Query 029094
Match_columns 199
No_of_seqs 109 out of 447
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 07:24:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029094.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029094hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3142 Prenylated rab accepto 100.0 6.5E-49 1.4E-53 322.8 16.7 181 6-186 1-186 (187)
2 PF03208 PRA1: PRA1 family pro 100.0 1.2E-37 2.6E-42 248.5 17.0 148 31-178 2-151 (153)
3 COG5130 YIP3 Prenylated rab ac 99.9 1.2E-23 2.6E-28 165.4 10.0 144 30-174 22-165 (169)
4 KOG4050 Glutamate transporter 99.9 1.1E-22 2.4E-27 162.9 12.8 137 31-168 13-155 (188)
5 COG1575 MenA 1,4-dihydroxy-2-n 78.6 14 0.00031 33.1 8.4 107 56-168 90-197 (303)
6 PF02300 Fumarate_red_C: Fumar 65.5 36 0.00078 26.8 7.0 49 85-133 62-116 (129)
7 PRK07419 1,4-dihydroxy-2-napht 60.9 87 0.0019 27.8 9.5 19 109-127 136-154 (304)
8 COG1955 FlaJ Archaeal flagella 56.8 1E+02 0.0022 29.8 9.5 54 25-78 123-176 (527)
9 PRK13591 ubiA prenyltransferas 56.4 1.4E+02 0.003 26.8 10.0 13 40-52 77-91 (307)
10 PRK04987 fumarate reductase su 55.6 71 0.0015 25.2 7.0 51 83-133 61-117 (130)
11 PF01040 UbiA: UbiA prenyltran 49.8 1.4E+02 0.0031 24.4 8.7 13 85-97 88-100 (257)
12 PRK11715 inner membrane protei 47.4 2.2E+02 0.0047 26.9 10.1 87 71-162 304-399 (436)
13 PF09991 DUF2232: Predicted me 47.0 1.3E+02 0.0027 25.4 8.0 40 129-168 44-83 (290)
14 PF06123 CreD: Inner membrane 44.2 2.7E+02 0.0058 26.2 10.2 24 71-94 298-330 (430)
15 PLN02922 prenyltransferase 43.6 2.4E+02 0.0052 25.1 9.9 32 90-125 125-156 (315)
16 cd00546 QFR_TypeD_subunitC Qui 40.2 1E+02 0.0022 24.2 5.7 51 83-133 57-113 (124)
17 TIGR00751 menA 1,4-dihydroxy-2 38.8 2.6E+02 0.0056 24.5 8.9 32 90-125 111-142 (284)
18 PRK13603 fumarate reductase su 38.2 1.1E+02 0.0024 24.0 5.7 51 83-133 57-113 (126)
19 PF05879 RHD3: Root hair defec 35.0 77 0.0017 31.8 5.4 26 82-107 665-690 (742)
20 TIGR03750 conj_TIGR03750 conju 34.6 2.1E+02 0.0045 21.9 6.7 51 108-158 8-63 (111)
21 PF09622 DUF2391: Putative int 34.5 1.1E+02 0.0024 26.9 5.8 46 124-169 70-126 (267)
22 PRK06041 flagellar assembly pr 33.9 3.8E+02 0.0083 25.9 9.8 56 25-80 145-200 (553)
23 COG4605 CeuC ABC-type enteroch 33.4 1.9E+02 0.004 26.1 7.0 43 38-82 145-187 (316)
24 KOG0054 Multidrug resistance-a 32.7 1.6E+02 0.0035 31.9 7.5 65 37-104 902-973 (1381)
25 PF11368 DUF3169: Protein of u 32.3 92 0.002 26.5 4.9 44 63-106 190-237 (248)
26 cd01785 PDZ_GEF_RA Ubiquitin-l 32.1 9.6 0.00021 27.7 -1.0 24 49-72 61-84 (85)
27 PF03522 KCl_Cotrans_1: K-Cl C 30.4 20 0.00043 21.2 0.3 18 160-178 5-22 (30)
28 TIGR02235 menA_cyano-plnt 1,4- 30.0 3.8E+02 0.0082 23.4 9.8 17 109-125 123-139 (285)
29 PF02411 MerT: MerT mercuric t 28.1 2.8E+02 0.006 21.3 6.5 21 87-107 50-71 (116)
30 PRK13751 putative mercuric tra 28.0 2.6E+02 0.0057 21.5 6.2 20 88-107 51-71 (116)
31 PF14256 YwiC: YwiC-like prote 27.5 2.9E+02 0.0063 21.3 6.7 52 122-173 61-112 (129)
32 COG4452 CreD Inner membrane pr 26.4 5.5E+02 0.012 24.2 9.7 24 71-94 298-330 (443)
33 PRK10952 glycine betaine trans 26.2 5E+02 0.011 23.6 13.4 20 87-106 104-123 (355)
34 COG5415 Predicted integral mem 25.8 4.4E+02 0.0095 22.8 7.7 44 56-99 28-79 (251)
35 PF12264 Waikav_capsid_1: Waik 24.7 41 0.00088 27.7 1.3 25 47-71 45-69 (197)
36 CHL00114 psbX photosystem II p 24.7 88 0.0019 19.6 2.5 21 140-160 2-22 (39)
37 PF11990 DUF3487: Protein of u 24.3 3.3E+02 0.0073 20.9 6.8 20 107-126 10-29 (121)
38 PF02714 DUF221: Domain of unk 23.3 4.7E+02 0.01 22.6 7.9 22 87-108 265-286 (325)
39 PF06645 SPC12: Microsomal sig 23.3 2.7E+02 0.0059 19.5 5.6 29 130-158 21-49 (76)
40 PF04140 ICMT: Isoprenylcystei 23.1 2.7E+02 0.0058 20.1 5.3 19 72-90 48-67 (94)
41 PF04530 Viral_Beta_CD: Viral 22.9 1.1E+02 0.0023 24.0 3.2 28 56-83 34-61 (122)
42 COG0382 UbiA 4-hydroxybenzoate 22.4 5.1E+02 0.011 22.3 11.6 27 143-169 166-192 (289)
43 PF00664 ABC_membrane: ABC tra 22.2 3.8E+02 0.0083 20.9 7.6 21 53-73 95-115 (275)
44 PRK12847 ubiA 4-hydroxybenzoat 22.1 3.2E+02 0.007 23.5 6.5 10 86-95 111-120 (285)
45 PF06596 PsbX: Photosystem II 22.1 1.3E+02 0.0028 18.9 2.8 20 140-159 2-21 (39)
46 TIGR02203 MsbA_lipidA lipid A 21.9 5.1E+02 0.011 24.3 8.3 21 53-73 108-128 (571)
47 PF05777 Acp26Ab: Drosophila a 21.7 67 0.0015 23.4 1.8 15 72-86 2-16 (90)
48 PF08372 PRT_C: Plant phosphor 21.6 2.9E+02 0.0063 22.3 5.7 37 59-95 82-121 (156)
49 KOG1134 Uncharacterized conser 21.5 8.4E+02 0.018 24.6 10.0 44 82-125 566-614 (728)
50 PRK13823 conjugal transfer pro 21.4 2.9E+02 0.0064 20.4 5.2 49 110-165 13-62 (94)
51 KOG1606 Stationary phase-induc 21.2 78 0.0017 27.5 2.3 37 31-67 106-147 (296)
52 PF09726 Macoilin: Transmembra 21.0 4E+02 0.0087 26.7 7.5 38 69-106 75-112 (697)
53 PF10318 7TM_GPCR_Srh: Serpent 20.2 4.6E+02 0.01 22.3 7.1 20 47-67 145-164 (302)
No 1
>KOG3142 consensus Prenylated rab acceptor 1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.5e-49 Score=322.83 Aligned_cols=181 Identities=49% Similarity=0.811 Sum_probs=166.3
Q ss_pred CCCCCCCcCCCCCC-CCchhhHHhhh----hhhcCCCCChhhhhCCCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHHHH
Q 029094 6 PTNYGSATTTTNPT-TTTSLSFFSRA----ESLTATRRPWREFFNTSALSLPADYNDAISRARRNASYFRVNYAVVMLFI 80 (199)
Q Consensus 6 ~~~~~~~~~~~~~~-~~~~~~~~~~~----~~~l~~~RPw~eF~d~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~ 80 (199)
|+++|+.|+++.+. ..+.++..+|. +..+++.|||+||+|.++|++|++++|+.+|+++|+.|||.||.+++.++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lst~RpW~ef~d~~~fs~P~s~s~a~sRi~~Nl~yF~~NY~~iv~~~ 80 (187)
T KOG3142|consen 1 MTNQGAPPPSSSPSQALSVESISSRAKQTIQSGLSTRRPWSEFFDRSAFSRPRSLSDATSRIKRNLSYFRVNYVIIVAIL 80 (187)
T ss_pred CCCCCCCCCCCCcccccchhhHHHHHHHHHHHHHhccCCHHHHHcccccCCCccHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 56788887655443 22233455544 77789999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEeccccchHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh
Q 029094 81 LFLSLLWHPVSMIVFIVVFVLWLFFYFARDDPVVVFNQTLDDKFVLGCLTLVTVLALILTDVGTNVLVGLIVGVVLVGLH 160 (199)
Q Consensus 81 ~~i~ll~~P~~Li~l~~~~~~~~~i~~~~~~p~~i~g~~~~~~~v~~~l~~vs~~ll~~~~~~~~l~~~l~~s~~vvl~H 160 (199)
..+++++||++|+++++++++|+++|+.||+|++++||+++++++++++++++++++|+++++.+++|++++|+++|++|
T Consensus 81 ~~~sLi~~P~~Livl~~lv~~w~~LY~~rd~pLvlfgr~i~d~~~l~~L~~~ti~~lflt~~~~~l~~~l~~g~~vv~~H 160 (187)
T KOG3142|consen 81 LFLSLITHPLSLIVLLALVAAWLFLYFLRDEPLVLFGRQISDREVLIGLVLITIPVLFLTSAGSNLLWALGAGLVVVLIH 160 (187)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHheeeecCCCeEEeeEEecCcchhhhHHHHHHHHHHHhhHHHHHHHHHHHhHHHHHhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCCCCCccccccccCCceeecc
Q 029094 161 ASFRATDDLFLDEESAAEGGLVSVLG 186 (199)
Q Consensus 161 A~~R~~~~~~~de~~~~~~~~~~~~~ 186 (199)
|+||++||+|+||||+..+|+.|+.+
T Consensus 161 aafr~~ddLF~dee~~~~~gl~s~~~ 186 (187)
T KOG3142|consen 161 AAFRNTDDLFLDEEEAAASGLLSFSS 186 (187)
T ss_pred HHHhChHhhhhhhhhcccccccccCC
Confidence 99999999999999999889998764
No 2
>PF03208 PRA1: PRA1 family protein; InterPro: IPR004895 This family includes yeast hypothetical proteins and the uncharacterised rat prenylated rab acceptor protein PRA1.
