Query 046724
Match_columns 197
No_of_seqs 56 out of 58
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 03:53:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046724hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2383 Predicted ATPase [Gene 98.1 2.8E-06 6.2E-11 80.1 4.2 42 82-124 34-76 (467)
2 PF03969 AFG1_ATPase: AFG1-lik 97.6 4.6E-05 1E-09 68.6 3.6 41 83-124 2-42 (362)
3 COG1485 Predicted ATPase [Gene 96.5 0.0034 7.5E-08 58.3 4.5 41 83-124 10-50 (367)
4 KOG0930 Guanine nucleotide exc 62.4 11 0.00023 35.7 4.0 143 3-161 139-286 (395)
5 PF05280 FlhC: Flagellar trans 59.5 3.3 7.2E-05 34.7 0.2 50 109-193 38-87 (175)
6 PRK12860 transcriptional activ 49.6 15 0.00032 31.7 2.6 49 108-191 37-85 (189)
7 TIGR03142 cytochro_ccmI cytoch 44.8 12 0.00026 28.7 1.2 36 84-120 44-79 (117)
8 PRK12722 transcriptional activ 43.3 22 0.00047 30.7 2.6 49 109-192 38-86 (187)
9 PF09451 ATG27: Autophagy-rela 41.3 7.2 0.00016 33.8 -0.5 49 134-182 195-243 (268)
10 cd00419 Ferrochelatase_C Ferro 36.1 52 0.0011 25.9 3.6 42 99-143 35-76 (135)
11 PF10775 ATP_sub_h: ATP syntha 26.9 45 0.00097 24.7 1.7 15 111-125 13-28 (67)
12 PF00392 GntR: Bacterial regul 25.7 89 0.0019 20.9 2.9 27 86-112 7-35 (64)
13 PF13076 DUF3940: Protein of u 25.1 92 0.002 20.7 2.8 28 89-117 8-37 (38)
14 PF00762 Ferrochelatase: Ferro 22.6 84 0.0018 28.1 2.9 40 99-143 201-240 (316)
15 PF08269 Cache_2: Cache domain 22.1 86 0.0019 22.3 2.4 30 84-114 22-51 (95)
16 PF12273 RCR: Chitin synthesis 22.0 10 0.00022 29.4 -2.6 18 144-161 3-20 (130)
17 KOG2383 Predicted ATPase [Gene 22.0 50 0.0011 32.4 1.5 107 1-136 5-111 (467)
18 KOG1612 Exosomal 3'-5' exoribo 21.8 1.8E+02 0.0039 27.0 4.9 45 98-150 96-140 (288)
19 KOG4634 Mitochondrial F1F0-ATP 21.6 1.3E+02 0.0027 24.4 3.4 36 84-119 41-77 (105)
20 COG4840 Uncharacterized protei 21.2 59 0.0013 24.7 1.4 30 90-120 21-50 (71)
21 COG3945 Uncharacterized conser 20.9 56 0.0012 28.7 1.4 37 82-124 75-113 (189)
No 1
>KOG2383 consensus Predicted ATPase [General function prediction only]
Probab=98.09 E-value=2.8e-06 Score=80.12 Aligned_cols=42 Identities=36% Similarity=0.536 Sum_probs=36.7
Q ss_pred CCChHHHHHHhhcCCccCCChhHHHHHHHHHHHHHHHhh-cccc
Q 046724 82 AGPLVEYERRIIAGELLDGDVCQLGTLGELQRLYDELVE-SADA 124 (197)
Q Consensus 82 ~GPL~EYerRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~-Y~p~ 124 (197)
.+|+.+|+++|+.|.|+. |++|++++..+.+||+++.. |.|+
T Consensus 34 ~tpl~~y~k~V~~g~l~~-d~yq~~~~~~~~~L~~~~~e~y~p~ 76 (467)
T KOG2383|consen 34 LTPLKEYSKLVNTGTLKS-DPYQRKTVSAFERLYHELIEYYDPR 76 (467)
T ss_pred cCcchHHHhHhccCcccC-CchhhhhHHHHHHHHhhhhhhcCcc
Confidence 379999999999999999 99999999999999995544 4444
No 2
>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP. AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding
Probab=97.61 E-value=4.6e-05 Score=68.58 Aligned_cols=41 Identities=39% Similarity=0.611 Sum_probs=39.6
Q ss_pred CChHHHHHHhhcCCccCCChhHHHHHHHHHHHHHHHhhcccc
