Query T0600 3NJA, Chromobacterium violaceum ATCC 12472, 125 residues
Match_columns 125
No_of_seqs 125 out of 10427
Neff 10.3
Searched_HMMs 11830
Date Mon Jul 5 09:08:19 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0600.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0600.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08447 PAS_3: PAS fold; Int 99.6 6.9E-16 5.8E-20 101.9 7.2 89 29-117 1-91 (91)
2 PF08448 PAS_4: PAS fold; Int 99.6 1.9E-15 1.6E-19 99.6 6.9 110 13-125 1-110 (110)
3 PF00989 PAS: PAS fold; Inter 99.5 3E-14 2.5E-18 93.2 8.8 112 7-120 1-113 (113)
4 PF07310 PAS_5: PAS domain; I 94.4 0.11 9.1E-06 26.0 8.1 99 15-118 37-137 (137)
5 PF08670 MEKHLA: MEKHLA domain 91.4 0.31 2.6E-05 23.5 9.9 111 5-119 30-144 (148)
6 PF08348 PAS_6: YheO-like PAS 90.6 0.19 1.6E-05 24.7 5.0 44 78-123 66-109 (118)
7 PF09884 DUF2111: Uncharacteri 48.2 6.5 0.00055 16.4 3.9 37 84-121 47-83 (84)
8 PF00944 Peptidase_S3: Alphavi 17.6 24 0.002 13.4 1.8 17 98-114 107-123 (158)
9 PF08446 PAS_2: PAS fold; Int 15.7 27 0.0022 13.2 3.5 49 20-70 18-68 (108)
10 PF00949 Peptidase_S7: Peptida 15.5 14 0.0012 14.7 0.1 23 98-120 114-136 (151)
No 1
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL , FAD in the redox potential sensor NifL , and a 4-hydroxycinnamyl chromophore in photoactive yellow protein . Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses . ; PDB: 3h9w_A 3eeh_A 2vlg_C 1g28_C 1jnu_D 1n9n_A 1n9l_A 1n9o_A 2a24_A 3f1o_A ....
Probab=99.60 E-value=6.9e-16 Score=101.94 Aligned_cols=89 Identities=31% Similarity=0.547 Sum_probs=83.9
Q ss_pred EEEEEHHHHHHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCEEEEEECCCCCCCCCCCCCEEEECC
Q ss_conf 8998168987411351224-5876689998875103789999999-9875045632578604433332223550056889
Q T0600 29 RLEWSQAVHDIFGTDSATF-DATEDAYFQRVHPDDRARVRRELDR-HVLGDRPFDVEYRIVRPDGQVRELLERNHIQRQA 106 (125)
Q Consensus 29 ~~~~s~~~~~~~g~~~~~~-~~~~~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~e~r~~~~~g~~~w~~~~~~~~~d~ 106 (125)
.++||+++++++|++++++ ......|..++||+|+..+.+.+.. +...+..++.|+|+++++|+.+|+..++.+++|+
T Consensus 1 ~~~~s~~~~~i~Gy~~~e~~~~~~~~~~~~ihpeD~~~~~~~~~~~~~~~~~~~~~e~r~~~~~G~~~wv~~~~~~~~d~ 80 (91)
T PF08447_consen 1 IVYVSDAFYEILGYSPEELGKSSPDTWFDLIHPEDRERVRQAIERASLRNGEPFSFEYRIRTKDGSYRWVHSRGRPIRDE 80 (91)
T ss_dssp EEEE-THHHHHHT--HHHHTCB-HHHGGGGBGHHHHHHHHHHHHHHHHHCTTCEEEEEEEEGTTSTEEEEEEEEEEEETT
T ss_pred CEEEEHHHHHHHCCCHHHHCCCCHHHHHHEECCCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEEEEECC
T ss_conf 99980799998799989984677778976279124999999987543034552359999997999899999999999999
Q ss_pred CCCEEEEEEEE
Q ss_conf 99689998888
Q T0600 107 SGQVDHLWGTV 117 (125)
Q Consensus 107 ~g~~~~~vG~~ 117 (125)
+|++++++|++
T Consensus 81 ~g~~~~~~G~~ 91 (91)
T PF08447_consen 81 NGKPVRLVGVN 91 (91)
T ss_dssp TTCEEEEEEEE
T ss_pred CCCEEEEEEEC
T ss_conf 99999999989
No 2
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3fc7_A 3fg8_F 2r78_D 3bwl_D.
Probab=99.57 E-value=1.9e-15 Score=99.55 Aligned_cols=110 Identities=23% Similarity=0.300 Sum_probs=97.5
Q ss_pred HHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCC
Q ss_conf 98619818998648998998168987411351224587668999887510378999999998750456325786044333
Q T0600 13 ESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQ 92 (125)
Q Consensus 13 ~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~ 92 (125)
+++++++++.+|.+++.+++|+++++++|++++++.+.... +++++++...+...+..++.++.....+..+.. +|.
