Query 024669
Match_columns 264
No_of_seqs 65 out of 67
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 06:29:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024669.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024669hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4094 Predicted membrane pro 100.0 3.6E-30 7.9E-35 225.9 1.5 110 145-264 2-112 (219)
2 PF07298 NnrU: NnrU protein; 99.6 5.2E-16 1.1E-20 131.2 0.8 103 146-264 1-105 (191)
3 cd03500 SQR_TypeA_SdhD_like Su 68.7 13 0.00029 28.1 5.0 83 98-186 8-90 (106)
4 PF04191 PEMT: Phospholipid me 65.2 1.9 4E-05 31.6 -0.2 17 247-263 39-55 (106)
5 PF10242 L_HGMIC_fpl: Lipoma H 55.3 13 0.00027 31.4 3.0 31 83-114 137-167 (181)
6 PF06966 DUF1295: Protein of u 53.6 5.2 0.00011 34.7 0.5 17 247-263 152-168 (235)
7 PF09878 DUF2105: Predicted me 49.4 9.7 0.00021 34.8 1.5 76 136-233 106-183 (212)
8 PF11446 DUF2897: Protein of u 41.8 14 0.00031 27.0 1.1 28 146-173 5-32 (55)
9 PRK10179 formate dehydrogenase 34.9 34 0.00073 29.6 2.5 67 91-163 107-174 (217)
10 KOG4026 Uncharacterized conser 29.3 50 0.0011 30.2 2.7 35 83-118 141-175 (207)
11 PF09622 DUF2391: Putative int 28.5 2.6E+02 0.0056 26.1 7.3 94 100-202 138-238 (267)
12 PF01292 Ni_hydr_CYTB: Prokary 27.7 33 0.00072 26.8 1.2 71 97-169 100-172 (182)
13 PRK13628 serine/threonine tran 25.6 1E+02 0.0022 29.4 4.2 58 98-167 14-74 (402)
14 TIGR02968 succ_dehyd_anc succi 25.4 72 0.0016 24.4 2.7 56 127-183 32-87 (105)
15 COG2020 STE14 Putative protein 23.9 41 0.0009 28.3 1.2 21 243-263 100-120 (187)
16 TIGR02125 CytB-hydogenase Ni/F 23.4 80 0.0017 25.8 2.7 67 97-164 115-189 (211)
17 PF00033 Cytochrom_B_N: Cytoch 23.4 83 0.0018 24.4 2.7 71 96-167 104-176 (188)
18 TIGR01583 formate-DH-gamm form 23.1 75 0.0016 26.8 2.6 67 93-164 104-171 (204)
19 cd03493 SQR_QFR_TM Succinate:q 22.5 1.2E+02 0.0025 21.0 3.1 50 124-174 23-72 (98)
20 PF06472 ABC_membrane_2: ABC t 22.3 51 0.0011 28.9 1.5 77 96-175 19-96 (281)
21 COG3736 VirB8 Type IV secretor 21.3 66 0.0014 29.5 2.1 36 92-129 33-84 (239)
22 PF01146 Caveolin: Caveolin; 20.6 52 0.0011 28.2 1.1 21 176-196 70-90 (148)
23 cd03494 SQR_TypeC_SdhD Succina 20.5 2.4E+02 0.0052 21.9 4.7 53 129-182 28-80 (99)
24 PRK14749 hypothetical protein; 20.2 40 0.00087 22.8 0.3 20 105-124 3-26 (30)
No 1
>COG4094 Predicted membrane protein [Function unknown]
Probab=99.95 E-value=3.6e-30 Score=225.88 Aligned_cols=110 Identities=32% Similarity=0.506 Sum_probs=107.3
Q ss_pred HHHHHHHHHHHHHhccccccccchhhhhcchhhhhhhhcccchhHHHHHHHhhhccccceeeceecCCCceeehhhhhhh
Q 024669 145 VVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVYFINHRYDGMQLWQLQGAPGVHQIVWLSSF 224 (264)
Q Consensus 145 ~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~RayRvlFA~vSLPLAv~~I~YFinHRYDGvqLW~lqgvpgv~~lVW~lsa 224 (264)
.+|++.++.|...||+-+ ++++||-.++..|.|++...+.||.||||||+++|++|+++|+.+++|..++
