Query 039401
Match_columns 168
No_of_seqs 131 out of 314
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 09:17:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2981 Protein involved in au 99.9 8.8E-28 1.9E-32 199.6 9.2 118 41-166 148-275 (295)
2 PF03987 Autophagy_act_C: Auto 99.9 3.8E-25 8.3E-30 149.1 6.8 62 68-136 1-62 (62)
3 KOG4741 Uncharacterized conser 99.9 4.1E-23 9E-28 161.6 1.5 104 49-168 50-153 (173)
4 KOG3558 Hypoxia-inducible fact 36.8 14 0.00031 35.8 0.6 29 114-144 151-180 (768)
5 PF00971 EIAV_GP90: EIAV coat 28.7 22 0.00047 31.2 0.4 14 70-83 276-289 (385)
6 PRK11835 hypothetical protein; 21.5 65 0.0014 24.3 1.7 20 125-144 78-97 (114)
7 PF14473 RD3: RD3 protein 19.8 11 0.00023 29.2 -2.9 32 114-145 69-100 (133)
8 PF05768 DUF836: Glutaredoxin- 17.1 42 0.00091 22.8 -0.1 26 75-100 48-79 (81)
9 PF13989 YejG: YejG-like prote 16.1 1.1E+02 0.0023 22.8 1.8 20 125-144 75-94 (106)
10 KOG3563 Forkhead/HNF-3-related 15.4 99 0.0021 28.1 1.7 16 86-101 188-203 (454)
No 1
>KOG2981 consensus Protein involved in autophagocytosis during starvation [General function prediction only]
Probab=99.95 E-value=8.8e-28 Score=199.63 Aligned_cols=118 Identities=26% Similarity=0.470 Sum_probs=99.5
Q ss_pred CCCCCCCCCCcccccc---cC----C--CCeEEEEEEEEEeCCCCCeEEEEEEecCCCCCCCHHHHHhhCCcchhhhhcc
Q 039401 41 SCFKEEEPTDSATLVQ---NY----D--CDKHYYDFHVIYNASYRVPVLYFRAYCSGGQPLVLDEIEKGLPSCSAKALSE 111 (168)
Q Consensus 41 ~~~~~~~~~D~~~~~~---~~----~--~~~~~~e~~I~YS~sYqVPvLyf~~~~~~g~pL~leei~~~lp~~~~~~l~~ 111 (168)
.|++.++.+|.++++. +. . -+.|+||++|+|+++||+|+||++||+++|+||+.++|+++++++++
T Consensus 148 e~~e~d~~edp~~~~s~~~~~~~dd~gil~tRtYDL~I~YdkyYqtPRl~l~Gyde~r~pLt~E~myEDvS~Dha----- 222 (295)
T KOG2981|consen 148 ELEESDEEEDPATFVSKAVAGLADDSGILQTRTYDLYITYDKYYQTPRLWLVGYDENRQPLTVEQMYEDVSQDHA----- 222 (295)
T ss_pred cccccccccCHHHHhhhhccccccccccceeeEEEEEEEeeccccCceEEEEEecCCCCcCCHHHHHHHhhhhhc-----
Confidence 4555555555455533 11 1 25799999999999999999999999999999999999999998874
Q ss_pred CCeeeeeeecCCCCCCC-eEEEecCCchHHHHHhhcccccccCCcccccchhhhhc
Q 039401 112 SKWTFITHEEHPYLNRP-WYKLHPCGTSEWMKLLFLGDTTQKKNGVAIELYLVAWF 166 (168)
Q Consensus 112 ~~~~~IT~~~HP~l~~p-~~~IHPC~Ta~~m~~l~~~~~~~~~~~~~~~~YL~~WL 166 (168)
.++||++.||++..+ ..+||||+||++|+.|++..+ .++.++.+++||.+||
T Consensus 223 --~KTvTiE~hPh~~~~~m~SVHPCkHa~vMkklI~~~~-e~g~~l~Vd~YL~lFL 275 (295)
T KOG2981|consen 223 --KKTVTIEKHPHLPGPNMASVHPCKHAEVMKKLIDQVR-ERGDELGVDQYLILFL 275 (295)
T ss_pred --cCeEEeccCCCCCCCCccccccchhHHHHHHHHHHHH-hcCCCcceehhHHHHH
Confidence 789999999999777 999999999999999998744 5677889999999997
No 2
>PF03987 Autophagy_act_C: Autophagocytosis associated protein, active-site domain ; InterPro: IPR007135 Proteins in this entry belong to the Atg3 group of proteins and the Atg3 conjugation enzymes. 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 []. Atg3 is the E2 enzyme for the LC3 lipidation process []. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place []. Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long alpha-helical structure that protrudes from the core region as far as 30 A []. It interacts with atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of atg8. It also interacts with the C-terminal region of the E1-like atg7 enzyme. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex [].; PDB: 2DYT_A.