T Consensus 1 l~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~ 77 (110)
T PF08448_consen 1 LDNIPDGIFILDPDGRIIYANRAFEDLFGYSPEELLGKPLW--ELFPPEDREDFQAALRQALEGGKPVQFEEEIHR-DGE 77 (110)
T ss_dssp HHHSSSEEEEEETT-BEEEE-HHHHHHHT--HHHHTT-BGG--GTSCCHHHHHHHHHHHHHHHT-EEEEEEEEESS----
T ss_pred CCCCCHHHEEECCCCEEEEEHHHHHHHHCCCHHHHCCCCHH--HHCCCHHHHHHHHHHHHHHCCCCEEEEEEEEEC-CCC
T ss_conf 99987152899898959977699998859298998599447--847710002368899998646980899999952-787
Q ss_pred CCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC
Q ss_conf 322235500568899968999888873211249
Q T0600 93 VRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125)
Q Consensus 93 ~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125)
.+|+.++..|++|++|++.++++++.|||++||
T Consensus 78 ~~~~~~~~~p~~d~~g~~~~~i~~~~DiTe~kr 110 (110)
T PF08448_consen 78 ERWFEVTLSPVRDEDGEVQGVIVIARDITERKR 110 (110)
T ss_dssp EEEEEEEEEEC-CTTTTTCEEEEEEEEETT---
T ss_pred CEEEEEEEEEEECCCCCEEEEEEEEEECCHHHC
T ss_conf 199999999968799989799999997874319
No 3
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs . In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand . Probably the most surprising identification of a PAS domain was that in EAG-like K^+-channels . ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1ll8_A 1wa9_B 3gec_A 1v9z_B 1s67_U 1vb6_A 1s66_L 1v9y_B 3b33_A 2w0n_A ....
Probab=99.50 E-value=3e-14 Score=93.20 Aligned_cols=112 Identities=20% Similarity=0.290 Sum_probs=97.0
Q ss_pred HHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCEEEE
Q ss_conf 9999999861981899864899899816898741135122458766899988751037899999999875045-632578
Q T0600 7 KLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP-FDVEYR 85 (125)
Q Consensus 7 ~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~e~r 85 (125)
|+++.+++.++.|++.+|.+++.+++|+++++++|++++++.+. .+..++++++.......+...+..+.. ...+.+
T Consensus 1 e~~~~ii~~~~~~i~v~d~~g~I~~~N~a~~~l~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (113)
T PF00989_consen 1 ERFRAIIESSPDGIFVVDADGRILYVNSAAEELFGYSPEELIGK--SIFDLFHPDDREEFRDQLSQLLQQGESSESFEVR 78 (113)
T ss_dssp HHHHHHHHTTSSEEEEEETTSBEEEETHHHHHHCTS-HHHHTTS--BGGGGCSTTTHHHHHHHHHHHHHHTC-BEEEEEE
T ss_pred CHHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHCCCHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 97899977384429999595989999889999879595884799--6999458523667999999999838983468999
Q ss_pred EECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEC
Q ss_conf 60443333222355005688999689998888732
Q T0600 86 IVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDM 120 (125)
Q Consensus 86 ~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DI 120 (125)
+..++|+.+|+.+++.|+++.+|++.+++++++||
T Consensus 79 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 79 FNLRDGSIIWIEVSASPIRDEDGEIIGIIGIFRDI 113 (113)
T ss_dssp EEESTSCEEEEEEEEEEEEETTEEEEEEEEEEEEC
T ss_pred EEECCCCEEEEEEEEEEEEECCCCEEEEEEEEECC
T ss_conf 99449969999999999991999999999999919
No 4
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=94.36 E-value=0.11 Score=25.97 Aligned_cols=99 Identities=21% Similarity=0.200 Sum_probs=76.4
Q ss_pred HCCCEEEEEECCCCEEE--EEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCC
Q ss_conf 61981899864899899--8168987411351224587668999887510378999999998750456325786044333
Q T0600 15 DAGIGSWVLHMESGRLE--WSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQ 92 (125)
Q Consensus 15 ~a~~g~w~~d~~~~~~~--~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~ 92 (125)
...+.+.+.+..++..| +-..+++++|.+ +.+. .+.++..++.+..+...+..+.....+..........+|.
