Query 031133
Match_columns 165
No_of_seqs 171 out of 413
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:42:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031133.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031133hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14009 DUF4228: Domain of un 100.0 3.8E-38 8.3E-43 244.8 12.7 153 1-163 1-181 (181)
2 PRK08053 sulfur carrier protei 73.9 9.3 0.0002 25.3 4.7 55 15-69 3-62 (66)
3 PRK06944 sulfur carrier protei 72.0 14 0.00031 23.9 5.2 54 15-68 3-60 (65)
4 PF02824 TGS: TGS domain; Int 70.9 8.5 0.00019 25.1 3.9 25 12-36 1-25 (60)
5 TIGR01683 thiS thiamine biosyn 59.6 23 0.00049 23.1 4.3 55 15-69 1-60 (64)
6 PRK05659 sulfur carrier protei 55.0 13 0.00029 24.1 2.6 22 15-36 3-24 (66)
7 PF01402 RHH_1: Ribbon-helix-h 54.8 26 0.00057 20.3 3.6 33 100-133 1-34 (39)
8 PRK07440 hypothetical protein; 51.3 17 0.00037 24.6 2.7 54 14-67 6-64 (70)
9 cd00565 ThiS ThiaminS ubiquiti 50.6 48 0.001 21.5 4.8 23 15-37 2-24 (65)
10 PRK05863 sulfur carrier protei 39.7 33 0.00071 22.6 2.6 22 15-36 3-24 (65)
11 PRK06083 sulfur carrier protei 39.7 31 0.00067 24.3 2.6 22 15-36 21-42 (84)
12 cd01668 TGS_RelA_SpoT TGS_RelA 39.4 42 0.0009 20.7 3.0 24 13-36 2-25 (60)
13 PF00812 Ephrin: Ephrin; Inte 38.1 43 0.00094 26.1 3.4 24 49-72 96-119 (145)
14 cd00178 STI Soybean trypsin in 38.0 24 0.00052 27.9 2.0 18 54-71 6-23 (172)
15 PF00197 Kunitz_legume: Trypsi 37.9 28 0.0006 27.6 2.4 19 54-72 6-24 (176)
16 PRK07696 sulfur carrier protei 34.1 45 0.00097 22.2 2.6 22 15-36 3-25 (67)
17 PRK08364 sulfur carrier protei 33.7 1.4E+02 0.0029 19.9 5.0 51 16-69 8-66 (70)
18 PRK06437 hypothetical protein; 30.4 1.6E+02 0.0035 19.4 4.9 52 15-69 5-63 (67)
19 smart00452 STI Soybean trypsin 28.0 44 0.00096 26.5 2.0 18 54-71 5-22 (172)
20 PF00325 Crp: Bacterial regula 27.8 56 0.0012 19.1 1.9 28 103-133 1-28 (32)
21 PF13545 HTH_Crp_2: Crp-like h 27.4 1.2E+02 0.0025 19.7 3.7 38 96-136 20-57 (76)
22 cd02980 TRX_Fd_family Thioredo 26.7 75 0.0016 20.7 2.7 33 1-36 44-76 (77)
23 COG5568 Uncharacterized small 25.9 58 0.0013 23.2 2.0 18 22-39 23-40 (85)
24 PRK06488 sulfur carrier protei 25.7 75 0.0016 20.6 2.5 54 15-69 3-61 (65)
25 PHA02843 hypothetical protein; 23.8 32 0.0007 23.2 0.4 14 1-14 1-14 (73)
26 COG2104 ThiS Sulfur transfer p 22.6 1.2E+02 0.0026 20.6 3.1 24 14-37 4-27 (68)
27 PF05595 DUF771: Domain of unk 21.1 1.8E+02 0.004 20.4 4.0 31 102-132 3-34 (91)
28 TIGR03697 NtcA_cyano global ni 20.4 88 0.0019 23.7 2.4 38 96-136 135-172 (193)
29 cd01775 CYR1_RA Ubiquitin doma 20.2 1.9E+02 0.0041 21.2 3.9 32 11-42 4-37 (97)
No 1
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=100.00 E-value=3.8e-38 Score=244.80 Aligned_cols=153 Identities=35% Similarity=0.603 Sum_probs=112.8
Q ss_pred CCCcccC------CCceeEEEecCCcEEEEeCCccHHHHHhhcCCcEEeCCC-----CCccCCCCCCccCCCCeEEEeeC
Q 031133 1 MGNCLML------EEKVIKVMKTDGKILEYKAPMKVQDVLAEFAGHAISDSF-----PEIRHLMPDFKLLGGNLYFLVPV 69 (165)
Q Consensus 1 MGNC~~~------~~~~iKV~~~dG~v~e~~~Pv~a~evl~~~Pgh~v~~s~-----~~~~~L~~de~L~~G~lYfLlP~ 69 (165)
||||++. ..++||||++||+|++|+.||+|+|||.+|||||||++. ..+++|+||++|++|++|||||.