Q 046724 83 GPLVEYERRIIAGELLDGDVCQLGTLGELQRLYDELVESADA 124 (197)
Q Consensus 83 GPL~EYerRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~Y~p~ 124 (197)
.|+++|+.+|++|.+++ |+.|++.+++||.||++|..+.++
T Consensus 2 tp~~~y~~~~~~~~~~~-D~~q~~~~~~l~~l~~~l~~~~~~ 42 (362)
T PF03969_consen 2 TPLERYQARVAQGELFP-DPAQRQAIEHLDRLYQELQKYKPA 42 (362)
T ss_pred ChHHHHHHHhcCCCCCC-CHHHHHHHHhHHHHHHHHHhcccc
Confidence 59999999999999999 999999999999999999999886
No 3
>COG1485 Predicted ATPase [General function prediction only]
Probab=96.47 E-value=0.0034 Score=58.29 Aligned_cols=41 Identities=37% Similarity=0.558 Sum_probs=36.6
Q ss_pred CChHHHHHHhhcCCccCCChhHHHHHHHHHHHHHHHhhcccc
Q 046724 83 GPLVEYERRIIAGELLDGDVCQLGTLGELQRLYDELVESADA 124 (197)
Q Consensus 83 GPL~EYerRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~Y~p~ 124 (197)
.|.+.|++.++.|.+.+ |+.|..++++|++||+++....+.
T Consensus 10 sp~~~y~~~~~~~~~~~-D~aQ~~a~~~Ldrl~~~~~~~~~~ 50 (367)
T COG1485 10 SPVERYAQLVPAGTFQP-DPAQPAAAAALDRLYDELVAPRSA 50 (367)
T ss_pred CHHHHHHHhcccCCCCC-ChHHHHHHHHHHHHHHHhhccccc
Confidence 69999999999999999 999999999999999966554443
No 4
>KOG0930 consensus Guanine nucleotide exchange factor Cytohesin, contains PH and Sec7 domains [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.42 E-value=11 Score=35.73 Aligned_cols=143 Identities=17% Similarity=0.137 Sum_probs=81.8
Q ss_pred hhhhhHHHHHHHHhhhccccCcccccCCccccccccccccccccccchhhhhhhhhhHhhhhhhhHhhhccccccccCCC
Q 046724 3 RIAGSARYFRSALWHRKFDYWSSFTTRPKDLTENYHNCAYGVTNNAEIESFLRSKFMVSRALSTDAAASASIGEVHRAAA 82 (197)
Q Consensus 3 ~v~~S~r~~r~~~~h~~~~~~~~~~~~~~~li~~~~~~~~~v~~n~e~~~~~~p~~~~~R~~~t~aAas~s~~dv~~~~~ 82 (197)
++|..||||---|+.-|-++ ..-+.-.+.-+-|-+|..||-+|+++---+ ...-+ |..+ +..+.||.+ -
T Consensus 139 nlVqALRQfLwSFRLPGEaQ--KIdRmmEaFA~rYclcNPgvfqstDtcyvl-sfs~I---MlNT---sLHNpNVrD--k 207 (395)
T KOG0930|consen 139 NLVQALRQFLWSFRLPGEAQ--KIDRMMEAFAQRYCLCNPGVFQSTDTCYVL-SFAII---MLNT---SLHNPNVKD--K 207 (395)
T ss_pred hHHHHHHHHHHHhcCCchHH--HHHHHHHHHHHHHhccCCcccccCceeeee-eehhh---hhcc---cccCCCCCC--C
Confidence 35677887765555433222 233333455677889999999998876322 22222 2222 244556654 2
Q ss_pred CChHHHHHHhhcCCccCCChhHHHHHHHHHHHHHHHhhccccccccccc----cCCCCCCCCcccccce-eeeeehhhee
Q 046724 83 GPLVEYERRIIAGELLDGDVCQLGTLGELQRLYDELVESADACKLDRYS----SSEKSGDSPVSLQESV-AVVTFTATIF 157 (197)
Q Consensus 83 GPL~EYerRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~Y~p~c~LDRy~----~s~ksg~sgwl~s~Fv-~~~~~~~~~~ 157 (197)
-|++-|- -.+.|-+--||- .++.|-.||+.+++-.=.+-=|--+ .=-.+-+-|||.++-- -|.|.----|
T Consensus 208 P~lErfi-~MNrgineggdl----pee~LrnlyeSi~~epFkIPeddgndlthtffnpdREGWLlKlgg~rvktWKrRWF 282 (395)
T KOG0930|consen 208 PTLERFI-AMNRGINEGGDL----PEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGNRVKTWKRRWF 282 (395)
T ss_pred ccHHHHH-HHhhccccCCCC----cHHHHHHHHHHhcCCCCCCCcccCCcchhhccCccccceeeeecCCcccchhheeE
