Query 016821
Match_columns 382
No_of_seqs 188 out of 373
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:07:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016821hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03080 DUF239: Domain of unk 100.0 3.4E-48 7.4E-53 365.8 12.6 134 244-377 1-140 (229)
2 PF14365 DUF4409: Domain of un 100.0 6.8E-39 1.5E-43 275.5 5.9 107 131-239 1-117 (117)
3 PRK09510 tolA cell envelope in 33.7 71 0.0015 33.5 5.1 21 68-88 14-34 (387)
4 PF07438 DUF1514: Protein of u 32.9 46 0.001 26.7 2.8 55 69-127 3-63 (66)
5 TIGR02794 tolA_full TolA prote 22.3 1E+02 0.0023 31.6 4.0 20 68-87 3-22 (346)
6 PF13987 YedD: YedD-like prote 19.7 43 0.00094 29.2 0.5 22 123-144 23-45 (111)
7 PF11239 DUF3040: Protein of u 18.6 99 0.0022 24.9 2.4 17 107-123 4-20 (82)
8 COG1512 Beta-propeller domains 17.2 2.2E+02 0.0047 28.5 4.8 24 116-139 50-78 (271)
9 KOG2557 Uncharacterized conser 15.4 80 0.0017 33.3 1.3 21 284-304 278-298 (427)
10 PF05687 DUF822: Plant protein 15.1 90 0.0019 28.8 1.4 34 284-332 57-90 (150)
No 1
>PF03080 DUF239: Domain of unknown function (DUF239); InterPro: IPR004314 This is a family of plant proteins, a small number of which are putative peptidases (see for example Q9XIN9 from SWISSPROT). However, the structure of the protein PDB3:3eu8 has an alpha-alpha toroid fold and is similar to a glucoamylase, PDB:1ayx. Such glucoamylases are involved in breaking down complex sugars (e.g. starch). The biologically relevant state is likely to be monomeric. The putative active site is located at the centre of the toroid with a well defined large cavity. Further structural comparisons also show relationships with other glycohydrolases.
Probab=100.00 E-value=3.4e-48 Score=365.84 Aligned_cols=134 Identities=53% Similarity=0.942 Sum_probs=127.6
Q ss_pred eeeeEEEEEeeccccccCCccceeeeeeeeCcCCCCccEEEEeeEECccccCCCccEEEEEEccCCCCcccccccCCCce
Q 016821 244 YYGAKASINVWAPRVVNQYEFSLSQMWVISGSFGDDLNTIEAGWQVSPELYGDNYPRFFTYWTTDAYQATGCYNLLCSGF 323 (382)
Q Consensus 244 yyGa~AtInVw~P~V~~~~qfSlsqIwv~sG~~~~~~nsIeaGW~V~P~lYGD~~pRlFtyWT~D~y~~TGCYNl~CpGF 323 (382)
|||++|+||||+|+|+.++|||++||||.+|..++.+|+|||||+|+|+||||++||||+|||+|+|++|||||++||||
T Consensus 1 y~G~~a~i~v~~p~v~~~~q~S~~~i~i~~g~~~~~~~~i~~GW~V~P~lygd~~~~lf~~wt~d~~~~tgCyN~~CpGF 80 (229)
T PF03080_consen 1 YYGARATISVWNPKVQQPDQFSLSQIWISNGSDDDSLNSIEAGWQVYPSLYGDSRTRLFVYWTADGYQKTGCYNLDCPGF 80 (229)
T ss_pred CeeeEEEEECcCCccCCccceeheeEEEEecCCCCCCcEEEEeeeccccccCCCceEEEEEEEccCCCCcceeCCCCCcE
Confidence 79999999999999998779999999999997567799999999999999999999999999999999999999999999
Q ss_pred EEecCccccCccccccccCCCceEEEEEEEEEE-----eee-ecCccccccCcccccccc
Q 016821 324 VQTNNRIAIGAAISPTSSYNGGQFDISLLIWKL-----MVL-VTNRDKIRLPDPEFDLSR 377 (382)
Q Consensus 324 VQvs~~I~lG~~i~PvS~ygG~Qy~i~i~I~KD-----~~~-~~~~~~gy~p~~~f~~~~ 377 (382)
|||+++|+||++|+|+|+++|.|++|.+.|+|| ||+ +.++.|||||++||+.++
T Consensus 81 Vq~s~~i~~G~~~~~~S~~gG~q~~i~~~i~kD~~~gnWWL~~~~~~IGYwP~sLF~~l~ 140 (229)
T PF03080_consen 81 VQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYGGEPIGYWPKSLFTSLA 140 (229)
