Query 032911
Match_columns 130
No_of_seqs 124 out of 1031
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 07:28:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032911.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032911hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00146 40S ribosomal protein 100.0 7.4E-50 1.6E-54 288.0 12.9 130 1-130 1-130 (130)
2 COG0096 RpsH Ribosomal protein 100.0 8.2E-50 1.8E-54 286.9 12.5 124 1-130 1-132 (132)
3 PTZ00158 40S ribosomal protein 100.0 2.9E-49 6.3E-54 284.5 13.0 130 1-130 1-130 (130)
4 PRK04034 rps8p 30S ribosomal p 100.0 3.1E-48 6.6E-53 279.6 12.7 129 1-130 1-130 (130)
5 CHL00042 rps8 ribosomal protei 100.0 4.2E-45 9E-50 263.9 13.0 121 3-130 2-132 (132)
6 PRK00136 rpsH 30S ribosomal pr 100.0 5.4E-44 1.2E-48 257.4 13.1 121 1-130 1-130 (130)
7 PF00410 Ribosomal_S8: Ribosom 100.0 3.4E-43 7.3E-48 252.6 11.1 119 5-130 1-129 (129)
8 KOG1754 40S ribosomal protein 100.0 1.6E-38 3.5E-43 224.8 9.8 130 1-130 1-130 (130)
9 PF09639 YjcQ: YjcQ protein; 62.0 4.5 9.7E-05 26.9 1.2 25 31-55 24-48 (88)
10 PF09879 DUF2106: Predicted me 47.8 8.5 0.00018 28.4 0.7 18 97-114 105-122 (153)
11 PF10264 Stork_head: Winged he 45.1 28 0.00061 23.1 2.8 37 11-48 32-68 (80)
12 PF08438 MMR_HSR1_C: GTPase of 40.1 35 0.00076 23.8 2.9 37 8-48 11-47 (109)
13 PF03551 PadR: Transcriptional 35.7 1.1E+02 0.0024 19.0 5.0 26 29-54 29-54 (75)
14 PF14947 HTH_45: Winged helix- 35.4 30 0.00065 22.1 1.8 43 3-48 4-50 (77)
15 PF13732 DUF4162: Domain of un 33.9 61 0.0013 20.3 3.2 31 23-54 43-73 (84)
16 COG2519 GCD14 tRNA(1-methylade 32.3 78 0.0017 25.4 4.0 43 6-48 173-215 (256)
17 COG4037 Predicted membrane pro 29.4 25 0.00055 25.8 0.8 18 97-114 109-126 (163)
18 TIGR03433 padR_acidobact trans 27.4 1.4E+02 0.0031 19.7 4.2 25 30-54 38-62 (100)
19 PF13601 HTH_34: Winged helix 26.4 1.1E+02 0.0023 19.8 3.3 35 29-65 27-61 (80)
20 TIGR02889 spore_YpeB germinati 25.0 69 0.0015 27.6 2.8 22 107-128 369-407 (435)
21 PHA02943 hypothetical protein; 23.5 1.3E+02 0.0027 22.7 3.5 23 31-53 38-60 (165)
22 PF02813 Retro_M: Retroviral M 23.2 43 0.00093 22.4 0.9 22 29-50 20-41 (86)
23 PF01726 LexA_DNA_bind: LexA D 22.6 77 0.0017 19.7 2.0 20 29-48 38-57 (65)
24 PF13412 HTH_24: Winged helix- 22.3 78 0.0017 17.8 1.9 18 31-48 31-48 (48)
25 PF09339 HTH_IclR: IclR helix- 20.3 93 0.002 17.9 2.0 17 32-48 33-49 (52)
26 PF02082 Rrf2: Transcriptional 20.1 93 0.002 19.8 2.1 20 31-50 39-58 (83)
No 1
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=100.00 E-value=7.4e-50 Score=287.99 Aligned_cols=130 Identities=93% Similarity=1.400 Sum_probs=123.9
Q ss_pred CcccchHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccCCCccccccee
Q 032911 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~~~~~I~pRvy 80 (130)
|++||++|||||+||||+++++++|.++|+||++++|+++|++||||++|+..+++....++++|||..+++++|+||+|
T Consensus 1 m~~~~~iad~lt~IrNa~~a~~~~v~~~p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lk~~i~~~~~IS~Rvy 80 (130)
T PLN00146 1 MVRRSVLNDALKTMYNAEKRGKRQVLIRPSSKVVIKFLKVMQKHGYIGEFEVVDDHRSGKIVVELNGRLNKCGVISPRFD 80 (130)
T ss_pred CCCcChHHHHHHHhHhHHHcCCCeEEEEcChHHHHHHHHHHHHCCCCcceEEEecCCcceEEEEEcccccCCcEEEcCEe