Probab=100.00 E-value=1.2e-37 Score=248.45 Aligned_cols=148 Identities=38% Similarity=0.681 Sum_probs=139.0
Q ss_pred hhhcCCCCChhhhhCCCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 029094 31 ESLTATRRPWREFFNTSALSLPADYNDAISRARRNASYFRVNYAVVMLFILFLSLLWHPVSMIVFIVVFVLWLFFYFARD 110 (199)
Q Consensus 31 ~~~l~~~RPw~eF~d~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i~ll~~P~~Li~l~~~~~~~~~i~~~~~ 110 (199)
+++++++|||+||||.++|+.|+|.+++.+|+++|+.|||+||++++++++++++++||..++++++++++|++++..++
T Consensus 2 ~~~~~~~Rpw~eF~~~~~fs~P~~~~~~~~Ri~~Nl~~F~~NY~~i~~~~~~~~ll~~P~~l~~~~~~~~~~~~~~~~~~ 81 (153)
T PF03208_consen 2 QSRLSPLRPWREFFDTSRFSVPSSFSEAKSRIKRNLSYFQTNYLLIFLLLFLIFLLTNPFFLLVLLLVVALWAFIYKSRK 81 (153)
T ss_pred ccccCCCCCHHHHhCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999998875
Q ss_pred --CCeEeccccchHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhhcccCCCCCcccccccc
Q 029094 111 --DPVVVFNQTLDDKFVLGCLTLVTVLALILTDVGTNVLVGLIVGVVLVGLHASFRATDDLFLDEESAAE 178 (199)
Q Consensus 111 --~p~~i~g~~~~~~~v~~~l~~vs~~ll~~~~~~~~l~~~l~~s~~vvl~HA~~R~~~~~~~de~~~~~ 178 (199)
+|+.+.|+++++++++.++.+++++++++++++.+++|++++++++|++||++|+||+++.+|+|.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~l~~~~~lvl~HA~~r~~~~~~~~e~~~~~ 151 (153)
T PF03208_consen 82 ENDPIVIGGRKISPRQVLLALLIVSILLLFFTSAGLTLFWSLGASVLLVLLHASFREPDLKNKEENEIES 151 (153)
T ss_pred cCcchhccCcccCHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcCCccchhhhhHHhc
Confidence 78999999999999999999999999999999999999999999999999999999988777776653
No 3
>COG5130 YIP3 Prenylated rab acceptor 1 and related proteins [Intracellular trafficking and secretion / Signal transduction mechanisms]
Probab=99.90 E-value=1.2e-23 Score=165.39 Aligned_cols=144 Identities=22% Similarity=0.189 Sum_probs=131.1
Q ss_pred hhhhcCCCCChhhhhCCCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 029094 30 AESLTATRRPWREFFNTSALSLPADYNDAISRARRNASYFRVNYAVVMLFILFLSLLWHPVSMIVFIVVFVLWLFFYFAR 109 (199)
Q Consensus 30 ~~~~l~~~RPw~eF~d~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i~ll~~P~~Li~l~~~~~~~~~i~~~~ 109 (199)
.++.++..|.-+||||..|.++|++++|+++|+-.|+.||+.||..+...+..|.+++||.+++++.+.+++-+.+.+.|
T Consensus 22 ~~q~L~~~~~~~eFfni~rIs~PqNf~eaqsRv~~Nl~rFssnYlaiia~l~iy~ll~nllLlivIgivvaGvygi~kl~ 101 (169)
T COG5130 22 IKQALGDKDVTREFFNIGRISVPQNFNEAQSRVFANLDRFSSNYLAIIAILTIYYLLYNLLLLIVIGIVVAGVYGIRKLR 101 (169)
T ss_pred HHHHhcCcccHHHHhccccccCCcchHHHHHHHHhhHHHHhhhHHHHHHHHHHHHHHHhHHHHHHHhhhhheeeehhhcc
Confidence 35668889999999999999999999999999999999999999999999999999999999998888888777788889
Q ss_pred CCCeEeccccchHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhhcccCCCCCcccc
Q 029094 110 DDPVVVFNQTLDDKFVLGCLTLVTVLALILTDVGTNVLVGLIVGVVLVGLHASFRATDDLFLDEE 174 (199)
Q Consensus 110 ~~p~~i~g~~~~~~~v~~~l~~vs~~ll~~~~~~~~l~~~l~~s~~vvl~HA~~R~~~~~~~de~ 174 (199)
++|++..-+..+..+.|++++.+.+++.++.+...+++|..++|.++++.||++..++-. .|+|
T Consensus 102 g~~lv~~~~~~~~~~ly~glvcvlip~gffaspI~tllwl~gas~v~vfgHAal~e~p~e-~~fe 165 (169)
T COG5130 102 GRPLVCNIELEPRSVLYAGLVCVLIPFGFFASPIVTLLWLSGASGVVVFGHAALLEEPLE-KDFE 165 (169)
T ss_pred cCccccccceeecchhhhhHHHHHHHHHHHHhHHHHHHHHHhcceeEeechHHHcCCccc-cchh
Confidence 999888777778888899999999999999999999999999999999999999998654 3443
No 4
>KOG4050 consensus Glutamate transporter EAAC1-interacting protein GTRAP3-18 [Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.89 E-value=1.1e-22 Score=162.88 Aligned_cols=137 Identities=20% Similarity=0.284 Sum_probs=109.4
Q ss_pred hhhcCCCCChhhhh-CCCCCCCC--CChHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH
Q 029094 31 ESLTATRRPWREFF-NTSALSLP--ADYNDAISRARRNASYFRVNYAVVMLFILFLSLLWHPVSMIVFIVVF--VLWLFF 105 (199)
Q Consensus 31 ~~~l~~~RPw~eF~-d~~~fs~P--~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i~ll~~P~~Li~l~~~~--~~~~~i 105 (199)
..+++++|.|+||+ +..||.+| +|+++|++|+.+|+.|||+||+++++.++.+..+.+|..++..++.. +....+
T Consensus 13 ~v~lpPlRa~ddF~lgS~Rfa~Pd~~D~~kW~nRVisNLLYyQTNYfv~~it~~~l~~f~sp~~iilglivvvlvi~~li 92 (188)
T KOG4050|consen 13 GVELPPLRALDDFLLGSDRFARPDFNDFKKWNNRVISNLLYYQTNYFVTFITLFLLHGFISPQDIILGLIVVVLVIGTLI 92 (188)
T ss_pred CCCCCcchhHHHhccCcccccCCCCccHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999 69999999 89999999999999999999999999999999999999877643321 111122
Q ss_pred HHh-CCCCeEeccccchHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhhcccCCC
Q 029094 106 YFA-RDDPVVVFNQTLDDKFVLGCLTLVTVLALILTDVGTNVLVGLIVGVVLVGLHASFRATDD 168 (199)
Q Consensus 106 ~~~-~~~p~~i~g~~~~~~~v~~~l~~vs~~ll~~~~~~~~l~~~l~~s~~vvl~HA~~R~~~~ 168 (199)
+.. .++.++...++++ ...+++...+++++++++++..++.+++..+++++++||++|.|+-
T Consensus 93 wa~~~~a~~krmr~~hp-~~~l~gvllv~yfli~v~~~vlv~~F~il~Pv~L~lvHASLRLRni 155 (188)
T KOG4050|consen 93 WAASADANIKRMRTDHP-LVTLAGVLLVGYFLISVFGGVLVFAFAILFPVLLVLVHASLRLRNI 155 (188)
T ss_pred HHHhccHHHHHHhhcCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 222 2333333334433 4445668888999999999999999999999999999999999973
No 5
>COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]
Probab=78.60 E-value=14 Score=33.09 Aligned_cols=107 Identities=15% Similarity=0.091 Sum_probs=52.2
Q ss_pred HHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhCCCCeEeccccchHHHHHHHHHHHHH
Q 029094 56 NDAISRARRNASYFRVNYAVVMLFILFLSLLWHPV-SMIVFIVVFVLWLFFYFARDDPVVVFNQTLDDKFVLGCLTLVTV 134 (199)
Q Consensus 56 ~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i~ll~~P~-~Li~l~~~~~~~~~i~~~~~~p~~i~g~~~~~~~v~~~l~~vs~ 134 (199)
++.+.|+.-++.-+ -|....++...++..+++. +.+.+++++++|.| ...|...+-..+.+-.+.+++-.+.+
T Consensus 90 ~~~k~~~~l~l~l~--~~~g~~llg~~~~~~s~~~~l~lG~l~~~~g~~Y----TgGp~PlgY~gLGEi~~~vffG~l~v 163 (303)
T COG1575 90 QSMKPALILSLALF--LLAGLALLGVILAALSDWLVLLLGLLCIAAGILY----TGGPFPLGYMGLGEIFVGVFFGPLIV 163 (303)
