Query psy16712
Match_columns 221
No_of_seqs 115 out of 321
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 20:05:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16712.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16712hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3767|consensus 100.0 1.6E-93 3.6E-98 641.5 16.4 219 3-221 107-328 (328)
2 TIGR00798 mtc tricarboxylate c 100.0 2.7E-92 5.7E-97 639.2 16.7 219 3-221 97-318 (318)
3 PF03820 Mtc: Tricarboxylate c 100.0 3.3E-92 7.1E-97 638.5 16.8 219 3-221 89-308 (308)
4 TIGR03171 soxL2 Rieske iron-su 71.8 7.1 0.00015 36.5 4.9 82 20-122 39-121 (321)
5 PF05239 PRC: PRC-barrel domai 57.7 7.3 0.00016 27.5 1.7 21 95-116 4-24 (79)
6 PF10049 DUF2283: Protein of u 52.6 7 0.00015 26.4 0.9 21 96-116 23-44 (50)
7 KOG4355|consensus 34.7 18 0.00038 35.3 0.9 54 111-169 247-308 (547)
8 PF13721 SecD-TM1: SecD export 33.3 1.4E+02 0.0031 22.9 5.7 60 157-219 2-69 (101)
9 PF09339 HTH_IclR: IclR helix- 31.9 31 0.00067 22.8 1.5 46 102-160 4-52 (52)
10 PF11141 DUF2914: Protein of u 31.6 27 0.00057 25.0 1.2 13 104-116 48-60 (66)
11 PF05979 DUF896: Bacterial pro 30.6 19 0.00041 26.1 0.3 17 100-116 45-61 (65)
12 PF00571 CBS: CBS domain CBS d 30.3 19 0.00042 23.3 0.3 15 101-115 30-44 (57)
13 PRK01546 hypothetical protein; 29.6 28 0.0006 26.3 1.0 18 101-118 49-66 (79)
14 PF12396 DUF3659: Protein of u 28.3 36 0.00077 24.5 1.4 17 100-116 39-55 (64)
15 PRK13454 F0F1 ATP synthase sub 27.8 36 0.00078 28.7 1.6 20 4-23 20-40 (181)
16 COG1873 Protein implicated in 27.7 39 0.00084 25.6 1.6 23 93-116 4-26 (87)
17 PRK03759 isopentenyl-diphospha 24.7 38 0.00083 28.2 1.2 20 104-123 8-27 (184)
18 PRK01631 hypothetical protein; 24.6 39 0.00085 25.3 1.0 19 100-118 46-64 (76)
19 PF09048 Cro: Cro; InterPro: 24.4 33 0.00072 24.5 0.6 24 113-136 12-35 (59)
20 PRK02539 hypothetical protein; 23.1 42 0.00092 25.6 1.0 18 101-118 48-65 (85)
21 PF07411 DUF1508: Domain of un 22.3 93 0.002 20.8 2.5 23 106-128 10-37 (49)
22 PF14985 TM140: TM140 protein 22.3 89 0.0019 26.7 2.8 22 178-199 159-180 (181)
23 PRK14472 F0F1 ATP synthase sub 21.0 67 0.0015 26.6 1.9 18 3-23 10-27 (175)
24 PF12860 PAS_7: PAS fold 20.2 73 0.0016 23.6 1.8 24 99-122 3-26 (115)
No 1
>KOG3767|consensus
Probab=100.00 E-value=1.6e-93 Score=641.47 Aligned_cols=219 Identities=55% Similarity=0.850 Sum_probs=217.0