T Consensus 2 ~~lvl~l~lFl~~Hsv~~----------~~p~~R~~~i~~~g~~a~~glys~vs~~~lglvi~~~~~v~~v~~~lw~p~a 71 (219)
T COG4094 2 LILVLGLVLFLGLHSVRV----------AAPAFRARLIAASGKLAWRGLYSFVSLRGLGLVIWAVQVVRGVPPMLWDPPA 71 (219)
T ss_pred hHHHHHHHHHHHHhcccc----------ccHHHHHHHHHhcCCcceehHHHHHHHHhhhhhheeeeccCCCCcceeCcHH
Confidence 578899999999999976 8999999999999999999999999999999999999999999999999999
Q ss_pred hh-hhhccccccceeeeeccCCCceeeeeceeeeeecCCCC
Q 024669 225 VS-FFFLYPSTFNLLEVAAVDEPKMHLWETGVMRITRHPQV 264 (264)
Q Consensus 225 IS-FlFLYPaTFNLLEIAAV~KPqvHLyETGIiRITRHPQm 264 (264)
.| |+++||+|||++|++|.+||+.|+||++|+||||||||
T Consensus 72 ~~~h~~l~~a~~~l~~l~A~~~p~~~~~~g~Ii~itRHP~l 112 (219)
T COG4094 72 WSRHLALLLATFALILLAAGLKPAQHLYEGRIIRITRHPQL 112 (219)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccccccCCceEEEecCchh
Confidence 99 99999999999999999999999999999999999997
No 2
>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=99.56 E-value=5.2e-16 Score=131.19 Aligned_cols=103 Identities=26% Similarity=0.393 Sum_probs=96.8
Q ss_pred HHHHHHHHHHHHhccc--cccccchhhhhcchhhhhhhhcccchhHHHHHHHhhhccccceeeceecCCCceeehhhhhh
Q 024669 146 VMLVLILIFATVHSGL--ASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVYFINHRYDGMQLWQLQGAPGVHQIVWLSS 223 (264)
Q Consensus 146 vmL~Lll~FAi~HSGl--AsLR~~gE~~IG~RayRvlFA~vSLPLAv~~I~YFinHRYDGvqLW~lqgvpgv~~lVW~ls 223 (264)
++++.++.|+..||.. ..+|++.++.+|+|.||.+|+++|+..-+.+|.++-++|++ .++|+.+ |+.+.+++++.
T Consensus 1 ~li~~l~lF~~~Hs~~~~p~~R~~l~~~lG~~~y~~~ysllSl~~l~lii~~~~~a~~~-~~lw~~~--~~~~~l~~~lm 77 (191)
T PF07298_consen 1 LLILGLALFLGQHSVPARPGLRARLIARLGERGYRGLYSLLSLAGLVLIIWGYRSAPFV-PPLWDPP--PWLRHLANLLM 77 (191)
T ss_pred CHHHHHHHHHHHHhhhccHhhhHHHHHHcCchhhHHHHHHHHHHHHHHHHHHHHhCCCC-CcccCCc--hhHHHHHHHHH
Confidence 3567788999999995 78999999999999999999999999999999999999999 9999999 99999999999
Q ss_pred hhhhhhccccccceeeeeccCCCceeeeeceeeeeecCCCC
Q 024669 224 FVSFFFLYPSTFNLLEVAAVDEPKMHLWETGVMRITRHPQV 264 (264)
Q Consensus 224 aISFlFLYPaTFNLLEIAAV~KPqvHLyETGIiRITRHPQm 264 (264)
.++|++++.++++-.+.. |.|+|||||+
T Consensus 78 ~~a~il~~~a~~~~~~~~-------------i~r~~RHP~l 105 (191)
T PF07298_consen 78 LLAFILLVAALFPPNPFS-------------IYRITRHPML 105 (191)
T ss_pred HHHHHHHHHHhccCcchH-------------HHHHhcCchH
Confidence 999999999999887766 9999999995
No 3
>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=68.67 E-value=13 Score=28.05 Aligned_cols=83 Identities=16% Similarity=0.097 Sum_probs=47.4
Q ss_pred cceehhhHHHHHHHHHHHhhheeeeeCCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccchhhhhcchhh
Q 024669 98 QKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAY 177 (264)
Q Consensus 98 Qk~~sW~yF~~ilgvVL~~l~v~Widp~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~Ray 177 (264)
|++++++.+-.+..-+.......+ +-+.+|-+..+.+++.- +..+.+++..+..+=+...+|.--|+.+-.+..