Confidence 2444442 234444444452 3678999999998753221111100 1124668899998876 6777777788
Q ss_pred eecc
Q 046724 158 ILTC 161 (197)
Q Consensus 158 ~~~~ 161 (197)
|||-
T Consensus 283 iLtd 286 (395)
T KOG0930|consen 283 ILTD 286 (395)
T ss_pred Eeec
Confidence 8873
No 5
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=59.49 E-value=3.3 Score=34.73 Aligned_cols=50 Identities=22% Similarity=0.369 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhccccccccccccCCCCCCCCcccccceeeeeehhheeeeccceeeeecccCCCCcCCCchhhhHHHhh
Q 046724 109 GELQRLYDELVESADACKLDRYSSSEKSGDSPVSLQESVAVVTFTATIFILTCQRIVPLWGSRDWENNVDGPIFLSIALQ 188 (197)
Q Consensus 109 q~LQ~LYdeLk~Y~p~c~LDRy~~s~ksg~sgwl~s~Fv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (197)
+.|.+||.||++-.||++.=+ .+-.||- .|..|+|+-+|..|-..
T Consensus 38 ~rl~~Lykel~G~sppkG~lP-------~S~~wf~----------------------------t~~~~ihaSlf~~lY~~ 82 (175)
T PF05280_consen 38 ERLRRLYKELHGVSPPKGMLP-------FSTDWFM----------------------------TWQPNIHASLFMNLYRF 82 (175)
T ss_dssp HHHHHHHHHHCSS----S------------THHHH----------------------------SCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCCCCC-------CchhHHh----------------------------cchHHHHHHHHHHHHHH
Confidence 567899999999999854322 2223422 48889999999999888
Q ss_pred hhhcc
Q 046724 189 LEKEE 193 (197)
Q Consensus 189 ~~~~~ 193 (197)
+.++.
T Consensus 83 l~~~~ 87 (175)
T PF05280_consen 83 LRKNA 87 (175)
T ss_dssp HHHCT
T ss_pred HHhcC
Confidence 87653
No 6
>PRK12860 transcriptional activator FlhC; Provisional
Probab=49.59 E-value=15 Score=31.74 Aligned_cols=49 Identities=18% Similarity=0.214 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhhccccccccccccCCCCCCCCcccccceeeeeehhheeeeccceeeeecccCCCCcCCCchhhhHHHh
Q 046724 108 LGELQRLYDELVESADACKLDRYSSSEKSGDSPVSLQESVAVVTFTATIFILTCQRIVPLWGSRDWENNVDGPIFLSIAL 187 (197)
Q Consensus 108 Iq~LQ~LYdeLk~Y~p~c~LDRy~~s~ksg~sgwl~s~Fv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 187 (197)
.+.|.+||.|+++-.|||+.=+ .+--|| - +|..|+|+-+|..|-.
T Consensus 37 ~~rl~~Lyke~~G~SpPkG~lP-------~S~dWF---------------------------~-tw~~nihsSlf~~iY~ 81 (189)
T PRK12860 37 RDRLIRLYKEVRGVSPPKGMLP-------FSTDWF---------------------------M-TWLANIHASLFYNAYR 81 (189)
T ss_pred HHHHHHHHHHHcCCCCCCCCCC-------CchHHH---------------------------c-CchhhhHHHHHHHHHH
Confidence 3678899999999999965333 112232 2 7999999999999988
Q ss_pred hhhh
Q 046724 188 QLEK 191 (197)
Q Consensus 188 ~~~~ 191 (197)
.+-+
T Consensus 82 ~l~~ 85 (189)
T PRK12860 82 FLKN 85 (189)
T ss_pred HHHh
Confidence 7754
No 7
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=44.76 E-value=12 Score=28.72 Aligned_cols=36 Identities=22% Similarity=0.276 Sum_probs=25.6
Q ss_pred ChHHHHHHhhcCCccCCChhHHHHHHHHHHHHHHHhh
Q 046724 84 PLVEYERRIIAGELLDGDVCQLGTLGELQRLYDELVE 120 (197)
Q Consensus 84 PL~EYerRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~ 120 (197)
=+.|.|+-.++|.|-+ ++|+.--.+--++|-++...
