Query 009024
Match_columns 546
No_of_seqs 235 out of 519
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 19:29:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009024.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009024hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04784 DUF547: Protein of un 100.0 8.6E-38 1.9E-42 280.5 10.5 110 329-465 1-117 (117)
2 PF14389 Lzipper-MIP1: Leucine 99.7 9.8E-19 2.1E-23 150.2 3.1 82 40-123 6-88 (88)
3 PF09457 RBD-FIP: FIP domain ; 63.0 13 0.00028 28.9 4.0 33 91-123 2-41 (48)
4 PF06698 DUF1192: Protein of u 58.1 15 0.00032 29.9 3.7 25 90-114 22-46 (59)
5 PRK11020 hypothetical protein; 39.6 18 0.0004 33.0 1.7 49 47-109 3-51 (118)
6 KOG4010 Coiled-coil protein TP 36.6 55 0.0012 32.5 4.6 29 91-119 46-81 (208)
7 PF13107 DUF3964: Protein of u 30.6 25 0.00055 31.2 1.1 16 330-346 89-104 (109)
8 PRK14127 cell division protein 30.0 90 0.0019 28.4 4.5 34 87-120 35-68 (109)
9 PRK10265 chaperone-modulator p 24.8 93 0.002 27.4 3.7 23 90-112 72-94 (101)
10 PF05377 FlaC_arch: Flagella a 20.9 1.5E+02 0.0034 23.8 3.8 26 88-117 20-45 (55)
11 PRK11239 hypothetical protein; 20.8 1.6E+02 0.0034 29.9 4.8 30 88-117 182-211 (215)
12 COG3132 Uncharacterized protei 20.8 1.2E+02 0.0025 30.2 3.7 25 91-115 187-211 (215)
13 PF07106 TBPIP: Tat binding pr 20.6 1.3E+02 0.0029 28.5 4.1 28 90-117 110-137 (169)
No 1
>PF04784 DUF547: Protein of unknown function, DUF547; InterPro: IPR006869 This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans and Arabidopsis thaliana (Mouse-ear cress).
Probab=100.00 E-value=8.6e-38 Score=280.54 Aligned_cols=110 Identities=45% Similarity=0.684 Sum_probs=101.1
Q ss_pred ccCCCCCchhhHHHHHHHHHHHHHHHHHHHhCCCCCcccc----c-cceeEEEeCCEeecHHHHHhhhhcCCCCCChhhh
Q 009024 329 KIDPRKMKREEKLAFWINIHNALVMHAYLAYGTRNSVKST----S-IMKAAYNVGGQYVDAYVIQSSILGIRPHFSAPWL 403 (546)
Q Consensus 329 ~Vd~~~Ls~eEKLAFWINiYNaLvmHa~L~~GiP~s~k~~----~-~~ka~Y~VGG~~~Sl~dIEh~ILR~~~~~p~~~~ 403 (546)
+||++.|+++||+|||||+||+|+||++|++|+|.++.++ . |.+..|+|||+.+||+||||+|||++.+
T Consensus 1 ~v~~~~l~~~e~lAFwIN~yNal~~h~~l~~~~~~s~~~~~~~~~~~~~~~y~Igg~~~SL~dIe~~ILR~~~~------ 74 (117)
T PF04784_consen 1 RVDLSSLSREEKLAFWINLYNALVLHAILENGPPKSILDRKLGGSFFSKVRYNIGGQRFSLDDIEHGILRGNRP------ 74 (117)
T ss_pred CcChHHCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHhhcccccccceEEEECCEEecHHHHHHhhccCCCC------
Confidence 5899999999999999999999999999999988555433 4 9999999999999999999999997532
Q ss_pred hhhcCCCCCCCCCcccccccCCCCCceeeeeeccCCCCCCCcc--eeccccHHHHHHHHHHHHh
Q 009024 404 QALFSPGRKLKTGSTKHVYALEYPEPLVHFALCSGAYSDPGVR--VYTAKNVFRDLKLAKEEFI 465 (546)
Q Consensus 404 ~~L~~~~~k~k~~d~r~~~~l~~~DPrIhFAL~cGs~SsP~lR--vYta~~v~~qLe~A~~efL 465 (546)
.+.||||||||+||++|||+|| +|||++|++||++|+++||
T Consensus 75 ---------------------~~~DprihFaL~cgs~s~P~lr~~~yt~~~l~~qL~~a~~~fi 117 (117)
T PF04784_consen 75 ---------------------PWPDPRIHFALNCGSKSCPPLRREAYTAENLDEQLEEAAREFI 117 (117)
T ss_pred ---------------------CCCCCceeeeeecCCCCChhhhhhccCHHHHHHHHHHHHHhhC
Confidence 1799999999999999999999 9999999999999999997
No 2
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=99.73 E-value=9.8e-19 Score=150.15 Aligned_cols=82 Identities=32% Similarity=0.480 Sum_probs=74.2
Q ss_pred cCCCCcCCcchhHHhhhcCCCCCcccchhhhhhcccCccCC-CCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 40 VSPGLSSLSNPIVRLERTLPHQPSLCSHSEEATSFQSIKSI-PSHGSTAPKSSAELMKEIAVLEAEIMHLERYLLSLYRT 118 (546)