T Consensus 8 qRiTgv~L~~~l~~hi~~~~~~~~-----~~~~~~~~~~~~~~~p~-~~i~~~lll~~~~~H~~~Glr~il~Dy~~~~~~ 81 (106)
T cd03500 8 QRITGVFLVFLLAGHFWVQHMDNG-----GDVIDFAFVANRLASPL-WKVWDLLLLVLALLHGGNGLRNILLDYVRRPRL 81 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-----CCccCHHHHHHHHcChH-HHHHHHHHHHHHHHHHHHhHHHHHHHHccCchH
Confidence 555655555444333333332221 23345555555555333 444555666677777899999999998776666
Q ss_pred hhhhhcccc
Q 024669 178 RVLFAGVSL 186 (264)
Q Consensus 178 RvlFA~vSL 186 (264)
|..+-.+..
T Consensus 82 r~~~~~~~~ 90 (106)
T cd03500 82 RRAVKGLLY 90 (106)
T ss_pred HHHHHHHHH
Confidence 765544433
No 4
>PF04191 PEMT: Phospholipid methyltransferase ; InterPro: IPR007318 The Saccharomyces cerevisiae (Baker's yeast) phospholipid methyltransferase (2.1.1.16 from EC) has a broad substrate specificity of unsaturated phospholipids [].; GO: 0008170 N-methyltransferase activity, 0006644 phospholipid metabolic process
Probab=65.25 E-value=1.9 Score=31.64 Aligned_cols=17 Identities=41% Similarity=0.563 Sum_probs=14.7
Q ss_pred ceeeeeceeeeeecCCC
Q 024669 247 KMHLWETGVMRITRHPQ 263 (264)
Q Consensus 247 qvHLyETGIiRITRHPQ 263 (264)
.-+|-.+|+=|.+|||+
T Consensus 39 ~~~Lvt~G~Y~~vRhPm 55 (106)
T PF04191_consen 39 PQRLVTTGPYRYVRHPM 55 (106)
T ss_pred CCcccccCCccCcCChH
Confidence 34499999999999997
No 5
>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=55.27 E-value=13 Score=31.39 Aligned_cols=31 Identities=32% Similarity=0.649 Sum_probs=26.3
Q ss_pred cccccccccceecCccceehhhHHHHHHHHHH
Q 024669 83 ATLAGEDSAAFDLKNQKLTSWVYFSVILGVVL 114 (264)
Q Consensus 83 ~~lVGEDsA~F~~~~Qk~~sW~yF~~ilgvVL 114 (264)
-.+=||||..|++++= --.|.|..+++|++.
T Consensus 137 ~~~CG~~s~~y~~g~C-~~gwa~~la~~~~~~ 167 (181)
T PF10242_consen 137 RQLCGPDSDPYKLGDC-SLGWAYYLAIIGVAD 167 (181)
T ss_pred HhhhcCCCCceeCCCC-CCChHHHHHHHHHHH
Confidence 3577999999999975 668999999999953
No 6
>PF06966 DUF1295: Protein of unknown function (DUF1295); InterPro: IPR010721 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.