T Consensus 1 MGn~~~~~~~~~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h~v~~~~~~~~~~~~~~l~~d~~L~~G~~Y~llP~ 80 (181)
T PF14009_consen 1 MGNCVSCCLASSSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGHFVCDSDSFRFGRRIKPLPPDEELQPGQIYFLLPM 80 (181)
T ss_pred CCCcccccccccCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCCEEeccccccCCCcccCCCccCeecCCCEEEEEEc
Confidence 9999974 689999999999999999999999999999999998774 24689999999999999999999
Q ss_pred CCCCCcc---ccceeecchhhhh--------------cCcCCCCceEEEEEEEcHHHHHHHHHHhcCCcccHHHHHHHHh
Q 031133 70 PLPSPKV---EKKKVRFSEEEAR--------------DGAKETSSVVRIKVVISKQELQDLQMLQKGGVVSVQDVASWLQ 132 (165)
Q Consensus 70 ~~~~~~~---~~~~vr~~~~~~e--------------~~~~~~~~~~rvKi~itk~~l~~l~~~~~~~~~s~e~~l~~l~ 132 (165)
++..... ....+.+...... .....++|.++||++++|+||++ ++.++ +.+++++.+.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~rvki~isk~el~~--~l~~~---s~~~~~~~~~ 155 (181)
T PF14009_consen 81 SRLQSVLSASDMASLASSASSASSSSSARKSSSRPFSRSRSSNGGVVRVKIVISKEELEE--LLSEG---SDEEMLSESC 155 (181)
T ss_pred cccCcccccchhcccccchhhccccccccccccccccccccccCcccccccccCHHHHHH--HHhcc---ccchhhhhhh
Confidence 9865421 1222222221110 11355678999999999999999 55533 4455555544
Q ss_pred hcccccccccccccCCCCCCCccccCCCCCC
Q 031133 133 GKQSTNSQAVGFQDGGNNNEGWKPELESIPE 163 (165)
Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~WrP~LeSIpE 163 (165)
........ ......++|||+||||||
T Consensus 156 ~~~~~~~~-----~~~~~~~~WrP~LesI~E 181 (181)
T PF14009_consen 156 RRPRRRSS-----RRGSRSRSWRPALESIPE 181 (181)
T ss_pred cccccccc-----ccCCCCCCccCCCCCcCc
Confidence 43221100 123456899999999998
No 2
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=73.87 E-value=9.3 Score=25.27 Aligned_cols=55 Identities=18% Similarity=0.248 Sum_probs=34.1
Q ss_pred EecCCcEEEEeCCccHHHHHhh----cCCcEEeCCCCCc-cCCCCCCccCCCCeEEEeeC
Q 031133 15 MKTDGKILEYKAPMKVQDVLAE----FAGHAISDSFPEI-RHLMPDFKLLGGNLYFLVPV 69 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~----~Pgh~v~~s~~~~-~~L~~de~L~~G~lYfLlP~ 69 (165)
+..||+..++..++++.+++.. +++-+|.--...+ +.-.++..|..|--..+++.
T Consensus 3 i~vNg~~~~~~~~~tl~~ll~~l~~~~~~vaVavN~~iv~r~~w~~~~L~~gD~Ieii~~ 62 (66)
T PRK08053 3 ILFNDQPMQCAAGQTVHELLEQLNQLQPGAALAINQQIIPREQWAQHIVQDGDQILLFQV 62 (66)
T ss_pred EEECCeEEEcCCCCCHHHHHHHcCCCCCcEEEEECCEEeChHHcCccccCCCCEEEEEEE
Confidence 5789999999999999999975 3333332111111 23345556777755555554
No 3
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=72.01 E-value=14 Score=23.85 Aligned_cols=54 Identities=20% Similarity=0.202 Sum_probs=33.2
Q ss_pred EecCCcEEEEeCCccHHHHHhhc---CCcEEeCCCCCc-cCCCCCCccCCCCeEEEee
Q 031133 15 MKTDGKILEYKAPMKVQDVLAEF---AGHAISDSFPEI-RHLMPDFKLLGGNLYFLVP 68 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~~---Pgh~v~~s~~~~-~~L~~de~L~~G~lYfLlP 68 (165)
|..||+..++....++++++..+ |+..+.--...+ +.-..+..|..|--.-++|
T Consensus 3 i~vNg~~~~~~~~~tl~~ll~~l~~~~~~~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 3 IQLNQQTLSLPDGATVADALAAYGARPPFAVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred EEECCEEEECCCCCcHHHHHHhhCCCCCeEEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 57899999999999999999754 333331111111 2234466677775444444
No 4
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=70.92 E-value=8.5 Score=25.13 Aligned_cols=25 Identities=36% Similarity=0.375 Sum_probs=22.4
Q ss_pred eEEEecCCcEEEEeCCccHHHHHhh
Q 031133 12 IKVMKTDGKILEYKAPMKVQDVLAE 36 (165)
Q Consensus 12 iKV~~~dG~v~e~~~Pv~a~evl~~ 36 (165)
|+|..+||++.+|...+|+.|+-..