T Consensus 37 Lp~i~ile~~~~~~~r~RLaGt~i~~~~G~d---~tG~--~~~~l~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~~~ 111 (137)
T PF07310_consen 37 LPHIFILEVEDPGRFRYRLAGTRIVELFGRD---LTGR--RLDELFAPEDRERVFRALRAVVDEPCPVRARGRARTEDGR 111 (137)
T ss_pred HCCEEEEEEECCCCEEEEEECHHHHHHHCCC---CCCC--CHHHHCCHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCC
T ss_conf 1962999982899579999668999981998---8898--9778418166999999999998189529999787248998
Q ss_pred CCCCCCCCEEEECCCCCEEEEEEEEE
Q ss_conf 32223550056889996899988887
Q T0600 93 VRELLERNHIQRQASGQVDHLWGTVI 118 (125)
Q Consensus 93 ~~w~~~~~~~~~d~~g~~~~~vG~~~ 118 (125)
...++.-.-|+.++.|.+.+++|.+.
T Consensus 112 ~~~~e~l~LPL~~~~g~v~~ilG~l~ 137 (137)
T PF07310_consen 112 YLRFERLLLPLRDDDGEVDRILGALA 137 (137)
T ss_pred EEEEEEEECCCCCCCCCCCEEEEECC
T ss_conf 33556897235889998067977239
No 5
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=91.36 E-value=0.31 Score=23.52 Aligned_cols=111 Identities=12% Similarity=0.038 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHCCCEEEEEECCC--CEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf 89999999986198189986489--9899816898741135122458766899988751037899999999875045632
Q T0600 5 AEKLLHTAESDAGIGSWVLHMES--GRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDV 82 (125)
Q Consensus 5 SE~~l~~~~~~a~~g~w~~d~~~--~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 82 (125)
+|+.++.+.. ++..+...+.+. ..+|.|.+..+|++++-.++.+.+... ...+..++.....+..+.+.|-....
T Consensus 30 ~~~~~~~L~~-~p~ail~h~~~~dPvf~yaN~aaL~m~E~tw~~l~~lpsr~--tae~~~r~~r~~~l~~v~~qG~~~~y 106 (148)
T PF08670_consen 30 SEELAKALWH-APFAILCHSTKADPVFIYANQAALDMWETTWDELQDLPSRK--TAEEPERKERQSLLDQVMQQGYACLY 106 (148)
T ss_pred HHHHHHHHHC-CCCEEEECCCCCCCEEEECCHHHHHHHCCCHHHHHCCCHHH--CCCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 6899999971-99779984788897687610899999718899984697765--16935089999889999981850078
Q ss_pred E-EEEECCCCCCCCCCCC-CEEEECCCCCEEEEEEEEEE
Q ss_conf 5-7860443333222355-00568899968999888873
Q T0600 83 E-YRIVRPDGQVRELLER-NHIQRQASGQVDHLWGTVID 119 (125)
Q Consensus 83 e-~r~~~~~g~~~w~~~~-~~~~~d~~g~~~~~vG~~~D 119 (125)
- .| ....|+.++++-- +=-+.|++|.+.+.-.++.+
T Consensus 107 ~GIR-iss~Grrf~ie~A~~W~v~d~~g~~~gqAa~F~n 144 (148)
T PF08670_consen 107 SGIR-ISSMGRRFSIEQAVAWKVLDEDGNYHGQAAMFSN 144 (148)
T ss_pred CEEE-ECCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEE
T ss_conf 8578-8289976898026998788578888999999611
No 6
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=90.57 E-value=0.19 Score=24.66 Aligned_cols=44 Identities=20% Similarity=0.204 Sum_probs=36.9
Q ss_pred CCCCEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHH
Q ss_conf 4563257860443333222355005688999689998888732112
Q T0600 78 RPFDVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEH 123 (125)
Q Consensus 78 ~~~~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITer 123 (125)
...-.-|..+.++| +-++....+++|++|+++++.++-.|+|.-
T Consensus 66 ~~~~~~Y~~~~~dG--r~lkSsT~~ird~~g~~iG~LCIN~D~s~~ 109 (118)
T PF08348_consen 66 EDDIVNYKTRTKDG--RTLKSSTIFIRDENGKPIGALCINFDISAL 109 (118)
T ss_pred CCCCCCEEEECCCC--CEEEEEEEEEECCCCCEEEEEEEEECCHHH
T ss_conf 86144605678999--898999999999999999999997576789
No 7
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111)
Probab=48.24 E-value=6.5 Score=16.45 Aligned_cols=37 Identities=22% Similarity=0.243 Sum_probs=29.9
Q ss_pred EEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH
Q ss_conf 78604433332223550056889996899988887321
Q T0600 84 YRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125)
Q Consensus 84 ~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125)
.+.....|.+.=+-+-..|+++.+|+++..+|++ |+|
T Consensus 47 ~r~~p~~G~Y~G~pVvVaPI~~~dg~viaAiGIV-Dlt 83 (84)
T PF09884_consen 47 IRVTPISGPYKGVPVVVAPIKDEDGKVIAAIGIV-DLT 83 (84)
T ss_pred EEECCCCCCCCCCEEEEEEEECCCCCEEEEEEEE-ECC
T ss_conf 9845687643793389986665899699998998-715
No 8
>PF00944 Peptidase_S3: Alphavirus core protein ; InterPro: IPR000930 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. Togavirin, also known as Sindbis virus core endopeptidase, is a serine protease resident at the N-terminus of the p130 polyprotein of togaviruses . The endopeptidase signature identifies the peptidase as belonging to the MEROPS peptidase family S3 (togavirin family, clan PA(S)). The polyprotein also includes structural proteins for the nucleocapsid core and for the glycoprotein spikes . Togavirin is only active while part of the polyprotein, cleavage at a Trp-Ser bond resulting in total lack of activity . Mutagenesis studies have identified the location of the His-Asp-Ser catalytic triad, and X-ray studies have revealed the protein fold to be similar to that of chymotrypsin , .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 1wyk_A 1svp_A 1kxd_A 1ld4_A 1kxf_A 1z8y_Q 2snw_A 1kxb_A 1kxc_A 2snv_A ....
