137 (207)
++-.++.+.|.....+++..+.+..++++.|. |+.|++.+.
T Consensus 5 ~LYrsris~~~~~~lvlaaLvav~v~l~~s~~---g~~~~~~l~ 45 (53)
T PF12555_consen 5 RLYRSRISGWALALLVLAALVAVAVALLISPA---GQSFLDLLA 45 (53)
T ss_pred HHhcCCCchHHHHHHHHHHHHHHHHHHHhCcc---HHHHHHHHH
Confidence 34456788888888899999999999998775 488887664
No 27
>PF03839 Sec62: Translocation protein Sec62; InterPro: IPR004728 Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins have been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane
Probab=33.24 E-value=45 Score=29.19 Aligned_cols=32 Identities=19% Similarity=0.368 Sum_probs=24.4
Q ss_pred ccceecCcccchhHHH-HHHHHHHHHHHhhhee
Q 028579 90 SAAFDLKNQKLTSWVY-FSVILGVVLFLLQLLW 121 (207)
Q Consensus 90 sAvF~l~~Qk~~SW~y-F~~iLgvVL~~L~v~W 121 (207)
--++.++.-+...|++ +.+++|++..+|+.+|
T Consensus 99 ~YvW~ye~~~~~~~l~~~~~~~~v~a~~lFPlW 131 (224)
T PF03839_consen 99 YYVWIYEPSPLMQYLIGALLLVGVIAICLFPLW 131 (224)
T ss_pred EEEEEecCCcHHHHHHHHHHHHHHHHHHhhhcC
Confidence 3445566666778888 7788888889999998
No 28
>PRK01663 C4-dicarboxylate transporter DctA; Reviewed
Probab=33.06 E-value=1.7e+02 Score=27.16 Aligned_cols=64 Identities=30% Similarity=0.500 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHhhh---eeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhhhhhHH
Q 028579 103 WVYFSVILGVVLFLLQL---LWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRV 179 (207)
Q Consensus 103 W~yF~~iLgvVL~~L~v---~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGaRayRV 179 (207)
++.-+.++|+++.++.- .|++| .|+-|+..+ -|+.+-++|.-+=+|.+++.+. +..|....|.
T Consensus 12 ~iligl~lGi~~G~~~~~~~~~l~~---iG~iFl~lL---------km~VvPLVf~Sii~gI~~l~~~--~~lg~i~~~~ 77 (428)
T PRK01663 12 QVLVAIIIGILLGHFYPELGAQMKP---LGDGFIKLI---------KMIIAPIIFCTVVTGIAGMGDM--KKVGRVGGKA 77 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh---hHHHHHHHH---------HHHHHHHHHHHHHHHHHhCccc--cccchhHHHH
Confidence 46667777877776643 45544 789998875 4667777788788889988753 5566666665
Q ss_pred H
Q 028579 180 L 180 (207)
Q Consensus 180 l 180 (207)
+
T Consensus 78 ~ 78 (428)
T PRK01663 78 L 78 (428)
T ss_pred H
Confidence 4
No 29
>PF04024 PspC: PspC domain; InterPro: IPR007168 This domain is found in Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length.
Probab=33.05 E-value=54 Score=23.11 Aligned_cols=28 Identities=11% Similarity=0.146 Sum_probs=21.5
Q ss_pred hhhhhHHHHhhcchhHHHHHHHHHHHHH
Q 028579 173 GARAYRVLFAGVSLPLAVSTIVSSNLLI 200 (207)
Q Consensus 173 GaRayRVlFA~vSLPLAv~~IvYFi~~~ 200 (207)
-+...|++|.+..+-....+++|+++-+
T Consensus 27 d~~~vRl~~v~l~~~~~~~~l~Y~~~w~ 54 (61)
T PF04024_consen 27 DPTLVRLIFVVLTFFTGGGILLYLILWL 54 (61)
T ss_pred CHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 3567899999988855558889988754
No 30
>PRK12369 putative transporter; Reviewed
Probab=29.64 E-value=1e+02 Score=27.69 Aligned_cols=75 Identities=17% Similarity=0.189 Sum_probs=44.5
Q ss_pred CcccchhHHHHH--HHHHHHHHHhhh-eeeeCCCCchhhHHHHHhcc-------CCChHHHHHHHHHHHHHHhccccccc
Q 028579 96 KNQKLTSWVYFS--VILGVVLFLLQL-LWIDNSTGYGKAFIDSVSSL-------SDSHEVVMLVLILIFATVHSGLASLR 165 (207)
Q Consensus 96 ~~Qk~~SW~yF~--~iLgvVL~~L~v-~WIdpsTG~G~~Fidavssl-------s~Sh~~VML~LlliFAi~HSGlAsLR 165 (207)
.++|...|.+++ ++++..++...+ +|+ +=..++|-|+++.- ..+.=+-.+...++.+++...++.+.
