Query 032980
Match_columns 129
No_of_seqs 118 out of 1021
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:18:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032980.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032980hhsearch_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 2.3E-50 5E-55 289.9 14.1 128 1-129 1-130 (130)
2 PTZ00158 40S ribosomal protein 100.0 5.6E-50 1.2E-54 287.5 14.1 129 1-129 1-130 (130)
3 COG0096 RpsH Ribosomal protein 100.0 4.2E-50 9.1E-55 287.6 12.7 122 1-129 1-132 (132)
4 PRK04034 rps8p 30S ribosomal p 100.0 1.2E-48 2.7E-53 280.9 13.7 128 1-129 1-130 (130)
5 CHL00042 rps8 ribosomal protei 100.0 6.7E-47 1.5E-51 272.5 13.1 122 1-129 1-132 (132)
6 PRK00136 rpsH 30S ribosomal pr 100.0 2.1E-45 4.6E-50 264.1 13.2 121 1-129 1-130 (130)
7 PF00410 Ribosomal_S8: Ribosom 100.0 3.3E-44 7.1E-49 257.3 11.7 119 4-129 1-129 (129)
8 KOG1754 40S ribosomal protein 100.0 4.3E-40 9.4E-45 232.1 11.0 129 1-129 1-130 (130)
9 PF09639 YjcQ: YjcQ protein; 58.7 4.6 0.0001 26.7 0.8 46 8-54 3-48 (88)
10 PF10264 Stork_head: Winged he 55.9 6.6 0.00014 26.1 1.1 36 10-46 32-67 (80)
11 PF08438 MMR_HSR1_C: GTPase of 49.0 28 0.00061 24.3 3.5 37 7-47 11-47 (109)
12 COG2519 GCD14 tRNA(1-methylade 47.4 35 0.00075 27.4 4.2 42 6-47 174-215 (256)
13 COG1244 Predicted Fe-S oxidore 44.1 27 0.00058 29.2 3.2 41 4-45 221-261 (358)
14 PHA02745 hypothetical protein; 43.5 13 0.00028 29.6 1.2 29 61-89 138-170 (265)
15 PF09879 DUF2106: Predicted me 38.5 15 0.00032 27.1 0.8 16 97-112 106-121 (153)
16 PF13732 DUF4162: Domain of un 34.1 55 0.0012 20.5 2.9 31 22-53 43-73 (84)
17 COG1591 Holliday junction reso 32.7 95 0.0021 22.6 4.2 56 29-90 6-73 (137)
18 PF02813 Retro_M: Retroviral M 31.5 35 0.00075 22.7 1.6 22 28-49 20-41 (86)
19 PHA02943 hypothetical protein; 27.7 80 0.0017 23.6 3.2 24 29-52 37-60 (165)
20 COG4037 Predicted membrane pro 23.6 38 0.00082 24.8 0.8 18 96-113 109-126 (163)
21 PRK15453 phosphoribulokinase; 22.9 95 0.0021 25.3 3.0 34 6-40 242-275 (290)
22 PF13601 HTH_34: Winged helix 22.6 1.1E+02 0.0025 19.5 2.9 24 29-53 28-51 (80)
23 cd02029 PRK_like Phosphoribulo 22.0 1E+02 0.0022 25.0 3.0 34 6-40 236-269 (277)
24 PF08643 DUF1776: Fungal famil 21.8 73 0.0016 26.0 2.2 33 19-51 1-35 (299)
25 PF02618 YceG: YceG-like famil 21.4 1.3E+02 0.0029 24.1 3.6 44 5-50 55-98 (297)
26 TIGR03433 padR_acidobact trans 21.2 1.7E+02 0.0037 19.3 3.6 41 7-52 21-61 (100)
27 cd08788 CARD_NOD2_2_CARD15 Cas 21.1 56 0.0012 21.7 1.2 22 30-51 13-34 (81)
No 1
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=100.00 E-value=2.3e-50 Score=289.90 Aligned_cols=128 Identities=53% Similarity=0.911 Sum_probs=122.8
Q ss_pred CCC-chHHHHHHHhhhhhhcCCceEE-eecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccCCccccccce
Q 032980 1 MGR-RILNNALRAIVNAERRGKATVE-LQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCRALTYRQ 78 (129)
Q Consensus 1 M~~-d~lad~lt~IrNa~~a~~~~v~-i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRv 78 (129)
|++ ||+||||||||||++++|+.|. + |+||++.+||++|++||||++|++.+++..+.++++|||..+++++||||+
T Consensus 1 m~~~~~iad~lt~IrNa~~a~~~~v~~~-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lk~~i~~~~~IS~Rv 79 (130)
T PLN00146 1 MVRRSVLNDALKTMYNAEKRGKRQVLIR-PSSKVVIKFLKVMQKHGYIGEFEVVDDHRSGKIVVELNGRLNKCGVISPRF 79 (130)
T ss_pred CCCcChHHHHHHHhHhHHHcCCCeEEEE-cChHHHHHHHHHHHHCCCCcceEEEecCCcceEEEEEcccccCCcEEEcCE