T Consensus 1 I~v~lpdG~~~~~~~g~T~~d~A~~ 25 (60)
T PF02824_consen 1 IRVYLPDGSIKELPEGSTVLDVAYS 25 (60)
T ss_dssp EEEEETTSCEEEEETTBBHHHHHHH
T ss_pred CEEECCCCCeeeCCCCCCHHHHHHH
Confidence 6788899999999999999998765
No 5
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=59.62 E-value=23 Score=23.10 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=32.8
Q ss_pred EecCCcEEEEeCCccHHHHHhhcC---CcEE--eCCCCCccCCCCCCccCCCCeEEEeeC
Q 031133 15 MKTDGKILEYKAPMKVQDVLAEFA---GHAI--SDSFPEIRHLMPDFKLLGGNLYFLVPV 69 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~~P---gh~v--~~s~~~~~~L~~de~L~~G~lYfLlP~ 69 (165)
+..||+..++..+.++.+++...- ..++ .+..-..+.-.++..|..|--.-++|.
T Consensus 1 i~iNg~~~~~~~~~tv~~ll~~l~~~~~~v~v~vN~~iv~~~~~~~~~L~~gD~veii~~ 60 (64)
T TIGR01683 1 ITVNGEPVEVEDGLTLAALLESLGLDPRRVAVAVNGEIVPRSEWDDTILKEGDRIEIVTF 60 (64)
T ss_pred CEECCeEEEcCCCCcHHHHHHHcCCCCCeEEEEECCEEcCHHHcCceecCCCCEEEEEEe
Confidence 467999999999999999998642 2222 111111112234456777755555554
No 6
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=55.04 E-value=13 Score=24.13 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=20.1
Q ss_pred EecCCcEEEEeCCccHHHHHhh
Q 031133 15 MKTDGKILEYKAPMKVQDVLAE 36 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~ 36 (165)
+..||+..++..+.++++++..
T Consensus 3 i~vNG~~~~~~~~~tl~~lL~~ 24 (66)
T PRK05659 3 IQLNGEPRELPDGESVAALLAR 24 (66)
T ss_pred EEECCeEEEcCCCCCHHHHHHh
Confidence 6789999999999999999975
No 7
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=54.83 E-value=26 Score=20.28 Aligned_cols=33 Identities=21% Similarity=0.199 Sum_probs=25.7
Q ss_pred EEEEEEcHHHHHHHHHHhc-CCcccHHHHHHHHhh
Q 031133 100 RIKVVISKQELQDLQMLQK-GGVVSVQDVASWLQG 133 (165)
Q Consensus 100 rvKi~itk~~l~~l~~~~~-~~~~s~e~~l~~l~~ 133 (165)
||.|.|+.++.++|-.+.+ .| .|..+++..+..