Q ss_pred CccccccCCCchhHHHHHHHhhhhhhhhhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHhHhhhccc---hhhhhhc
Q psy16712 3 SEWKFTIRRSTPAVVFWQWFNQSFNAVVNYTNRSGGSPVDESLLIKSYCAATGSAVATALSLNHLAKKAP---PIFARLV 79 (221)
Q Consensus 3 ~~~ml~~~~s~~~~iFwQw~NQS~Na~vNY~NRnas~~~s~~~l~~sY~~A~~~a~~~Algl~~~~~~~~---~l~~r~v 79 (221)
.|+||+||+++|++|||||+||||||+|||+|||+++++|.+|++.||++||++||++|||||+++||.+ |+++|||
T Consensus 107 tggmLt~y~~~p~vvFwQW~NQSfNA~VNytNrsg~~~~t~~ql~~sY~~Att~A~s~AlGLn~~vk~~~~l~PligRlV 186 (328)
T KOG3767|consen 107 TGGMLTPYRTTPGVVFWQWFNQSFNAAVNYTNRSGNSPTTLSQLITSYCAATTGACSTALGLNYLVKKANNLTPLIGRLV 186 (328)
T ss_pred hhhhcccCCCCCeeeeHHHhhhHHHHHHhhcccCCCCCCchHHHHHHHHHHHHHHHHHHhhHHHHHhhcccCCcHHhhhc
Confidence 5899999999999999999999999999999999999999999999999999999999999999999986 9999999
Q ss_pred hHHHHhhhhccccccccchhhhcCcceecCCCceeeehHHHHHHhhhHhHhhhhhhcccccchHHHHHHHHHhhhhhccc
Q psy16712 80 PFSAVAAANMVNIPFMRNKEITDGLPVYDANNNLIGNSQKAAVTGISMVVVSRIGMATPGMIGIPVILNYLERKGTIRHL 159 (221)
Q Consensus 80 Pf~AVA~An~~Ni~~mR~~El~~GI~V~D~~G~~vG~S~~Aa~~Ai~~t~~SRi~~~~P~m~lpp~im~~lek~~~~~~~ 159 (221)
||+|||+|||+||||||++|+++||+|+|||||++|+||+||++||.||++|||+|++|.|++||+||++|||+.|++++
T Consensus 187 PfaAva~An~iNIpmMR~~El~~GI~V~D~~g~~lG~Sk~AA~~aI~qv~lSRI~ma~P~mvipPvim~~lek~~~~~~~ 266 (328)
T KOG3767|consen 187 PFAAVAAANCINIPMMRSNELREGIDVFDENGNVLGKSKKAAKQAITQVVLSRIVMAMPSMVIPPVIMNRLEKTAYLRKR 266 (328)
T ss_pred cHHHHHHhccceeeecchhhHhcCceeecCCCCEecccHHHHHHHHHHHHHHHHHhcCccccccHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhHHHHHHHHHHHHHhhccchhccccCCCccccCCCcHHHHHHHhcCCCCCceEEeecCC
Q psy16712 160 KWAPTAIQIGLLAVFLTFTTPMCCALFPQQTPIQISSLEPELQERAKKLNPPPTVGYYNKGL 221 (221)
Q Consensus 160 p~l~~p~~~~l~~~~l~~~~P~a~AlFPQ~~~i~~~~LEpe~~~~~~~~g~~~~~vyyNKGL 221 (221)
||+.+|+|+++|+++|+|++|+|||+|||+++|++++||+|+|+.++|.++++++|||||||
T Consensus 267 p~~~~plq~~l~g~~l~~a~Pl~calFPQ~s~I~~~~LE~~~q~~i~e~~~~~~~vy~NKGL 328 (328)
T KOG3767|consen 267 PGMLAPLQTLLCGLALGFATPLACALFPQKSAIQVTKLEPELQQLIPELANPPEIVYYNKGL 328 (328)
T ss_pred ccccchHHHHHHHHHHHHHhhHHhhhcccccccccccccHHHhhhhhhcCCCceEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999998
No 2
>TIGR00798 mtc tricarboxylate carrier. The MTC family consists of a limited number of homologues, all from eukaryotes. A single member of the family has been functionally characterized, the tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism.