Confidence 99999999999999999999999997339999999999999999999999988776677899999998888999999999
Q ss_pred cccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 81 VGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 81 ~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
++.++|+++..+++|++|+|++|||||+|||||+||+++|+|||+||+||
T Consensus 81 ~~~~~l~~v~~~~~~~~g~Gi~IlSTskGimt~~eAr~~~vGGEvL~~vy 130 (130)
T PLN00146 81 VKVKEIEAWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
T ss_pred cCcchhhHHHhccCCCCCCEEEEEECCCccccHHHHHHcCCCCEEEEEEC
Confidence 99999999988999999999999999999999999999999999999998
No 2
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.2e-50 Score=286.91 Aligned_cols=124 Identities=42% Similarity=0.677 Sum_probs=113.6
Q ss_pred CcccchHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccCCCccccccee
Q 032911 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~~~~~I~pRvy 80 (130)
|+++|+|||||||||||.++++..|.+ |+||+..+||++|++||||++|++.++++++.++|+|||+.+++|+|+
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~v~~-P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~~~~v~Lky~~n~~~vI~---- 75 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEVVSM-PASKLKGAILKVLKKEGYIKDFEVIDDGRKGKLRVQLKYRINGCGVIS---- 75 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccceeec-chHHHHHHHHHHHHHcCCcceEEEEeCCcceEEEEEEEeccCCCcccc----
Confidence 889999999999999999998888987 999999999999999999999999999999999999999988899999
Q ss_pred cccceeecccc------ccCCC--CcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 81 VGVKEIEGWTA------RLLPS--RQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 81 ~~~~~isk~~~------r~l~~--~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
..+.+|+|+. +.||+ +|+|++|||||+|||||+|||++|+|||||||||
T Consensus 76 -~~~rVSkpg~rvy~~~~~LP~v~~g~Gi~IvSTs~GVMtd~eAr~~~vGGevLcyV~ 132 (132)
T COG0096 76 -PIKRVSKPGLRVYEKKRELPAVLNGLGIAIVSTSKGVMTDKEARKKGVGGEVLCYVW 132 (132)
T ss_pred -cceecCCCCceeecChhhhhhhhcCceEEEEEcCCCccChHHHHHcCCCcEEEEEEC
Confidence 4555555543 33566 8899999999999999999999999999999999
No 3
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=100.00 E-value=2.9e-49 Score=284.52 Aligned_cols=130 Identities=77% Similarity=1.242 Sum_probs=124.4
Q ss_pred CcccchHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccCCCccccccee
Q 032911 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~~~~~I~pRvy 80 (130)
|+.||++|||||+||||++++|++|.++|+||++++|+++|++||||++|++.+++....+.++|+.+.+++.+|+||+|
T Consensus 1 m~~~~~iadmlt~IrNa~~~~~~~V~v~p~Skl~~~il~IL~~eGyI~~~~~~~~~~~~~i~v~l~~rIsk~g~IS~RvY 80 (130)
T PTZ00158 1 MVRMSVLADCLRSIVNAEKQGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIVDDHRSGKIVVNLNGRLNKCGVISPRFD 80 (130)
T ss_pred CCcccHHHHHHHhhhhHHhCCCCeEEEeCCcHHHHHHHHHHHHCCcccceEEEecCCEEEEEEEEcCccccCCCCccceE
Confidence 89999999999999999999999999669999999999999999999999988777667889999988888889999999
Q ss_pred cccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 81 VGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 81 ~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