Probab=17.63 E-value=24 Score=13.45 Aligned_cols=17 Identities=18% Similarity=0.151 Sum_probs=14.0
Q ss_pred CCCEEEECCCCCEEEEE
Q ss_conf 55005688999689998
Q T0600 98 ERNHIQRQASGQVDHLW 114 (125)
Q Consensus 98 ~~~~~~~d~~g~~~~~v 114 (125)
.+++|+.|..|+++.++
T Consensus 107 DSGRpi~DN~GrVVaIV 123 (158)
T PF00944_consen 107 DSGRPILDNSGRVVAIV 123 (158)
T ss_dssp ----EEE-----EEEEE
T ss_pred CCCCCCCCCCCCEEEEE
T ss_conf 88982276888699999
No 9
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0007600 sensory perception, 0018298 protein-chromophore linkage, 0045449 regulation of transcription; PDB: 1ztu_A 2o9b_A 2o9c_A 2ool_A 2vea_A 3c2w_F.
Probab=15.66 E-value=27 Score=13.17 Aligned_cols=49 Identities=16% Similarity=0.267 Sum_probs=31.6
Q ss_pred EEEEECCC-CEEEEEHHHHHHHCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89986489-9899816898741135-122458766899988751037899999
Q T0600 20 SWVLHMES-GRLEWSQAVHDIFGTD-SATFDATEDAYFQRVHPDDRARVRREL 70 (125)
Q Consensus 20 ~w~~d~~~-~~~~~s~~~~~~~g~~-~~~~~~~~~~~~~~i~~~~~~~~~~~~ 70 (125)
+...|..+ ....+|.++..++|.+ ++...+. .+.+++.++....+...+
T Consensus 18 LLa~d~~~~~I~~~SeN~~~~lg~~~~~~llG~--~l~~ll~~~~~~~l~~~~ 68 (108)
T PF08446_consen 18 LLALDPPDLRIIQASENIADLLGIPPPEDLLGR--PLSDLLSPESAHRLREAL 68 (108)
T ss_dssp EEEEETTTTEEEEEETTHHHHHSS--HCCHTT---CHHHHSCCCCHHHHHHHC
T ss_pred EEEEECCCCEEEEECCCHHHHHCCCCHHHHCCC--CHHHHHCHHHHHHHHHHH
T ss_conf 999987898899986698998587320645189--899985977899999865
No 10
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This signature identifies serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N-terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase , , .; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2bhr_B 2fom_B 2bmf_B 2vbc_A 3e90_D 2ggv_B 2fp7_B 2ijo_B 1bef_A 2qid_A ....
Probab=15.54 E-value=14 Score=14.72 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=17.7
Q ss_pred CCCEEEECCCCCEEEEEEEEEEC
Q ss_conf 55005688999689998888732
Q T0600 98 ERNHIQRQASGQVDHLWGTVIDM 120 (125)
Q Consensus 98 ~~~~~~~d~~g~~~~~vG~~~DI 120 (125)
.++.|++|.+|+++++.|-...+
T Consensus 114 sSGSPI~N~~g~vvGlYg~g~~~ 136 (151)
T PF00949_consen 114 SSGSPIFNKNGQVVGLYGNGVVI 136 (151)
T ss_dssp -----EEE----B--------B-
T ss_pred CCCCCEECCCCCEEEEEECEEEE
T ss_conf 97881587899799998450885
Done!