T ss_pred ccCCHHHHHHHHHH--HHHHHHHHHHHHHHHhhhHHHHHHHHHHHheeee----ccCCcCcccCCHHHHHHHHHHHHHHH
Confidence 34445555444332 2333344444444556666 33334444455433 45565555555666666555555554
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHhhhcccCCC
Q 029094 135 LALILTDVGTNVLVGLIVGVVLVGLHASFRATDD 168 (199)
Q Consensus 135 ~ll~~~~~~~~l~~~l~~s~~vvl~HA~~R~~~~ 168 (199)
..-++......-...+..|+.+.+.-+.....|+
T Consensus 164 ~g~~yiqt~~~~~~~ll~slp~gil~~~Il~aNN 197 (303)
T COG1575 164 LGAYYIQTGRLSWAILLPSLPVGILIANILLANN 197 (303)
T ss_pred HHHHHHhcccchHHHHHHHHHHHHHHHHHHHhcc
Confidence 4445444433333355555555555555555443
No 6
>PF02300 Fumarate_red_C: Fumarate reductase subunit C; InterPro: IPR003510 Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 15kDa hydrophobic subunit C.; GO: 0016020 membrane; PDB: 1KFY_O 1L0V_O 3P4S_O 2B76_O 3CIR_O 3P4R_C 1KF6_O 3P4P_C 3P4Q_C.
Probab=65.52 E-value=36 Score=26.85 Aligned_cols=49 Identities=20% Similarity=0.371 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHh-CCCCeEeccccchHHHHHHHHHHHH
Q 029094 85 LLWHPVSMIVFIVVFVLWL-----FFYFA-RDDPVVVFNQTLDDKFVLGCLTLVT 133 (199)
Q Consensus 85 ll~~P~~Li~l~~~~~~~~-----~i~~~-~~~p~~i~g~~~~~~~v~~~l~~vs 133 (199)
.+.||+.++.=++..++.+ ++... +.-|+.++|+.++++.+..+..+++
T Consensus 62 fl~nP~vv~lnliaLaa~L~Ha~TwF~l~Pkam~i~v~~~~v~~~~i~~~~w~~~ 116 (129)
T PF02300_consen 62 FLQNPIVVILNLIALAAALLHAKTWFELAPKAMPIIVGGERVPPRPIVKGLWAAT 116 (129)
T ss_dssp HHTSHHHHHHHHHHHHHHHHHHHHHHHHGGGG---EETTEE--SHHHHHHHHHHH
T ss_pred HHcCcHHHHHHHHHHHHHHHHHHHHHHHchhhhhhhcCCeeCCHHHHHHHHHHHH
Confidence 3568887776443322221 11111 3347888999999987765444433
No 7
>PRK07419 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional
Probab=60.93 E-value=87 Score=27.84 Aligned_cols=19 Identities=16% Similarity=0.163 Sum_probs=9.6
Q ss_pred CCCCeEeccccchHHHHHH
Q 029094 109 RDDPVVVFNQTLDDKFVLG 127 (199)
Q Consensus 109 ~~~p~~i~g~~~~~~~v~~ 127 (199)
...|.....+-..+-.+.+
T Consensus 136 T~gP~~l~y~gLGE~~v~l 154 (304)
T PRK07419 136 QGPPFRLGYQGLGEPLCFL 154 (304)
T ss_pred cCCCcccCCCCchHHHHHH
Confidence 4455555555555544444
No 8
>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=56.80 E-value=1e+02 Score=29.80 Aligned_cols=54 Identities=15% Similarity=0.292 Sum_probs=45.3
Q ss_pred hHHhhhhhhcCCCCChhhhhCCCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHH
Q 029094 25 SFFSRAESLTATRRPWREFFNTSALSLPADYNDAISRARRNASYFRVNYAVVML 78 (199)
Q Consensus 25 ~~~~~~~~~l~~~RPw~eF~d~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~ 78 (199)
||+.|-...+..--+-.||+.++....=++.+...+|..++++-|+.=|.-+..
T Consensus 123 dfL~Rla~ai~sGe~~~eFl~~E~~~~~~~y~~~Yer~LeSl~~~~diY~sll~ 176 (527)
T COG1955 123 DFLDRLAYALDSGEDLKEFLEREQDTTMDEYETEYERALESLDVWKDIYVSLLV 176 (527)
T ss_pred HHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678887777788889999997776666688899999999999999999986654
No 9
>PRK13591 ubiA prenyltransferase; Provisional
Probab=56.35 E-value=1.4e+02 Score=26.82 Aligned_cols=13 Identities=8% Similarity=0.130 Sum_probs=8.8
Q ss_pred hhhhhC--CCCCCCC
Q 029094 40 WREFFN--TSALSLP 52 (199)
Q Consensus 40 w~eF~d--~~~fs~P 52 (199)
-+|++| .++.+.|
T Consensus 77 iNd~~D~eiD~IN~P 91 (307)
T PRK13591 77 LDRALDSEEDAVNRS 91 (307)
T ss_pred HhhhccchhhhccCc
Confidence 357777 4567877
No 10
>PRK04987 fumarate reductase subunit C; Provisional
Probab=55.61 E-value=71 Score=25.23 Aligned_cols=51 Identities=24% Similarity=0.412 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HHHh-CCCCeEeccccchHHHHHHHHHHHH
Q 029094 83 LSLLWHPVSMIVFIVVFVLWLF-----FYFA-RDDPVVVFNQTLDDKFVLGCLTLVT 133 (199)
Q Consensus 83 i~ll~~P~~Li~l~~~~~~~~~-----i~~~-~~~p~~i~g~~~~~~~v~~~l~~vs 133 (199)
+..+.||+.++.=++..++.++ +... +.-|+.+.|+.++++.+..++.+++
T Consensus 61 ~~flqnPiv~~lniiaL~a~LlHa~TwF~~~Pka~~i~v~~~~l~~~~ii~~~wa~~ 117 (130)
T PRK04987 61 VSFLQNPIVVILNIITLAAALLHTKTWFEMAPKAANIIVKDEKMGPEPIIKALWAVT 117 (130)
T ss_pred HHHHhCcHHHHHHHHHHHHHHHHHHHHHHHcchhheeeecCccCChHHHHHHHHHHH
Confidence 3446789887764443322221 1111 2346778888888877655444443
No 11
>PF01040 UbiA: UbiA prenyltransferase family; InterPro: IPR000537 The UbiA family of prenyltransferases includes bacterial 4-hydroxybenzoate octaprenyltransferase (gene ubiA); yeast mitochondrial para-hydroxybenzoate--polyprenyltransferase (gene COQ2); and protohaem IX farnesyltransferase (haem O synthase) from yeast and mammals(gene COX10), and from bacteria (genes cyoE or ctaB) [, ]. These are integral membrane proteins, which probably contain seven transmembrane segments. The signature is also found in cytochrome C oxidase assembly factor. The complexity of cytochrome C oxidase requires assistance in building the complex, and this is carried out by the cytochrome C oxidase assembly factor.; GO: 0004659 prenyltransferase activity, 0016021 integral to membrane
Probab=49.80 E-value=1.4e+02 Score=24.42 Aligned_cols=13 Identities=23% Similarity=0.600 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHH
Q 029094 85 LLWHPVSMIVFIV 97 (199)
Q Consensus 85 ll~~P~~Li~l~~ 97 (199)
...+|..++..++
T Consensus 88 ~~~~~~~~~~~~~ 100 (257)
T PF01040_consen 88 LLLGPWFLLILLL 100 (257)
T ss_pred HhcCchhHHHHHH
Confidence 4456665554433
No 12
>PRK11715 inner membrane protein; Provisional
Probab=47.40 E-value=2.2e+02 Score=26.90 Aligned_cols=87 Identities=20% Similarity=0.419 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHhCCCCeEeccccchHHHHHHHHHHHHHHHHHHhh
Q 029094 71 VNYAVVMLFILFLSLL---------WHPVSMIVFIVVFVLWLFFYFARDDPVVVFNQTLDDKFVLGCLTLVTVLALILTD 141 (199)
Q Consensus 71 ~NY~~i~~~~~~i~ll---------~~P~~Li~l~~~~~~~~~i~~~~~~p~~i~g~~~~~~~v~~~l~~vs~~ll~~~~ 141 (199)
..|.++++++.+.+++ .||+.-+...+..+.++.+-..=.+.+. +......++++++..+-+|...