Probab=100.00 E-value=2.7e-92 Score=639.22 Aligned_cols=219 Identities=52% Similarity=0.841 Sum_probs=215.7
Q ss_pred CccccccCCCchhHHHHHHHhhhhhhhhhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHhHhhhcc---chhhhhhc
Q psy16712 3 SEWKFTIRRSTPAVVFWQWFNQSFNAVVNYTNRSGGSPVDESLLIKSYCAATGSAVATALSLNHLAKKA---PPIFARLV 79 (221)
Q Consensus 3 ~~~ml~~~~s~~~~iFwQw~NQS~Na~vNY~NRnas~~~s~~~l~~sY~~A~~~a~~~Algl~~~~~~~---~~l~~r~v 79 (221)
.|+||+||+++++++||||+||||||+|||+|||+|+|+|++|++.+|++||++||++|+|||++++|. +|+++|+|
T Consensus 97 ~~gMl~p~~t~~~~iFWQw~NQS~Na~vNyaNrNas~~~s~~ql~~sY~~Av~~a~~~AlgLn~~v~k~~~~~pll~R~V 176 (318)
T TIGR00798 97 TGGMLTPYRSTPGVVFWQWINQSFNAAVNYTNRSGDSPLTLSQLLVSYCAAVTGACGVALGLNMMVKKSPSLSPLIGRLV 176 (318)
T ss_pred HhHhhcCCCCCchhHHHHHhhhhhHHHHHhhccCCCCCCCHHHHHHHHHHHHHHHHHHHHhHHHHHhhhccccHHHHHhC
Confidence 589999999999999999999999999999999999999999999999999999999999999999765 68999999
Q ss_pred hHHHHhhhhccccccccchhhhcCcceecCCCceeeehHHHHHHhhhHhHhhhhhhcccccchHHHHHHHHHhhhhhccc
Q psy16712 80 PFSAVAAANMVNIPFMRNKEITDGLPVYDANNNLIGNSQKAAVTGISMVVVSRIGMATPGMIGIPVILNYLERKGTIRHL 159 (221)
Q Consensus 80 Pf~AVA~An~~Ni~~mR~~El~~GI~V~D~~G~~vG~S~~Aa~~Ai~~t~~SRi~~~~P~m~lpp~im~~lek~~~~~~~ 159 (221)
||+|||+||++||++||++|+++||+|+|+||+++|+||+||++||+||++||++|++|+|++||++|+.|||++|++|+
T Consensus 177 Pf~AVa~An~~Ni~lMR~~El~~GI~V~D~~G~~vG~Sk~Aa~~Av~eta~SRv~~~~P~m~lpPlim~~l~k~~~l~~~ 256 (318)
T TIGR00798 177 PFAAVAVANAINIPMMRGNELTEGIEVFDEDGETVGKSKKAAALAIAQVVLSRVIMAVPDMVMPPLIMNRLERTAWLRAR 256 (318)
T ss_pred cHHHHHHhcccchHhhhhHHHhcCceeECCCCCccchhHHHHHHHHHHHHHHHHHHhchHhhccHHHHHHHhhhHHhhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhHHHHHHHHHHHHHhhccchhccccCCCccccCCCcHHHHHHHhcCCCCCceEEeecCC
Q psy16712 160 KWAPTAIQIGLLAVFLTFTTPMCCALFPQQTPIQISSLEPELQERAKKLNPPPTVGYYNKGL 221 (221)
Q Consensus 160 p~l~~p~~~~l~~~~l~~~~P~a~AlFPQ~~~i~~~~LEpe~~~~~~~~g~~~~~vyyNKGL 221 (221)
|++..|+|+++|+++|+||+|+|||+|||+++|++++||||||++++++|+++++|||||||
T Consensus 257 p~l~~pi~~~l~~~~l~~~lP~a~alFPQ~~~I~~~~LEpe~~~~~~~~~~~~~~v~yNKGL 318 (318)
T TIGR00798 257 PWMQIPIQTLLCGLGLAFATPLACALFPQKSAISVDKLEPSLQNLIQKLGNPPKVVYYNKGL 318 (318)
T ss_pred chhhchHHHHHHHHHHHHHHHHHHHhccccccCcHHhcCHHHHHhhhccCCCCceEEeCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999998
No 3
>PF03820 Mtc: Tricarboxylate carrier; InterPro: IPR004686 The MTC family consists of a limited number of homologues, all from eukaryotes. One member of the family has been functionally characterised as a tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. The rest of the characterised proteins appear to be sideroflexins involved in iron transport.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016020 membrane
Probab=100.00 E-value=3.3e-92 Score=638.53 Aligned_cols=219 Identities=52% Similarity=0.862 Sum_probs=216.6
Q ss_pred CccccccCCCchhHHHHHHHhhhhhhhhhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHhHhh-hccchhhhhhchH
Q psy16712 3 SEWKFTIRRSTPAVVFWQWFNQSFNAVVNYTNRSGGSPVDESLLIKSYCAATGSAVATALSLNHLA-KKAPPIFARLVPF 81 (221)