Confidence 776 9999999999999999999997 6 999999999999999999999998776667789999999989999999999
Q ss_pred eecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 79 DIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 79 y~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
|++.+|||+|..|++|+.|+|++|+|||+|||||+||+++++|||+||+||
T Consensus 80 y~~~~~l~~v~~~~~~~~g~Gi~IlSTskGimt~~eAr~~~vGGEvL~~vy 130 (130)
T PLN00146 80 DVKVKEIEAWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
T ss_pred ecCcchhhHHHhccCCCCCCEEEEEECCCccccHHHHHHcCCCCEEEEEEC
Confidence 999999999999999999999999999999999999999999999999998
No 2
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=100.00 E-value=5.6e-50 Score=287.48 Aligned_cols=129 Identities=47% Similarity=0.827 Sum_probs=123.7
Q ss_pred CCC-chHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccCCcccccccee
Q 032980 1 MGR-RILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCRALTYRQD 79 (129)
Q Consensus 1 M~~-d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy 79 (129)
|+. ||+|||||+||||++++|++|.+.|+||++.+||++|++||||.+|++.+++....+.+.|+-+.++|+.||||+|
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 774 9999999999999999999999559999999999999999999999988776677889999999999999999999
Q ss_pred ecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 80 IKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 80 ~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
++++|||+|.+||+|.+|+|++|||||+|||||+||+++++|||+||+||
T Consensus 81 ~~~~~ip~v~~~~lp~~glGi~IlSTSkGImt~~eAr~~~vGGEvLc~v~ 130 (130)
T PTZ00158 81 VTLGEFEKWANNILPSRQFGHVVLTTSYGIMDHEEARRRHTGGKILGFFY 130 (130)
T ss_pred CCcchhhHHhcCCCccccceEEEEECCCCccChHHHHHcCCCceEEEEEC
Confidence 99999999999999999999999999999999999999999999999998
No 3
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.2e-50 Score=287.63 Aligned_cols=122 Identities=36% Similarity=0.574 Sum_probs=117.8
Q ss_pred CCC-chHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccCCccccc----
Q 032980 1 MGR-RILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCRALT---- 75 (129)
Q Consensus 1 M~~-d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~k~~~Is---- 75 (129)
|++ |||||||||||||.+++|..|.+ |+||+..+||++|++||||++|++.++++++.++|+|||+.+++|+|+
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~v~~-P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~~~~v~Lky~~n~~~vI~~~~r 79 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEVVSM-PASKLKGAILKVLKKEGYIKDFEVIDDGRKGKLRVQLKYRINGCGVISPIKR 79 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccceeec-chHHHHHHHHHHHHHcCCcceEEEEeCCcceEEEEEEEeccCCCccccccee
Confidence 565 99999999999999999999998 999999999999999999999999999889999999999999999998
Q ss_pred ---c--ceeecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 76 ---Y--RQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 ---p--Rvy~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
| |+|.+.++||++.+ |+|++|||||+|||||+|||++|+|||+|||||
T Consensus 80 VSkpg~rvy~~~~~LP~v~~------g~Gi~IvSTs~GVMtd~eAr~~~vGGevLcyV~ 132 (132)
T COG0096 80 VSKPGLRVYEKKRELPAVLN------GLGIAIVSTSKGVMTDKEARKKGVGGEVLCYVW 132 (132)
T ss_pred cCCCCceeecChhhhhhhhc------CceEEEEEcCCCccChHHHHHcCCCcEEEEEEC
Confidence 5 99999999999999 799999999999999999999999999999999
No 4