Probab=53.57 E-value=5.2 Score=34.72 Aligned_cols=17 Identities=41% Similarity=0.698 Sum_probs=15.1
Q ss_pred ceeeeeceeeeeecCCC
Q 024669 247 KMHLWETGVMRITRHPQ 263 (264)
Q Consensus 247 qvHLyETGIiRITRHPQ 263 (264)
+-++..+|.=|.+|||.
T Consensus 152 ~g~~~~~GLw~~sRHPN 168 (235)
T PF06966_consen 152 KGKFCTTGLWRYSRHPN 168 (235)
T ss_pred CCccccCCeeeeeeCch
Confidence 36789999999999996
No 7
>PF09878 DUF2105: Predicted membrane protein (DUF2105); InterPro: IPR019212 This entry represents a protein found in various hypothetical archaeal proteins, has no known function.
Probab=49.42 E-value=9.7 Score=34.80 Aligned_cols=76 Identities=26% Similarity=0.662 Sum_probs=50.5
Q ss_pred hhccCCChHHHHHHHHHHHHHHhccccccccchhhhhcchhhhhhhhcccchhHHHHHHHhhhccccceeeceecCCCce
Q 024669 136 VSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFAGVSLPLAVSTIVYFINHRYDGMQLWQLQGAPGV 215 (264)
Q Consensus 136 vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~RayRvlFA~vSLPLAv~~I~YFinHRYDGvqLW~lqgvpgv 215 (264)
+|-+..++ -.+...+.+|.+.-||-. |-.++ |.-++.||+.+|+.|.+.-+..|+.|+
T Consensus 106 mEVl~TaP-~fiaiiLvvYG~iLSGFT-----GGAVa----------------a~GllfY~ls~~~~g~~~~~wegi~~~ 163 (212)
T PF09878_consen 106 MEVLRTAP-KFIAIILVVYGAILSGFT-----GGAVA----------------ASGLLFYFLSRRVRGLPIFVWEGIEGV 163 (212)
T ss_pred eeeeccch-HHHHHHHHHHHHHHcCCc-----cHHHH----------------HhhHHHHHHhhhhcCCcceeeehhhhh
Confidence 34455555 334456667777777742 22222 344678999999999998777888888
Q ss_pred eehhhhhhhhhh--hhcccc
Q 024669 216 HQIVWLSSFVSF--FFLYPS 233 (264)
Q Consensus 216 ~~lVW~lsaISF--lFLYPa 233 (264)
..+.|.+-.+.| ||+.|.
T Consensus 164 SGiaWalWi~gF~~Ff~~P~ 183 (212)
T PF09878_consen 164 SGIAWALWIAGFIGFFLFPQ 183 (212)
T ss_pred hhHHHHHHHHHHHHHHHhHH
Confidence 888777766655 456665
No 8
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=41.81 E-value=14 Score=27.03 Aligned_cols=28 Identities=11% Similarity=0.324 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHhccccccccchhhhhc
Q 024669 146 VMLVLILIFATVHSGLASLRDMGEKVIG 173 (264)
Q Consensus 146 vmL~Lll~FAi~HSGlAsLR~~gE~~IG 173 (264)
+.++++++|+++=|++|.||..|--+++
T Consensus 5 ~wlIIviVlgvIigNia~LK~sAk~K~~ 32 (55)
T PF11446_consen 5 PWLIIVIVLGVIIGNIAALKYSAKMKFP 32 (55)
T ss_pred hhHHHHHHHHHHHhHHHHHHHhcccCCC
Confidence 4567889999999999999998874433
No 9
>PRK10179 formate dehydrogenase-N subunit gamma; Provisional
Probab=34.87 E-value=34 Score=29.56 Aligned_cols=67 Identities=15% Similarity=0.218 Sum_probs=39.2
Q ss_pred cceecCccceehhhHHHHHHHHHHHhhheeeee-CCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccc
Q 024669 91 AAFDLKNQKLTSWVYFSVILGVVLFLLQLLWID-NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLAS 163 (264)
Q Consensus 91 A~F~~~~Qk~~sW~yF~~ilgvVL~~l~v~Wid-p~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAs 163 (264)
..||-+ ||+.-|..+.+++..++..+. +|.. ..+.++.. .+.-...=|.+.| .++++|.++|--+|.