Q Consensus 3 ~~~ml~~~~s~~~~iFwQw~NQS~Na~vNY~NRnas~~~s~~~l~~sY~~A~~~a~~~Algl~~~~-~~~~~l~~r~vPf 81 (221)
.|+||+||+|++++|||||+||||||+|||+|||+|+++|++|++.||++||++||++|+|||+++ ++++|+++|+|||
T Consensus 89 ~~~mL~~~~s~~~~ifwQw~NQS~Na~vNy~Nrnas~~~~~~~l~~sY~~At~~a~~~Algl~~~~~~~~~pl~~r~vPf 168 (308)
T PF03820_consen 89 TGGMLTPYKSTPAVIFWQWVNQSYNAAVNYTNRNASSPISTSQLLTSYVGATTSAVGTALGLNRLVKKNASPLLGRLVPF 168 (308)
T ss_pred HHHHhccCcchHHHHHHHHHHhHHHHHHhhhccCCCCcccHHHHHHhHHhhhHHHHHHHHHHHHHHhccccHHHHHHhhH
Confidence 589999999999999999999999999999999999999999999999999999999999999999 7778999999999
Q ss_pred HHHhhhhccccccccchhhhcCcceecCCCceeeehHHHHHHhhhHhHhhhhhhcccccchHHHHHHHHHhhhhhcccCc
Q psy16712 82 SAVAAANMVNIPFMRNKEITDGLPVYDANNNLIGNSQKAAVTGISMVVVSRIGMATPGMIGIPVILNYLERKGTIRHLKW 161 (221)
Q Consensus 82 ~AVA~An~~Ni~~mR~~El~~GI~V~D~~G~~vG~S~~Aa~~Ai~~t~~SRi~~~~P~m~lpp~im~~lek~~~~~~~p~ 161 (221)
+|||+||++||++||++|+++||+|+|||||++|+||+||++||+||++||++|++|+|++||++|+.|||++|++|+||
T Consensus 169 ~AVA~An~~Nv~~mR~~El~~GI~V~D~~G~~vG~Sk~Aa~~Av~~t~~SRi~~~~P~m~lpPlim~~l~r~~~~~~~p~ 248 (308)
T PF03820_consen 169 AAVAAANCINVPLMRSNELENGIEVFDEDGNVVGKSKKAARKAVSQTALSRIVMAAPSMLLPPLIMNRLERTPFLKRNPW 248 (308)
T ss_pred HHHHHhhhcchHhcCHHHHcccceeECCCCCEeeEEhHHHHHHHHHHHHHHHHHhchhhhCcHHHHHHHHHhHHHHhCch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhhccchhccccCCCccccCCCcHHHHHHHhcCCCCCceEEeecCC
Q psy16712 162 APTAIQIGLLAVFLTFTTPMCCALFPQQTPIQISSLEPELQERAKKLNPPPTVGYYNKGL 221 (221)
Q Consensus 162 l~~p~~~~l~~~~l~~~~P~a~AlFPQ~~~i~~~~LEpe~~~~~~~~g~~~~~vyyNKGL 221 (221)
+..|+|+++++++|+||+|+|||+|||+++|++++||||+|++++|+|+++++|||||||
T Consensus 249 ~~~p~~~~l~~~~l~~~~P~a~AlFPQ~~si~~~~LEpe~~~~~~~~g~~~~~vyyNKGL 308 (308)
T PF03820_consen 249 LNAPIQLALIGLCLGFMLPLACALFPQRSSISVSKLEPELQELTEKKGPPPTTVYYNKGL 308 (308)
T ss_pred hhhhHHhHHHHHHHHHhhhhHHhhcccccccchHhcCHHHHHHHhhcCCCCCEEEeCCCC
Confidence 999999999999999999999999999999999999999999999999999999999998
No 4
>TIGR03171 soxL2 Rieske iron-sulfur protein SoxL2. This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system.
Probab=71.79 E-value=7.1 Score=36.48 Aligned_cols=82 Identities=24% Similarity=0.285 Sum_probs=51.1
Q ss_pred HHHhhhhhhhhhhccCCCCCC-CchhHHHHHHHHHHHHHHHHHHHHhHhhhccchhhhhhchHHHHhhhhccccccccch
Q psy16712 20 QWFNQSFNAVVNYTNRSGGSP-VDESLLIKSYCAATGSAVATALSLNHLAKKAPPIFARLVPFSAVAAANMVNIPFMRNK 98 (221)
Q Consensus 20 Qw~NQS~Na~vNY~NRnas~~-~s~~~l~~sY~~A~~~a~~~Algl~~~~~~~~~l~~r~vPf~AVA~An~~Ni~~mR~~ 98 (221)
.|+|.-=--++||+|.|-..+ ++.++++. .|++++.+.+. +. ++ |+++.|+| ++.+.+...
T Consensus 39 ~~~~~~~~~~~~~~~~~~~~vD~~RR~fL~---~al~gAga~a~-~~-av----Plv~~l~P-P~~a~atG~-------- 100 (321)
T TIGR03171 39 EFVNKGEDYLFNYVNKNVGGVDEGRRKFLK---GLIFGIAAAAV-VG-II----PGLRVLVP-PTVAAASGF-------- 100 (321)
T ss_pred HHHhhhhHHHhhhhhcccCCCCccHHHHHH---HHHHHHHHHHh-hh-hh----hheecccC-chhhhccCC--------
Confidence 466777778999999997655 56677777 35555544222 21 22 67888888 444433211
Q ss_pred hhhcCcceecCCCceeeehHHHHH
Q psy16712 99 EITDGLPVYDANNNLIGNSQKAAV 122 (221)
Q Consensus 99 El~~GI~V~D~~G~~vG~S~~Aa~ 122 (221)
.++-+.|++|+.+=.|.....