T Consensus 7 ~~~~~~~~~ll~~~~~i~l~l~~v~~~v~~---n~w~~~fy~aL~~~~~~~~~~~~~~f~~~l~~f~~~~~~~v~~~v~~ 83 (326)
T PRK12369 7 ASKKWALWAYGGLFFILLSLWYQVSLNVAI---NEWYGDFYDLLQKAKIEPNNHTAGDFWASILSFLAIAMPYVLIATVV 83 (326)
T ss_pred cCCcHHHHHHHHHHHHHHHHHHHHHHhhhh---hHHhHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778999988 566655543322 232 22468999999984 22221333444456666666677666
Q ss_pred chhhhhhh
Q 028579 166 DMGEKVIG 173 (207)
Q Consensus 166 ~~gEk~IG 173 (207)
.+-.++++
T Consensus 84 ~~~~~~l~ 91 (326)
T PRK12369 84 DYFASHYA 91 (326)
T ss_pred HHHHHHHH
Confidence 66666665
No 31
>PF06472 ABC_membrane_2: ABC transporter transmembrane region 2; InterPro: IPR010509 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This region covers the N terminus and first two membrane regions of a small family of ABC transporters. Mutations in this domain in P28288 from SWISSPROT are believed responsible for Zellweger Syndrome-2 []; mutations in P33897 from SWISSPROT are responsible for recessive X-linked adrenoleukodystrophy []. A Saccharomyces cerevisiae protein containing this domain is involved in the import of long-chain fatty acids [].; GO: 0006810 transport, 0016020 membrane
Probab=28.50 E-value=1e+02 Score=26.11 Aligned_cols=77 Identities=17% Similarity=0.267 Sum_probs=55.5
Q ss_pred CcccchhHHHHHHHHHHHHHHhh-heeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhh
Q 028579 96 KNQKLTSWVYFSVILGVVLFLLQ-LLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGA 174 (207)
Q Consensus 96 ~~Qk~~SW~yF~~iLgvVL~~L~-v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGa 174 (207)
.+++...|.++.++++..+.--+ -+|+.. ..++|.+++...-...=+..++..++-+++.+.+.+...+-++.+.-
T Consensus 19 ~~~~~~~~~ll~~ll~l~l~~~~lsv~~~~---~~g~~~~aL~~~d~~~f~~~l~~~~~l~~~~~~l~~~~~yl~~~L~l 95 (281)
T PF06472_consen 19 PSERWKAWLLLLVLLLLLLARVYLSVRINF---WNGDFYNALQQKDLQAFWRLLLLFLLLAIASALLNSILKYLRQRLAL 95 (281)
T ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHH---HhhHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778899999888776654322 244433 34689999999777665566666777788888888888888887765
Q ss_pred h
Q 028579 175 R 175 (207)
Q Consensus 175 R 175 (207)
|
T Consensus 96 ~ 96 (281)
T PF06472_consen 96 R 96 (281)
T ss_pred H
Confidence 4
No 32
>PF08173 YbgT_YccB: Membrane bound YbgT-like protein; InterPro: IPR012994 This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in Escherichia coli. Members have a consensus motif (MWYFXW), which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to proteobacteria [].
Probab=28.49 E-value=42 Score=21.45 Aligned_cols=21 Identities=38% Similarity=0.914 Sum_probs=13.9
Q ss_pred HHHHHHHH----HHHHhhheeeeCC
Q 028579 105 YFSVILGV----VLFLLQLLWIDNS 125 (207)
Q Consensus 105 yF~~iLgv----VL~~L~v~WIdps 125 (207)
||+=|||+ .+++++.+|++..
T Consensus 3 YfaWilG~~lA~~~~i~~a~wlE~~ 27 (28)
T PF08173_consen 3 YFAWILGVLLACAFGILNAMWLEKR 27 (28)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 66666655 4567888888753
No 33
>PRK13872 conjugal transfer protein TrbF; Provisional
Probab=27.38 E-value=61 Score=27.03 Aligned_cols=29 Identities=31% Similarity=0.367 Sum_probs=18.1
Q ss_pred cccchhhhhhh-----hhhhHHHHhhcchhHHHHHH
Q 028579 163 SLRDMGEKVIG-----ARAYRVLFAGVSLPLAVSTI 193 (207)
Q Consensus 163 sLR~~gEk~IG-----aRayRVlFA~vSLPLAv~~I 193 (207)
+=|.|-| ++| +|+||++ |++++=++++.+
T Consensus 23 a~~~wee-r~~~~~~~~~~w~~v-a~~~l~i~~~~v 56 (228)
T PRK13872 23 AAQVWDE-RIGSARVQARNWRLM-AFGCLALSAGLA 56 (228)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 3466665 666 7789965 555666555543
No 34
>PF09900 DUF2127: Predicted membrane protein (DUF2127); InterPro: IPR021125 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Probab=27.25 E-value=68 Score=25.53 Aligned_cols=51 Identities=20% Similarity=0.231 Sum_probs=36.3
Q ss_pred eeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhc----ccccccchhhh
Q 028579 120 LWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHS----GLASLRDMGEK 170 (207)
Q Consensus 120 ~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HS----GlAsLR~~gEk 170 (207)
.=.||+.-+...+++..+.+++++-..+-..++.+|+++- ||=--|.|||-
T Consensus 43 l~~dp~~~~~~~ll~~~~~~~~~~l~~~a~~~~~Ya~l~lvea~GLw~~k~Wae~ 97 (141)
T PF09900_consen 43 LHLDPASRLPHLLLHAAQHLSPSTLHFAALYLLAYALLRLVEAYGLWRGKRWAEW 97 (141)
T ss_pred hCcCchhhHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHcCchHhH
Confidence 4479999999999999999999984444444455555542 44456777774
No 35
>PF11137 DUF2909: Protein of unknown function (DUF2909); InterPro: IPR021313 This is a family of proteins conserved in Proteobacteria of unknown function.
