Query 040197
Match_columns 416
No_of_seqs 179 out of 389
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 06:03:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040197.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040197hhsearch_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 9.7E-83 2.1E-87 609.1 24.7 226 180-409 1-229 (229)
2 PF14365 DUF4409: Domain of un 100.0 3.1E-35 6.8E-40 254.3 7.0 112 54-175 1-117 (117)
3 PF07653 SH3_2: Variant SH3 do 62.2 7.9 0.00017 28.5 2.7 36 274-314 16-51 (55)
4 PTZ00459 mucin-associated surf 45.8 12 0.00026 37.6 1.8 20 1-20 1-21 (291)
5 PF14604 SH3_9: Variant SH3 do 34.1 44 0.00094 24.2 2.7 21 293-314 27-47 (49)
6 PF00018 SH3_1: SH3 domain; I 29.6 75 0.0016 22.5 3.3 34 274-312 14-48 (48)
7 COG4913 Uncharacterized protei 22.4 51 0.0011 37.4 1.8 36 35-74 869-904 (1104)
8 PF07204 Orthoreo_P10: Orthore 18.4 1E+02 0.0022 26.1 2.4 21 27-47 66-86 (98)
9 PF12273 RCR: Chitin synthesis 18.2 80 0.0017 27.5 1.9 9 9-17 9-17 (130)
10 COG1512 Beta-propeller domains 17.2 1.4E+02 0.003 29.9 3.5 34 28-61 41-77 (271)
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=9.7e-83 Score=609.11 Aligned_cols=226 Identities=47% Similarity=0.963 Sum_probs=213.7
Q ss_pred eeeeEEEEEeecCCccCCCCceEEEEEeeeCC-CCccceEEEeEEEcCceeCCCceEEEEEEeeCCCCccCccCCCCCcc
Q 040197 180 FSGAKGDIKVWNPFVESDDEYSTSRVSLQSGP-YYDFESIESGWAVNPRVYGDRKTRLFVYWTADASKTTGCFDVTCPGF 258 (416)
Q Consensus 180 ~~G~~a~i~V~~P~v~~~~q~S~s~iwi~~g~-~~~~n~IeaGW~V~P~lYgD~~~rlf~yWt~d~y~~tGCyNl~CpGF 258 (416)
|||++|+||||+|+|+.++|||++||||++++ .+.+|+|||||+|+|+||||++||||+|||+|+|++|||||++||||
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 79999999999999998789999999999999 78899999999999999999999999999999999999999999999
Q ss_pred EEeecccccCcccccccCCCCceeEEEEEEeeCCCCCCeEEEeCCcceeeeeCccccccCcCCceEEEEeeEEeccCCCC
Q 040197 259 VQVSNEIALGAAIYPISNPNGLPYQITIYLFKDPDTGNWWMQYGEKINVGYWPPKLFSLLPSGAESAEWGGEVYSSKLEN 338 (416)
Q Consensus 259 VQvs~~i~lG~~i~pvS~~gG~q~~i~i~I~kD~~tgnWWL~~g~~~~IGYWP~sLF~~L~~~A~~V~wGGeV~~~~~~~ 338 (416)
|||+++|+||++|+|+|+++|+|++|+|+|+||+.+|||||+++++ .|||||++||++|+++|+.|+|||||++++.
T Consensus 81 Vq~s~~i~~G~~~~~~S~~gG~q~~i~~~i~kD~~~gnWWL~~~~~-~IGYwP~sLF~~l~~~A~~v~wGGeV~~~~~-- 157 (229)
T PF03080_consen 81 VQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYGGE-PIGYWPKSLFTSLADGATEVEWGGEVYSPPG-- 157 (229)
T ss_pred EEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEecc-eeeeehHHhhhhhhcCceEEEEEEEEeCCCC--
Confidence 9999999999999999999999999999999999999999999876 7999999999999999999999999998874
Q ss_pred CCCCCCCCCCCCCCCCCCCceEEEeccEEEcCCCCccCCc--ceeecccCCCceEEeecCccCCCCEEEEeCC
Q 040197 339 PPHTATAMGNGHFPDYISGNSGSVKRIRILDNSRTLKFPE--WVYSYTDQYNCYGVDYVGDYIVDPEFYFGGP 409 (416)
Q Consensus 339 ~~~tsp~MGSG~fp~~g~~~Aay~~ni~ivd~~~~~~~p~--~~~~~~d~p~CY~v~~~~~~~~~~~f~yGGP 409 (416)
+||+|||||||||++++++|||||||+++|.+++.+.+. .+++++|+|+||++....+..++.+||||||
T Consensus 158 -~~~sppMGSG~fp~~g~~~aAy~~~i~~~d~~~~~~~~~~~~~~~~~~~~~CY~~~~~~~~~~g~~f~yGGP 229 (229)