T Consensus 1 Riti~l~~~~~~~l~~~a~~~g-~s~s~~ir~ai~ 34 (39)
T PF01402_consen 1 RITIRLPDELYERLDELAKELG-RSRSELIREAIR 34 (39)
T ss_dssp EEEEEEEHHHHHHHHHHHHHHT-SSHHHHHHHHHH
T ss_pred CeEEEeCHHHHHHHHHHHHHHC-cCHHHHHHHHHH
Confidence 7889999999999777763 35 788888777654
No 8
>PRK07440 hypothetical protein; Provisional
Probab=51.27 E-value=17 Score=24.56 Aligned_cols=54 Identities=15% Similarity=0.250 Sum_probs=32.6
Q ss_pred EEecCCcEEEEeCCccHHHHHhh--cCCc--EEe-CCCCCccCCCCCCccCCCCeEEEe
Q 031133 14 VMKTDGKILEYKAPMKVQDVLAE--FAGH--AIS-DSFPEIRHLMPDFKLLGGNLYFLV 67 (165)
Q Consensus 14 V~~~dG~v~e~~~Pv~a~evl~~--~Pgh--~v~-~s~~~~~~L~~de~L~~G~lYfLl 67 (165)
-+..||+..++..+.++.+++.+ ++.. +|. +..-..+...++..|..|--.-++
T Consensus 6 ~i~vNG~~~~~~~~~tl~~lL~~l~~~~~~vav~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 6 TLQVNGETRTCSSGTSLPDLLQQLGFNPRLVAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred EEEECCEEEEcCCCCCHHHHHHHcCCCCCeEEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 46679999999999999999976 3322 221 221111334456666666444443
No 9
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=50.61 E-value=48 Score=21.52 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=20.4
Q ss_pred EecCCcEEEEeCCccHHHHHhhc
Q 031133 15 MKTDGKILEYKAPMKVQDVLAEF 37 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~~ 37 (165)
+..||+..++..+.++.+++...
T Consensus 2 i~iNg~~~~~~~~~tv~~ll~~l 24 (65)
T cd00565 2 ITVNGEPREVEEGATLAELLEEL 24 (65)
T ss_pred EEECCeEEEcCCCCCHHHHHHHc
Confidence 56799999999999999999764
No 10
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=39.66 E-value=33 Score=22.58 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=19.9
Q ss_pred EecCCcEEEEeCCccHHHHHhh
Q 031133 15 MKTDGKILEYKAPMKVQDVLAE 36 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~ 36 (165)
+..||+..++..+.++.+++..
T Consensus 3 i~vNG~~~~~~~~~tl~~ll~~ 24 (65)
T PRK05863 3 VVVNEEQVEVDEQTTVAALLDS 24 (65)
T ss_pred EEECCEEEEcCCCCcHHHHHHH
Confidence 5679999999999999999976
No 11
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=39.65 E-value=31 Score=24.33 Aligned_cols=22 Identities=5% Similarity=0.285 Sum_probs=20.3
Q ss_pred EecCCcEEEEeCCccHHHHHhh
Q 031133 15 MKTDGKILEYKAPMKVQDVLAE 36 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~ 36 (165)
+..||+..++..+.++.+++..
T Consensus 21 I~VNG~~~~~~~~~tl~~LL~~ 42 (84)
T PRK06083 21 ISINDQSIQVDISSSLAQIIAQ 42 (84)
T ss_pred EEECCeEEEcCCCCcHHHHHHH
Confidence 6789999999999999999976
No 12
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=39.37 E-value=42 Score=20.69 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=20.9
Q ss_pred EEEecCCcEEEEeCCccHHHHHhh
Q 031133 13 KVMKTDGKILEYKAPMKVQDVLAE 36 (165)
Q Consensus 13 KV~~~dG~v~e~~~Pv~a~evl~~ 36 (165)
-|..+||..++|..++++.+++..
T Consensus 2 ~~~~~~g~~~~~~~~~t~~~~~~~ 25 (60)
T cd01668 2 YVFTPKGEIIELPAGATVLDFAYA 25 (60)
T ss_pred EEECCCCCEEEcCCCCCHHHHHHH
Confidence 467789999999999999998865
No 13
>PF00812 Ephrin: Ephrin; InterPro: IPR001799 Ephrins are a family of proteins [] that are ligands of class V (EPH-related) receptor protein-tyrosine kinases (see IPR001426 from INTERPRO). These receptors and their ligands have been implicated in regulating neuronal axon guidance and in patterning of the developing nervous system and may also serve a patterning and compartmentalisation role outside of the nervous system as well. Ephrins are membrane-attached proteins of 205 to 340 residues. Attachment appears to be crucial for their normal function. Type-A ephrins are linked to the membrane via a glycosylphosphatidylinositol (GPI)-linkage, while type-B ephrins are type-I membrane proteins.; GO: 0016020 membrane; PDB: 3HEI_P 3CZU_B 3MBW_B 1KGY_E 1IKO_P 2WO3_B 2I85_A 2VSK_B 3GXU_B 2VSM_B ....
Probab=38.07 E-value=43 Score=26.08 Aligned_cols=24 Identities=8% Similarity=0.235 Sum_probs=18.3
Q ss_pred ccCCCCCCccCCCCeEEEeeCCCC
Q 031133 49 IRHLMPDFKLLGGNLYFLVPVPLP 72 (165)
Q Consensus 49 ~~~L~~de~L~~G~lYfLlP~~~~ 72 (165)
+.|++-+-+.+||+-||.+-.+..