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=100.00 E-value=1.2e-48 Score=280.91 Aligned_cols=128 Identities=41% Similarity=0.676 Sum_probs=121.7
Q ss_pred CC-CchHHHHHHHhhhhhhcCCceEE-eecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccCCccccccce
Q 032980 1 MG-RRILNNALRAIVNAERRGKATVE-LQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCRALTYRQ 78 (129)
Q Consensus 1 M~-~d~lad~lt~IrNa~~a~~~~v~-i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRv 78 (129)
|+ .|+||||||+||||++|+++.|. + |+|+++.+||++|++||||++|++.++++++.+.++|||..+++++|+||+
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 65 49999999999999999999985 7 999999999999999999999998777667788999999888899999999
Q ss_pred eecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 79 DIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 79 y~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
|++.+|||++..+++|+.++|++|||||+|||||+||+++++|||+||+||
T Consensus 80 y~~~~~l~~~~~~~l~~~~lGi~IlSTskGImt~~eA~~~~vGGEvL~~v~ 130 (130)
T PRK04034 80 PVKYDEFEKWEKRYLPARDFGILIVSTSKGVMSHKEAREKGIGGVLLAYVY 130 (130)
T ss_pred EcCHhHhHHHHhccCCCCCceEEEEECCCCceeHHHHHHcCCCCEEEEEEC
Confidence 999999999999999999999999999999999999999999999999999
No 5
>CHL00042 rps8 ribosomal protein S8
Probab=100.00 E-value=6.7e-47 Score=272.54 Aligned_cols=122 Identities=24% Similarity=0.352 Sum_probs=113.7
Q ss_pred CCCchHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccC-Cccccc----
Q 032980 1 MGRRILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVN-DCRALT---- 75 (129)
Q Consensus 1 M~~d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~-k~~~Is---- 75 (129)
|..|+||||||+||||++|++++|.+ |+|+++.+||++|++||||++|++.+++.++.++|+|||+.+ +.|+|+
T Consensus 1 m~~d~iad~lt~IrNa~~a~~~~v~i-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lky~~~~~~pvi~~i~~ 79 (132)
T CHL00042 1 MGNDTIADMLTRIRNANMVKKGTVRI-PATNITENIVKILLREGFIENVREHRENNKYFLVLTLKYRGNKKKPYITTLKR 79 (132)
T ss_pred CCcchHHHHHHHhHHHHHCCCCEEEE-eccHHHHHHHHHHHHCCcccceEEEecCCeeEEEEEEEeecCCCceeccccEE
Confidence 77799999999999999999999999 999999999999999999999999877777889999999853 246554
Q ss_pred ---c--ceeecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 76 ---Y--RQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 ---p--Rvy~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
| |+|++.+|||++.+ |+|++|||||+|||||+||+++++|||+||+||
T Consensus 80 iSkPg~Rvy~~~~~L~~~~~------g~G~~IlSTskGimt~~eA~~~~iGGe~L~~v~ 132 (132)
T CHL00042 80 ISKPGLRIYSNYKEIPRVLG------GMGIVILSTSKGIMTDREARLKGIGGEILCYIW 132 (132)
T ss_pred EcCCCceeEcCHhHHHHHhC------CCcEEEEECCCCcccHHHHHHcCCCCEEEEEEC
Confidence 7 99999999999998 799999999999999999999999999999999
No 6
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=100.00 E-value=2.1e-45 Score=264.06 Aligned_cols=121 Identities=26% Similarity=0.387 Sum_probs=113.3
Q ss_pred CCCchHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccCCccccc-----
Q 032980 1 MGRRILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCRALT----- 75 (129)
Q Consensus 1 M~~d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~k~~~Is----- 75 (129)
|..|+||||||+||||++|++.+|.+ |+|+++.+||++|++||||++|++.++++..+++|+|||+.+ +|+|+
T Consensus 1 m~~d~i~d~lt~IrNa~~~~~~~v~i-p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lky~~~-~pvi~~i~~I 78 (130)
T PRK00136 1 SMTDPIADMLTRIRNAQMAKHETVSM-PASKLKVAIAEILKEEGYIKDYEVEEDGKQGILRITLKYGEG-EPVIEGIKRV 78 (130)