Probab=99.92 E-value=3.8e-25 Score=149.10 Aligned_cols=62 Identities=53% Similarity=1.018 Sum_probs=48.2
Q ss_pred EEEEeCCCCCeEEEEEEecCCCCCCCHHHHHhhCCcchhhhhccCCeeeeeeecCCCCCCCeEEEecCC
Q 039401 68 HVIYNASYRVPVLYFRAYCSGGQPLVLDEIEKGLPSCSAKALSESKWTFITHEEHPYLNRPWYKLHPCG 136 (168)
Q Consensus 68 ~I~YS~sYqVPvLyf~~~~~~g~pL~leei~~~lp~~~~~~l~~~~~~~IT~~~HP~l~~p~~~IHPC~ 136 (168)
||+||++||||+||||+|+++|.||++++|+++++.... ..+||+++||++|.|||+||||+
T Consensus 1 ~I~Ys~~YqvP~L~f~~~~~~g~~l~~~~~~~~~~~~~~-------~~~it~~~HP~l~~p~~~iHPC~ 62 (62)
T PF03987_consen 1 HITYSPSYQVPVLYFRGYDEDGSPLSLEEVYEDLSPDSA-------DSTITQEEHPILGIPWYSIHPCD 62 (62)
T ss_dssp EEEEETTTTEEEEEEEEEETT--B--HHHHHTTS-TTTH-------HHHEEEEE-TTBSS-EEEE-S-S
T ss_pred CEEecCccCCCEEEEEEECCCCCCCCHHHHHHhhccccc-------cceeecccCCCCCCceEEEcCCC
Confidence 799999999999999999999999999999999965554 33499999999999999999996
No 3
>KOG4741 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.86 E-value=4.1e-23 Score=161.63 Aligned_cols=104 Identities=36% Similarity=0.669 Sum_probs=87.1
Q ss_pred CCcccccccCCCCeEEEEEEEEEeCCCCCeEEEEEEecCCCCCCCHHHHHhhCCcchhhhhccCCeeeeeeecCCCCCCC
Q 039401 49 TDSATLVQNYDCDKHYYDFHVIYNASYRVPVLYFRAYCSGGQPLVLDEIEKGLPSCSAKALSESKWTFITHEEHPYLNRP 128 (168)
Q Consensus 49 ~D~~~~~~~~~~~~~~~e~~I~YS~sYqVPvLyf~~~~~~g~pL~leei~~~lp~~~~~~l~~~~~~~IT~~~HP~l~~p 128 (168)
++..++-+.+. +.+..+.||.|+.+||||+|||+.+..+|+||..-.|-+ .++..+.++.+..||+.+||+||.|
T Consensus 50 a~~s~i~t~~d-~vi~~e~hilyn~kyqvp~lwf~f~~~ngrpl~~r~v~E----i~~t~l~e~~~~~Itq~eHP~Lg~p 124 (173)
T KOG4741|consen 50 AKQSAICTFDD-QVINREAHFLYNRKYQVPELWFMFYCRNGRPLRVRQVAE----ILGTKLEENDAIVITQSEHPTLGIP 124 (173)
T ss_pred eeeeeeeehhH-HHhhhhheEEEEeeecchhheeehhhcCCCchhhhhhHH----hhcCccccCccceeeeccCCcccce
Confidence 34444444444 789999999999999999999999999999999885444 4555566778899999999999999
Q ss_pred eEEEecCCchHHHHHhhcccccccCCcccccchhhhhccC
Q 039401 129 WYKLHPCGTSEWMKLLFLGDTTQKKNGVAIELYLVAWFSV 168 (168)
Q Consensus 129 ~~~IHPC~Ta~~m~~l~~~~~~~~~~~~~~~~YL~~WLsv 168 (168)
+|-||||+|+++|+.+... .+|+++|||+
T Consensus 125 yy~LHPC~Tse~mke~~k~-----------sNyilswiS~ 153 (173)
T KOG4741|consen 125 YYKLHPCDTSELMKEIPKR-----------SNYILSWISA 153 (173)
T ss_pred eeeecCCcHHHHHhhcCCc-----------hHHHHHHHHH