Probab=27.21 E-value=1.5e+02 Score=21.63 Aligned_cols=32 Identities=19% Similarity=0.268 Sum_probs=14.6
Q ss_pred HHHHHHhcccccccchhh--hhhhhhhhHHHHhh
Q 028579 152 LIFATVHSGLASLRDMGE--KVIGARAYRVLFAG 183 (207)
Q Consensus 152 liFAi~HSGlAsLR~~gE--k~IGaRayRVlFA~ 183 (207)
+++...-.-..-+|+.++ +..=.=.+||.|+.
T Consensus 12 ii~sL~saL~~l~kd~~~~~rm~~~L~~RV~lS~ 45 (63)
T PF11137_consen 12 IIASLFSALFFLVKDKGSSKRMVKALGRRVGLSA 45 (63)
T ss_pred HHHHHHHHHHHHhhCCCCCchHHHHHHHHHHHHH
Confidence 344443333344566543 23333346776654
No 36
>KOG4193 consensus G protein-coupled receptors [Signal transduction mechanisms]
Probab=27.19 E-value=70 Score=31.49 Aligned_cols=80 Identities=24% Similarity=0.404 Sum_probs=52.4
Q ss_pred hHHHHHHHHHHHHHHhhhe----------eeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhh
Q 028579 102 SWVYFSVILGVVLFLLQLL----------WIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKV 171 (207)
Q Consensus 102 SW~yF~~iLgvVL~~L~v~----------WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~ 171 (207)
.|+.=+++.|++..+=+.. |||..++++-.|+.=+.-+---- .+|+++.+. .+=-....+++.++++
T Consensus 434 gwg~Pavvv~Isa~~~~~~~~~~~~~~~CWl~~~~~~~~~F~GPv~~ii~~N-i~~Fv~t~~--~l~~~~~~~~~~~~~~ 510 (610)
T KOG4193|consen 434 GWGVPAVVVGVSALVDPDLEGQYGTPRVCWLDTQNGFIWSFLGPVTLIILVN-IVMFVVTLK--KLLRRLSKLQPIASKL 510 (610)
T ss_pred HhhhhHHHHhheeEEeccCccccccCCceEEecCCceEEEEehHHHHHHHHH-HHHHHHHHH--HHhhcccccCcchhhH
Confidence 4555566666665555555 99999999999888765433222 333332222 2234567889999999
Q ss_pred hhhhhhHHHHhhc
Q 028579 172 IGARAYRVLFAGV 184 (207)
Q Consensus 172 IGaRayRVlFA~v 184 (207)
.+-+.+|-..++.
T Consensus 511 ~~~~~~~~~l~L~ 523 (610)
T KOG4193|consen 511 ENISLIRSALALL 523 (610)
T ss_pred HHHHHHHHHHHHH
Confidence 9998888766654
No 37
>PRK10621 hypothetical protein; Provisional
Probab=26.94 E-value=66 Score=26.92 Aligned_cols=36 Identities=22% Similarity=0.153 Sum_probs=24.5
Q ss_pred hhhhhhhhhhHHHHhhcchhHHHHHHHHHHHHHHHhhc
Q 028579 168 GEKVIGARAYRVLFAGVSLPLAVSTIVSSNLLIQSILH 205 (207)
Q Consensus 168 gEk~IGaRayRVlFA~vSLPLAv~~IvYFi~~~~~~~~ 205 (207)
--+++++|.+|.+|+.+-+=.++-.+ |-.+. |.|+|
T Consensus 226 l~~~~~~~~lr~~~~~ll~~~~i~~~-~~~~~-~~~~~ 261 (266)
T PRK10621 226 LVLSKGQKLIRPMIVIVSAVMSAKLL-YDSHG-QEILH 261 (266)
T ss_pred HHHHcCchHhHHHHHHHHHHHHHHHH-HHHHh-HHHHH
Confidence 34568999999999987765555544 22223 88876
No 38
>TIGR01299 synapt_SV2 synaptic vesicle protein SV2. This model describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by pfam model pfam00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices.