++.++|+++..++||.+|+|++|||||+|||||+|||++++|||+||+||
T Consensus 81 ~~~~~ip~v~~~~lp~~glGi~IlSTSkGImt~~eAr~~~vGGEvLc~v~ 130 (130)
T PTZ00158 81 VTLGEFEKWANNILPSRQFGHVVLTTSYGIMDHEEARRRHTGGKILGFFY 130 (130)
T ss_pred CCcchhhHHhcCCCccccceEEEEECCCCccChHHHHHcCCCceEEEEEC
Confidence 99999999998999999999999999999999999999999999999997
No 4
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=100.00 E-value=3.1e-48 Score=279.56 Aligned_cols=129 Identities=53% Similarity=0.926 Sum_probs=122.1
Q ss_pred CcccchHHHHHHhhhhhhhhCcccee-ecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccCCCcccccce
Q 032911 1 MVRVSVLNDALKSMYNAEKRGKRQVM-IRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVISPRF 79 (130)
Q Consensus 1 m~~~~~l~d~lt~IrNa~~a~~~~v~-~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~~~~~I~pRv 79 (130)
|+++|++|||||+||||++|++++|. + |+|+++++||++|++||||++|++.++++++.+.++|||..+++++|+||+
T Consensus 1 m~~~d~iad~lt~IrNa~~a~~~~v~~~-p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lk~~~~~~~~IkPRv 79 (130)
T PRK04034 1 MVLLDPLANALSTIKNAEMVGKKEVIIK-PASKLIGNVLRVMQDEGYIGEFEYIDDGRAGKFKVELLGRINKCGAIKPRY 79 (130)
T ss_pred CCcccHHHHHHHHhHhHHHcCCceEEEE-cccHHHHHHHHHHHHCCCceEEEEEcCCCccceEEEECCccCCCCcCCCCe
Confidence 77789999999999999999999985 6 999999999999999999999998776667789999999877789999999
Q ss_pred ecccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 80 DVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 80 y~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
|++.++|+++..+++|++|+|++|||||+|||||+||+++++|||+||+||
T Consensus 80 y~~~~~l~~~~~~~l~~~~lGi~IlSTskGImt~~eA~~~~vGGEvL~~v~ 130 (130)
T PRK04034 80 PVKYDEFEKWEKRYLPARDFGILIVSTSKGVMSHKEAREKGIGGVLLAYVY 130 (130)
T ss_pred EcCHhHhHHHHhccCCCCCceEEEEECCCCceeHHHHHHcCCCCEEEEEEC
Confidence 999999999888899999999999999999999999999999999999999
No 5
>CHL00042 rps8 ribosomal protein S8
Probab=100.00 E-value=4.2e-45 Score=263.89 Aligned_cols=121 Identities=29% Similarity=0.438 Sum_probs=106.6
Q ss_pred ccchHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccC-CCcccc-----
Q 032911 3 RVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLN-KCGVIS----- 76 (130)
Q Consensus 3 ~~~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~-~~~~I~----- 76 (130)
++|++|||||+||||++|++.+|.+ |+|+++++||++|++||||++|++.+++.++.++|+|||+.+ ..|+|+
T Consensus 2 ~~d~iad~lt~IrNa~~a~~~~v~i-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lky~~~~~~pvi~~i~~i 80 (132)
T CHL00042 2 GNDTIADMLTRIRNANMVKKGTVRI-PATNITENIVKILLREGFIENVREHRENNKYFLVLTLKYRGNKKKPYITTLKRI 80 (132)
T ss_pred CcchHHHHHHHhHHHHHCCCCEEEE-eccHHHHHHHHHHHHCCcccceEEEecCCeeEEEEEEEeecCCCceeccccEEE
Confidence 4799999999999999999999999 999999999999999999999999877777889999999853 258886
Q ss_pred --c--ceecccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 77 --P--RFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 77 --p--Rvy~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
| |+|++.++++++. +|+|++|||||+|||||+||+++++|||+||+||
T Consensus 81 SkPg~Rvy~~~~~L~~~~------~g~G~~IlSTskGimt~~eA~~~~iGGe~L~~v~ 132 (132)
T CHL00042 81 SKPGLRIYSNYKEIPRVL------GGMGIVILSTSKGIMTDREARLKGIGGEILCYIW 132 (132)