T ss_pred CCcChHHHHHHHHHHHHHcCCCeEEe-cccHHHHHHHHHHHHCCcccceEEEecCCcceEEEEEecCCC-CcccccceEe
Confidence 77799999999999999999999998 999999999999999999999999876556679999999865 67775
Q ss_pred --c--ceeecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 76 --Y--RQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 --p--Rvy~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
| |+|++.+||+++.+ |+|++|+|||+|||||+||+++++|||+||+||
T Consensus 79 SkPg~Riy~~~~~l~~~~~------g~G~~IlSTs~Gimt~~eA~~~~iGGeiL~~v~ 130 (130)
T PRK00136 79 SKPGLRVYKKKDELPKVLN------GLGIAIVSTSKGVMTDREARKAGVGGEVLCYVW 130 (130)
T ss_pred cCCCcceEcCHhHHHHHHC------CCCEEEEEcCCCeeeHHHHHHhCCCCEEEEEEC
Confidence 7 99999999999998 799999999999999999999999999999998
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=3.3e-44 Score=257.29 Aligned_cols=119 Identities=34% Similarity=0.472 Sum_probs=110.9
Q ss_pred chHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeCCCc-ceEEEEEecccCCccccc-------
Q 032980 4 RILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRV-GKIKVELLGRVNDCRALT------- 75 (129)
Q Consensus 4 d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~-~~i~I~Lky~~~k~~~Is------- 75 (129)
|+|||+|++||||++++++.|.+ |+|+++.++|++|++||||++|++.++++. ++++|+|||+.++.|+|+
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 89999999999999999999999 999999999999999999999999887764 679999999655556655
Q ss_pred c--ceeecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 76 Y--RQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 p--Rvy~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
| |+|++.+||+++.+ |+|++|+|||+||||++||+++++|||+||+||
T Consensus 80 p~~r~y~~~~~L~~~~~------g~g~~IlSTskGImt~~eA~~~~vGGevL~~V~ 129 (129)
T PF00410_consen 80 PGRRVYISYKELPKVKN------GLGILILSTSKGIMTHREARKLNVGGEVLCYVW 129 (129)
T ss_dssp TTCCCEESGTGSHHSCT------TTSEEEEEETTEEEEHHHHHHHTSEEEEEEEEE
T ss_pred CCcceecCHHHHHHHhC------CCeEEEEEcCCCcEeHHHHHHcCCCCEEEEEEC
Confidence 4 99999999999997 799999999999999999999999999999998
No 8
>KOG1754 consensus 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-40 Score=232.09 Aligned_cols=129 Identities=48% Similarity=0.876 Sum_probs=126.6
Q ss_pred CCC-chHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeCCCcceEEEEEecccCCcccccccee
Q 032980 1 MGR-RILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCRALTYRQD 79 (129)
Q Consensus 1 M~~-d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy 79 (129)
|+. +.|||+|..|+||.++||++|.+.|+|+....||.+|+++|||.+|++.+|++++++.|+|..|.|+|++||||+.
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 565 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccchhhhhcccCCCCCceEEEEECCCCcccHHHHHHcCCCeEEEEEEC
Q 032980 80 IKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 80 ~~~~~l~~~~~~~~~~~~~Gi~IlSTs~Gimt~~eA~~~~~GGevL~~v~ 129 (129)
++.++|++|.+..+|++++|+.+++||.|+|+|+||+.+++|||+||++|
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=58.69 E-value=4.6 Score=26.74 Aligned_cols=46 Identities=20% Similarity=0.327 Sum_probs=24.8
Q ss_pred HHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEEeC
Q 032980 8 NALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDP 54 (129)
Q Consensus 8 d~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~~ 54 (129)
..|+.+-.+...+...=. .-.+..-..++.-|.++|||.|+.+...
