Query 001195
Match_columns 1126
No_of_seqs 43 out of 45
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 18:24:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001195.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001195hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01666 YCCS hypothetical me 81.9 3 6.6E-05 52.8 7.2 77 62-138 4-80 (704)
2 TIGR01667 YCCS_YHJK integral m 65.6 13 0.00028 47.4 6.9 98 63-163 5-102 (701)
3 PF15176 LRR19-TM: Leucine-ric 37.0 35 0.00075 33.9 3.2 25 867-891 16-43 (102)
4 PF12270 Cyt_c_ox_IV: Cytochro 35.2 49 0.0011 34.5 4.1 33 715-747 72-105 (137)
5 KOG0260 RNA polymerase II, lar 31.6 68 0.0015 43.1 5.4 10 59-68 1582-1591(1605)
6 PF15061 DUF4538: Domain of un 30.3 49 0.0011 29.9 2.8 30 647-676 5-34 (58)
7 PF11177 DUF2964: Protein of u 30.0 61 0.0013 29.7 3.4 49 362-410 9-57 (62)
8 PF09877 DUF2104: Predicted me 25.3 3.8E+02 0.0082 26.8 8.0 94 358-453 2-99 (99)
9 COG0368 CobS Cobalamin-5-phosp 21.1 1.1E+02 0.0025 34.5 4.3 87 801-890 9-122 (246)
10 KOG0569 Permease of the major 20.5 8.1E+02 0.018 30.5 11.5 62 753-816 148-211 (485)
No 1
>TIGR01666 YCCS hypothetical membrane protein, TIGR01666. This model represents a clade of sequences from gamma and beta proteobacteria. These proteins are 700 amino acids long and many have been annotated as putative membrane proteins. The gene from Salmonella has been annotated as a putative efflux transporter. The gene from E. coli has the name yccS.
Probab=81.91 E-value=3 Score=52.80 Aligned_cols=77 Identities=26% Similarity=0.215 Sum_probs=68.0
Q ss_pred cCCCCchhHHHHHHHHhHHHHHHhhCCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHhhcccccc
Q 001195 62 SPSSFAHNARIAIALVPCAAFLLDLGGSPVVTTITLGLMLAYIIDSLNFKSGSFFGVWFSLIASQIAFFFSSSLFVT 138 (1126)
Q Consensus 62 ~~~sf~hN~RIa~aL~P~l~~ll~~GG~~~l~~Lt~Glmv~YilD~l~~~~ga~~~iW~tl~~a~la~~~s~~~~~~ 138 (1126)
...+|.|+-||.+++.+++++...+|=......+++|++.+-+.|.-+-.+|=+-.+-.|++|+.++.+....++-.
T Consensus 4 ~~~~~~~~lri~ia~~~~~~~~~~~~~~~~~~~l~LG~ia~al~D~d~~~~~R~~~l~~t~~~f~i~sl~v~ll~~~ 80 (704)
T TIGR01666 4 LNAKVIYTIPIFIALNGAAVGIWFFDISSQSMPLILGIIAAALVDLDDRLTGRLKNVIFTLICFSIASFSVELLFGK 80 (704)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34679999999999999999999999888889999999999999999999999999999999998888877654433
No 2
>TIGR01667 YCCS_YHJK integral membrane protein, YccS/YhfK family. TMHMM on members of this model shows a consensus of 11 transmembrane helices separated into two clusters, an N-terminal cluster of 6 and a central cluster of 5. This would indicate two non-membrane domains one on each side of the membrane
Probab=65.57 E-value=13 Score=47.38 Aligned_cols=98 Identities=19% Similarity=0.149 Sum_probs=77.4
Q ss_pred CCCCchhHHHHHHHHhHHHHHHhhCCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHhhccccccccch
Q 001195 63 PSSFAHNARIAIALVPCAAFLLDLGGSPVVTTITLGLMLAYIIDSLNFKSGSFFGVWFSLIASQIAFFFSSSLFVTFNSI 142 (1126)
Q Consensus 63 ~~sf~hN~RIa~aL~P~l~~ll~~GG~~~l~~Lt~Glmv~YilD~l~~~~ga~~~iW~tl~~a~la~~~s~~~~~~~~s~ 142 (1126)
..+|.|+-||.+++.++.+....+|-......+++|++.+-+.|.-+-.+|=+-.+-.|.+|+.++.+....++-.|
T Consensus 5 ~~~~~~~l~v~ia~~~~~~~~~~~g~~~~~i~l~lG~ia~~l~D~~~~~~~R~~~l~it~~~f~i~sl~v~ll~~~p--- 81 (701)
T TIGR01667 5 NQKLVYCLPVFIALMGAELRIWWFGLLFLLIPLCLGIIAAGLDDLDDRLTGRLKNLIITLSCFSIASFLVQLLFPKP--- 81 (701)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhCCccHHHHHHHhhHhhccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHhcch---
Confidence 46789999999999999988888998888999999999999999999999999999999999988888887644332
Q ss_pred hhhHHHHHHHHHhHHHHhhhh
Q 001195 143 PLGLLATFLCAYTNFLIGTWA 163 (1126)
Q Consensus 143 ~~~~~~lll~~~~~fL~G~Wa 163 (1126)
.....++..+.....++|.|.
T Consensus 82 ~~~~~~l~~~tf~~~mlga~G 102 (701)
T TIGR01667 82 WLFPFLLTLLTFGFILLGALG 102 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 222333444444555565554
No 3
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=37.03 E-value=35 Score=33.87 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=18.9
Q ss_pred hhhhHhHH---HHHHHHHHHHHHHHhhh
Q 001195 867 ARTSLLGL---YAAIFMLIALEIKFELA 891 (1126)
Q Consensus 867 ~r~sLLgv---~a~~~LlIA~~lKfkl~ 891 (1126)
++.-|+|| ...+++|||+++||++=
T Consensus 16 sW~~LVGVv~~al~~SlLIalaaKC~~~ 43 (102)
T PF15176_consen 16 SWPFLVGVVVTALVTSLLIALAAKCPVW 43 (102)
T ss_pred ccHhHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 34445554 56799999999999986
No 4
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=35.16 E-value=49 Score=34.47 Aligned_cols=33 Identities=30% Similarity=0.457 Sum_probs=27.0
Q ss_pred cC-cccchhhhhcccCCCchhHHHHHHHHHHHHh
Q 001195 715 QS-ADDISIYGFMASKPTWPSWLIILAILLTLAA 747 (1126)
Q Consensus 715 ~e-~dD~~iyg~~~~~~~wp~WLLi~a~l~~l~~ 747 (1126)
.| +|+++.||++.-+.-||-|+=.++.++.+.-
T Consensus 72 aEI~dgAGe~GfFsP~SwWPl~la~~~al~~lGl 105 (137)
T PF12270_consen 72 AEIADGAGELGFFSPHSWWPLVLAAAAALVFLGL 105 (137)
T ss_pred cccccCCCCcCcCCCccHhHHHHHHHHHHHHHHH
Confidence 44 7889999999999999999888777766643
No 5
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=31.58 E-value=68 Score=43.07 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=4.2
Q ss_pred ccccCCCCch
Q 001195 59 SRFSPSSFAH 68 (1126)
Q Consensus 59 ~rf~~~sf~h 68 (1126)
..|+|.+++|
T Consensus 1582 ~~ysp~sp~y 1591 (1605)
T KOG0260|consen 1582 PSYSPTSPSY 1591 (1605)
T ss_pred CCCCCCCCCC
Confidence 3344444444
No 6
>PF15061 DUF4538: Domain of unknown function (DUF4538)
Probab=30.31 E-value=49 Score=29.94 Aligned_cols=30 Identities=23% Similarity=0.111 Sum_probs=24.4
Q ss_pred CCchHHHHHHHHHHhhhhhhhhhhccCchh
Q 001195 647 PSDGLLLGFCIILTGLACVPIVALHFSHVL 676 (1126)
Q Consensus 647 psd~~llG~~~l~~g~~~~Piv~~h~s~~~ 676 (1126)
.--++++|+++-+.|++|+||..+-+=|..