T ss_pred cCCCceeEcCHhHHHHHh------CCCcEEEEECCCCcccHHHHHHcCCCCEEEEEEC
Confidence 4 5555555553332 8999999999999999999999999999999999
No 6
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=100.00 E-value=5.4e-44 Score=257.43 Aligned_cols=121 Identities=27% Similarity=0.469 Sum_probs=107.4
Q ss_pred CcccchHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccCCCcccc----
Q 032911 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVIS---- 76 (130)
Q Consensus 1 m~~~~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~~~~~I~---- 76 (130)
|+ +|+++||||+||||+++++.+|.+ |+|+++.+||++|++||||++|+..+++++.+++|+|||+.+ +|+|+
T Consensus 1 m~-~d~i~d~lt~IrNa~~~~~~~v~i-p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lky~~~-~pvi~~i~~ 77 (130)
T PRK00136 1 SM-TDPIADMLTRIRNAQMAKHETVSM-PASKLKVAIAEILKEEGYIKDYEVEEDGKQGILRITLKYGEG-EPVIEGIKR 77 (130)
T ss_pred CC-cChHHHHHHHHHHHHHcCCCeEEe-cccHHHHHHHHHHHHCCcccceEEEecCCcceEEEEEecCCC-CcccccceE
Confidence 54 599999999999999999999998 999999999999999999999998876556679999999865 69986
Q ss_pred ---c--ceecccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 77 ---P--RFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 77 ---p--Rvy~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
| |+|++.++|+++. +|+|++|+|||+|||||+||+++++|||+||+||
T Consensus 78 ISkPg~Riy~~~~~l~~~~------~g~G~~IlSTs~Gimt~~eA~~~~iGGeiL~~v~ 130 (130)
T PRK00136 78 VSKPGLRVYKKKDELPKVL------NGLGIAIVSTSKGVMTDREARKAGVGGEVLCYVW 130 (130)
T ss_pred ecCCCcceEcCHhHHHHHH------CCCCEEEEEcCCCeeeHHHHHHhCCCCEEEEEEC
Confidence 4 5666655554443 8999999999999999999999999999999999
No 7
>PF00410 Ribosomal_S8: Ribosomal protein S8; InterPro: IPR000630 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S8 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S8 is known to bind directly to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups eubacterial, algal and plant chloroplast, cyanelle, archaebacterial and Marchantia polymorpha mitochondrial S8; mammalian and plant S15A; and yeast S22 (S24) ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_H 3O30_O 3O2Z_O 3IZB_H 3U5G_W 3U5C_W 3OTO_H 1AN7_A 2HGR_K 3BBN_H ....
Probab=100.00 E-value=3.4e-43 Score=252.64 Aligned_cols=119 Identities=42% Similarity=0.656 Sum_probs=107.4
Q ss_pred chHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCcc-ceEEEEEcCccCCCcccc-------
Q 032911 5 SVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRA-GKIVVELNGRLNKCGVIS------- 76 (130)
Q Consensus 5 ~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~-~~i~i~Lky~~~~~~~I~------- 76 (130)
|++||||++||||+++++++|.+ |+|++++++|++|++||||++|++.++++. ++++|+|||..++.|+|+
T Consensus 1 D~lad~l~~I~Na~~~~~~~v~i-p~sk~~~~il~iL~~eGyI~~f~~~~~~~~~~~i~I~Lky~~~~~~~i~~i~~iSk 79 (129)
T PF00410_consen 1 DPLADLLTRIRNASRARKRFVII-PYSKLNLSILKILKKEGYISGFEIIDDNRNGKRIWIELKYRRNGKPVIKKIKRISK 79 (129)
T ss_dssp SHHHHHHHHHHHHHHTTCSEEEE-EHCHHHHHHHHHHHHTTSEEEEEEEESSSSEEEEEEEESBCSSSSBSSSEEEESSB
T ss_pred CcHHHHHHHhHHHHHCCCCEEEe-cccHHHHHHHHHHhhccccceeEeeccCCCceEEEEEEccccccchhhhhhhcccC
Confidence 79999999999999999999999 999999999999999999999999887764 679999999545568875