T Consensus 101 ---pk~La~D~~GnPIKASdL~vn 121 (321)
T TIGR03171 101 ---PKSLLVDSSGNPIKASSIPVN 121 (321)
T ss_pred ---CceEEecCCCCeeeHHHccCC
Confidence 136667999998866665443
No 5
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [].; PDB: 2QGG_A 3H9N_A 2WJN_H 2PRC_H 5PRC_H 2X5V_H 1DXR_H 1R2C_H 3G7F_H 1PRC_H ....
Probab=57.69 E-value=7.3 Score=27.52 Aligned_cols=21 Identities=33% Similarity=0.471 Sum_probs=16.5
Q ss_pred ccchhhhcCcceecCCCceeee
Q psy16712 95 MRNKEITDGLPVYDANNNLIGN 116 (221)
Q Consensus 95 mR~~El~~GI~V~D~~G~~vG~ 116 (221)
+|.+|+ .|-+|+|.+|+.+|+
T Consensus 4 ~~~s~l-~g~~V~~~~G~~iG~ 24 (79)
T PF05239_consen 4 FRLSEL-IGKEVIDRDGEKIGK 24 (79)
T ss_dssp GCHHHH-TTSEEEETTSCEEEE
T ss_pred EEhHHc-cCCEEEcCCCCEEEE
Confidence 455554 499999999999995
No 6
>PF10049 DUF2283: Protein of unknown function (DUF2283); InterPro: IPR019270 Members of this family of hypothetical proteins have no known function.
Probab=52.63 E-value=7 Score=26.38 Aligned_cols=21 Identities=29% Similarity=0.751 Sum_probs=18.0
Q ss_pred cchhhhcCcce-ecCCCceeee
Q psy16712 96 RNKEITDGLPV-YDANNNLIGN 116 (221)
Q Consensus 96 R~~El~~GI~V-~D~~G~~vG~ 116 (221)
++.|+..||-+ +|++|+.+|.
T Consensus 23 ~s~e~~~~iild~d~~G~ivGI 44 (50)
T PF10049_consen 23 ESEELDDGIILDYDEDGRIVGI 44 (50)
T ss_pred eeEEecCCEEEEECCCCCEEEE
Confidence 67788889988 8999999985
No 7
>KOG4355|consensus
Probab=34.68 E-value=18 Score=35.26 Aligned_cols=54 Identities=28% Similarity=0.276 Sum_probs=39.8
Q ss_pred CceeeehHHH----HHHhhhHhHhhhhhhcccccchHHHHHHHHHhhhhhcccCc----hhHHHHHH
Q psy16712 111 NNLIGNSQKA----AVTGISMVVVSRIGMATPGMIGIPVILNYLERKGTIRHLKW----APTAIQIG 169 (221)
Q Consensus 111 G~~vG~S~~A----a~~Ai~~t~~SRi~~~~P~m~lpp~im~~lek~~~~~~~p~----l~~p~~~~ 169 (221)
|..+|+|--- ..+-|-|-+.+|+- |..||.|.+.|+...+..|+|+ ++.|+|.+
T Consensus 247 grdig~slp~ll~klv~~iPe~cmlr~g-----mTnpP~ilehl~e~a~vlrhp~vYsflhvpvqsg 308 (547)
T KOG4355|consen 247 GRDIGKSLPKLLWKLVEVIPESCMLRAG-----MTNPPYILEHLEEAAFVLRHPRVYSFLHVPVQSG 308 (547)
T ss_pred hhhhhhhhHHHHHHHHHhcchhhhhhhc-----CCCCchHHHHHHHHHHHhcCCeEEEEEecccccC
Confidence 5778888643 34444555667764 5778999999999998888884 77888764
No 8
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=33.33 E-value=1.4e+02 Score=22.89 Aligned_cols=60 Identities=13% Similarity=0.110 Sum_probs=40.4
Q ss_pred cccCchhHHHHHHHHHHHHHhhccchhccccCCCccccCC------Cc--HHHHHHHhcCCCCCceEEeec
Q psy16712 157 RHLKWAPTAIQIGLLAVFLTFTTPMCCALFPQQTPIQISS------LE--PELQERAKKLNPPPTVGYYNK 219 (221)
Q Consensus 157 ~~~p~l~~p~~~~l~~~~l~~~~P~a~AlFPQ~~~i~~~~------LE--pe~~~~~~~~g~~~~~vyyNK 219 (221)
.|+|+.+--+=+..+.+++..++| -+||....++++. ++ .++++..+++|-+++.+....