T Consensus 44 qL~ELe~d~~~G~l~~-~e~~~~~~El~rrLL~d~~~ 79 (117)
T TIGR03142 44 RLAELERDLAEGLLDE-AEAEAARAELQRRLLADIPA 79 (117)
T ss_pred HHHHHHHHHHcCCCCH-HHHHHHHHHHHHHHHHCccc
Confidence 5788888899999988 66666555555566666443
No 8
>PRK12722 transcriptional activator FlhC; Provisional
Probab=43.26 E-value=22 Score=30.66 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhhccccccccccccCCCCCCCCcccccceeeeeehhheeeeccceeeeecccCCCCcCCCchhhhHHHhh
Q 046724 109 GELQRLYDELVESADACKLDRYSSSEKSGDSPVSLQESVAVVTFTATIFILTCQRIVPLWGSRDWENNVDGPIFLSIALQ 188 (197)
Q Consensus 109 q~LQ~LYdeLk~Y~p~c~LDRy~~s~ksg~sgwl~s~Fv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (197)
+.|.+||.|+++-.|||+.=+ -+--||- .|..|+|+-+|..|-..
T Consensus 38 ~rl~~Lyke~~G~spPkG~lP-------~S~dWF~----------------------------tw~~nihsSlf~~iY~~ 82 (187)
T PRK12722 38 ERLIKLYKELRGVSPPKGMLP-------FSTDWFM----------------------------TWEPNIHSSLFYNIYQF 82 (187)
T ss_pred HHHHHHHHHHcCCCCCCCCCC-------CchHHHc----------------------------ccchhhHHHHHHHHHHH
Confidence 567889999999999965333 1122422 48999999999999887
Q ss_pred hhhc
Q 046724 189 LEKE 192 (197)
Q Consensus 189 ~~~~ 192 (197)
+-+.
T Consensus 83 l~~~ 86 (187)
T PRK12722 83 LLKT 86 (187)
T ss_pred HHHc
Confidence 7653
No 9
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=41.25 E-value=7.2 Score=33.76 Aligned_cols=49 Identities=16% Similarity=0.112 Sum_probs=35.0
Q ss_pred CCCCCCCcccccceeeeeehhheeeeccceeeeecccCCCCcCCCchhh
Q 046724 134 EKSGDSPVSLQESVAVVTFTATIFILTCQRIVPLWGSRDWENNVDGPIF 182 (197)
Q Consensus 134 ~ksg~sgwl~s~Fv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (197)
.+++.+|||.-+|+.++.+++.-||+.--.-.-.-+.|+||--.|+-.+
T Consensus 195 ~~~~~~g~f~wl~i~~~l~~~~Y~i~g~~~n~~~~g~~g~e~iP~~dfw 243 (268)
T PF09451_consen 195 DSSGGWGFFTWLFIILFLFLAAYLIFGSWYNYNRYGARGFELIPHFDFW 243 (268)
T ss_pred CccccccHHHHHHHHHHHHHHHHhhhhhheeeccCCCCCceecccHhHH
Confidence 3477888887788888888877777766555556688899766666333
No 10
>cd00419 Ferrochelatase_C Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=36.06 E-value=52 Score=25.87 Aligned_cols=42 Identities=10% Similarity=-0.085 Sum_probs=30.1
Q ss_pred CCChhHHHHHHHHHHHHHHHhhccccccccccccCCCCCCCCccc
Q 046724 99 DGDVCQLGTLGELQRLYDELVESADACKLDRYSSSEKSGDSPVSL 143 (197)
Q Consensus 99 dGD~hQr~iIq~LQ~LYdeLk~Y~p~c~LDRy~~s~ksg~sgwl~ 143 (197)
.||+++.++.+.-+.|-+.|.. +. .-=....+++.|++.|+.