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-IWRPYFAQYFPMQ---VVRYSLLIHAAAG-IILIHAILIHMYMAF 174 (217)
T ss_pred cccCHH-HHHHHHHHHHHHHHHHHHHHH-HHHHhhhhhCCHH---HHHHHHHHHHHHH-HHHHHHHHHHHHHHh
Confidence 346665 889999877766666666655 4521 12222222 2222224464444 567888899998874
No 10
>KOG4026 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.27 E-value=50 Score=30.15 Aligned_cols=35 Identities=20% Similarity=0.586 Sum_probs=29.8
Q ss_pred cccccccccceecCccceehhhHHHHHHHHHHHhhh
Q 024669 83 ATLAGEDSAAFDLKNQKLTSWVYFSVILGVVLFLLQ 118 (264)
Q Consensus 83 ~~lVGEDsA~F~~~~Qk~~sW~yF~~ilgvVL~~l~ 118 (264)
-..=||++-.|++++=++ .|.|..+|+|+++..+-
T Consensus 141 r~~CG~~a~ky~lG~CsI-gWaY~lAIig~~daliL 175 (207)
T KOG4026|consen 141 RRMCGAKAGKYYLGDCSI-GWAYYLAIIGILDALIL 175 (207)
T ss_pred HHHhccccCCccCccccc-cHHHHHHHHHHHHHHHH
Confidence 447899999999999855 69999999999987653
No 11
>PF09622 DUF2391: Putative integral membrane protein (DUF2391); InterPro: IPR024464 Members of this protein family are found in archaea and bacteria. Their function is unknown.
Probab=28.54 E-value=2.6e+02 Score=26.10 Aligned_cols=94 Identities=17% Similarity=0.219 Sum_probs=45.4
Q ss_pred eehhhHHH-HHHHHHHHhhheeeeeCCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHh-----ccccccccchh-hhh
Q 024669 100 LTSWVYFS-VILGVVLFLLQLLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVH-----SGLASLRDMGE-KVI 172 (264)
Q Consensus 100 ~~sW~yF~-~ilgvVL~~l~v~Widp~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~H-----SGlAsLR~~gE-~~I 172 (264)
-..|...+ -++|.++..++++== +.-.+=-.++++-|.+.+++ +..++.| +|....+++-| .-+
T Consensus 138 ~~~~~Dl~q~~vGA~~lA~p~apT-------eEvw~lA~~ms~~~~l~l~~--~sL~i~y~fvy~a~f~~~~~~~~~~g~ 208 (267)
T PF09622_consen 138 RGYLADLGQMIVGALFLAFPFAPT-------EEVWLLAAKMSPWHALALVL--LSLAIMYLFVYKAGFRGQHKREEQRGI 208 (267)
T ss_pred cccHHHHHHHHHHHHHHhcCcCcc-------hHHHHHHHhCCHHHHHHHHH--HHHHHHHHHHHhhccCCccchhhccCc
Confidence 34455544 467888888887521 23333335666777544433 3333333 45443333332 335
Q ss_pred cchhhhhhhhcccchhHHHHHHHhhhcccc
Q 024669 173 GARAYRVLFAGVSLPLAVSTIVYFINHRYD 202 (264)
Q Consensus 173 G~RayRvlFA~vSLPLAv~~I~YFinHRYD 202 (264)
+.|..|.....--+-+.++++.-+.-+|+|
T Consensus 209 ~~~~l~~tivsY~isl~vsl~~L~~f~~~~ 238 (267)
T PF09622_consen 209 FQRFLRFTIVSYLISLLVSLLMLWFFGRLD 238 (267)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 566666543333333333333222225665
No 12
>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=27.70 E-value=33 Score=26.85 Aligned_cols=71 Identities=21% Similarity=0.289 Sum_probs=41.3
Q ss_pred ccceehhhHHHHHHHHHHHhhheeeeeCCCCcch--hHHHHhhccCCChHHHHHHHHHHHHHHhccccccccchh
Q 024669 97 NQKLTSWVYFSVILGVVLFLLQLLWIDNSTGYGK--AFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGE 169 (264)
Q Consensus 97 ~Qk~~sW~yF~~ilgvVL~~l~v~Widp~TG~G~--~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE 169 (264)
-||..-|+.+...+..++..+...+ ...+|++- ...+.......=|++.+..++ +|.++|-.+|-......