Probab=26.87 E-value=1.6e+02 Score=29.32 Aligned_cols=23 Identities=13% Similarity=0.200 Sum_probs=17.9
Q ss_pred hhhHHHHhhcchhHHHHHHHHHH
Q 028579 175 RAYRVLFAGVSLPLAVSTIVSSN 197 (207)
Q Consensus 175 RayRVlFA~vSLPLAv~~IvYFi 197 (207)
+.||++|...++|..+.++.+|+
T Consensus 331 ~gWR~l~~i~~lp~ll~ll~~~~ 353 (742)
T TIGR01299 331 HSWRVFVIVCAFPCVFAIGALTF 353 (742)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHH
Confidence 56999999999998776665554
No 39
>PF00854 PTR2: POT family; InterPro: IPR000109 This entry represents the POT (proton-dependent oligopeptide transport) family, which all appear to be proton dependent transporters. The transport of peptides into cells is a well-documented biological phenomenon which is accomplished by specific, energy-dependent transporters found in a number of organisms as diverse as bacteria and humans. The POT family of proteins is distinct from the ABC-type peptide transporters and was uncovered by sequence analyses of a number of recently discovered peptide transport proteins []. These proteins that seem to be mainly involved in the intake of small peptides with the concomitant uptake of a proton []. These integral membrane proteins are predicted to comprise twelve transmembrane regions.; GO: 0005215 transporter activity, 0006857 oligopeptide transport, 0016020 membrane; PDB: 4APS_A 2XUT_C.
Probab=25.85 E-value=1e+02 Score=26.07 Aligned_cols=37 Identities=16% Similarity=0.389 Sum_probs=31.4
Q ss_pred ccchhHHHHHHHHHHHHHHhhheeeeCCCCchhhHHH
Q 028579 98 QKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGKAFID 134 (207)
Q Consensus 98 Qk~~SW~yF~~iLgvVL~~L~v~WIdpsTG~G~~Fid 134 (207)
++.-+|.|++.-+|..++.....||...-||.-.|.-
T Consensus 71 ~~~F~~fY~~in~G~~~~~~~~~~i~~~~~~~~~f~i 107 (372)
T PF00854_consen 71 DSFFNWFYWGINIGSLFSPTLVPYIQQNYGWFLGFGI 107 (372)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCCHHHHCS-HHHHHHH
T ss_pred hhhHHHHHHHHhhhhHhhcccchhhccccchhhhhhH
Confidence 3345699999999999999999999999999988853
No 40
>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=25.83 E-value=2.5e+02 Score=20.06 Aligned_cols=64 Identities=19% Similarity=0.170 Sum_probs=37.7
Q ss_pred hhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhh-hhhhhhHHHHhhcchhHHHHHH
Q 028579 129 GKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKV-IGARAYRVLFAGVSLPLAVSTI 193 (207)
Q Consensus 129 G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~-IGaRayRVlFA~vSLPLAv~~I 193 (207)
+++|-+.+..++ +.-...+-+++.+++..-+.-.+|..-+.. .|.+-|+-...-+++=+++++.
T Consensus 32 ~~~y~~~~~~~~-~p~~~~~~~l~~~~~~~H~~~Gir~~~~d~g~~~~~~~~~~~~~~~~~~vv~~ 96 (101)
T cd03501 32 PETYNAVIATYK-SPIFKLGEFGLVAAVVFHALNGIRLILVDFGSGGPRYQRQLFYIVLVLTVVLI 96 (101)
T ss_pred HHHHHHHHHHHH-ChHHHHHHHHHHHHHHHHHHHhHHHHHHHhcccchHHHHHHHHHHHHHHHHHH
Confidence 456655555554 453344445556666666677777777666 4665577666655555555444
No 41
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=25.32 E-value=43 Score=25.68 Aligned_cols=15 Identities=40% Similarity=1.054 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHh
Q 028579 103 WVYFSVILGVVLFLL 117 (207)
Q Consensus 103 W~yF~~iLgvVL~~L 117 (207)
|+.|++|+.+++.+|
T Consensus 2 W~l~~iii~~i~l~~ 16 (130)
T PF12273_consen 2 WVLFAIIIVAILLFL 16 (130)
T ss_pred eeeHHHHHHHHHHHH
Confidence 788877665544443
No 42
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=24.76 E-value=90 Score=28.70 Aligned_cols=25 Identities=24% Similarity=0.590 Sum_probs=22.3
Q ss_pred chhHHHHHHHHHHHHHHhhheeeeC
Q 028579 100 LTSWVYFSVILGVVLFLLQLLWIDN 124 (207)
Q Consensus 100 ~~SW~yF~~iLgvVL~~L~v~WIdp 124 (207)
..+|+++.++|+|+.+|+|-+|..+
T Consensus 155 ~~~~lf~ii~l~vla~ivY~~~~~~ 179 (318)
T PF06682_consen 155 GGSWLFWIIFLLVLAFIVYSLFLSC 179 (318)
T ss_pred CcchhhhHHHHHHHHHHHHHHHhcc
Confidence 3789999999999999999999954
No 43
>TIGR02185 Trep_Strep conserved hypothetical integral membrane protein TIGR02185. This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6.