T Consensus 304 ~KYgiLFI~LTF~~fFlfE~~~~~~iHpiQYlLVGlAl~lFYLLLLSlSEHig-----F~~AYliAa~a~v~li~~Y~~~ 378 (436)
T PRK11715 304 VKYAILFIALTFAAFFLFELLKKLRIHPVQYLLVGLALVLFYLLLLSLSEHIG-----FTLAYLIAALACVLLIGFYLSA 378 (436)
T ss_pred HhHHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHHHHHHHHHHHHhhhc-----hHHHHHHHHHHHHHHHHHHHHH
Confidence 4577777777666654 3898554332222222221111122211 2223333444455555555555
Q ss_pred hhHHHHHHHHHHHHHHHHhhh
Q 029094 142 VGTNVLVGLIVGVVLVGLHAS 162 (199)
Q Consensus 142 ~~~~l~~~l~~s~~vvl~HA~ 162 (199)
+...--.++.++..+..+=|.
T Consensus 379 vl~~~k~g~~~~~~L~~LYg~ 399 (436)
T PRK11715 379 VLRSWKRGLLFAAALAALYGV 399 (436)
T ss_pred HHhcchHHHHHHHHHHHHHHH
Confidence 444444444444444443333
No 13
>PF09991 DUF2232: Predicted membrane protein (DUF2232); InterPro: IPR018710 This family of bacterial and eukaryotic proteins has no known fucntion; however this signature belongs to a Pfam Gx transporter clan.
Probab=47.00 E-value=1.3e+02 Score=25.41 Aligned_cols=40 Identities=18% Similarity=0.136 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhhcccCCC
Q 029094 129 LTLVTVLALILTDVGTNVLVGLIVGVVLVGLHASFRATDD 168 (199)
Q Consensus 129 l~~vs~~ll~~~~~~~~l~~~l~~s~~vvl~HA~~R~~~~ 168 (199)
.++..+....+.+....+++.+..+..-.+.+-.+|++.+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~lg~~~~~~~~ 83 (290)
T PF09991_consen 44 LLAAAVLLALFGGPVSALFYLLFFGLPGLVLGYLLRKKRS 83 (290)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 3333344334455566677777766666666666666543
No 14
>PF06123 CreD: Inner membrane protein CreD; InterPro: IPR010364 This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with a Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA [].
Probab=44.25 E-value=2.7e+02 Score=26.23 Aligned_cols=24 Identities=25% Similarity=0.746 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHH---------HHHHHHHH
Q 029094 71 VNYAVVMLFILFLSLL---------WHPVSMIV 94 (199)
Q Consensus 71 ~NY~~i~~~~~~i~ll---------~~P~~Li~ 94 (199)
.-|.++++.+.+.+++ .||+.-+.
T Consensus 298 ~KYgiLFI~LTF~~fflfE~~~~~~iHpiQY~L 330 (430)
T PF06123_consen 298 VKYGILFIGLTFLAFFLFELLSKLRIHPIQYLL 330 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHH
Confidence 3477777777666654 38985443
No 15
>PLN02922 prenyltransferase
Probab=43.59 E-value=2.4e+02 Score=25.15 Aligned_cols=32 Identities=13% Similarity=0.313 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCeEeccccchHHHH
Q 029094 90 VSMIVFIVVFVLWLFFYFARDDPVVVFNQTLDDKFV 125 (199)
Q Consensus 90 ~~Li~l~~~~~~~~~i~~~~~~p~~i~g~~~~~~~v 125 (199)
++++.+++++.+|. | ...|..+..+-..+-.+
T Consensus 125 ~l~iG~~g~~~~~~--Y--t~gP~pl~y~gLGE~~v 156 (315)
T PLN02922 125 VILLLAAAILCGYV--Y--QCPPFRLSYKGLGEPLC 156 (315)
T ss_pred HHHHHHHHHHHHHH--H--hcCCcccccCcchHHHH
Confidence 33333444444443 3 34555555555554444
No 16
>cd00546 QFR_TypeD_subunitC Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits.
Probab=40.16 E-value=1e+02 Score=24.17 Aligned_cols=51 Identities=22% Similarity=0.328 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HHHh-CCCCeEeccccchHHHHHHHHHHHH
Q 029094 83 LSLLWHPVSMIVFIVVFVLWLF-----FYFA-RDDPVVVFNQTLDDKFVLGCLTLVT 133 (199)
Q Consensus 83 i~ll~~P~~Li~l~~~~~~~~~-----i~~~-~~~p~~i~g~~~~~~~v~~~l~~vs 133 (199)
+..+.||+.++.=++..++.++ +... +.-|+.++|+.++++.+..+..+++
T Consensus 57 ~~flqnPiv~~lniiaL~a~L~Ha~TwF~~~Pkam~i~v~~~~l~~~~iv~~~wa~~ 113 (124)
T cd00546 57 VSFLQNPIVVLLNIIALAAALLHAKTWFEMAPKVMNIIVKGERVPPEAITKALWAVT 113 (124)
T ss_pred HHHHhCcHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCccCChHHHHHHHHHHH
Confidence 3445789887764443322221 1111 2335777888888877655444443
No 17
>TIGR00751 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase. This membrane-associated enzyme converts 1,4-dihydroxy-2-naphthoic acid (DHNA) to demethylmenaquinone, a step in menaquinone biosynthesis.
Probab=38.82 E-value=2.6e+02 Score=24.46 Aligned_cols=32 Identities=13% Similarity=-0.058 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCeEeccccchHHHH
Q 029094 90 VSMIVFIVVFVLWLFFYFARDDPVVVFNQTLDDKFV 125 (199)
Q Consensus 90 ~~Li~l~~~~~~~~~i~~~~~~p~~i~g~~~~~~~v 125 (199)
+.++.++..+.+|. | ...|.....+-..+-.+
T Consensus 111 ~l~lg~~~~~~~~~--Y--t~gP~~l~y~gLGE~~v 142 (284)
T TIGR00751 111 FIALGALCIAAAIT--Y--TVGSKPYGYAGLGDISV 142 (284)
T ss_pred HHHHHHHHHHHhHh--h--cCCCCccccCchHHHHH
Confidence 34444444444443 3 34444444343444333
No 18
>PRK13603 fumarate reductase subunit C; Provisional
Probab=38.23 E-value=1.1e+02 Score=24.02 Aligned_cols=51 Identities=22% Similarity=0.229 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HHHh-CCCCeEeccccchHHHHHHHHHHHH
Q 029094 83 LSLLWHPVSMIVFIVVFVLWLF-----FYFA-RDDPVVVFNQTLDDKFVLGCLTLVT 133 (199)
Q Consensus 83 i~ll~~P~~Li~l~~~~~~~~~-----i~~~-~~~p~~i~g~~~~~~~v~~~l~~vs 133 (199)
+..+.||+.++.=++..++.++ +... +.-|+.+.|+.++++.+..+..+++
T Consensus 57 ~~flqnPivv~lniiaL~a~L~Ha~TwF~~~Pkam~I~v~~~~l~~~~iv~~~wa~~ 113 (126)
T PRK13603 57 LDFSANPVVVVLNVVALSFLLLHAVTWFGSAPRAMVIQVRGRRVPARAVLAGHYAAW 113 (126)
T ss_pred HHHHhCcHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCcCChHHHHHHHHHHH
Confidence 3446789887764443322221 1111 2335777888888877655444443
No 19
>PF05879 RHD3: Root hair defective 3 GTP-binding protein (RHD3); InterPro: IPR008803 This family consists of several eukaryotic root hair defective 3 like GTP-binding proteins. It has been speculated that the RHD3 protein is a member of a novel class of GTP-binding proteins that is widespread in eukaryotes and required for regulated cell enlargement []. The family also contains the homologous Saccharomyces cerevisiae synthetic construct enhancement of YOP1 (SEY1) protein which is involved in membrane trafficking [].; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=34.99 E-value=77 Score=31.77 Aligned_cols=26 Identities=15% Similarity=0.441 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029094 82 FLSLLWHPVSMIVFIVVFVLWLFFYF 107 (199)
Q Consensus 82 ~i~ll~~P~~Li~l~~~~~~~~~i~~ 107 (199)
++.++.||+.+.++++++++.+.+|.