T PF03080_consen 158 -RHTSPPMGSGHFPSEGFGKAAYFRNIQVVDSNGQFVDPNDDLLEVFADNPSCYDVSYIGDGDWGYYFFYGGP 229 (229)
T ss_pred -CCCCCCccCCcCCCCCCCccEEEEEEEEEcCCCCCcCCcccceeEccCCCCceeEeeccCCCcccEEEeeCC
Confidence 589999999999999999999999999999999988774 5778999999999998654224499999999
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=3.1e-35 Score=254.35 Aligned_cols=112 Identities=49% Similarity=0.864 Sum_probs=87.8
Q ss_pred eEECCCCCeEeeeecCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCcccccccccccccCCCCCcceeeeeec
Q 040197 54 SIQSEDGDIIDCVCIYKQPAFDHPALKDHIIQMTPTYDPNGKTVTTGSADTETSTTVMASQIWRKNGSCPEGTIPVRRIH 133 (416)
Q Consensus 54 ti~s~dGdi~DCVdi~kQPAfdHPlLKnH~iQ~~Ps~~p~~~~~~~~~~~~~~~~~~~~~q~~~~~~~CP~GTVPIrR~~ 133 (416)
||+|+|||||||||||||||||||||| ++||+|++.|+....... . +.+... .+|+|+++++||+|||||||++
T Consensus 1 tI~s~dGdi~DCVdi~kQPAfdHPlLK--~~q~~Ps~~p~~~~~~~~-~--~~~~~~-~~q~w~~~g~CP~GTVPIrRtt 74 (117)
T PF14365_consen 1 TIQSPDGDIIDCVDIYKQPAFDHPLLK--NIQMRPSSYPKGISSKES-S--SSSSKP-ISQLWHQNGSCPEGTVPIRRTT 74 (117)
T ss_pred CccCCCCCeEeCEeccccccccCchhc--CcccCcchhhhhcccccc-c--cccccc-chhhhccccCCcCCceeeecCC
Confidence 699999999999999999999999999 478999999987654311 1 122333 7899999999999999999999
Q ss_pred -----cCCCccccCCCCCCccccccccccCCCCCCCCCCceEEEEEE
Q 040197 134 -----NSNSFEGYGRKQPSFYHRVKQLNDIKQPNLQQPNHSKAILLT 175 (416)
Q Consensus 134 -----ra~s~~~f~~k~~~~~~~~~~~n~~~~~~~~~~~h~~a~~~~ 175 (416)
|++|+.+||+|.++...... ....+...++|+||++++
T Consensus 75 ~~dllr~~s~~~~g~k~~~~~~~~~----~~~~~~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 75 KEDLLRAKSFKRFGRKPPSSISSPS----SNKPDISSNGHEHAIAYV 117 (117)
T ss_pred HHHHhhhhhHHHcCCcCCCCcCCcc----ccCCCCCCCCCceEEEeC
Confidence 99999999999875432211 001224568999999974
No 3
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=62.16 E-value=7.9 Score=28.48 Aligned_cols=36 Identities=19% Similarity=0.537 Sum_probs=22.9
Q ss_pred ccCCCCceeEEEEEEeeCCCCCCeEEEeCCcceeeeeCccc
Q 040197 274 ISNPNGLPYQITIYLFKDPDTGNWWMQYGEKINVGYWPPKL 314 (416)
Q Consensus 274 vS~~gG~q~~i~i~I~kD~~tgnWWL~~g~~~~IGYWP~sL 314 (416)
+|.--|... .|.++...++||+-..++ ..||.|++.
T Consensus 16 Ls~~~Gd~i----~v~~~~~~~~ww~~~~~g-~~G~~P~~~ 51 (55)
T PF07653_consen 16 LSFKKGDVI----EVLGEKDDDGWWLGENNG-RRGWFPSSY 51 (55)
T ss_dssp -EB-TTEEE----EEEEEECSTSEEEEEETT-EEEEEEGGG
T ss_pred eEEecCCEE----EEEEeecCCCEEEEEECC-cEEEEcHHH
Confidence 455555543 344566788999876644 489999875
No 4
>PTZ00459 mucin-associated surface protein (MASP); Provisional
Probab=45.85 E-value=12 Score=37.57 Aligned_cols=20 Identities=15% Similarity=0.257 Sum_probs=15.6
Q ss_pred CcccchhHHHHHH-HHHHHhh
Q 040197 1 MEYILGCKGFIIL-LGVTFVI 20 (416)
Q Consensus 1 ~~~~~~~~~~~~~-l~~~~~l 20 (416)
|-|||.-||+++| ||+|++-
T Consensus 1 MaMmMTGRVLLVCALCVLWCg 21 (291)
T PTZ00459 1 MAMMMTGRVLLVCALCVLWCG 21 (291)
T ss_pred CccchhchHHHHHHHHHHhcC
Confidence 8899999998876 6666543
No 5
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=34.05 E-value=44 Score=24.18 Aligned_cols=21 Identities=19% Similarity=0.711 Sum_probs=15.7
Q ss_pred CCCCeEEEeCCcceeeeeCccc
Q 040197 293 DTGNWWMQYGEKINVGYWPPKL 314 (416)