T Consensus 96 fSP~p~G~EF~pG~~YY~ISts~g 119 (145)
T PF00812_consen 96 FSPFPLGLEFQPGHDYYYISTSTG 119 (145)
T ss_dssp S-SSTTSSS--TTEEEEEEEEESS
T ss_pred CCCCCCCeeecCCCeEEEEEccCC
Confidence 589999999999999999988643
No 14
>cd00178 STI Soybean trypsin inhibitor (Kunitz) family of protease inhibitors. Inhibit proteases by binding with high affinity to their active sites. Trefoil fold, common to interleukins and fibroblast growth factors.
Probab=37.95 E-value=24 Score=27.95 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=15.9
Q ss_pred CCCccCCCCeEEEeeCCC
Q 031133 54 PDFKLLGGNLYFLVPVPL 71 (165)
Q Consensus 54 ~de~L~~G~lYfLlP~~~ 71 (165)
.+++|++|.-||++|...
T Consensus 6 ~G~~l~~g~~YyI~p~~~ 23 (172)
T cd00178 6 DGNPLRNGGRYYILPAIR 23 (172)
T ss_pred CCCCCcCCCeEEEEEcee
Confidence 368899999999999976
No 15
>PF00197 Kunitz_legume: Trypsin and protease inhibitor; InterPro: IPR002160 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The Kunitz-type soybean trypsin inhibitor (STI) family consists mainly of proteinase inhibitors from Leguminosae seeds []. They belong to MEROPS inhibitor family I3, clan IC. They exhibit proteinase inhibitory activity against serine proteinases; trypsin (MEROPS peptidase family S1, IPR001254 from INTERPRO) and subtilisin (MEROPS peptidase family S8, IPR000209 from INTERPRO), thiol proteinases (MEROPS peptidase family C1, IPR000668 from INTERPRO) and aspartic proteinases (MEROPS peptidase family A1, IPR001461 from INTERPRO) []. Inhibitors from cereals are active against subtilisin and endogenous alpha-amylases, while some also inhibit tissue plasminogen activator. The inhibitors are usually specific for either trypsin or chymotrypsin, and some are effective against both. They are thought to protect the seeds against consumption by animal predators, while at the same time existing as seed storage proteins themselves - all the actively inhibitory members contain 2 disulphide bridges. The existence of a member with no inhibitory activity, winged bean albumin 1, suggests that the inhibitors may have evolved from seed storage proteins. Proteins from the Kunitz family contain from 170 to 200 amino acid residues and one or two intra-chain disulphide bonds. The best conserved region is found in their N-terminal section. The crystal structures of soybean trypsin inhibitor (STI), trypsin inhibitor DE-3 from the Kaffir tree Erythrina caffra (ETI) [] and the bifunctional proteinase K/alpha-amylase inhibitor from wheat (PK13) have been solved, showing them to share the same 12-stranded beta-sheet structure as those of interleukin-1 and heparin-binding growth factors []. The beta-sheets are arranged in 3 similar lobes around a central axis, 6 strands forming an anti-parallel beta-barrel. Despite the structural similarity, STI shows no interleukin-1 bioactivity, presumably as a result of their primary sequence disparities. The active inhibitory site containing the scissile bond is located in the loop between beta-strands 4 and 5 in STI and ETI. The STIs belong to a superfamily that also contains the interleukin-1 proteins, heparin binding growth factors (HBGF) and histactophilin, all of which have very similar structures, but share no sequence similarity with the STI family.; GO: 0004866 endopeptidase inhibitor activity; PDB: 3TC2_B 3S8J_A 3S8K_A 1TIE_A 2GZB_A 3E8L_C 2IWT_B 3BX1_C 1AVA_D 3IIR_A ....
Probab=37.86 E-value=28 Score=27.61 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=15.1
Q ss_pred CCCccCCCCeEEEeeCCCC
Q 031133 54 PDFKLLGGNLYFLVPVPLP 72 (165)
Q Consensus 54 ~de~L~~G~lYfLlP~~~~ 72 (165)
.+.+|++|.-||++|+...