T Consensus 2 N~yp~WKyllil~vl~~~~lyALP---nlyge~pAvqIs~~~~~~~~~~~~~v~~~L~~~~I~~k~i~~~~ 69 (101)
T PF13721_consen 2 NRYPLWKYLLILVVLLLGALYALP---NLYGEDPAVQISASSAGVQLPDAFQVEQALKAAGIAVKSIEQEG 69 (101)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhh---hccCCCCcEEEecCCCCccCChHHHHHHHHHHCCCCcceEEeeC
Confidence 466766655655666777788888 5888888887765 32 356666777777776665543
No 9
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=31.94 E-value=31 Score=22.81 Aligned_cols=46 Identities=17% Similarity=0.219 Sum_probs=32.9
Q ss_pred cCcceec---CCCceeeehHHHHHHhhhHhHhhhhhhcccccchHHHHHHHHHhhhhhcccC
Q psy16712 102 DGLPVYD---ANNNLIGNSQKAAVTGISMVVVSRIGMATPGMIGIPVILNYLERKGTIRHLK 160 (221)
Q Consensus 102 ~GI~V~D---~~G~~vG~S~~Aa~~Ai~~t~~SRi~~~~P~m~lpp~im~~lek~~~~~~~p 160 (221)
+++.|.| +.+..++.+.+|.+-++....+.|++ ..|++.+|+.|.|
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L-------------~tL~~~g~v~~dp 52 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLL-------------QTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHH-------------HHHHHTTSEEECS
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHH-------------HHHHHCcCeecCc
Confidence 3444444 56666899999999999999999964 5567777776654
No 10
>PF11141 DUF2914: Protein of unknown function (DUF2914); InterPro: IPR022606 This bacterial family of proteins has no known function.
Probab=31.64 E-value=27 Score=24.96 Aligned_cols=13 Identities=23% Similarity=0.608 Sum_probs=11.6
Q ss_pred cceecCCCceeee
Q psy16712 104 LPVYDANNNLIGN 116 (221)
Q Consensus 104 I~V~D~~G~~vG~ 116 (221)
++|.|+||+++|.
T Consensus 48 V~V~~~~G~~l~~ 60 (66)
T PF11141_consen 48 VEVVDEDGQVLGS 60 (66)
T ss_pred EEEEcCCCCEEEE
Confidence 6899999999985
No 11
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=30.57 E-value=19 Score=26.14 Aligned_cols=17 Identities=12% Similarity=0.249 Sum_probs=3.5
Q ss_pred hhcCcceecCCCceeee
Q psy16712 100 ITDGLPVYDANNNLIGN 116 (221)
Q Consensus 100 l~~GI~V~D~~G~~vG~ 116 (221)
-.++|.|.|+||+.|-.
T Consensus 45 ~L~~i~ivD~~G~dVTP 61 (65)
T PF05979_consen 45 QLENIKIVDPDGNDVTP 61 (65)
T ss_dssp CSSTT------------
T ss_pred HhcceeEECCCCCCCCh
Confidence 34799999999998743
No 12
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=30.32 E-value=19 Score=23.25 Aligned_cols=15 Identities=40% Similarity=0.769 Sum_probs=12.9
Q ss_pred hcCcceecCCCceee
Q psy16712 101 TDGLPVYDANNNLIG 115 (221)
Q Consensus 101 ~~GI~V~D~~G~~vG 115 (221)
...++|.|++|+.+|
T Consensus 30 ~~~~~V~d~~~~~~G 44 (57)
T PF00571_consen 30 ISRLPVVDEDGKLVG 44 (57)
T ss_dssp SSEEEEESTTSBEEE
T ss_pred CcEEEEEecCCEEEE
Confidence 456899999999998
No 13
>PRK01546 hypothetical protein; Provisional
Probab=29.56 E-value=28 Score=26.29 Aligned_cols=18 Identities=11% Similarity=0.257 Sum_probs=14.5
Q ss_pred hcCcceecCCCceeeehH
Q psy16712 101 TDGLPVYDANNNLIGNSQ 118 (221)