T Consensus 100 ~~~~~~~~~~~~~~~~~iTG~~~~~-~~~~~~~~~~~~~~~~~~~~~vH~~~a~~~i-~~i~~Hv~~a~~~~~~~ 172 (182)
T PF01292_consen 100 GQKIVHWVLYLLLLLLPITGLLLWF-ASAEGFPLFAASPGGAQIARSVHFFLAWLLI-AFIILHVYAALFHHFRW 172 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-hhcccCccccccchHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhhhH
Confidence 3566777777777766666554433 32333322 112222233344766665555 99999999887776554
No 13
>PRK13628 serine/threonine transporter SstT; Provisional
Probab=25.59 E-value=1e+02 Score=29.39 Aligned_cols=58 Identities=22% Similarity=0.403 Sum_probs=42.7
Q ss_pred cceehhhHHHHHHHHHHHhhh---eeeeeCCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccc
Q 024669 98 QKLTSWVYFSVILGVVLFLLQ---LLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDM 167 (264)
Q Consensus 98 Qk~~sW~yF~~ilgvVL~~l~---v~Widp~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~ 167 (264)
.++.-|+.-+.++|+++.... ..|+.| .|+-|++.+. |+..-++|.-+=+|.+++++.
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 346667888888888887654 246655 7999998764 566777888888888888764
No 14
>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=25.39 E-value=72 Score=24.36 Aligned_cols=56 Identities=11% Similarity=0.157 Sum_probs=37.7
Q ss_pred CcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccchhhhhcchhhhhhhhc
Q 024669 127 GYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFAG 183 (264)
Q Consensus 127 G~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~RayRvlFA~ 183 (264)
+-+.+|-+..+-++... .-.+..++.+++.+=+...+|.--|..+....-|..--.