Confidence 9999999999999998532 2999999985
No 4
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=36.82 E-value=14 Score=35.78 Aligned_cols=29 Identities=21% Similarity=0.394 Sum_probs=20.6
Q ss_pred eeeeeeecCCCCCCC-eEEEecCCchHHHHHh
Q 039401 114 WTFITHEEHPYLNRP-WYKLHPCGTSEWMKLL 144 (168)
Q Consensus 114 ~~~IT~~~HP~l~~p-~~~IHPC~Ta~~m~~l 144 (168)
+-++||.+ ++|.- |=|||||++.++-+.+
T Consensus 151 yLGLSQvE--LTG~SvFDfiHP~DheE~~eqL 180 (768)
T KOG3558|consen 151 YLGLSQVE--LTGSSVFDFIHPCDHEEIAEQL 180 (768)
T ss_pred hhCcccee--eecchhhhccCccCHHHHHHHh
Confidence 33444544 45554 7799999999999887
No 5
>PF00971 EIAV_GP90: EIAV coat protein, gp90; InterPro: IPR001361 Equine infectious anemia virus(EIAV) belongs to the family retroviridae. EIAV gp90 is hypervariable in the carboxyl-end region and more stable in the amino-end region. This variability is a pathogenicity factor that allows the evasion of the host's immune response [].; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=28.69 E-value=22 Score=31.23 Aligned_cols=14 Identities=36% Similarity=0.762 Sum_probs=12.3
Q ss_pred EEeCCCCCeEEEEE
Q 039401 70 IYNASYRVPVLYFR 83 (168)
Q Consensus 70 ~YS~sYqVPvLyf~ 83 (168)
-|+-+||||++|--
T Consensus 276 dYtg~YQvPifY~c 289 (385)
T PF00971_consen 276 DYTGIYQVPIFYTC 289 (385)
T ss_pred CccceEeeeeEEEe
Confidence 58999999999974
No 6
>PRK11835 hypothetical protein; Provisional
Probab=21.53 E-value=65 Score=24.26 Aligned_cols=20 Identities=15% Similarity=-0.031 Sum_probs=17.6
Q ss_pred CCCCeEEEecCCchHHHHHh
Q 039401 125 LNRPWYKLHPCGTSEWMKLL 144 (168)
Q Consensus 125 l~~p~~~IHPC~Ta~~m~~l 144 (168)
-|.|++|||.++-..+|=.+
T Consensus 78 eGepCLFv~~~DE~aa~CrL 97 (114)
T PRK11835 78 EGEPCLFVNRQDESAATCRL 97 (114)
T ss_pred cCCceEEEecccchhhheee
Confidence 48999999999999998655
No 7
>PF14473 RD3: RD3 protein
Probab=19.84 E-value=11 Score=29.24 Aligned_cols=32 Identities=19% Similarity=0.154 Sum_probs=24.2
Q ss_pred eeeeeeecCCCCCCCeEEEecCCchHHHHHhh
Q 039401 114 WTFITHEEHPYLNRPWYKLHPCGTSEWMKLLF 145 (168)
Q Consensus 114 ~~~IT~~~HP~l~~p~~~IHPC~Ta~~m~~l~ 145 (168)
...|+.+++=-|...|-.||||.++.++..+-
T Consensus 69 ~~~i~~~ErlqLE~lCski~P~~~g~vI~RFR 100 (133)