T Consensus 6 ~G~~l~~g~~YyI~p~~~~ 24 (176)
T PF00197_consen 6 DGNPLRNGGEYYILPAIRG 24 (176)
T ss_dssp TSCB-BTTSEEEEEESSTG
T ss_pred CCCCCcCCCCEEEEeCccC
Confidence 3678999999999998653
No 16
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=34.13 E-value=45 Score=22.17 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=19.0
Q ss_pred EecCCcEEEEeCC-ccHHHHHhh
Q 031133 15 MKTDGKILEYKAP-MKVQDVLAE 36 (165)
Q Consensus 15 ~~~dG~v~e~~~P-v~a~evl~~ 36 (165)
+..||+..++..+ .++++++..
T Consensus 3 I~vNG~~~~~~~~~~tv~~lL~~ 25 (67)
T PRK07696 3 LKINGNQIEVPESVKTVAELLTH 25 (67)
T ss_pred EEECCEEEEcCCCcccHHHHHHH
Confidence 5679999999987 789999975
No 17
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=33.71 E-value=1.4e+02 Score=19.85 Aligned_cols=51 Identities=24% Similarity=0.338 Sum_probs=32.7
Q ss_pred ecCCc----EEEEeCCccHHHHHhhcC----CcEEeCCCCCccCCCCCCccCCCCeEEEeeC
Q 031133 16 KTDGK----ILEYKAPMKVQDVLAEFA----GHAISDSFPEIRHLMPDFKLLGGNLYFLVPV 69 (165)
Q Consensus 16 ~~dG~----v~e~~~Pv~a~evl~~~P----gh~v~~s~~~~~~L~~de~L~~G~lYfLlP~ 69 (165)
..+|+ .+++....++++++.+.- +.+|.--. ..+++++.|..|--.-++|.
T Consensus 8 ~vng~~~~~~~~~~~~~tv~~ll~~l~~~~~~v~v~vNg---~iv~~~~~l~~gD~Veii~~ 66 (70)
T PRK08364 8 KVIGRGIEKEIEWRKGMKVADILRAVGFNTESAIAKVNG---KVALEDDPVKDGDYVEVIPV 66 (70)
T ss_pred EEeccccceEEEcCCCCcHHHHHHHcCCCCccEEEEECC---EECCCCcCcCCCCEEEEEcc
Confidence 44787 677788899999997642 11221111 33467888888876666665
No 18
>PRK06437 hypothetical protein; Provisional
Probab=30.35 E-value=1.6e+02 Score=19.45 Aligned_cols=52 Identities=13% Similarity=0.296 Sum_probs=32.8
Q ss_pred EecCC---cEEEEeCCccHHHHHhhc--C--CcEEeCCCCCccCCCCCCccCCCCeEEEeeC
Q 031133 15 MKTDG---KILEYKAPMKVQDVLAEF--A--GHAISDSFPEIRHLMPDFKLLGGNLYFLVPV 69 (165)
Q Consensus 15 ~~~dG---~v~e~~~Pv~a~evl~~~--P--gh~v~~s~~~~~~L~~de~L~~G~lYfLlP~ 69 (165)
|..|| +..++..+.++++++.+. + +.++..- -.+++++..|..|--.-++|.
T Consensus 5 ~~v~g~~~~~~~i~~~~tv~dLL~~Lgi~~~~vaV~vN---g~iv~~~~~L~dgD~Veiv~~ 63 (67)
T PRK06437 5 IRVKGHINKTIEIDHELTVNDIIKDLGLDEEEYVVIVN---GSPVLEDHNVKKEDDVLILEV 63 (67)
T ss_pred EEecCCcceEEEcCCCCcHHHHHHHcCCCCccEEEEEC---CEECCCceEcCCCCEEEEEec
Confidence 55678 568888889999999863 2 1222211 134458888888855555554
No 19
>smart00452 STI Soybean trypsin inhibitor (Kunitz) family of protease inhibitors.
Probab=27.95 E-value=44 Score=26.49 Aligned_cols=18 Identities=22% Similarity=0.445 Sum_probs=15.8
Q ss_pred CCCccCCCCeEEEeeCCC
Q 031133 54 PDFKLLGGNLYFLVPVPL 71 (165)
Q Consensus 54 ~de~L~~G~lYfLlP~~~ 71 (165)
.+.+|++|.-||++|...