T Consensus 32 ~~~~~y~~~~~~~~~~~-~~i~~~l~~~~~~~H~~~Glr~ii~Dy~~~~~~r~~l~~ 87 (105)
T TIGR02968 32 LPGLTYEAWRALFAHPW-MKIFTLLALLALLYHAWIGMRVVLEDYVKPEGLRLVLQV 87 (105)
T ss_pred cCCCCHHHHHHHHhChH-HHHHHHHHHHHHHHHHHHhHHHHHHHHccchHHHHHHHH
Confidence 34445655555555444 445555666777777889999999999888777765433
No 15
>COG2020 STE14 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=23.87 E-value=41 Score=28.32 Aligned_cols=21 Identities=33% Similarity=0.388 Sum_probs=16.5
Q ss_pred cCCCceeeeeceeeeeecCCC
Q 024669 243 VDEPKMHLWETGVMRITRHPQ 263 (264)
Q Consensus 243 V~KPqvHLyETGIiRITRHPQ 263 (264)
..+..=.|=.||+=|++|||+
T Consensus 100 ~~~~~~~LVttG~Y~~VRHP~ 120 (187)
T COG2020 100 KARKGHELVTTGPYSIVRHPI 120 (187)
T ss_pred CCCCCCeeEecCCcceecCcH
Confidence 334455688899999999996
No 16
>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=23.39 E-value=80 Score=25.77 Aligned_cols=67 Identities=22% Similarity=0.238 Sum_probs=38.5
Q ss_pred ccceehhhHHHHHHHHHHHhhheeeeeC-CCCcchhHHHHhh-------ccCCChHHHHHHHHHHHHHHhcccccc
Q 024669 97 NQKLTSWVYFSVILGVVLFLLQLLWIDN-STGYGKAFIDSVS-------SLSDSHEVVMLVLILIFATVHSGLASL 164 (264)
Q Consensus 97 ~Qk~~sW~yF~~ilgvVL~~l~v~Widp-~TG~G~~fi~~vs-------~ls~Sh~~vmL~Lll~FAi~HSGlAsL 164 (264)
.||+.-|+.+..++..++..+...+-++ ..|+.-.+.+.+. .+..=|+ ++..+++.|.++|-.+|-.
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 4677788777777777777765544222 2333322222211 1123364 5556777899999998764
No 17
>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=23.38 E-value=83 Score=24.42 Aligned_cols=71 Identities=17% Similarity=0.144 Sum_probs=38.8
Q ss_pred CccceehhhHHHHHHHHHHHhhhe--eeeeCCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccc
Q 024669 96 KNQKLTSWVYFSVILGVVLFLLQL--LWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDM 167 (264)
Q Consensus 96 ~~Qk~~sW~yF~~ilgvVL~~l~v--~Widp~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~ 167 (264)
.-||..-|+.+.+++...+..+.. .+.-+-.+....-.+..+-...-|.+.+ .+++.|.++|-.+|.....
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 1111222222333344444556685555 4555889999888766544
No 18
>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=23.08 E-value=75 Score=26.76 Aligned_cols=67 Identities=15% Similarity=0.208 Sum_probs=38.8
Q ss_pred eecCccceehhhHHHHHHHHHHHhhheeeee-CCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhcccccc
Q 024669 93 FDLKNQKLTSWVYFSVILGVVLFLLQLLWID-NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASL 164 (264)
Q Consensus 93 F~~~~Qk~~sW~yF~~ilgvVL~~l~v~Wid-p~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsL 164 (264)
||. .||+.-|+.+.+.+..++..+...=.+ |..+++..-.+. ...=| ..+..++++|.++|-.+|..
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 544 478999987776666665554332001 222333333333 23456 44445778889999999876
No 19
>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=22.46 E-value=1.2e+02 Score=20.99 Aligned_cols=50 Identities=22% Similarity=0.164 Sum_probs=31.0
Q ss_pred CCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccchhhhhcc
Q 024669 124 NSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGA 174 (264)
Q Consensus 124 p~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~ 174 (264)
-..+.+.++ +.+...-++.-...+.+++.++..+-+...+|.-.|...-.