T Consensus 665 ~m~vLrnPl~~~l~li~~~~~~~~~~ 690 (742)
T PF05879_consen 665 FMAVLRNPLYFTLLLILGGGFYVLYQ 690 (742)
T ss_pred HHHHHHChHHHHHHHHHHHHHHHHHH
Confidence 35667899988887777776666664
No 20
>TIGR03750 conj_TIGR03750 conjugative transfer region protein, TIGR03750 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=34.61 E-value=2.1e+02 Score=21.90 Aligned_cols=51 Identities=24% Similarity=0.277 Sum_probs=25.9
Q ss_pred hCCCCeEeccccchHHHHHHHH-----HHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 029094 108 ARDDPVVVFNQTLDDKFVLGCL-----TLVTVLALILTDVGTNVLVGLIVGVVLVG 158 (199)
Q Consensus 108 ~~~~p~~i~g~~~~~~~v~~~l-----~~vs~~ll~~~~~~~~l~~~l~~s~~vvl 158 (199)
.+.+|.++.|-+.++--+.+++ .++++++.++++....+-.+..++.++++
T Consensus 8 LN~ePvV~rGlT~~El~~~~~~~~~~gl~~g~~l~~~~~~w~~~p~~~lig~~l~v 63 (111)
T TIGR03750 8 LNREPVVFRGLTADELGVAAGVGLAAGLVLGLLLALLAGPWALIPTGALLGPILVV 63 (111)
T ss_pred hcCCCceecccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888988666654443322 33444444445544344344444433333
No 21
>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=34.46 E-value=1.1e+02 Score=26.95 Aligned_cols=46 Identities=13% Similarity=0.110 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHhh-----------hhHHHHHHHHHHHHHHHHhhhcccCCCC
Q 029094 124 FVLGCLTLVTVLALILTD-----------VGTNVLVGLIVGVVLVGLHASFRATDDL 169 (199)
Q Consensus 124 ~v~~~l~~vs~~ll~~~~-----------~~~~l~~~l~~s~~vvl~HA~~R~~~~~ 169 (199)
..++.-.+++..++++.+ .+..++-++-++....+..+-+...++.
T Consensus 70 ~A~~ig~v~a~~~L~~l~~l~~~~~~~e~lgkiiv~~vP~siGa~la~~~L~~~~~~ 126 (267)
T PF09622_consen 70 EALAIGAVVAAAVLTLLGKLTLDTPPREALGKIIVQSVPASIGAALARSQLGGDSDE 126 (267)
T ss_pred HHHHHHHHHHHHHHHHHhhCCCCCCHHHHhHhheeeEecHHHHHHHHHHHcCCCCCc
Confidence 334444455555555554 2455666777889999999999887654
No 22
>PRK06041 flagellar assembly protein J; Reviewed
Probab=33.86 E-value=3.8e+02 Score=25.87 Aligned_cols=56 Identities=20% Similarity=0.348 Sum_probs=36.2
Q ss_pred hHHhhhhhhcCCCCChhhhhCCCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHHHH
Q 029094 25 SFFSRAESLTATRRPWREFFNTSALSLPADYNDAISRARRNASYFRVNYAVVMLFI 80 (199)
Q Consensus 25 ~~~~~~~~~l~~~RPw~eF~d~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~ 80 (199)
+|+.+....+..--+.+||+..+.-..=++.+...+|..+++.-+..=|+.+++..
T Consensus 145 ~fl~~l~~~i~sG~~l~~fL~~e~~~~~~~~~~~~~~~le~L~~~~E~Yvt~lvs~ 200 (553)
T PRK06041 145 DFLDRLAYSIDSGEPLKEFLKQEQDTVMEDYKTFYERALYSLDVWKDLYVSLLLSV 200 (553)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555544455555667777422222224566678899999999999998776643
No 23
>COG4605 CeuC ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]
Probab=33.38 E-value=1.9e+02 Score=26.14 Aligned_cols=43 Identities=16% Similarity=0.237 Sum_probs=34.2
Q ss_pred CChhhhhCCCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHHHHHH
Q 029094 38 RPWREFFNTSALSLPADYNDAISRARRNASYFRVNYAVVMLFILF 82 (199)
Q Consensus 38 RPw~eF~d~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~~~ 82 (199)
|+.+.|+ ++.==|+.+..+++|+-.+.+.=.++++.+...+.+
T Consensus 145 rSiSsfm--q~liDPneF~~lQ~~mFAsFn~int~ll~i~a~i~~ 187 (316)
T COG4605 145 RSISSFM--QRLIDPNEFAILQARMFASFNNINTELLAIAAIILL 187 (316)
T ss_pred HHHHHHH--HHHcChHHHHHHHHHHHhhhhccCccHHHHHHHHHH
Confidence 5666777 566778999999999999999988888877665543
No 24
>KOG0054 consensus Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]
Probab=32.69 E-value=1.6e+02 Score=31.88 Aligned_cols=65 Identities=20% Similarity=0.261 Sum_probs=47.6
Q ss_pred CCChhhhhC-------CCCCCCCCChHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029094 37 RRPWREFFN-------TSALSLPADYNDAISRARRNASYFRVNYAVVMLFILFLSLLWHPVSMIVFIVVFVLWLF 104 (199)
Q Consensus 37 ~RPw~eF~d-------~~~fs~P~s~~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i~ll~~P~~Li~l~~~~~~~~~ 104 (199)
.|..-.||| .+||| +|.+.+-.++-..+..|-.|.+-+..++.+++ +..|..++..+.+.+++++
T Consensus 902 lrapm~FFdtTP~GRILNRFS--kD~~~vD~~Lp~~~~~~~~~~~~~l~~~~vi~-~~~P~fli~~~pl~v~~~~ 973 (1381)
T KOG0054|consen 902 LRAPMSFFDTTPTGRILNRFS--KDIDTVDVLLPFTLEFFLQSLLNVLGILVVIS-YVTPWFLIAIIPLGVIYYF 973 (1381)
T ss_pred HhCcchhcCCCCccchhhhcc--cchHHHHHhhHHHHHHHHHHHHHHHHHHHHhh-HHhHHHHHHHHHHHHHHHH
Confidence 466677898 36777 68888888999999999888888777665554 4567777766666555554
No 25
>PF11368 DUF3169: Protein of unknown function (DUF3169); InterPro: IPR021509 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=32.26 E-value=92 Score=26.51 Aligned_cols=44 Identities=14% Similarity=0.495 Sum_probs=23.2
Q ss_pred HHhHHhH-HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029094 63 RRNASYF-RVNYAVVM---LFILFLSLLWHPVSMIVFIVVFVLWLFFY 106 (199)
Q Consensus 63 ~~Nl~yF-~~NY~~i~---~~~~~i~ll~~P~~Li~l~~~~~~~~~i~ 106 (199)
+.+..-| +.|..++. +++.++++.++-.-+++++++.+.|.|..