T ss_pred EEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEecceeeeehHHhhhhhh
Confidence 999999999999999999999999999999997 665 677899999999999865
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=6.8e-39 Score=275.47 Aligned_cols=107 Identities=56% Similarity=0.941 Sum_probs=87.7
Q ss_pred EEeCCCCCeEEeeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCcccceeeeccCCCCCCCCceeeeecCchhh
Q 016821 131 TIQSPDGDIIDCVETHLQPAFDHPKLKGQRPLDPPARPNGHNPS----GMITEEFQLWSFSGESCPEGTIPIRRTTEQDV 206 (382)
Q Consensus 131 TIqs~DGDiiDCVdI~kQPAfdHPLLKNHkIq~pP~~p~~~~~~----~~~~~~~q~w~~~g~~CP~GTVPIrRtt~eDl 206 (382)
||+|+||||||||||||||||||||||+|+ +.|++.|++.... .......|+|+.+| +||+|||||||+++|||
T Consensus 1 tI~s~dGdi~DCVdi~kQPAfdHPlLK~~q-~~Ps~~p~~~~~~~~~~~~~~~~~q~w~~~g-~CP~GTVPIrRtt~~dl 78 (117)
T PF14365_consen 1 TIQSPDGDIIDCVDIYKQPAFDHPLLKNIQ-MRPSSYPKGISSKESSSSSSKPISQLWHQNG-SCPEGTVPIRRTTKEDL 78 (117)
T ss_pred CccCCCCCeEeCEeccccccccCchhcCcc-cCcchhhhhcccccccccccccchhhhcccc-CCcCCceeeecCCHHHH
Confidence 699999999999999999999999999654 3444677765543 22344579999888 89999999999999999
Q ss_pred cccccccccccccccccc------ccCCCCCceeEEEEE
Q 016821 207 LRATSVGKFGRKKIRRVR------RDTNSNGHEHAVGYV 239 (382)
Q Consensus 207 lRa~S~~~fg~k~~~~~~------~~~~~~gHe~Av~~~ 239 (382)
+||+|+.+||+|.+.... .+.+.+|||||++|+
T Consensus 79 lr~~s~~~~g~k~~~~~~~~~~~~~~~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 79 LRAKSFKRFGRKPPSSISSPSSNKPDISSNGHEHAIAYV 117 (117)
T ss_pred hhhhhHHHcCCcCCCCcCCccccCCCCCCCCCceEEEeC
Confidence 999999999999765432 234677999999985
No 3
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=33.69 E-value=71 Score=33.52 Aligned_cols=21 Identities=14% Similarity=0.113 Sum_probs=15.5
Q ss_pred CChHHHHHHHHHHHhhhhccc
Q 016821 68 SPIIPIFVSYLLVLSSSICLV 88 (382)
Q Consensus 68 ~~~~~~~~~~~l~~~~~~~~~ 88 (382)
+.+||+++|+|||++|++++.
T Consensus 14 aiiiSv~LHvlLi~lLi~gs~ 34 (387)
T PRK09510 14 AIIISVVLHIILFALLIWSSF 34 (387)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 357888999998888765543
No 4
>PF07438 DUF1514: Protein of unknown function (DUF1514); InterPro: IPR009999 This entry is represented by Bacteriophage phi PVL, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown.
Probab=32.86 E-value=46 Score=26.70 Aligned_cols=55 Identities=20% Similarity=0.248 Sum_probs=27.6
Q ss_pred ChHHHHHHHHHHHhhhhcccccc---CCCCCCccccc---cccCchHHHHHHHHHHHHHHhhcCC
Q 016821 69 PIIPIFVSYLLVLSSSICLVHSS---DTGKNLNATNQ---TTLRPEEELHKLKFIRAHLNKINKP 127 (382)
Q Consensus 69 ~~~~~~~~~~l~~~~~~~~~~~~---~~~~~~~~~~~---~~~~~~~~~~~~~~i~~~Lk~iNKp 127 (382)
+++++.++.+||+++ .+.|- +.+.- --+|. ..|......+.+++.|..+++|||.
T Consensus 3 IiiSIvLai~lLI~l---~~ns~lr~eieal-kY~N~yL~~~~v~~~g~~gl~~~~~e~~r~~~~ 63 (66)
T PF07438_consen 3 IIISIVLAIALLISL---SVNSELRKEIEAL-KYMNDYLFDQFVRDNGYEGLEEYEIEIERIKKD 63 (66)
T ss_pred hhHHHHHHHHHHHHH---hhhHHHHHHHHHH-HHHHHHHHHHHhhccCcchHHHHHHHHHHHHHH
Confidence 577888888888877 23321 00000 00110 1122222233456778888888875
No 5
>TIGR02794 tolA_full TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB.
