Query 042587
Match_columns 99
No_of_seqs 107 out of 122
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:37:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042587.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042587hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3142 Prenylated rab accepto 99.9 2.9E-26 6.4E-31 174.1 5.4 81 1-82 94-186 (187)
2 PF03208 PRA1: PRA1 family pro 99.1 3.3E-10 7.1E-15 80.2 6.2 71 2-72 66-150 (153)
3 PF14256 YwiC: YwiC-like prote 66.8 31 0.00068 24.6 6.3 66 3-68 28-112 (129)
4 KOG4050 Glutamate transporter 60.4 24 0.00051 27.6 5.0 42 19-60 111-152 (188)
5 PRK13823 conjugal transfer pro 44.7 61 0.0013 22.4 4.6 42 16-60 21-62 (94)
6 CHL00114 psbX photosystem II p 44.3 28 0.0006 21.0 2.5 22 34-55 1-22 (39)
7 cd00867 Trans_IPPS Trans-Isopr 35.1 34 0.00073 24.9 2.2 28 44-72 20-47 (236)
8 PF06596 PsbX: Photosystem II 34.5 59 0.0013 19.5 2.8 21 34-54 1-21 (39)
9 PF09964 DUF2198: Uncharacteri 31.6 1.6E+02 0.0035 19.8 4.9 33 22-54 5-37 (74)
10 PF10112 Halogen_Hydrol: 5-bro 25.9 2.1E+02 0.0047 20.9 5.2 35 20-54 12-46 (199)
11 PF10960 DUF2762: Protein of u 22.3 59 0.0013 21.4 1.5 13 3-15 15-27 (71)
12 PF13398 Peptidase_M50B: Pepti 21.5 3.5E+02 0.0076 20.1 6.0 37 29-67 128-164 (200)
13 PF09813 Coiled-coil_56: Coile 20.8 66 0.0014 22.9 1.5 34 38-71 49-84 (100)
No 1
>KOG3142 consensus Prenylated rab acceptor 1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=2.9e-26 Score=174.12 Aligned_cols=81 Identities=36% Similarity=0.563 Sum_probs=77.8
Q ss_pred ChhHHHHHHHHHHHh------------cChhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCCCccccc
Q 042587 1 MLLGLLSSLIFAHIF------------RDHETLSVLIILSVFIIFLTSIRSVLILGLMAGDGLSCAHGVFRVLEDLVLDE 68 (99)
Q Consensus 1 vll~l~aaWlfLYf~------------sDr~vL~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~HaAfR~~dDLFlDe 68 (99)
+++++.++|+||||+ |||+++++|+++|++++|+|++++|++.++++|+++|+.|||||+|||||+||
T Consensus 94 vl~~lv~~w~~LY~~rd~pLvlfgr~i~d~~~l~~L~~~ti~~lflt~~~~~l~~~l~~g~~vv~~Haafr~~ddLF~de 173 (187)
T KOG3142|consen 94 VLLALVAAWLFLYFLRDEPLVLFGRQISDREVLIGLVLITIPVLFLTSAGSNLLWALGAGLVVVLIHAAFRNTDDLFLDE 173 (187)
T ss_pred HHHHHHHHHHheeeecCCCeEEeeEEecCcchhhhHHHHHHHHHHHhhHHHHHHHHHHHhHHHHHhHHHHhChHhhhhhh
Confidence 468899999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCceeeecC
Q 042587 69 QEPSANTRFLSFPD 82 (99)
Q Consensus 69 ~e~~~~~gllSfl~ 82 (99)
||+. ++|++|+.+
T Consensus 174 e~~~-~~gl~s~~~ 186 (187)
T KOG3142|consen 174 EEAA-ASGLLSFSS 186 (187)
T ss_pred hhcc-cccccccCC
Confidence 9998 789999875
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=99.07 E-value=3.3e-10 Score=80.16 Aligned_cols=71 Identities=27% Similarity=0.269 Sum_probs=62.2
Q ss_pred hhHHHHHHHHHHHh--------------cChhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCCCcccc
Q 042587 2 LLGLLSSLIFAHIF--------------RDHETLSVLIILSVFIIFLTSIRSVLILGLMAGDGLSCAHGVFRVLEDLVLD 67 (99)
Q Consensus 2 ll~l~aaWlfLYf~--------------sDr~vL~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~HaAfR~~dDLFlD 67 (99)
++.+..+|.++|.. +++.++..+.++++..+++++.+.+++.++++++.++++||+||+|||.+-+
T Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~l~~~~~lvl~HA~~r~~~~~~~~ 145 (153)
T PF03208_consen 66 LLLVVALWAFIYKSRKENDPIVIGGRKISPRQVLLALLIVSILLLFFTSAGLTLFWSLGASVLLVLLHASFREPDLKNKE 145 (153)
T ss_pred HHHHHHHHHHHhhhcccCcchhccCcccCHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcCCccchhh
Confidence 34566788888876 6677889999999999999999999999999999999999999999998877
Q ss_pred cCCCC
Q 042587 68 EQEPS 72 (99)
Q Consensus 68 e~e~~ 72 (99)
|+|..