T Consensus 5 ~G~~l~~G~~YyI~p~~~ 22 (172)
T smart00452 5 DGNPLRNGGTYYILPAIR 22 (172)
T ss_pred CCCCCcCCCcEEEEEccc
Confidence 467899999999999975
No 20
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=27.76 E-value=56 Score=19.08 Aligned_cols=28 Identities=18% Similarity=0.324 Sum_probs=14.1
Q ss_pred EEEcHHHHHHHHHHhcCCcccHHHHHHHHhh
Q 031133 103 VVISKQELQDLQMLQKGGVVSVQDVASWLQG 133 (165)
Q Consensus 103 i~itk~~l~~l~~~~~~~~~s~e~~l~~l~~ 133 (165)
|.+|++|+...+-++. .++-.++..+.+
T Consensus 1 l~mtr~diA~~lG~t~---ETVSR~l~~l~~ 28 (32)
T PF00325_consen 1 LPMTRQDIADYLGLTR---ETVSRILKKLER 28 (32)
T ss_dssp EE--HHHHHHHHTS-H---HHHHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCcH---HHHHHHHHHHHH
Confidence 5789999999332221 244445555544
No 21
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=27.40 E-value=1.2e+02 Score=19.69 Aligned_cols=38 Identities=21% Similarity=0.348 Sum_probs=28.3
Q ss_pred CceEEEEEEEcHHHHHHHHHHhcCCcccHHHHHHHHhhccc
Q 031133 96 SSVVRIKVVISKQELQDLQMLQKGGVVSVQDVASWLQGKQS 136 (165)
Q Consensus 96 ~~~~rvKi~itk~~l~~l~~~~~~~~~s~e~~l~~l~~~~~ 136 (165)
.+...+.+-+|+++|.. ++.-.. .++..++..|.+++-
T Consensus 20 ~~~~~~~~~lt~~~iA~--~~g~sr-~tv~r~l~~l~~~g~ 57 (76)
T PF13545_consen 20 GDGIRIPLPLTQEEIAD--MLGVSR-ETVSRILKRLKDEGI 57 (76)
T ss_dssp TTEEEEEEESSHHHHHH--HHTSCH-HHHHHHHHHHHHTTS
T ss_pred CCCceEEecCCHHHHHH--HHCCCH-HHHHHHHHHHHHCCC
Confidence 46778999999999999 553112 478888888877643
No 22
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=26.69 E-value=75 Score=20.72 Aligned_cols=33 Identities=24% Similarity=0.483 Sum_probs=17.0
Q ss_pred CCCcccCCCceeEEEecCCcEEEEeCCccHHHHHhh
Q 031133 1 MGNCLMLEEKVIKVMKTDGKILEYKAPMKVQDVLAE 36 (165)
Q Consensus 1 MGNC~~~~~~~iKV~~~dG~v~e~~~Pv~a~evl~~ 36 (165)
||+|-. ..+-++.++|.++..-.|-.+.+|+.+
T Consensus 44 lg~C~~---~P~v~i~~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 44 LGACGL---APVVVVYPDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred cCcccC---CCEEEEeCCCeEEccCCHHHHHHHHHh
Confidence 455532 233444466765555555555556554
No 23
>COG5568 Uncharacterized small protein [Function unknown]
Probab=25.87 E-value=58 Score=23.23 Aligned_cols=18 Identities=17% Similarity=0.431 Sum_probs=15.2
Q ss_pred EEEeCCccHHHHHhhcCC
Q 031133 22 LEYKAPMKVQDVLAEFAG 39 (165)
Q Consensus 22 ~e~~~Pv~a~evl~~~Pg 39 (165)
.-|-++|++.||+..||.
T Consensus 23 v~YvRkirs~el~r~fPe 40 (85)
T COG5568 23 VAYVRKIRSDELLRCFPE 40 (85)
T ss_pred eEEEEeccHHHHHhhCCC
Confidence 346779999999999993
No 24
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=25.66 E-value=75 Score=20.59 Aligned_cols=54 Identities=17% Similarity=0.236 Sum_probs=31.5
Q ss_pred EecCCcEEEEeCCccHHHHHhhc--CCcEE-e--CCCCCccCCCCCCccCCCCeEEEeeC
Q 031133 15 MKTDGKILEYKAPMKVQDVLAEF--AGHAI-S--DSFPEIRHLMPDFKLLGGNLYFLVPV 69 (165)
Q Consensus 15 ~~~dG~v~e~~~Pv~a~evl~~~--Pgh~v-~--~s~~~~~~L~~de~L~~G~lYfLlP~ 69 (165)
+..||+..++ .+.++.+++..+ +...+ + +..-..+.-.++..|..|--.-++|.