T Consensus 35 ~gd~Y~~~~~~~~~~v~~~l~~--~~-~~~~~~fqS~~g~~~Wl~ 76 (135)
T cd00419 35 KGDPYPDQCEETARLVAERLGL--PF-DEYELAYQSRFGPGEWLE 76 (135)
T ss_pred CCCCHHHHHHHHHHHHHHHhCC--CC-CCEEEEecCCCCCCCCCC
Confidence 5899999999888888888863 11 001223788888899986
No 11
>PF10775 ATP_sub_h: ATP synthase complex subunit h; InterPro: IPR019711 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit H found in the F0 complex of F-ATPases from fungal mitochondria. Subunit H is homologous to the mammalian factor F6, and is essential for the correct assembly and/or functioning of F-ATPases, since yeast cells lacking it are not able to grow on non-fermentable carbon sources. Subunit H occupies a central place in the peripheral stalk between the F1 sector and the membrane [].
Probab=26.86 E-value=45 Score=24.68 Aligned_cols=15 Identities=33% Similarity=0.370 Sum_probs=12.7
Q ss_pred HHHHH-HHHhhccccc
Q 046724 111 LQRLY-DELVESADAC 125 (197)
Q Consensus 111 LQ~LY-deLk~Y~p~c 125 (197)
+|+|| .|||.|.|++
T Consensus 13 VQDLYLkELKayKp~p 28 (67)
T PF10775_consen 13 VQDLYLKELKAYKPPP 28 (67)
T ss_pred HHHHHHHHHHhcCCCC
Confidence 57788 7999999995
No 12
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=25.70 E-value=89 Score=20.93 Aligned_cols=27 Identities=19% Similarity=0.251 Sum_probs=18.5
Q ss_pred HHHHHHhhcCCccCCCh--hHHHHHHHHH
Q 046724 86 VEYERRIIAGELLDGDV--CQLGTLGELQ 112 (197)
Q Consensus 86 ~EYerRV~sGeLrdGD~--hQr~iIq~LQ 112 (197)
+....+|.+|++.+||. -.+++.+.++
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~ 35 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYG 35 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhc
Confidence 34567899999999984 4666666553
No 13
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=25.08 E-value=92 Score=20.65 Aligned_cols=28 Identities=39% Similarity=0.484 Sum_probs=22.6
Q ss_pred HHHhhcCCccCCChhHH--HHHHHHHHHHHH
Q 046724 89 ERRIIAGELLDGDVCQL--GTLGELQRLYDE 117 (197)
Q Consensus 89 erRV~sGeLrdGD~hQr--~iIq~LQ~LYde 117 (197)
++.|+.|--+.+| .|. -++++|+.+|+.
T Consensus 8 ~~Li~~Giyk~~d-rqL~Eltl~ELe~ey~~ 37 (38)
T PF13076_consen 8 EKLIQSGIYKKED-RQLYELTLSELEKEYER 37 (38)
T ss_pred HHHHHcCCcCccc-hHHHHcCHHHHHHHHHc
Confidence 5788999999966 554 489999999975
No 14
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=22.56 E-value=84 Score=28.11 Aligned_cols=40 Identities=13% Similarity=0.033 Sum_probs=27.3
Q ss_pred CCChhHHHHHHHHHHHHHHHhhccccccccccccCCCCCCCCccc
Q 046724 99 DGDVCQLGTLGELQRLYDELVESADACKLDRYSSSEKSGDSPVSL 143 (197)
Q Consensus 99 dGD~hQr~iIq~LQ~LYdeLk~Y~p~c~LDRy~~s~ksg~sgwl~ 143 (197)
.||+++.++.+..+.|=+.| ++.+ =+...|++.|++.|+.
T Consensus 201 ~GdpY~~~~~~t~~~i~~~l-~~~~----~~~~fQS~~g~~~WL~ 240 (316)
T PF00762_consen 201 KGDPYPAQCEETARLIAERL-GLPE----WRLAFQSRFGPGEWLG 240 (316)
T ss_dssp CT-SHHHHHHHHHHHHHHHT-TTSS----EEEEEES-SSSS-BSS
T ss_pred CCCChHHHHHHHHHHHHHHc-CCCc----eEEEEECCCCCCCCcc
Confidence 58999999999998888888 2222 1223778888999987
No 15
>PF08269 Cache_2: Cache domain; InterPro: IPR013163 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions []. This entry is composed of the type 2 Cache domain.; PDB: 2QHK_A 4EXO_A.