Probab=24.54 E-value=1.6e+02 Score=24.31 Aligned_cols=17 Identities=18% Similarity=0.303 Sum_probs=14.0
Q ss_pred CCchhhHHHHHhccCCC
Q 028579 126 TGYGKAFIDSVSSLSDS 142 (207)
Q Consensus 126 TG~G~~Fidavssls~S 142 (207)
.|.+++|+|.+.+..+.
T Consensus 142 ~~~~~~y~~~~~~~~~~ 158 (189)
T TIGR02185 142 RGDSAEYIDQYIKYVSA 158 (189)
T ss_pred cCCcHHHHHHHHHhcch
Confidence 57788999999998843
No 44
>TIGR03745 conj_TIGR03745 integrating conjugative element membrane protein, PFL_4702 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition.
Probab=23.23 E-value=1.5e+02 Score=23.80 Aligned_cols=58 Identities=16% Similarity=0.206 Sum_probs=37.5
Q ss_pred eCCCCchhhHHHHHhccCCChHHHHHHHHH-HHHHHhcccccccchhhhhhhhhhhHHHH
Q 028579 123 DNSTGYGKAFIDSVSSLSDSHEVVMLVLIL-IFATVHSGLASLRDMGEKVIGARAYRVLF 181 (207)
Q Consensus 123 dpsTG~G~~Fidavssls~Sh~~VML~Lll-iFAi~HSGlAsLR~~gEk~IGaRayRVlF 181 (207)
+|++|=|+..++.+.+.--+- ++.++|++ ..|..--.-+++-...|-.-|.--|.=+=
T Consensus 22 ~PS~G~g~g~~~tik~Y~~dg-~~llgL~i~a~aFi~Va~~a~~ty~Ei~~Gk~~W~~fg 80 (104)
T TIGR03745 22 APSRGGGSGIMQTIKNYGYDG-GILLGLLIAAIAFIGVAYHALGTYHEIRTGKATWGDFG 80 (104)
T ss_pred CCCCCCCcCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHcchhhHHhCc
Confidence 699999999999999887665 55555554 22222222345556666666777776443
No 45
>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=22.76 E-value=1.8e+02 Score=22.05 Aligned_cols=49 Identities=22% Similarity=0.279 Sum_probs=30.2
Q ss_pred eeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhh
Q 028579 121 WIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEK 170 (207)
Q Consensus 121 WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk 170 (207)
|+.-..+..++| |.+.+.-++.-.-.+..++.+++.+-++.-+|--.-.
T Consensus 41 ~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~yH~~nGiRhl~~D 89 (120)
T TIGR02970 41 WLSLSLSSPESF-ATVHALLSSPLGKLILWGLLWALLYHLLAGIRHLLWD 89 (120)
T ss_pred HHHHHhcCHHHH-HHHHHHHhCHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 443233333455 6666665555345555677889998889999964433
No 46
>PF10864 DUF2663: Protein of unknown function (DUF2663); InterPro: IPR020210 This entry represents a group of uncharacterised transmembrane proteins.
Probab=22.36 E-value=1.2e+02 Score=24.88 Aligned_cols=40 Identities=25% Similarity=0.228 Sum_probs=25.4
Q ss_pred hhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhh
Q 028579 130 KAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKV 171 (207)
Q Consensus 130 ~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~ 171 (207)
+.|-..++.+.++. +.|.+++.++.+-...-.++.++||-
T Consensus 45 ~s~~~~~s~~~~~~--~~l~~ll~~~~~~~~~~~~~kK~eKA 84 (130)
T PF10864_consen 45 YSFSSFLSAILGSP--VHLFWLLALAFSYWAMYYLKKKEEKA 84 (130)
T ss_pred cCHHHHHHHHHcCh--HHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence 66777777777776 34444455555556667777777763
No 47
>PRK09039 hypothetical protein; Validated
Probab=22.14 E-value=86 Score=28.22 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=19.7
Q ss_pred hHHHHHhccCCChHHHHHHHHHHHHHHhc
Q 028579 131 AFIDSVSSLSDSHEVVMLVLILIFATVHS 159 (207)
Q Consensus 131 ~Fidavssls~Sh~~VML~LlliFAi~HS 159 (207)
-|||++++| =.|++.+|.+|-++..
T Consensus 18 g~vd~~~~l----l~~~~f~l~~f~~~q~ 42 (343)
T PRK09039 18 GFVDALSTL----LLVIMFLLTVFVVAQF 42 (343)
T ss_pred hHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 489999987 3677788889988764
No 48
>PF11877 DUF3397: Protein of unknown function (DUF3397); InterPro: IPR024515 This family of bacterial proteins is currently functionally uncharacterised.