Q ss_pred c--ceecccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 77 P--RFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 77 p--Rvy~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
| |+|++.+++++.. +|+|++|+|||+|||||+||+++++|||+||+||
T Consensus 80 p~~r~y~~~~~L~~~~------~g~g~~IlSTskGImt~~eA~~~~vGGevL~~V~ 129 (129)
T PF00410_consen 80 PGRRVYISYKELPKVK------NGLGILILSTSKGIMTHREARKLNVGGEVLCYVW 129 (129)
T ss_dssp TTCCCEESGTGSHHSC------TTTSEEEEEETTEEEEHHHHHHHTSEEEEEEEEE
T ss_pred CCcceecCHHHHHHHh------CCCeEEEEEcCCCcEeHHHHHHcCCCCEEEEEEC
Confidence 4 7777777776533 8999999999999999999999999999999999
No 8
>KOG1754 consensus 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-38 Score=224.75 Aligned_cols=130 Identities=84% Similarity=1.317 Sum_probs=128.4
Q ss_pred CcccchHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEEcCccCCCccccccee
Q 032911 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~~~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~Lky~~~~~~~I~pRvy 80 (130)
|++++.|||+|..|+||.+++|++|.+.|.|+....+|.+|.+||||.+|++.++++.+++.|.|..+.|+|++|+||+-
T Consensus 1 m~~~~vLaDalksinNA~krGK~qvlirp~Skvii~FL~vmmkhGyIg~fei~ddhragkivv~L~gRlNkcg~Isprfd 80 (130)
T KOG1754|consen 1 MVRMNVLADALKSINNAEKRGKRQVLIRPSSKVIIRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFD 80 (130)
T ss_pred CchHHHHHHHHHHhhhHHhcCCceEEecccHHHHHHHHHHHHHcCcccceEEecCCccceEEEecccccccccccccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccceeeccccccCCCCcceEEEEECCCCcccHHHHHHcCCCcEEEEEEC
Q 032911 81 VGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
Q Consensus 81 ~~~~~isk~~~r~l~~~g~Gi~IlSTskGimt~~eAr~~~lGGevLc~V~ 130 (130)
++.+++++|..+.+|+.++|+.+++||.|+|+|+||+.+++|||+||++|
T Consensus 81 V~lkdlek~~n~llpsrqfg~ivltts~Gimdh~ear~k~~gg~ilg~~~ 130 (130)
T KOG1754|consen 81 VKLKDLEKWTNSLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKILGFFY 130 (130)
T ss_pred cccchHHHHHhccCccceeeEEEEecccccccHHHHhHhhcCcccceeeC
Confidence 99999999999999999999999999999999999999999999999998
No 9
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=61.96 E-value=4.5 Score=26.89 Aligned_cols=25 Identities=24% Similarity=0.311 Sum_probs=18.9
Q ss_pred cHHHHHHHHHhccCCceeeeEEeeC
Q 032911 31 SKVIIKFLLVMQKHGYIGEFEYVDD 55 (130)
Q Consensus 31 sk~~~~il~iL~~eGyI~~~~~~~~ 55 (130)
+..-..++.-|.++|||+|+.+...
T Consensus 24 ~~~~~~il~~L~d~GyI~G~~~~~~ 48 (88)
T PF09639_consen 24 DSYWSDILRMLQDEGYIKGVSVVRY 48 (88)
T ss_dssp HHHHHHHHHHHHHHTSEE--EESSS
T ss_pred HHHHHHHHHHHHHCCCccceEEEec
Confidence 4666789999999999999988653
No 10
>PF09879 DUF2106: Predicted membrane protein (DUF2106); InterPro: IPR011313 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure. This entry represents small membrane proteins that are predicted to be the EhaF transmembrane subunits of multi-subunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Probab=47.78 E-value=8.5 Score=28.41 Aligned_cols=18 Identities=28% Similarity=0.580 Sum_probs=15.1
Q ss_pred CcceEEEEECCCCcccHH
Q 032911 97 RQFGYIVLTTSAGIMDHE 114 (130)
Q Consensus 97 ~g~Gi~IlSTskGimt~~ 114 (130)
.=+|..|+|||.||++..