T Consensus 3 i~~Ng~~~~~-~~~tl~~Ll~~l~~~~~~vavavN~~iv~~~~~~~~~L~dgD~Ieiv~~ 61 (65)
T PRK06488 3 LFVNGETLQT-EATTLALLLAELDYEGNWLATAVNGELVHKEARAQFVLHEGDRIEILSP 61 (65)
T ss_pred EEECCeEEEc-CcCcHHHHHHHcCCCCCeEEEEECCEEcCHHHcCccccCCCCEEEEEEe
Confidence 5679999999 568999999763 22212 1 11111122334667777765555554
No 25
>PHA02843 hypothetical protein; Provisional
Probab=23.77 E-value=32 Score=23.21 Aligned_cols=14 Identities=50% Similarity=0.741 Sum_probs=10.1
Q ss_pred CCCcccCCCceeEE
Q 031133 1 MGNCLMLEEKVIKV 14 (165)
Q Consensus 1 MGNC~~~~~~~iKV 14 (165)
||||.-.+.+.||-
T Consensus 1 mgncsrkqnknikt 14 (73)
T PHA02843 1 MGNCSRKQNKNIKT 14 (73)
T ss_pred CCccchhhccCccc
Confidence 89998766666653
No 26
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=22.58 E-value=1.2e+02 Score=20.56 Aligned_cols=24 Identities=29% Similarity=0.473 Sum_probs=20.5
Q ss_pred EEecCCcEEEEeCCccHHHHHhhc
Q 031133 14 VMKTDGKILEYKAPMKVQDVLAEF 37 (165)
Q Consensus 14 V~~~dG~v~e~~~Pv~a~evl~~~ 37 (165)
-+..||+-.++..+.|++++|.+.
T Consensus 4 ~i~~ng~~~e~~~~~tv~dLL~~l 27 (68)
T COG2104 4 TIQLNGKEVEIAEGTTVADLLAQL 27 (68)
T ss_pred EEEECCEEEEcCCCCcHHHHHHHh
Confidence 345689999999999999999773
No 27
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=21.07 E-value=1.8e+02 Score=20.42 Aligned_cols=31 Identities=26% Similarity=0.379 Sum_probs=23.5
Q ss_pred EEEEcHHHHHHHHHHhcCCc-ccHHHHHHHHh
Q 031133 102 KVVISKQELQDLQMLQKGGV-VSVQDVASWLQ 132 (165)
Q Consensus 102 Ki~itk~~l~~l~~~~~~~~-~s~e~~l~~l~ 132 (165)
+|.|+|.++++|......+. -++.++...+.
T Consensus 3 ~vii~k~ey~el~~~~~~~~~W~~~dl~k~~~ 34 (91)
T PF05595_consen 3 KVIIDKEEYEELKKKDLEGKWWDMKDLRKRTG 34 (91)
T ss_pred eEEeeHHHHHHHHHHhhccceeeHHHHHHHHC
Confidence 68999999999766555554 48888877773
No 28
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=20.37 E-value=88 Score=23.69 Aligned_cols=38 Identities=18% Similarity=0.198 Sum_probs=27.3
Q ss_pred CceEEEEEEEcHHHHHHHHHHhcCCcccHHHHHHHHhhccc
Q 031133 96 SSVVRIKVVISKQELQDLQMLQKGGVVSVQDVASWLQGKQS 136 (165)
Q Consensus 96 ~~~~rvKi~itk~~l~~l~~~~~~~~~s~e~~l~~l~~~~~ 136 (165)
.+...+.+.+|++||..++-.+. .++..+++.|..++-
T Consensus 135 ~~~~~~~~~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~ 172 (193)
T TIGR03697 135 QRGVTIDLRLSHQAIAEAIGSTR---VTITRLLGDLRKKKL 172 (193)
T ss_pred CCeEEecCCCCHHHHHHHhCCcH---HHHHHHHHHHHHCCC
Confidence 45567889999999999433332 377888888877643
No 29
>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase. CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.
Probab=20.18 E-value=1.9e+02 Score=21.23 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=24.8
Q ss_pred eeEEEecCCcEEEEeCCc--cHHHHHhhcCCcEE
Q 031133 11 VIKVMKTDGKILEYKAPM--KVQDVLAEFAGHAI 42 (165)
Q Consensus 11 ~iKV~~~dG~v~e~~~Pv--~a~evl~~~Pgh~v 42 (165)
.|||-+.||.-.-+..|+ ||+|++..--..+.
T Consensus 4 ~IRIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~ 37 (97)
T cd01775 4 CIRVFRSDGTFTTLSCPLNTTVSELIPQLAKKFY 37 (97)
T ss_pred EEEEEecCCcEEEEEcCCcCcHHHHHHHHHHhhc
Confidence 589999999988887765 89998877554433
Done!