Probab=22.10 E-value=86 Score=22.26 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=19.2
Q ss_pred ChHHHHHHhhcCCccCCChhHHHHHHHHHHH
Q 046724 84 PLVEYERRIIAGELLDGDVCQLGTLGELQRL 114 (197)
Q Consensus 84 PL~EYerRV~sGeLrdGD~hQr~iIq~LQ~L 114 (197)
=+..|..+..+|+|-+ ++-|..+++.|..+
T Consensus 22 ~i~~~~~~~~~g~ls~-eea~~~a~~~l~~~ 51 (95)
T PF08269_consen 22 LIESYYAQAQAGKLSE-EEAQQQAREALRAL 51 (95)
T ss_dssp HTHHHHHC-STT------TTHHHHHHHHHH-
T ss_pred HHHHHHHHHhcCCccH-HHHHHHHHHHHhcc
Confidence 5778999999999999 88898888888443
No 16
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=21.97 E-value=10 Score=29.41 Aligned_cols=18 Identities=6% Similarity=-0.029 Sum_probs=9.7
Q ss_pred ccceeeeeehhheeeecc
Q 046724 144 QESVAVVTFTATIFILTC 161 (197)
Q Consensus 144 s~Fv~~~~~~~~~~~~~~ 161 (197)
.+|+.+|.+...+|+++|
T Consensus 3 ~l~~iii~~i~l~~~~~~ 20 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFY 20 (130)
T ss_pred eeHHHHHHHHHHHHHHHH
Confidence 346555555555555554
No 17
>KOG2383 consensus Predicted ATPase [General function prediction only]
Probab=21.97 E-value=50 Score=32.36 Aligned_cols=107 Identities=16% Similarity=0.052 Sum_probs=62.6
Q ss_pred ChhhhhhHHHHHHHHhhhccccCcccccCCccccccccccccccccccchhhhhhhhhhHhhhhhhhHhhhccccccccC
Q 046724 1 MRRIAGSARYFRSALWHRKFDYWSSFTTRPKDLTENYHNCAYGVTNNAEIESFLRSKFMVSRALSTDAAASASIGEVHRA 80 (197)
Q Consensus 1 MR~v~~S~r~~r~~~~h~~~~~~~~~~~~~~~li~~~~~~~~~v~~n~e~~~~~~p~~~~~R~~~t~aAas~s~~dv~~~ 80 (197)
||..++++||+-....+.+|++ +.+.+..+..+++|..- |+.+.- ..-.+ .|...++. .+.
T Consensus 5 lrl~~~~~r~~~l~~~~~~y~~-~~~~~~~~tpl~~y~k~---V~~g~l-~~d~y-----q~~~~~~~------~~L--- 65 (467)
T KOG2383|consen 5 LRLAVRCFRRVPLRSRICRYSS-TAPHKFLLTPLKEYSKL---VNTGTL-KSDPY-----QRKTVSAF------ERL--- 65 (467)
T ss_pred HHhhHHHHhhhhhccccceeee-ccccccccCcchHHHhH---hccCcc-cCCch-----hhhhHHHH------HHH---
Confidence 4667788998888877787765 57777777777666442 111100 00000 01111110 111
Q ss_pred CCCChHHHHHHhhcCCccCCChhHHHHHHHHHHHHHHHhhccccccccccccCCCC
Q 046724 81 AAGPLVEYERRIIAGELLDGDVCQLGTLGELQRLYDELVESADACKLDRYSSSEKS 136 (197)
Q Consensus 81 ~~GPL~EYerRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~Y~p~c~LDRy~~s~ks 136 (197)
-+++++-|+-++.++.... + +++++++|+.-..+|++|++..+..+
T Consensus 66 ~~~~~e~y~p~~~~~~~~~-e---------~~r~i~~l~k~~~~~k~~~~~a~~~~ 111 (467)
T KOG2383|consen 66 YHELIEYYDPRLKQWSAKR-E---------EGRWIFELKKSFDDGKLDTPNASGQP 111 (467)
T ss_pred HhhhhhhcCccccccccch-h---------hhhHHHHHHHHHhccCCCCcccccCC
Confidence 1358888888888877776 3 34477777777778888888777443