T Consensus 105 ~y~GTTIvS~PGGIlDEI 122 (153)
T PF09879_consen 105 PYFGTTIVSHPGGILDEI 122 (153)
T ss_pred ccccceEecCCChhHHHH
Confidence 458999999999998753
No 11
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=45.08 E-value=28 Score=23.11 Aligned_cols=37 Identities=19% Similarity=0.201 Sum_probs=31.2
Q ss_pred HHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCcee
Q 032911 11 LKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 11 lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~ 48 (130)
...|+++....-..+.. |+.....+.|..|.+||-|-
T Consensus 32 ~E~l~~~L~~~yp~i~~-Ps~e~l~~~L~~Li~erkIY 68 (80)
T PF10264_consen 32 QETLREHLRKHYPGIAI-PSQEVLYNTLGTLIKERKIY 68 (80)
T ss_pred HHHHHHHHHHhCCCCCC-CCHHHHHHHHHHHHHcCcee
Confidence 34667777777777887 99999999999999999884
No 12
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=40.07 E-value=35 Score=23.83 Aligned_cols=37 Identities=16% Similarity=0.239 Sum_probs=23.4
Q ss_pred HHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCcee
Q 032911 8 NDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 8 ~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~ 48 (130)
.+.+.+|+..+ .....+ |.|-..+-.|+-+.++|||+
T Consensus 11 ~~ni~kl~~~~---~~~~vV-p~SA~aEl~Lr~a~k~g~I~ 47 (109)
T PF08438_consen 11 DENIEKLKEKY---PDEPVV-PTSAAAELALRKAAKAGLID 47 (109)
T ss_dssp HHHHHHHHHHH---TT-EEE-EE-HHHHHHHHS-SSS----
T ss_pred HhHHHHHHHhC---CCCcee-eccHHHHHHHHHHHHCCCEE
Confidence 45677888765 233444 99999999999999999998
No 13
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=35.66 E-value=1.1e+02 Score=18.95 Aligned_cols=26 Identities=15% Similarity=0.050 Sum_probs=22.1
Q ss_pred CCcHHHHHHHHHhccCCceeeeEEee
Q 032911 29 PSSKVIIKFLLVMQKHGYIGEFEYVD 54 (130)
Q Consensus 29 p~sk~~~~il~iL~~eGyI~~~~~~~ 54 (130)
+........|.-|.++|+|+......
T Consensus 29 i~~g~lY~~L~~Le~~gli~~~~~~~ 54 (75)
T PF03551_consen 29 ISPGSLYPALKRLEEEGLIESRWEEE 54 (75)
T ss_dssp TTHHHHHHHHHHHHHTTSEEEEEEEE
T ss_pred cChhHHHHHHHHHHhCCCEEEeeecc
Confidence 55777889999999999999887664
No 14
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=35.40 E-value=30 Score=22.09 Aligned_cols=43 Identities=21% Similarity=0.412 Sum_probs=26.8
Q ss_pred ccchHHHHHHhhhhhhhhCccce----eecCCcHHHHHHHHHhccCCcee
Q 032911 3 RVSVLNDALKSMYNAEKRGKRQV----MIRPSSKVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 3 ~~~~l~d~lt~IrNa~~a~~~~v----~~~p~sk~~~~il~iL~~eGyI~ 48 (130)
.++++.|.|..+.++... ...+ -+ + .......++.|.+.|+|+
T Consensus 4 ~~~Ii~~IL~~l~~~~~~-~t~i~~~~~L-~-~~~~~~yL~~L~~~gLI~ 50 (77)
T PF14947_consen 4 RLEIIFDILKILSKGGAK-KTEIMYKANL-N-YSTLKKYLKELEEKGLIK 50 (77)
T ss_dssp TTHHHHHHHHHH-TT-B--HHHHHTTST----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHcCCCC-HHHHHHHhCc-C-HHHHHHHHHHHHHCcCee
Confidence 467899999999654432 2222 22 2 344567899999999994
No 15
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=33.91 E-value=61 Score=20.31 Aligned_cols=31 Identities=16% Similarity=0.279 Sum_probs=24.7
Q ss_pred cceeecCCcHHHHHHHHHhccCCceeeeEEee
Q 032911 23 RQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVD 54 (130)
Q Consensus 23 ~~v~~~p~sk~~~~il~iL~~eGyI~~~~~~~ 54 (130)
-.+.+ .......++++.|.++|+|..|+...
T Consensus 43 ~~i~l-~~~~~~~~ll~~l~~~g~I~~f~~~~ 73 (84)
T PF13732_consen 43 LRIKL-EDEETANELLQELIEKGIIRSFEEEE 73 (84)
T ss_pred EEEEE-CCcccHHHHHHHHHhCCCeeEEEEcC
Confidence 35555 56667789999999999999998754
No 16
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=32.25 E-value=78 Score=25.45 Aligned_cols=43 Identities=19% Similarity=0.294 Sum_probs=37.5
Q ss_pred hHHHHHHhhhhhhhhCccceeecCCcHHHHHHHHHhccCCcee
Q 032911 6 VLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 6 ~l~d~lt~IrNa~~a~~~~v~~~p~sk~~~~il~iL~~eGyI~ 48 (130)
-..|.+-++.++.+.+-..|...|+.......++.|.+.||..