Probab=21.91 E-value=3.1e+02 Score=20.92 Aligned_cols=38 Identities=26% Similarity=0.310 Sum_probs=25.8
Q ss_pred cccccchhh---hhhhhhhhHHHHhhcchhHHHHHHHHHHHHHHHhhc
Q 028579 161 LASLRDMGE---KVIGARAYRVLFAGVSLPLAVSTIVSSNLLIQSILH 205 (207)
Q Consensus 161 lAsLR~~gE---k~IGaRayRVlFA~vSLPLAv~~IvYFi~~~~~~~~ 205 (207)
+...|..+| ++.-...||..|.. ..+.|..+++-.+.|
T Consensus 76 ~~~~~~~~~i~~~k~~k~~WR~~Fll-------~~~~Yi~l~i~~ii~ 116 (116)
T PF11877_consen 76 IYQARKKGEISYKKFFKKFWRLGFLL-------TFFLYIGLLIIGIIK 116 (116)
T ss_pred HHHHHHcCcchhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHC
Confidence 345666666 45566789999875 456777777776654
No 49
>PF15383 TMEM237: Transmembrane protein 237
Probab=21.69 E-value=2.5e+02 Score=24.97 Aligned_cols=67 Identities=16% Similarity=0.190 Sum_probs=41.0
Q ss_pred CCCCchhhHHHHHhccC-CChHHHHHHHHHH-------HHHHhcccccccchhhhhhhhhhhHHHHhhcchhHHHHHHHH
Q 028579 124 NSTGYGKAFIDSVSSLS-DSHEVVMLVLILI-------FATVHSGLASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVS 195 (207)
Q Consensus 124 psTG~G~~Fidavssls-~Sh~~VML~Llli-------FAi~HSGlAsLR~~gEk~IGaRayRVlFA~vSLPLAv~~IvY 195 (207)
+..+=++.|+..-+.++ +-|...++++.++ +.+.|..++.+|. + ..--|.|+..++|
T Consensus 122 ~~~~~~~~lL~~Y~~la~p~~~~fY~l~~is~VSafDr~dl~~~~~~~~r~-------------~--~~~~~~~lai~ly 186 (253)
T PF15383_consen 122 YQLSTVSNLLSQYSPLAYPAQSLFYFLLAISTVSAFDRYDLAHFSMAHLRG-------------F--LKLDPGALAILLY 186 (253)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHhhcccHHHHHh-------------h--hccCchHHHHHHH
Confidence 33344568999999998 6665655554442 2344554444332 2 2344677778899
Q ss_pred HHHHHHHhhc
Q 028579 196 SNLLIQSILH 205 (207)
Q Consensus 196 Fi~~~~~~~~ 205 (207)
|+-++-+...
T Consensus 187 ~~~lvlsls~ 196 (253)
T PF15383_consen 187 FIALVLSLSC 196 (253)
T ss_pred HHHHHHHHHH
Confidence 9988876543
No 50
>PF09605 Trep_Strep: Hypothetical bacterial integral membrane protein (Trep_Strep); InterPro: IPR011733 This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
Probab=21.52 E-value=1.5e+02 Score=24.35 Aligned_cols=58 Identities=21% Similarity=0.448 Sum_probs=33.6
Q ss_pred CcccchhHHHHHHHHHHHHHHhhheeeeC--------CCCchhhHHHHHhccCCChHHHHHHHHHHHH
Q 028579 96 KNQKLTSWVYFSVILGVVLFLLQLLWIDN--------STGYGKAFIDSVSSLSDSHEVVMLVLILIFA 155 (207)
Q Consensus 96 ~~Qk~~SW~yF~~iLgvVL~~L~v~WIdp--------sTG~G~~Fidavssls~Sh~~VML~LlliFA 155 (207)
++.+..-+.|---.++.. ...-..|+++ +.|+|.+|+|.+.++.+.. ...+.++..|.
T Consensus 102 ~~~~~~~iay~vf~~~~~-g~~~p~~~~~~~y~~~~~~~~~~~~y~~~~~~~~~~~-~~~~~~~~~~v 167 (186)
T PF09605_consen 102 KSKKRNTIAYAVFSLGYM-GPYLPIWFMRDAYLAAMIAKGMGAEYADTMISFFTPW-MLIIIIIITFV 167 (186)
T ss_pred CcHHHHHHHHHHHHHHHH-hhHHHHHHhHHHHHHHHHHcCCCHHHHHHHHHHcchH-HHHHHHHHHHH
Confidence 333333344433333444 4555566655 4699999999999998775 33333333333
No 51
>PRK15006 thiosulfate reductase cytochrome B subunit; Provisional
Probab=21.48 E-value=65 Score=27.91 Aligned_cols=73 Identities=18% Similarity=0.088 Sum_probs=38.3
Q ss_pred cccceecCcccchhHH-HHHHHHHHHHHHhhhe---eeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccc
Q 028579 89 DSAAFDLKNQKLTSWV-YFSVILGVVLFLLQLL---WIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASL 164 (207)
Q Consensus 89 DsAvF~l~~Qk~~SW~-yF~~iLgvVL~~L~v~---WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsL 164 (207)
+..-||-. ||+.-|. .+..++..++..+... |. +..--|. ..-...-|++.+ .++++|.++|--++..