No 18
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=21.75 E-value=1.8e+02 Score=27.05 Aligned_cols=45 Identities=20% Similarity=0.135 Sum_probs=31.0
Q ss_pred cCCChhHHHHHHHHHHHHHHHhhccccccccccccCCCCCCCCcccccceeee
Q 046724 98 LDGDVCQLGTLGELQRLYDELVESADACKLDRYSSSEKSGDSPVSLQESVAVV 150 (197)
Q Consensus 98 rdGD~hQr~iIq~LQ~LYdeLk~Y~p~c~LDRy~~s~ksg~sgwl~s~Fv~~~ 150 (197)
|.||+.=..+...||++|.. +..++|=-+-+-+.| .-|++||-++
T Consensus 96 Rggde~~~eltsaLq~~l~~-----~~sgv~ls~L~lt~~---~~W~i~VDvl 140 (288)
T KOG1612|consen 96 RGGDELVEELTSALQRVLNS-----LGSGVDLSKLQLTPG---YCWKIYVDVL 140 (288)
T ss_pred CChhhHHHHHHHHHHHHHhC-----cCcccchhheeccCC---eeEEEEEeEE
Confidence 67899999999999999987 343333322333333 6678888874
No 19
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=21.60 E-value=1.3e+02 Score=24.43 Aligned_cols=36 Identities=31% Similarity=0.410 Sum_probs=28.3
Q ss_pred ChHHHHHHhhcCCccCCC-hhHHHHHHHHHHHHHHHh
Q 046724 84 PLVEYERRIIAGELLDGD-VCQLGTLGELQRLYDELV 119 (197)
Q Consensus 84 PL~EYerRV~sGeLrdGD-~hQr~iIq~LQ~LYdeLk 119 (197)
-+.||.++-.+|.|.|-| ++|++.=++|.+|-...-
T Consensus 41 KvREy~~ks~~Gklvds~pe~e~eLk~el~rla~qfg 77 (105)
T KOG4634|consen 41 KVREYKKKSPAGKLVDSDPEYEQELKEELFRLAQQFG 77 (105)
T ss_pred HHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 467999999999999977 578777777777765543
No 20
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.19 E-value=59 Score=24.68 Aligned_cols=30 Identities=17% Similarity=0.253 Sum_probs=26.1
Q ss_pred HHhhcCCccCCChhHHHHHHHHHHHHHHHhh
Q 046724 90 RRIIAGELLDGDVCQLGTLGELQRLYDELVE 120 (197)
Q Consensus 90 rRV~sGeLrdGD~hQr~iIq~LQ~LYdeLk~ 120 (197)
.-|+-|.|.| +++--.=.++|-++|+.++.
T Consensus 21 nmvN~gvl~~-e~~d~~~~edLtdiy~mvkk 50 (71)
T COG4840 21 NMVNVGVLDP-EKYDNANYEDLTDIYDMVKK 50 (71)
T ss_pred hhhhhhccCH-HhcccccHHHHHHHHHHHHH
Confidence 3478899999 88888899999999999975
No 21
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=20.92 E-value=56 Score=28.67 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=29.0
Q ss_pred CCChHHHHHHhhcCCccCCChhH--HHHHHHHHHHHHHHhhcccc
Q 046724 82 AGPLVEYERRIIAGELLDGDVCQ--LGTLGELQRLYDELVESADA 124 (197)
Q Consensus 82 ~GPL~EYerRV~sGeLrdGD~hQ--r~iIq~LQ~LYdeLk~Y~p~ 124 (197)
||| |++-...|-+.. || |.+|..|+++|+++++-...
T Consensus 75 g~~---~~~~~i~~m~~E---H~~~R~i~r~lee~~~~~kngd~~ 113 (189)
T COG3945 75 GGP---FEEGPIYVMTVE---HGEGRYIIRDLEEAYERLKNGDED 113 (189)
T ss_pred CCC---cccCceeeehhh---hhhHHHHHHHHHHHHHHHHccccc
Confidence 467 666666777777 65 45999999999999998665
Done!