T Consensus 173 ~PW~~le~~~~~Lkpgg~~~~y~P~veQv~kt~~~l~~~g~~~ 215 (256)
T COG2519 173 DPWNVLEHVSDALKPGGVVVVYSPTVEQVEKTVEALRERGFVD 215 (256)
T ss_pred ChHHHHHHHHHHhCCCcEEEEEcCCHHHHHHHHHHHHhcCccc
Confidence 3468888999999988777777899999999999999998875
No 17
>COG4037 Predicted membrane protein [Function unknown]
Probab=29.39 E-value=25 Score=25.75 Aligned_cols=18 Identities=33% Similarity=0.683 Sum_probs=15.3
Q ss_pred CcceEEEEECCCCcccHH
Q 032911 97 RQFGYIVLTTSAGIMDHE 114 (130)
Q Consensus 97 ~g~Gi~IlSTskGimt~~ 114 (130)
.-+|..|+|+|.|+++..
T Consensus 109 ~yfGTtIvS~PGGilDEI 126 (163)
T COG4037 109 RYFGTTIVSHPGGILDEI 126 (163)
T ss_pred EEcccEEecCCChhHHHH
Confidence 458999999999998754
No 18
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=27.44 E-value=1.4e+02 Score=19.72 Aligned_cols=25 Identities=12% Similarity=0.096 Sum_probs=19.3
Q ss_pred CcHHHHHHHHHhccCCceeeeEEee
Q 032911 30 SSKVIIKFLLVMQKHGYIGEFEYVD 54 (130)
Q Consensus 30 ~sk~~~~il~iL~~eGyI~~~~~~~ 54 (130)
.......+|.-|.++|+|......+
T Consensus 38 ~~gtlY~~L~rLe~~GlI~~~~~~~ 62 (100)
T TIGR03433 38 EEGSLYPALHRLERRGWIAAEWGES 62 (100)
T ss_pred CCCcHHHHHHHHHHCCCeEEEeeec
Confidence 3455789999999999999864433
No 19
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=26.39 E-value=1.1e+02 Score=19.76 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=19.7
Q ss_pred CCcHHHHHHHHHhccCCceeeeEEeeCCccceEEEEE
Q 032911 29 PSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVEL 65 (130)
Q Consensus 29 p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~i~L 65 (130)
+.+++. .-++.|.++|||+--....+ +..+-++.|
T Consensus 27 t~g~Ls-~hL~~Le~~GyV~~~k~~~~-~~p~t~~~l 61 (80)
T PF13601_consen 27 TDGNLS-KHLKKLEEAGYVEVEKEFEG-RRPRTWYSL 61 (80)
T ss_dssp -HHHHH-HHHHHHHHTTSEEEEEE-SS-S--EEEEEE
T ss_pred CHHHHH-HHHHHHHHCCCEEEEEeccC-CCCeEEEEE
Confidence 434443 45789999999996544332 234455554
No 20
>TIGR02889 spore_YpeB germination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function.