T Consensus 5 ~r~~~~~ggfVg~iG~a~Ypi~~~Pmm~~e 34 (58)
T PF15061_consen 5 WRYALFVGGFVGLIGAALYPIYFRPMMNPE 34 (58)
T ss_pred ccchhhHHHHHHHHHHHHhhhhcccccChH
Confidence 334789999999999999999998764443
No 7
>PF11177 DUF2964: Protein of unknown function (DUF2964); InterPro: IPR021347 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=30.03 E-value=61 Score=29.69 Aligned_cols=49 Identities=24% Similarity=0.353 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhhhHHHhccc
Q 001195 362 LLVTTTMLGGATGAGAYALGMISDASSSVAFTALAVVVSAAAAIVVGFP 410 (1126)
Q Consensus 362 ilVTvalyg~a~~~~~~~~G~~gd~v~s~a~~~~~v~~s~a~~i~~G~P 410 (1126)
++-|++++.++++...-.-|++-|.-....++..++++++++-.+.--|
T Consensus 9 vlAtiavFiaLagl~~~I~GlLfD~~~~~~yg~~al~~Gv~~fV~~Lnp 57 (62)
T PF11177_consen 9 VLATIAVFIALAGLAAVIHGLLFDEERVFRYGVIALVVGVAGFVVMLNP 57 (62)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhccccchhHHHHHHHHHHHHHHHHhCCC
Confidence 3448888888888888888999986666678888888877776665544
No 8
>PF09877 DUF2104: Predicted membrane protein (DUF2104); InterPro: IPR019211 This entry is found in various hypothetical archaeal proteins, has no known function.
Probab=25.29 E-value=3.8e+02 Score=26.82 Aligned_cols=94 Identities=15% Similarity=0.202 Sum_probs=63.5
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhhhHH--HhcccchhhhhhHHHHHHHHHhh--hcCCC
Q 001195 358 PVNYLLVTTTMLGGATGAGAYALGMISDASSSVAFTALAVVVSAAAAI--VVGFPLVFIAVPSIAGFYLARFF--TKKSL 433 (1126)
Q Consensus 358 P~nyilVTvalyg~a~~~~~~~~G~~gd~v~s~a~~~~~v~~s~a~~i--~~G~P~~~lP~pvi~~~~~~~f~--~~k~~ 433 (1126)
|++++.-+++..-|...+..+--++-.+..-..-.-..++++|+.|++ ++..| ..+.-...++.+.-|- -|-.=
T Consensus 2 ~~~~li~~i~fiiGs~~GL~ySYkKy~~P~v~k~iD~~ALv~aiiG~~~~~vn~~--~~~~~~~ig~~li~~~~GmRPGY 79 (99)
T PF09877_consen 2 PFILLIYIILFIIGSFLGLEYSYKKYREPFVEKKIDKLALVLAIIGGLILAVNSP--SSPILYTIGAFLIGFPLGMRPGY 79 (99)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHhccchhhhcccHHHHHHHHHHHHHHHhcCc--chhHHHHHHHHHHhhhccCCCCC
Confidence 567777788888888888888888877744444445577788888988 77777 4555555555554444 33344
Q ss_pred CceEEeeecchhHHHHHhhh
Q 001195 434 PSYFAFVSLSSMMVIWFVMH 453 (1126)
Q Consensus 434 ~~y~~Fvv~~~l~~~WFv~~ 453 (1126)
+.+=+++......+.|++.|
T Consensus 80 Gr~E~~iG~iiA~l~~~l~~ 99 (99)
T PF09877_consen 80 GRIETVIGLIIALLIYLLTW 99 (99)
T ss_pred CeehhhhhHHHHHHHHHHhC
Confidence 44657777777888887754
No 9
>COG0368 CobS Cobalamin-5-phosphate synthase [Coenzyme metabolism]
Probab=21.14 E-value=1.1e+02 Score=34.45 Aligned_cols=87 Identities=14% Similarity=0.159 Sum_probs=48.1
Q ss_pred heeeeeccCCC--Cc------chHHHHHHHHHHHHHHHHHhhcccccc---------------cccCCCCCCCccc---h
Q 001195 801 FVVFTHFPSAS--ST------KLLPWIFALLVALFPVTYLLEGQVRIK---------------SILGDNGFGDFEE---E 854 (1126)
Q Consensus 801 Fv~ft~~Psa~--s~------~~lp~v~~~~v~~fpv~yll~g~l~~~---------------~~l~~~~~~~~~~---~ 854 (1126)
|-.||-+|.++ .+ +..|.|...........|+..++.-.+ -.+|.|++-|++| .