T Consensus 190 ~~~yk~~~~ln~~ll~~~~~~l~i~s~~t~~~q~la~lvl~~I~iyi~ 237 (248)
T PF11368_consen 190 EASYKIYFKLNQYLLPILYILLFIYSLLTGENQLLAILVLIIIWIYIN 237 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHH
Confidence 3444434 44744433 33344555555555666666667776654
No 26
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=32.15 E-value=9.6 Score=27.71 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=20.5
Q ss_pred CCCCCChHHHHHHHHHhHHhHHHH
Q 029094 49 LSLPADYNDAISRARRNASYFRVN 72 (199)
Q Consensus 49 fs~P~s~~~~~~Ri~~Nl~yF~~N 72 (199)
=..|..++++.+||.-|=+||--|
T Consensus 61 rRLPdql~~La~RI~Ln~RYYLKn 84 (85)
T cd01785 61 RRLPDQLQNLAERIQLSSRYYLKN 84 (85)
T ss_pred ccCCHHHHHHHHhhcccceEEecc
Confidence 357899999999999999998544
No 27
>PF03522 KCl_Cotrans_1: K-Cl Co-transporter type 1 (KCC1); InterPro: IPR018491 The K-Cl co-transporter (KCC) mediates the coupled movement of K+ and Cl- ions across the plasma membrane of many animal cells. This transport is involved in the regulatory volume decrease in response to cell swelling in red blood cells, and has been proposed to play a role in the vectorial movement of Cl- across kidney epithelia. The transport process involves one for one electroneutral movement of K+ together with Cl-, and, in all known mammalian cells, the net movement is outward []. In neurones, it appears to play a unique role in maintaining low intracellular Cl-concentration, which is required for the functioning of Cl- dependent fast synaptic inhibition, mediated by certain neurotransmitters, such as gamma-aminobutyric acid (GABA) and glycine. Three isoforms of the K-Cl co-transporter have been described, termed KCC1 KCC2, and KCC3, containing 1085, 1116 and 1150 amino acids, respectively. They are predicted to have 12 transmembrane (TM) regions in a central hydrophobic domain, together with hydrophilic N- and C-termini that are likely cytoplasmic. Comparison of their sequences with those of other ion-tranporting membrane proteins reveals that they are part of a new superfamily of cation-chloride co-transporters, which includes the Na-Cl and Na-K-2Cl co-transporters. KCC1 and KCC3 are widely expressed in human tissues, while KCC2 is are expressed only in brain neurones, making it likely that this is the isoform responsible for maintaining low Cl- concentration in neurones [, , ]. KCC1 is widely expressed in human tissues, and when heterologously expressed, possesses the functional characteristics of the well-studied red blood cell K-Cl co-transporter, including stimulation by both swelling and N-ethylmaleimide. Several splice variants have also been identified. KCC3 is widely expressed in human tissues and, like KCC1, is stimulated by both swelling and N-ethylmaleimide. The induction of KCC3 is up-regulated by vascular endothelial growth factor and down-regulated by tumour necrosis factor. Defects in KCC3 are linked to agenesis of the corpus callosum with peripheral neuropathy []. This disorder is characterised by severe progressive sensorimotor neuropathy, mental retardation, dysmorphic features and complete or partial agenesis of the corpus callosum.; GO: 0005215 transporter activity, 0006811 ion transport, 0016020 membrane
Probab=30.45 E-value=20 Score=21.17 Aligned_cols=18 Identities=39% Similarity=0.691 Sum_probs=12.3
Q ss_pred hhhcccCCCCCcccccccc
Q 029094 160 HASFRATDDLFLDEESAAE 178 (199)
Q Consensus 160 HA~~R~~~~~~~de~~~~~ 178 (199)
|..+|. ++++.||||+..
T Consensus 5 ~S~lrl-~SlySDeeeE~~ 22 (30)
T PF03522_consen 5 HSILRL-ESLYSDEEEETE 22 (30)
T ss_pred cceeee-eccccCcccccc
Confidence 666666 466788887653
No 28
>TIGR02235 menA_cyano-plnt 1,4-dihydroxy-2-naphthoate phytyltransferase. This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I. The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility.
Probab=30.00 E-value=3.8e+02 Score=23.44 Aligned_cols=17 Identities=18% Similarity=0.210 Sum_probs=7.6
Q ss_pred CCCCeEeccccchHHHH
Q 029094 109 RDDPVVVFNQTLDDKFV 125 (199)
Q Consensus 109 ~~~p~~i~g~~~~~~~v 125 (199)
...|.....+-..+-.+
T Consensus 123 t~gP~~l~y~gLGE~~v 139 (285)
T TIGR02235 123 QGPPFRLGYQGLGEPIC 139 (285)
T ss_pred cCCCcccCCCCccHHHH
Confidence 34455444444444333
No 29
>PF02411 MerT: MerT mercuric transport protein; InterPro: IPR003457 MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerA).; GO: 0015097 mercury ion transmembrane transporter activity, 0015694 mercury ion transport, 0016020 membrane
Probab=28.14 E-value=2.8e+02 Score=21.27 Aligned_cols=21 Identities=10% Similarity=0.278 Sum_probs=11.7
Q ss_pred HHHHHHHH-HHHHHHHHHHHHH
Q 029094 87 WHPVSMIV-FIVVFVLWLFFYF 107 (199)
Q Consensus 87 ~~P~~Li~-l~~~~~~~~~i~~ 107 (199)
.+|.++.+ +++++.+|+-+|+
T Consensus 50 yRp~fi~~tl~~lg~a~~~~yr 71 (116)
T PF02411_consen 50 YRPYFIALTLLFLGYAFWRLYR 71 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc
Confidence 35655443 4555666666664
No 30
>PRK13751 putative mercuric transport protein; Provisional
Probab=28.01 E-value=2.6e+02 Score=21.55 Aligned_cols=20 Identities=20% Similarity=0.627 Sum_probs=10.3
Q ss_pred HHHHH-HHHHHHHHHHHHHHH
Q 029094 88 HPVSM-IVFIVVFVLWLFFYF 107 (199)
Q Consensus 88 ~P~~L-i~l~~~~~~~~~i~~ 107 (199)
+|.++ ++++++..+|+.+|+
T Consensus 51 r~~fi~~a~~~l~~a~~~~yr 71 (116)
T PRK13751 51 RPIFIGAALVALFFAWRRIYR 71 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHc
Confidence 44444 344445566665664
No 31
>PF14256 YwiC: YwiC-like protein
Probab=27.47 E-value=2.9e+02 Score=21.33 Aligned_cols=52 Identities=19% Similarity=0.176 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhhcccCCCCCccc
Q 029094 122 DKFVLGCLTLVTVLALILTDVGTNVLVGLIVGVVLVGLHASFRATDDLFLDE 173 (199)
Q Consensus 122 ~~~v~~~l~~vs~~ll~~~~~~~~l~~~l~~s~~vvl~HA~~R~~~~~~~de 173 (199)
.-.+|.++.++.....+........+..+.++++.+-+-.+-|++|-....|
T Consensus 61 ~~~~Yg~~a~~~~l~~l~~~p~ll~~~~~~~pl~~v~~~~~~~~~eRsLlnd 112 (129)
T PF14256_consen 61 WALIYGAIALVFGLPALLYAPRLLWWALLFLPLFAVNLYFAKRKRERSLLND 112 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcCchhHHHh
Confidence 3445555555554444444554444445666677777777777766443433
No 32
>COG4452 CreD Inner membrane protein involved in colicin E2 resistance [Defense mechanisms]
Probab=26.39 E-value=5.5e+02 Score=24.16 Aligned_cols=24 Identities=21% Similarity=0.703 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHH---------HHHHHHHH
Q 029094 71 VNYAVVMLFILFLSLL---------WHPVSMIV 94 (199)
Q Consensus 71 ~NY~~i~~~~~~i~ll---------~~P~~Li~ 94 (199)
.-|.++++.+.+..++ .||+.-+.
T Consensus 298 ~kYaIlfI~Ltf~afFifE~lt~~~~Hp~QY~L 330 (443)
T COG4452 298 TKYAILFIGLTFMAFFIFEVLTGQRLHPMQYLL 330 (443)
T ss_pred HHHHHHHHHHHHHHHhhhhhhcccccchHHHHH
Confidence 3466666655555443 38986554
No 33
>PRK10952 glycine betaine transporter membrane protein; Provisional
Probab=26.19 E-value=5e+02 Score=23.58 Aligned_cols=20 Identities=10% Similarity=0.363 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 029094 87 WHPVSMIVFIVVFVLWLFFY 106 (199)
Q Consensus 87 ~~P~~Li~l~~~~~~~~~i~ 106 (199)
.-|..++.++++.++|....
T Consensus 104 ~~p~~~~~~~~~~~~w~~~~ 123 (355)
T PRK10952 104 GMPAPVAIIVFALIAWQISG 123 (355)
T ss_pred hccHHHHHHHHHHHHHHHHH
Confidence 45666666777777776433
No 34
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=25.79 E-value=4.4e+02 Score=22.78 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=29.2
Q ss_pred HHHHHHHHHhHHhHHHHHHHHHHHHHHHHH--H------HHHHHHHHHHHHH
Q 029094 56 NDAISRARRNASYFRVNYAVVMLFILFLSL--L------WHPVSMIVFIVVF 99 (199)
Q Consensus 56 ~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i~l--l------~~P~~Li~l~~~~ 99 (199)
+....|++.-+..-|+||.+--+++..+.+ + +.|.+-|.+.+++
T Consensus 28 ~~~~~~~qs~l~~~~~r~tv~slAl~~l~~S~iy~~~~~y~~~~~It~~llg 79 (251)
T COG5415 28 DVALKKSQSILSQWQSRLTVYSLALTVLALSYIYWEYHGYRPYLVITALLLG 79 (251)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhccccchhHHHHHHHHh
Confidence 445667777888999999988777776632 2 3566555544443
No 35
>PF12264 Waikav_capsid_1: Waikavirus capsid protein 1; InterPro: IPR024379 This entry represents capsid protein 1 of Rice tungro spherical virus [].