Q Consensus 101 ~~GI~V~D~~G~~vG~S~ 118 (221)
.++|.|.|++|+.|-..|
T Consensus 49 L~~i~vvD~~G~dVTP~K 66 (79)
T PRK01546 49 LKGIKVVNEQGTDVTPAK 66 (79)
T ss_pred hccceEECCCCCCCCHHH
Confidence 479999999999885443
No 14
>PF12396 DUF3659: Protein of unknown function (DUF3659) ; InterPro: IPR022124 This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
Probab=28.28 E-value=36 Score=24.50 Aligned_cols=17 Identities=24% Similarity=0.546 Sum_probs=11.2
Q ss_pred hhcCcceecCCCceeee
Q psy16712 100 ITDGLPVYDANNNLIGN 116 (221)
Q Consensus 100 l~~GI~V~D~~G~~vG~ 116 (221)
.-+-=+|.|++|+++|+
T Consensus 39 vd~~G~I~d~~G~viGk 55 (64)
T PF12396_consen 39 VDEDGDILDKDGNVIGK 55 (64)
T ss_pred CCCCCCEECCCCCEEEE
Confidence 33334677888888886
No 15
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=27.83 E-value=36 Score=28.72 Aligned_cols=20 Identities=20% Similarity=0.301 Sum_probs=14.9
Q ss_pred ccccccCCC-chhHHHHHHHh
Q psy16712 4 EWKFTIRRS-TPAVVFWQWFN 23 (221)
Q Consensus 4 ~~ml~~~~s-~~~~iFwQw~N 23 (221)
|+|..+..+ .++++|||++|
T Consensus 20 ~gmp~ld~~t~~~q~~~~lI~ 40 (181)
T PRK13454 20 PGMPQLDFSTFPNQIFWLLVT 40 (181)
T ss_pred CCCCCCcHHhcchHHHHHHHH
Confidence 567766764 57889998886
No 16
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=27.71 E-value=39 Score=25.57 Aligned_cols=23 Identities=26% Similarity=0.430 Sum_probs=17.7
Q ss_pred ccccchhhhcCcceecCCCceeee
Q psy16712 93 PFMRNKEITDGLPVYDANNNLIGN 116 (221)
Q Consensus 93 ~~mR~~El~~GI~V~D~~G~~vG~ 116 (221)
..||-+|| .|-+|+|.+|..+|+
T Consensus 4 ~~~~~s~l-~gk~V~~~~G~~vG~ 26 (87)
T COG1873 4 EMMRLSEL-LGKEVITNDGKYVGT 26 (87)
T ss_pred hhheHHHh-cCcEEEcCCCeEEEE
Confidence 34566665 489999999999985
No 17
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=24.70 E-value=38 Score=28.16 Aligned_cols=20 Identities=25% Similarity=0.338 Sum_probs=16.5
Q ss_pred cceecCCCceeeehHHHHHH
Q psy16712 104 LPVYDANNNLIGNSQKAAVT 123 (221)
Q Consensus 104 I~V~D~~G~~vG~S~~Aa~~ 123 (221)
++++|+||+.+|...+...+
T Consensus 8 ~~~vd~~~~~~g~~~r~~~~ 27 (184)
T PRK03759 8 VVLLDEQGVPTGTAEKAAAH 27 (184)
T ss_pred EEEECCCCCCcccccHHHHH
Confidence 89999999999977666554
No 18
>PRK01631 hypothetical protein; Provisional
Probab=24.57 E-value=39 Score=25.32 Aligned_cols=19 Identities=16% Similarity=0.071 Sum_probs=15.1
Q ss_pred hhcCcceecCCCceeeehH
Q psy16712 100 ITDGLPVYDANNNLIGNSQ 118 (221)
Q Consensus 100 l~~GI~V~D~~G~~vG~S~ 118 (221)
..++|.|.|++|+.+-..|
T Consensus 46 ~L~~i~ivD~~G~dvTP~K 64 (76)
T PRK01631 46 ILLNTKIVDQNGLNVTPAA 64 (76)
T ss_pred HhcCceeECCCCCcCCHHH
Confidence 3589999999999885444
No 19
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=24.43 E-value=33 Score=24.51 Aligned_cols=24 Identities=21% Similarity=0.250 Sum_probs=19.7
Q ss_pred eeeehHHHHHHhhhHhHhhhhhhc
Q psy16712 113 LIGNSQKAAVTGISMVVVSRIGMA 136 (221)
Q Consensus 113 ~vG~S~~Aa~~Ai~~t~~SRi~~~ 136 (221)
..|+.|.|...+|.|+++|..+-+