T Consensus 146 e~~~~ 150 (153)
T PF03208_consen 146 ENEIE 150 (153)
T ss_pred hhHHh
Confidence 77654
No 3
>PF14256 YwiC: YwiC-like protein
Probab=66.84 E-value=31 Score=24.56 Aligned_cols=66 Identities=15% Similarity=0.054 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHh--------cChh-----------hhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCCC
Q 042587 3 LGLLSSLIFAHIF--------RDHE-----------TLSVLIILSVFIIFLTSIRSVLILGLMAGDGLSCAHGVFRVLED 63 (99)
Q Consensus 3 l~l~aaWlfLYf~--------sDr~-----------vL~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~HaAfR~~dD 63 (99)
+-++.+|++.|+. .+|. +-.+..++..+..+...-...-...+++...++-+--+.|+-|-
T Consensus 28 ~~L~~aw~~~yl~~~p~~~~~k~r~~~~~~~~~~~~~Yg~~a~~~~l~~l~~~p~ll~~~~~~~pl~~v~~~~~~~~~eR 107 (129)
T PF14256_consen 28 LPLLLAWLFGYLAFYPFLLWLKQRRRRRPRYLKWALIYGAIALVFGLPALLYAPRLLWWALLFLPLFAVNLYFAKRKRER 107 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcCch
Confidence 3578999999998 3332 22233333333333444445555556777777777777777554
Q ss_pred ccccc
Q 042587 64 LVLDE 68 (99)
Q Consensus 64 LFlDe 68 (99)
-.+.|
T Consensus 108 sLlnd 112 (129)
T PF14256_consen 108 SLLND 112 (129)
T ss_pred hHHHh
Confidence 43443
No 4
>KOG4050 consensus Glutamate transporter EAAC1-interacting protein GTRAP3-18 [Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=60.40 E-value=24 Score=27.56 Aligned_cols=42 Identities=19% Similarity=0.243 Sum_probs=30.7
Q ss_pred hhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccccc
Q 042587 19 ETLSVLIILSVFIIFLTSIRSVLILGLMAGDGLSCAHGVFRV 60 (99)
Q Consensus 19 ~vL~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~HaAfR~ 60 (99)
..+.+...+.-+.+.+-+.-...+-++...+.++.+||.+|-
T Consensus 111 ~~l~gvllv~yfli~v~~~vlv~~F~il~Pv~L~lvHASLRL 152 (188)
T KOG4050|consen 111 VTLAGVLLVGYFLISVFGGVLVFAFAILFPVLLVLVHASLRL 152 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666666555556667788899999999999884
No 5
>PRK13823 conjugal transfer protein TrbD; Provisional
Probab=44.69 E-value=61 Score=22.36 Aligned_cols=42 Identities=19% Similarity=0.211 Sum_probs=23.8
Q ss_pred cChhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccccc
Q 042587 16 RDHETLSVLIILSVFIIFLTSIRSVLILGLMAGDGLSCAHGVFRV 60 (99)
Q Consensus 16 sDr~vL~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~HaAfR~ 60 (99)
-|||..+.-..++....+-...+...+.++.+. ...|+..|.
T Consensus 21 a~R~l~i~~g~la~~l~~g~~~~~a~~~gl~lw---~v~h~~l~~ 62 (94)
T PRK13823 21 GDRELVMFSGLLAGILIFVAQTWRAALFGIALW---FGALFALRL 62 (94)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH
Confidence 689987777777766555333333333333332 455766663
No 6
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=44.26 E-value=28 Score=20.99 Aligned_cols=22 Identities=23% Similarity=0.225 Sum_probs=18.4
Q ss_pred hhhhHHHHHHHHHHHHHHHHhh
Q 042587 34 LTSIRSVLILGLMAGDGLSCAH 55 (99)
Q Consensus 34 lT~v~~nl~~al~ig~~lV~~H 55 (99)
+|..-+|.+.++..|.+++.+-
T Consensus 1 MTpSLsnF~~SL~~Ga~ivvip 22 (39)
T CHL00114 1 MTPSLSAFINSLLLGAIIVVIP 22 (39)
T ss_pred CChhHHHHHHHHHHHHHHhHHH
Confidence 5788899999999999887643
No 7
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=35.11 E-value=34 Score=24.89 Aligned_cols=28 Identities=18% Similarity=0.293 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhhcccccCCCcccccCCCC
Q 042587 44 GLMAGDGLSCAHGVFRVLEDLVLDEQEPS 72 (99)
Q Consensus 44 al~ig~~lV~~HaAfR~~dDLFlDe~e~~ 72 (99)
.+-.+.++-.+|++.|.-||+ .|+.+.+
T Consensus 20 ~~~~a~ave~l~~~~li~DDI-~D~~~~r 47 (236)
T cd00867 20 ALRLAAAVELLHAASLVHDDI-VDDSDLR 47 (236)
T ss_pred HHHHHHHHHHHHHHHHHHccc-ccCCccC
Confidence 346788999999999999998 8876655
No 8
>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=34.46 E-value=59 Score=19.52 Aligned_cols=21 Identities=29% Similarity=0.365 Sum_probs=14.0
Q ss_pred hhhhHHHHHHHHHHHHHHHHh
Q 042587 34 LTSIRSVLILGLMAGDGLSCA 54 (99)
Q Consensus 34 lT~v~~nl~~al~ig~~lV~~ 54 (99)
+|..-.|.+.++..|.++|..