Probab=24.99 E-value=69 Score=27.57 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=17.6
Q ss_pred CCCcccHHHHHHc---CC--------------CcEEEEE
Q 032911 107 SAGIMDHEEARRK---NV--------------GGKVLGF 128 (130)
Q Consensus 107 skGimt~~eAr~~---~l--------------GGevLc~ 128 (130)
|+--+|.+|||+. ++ |.|+|||
T Consensus 369 p~pkls~eeAr~~vnp~l~v~~~rLalIp~~~~~EvLcY 407 (435)
T TIGR02889 369 PKPKLTEEEARSKVNKHLKILSTRLAVIPNETNQEVLTY 407 (435)
T ss_pred CCCcCCHHHHHHhhCCCceeccceeEEEECCCCcEEEEE
Confidence 4567889999987 33 8999997
No 21
>PHA02943 hypothetical protein; Provisional
Probab=23.53 E-value=1.3e+02 Score=22.69 Aligned_cols=23 Identities=17% Similarity=0.169 Sum_probs=18.9
Q ss_pred cHHHHHHHHHhccCCceeeeEEe
Q 032911 31 SKVIIKFLLVMQKHGYIGEFEYV 53 (130)
Q Consensus 31 sk~~~~il~iL~~eGyI~~~~~~ 53 (130)
......+|.+|.+||+|+..+++
T Consensus 38 ~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 38 HSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred HHHHHHHHHHHHHcCceEEEeec
Confidence 45667899999999999987653
No 22
>PF02813 Retro_M: Retroviral M domain; InterPro: IPR004028 The Gag polyprotein directs the assembly and release of virus particles from infected cells. The Gag polyprotein has three domains required for activity: an N-terminal membrane-binding (M) domain that directs Gag to the plasma membrane, an interaction (I) domain involved in Gag aggregation, and a late assembly (L) domain that mediates the budding process []. During viral maturation, the Gag polyprotein is then cleaved into major structural proteins by the viral protease, yielding the matrix, capsid, nucleoprotein, and some smaller peptides. In Rous sarcoma virus (RSV), the M domain consists of the first 85 residues of the matrix protein. However, unlike other Gag polyproteins, the M domain of RSV Gag is not myristylated, but retains full activity [].This domain forms an alpha helical bundle structure []. This entry represents the M domain of the Gag polyprotein found in avian retroviruses. This entry also identifies Gag polyproteins from several avian endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; PDB: 1A6S_A.
Probab=23.16 E-value=43 Score=22.36 Aligned_cols=22 Identities=36% Similarity=0.446 Sum_probs=17.6
Q ss_pred CCcHHHHHHHHHhccCCceeee
Q 032911 29 PSSKVIIKFLLVMQKHGYIGEF 50 (130)
Q Consensus 29 p~sk~~~~il~iL~~eGyI~~~ 50 (130)
|.+|-.-+++..|.+||.+.+=
T Consensus 20 ps~Kei~a~Ls~L~~Eg~L~sP 41 (86)
T PF02813_consen 20 PSKKEIGAMLSLLQKEGLLTSP 41 (86)
T ss_dssp S-SSHHHHHHHTGGGTT-TT-G
T ss_pred CcHHHHHHHHHHHHHccCcCCh
Confidence 8899999999999999999853
No 23
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.61 E-value=77 Score=19.75 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=17.7
Q ss_pred CCcHHHHHHHHHhccCCcee
Q 032911 29 PSSKVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 29 p~sk~~~~il~iL~~eGyI~ 48 (130)
.++.....-|+.|.+.|||+
T Consensus 38 ~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 38 KSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp SSHHHHHHHHHHHHHTTSEE
T ss_pred CChHHHHHHHHHHHHCcCcc
Confidence 46778889999999999998
No 24
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=22.29 E-value=78 Score=17.77 Aligned_cols=18 Identities=17% Similarity=0.451 Sum_probs=14.0
Q ss_pred cHHHHHHHHHhccCCcee
Q 032911 31 SKVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 31 sk~~~~il~iL~~eGyI~ 48 (130)
.......++-|.++|||+
T Consensus 31 ~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 31 RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHCcCcC
Confidence 345567888999999985
No 25
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=20.30 E-value=93 Score=17.95 Aligned_cols=17 Identities=18% Similarity=0.544 Sum_probs=14.4
Q ss_pred HHHHHHHHHhccCCcee
Q 032911 32 KVIIKFLLVMQKHGYIG 48 (130)
Q Consensus 32 k~~~~il~iL~~eGyI~ 48 (130)
.....++..|.++||++
T Consensus 33 stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 33 STVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHCcCee
Confidence 35678999999999986
No 26
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=20.15 E-value=93 Score=19.79 Aligned_cols=20 Identities=25% Similarity=0.311 Sum_probs=16.9
Q ss_pred cHHHHHHHHHhccCCceeee
Q 032911 31 SKVIIKFLLVMQKHGYIGEF 50 (130)
Q Consensus 31 sk~~~~il~iL~~eGyI~~~ 50 (130)
-.....+++-|.++|+|++.
T Consensus 39 ~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 39 PSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHhhCCeeEec
Confidence 45678999999999999855
Done!