Probab=24.74 E-value=41 Score=27.68 Aligned_cols=25 Identities=40% Similarity=0.534 Sum_probs=23.1
Q ss_pred CCCCCCCChHHHHHHHHHhHHhHHH
Q 029094 47 SALSLPADYNDAISRARRNASYFRV 71 (199)
Q Consensus 47 ~~fs~P~s~~~~~~Ri~~Nl~yF~~ 71 (199)
+.|++|+|+=..++|++.=+.|||.
T Consensus 45 ~~~~lP~DlW~~NsRl~d~msYFQY 69 (197)
T PF12264_consen 45 KTFSLPSDLWAANSRLKDIMSYFQY 69 (197)
T ss_pred eeccCcHHHhhhhhHHHHHHHHhhe
Confidence 7899999999999999999999985
No 36
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=24.74 E-value=88 Score=19.64 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=16.0
Q ss_pred hhhhHHHHHHHHHHHHHHHHh
Q 029094 140 TDVGTNVLVGLIVGVVLVGLH 160 (199)
Q Consensus 140 ~~~~~~l~~~l~~s~~vvl~H 160 (199)
+.+..+++|++.++.+++++-
T Consensus 2 TpSLsnF~~SL~~Ga~ivvip 22 (39)
T CHL00114 2 TPSLSAFINSLLLGAIIVVIP 22 (39)
T ss_pred ChhHHHHHHHHHHHHHHhHHH
Confidence 456778899999888776644
No 37
>PF11990 DUF3487: Protein of unknown function (DUF3487); InterPro: IPR021877 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.
Probab=24.33 E-value=3.3e+02 Score=20.94 Aligned_cols=20 Identities=25% Similarity=0.175 Sum_probs=13.4
Q ss_pred HhCCCCeEeccccchHHHHH
Q 029094 107 FARDDPVVVFNQTLDDKFVL 126 (199)
Q Consensus 107 ~~~~~p~~i~g~~~~~~~v~ 126 (199)
..+.+|.++.|-+.++--+.
T Consensus 10 RLN~ePvV~rGlT~~El~~~ 29 (121)
T PF11990_consen 10 RLNREPVVFRGLTADELGLA 29 (121)
T ss_pred hhcCCCCeecCCCHHHHHHH
Confidence 34678998888666664433
No 38
>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length.; GO: 0016020 membrane
Probab=23.31 E-value=4.7e+02 Score=22.57 Aligned_cols=22 Identities=23% Similarity=0.203 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 029094 87 WHPVSMIVFIVVFVLWLFFYFA 108 (199)
Q Consensus 87 ~~P~~Li~l~~~~~~~~~i~~~ 108 (199)
..|+.+...++-++..+++++.
T Consensus 265 i~Plil~~~~~yf~l~y~v~ky 286 (325)
T PF02714_consen 265 IAPLILPFGLVYFLLKYFVDKY 286 (325)
T ss_pred hhhHHHHHHHHHHHHHHHHHHh
Confidence 5666555544445555555553
No 39
>PF06645 SPC12: Microsomal signal peptidase 12 kDa subunit (SPC12); InterPro: IPR009542 This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12).; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=23.30 E-value=2.7e+02 Score=19.54 Aligned_cols=29 Identities=17% Similarity=0.128 Sum_probs=15.2
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 029094 130 TLVTVLALILTDVGTNVLVGLIVGVVLVG 158 (199)
Q Consensus 130 ~~vs~~ll~~~~~~~~l~~~l~~s~~vvl 158 (199)
.+++.+.=|++......+.+.++++++++
T Consensus 21 ~iisfi~Gy~~q~~~~~~~~~~~g~~~~~ 49 (76)
T PF06645_consen 21 AIISFIVGYITQSFSYTFYIYGAGVVLTL 49 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444556655555555555554444
No 40
>PF04140 ICMT: Isoprenylcysteine carboxyl methyltransferase (ICMT) family ; InterPro: IPR007269 The isoprenylcysteine o-methyltransferase (2.1.1.100 from EC) carries out carboyxl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae (Baker's yeast) this methylation is carried out by Ste14p, an integral endoplasmic reticulum membrane protein. Ste14p is the founding member of the isoprenylcysteine carboxyl methyltransferase (ICMT) family, whose members share significant sequence homology [].; GO: 0004671 protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity, 0006481 C-terminal protein methylation, 0016021 integral to membrane; PDB: 4A2N_B.
Probab=23.05 E-value=2.7e+02 Score=20.13 Aligned_cols=19 Identities=16% Similarity=0.093 Sum_probs=10.7
Q ss_pred HHHH-HHHHHHHHHHHHHHH
Q 029094 72 NYAV-VMLFILFLSLLWHPV 90 (199)
Q Consensus 72 NY~~-i~~~~~~i~ll~~P~ 90 (199)
||.. +...+....++.|+.
T Consensus 48 ~Y~g~~~~~~~~~~ll~~~~ 67 (94)
T PF04140_consen 48 SYLGNIIWELGGQLLLFNAW 67 (94)
T ss_dssp HHHH-HHHHHHHHHHHHT-H
T ss_pred hHHHHHHHHHHHHHHHHhHH
Confidence 6666 444455566677773
No 41
>PF04530 Viral_Beta_CD: Viral Beta C/D like family; InterPro: IPR007617 This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Probab=22.94 E-value=1.1e+02 Score=23.95 Aligned_cols=28 Identities=18% Similarity=0.199 Sum_probs=19.2
Q ss_pred HHHHHHHHHhHHhHHHHHHHHHHHHHHH
Q 029094 56 NDAISRARRNASYFRVNYAVVMLFILFL 83 (199)
Q Consensus 56 ~~~~~Ri~~Nl~yF~~NY~~i~~~~~~i 83 (199)
++..+|...=+.-|..||.++++.+.++
T Consensus 34 e~t~~~~~~~~sv~~~~y~l~~~~v~~L 61 (122)
T PF04530_consen 34 EMTARRETTFLSVLNDNYVLFVCAVCML 61 (122)
T ss_pred hHhhhhhcchhhhhhhhHHHHHHHHHHH
Confidence 3334443334889999999988877665
No 42
>COG0382 UbiA 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]
Probab=22.37 E-value=5.1e+02 Score=22.31 Aligned_cols=27 Identities=11% Similarity=-0.012 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHHHHHhhhcccCCCC
Q 029094 143 GTNVLVGLIVGVVLVGLHASFRATDDL 169 (199)
Q Consensus 143 ~~~l~~~l~~s~~vvl~HA~~R~~~~~ 169 (199)
.....+......+-++.+..+.+-+|.
T Consensus 166 ~~~~~~l~~~~~l~~~~~~~i~~~~D~ 192 (289)
T COG0382 166 PLLAWLLLLAAILWTLGYDIIYAIQDI 192 (289)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 344455566667778888888887775
No 43
>PF00664 ABC_membrane: ABC transporter transmembrane region; InterPro: IPR001140 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). A variety of ATP-binding transport proteins have a six transmembrane helical region. They are all integral membrane proteins involved in a variety of transport systems. Members of this family include; the cystic fibrosis transmembrane conductance regulator (CFTR), bacterial leukotoxin secretion ATP-binding protein, multidrug resistance proteins, the yeast leptomycin B resistance protein, the mammalian sulphonylurea receptor and antigen peptide transporter 2. Many of these proteins have two such regions.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3G61_B 3G5U_B 3G60_A 3B60_D 3QF4_B 2HYD_A 2ONJ_A 4A82_B 4AA3_A 2YL4_A.
Probab=22.24 E-value=3.8e+02 Score=20.88 Aligned_cols=21 Identities=10% Similarity=0.085 Sum_probs=14.7
Q ss_pred CChHHHHHHHHHhHHhHHHHH
Q 029094 53 ADYNDAISRARRNASYFRVNY 73 (199)
Q Consensus 53 ~s~~~~~~Ri~~Nl~yF~~NY 73 (199)
.+.+|..+|+.++.+..+..|
T Consensus 95 ~~~g~l~~~i~~d~~~i~~~~ 115 (275)
T PF00664_consen 95 NSSGELLSRITNDIEQIENFL 115 (275)
T ss_dssp S-HHHHHHHHHHHHHHHHHHH
T ss_pred hcccccccccccccccccccc
Confidence 456899999998776655444
No 44
>PRK12847 ubiA 4-hydroxybenzoate polyprenyltransferase; Reviewed
Probab=22.12 E-value=3.2e+02 Score=23.53 Aligned_cols=10 Identities=10% Similarity=0.208 Sum_probs=5.1
Q ss_pred HHHHHHHHHH
Q 029094 86 LWHPVSMIVF 95 (199)
Q Consensus 86 l~~P~~Li~l 95 (199)
..+|..+...