T Consensus 1 mTpSL~nfl~Sl~aG~~iVv~ 21 (39)
T PF06596_consen 1 MTPSLSNFLLSLVAGAVIVVI 21 (39)
T ss_dssp --HHHHHHHHHHHHHH-HHHH
T ss_pred CCHhHHHHHHHHHhhhhhhhh
Confidence 477778999999998855543
No 9
>PF09964 DUF2198: Uncharacterized protein conserved in bacteria (DUF2198); InterPro: IPR019242 This family of various hypothetical archaeal proteins has no known function.
Probab=31.58 E-value=1.6e+02 Score=19.83 Aligned_cols=33 Identities=15% Similarity=0.247 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh
Q 042587 22 SVLIILSVFIIFLTSIRSVLILGLMAGDGLSCA 54 (99)
Q Consensus 22 ~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~ 54 (99)
..+..=-+.++++|.|+.|-.+|+.+-++++.+
T Consensus 5 ~Al~~P~lLVvlFtrVT~n~~vg~~lt~~Li~A 37 (74)
T PF09964_consen 5 LALFFPCLLVVLFTRVTYNHYVGTILTVALIAA 37 (74)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHH
Confidence 344555577788999999999999888877764
No 10
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=25.90 E-value=2.1e+02 Score=20.94 Aligned_cols=35 Identities=23% Similarity=0.344 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh
Q 042587 20 TLSVLIILSVFIIFLTSIRSVLILGLMAGDGLSCA 54 (99)
Q Consensus 20 vL~~L~v~Tv~~l~lT~v~~nl~~al~ig~~lV~~ 54 (99)
.+++.+.+.++++.+.+...+.+.++++|++.-..
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~ 46 (199)
T PF10112_consen 12 ILGVLIAAITFLVSFFGFDHSFLLSLLIGAVAFAV 46 (199)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 34444444444444444445555566666554433
No 11
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=22.30 E-value=59 Score=21.40 Aligned_cols=13 Identities=8% Similarity=0.237 Sum_probs=10.8
Q ss_pred hHHHHHHHHHHHh
Q 042587 3 LGLLSSLIFAHIF 15 (99)
Q Consensus 3 l~l~aaWlfLYf~ 15 (99)
.+++..|++.|..
T Consensus 15 fA~LFv~Ll~yvl 27 (71)
T PF10960_consen 15 FAVLFVWLLFYVL 27 (71)
T ss_pred HHHHHHHHHHHHH
Confidence 3677899999998
No 12
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=21.50 E-value=3.5e+02 Score=20.13 Aligned_cols=37 Identities=19% Similarity=0.157 Sum_probs=21.5
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCCCcccc
Q 042587 29 VFIIFLTSIRSVLILGLMAGDGLSCAHGVFRVLEDLVLD 67 (99)
Q Consensus 29 v~~l~lT~v~~nl~~al~ig~~lV~~HaAfR~~dDLFlD 67 (99)
+...+..+-+.+-.....+|...+. ++.|..||+|-+
T Consensus 128 ~~~~~~~~~~~~~~~~~~ig~~~~l--~~~~~i~~l~~~ 164 (200)
T PF13398_consen 128 IALWFFAPPWILRFILLFIGVFLLL--YSVRDIDDLFRR 164 (200)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHHHH--HHHcCHHHHhcC
Confidence 3333455555555555555555443 667778898733
No 13
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=20.77 E-value=66 Score=22.87 Aligned_cols=34 Identities=29% Similarity=0.369 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHhhc--ccccCCCcccccCCC
Q 042587 38 RSVLILGLMAGDGLSCAHG--VFRVLEDLVLDEQEP 71 (99)
Q Consensus 38 ~~nl~~al~ig~~lV~~Ha--AfR~~dDLFlDe~e~ 71 (99)
.-|++.|+.+|..++++-+ -..+-.|=|+||-|.
T Consensus 49 ~rN~~Tgl~L~~~v~gIY~YTi~sV~Qe~F~D~~ee 84 (100)
T PF09813_consen 49 RRNLLTGLALGAFVVGIYAYTIYSVKQEDFLDELEE 84 (100)
T ss_pred hhhHHHHHHHHHHHHHHHhheeeeechhhhHHHhhh
Confidence 3689999999988887765 345555778887544
Done!