T Consensus 12 ~~GQ~kaA~~lGV~Q~AIsKAlr~ 35 (59)
T PF09048_consen 12 EHGQAKAARALGVTQSAISKALRA 35 (59)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHHHC
T ss_pred HhChHHHHHHcCCcHHHHHHHHHc
Confidence 458999999999999999987654
No 20
>PRK02539 hypothetical protein; Provisional
Probab=23.10 E-value=42 Score=25.65 Aligned_cols=18 Identities=17% Similarity=0.399 Sum_probs=14.5
Q ss_pred hcCcceecCCCceeeehH
Q psy16712 101 TDGLPVYDANNNLIGNSQ 118 (221)
Q Consensus 101 ~~GI~V~D~~G~~vG~S~ 118 (221)
.++|.|.|++|+.|-..|
T Consensus 48 L~~i~ivD~~G~dVTP~K 65 (85)
T PRK02539 48 IEGIKIVDEEGNDVTPEK 65 (85)
T ss_pred hccceEECCCCCCCCHHH
Confidence 479999999999985443
No 21
>PF07411 DUF1508: Domain of unknown function (DUF1508); InterPro: IPR010879 This domain is found in a family of proteins, which have no known function. Members of this family are often found as tandem repeats and in some cases represent the whole protein.; PDB: 3BID_H 2K49_A 2K8E_A 2K7I_A.
Probab=22.30 E-value=93 Score=20.83 Aligned_cols=23 Identities=30% Similarity=0.416 Sum_probs=14.9
Q ss_pred eecCCCceee-----ehHHHHHHhhhHh
Q psy16712 106 VYDANNNLIG-----NSQKAAVTGISMV 128 (221)
Q Consensus 106 V~D~~G~~vG-----~S~~Aa~~Ai~~t 128 (221)
+.+.||++|+ .|+.++.++|..+
T Consensus 10 L~a~ng~viasse~Y~sk~~a~~~I~~V 37 (49)
T PF07411_consen 10 LKAGNGEVIASSEGYSSKADAEKGIESV 37 (49)
T ss_dssp EE-TTS-EEEEBEEBSSHHHHHHHHHHH
T ss_pred EEcCCCCEEEecCCcCCHHHHHHHHHHH
Confidence 4678999997 4567777777654
No 22
>PF14985 TM140: TM140 protein family
Probab=22.28 E-value=89 Score=26.73 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=17.9
Q ss_pred hccchhccccCCCccccCCCcH
Q psy16712 178 TTPMCCALFPQQTPIQISSLEP 199 (221)
Q Consensus 178 ~~P~a~AlFPQ~~~i~~~~LEp 199 (221)
-+=++..+||++++-+-+++|.
T Consensus 159 LlL~~~v~fp~r~~~~ks~~es 180 (181)
T PF14985_consen 159 LLLMATVVFPPRAKRDKSKLES 180 (181)
T ss_pred HHHHHHHhcCCccccchhhccC
Confidence 3445778999999999999984
No 23
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=21.02 E-value=67 Score=26.64 Aligned_cols=18 Identities=22% Similarity=0.514 Sum_probs=11.8
Q ss_pred CccccccCCCchhHHHHHHHh
Q psy16712 3 SEWKFTIRRSTPAVVFWQWFN 23 (221)
Q Consensus 3 ~~~ml~~~~s~~~~iFwQw~N 23 (221)
.|+|+.++ ++++|||++|
T Consensus 10 ~~~~~~~~---~~~~~~~~i~ 27 (175)
T PRK14472 10 SGGLLSPN---PGLIFWTAVT 27 (175)
T ss_pred cCCccCCC---HHHHHHHHHH
Confidence 35555433 4678999887
No 24
>PF12860 PAS_7: PAS fold
Probab=20.18 E-value=73 Score=23.57 Aligned_cols=24 Identities=21% Similarity=0.414 Sum_probs=18.9
Q ss_pred hhhcCcceecCCCceeeehHHHHH
Q psy16712 99 EITDGLPVYDANNNLIGNSQKAAV 122 (221)
Q Consensus 99 El~~GI~V~D~~G~~vG~S~~Aa~ 122 (221)
.+..||-|+|+||+.+-..+....
T Consensus 3 ~l~~Gv~v~D~~~rl~~~N~~~~~ 26 (115)
T PF12860_consen 3 SLPQGVAVFDSDGRLVFWNQRFRE 26 (115)
T ss_pred CcCceEEEEcCCCeEEeEcHHHHH
Confidence 367899999999999866665544
Done!