T Consensus 111 ~~~~~~~~~~ 120 (285)
T PRK12847 111 LLNKTTIYLS 120 (285)
T ss_pred HHhHHHHHHH
Confidence 3566654443
No 45
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=22.10 E-value=1.3e+02 Score=18.89 Aligned_cols=20 Identities=35% Similarity=0.517 Sum_probs=11.2
Q ss_pred hhhhHHHHHHHHHHHHHHHH
Q 029094 140 TDVGTNVLVGLIVGVVLVGL 159 (199)
Q Consensus 140 ~~~~~~l~~~l~~s~~vvl~ 159 (199)
+.+..++++++.++.++|++
T Consensus 2 TpSL~nfl~Sl~aG~~iVv~ 21 (39)
T PF06596_consen 2 TPSLSNFLLSLVAGAVIVVI 21 (39)
T ss_dssp -HHHHHHHHHHHHHH-HHHH
T ss_pred CHhHHHHHHHHHhhhhhhhh
Confidence 34556777777777644443
No 46
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.
Probab=21.93 E-value=5.1e+02 Score=24.26 Aligned_cols=21 Identities=10% Similarity=-0.002 Sum_probs=15.0
Q ss_pred CChHHHHHHHHHhHHhHHHHH
Q 029094 53 ADYNDAISRARRNASYFRVNY 73 (199)
Q Consensus 53 ~s~~~~~~Ri~~Nl~yF~~NY 73 (199)
.+.++..+|+...+...+.+|
T Consensus 108 ~~~g~~~~~l~~di~~i~~~~ 128 (571)
T TIGR02203 108 QPTGTLLSRITFDSEQVASAA 128 (571)
T ss_pred CCchHHHHHHHHHHHHHHHHH
Confidence 356889999987766666555
No 47
>PF05777 Acp26Ab: Drosophila accessory gland-specific peptide 26Ab (Acp26Ab); InterPro: IPR008392 This family consists of accessory gland-specific 26Ab peptides or male accessory gland secretory protein 355B from different Drosophila species. Drosophila males, like males of most other insects, transfer a group of specific proteins (Acp26Ab and Acp26Aa in Drosophila) to the females during mating. These proteins are produced primarily in the accessory gland and are likely to influence the female's reproduction [].; GO: 0007617 mating behavior, 0005576 extracellular region
Probab=21.66 E-value=67 Score=23.42 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHH
Q 029094 72 NYAVVMLFILFLSLL 86 (199)
Q Consensus 72 NY~~i~~~~~~i~ll 86 (199)
||+++..++.++|+.
T Consensus 2 nyf~~l~if~cicl~ 16 (90)
T PF05777_consen 2 NYFVVLCIFSCICLW 16 (90)
T ss_pred cchhhHHHHHHHHHH
Confidence 787777776666653
No 48
>PF08372 PRT_C: Plant phosphoribosyltransferase C-terminal; InterPro: IPR013583 This domain is found at the C terminus of phosphoribosyltransferases and phosphoribosyltransferase-like proteins. It contains putative transmembrane regions. It often appears together with calcium-ion dependent C2 domains (IPR000008 from INTERPRO).
Probab=21.63 E-value=2.9e+02 Score=22.34 Aligned_cols=37 Identities=19% Similarity=0.254 Sum_probs=26.0
Q ss_pred HHHHHHhHHh---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029094 59 ISRARRNASY---FRVNYAVVMLFILFLSLLWHPVSMIVF 95 (199)
Q Consensus 59 ~~Ri~~Nl~y---F~~NY~~i~~~~~~i~ll~~P~~Li~l 95 (199)
.+|+++=+.. ..+..+++++++.+++++.-|+-.+++
T Consensus 82 gERl~allsWrdP~aT~lf~~~clv~avvly~vP~r~l~l 121 (156)
T PF08372_consen 82 GERLQALLSWRDPRATALFVVFCLVAAVVLYFVPFRVLVL 121 (156)
T ss_pred HHHHHHhhccCCccHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 4555444444 567788888888888888889866643
No 49
>KOG1134 consensus Uncharacterized conserved protein [General function prediction only]
Probab=21.50 E-value=8.4e+02 Score=24.56 Aligned_cols=44 Identities=14% Similarity=0.063 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhC-----CCCeEeccccchHHHH
Q 029094 82 FLSLLWHPVSMIVFIVVFVLWLFFYFAR-----DDPVVVFNQTLDDKFV 125 (199)
Q Consensus 82 ~i~ll~~P~~Li~l~~~~~~~~~i~~~~-----~~p~~i~g~~~~~~~v 125 (199)
++..+..|+.+.-.++.++.-+++|+.+ +.+-.-+|+-.++.+.
T Consensus 566 i~YsviaPlILpF~lvyF~l~y~vyr~ql~yvy~~~yes~g~~wp~ih~ 614 (728)
T KOG1134|consen 566 ICYSVIAPLILPFGLVYFCLAYLVYRYQLIYVYNQKYESGGRFWPDIHR 614 (728)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHhhhhheeecccccccccchHHHHH
Confidence 3334467765555555555555566543 2344566666665443
No 50
>PRK13823 conjugal transfer protein TrbD; Provisional
Probab=21.44 E-value=2.9e+02 Score=20.40 Aligned_cols=49 Identities=12% Similarity=0.225 Sum_probs=22.2
Q ss_pred CCCeEeccccchHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH-HHHhhhccc
Q 029094 110 DDPVVVFNQTLDDKFVLGCLTLVTVLALILTDVGTNVLVGLIVGVVL-VGLHASFRA 165 (199)
Q Consensus 110 ~~p~~i~g~~~~~~~v~~~l~~vs~~ll~~~~~~~~l~~~l~~s~~v-vl~HA~~R~ 165 (199)
.+|.-++|-+ |++.++-..++..+.+ +....|+..+++++ ++.|..+|.
T Consensus 13 ~rp~Ll~Ga~---R~l~i~~g~la~~l~~----g~~~~~a~~~gl~lw~v~h~~l~~ 62 (94)
T PRK13823 13 NRPNLFMGGD---RELVMFSGLLAGILIF----VAQTWRAALFGIALWFGALFALRL 62 (94)
T ss_pred cccHhhCCcc---hHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4565555533 5544433333333222 22333344444444 666666654
No 51
>KOG1606 consensus Stationary phase-induced protein, SOR/SNZ family [Coenzyme transport and metabolism]
Probab=21.23 E-value=78 Score=27.47 Aligned_cols=37 Identities=27% Similarity=0.491 Sum_probs=29.7
Q ss_pred hhhcCCCCChhhhhCCCCCCCC-----CChHHHHHHHHHhHH
Q 029094 31 ESLTATRRPWREFFNTSALSLP-----ADYNDAISRARRNAS 67 (199)
Q Consensus 31 ~~~l~~~RPw~eF~d~~~fs~P-----~s~~~~~~Ri~~Nl~ 67 (199)
++..=++--|+.+.+..+|..| ++++|+..||++-..
T Consensus 106 ESEvlt~AD~~hhI~KhnFkvPFvCG~rdlGEALRRI~EGAA 147 (296)
T KOG1606|consen 106 ESEVLTPADWDHHIEKHNFKVPFVCGCRDLGEALRRIREGAA 147 (296)
T ss_pred hhhhcccccccchhhhhcCcCceeeccccHHHHHHHHhhchh
Confidence 3444456679999999999999 899999999987543
No 52
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=20.98 E-value=4e+02 Score=26.68 Aligned_cols=38 Identities=18% Similarity=0.482 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029094 69 FRVNYAVVMLFILFLSLLWHPVSMIVFIVVFVLWLFFY 106 (199)
Q Consensus 69 F~~NY~~i~~~~~~i~ll~~P~~Li~l~~~~~~~~~i~ 106 (199)
|..=++++++..-++|+++=|+-.+.+++....|+.+.
T Consensus 75 ~~~~~~~~~~~~d~~~~~~~p~~~~~~~~~~~v~~~~~ 112 (697)
T PF09726_consen 75 FSVFFVCIAFTSDLICLFFIPVHWLFFAASTYVWVQYV 112 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHh
Confidence 55555666666667888888888887777777776433
No 53
>PF10318 7TM_GPCR_Srh: Serpentine type 7TM GPCR chemoreceptor Srh; InterPro: IPR019422 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. Srh is part of the Str superfamily of chemoreceptors [].
Probab=20.20 E-value=4.6e+02 Score=22.26 Aligned_cols=20 Identities=25% Similarity=0.330 Sum_probs=15.1
Q ss_pred CCCCCCCChHHHHHHHHHhHH
Q 029094 47 SALSLPADYNDAISRARRNAS 67 (199)
Q Consensus 47 ~~fs~P~s~~~~~~Ri~~Nl~ 67 (199)
.-++.| |++++++++.++..
T Consensus 145 ~~~~~p-dQ~~~k~~~~~~~p 164 (302)
T PF10318_consen 145 IYLSIP-DQEEAKQEVLKKYP 164 (302)
T ss_pred HhcCCc-cHHHHHHHHHhhcc
Confidence 335777 88898888888775
Done!