Q Consensus 40 ~~~~~~~~~~~i~~L~k~L~~q~~~~~~~~l~~~~~~~~~~-~~~~~~~p~~~~eLi~EIA~LE~EV~~lE~~llsLYr~ 118 (546)
.+.++++|+|+|.+|+++|++|. +++.+|+.+...+.+. +..+.++|++++|||+|||+||+||++||+||++|||+
T Consensus 6 ~~~~r~~LeqeV~~Lq~~L~~E~--~~r~aLe~al~~~~~~~~~~~~~lp~~~keLL~EIA~lE~eV~~LE~~v~~L~~~ 83 (88)
T PF14389_consen 6 LHERRSALEQEVAELQKQLQEEQ--DLRRALEKALGRSSGSLPSSPSSLPKKAKELLEEIALLEAEVAKLEQKVLSLYRQ 83 (88)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHhCCCCcccCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999999988 7888888877776666 68899999999999999999999999999999999999
Q ss_pred HHHHh
Q 009024 119 AFEEH 123 (546)
Q Consensus 119 ~f~q~ 123 (546)
+|+||
T Consensus 84 l~~q~ 88 (88)
T PF14389_consen 84 LFQQR 88 (88)
T ss_pred HHhcC
Confidence 99885
No 3
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=62.95 E-value=13 Score=28.93 Aligned_cols=33 Identities=27% Similarity=0.344 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Q 009024 91 SAELMKEIAVLEAEIMH-------LERYLLSLYRTAFEEH 123 (546)
Q Consensus 91 ~~eLi~EIA~LE~EV~~-------lE~~llsLYr~~f~q~ 123 (546)
-.||+.++.-.|.++.+ ||.|+-+|--++.|++
T Consensus 2 ~eeL~~~l~~~e~~~~~k~~~v~eLe~YiD~LL~rVmE~~ 41 (48)
T PF09457_consen 2 REELISLLKKQEEENARKDSRVRELEDYIDNLLVRVMEQT 41 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 36899999999999999 9999999988877655
No 4
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=58.12 E-value=15 Score=29.90 Aligned_cols=25 Identities=48% Similarity=0.542 Sum_probs=22.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 90 SSAELMKEIAVLEAEIMHLERYLLS 114 (546)
Q Consensus 90 ~~~eLi~EIA~LE~EV~~lE~~lls 114 (546)
+..||=.=||.||.||.++|.++-.
T Consensus 22 Sv~EL~~RIa~L~aEI~R~~~~~~~ 46 (59)
T PF06698_consen 22 SVEELEERIALLEAEIARLEAAIAK 46 (59)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999988753
No 5
>PRK11020 hypothetical protein; Provisional
Probab=39.56 E-value=18 Score=33.01 Aligned_cols=49 Identities=33% Similarity=0.287 Sum_probs=33.5
Q ss_pred CcchhHHhhhcCCCCCcccchhhhhhcccCccCCCCCCCCCChhHHHHHHHHHHHHHHHHHHH
Q 009024 47 LSNPIVRLERTLPHQPSLCSHSEEATSFQSIKSIPSHGSTAPKSSAELMKEIAVLEAEIMHLE 109 (546)
Q Consensus 47 ~~~~i~~L~k~L~~q~~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~eLi~EIA~LE~EV~~lE 109 (546)
+++||.+|-.+|. .+.+.++.+..+--. .-..++.+||+.|+.||.+|-
T Consensus 3 ~K~Eiq~L~drLD-----~~~~Klaaa~~rgd~---------~~i~qf~~E~~~l~k~I~~lk 51 (118)
T PRK11020 3 EKNEIKRLSDRLD-----AIRHKLAAASLRGDA---------EKYAQFEKEKATLEAEIARLK 51 (118)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHHHHhcCCH---------HHHHHHHHHHHHHHHHHHHHH
Confidence 5789999988884 334444443222211 257789999999999999874
No 6
>KOG4010 consensus Coiled-coil protein TPD52 [General function prediction only]
Probab=36.59 E-value=55 Score=32.48 Aligned_cols=29 Identities=41% Similarity=0.471 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHH
Q 009024 91 SAELMKEIAVLEAEIMHL-------ERYLLSLYRTA 119 (546)
Q Consensus 91 ~~eLi~EIA~LE~EV~~l-------E~~llsLYr~~ 119 (546)
-.||-+|++-+|+||+-| |+|.-.|-|++
T Consensus 46 keelr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKL 81 (208)
T KOG4010|consen 46 KEELRTELAKVEEEIVTLRQVLAAKERHAAELKRKL 81 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 358899999999999987 55555577764
No 7
>PF13107 DUF3964: Protein of unknown function (DUF3964)
Probab=30.60 E-value=25 Score=31.16 Aligned_cols=16 Identities=25% Similarity=0.881 Sum_probs=11.7