T Consensus 172 ~~~k~Npg-qkl~y~~v~~~~~~~livTGl~l~~p~~~-~~~~~g~-----~~~~~~iH~~~a-~lli~fiivHIYl~~~ 243 (261)
T PRK15006 172 TQSKFNPL-QQLAYLGVMYGLVPLLLLTGLLCLYPQAV-GDVFPGV-----RYWLLQLHFALA-FISLFFIFGHLYLCTT 243 (261)
T ss_pred cccccCHH-HHHHHHHHHHHHHHHHHHHHHHHHhHhhc-ccccccH-----HHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 44467765 7888886 3455444444443321 21 1110011 111224464444 6678888999988765
Q ss_pred cchhh
Q 028579 165 RDMGE 169 (207)
Q Consensus 165 R~~gE 169 (207)
.+..|
T Consensus 244 ~~~~~ 248 (261)
T PRK15006 244 GRTPG 248 (261)
T ss_pred hhccc
Confidence 44443
No 52
>PF05425 CopD: Copper resistance protein D; InterPro: IPR008457 Copper sequestering activity displayed by some bacteria is determined by copper-binding protein products of the copper resistance operon (cop). CopD, together with CopC, perform copper uptake into the cytoplasm [].; GO: 0016021 integral to membrane
Probab=21.38 E-value=3.3e+02 Score=19.75 Aligned_cols=49 Identities=22% Similarity=0.558 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHHHHhhheeee------CCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhc
Q 028579 102 SWVYFSVILGVVLFLLQLLWID------NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHS 159 (207)
Q Consensus 102 SW~yF~~iLgvVL~~L~v~WId------psTG~G~~Fidavssls~Sh~~VML~LlliFAi~HS 159 (207)
||+-..++...++..++-.|.- ..|.||.-.+-. .+.+.+++..+..|-
T Consensus 8 s~~a~~av~~l~~TG~~~a~~~~~~~~l~~t~yG~~Ll~K---------~~L~~~~l~l~~~~~ 62 (105)
T PF05425_consen 8 SWIAWAAVAVLVVTGLVMAWLRLGFDALFTTPYGRLLLVK---------LALVLLMLALAAYNR 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCchhhccChhHHHHHHH---------HHHHHHHHHHHHHHH
Confidence 3444445555555666555554 236677554432 344555556666664
No 53
>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=21.33 E-value=3.5e+02 Score=20.05 Aligned_cols=80 Identities=16% Similarity=0.104 Sum_probs=42.0
Q ss_pred ccchhHHHHHHHHHHHHHHhhheeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchh-------hh
Q 028579 98 QKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMG-------EK 170 (207)
Q Consensus 98 Qk~~SW~yF~~iLgvVL~~L~v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~g-------Ek 170 (207)
|+++.++.+..++..+.... -...-..+|-...+-. ++.-.-++.+++.+++.+-...-+|.-. |+
T Consensus 22 hRiSGv~L~~~~~~~~~~~~------~~~~~~~~y~~~~~~~-~~~~~~~~~~~~~~~~~yH~~nGiRhll~D~g~~~~~ 94 (117)
T cd03499 22 HRITGVALFLGLPLLLWWLL------ASLSSPESFESVSALL-GSWLGKLVLFGLTWALFYHLLNGIRHLIWDLGKGLEL 94 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHH------HHhcCHHHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHHhhHHHHHHHccccCcH
Confidence 44455555444444433332 2222334454444433 3443556667788888888888888532 34
Q ss_pred hhhhhhhHHHHhhc
Q 028579 171 VIGARAYRVLFAGV 184 (207)
Q Consensus 171 ~IGaRayRVlFA~v 184 (207)
.-+.+..++.+++.
T Consensus 95 ~~~~~~~~~~~~~~ 108 (117)
T cd03499 95 KTVYKSGYAVLVLS 108 (117)
T ss_pred HHHHHHHHHHHHHH
Confidence 44455555555443
No 54
>TIGR00771 DcuC c4-dicarboxylate anaerobic carrier family protein. catalyzing fumarate-succinate exchange and fumarate uptake.
Probab=21.04 E-value=1.5e+02 Score=26.93 Aligned_cols=51 Identities=14% Similarity=-0.019 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhhheeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHH
Q 028579 105 YFSVILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFA 155 (207)
Q Consensus 105 yF~~iLgvVL~~L~v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFA 155 (207)
.++.++..+.++....|+=..+|..+...+++.+++.+....++.+.+++.