T Consensus 9 l~FlTriPvp~~d~~~~~r~~~~~PlVGl~iG~i~~~~~~~~~~~~~~~l~a~l~v~~~~~ltG~~HlDGLaD~aDgl~~ 88 (246)
T COG0368 9 LSFLTRIPVPGLDFEELRRAIRAFPLVGLLLGLIAALVAYILAPLFGPPLAAALAVLLLLLLTGGLHLDGLADTADGLMS 88 (246)
T ss_pred HHHHhcCCCCCCchhHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccchhhhhhhhhhhhhC
Confidence 44567777764 22 246666666666666665554432222 2567788888865 1
Q ss_pred h-hhHHHHHhhhhhhhhHhHHHHHHHHHHHHHHHHhh
Q 001195 855 D-RKLTTLLAVEGARTSLLGLYAAIFMLIALEIKFEL 890 (1126)
Q Consensus 855 ~-~~~~~~~~~e~~r~sLLgv~a~~~LlIA~~lKfkl 890 (1126)
. ++-..++.+|+.|.+. +++..+...+.+|.-.
T Consensus 89 ~~~~er~leiMkDsrvG~---~Gv~ali~vlll~~~~ 122 (246)
T COG0368 89 GGSRERKLEIMKDSRVGA---GGVAALILVLLLKVLA 122 (246)
T ss_pred CCCHHHHHHHHhCCCcCc---cHHHHHHHHHHHHHHH
Confidence 1 1223446678888554 4444455555666543
No 10
>KOG0569 consensus Permease of the major facilitator superfamily [Carbohydrate transport and metabolism]
Probab=20.46 E-value=8.1e+02 Score=30.52 Aligned_cols=62 Identities=16% Similarity=0.146 Sum_probs=32.2
Q ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHhhhhh--hHHHHHHHHHHhHhhheeeeeccCCCCcchH
Q 001195 753 PIKYIVELRAFYSIVMGIALGIYISAEFFLQAT--VLHALIVVTMVGTCVFVVFTHFPSASSTKLL 816 (1126)
Q Consensus 753 ~~~~~v~lR~~ys~~~G~~lGlYl~~eyf~~~~--~l~vll~~~~v~asvFv~ft~~Psa~s~~~l 816 (1126)
..+..+.-=.-.++.+|..+|--++++++++.. |+..+.+ .++.+.+.+..+. =-+.|||++
T Consensus 148 ~~RG~~g~~~~~~~~~g~ll~~~~~l~~ilGt~~~W~~l~~~-~~i~~~~~l~~l~-~~PESPk~L 211 (485)
T KOG0569|consen 148 NLRGALGTLLQIGVVIGILLGQVLGLPSLLGTEDLWPYLLAF-PLIPALLQLALLP-FLPESPKYL 211 (485)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHccHHhcCCCcchHHHHHH-HHHHHHHHHHHHh-cCCCCcchH
Confidence 444444444455677777888778888888443 2333332 3433222222221 125788865
Done!