Probab=22.30 E-value=1e+02 Score=31.58 Aligned_cols=20 Identities=10% Similarity=0.120 Sum_probs=14.7
Q ss_pred CChHHHHHHHHHHHhhhhcc
Q 016821 68 SPIIPIFVSYLLVLSSSICL 87 (382)
Q Consensus 68 ~~~~~~~~~~~l~~~~~~~~ 87 (382)
+.++|+++|+||+++|++..
T Consensus 3 a~~lSv~lHvlLi~lL~~g~ 22 (346)
T TIGR02794 3 AFLLSLLLHILLLGLLILGS 22 (346)
T ss_pred hHHHHHHHHHHHHHHHHHhh
Confidence 35788899999887775443
No 6
>PF13987 YedD: YedD-like protein
Probab=19.75 E-value=43 Score=29.19 Aligned_cols=22 Identities=27% Similarity=0.650 Sum_probs=16.5
Q ss_pred hhcCCcceE-EeCCCCCeEEeee
Q 016821 123 KINKPAVKT-IQSPDGDIIDCVE 144 (382)
Q Consensus 123 ~iNKp~vKT-Iqs~DGDiiDCVd 144 (382)
.+...|+.| |-|.+||..||--
T Consensus 23 lvSpeAiASLivt~~GdTLDCRQ 45 (111)
T PF13987_consen 23 LVSPEAIASLIVTKEGDTLDCRQ 45 (111)
T ss_pred ccChhheeEEEEccCCCccchhh
Confidence 455556655 7899999999953
No 7
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=18.65 E-value=99 Score=24.92 Aligned_cols=17 Identities=29% Similarity=0.391 Sum_probs=14.0
Q ss_pred chHHHHHHHHHHHHHHh
Q 016821 107 PEEELHKLKFIRAHLNK 123 (382)
Q Consensus 107 ~~~~~~~~~~i~~~Lk~ 123 (382)
+.+|-+.++|||++|..
T Consensus 4 Se~E~r~L~eiEr~L~~ 20 (82)
T PF11239_consen 4 SEHEQRRLEEIERQLRA 20 (82)
T ss_pred CHHHHHHHHHHHHHHHh
Confidence 35777889999999975
No 8
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=17.24 E-value=2.2e+02 Score=28.51 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=15.3
Q ss_pred HHHHHHHhhcCC-----cceEEeCCCCCe
Q 016821 116 FIRAHLNKINKP-----AVKTIQSPDGDI 139 (382)
Q Consensus 116 ~i~~~Lk~iNKp-----~vKTIqs~DGDi 139 (382)
++|++|+.|-+. +|-+|.|-+|+.
T Consensus 50 ~Leq~l~~L~~kt~~QiaVv~vpSt~g~~ 78 (271)
T COG1512 50 ALEQQLADLEQKTGAQIAVVTVPSTGGET 78 (271)
T ss_pred HHHHHHHHHHhccCCeEEEEEecCCCCCC
Confidence 477788888332 266777666653
No 9
>KOG2557 consensus Uncharacterized conserved protein, contains TLDc domain [Function unknown]
Probab=15.45 E-value=80 Score=33.26 Aligned_cols=21 Identities=29% Similarity=0.678 Sum_probs=17.5
Q ss_pred EEeeEECccccCCCccEEEEE
Q 016821 284 EAGWQVSPELYGDNYPRFFTY 304 (382)
Q Consensus 284 eaGW~V~P~lYGD~~pRlFty 304 (382)
.-+|-|+|++|||++.=||.-
T Consensus 278 Sq~we~~pQF~Gd~~~fLfqL 298 (427)
T KOG2557|consen 278 SQPWERYPQFYGDMKSFLFQL 298 (427)
T ss_pred cCcccccCccCCccceeeeee
Confidence 347999999999999877753
No 10
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=15.06 E-value=90 Score=28.78 Aligned_cols=34 Identities=29% Similarity=0.558 Sum_probs=0.0
Q ss_pred EEeeEECccccCCCccEEEEEEccCCCCcccccccCCCceEEecCcccc
Q 016821 284 EAGWQVSPELYGDNYPRFFTYWTTDAYQATGCYNLLCSGFVQTNNRIAI 332 (382)
Q Consensus 284 eaGW~V~P~lYGD~~pRlFtyWT~D~y~~TGCYNl~CpGFVQvs~~I~l 332 (382)
||||.|.|+ ..-|.+ ||-.....-.+..+....+
T Consensus 57 eAGw~Ve~D--------------GTtyr~-~~~~~~~~~~~g~s~~~sp 90 (150)
T PF05687_consen 57 EAGWTVEPD--------------GTTYRK-GCKPPEPMEIVGSSASASP 90 (150)
T ss_pred hCCEEEccC--------------CCeecc-CCCCCccccccccCCCCCC
Done!