Q Consensus 293 ~tgnWWL~~g~~~~IGYWP~sL 314 (416)
...+||+--.+. ..||+|++-
T Consensus 27 ~~~~W~~g~~~g-~~G~~P~~y 47 (49)
T PF14604_consen 27 SDDGWWYGRNTG-RTGLFPANY 47 (49)
T ss_dssp SSTSEEEEEETT-EEEEEEGGG
T ss_pred CCCCEEEEEECC-EEEEECHHh
Confidence 578899866533 599999863
No 6
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=29.57 E-value=75 Score=22.46 Aligned_cols=34 Identities=21% Similarity=0.471 Sum_probs=19.3
Q ss_pred ccCCCCceeEEEEEEeeCCCCCCeEEEeCCc-ceeeeeCc
Q 040197 274 ISNPNGLPYQITIYLFKDPDTGNWWMQYGEK-INVGYWPP 312 (416)
Q Consensus 274 vS~~gG~q~~i~i~I~kD~~tgnWWL~~g~~-~~IGYWP~ 312 (416)
+|..-|.... |.++ .+..||+-.... ...||.|+
T Consensus 14 Ls~~~Gd~i~----v~~~-~~~~Ww~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 14 LSFKKGDIIE----VLEK-SDDGWWKVRNESTGKEGWVPS 48 (48)
T ss_dssp SEB-TTEEEE----EEEE-SSSSEEEEEETTTTEEEEEEG
T ss_pred EeEECCCEEE----EEEe-cCCCEEEEEECCCCcEEEeeC
Confidence 3444455443 3343 344899876432 35999996
No 7
>COG4913 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.45 E-value=51 Score=37.40 Aligned_cols=36 Identities=19% Similarity=0.327 Sum_probs=26.8
Q ss_pred hhHHHHHhhhhcCCCCcceeEECCCCCeEeeeecCCCCCC
Q 040197 35 SSYIGRKVNHLNSNGNVVKSIQSEDGDIIDCVCIYKQPAF 74 (416)
Q Consensus 35 ~~ei~~~L~~lnk~~p~vkti~s~dGdi~DCVdi~kQPAf 74 (416)
..+||..++.||. .+.-|.-..|. |=||||-|||.-
T Consensus 869 r~~IeERIe~IN~---SL~~vdfn~gR-ylhIdi~kQp~p 904 (1104)
T COG4913 869 RALIEERIEAIND---SLRRVDFNSGR-YLHIDIAKQPVP 904 (1104)
T ss_pred HHHHHHHHHHHHH---HHhhccccCCc-eEEeecccCCCc
Confidence 6789999999997 34445444555 449999999873
No 8
>PF07204 Orthoreo_P10: Orthoreovirus membrane fusion protein p10; InterPro: IPR009854 This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction [].
Probab=18.43 E-value=1e+02 Score=26.08 Aligned_cols=21 Identities=10% Similarity=0.099 Sum_probs=15.7
Q ss_pred eeeeeccchhHHHHHhhhhcC
Q 040197 27 GEIISGQKSSYIGRKVNHLNS 47 (416)
Q Consensus 27 ~~~~~~~~~~ei~~~L~~lnk 47 (416)
.+....+...+-+|+|-.||+
T Consensus 66 ~K~K~~~~r~~~~reLval~~ 86 (98)
T PF07204_consen 66 AKHKTSAARNTFHRELVALTR 86 (98)
T ss_pred hhhhhHhhhhHHHHHHHHHhc
Confidence 344445567888999999998
No 9
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=18.15 E-value=80 Score=27.55 Aligned_cols=9 Identities=33% Similarity=0.047 Sum_probs=3.2
Q ss_pred HHHHHHHHH
Q 040197 9 GFIILLGVT 17 (416)
Q Consensus 9 ~~~~~l~~~ 17 (416)
|+++||++|
T Consensus 9 i~~i~l~~~ 17 (130)
T PF12273_consen 9 IVAILLFLF 17 (130)
T ss_pred HHHHHHHHH
Confidence 333333333
No 10
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=17.15 E-value=1.4e+02 Score=29.86 Aligned_cols=34 Identities=15% Similarity=0.324 Sum_probs=21.3
Q ss_pred eeeeccchhHHHHHhhhhcCCCC---cceeEECCCCC
Q 040197 28 EIISGQKSSYIGRKVNHLNSNGN---VVKSIQSEDGD 61 (416)
Q Consensus 28 ~~~~~~~~~ei~~~L~~lnk~~p---~vkti~s~dGd 61 (416)
..++.++...+|++|+.|-+... +|-+|.|-+|+
T Consensus 41 ~~Ls~~e~~~Leq~l~~L~~kt~~QiaVv~vpSt~g~ 77 (271)
T COG1512 41 GTLSAAERGALEQQLADLEQKTGAQIAVVTVPSTGGE 77 (271)
T ss_pred ccCChhhHHHHHHHHHHHHhccCCeEEEEEecCCCCC
Confidence 34556668889999999944222 25556555554
Done!