T Consensus 23 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~H~~~Gir~i~~D~~~~ 72 (98)
T cd03493 23 ALLGGPYAF-AEVVAFLSSPLGKLLYLLLLLALLYHALNGIRHLIWDYGKG 72 (98)
T ss_pred HHhcCHHHH-HHHHHHHhCHHHHHHHHHHHHHHHHHHHHhHHHHHHHcccc
Confidence 345555555 34444444553555556667777777888888888877543
No 20
>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=22.34 E-value=51 Score=28.95 Aligned_cols=77 Identities=17% Similarity=0.267 Sum_probs=53.9
Q ss_pred CccceehhhHHHHHHHHHHHhhh-eeeeeCCCCcchhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccchhhhhcc
Q 024669 96 KNQKLTSWVYFSVILGVVLFLLQ-LLWIDNSTGYGKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGA 174 (264)
Q Consensus 96 ~~Qk~~sW~yF~~ilgvVL~~l~-v~Widp~TG~G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~ 174 (264)
.+++...|.++.++++..+.--+ -+|+.. ..++|.+++.......=...++..++-+++.+.+.+...+.++.+.-
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 56778889999887776654322 234433 34689999999877775566666677778888888888887777654
Q ss_pred h
Q 024669 175 R 175 (264)
Q Consensus 175 R 175 (264)
|
T Consensus 96 ~ 96 (281)
T PF06472_consen 96 R 96 (281)
T ss_pred H
Confidence 3
No 21
>COG3736 VirB8 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]
Probab=21.34 E-value=66 Score=29.54 Aligned_cols=36 Identities=22% Similarity=0.310 Sum_probs=22.4
Q ss_pred ceecCccceehhhHHHHHHHHHHHhh----------------heeeeeCCCCcc
Q 024669 92 AFDLKNQKLTSWVYFSVILGVVLFLL----------------QLLWIDNSTGYG 129 (264)
Q Consensus 92 ~F~~~~Qk~~sW~yF~~ilgvVL~~l----------------~v~Widp~TG~G 129 (264)
++.++.++ +|++-.+++..++.++ |++|+|++||--
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 45555554 7766555444333322 789999999964
No 22
>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=20.58 E-value=52 Score=28.18 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=18.7
Q ss_pred hhhhhhhcccchhHHHHHHHh
Q 024669 176 AYRVLFAGVSLPLAVSTIVYF 196 (264)
Q Consensus 176 ayRvlFA~vSLPLAv~~I~YF 196 (264)
-||++=+++++|+|+++-++|
T Consensus 70 ~Yr~Ls~ilaiP~A~~~Gi~F 90 (148)
T PF01146_consen 70 CYRILSLILAIPLAFLWGILF 90 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999988777
No 23
>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=20.49 E-value=2.4e+02 Score=21.87 Aligned_cols=53 Identities=13% Similarity=0.183 Sum_probs=37.4
Q ss_pred chhHHHHhhccCCChHHHHHHHHHHHHHHhccccccccchhhhhcchhhhhhhh
Q 024669 129 GKAFIDSVSSLSDSHEVVMLVLILIFATVHSGLASLRDMGEKVIGARAYRVLFA 182 (264)
Q Consensus 129 G~~fi~~vs~ls~Sh~~vmL~Lll~FAi~HSGlAsLR~~gE~~IG~RayRvlFA 182 (264)
|.+|-+..+-++..- .-++.+++..+..|-....+|.--|..|.+..-|...-
T Consensus 28 ~~~y~~~~~~~~~p~-~~i~~~l~~~~~~~H~~~Glr~vi~DYv~~~~lr~~l~ 80 (99)
T cd03494 28 PLTYEAWSGLFSSLW-MKIFTLLALLALLLHAWIGLWDILTDYVKPAGLRLLLQ 80 (99)
T ss_pred CCCHHHHHHHHhCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence 455655555555433 44555667778888889999999999998877776543
No 24
>PRK14749 hypothetical protein; Provisional
Probab=20.18 E-value=40 Score=22.82 Aligned_cols=20 Identities=35% Similarity=0.806 Sum_probs=14.4
Q ss_pred HHHHHHHHH----HHhhheeeeeC
Q 024669 105 YFSVILGVV----LFLLQLLWIDN 124 (264)
Q Consensus 105 yF~~ilgvV----L~~l~v~Widp 124 (264)
||+=|||+. +.++|.+|++.
T Consensus 3 YfaWiLG~~lAc~f~ilna~w~E~ 26 (30)
T PRK14749 3 YLLWFVGILLMCSLSTLVLVWLDP 26 (30)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677777665 46788889874
Done!