T PF14473_consen 69 SYQISPGERLQLEDLCSKIPPCECGPVISRFR 100 (133)
T ss_pred cCCCCHHHHHHHHHHHhcCChhhhHHHHHHHH
Confidence 34555555555777899999999999997764
No 8
>PF05768 DUF836: Glutaredoxin-like domain (DUF836); InterPro: IPR008554 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This family contains several viral glutaredoxins, and many related bacterial and eukaryotic proteins of unknown function. The best characterised member of this family is G4L (P68460 from SWISSPROT) from Vaccinia virus (strain Western Reserve/WR) (VACV), which is necessary for virion morphogenesis and virus replication []. This is a cytomplasmic protein which functions as a shuttle in a redox pathway between membrane-associated E10R and L1R or F9L []. ; PDB: 1TTZ_A 1XPV_A 2FGX_A 2G2Q_C 1WJK_A.
Probab=17.06 E-value=42 Score=22.76 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=15.8
Q ss_pred CCCeEEEEEEe------cCCCCCCCHHHHHhh
Q 039401 75 YRVPVLYFRAY------CSGGQPLVLDEIEKG 100 (168)
Q Consensus 75 YqVPvLyf~~~------~~~g~pL~leei~~~ 100 (168)
|.+|||.+.+- ...+-+++.+++.+.
T Consensus 48 ~~IPVl~~~~~~~~~~~~~~~~~~d~~~L~~~ 79 (81)
T PF05768_consen 48 YRIPVLHIDGIRQFKEQEELKWRFDEEQLRAW 79 (81)
T ss_dssp TSTSEEEETT-GGGCTSEEEESSB-HHHHHHH
T ss_pred CCCCEEEEcCcccccccceeCCCCCHHHHHHH
Confidence 78999988772 222346777666554
No 9
>PF13989 YejG: YejG-like protein
Probab=16.06 E-value=1.1e+02 Score=22.82 Aligned_cols=20 Identities=25% Similarity=0.120 Sum_probs=17.4
Q ss_pred CCCCeEEEecCCchHHHHHh
Q 039401 125 LNRPWYKLHPCGTSEWMKLL 144 (168)
Q Consensus 125 l~~p~~~IHPC~Ta~~m~~l 144 (168)
-|.|++|||.++-+.+|=.+
T Consensus 75 eGepCLFv~~~DEsa~~CrL 94 (106)
T PF13989_consen 75 EGEPCLFVHREDESAAMCRL 94 (106)
T ss_pred cCCceEEEecccchhhheee
Confidence 48999999999999998654
No 10
>KOG3563 consensus Forkhead/HNF-3-related transcription factor [Transcription]
Probab=15.43 E-value=99 Score=28.10 Aligned_cols=16 Identities=25% Similarity=0.216 Sum_probs=12.9
Q ss_pred cCCCCCCCHHHHHhhC
Q 039401 86 CSGGQPLVLDEIEKGL 101 (168)
Q Consensus 86 ~~~g~pL~leei~~~l 101 (168)
+..++.|+|.||+++|
T Consensus 188 ~~pskmLTLSEIYqwI 203 (454)
T KOG3563|consen 188 QAPSKMLTLSEIYQWI 203 (454)
T ss_pred hCCccceeHHHHHHHH
Confidence 3456789999999985
Done!