Q ss_pred cCCCCCchhhHHHHHHH
Q 009024 330 IDPRKMKREEKLAFWIN 346 (546)
Q Consensus 330 Vd~~~Ls~eEKLAFWIN 346 (546)
|++..++ +|++|||+|
T Consensus 89 v~Lp~i~-~~~~AFW~N 104 (109)
T PF13107_consen 89 VNLPEIE-NQQMAFWFN 104 (109)
T ss_pred eeCchhh-HHHHHHHhh
Confidence 5555543 688999998
No 8
>PRK14127 cell division protein GpsB; Provisional
Probab=29.95 E-value=90 Score=28.36 Aligned_cols=34 Identities=24% Similarity=0.182 Sum_probs=25.2
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 87 APKSSAELMKEIAVLEAEIMHLERYLLSLYRTAF 120 (546)
Q Consensus 87 ~p~~~~eLi~EIA~LE~EV~~lE~~llsLYr~~f 120 (546)
+-+.-..|++||+.|++|+.+||+.|-.+-.++-
T Consensus 35 V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 35 VIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3345667788888999999999988877665443
No 9
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=24.84 E-value=93 Score=27.43 Aligned_cols=23 Identities=35% Similarity=0.355 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Q 009024 90 SSAELMKEIAVLEAEIMHLERYL 112 (546)
Q Consensus 90 ~~~eLi~EIA~LE~EV~~lE~~l 112 (546)
=+.+|+.+|+.|+.|+..|++++
T Consensus 72 lvl~LLd~i~~Lr~el~~L~~~l 94 (101)
T PRK10265 72 VALTLLDEIAHLKQENRLLRQRL 94 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999854
No 10
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=20.95 E-value=1.5e+02 Score=23.80 Aligned_cols=26 Identities=31% Similarity=0.567 Sum_probs=20.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 88 PKSSAELMKEIAVLEAEIMHLERYLLSLYR 117 (546)
Q Consensus 88 p~~~~eLi~EIA~LE~EV~~lE~~llsLYr 117 (546)
=++.++|-.+|..||+-| +.||+||-
T Consensus 20 k~en~~i~~~ve~i~env----k~ll~lYE 45 (55)
T PF05377_consen 20 KKENEEISESVEKIEENV----KDLLSLYE 45 (55)
T ss_pred HHHHHHHHHHHHHHHHHH----HHHHHHHH
Confidence 356778888888888888 78899994
No 11
>PRK11239 hypothetical protein; Provisional
Probab=20.84 E-value=1.6e+02 Score=29.89 Aligned_cols=30 Identities=27% Similarity=0.349 Sum_probs=22.1
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 88 PKSSAELMKEIAVLEAEIMHLERYLLSLYR 117 (546)
Q Consensus 88 p~~~~eLi~EIA~LE~EV~~lE~~llsLYr 117 (546)
+....+|-.+|+.||.||..|+..|-.|..
T Consensus 182 ~~~~~~Le~rv~~Le~eva~L~~~l~~l~~ 211 (215)
T PRK11239 182 NAVDGDLQARVEALEIEVAELKQRLDSLLA 211 (215)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566888888888888888887776643
No 12
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.76 E-value=1.2e+02 Score=30.16 Aligned_cols=25 Identities=36% Similarity=0.444 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 91 SAELMKEIAVLEAEIMHLERYLLSL 115 (546)
Q Consensus 91 ~~eLi~EIA~LE~EV~~lE~~llsL 115 (546)
..+|=++||.||.||..|++.|-+|
T Consensus 187 s~dlearv~aLe~eva~L~~rld~l 211 (215)
T COG3132 187 SSDLEARVEALEQEVAELRARLDSL 211 (215)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHH
Confidence 4569999999999999999887765
No 13
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=20.62 E-value=1.3e+02 Score=28.51 Aligned_cols=28 Identities=43% Similarity=0.453 Sum_probs=25.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009024 90 SSAELMKEIAVLEAEIMHLERYLLSLYR 117 (546)
Q Consensus 90 ~~~eLi~EIA~LE~EV~~lE~~llsLYr 117 (546)
.+.||..+|+.|+.|+..||..|-.|-.
T Consensus 110 t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 110 TNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5889999999999999999999888763
Done!