T Consensus 256 ~~~~v~~iI~aA~vF~~~L~~~Gi~~~l~~~l~~~~~~~~~~ll~~~l~~~ 306 (388)
T TIGR00771 256 SFANVVGLIVAASVFAAGLKTIGAVDAAISFAKESGLGNIFVMWGATIGPF 306 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 355677788888889999999999999999999998777444444444333
No 55
>PF00209 SNF: Sodium:neurotransmitter symporter family; InterPro: IPR000175 Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions []. Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na+ and Cl-, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na+ and the counter-transport of K+, with no apparent dependence on Cl- []. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters [, ]. Sequence analysis of the Na+/Cl- neurotransmitter superfamily reveals that it can be divided into four subfamilies, these being transporters for monoamines, the amino acids proline and glycine, GABA, and a group of orphan transporters [].; GO: 0005328 neurotransmitter:sodium symporter activity, 0006836 neurotransmitter transport, 0016021 integral to membrane; PDB: 2QEI_A 3F3C_A 3USP_A 3USK_A 3TU0_A 3GWW_A 3TT3_A 3F4J_A 3USJ_B 3GJC_B ....
Probab=21.02 E-value=5.6e+02 Score=23.65 Aligned_cols=67 Identities=19% Similarity=0.306 Sum_probs=39.7
Q ss_pred CCchhhHHHHHhccCCChHHHHHHHHHHHHHH-hcccccccchhhhhhhhhh---hHHHHhhcchhHHHHHH
Q 028579 126 TGYGKAFIDSVSSLSDSHEVVMLVLILIFATV-HSGLASLRDMGEKVIGARA---YRVLFAGVSLPLAVSTI 193 (207)
Q Consensus 126 TG~G~~Fidavssls~Sh~~VML~LlliFAi~-HSGlAsLR~~gEk~IGaRa---yRVlFA~vSLPLAv~~I 193 (207)
|.-|..++|.+.....+......+++...++. .-|...++..-|+.+|.|. |+++...+ .|.....+
T Consensus 405 t~~G~~~~~~~d~~~~~~~l~~~~l~e~i~v~wvyG~~~~~~di~~~~g~~~~~~w~~~w~~v-~Pi~ll~i 475 (523)
T PF00209_consen 405 TQGGIYIFDLLDDYVGSISLLIIALLECIAVGWVYGWDRFREDINEMLGFKPGKFWKFLWKYV-TPIILLVI 475 (523)
T ss_dssp BT---THHHHHHHHTTTHHHHHHHHHHHHHHHTTSTHHHHHHHHHTT-SS---THHHHHHHTH-HHHHHHHH
T ss_pred cccHHHhcchHhhcchhHHHHHHHHHHHHheeccccceehhhhhcccccccHHHHHHhhEEEe-ecccccce
Confidence 55678899999888877644544555445554 4678888888888888654 55555444 36655443
No 56
>PF09600 Cyd_oper_YbgE: Cyd operon protein YbgE (Cyd_oper_YbgE); InterPro: IPR011846 This entry describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria [].
Probab=20.93 E-value=3.8e+02 Score=20.28 Aligned_cols=58 Identities=21% Similarity=0.358 Sum_probs=35.2
Q ss_pred HHHHHHHHhhheeeeCCCCchhhHHHHHhccCCChHHHHHHHHHHHHHHhcccccccchhhhhhhhhhhHHHHh
Q 028579 109 ILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFA 182 (207)
Q Consensus 109 iLgvVL~~L~v~WIdpsTG~G~~Fidavssls~Sh~~VML~LlliFAi~HSGlAsLR~~gEk~IGaRayRVlFA 182 (207)
+|+.++++ .+..|| +.|-+..++.+... ..++..-.+-..+|. -.+||+ .+.||++|.
T Consensus 8 ilAl~la~--~v~~~P-----~~fA~~~g~~~~~~-~~ll~wavc~~~IhG--vGF~Pr------~~~Wr~lFs 65 (82)
T PF09600_consen 8 ILALALAA--CVFWDP-----NRFAAATGGFSHWL-APLLIWAVCAGWIHG--VGFRPR------SWIWRLLFS 65 (82)
T ss_pred HHHHHHHH--HHHcCH-----HHHHHHcCCCcHHH-HHHHHHHHHHHHhhc--cccchh------HHHHHHHHh
Confidence 44444443 345566 47888777766655 444444556667784 345554 478999994
No 57
>PF00586 AIRS: AIR synthase related protein, N-terminal domain; InterPro: IPR000728 This family includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; GO: 0003824 catalytic activity; PDB: 3VIU_A 2Z1T_A 2Z1U_A 3C9U_B 3C9S_A 3C9R_A 1VQV_A 3C9T_B 3M84_A 3QTY_A ....
Probab=20.80 E-value=50 Score=23.25 Aligned_cols=10 Identities=30% Similarity=0.684 Sum_probs=9.3
Q ss_pred cccccceecC
Q 028579 87 GEDSAAFDLK 96 (207)
Q Consensus 87 GEDsAvF~l~ 96 (207)
|||+|+.++.
T Consensus 1 GdDaavi~~~ 10 (96)
T PF00586_consen 1 GDDAAVIRIP 10 (96)
T ss_dssp TSSSEEEEET
T ss_pred CCceEEEEcC
Confidence 8999999998
Done!