T Consensus 3 kIL~~l~~~~~~~~~~~~-~~~~~~~~~il~~L~d~GyI~G~~~~~~ 48 (88)
T PF09639_consen 3 KILKYLYKCMKNGKEPDP-DITDSYWSDILRMLQDEGYIKGVSVVRY 48 (88)
T ss_dssp HHHHHHHHH-S---HHHH-TS-HHHHHHHHHHHHHHTSEE--EESSS
T ss_pred hHHHHHHHHHcCCCCCCc-chhHHHHHHHHHHHHHCCCccceEEEec
Confidence 345555555443333211 1234566788889999999999988654
No 10
>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=55.91 E-value=6.6 Score=26.05 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=32.0
Q ss_pred HHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcc
Q 032980 10 LRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYV 46 (129)
Q Consensus 10 lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI 46 (129)
..+|+++.+..-..+.+ |+.......|..|.+||.|
T Consensus 32 ~E~l~~~L~~~yp~i~~-Ps~e~l~~~L~~Li~erkI 67 (80)
T PF10264_consen 32 QETLREHLRKHYPGIAI-PSQEVLYNTLGTLIKERKI 67 (80)
T ss_pred HHHHHHHHHHhCCCCCC-CCHHHHHHHHHHHHHcCce
Confidence 45788888888888997 9999999999999999987
No 11
>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=49.01 E-value=28 Score=24.27 Aligned_cols=37 Identities=11% Similarity=0.139 Sum_probs=23.9
Q ss_pred HHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCccc
Q 032980 7 NNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVK 47 (129)
Q Consensus 7 ad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~ 47 (129)
.+.+.+|+..+ .....+ |.|-..+-+|+-+.++|||+
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 46677888755 445555 99999999999999999998
No 12
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=47.40 E-value=35 Score=27.38 Aligned_cols=42 Identities=21% Similarity=0.348 Sum_probs=37.3
Q ss_pred HHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCccc
Q 032980 6 LNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVK 47 (129)
Q Consensus 6 lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~ 47 (129)
..|++.++.++.+.+-..|...|+..........|.+.||+.
T Consensus 174 PW~~le~~~~~Lkpgg~~~~y~P~veQv~kt~~~l~~~g~~~ 215 (256)
T COG2519 174 PWNVLEHVSDALKPGGVVVVYSPTVEQVEKTVEALRERGFVD 215 (256)
T ss_pred hHHHHHHHHHHhCCCcEEEEEcCCHHHHHHHHHHHHhcCccc
Confidence 458899999999999887777899999999999999998865
No 13
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=44.15 E-value=27 Score=29.22 Aligned_cols=41 Identities=20% Similarity=0.447 Sum_probs=36.0
Q ss_pred chHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCc
Q 032980 4 RILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGY 45 (129)
Q Consensus 4 d~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGy 45 (129)
+.|.|++..|+ |...+-..+++.|.+-..--+.+.|++.|.
T Consensus 221 eAI~D~i~Si~-~~~~~~d~iSinptnVqKgTlvE~lw~~g~ 261 (358)
T COG1244 221 EAIEDVISSIV-AAKPGTDTISINPTNVQKGTLVEKLWRRGL 261 (358)
T ss_pred HHHHHHHHHHH-HhccCCCeEEecccccchhhHHHHHHHcCC
Confidence 56889999999 888999999998988888888999988875
No 14
>PHA02745 hypothetical protein; Provisional
Probab=43.46 E-value=13 Score=29.64 Aligned_cols=29 Identities=14% Similarity=0.046 Sum_probs=23.8
Q ss_pred EEEEecccCCccccc--c--ceeecccchhhhh
Q 032980 61 KVELLGRVNDCRALT--Y--RQDIKASEIEGYT 89 (129)
Q Consensus 61 ~I~Lky~~~k~~~Is--p--Rvy~~~~~l~~~~ 89 (129)
.=.||||.+.++++. | .||++..+|....
T Consensus 138 RWTLKyR~~~pGLVEL~P~SgVYV~~~~L~~C~ 170 (265)
T PHA02745 138 RWTLKHRYPGSGLVELLPHSGVYINAINLSNCK 170 (265)
T ss_pred cceeeccCCCCCcEEeecCCceEEeHHHHHHHH
Confidence 347999999988888 7 9999998886544
No 15
>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=38.55 E-value=15 Score=27.12 Aligned_cols=16 Identities=31% Similarity=0.843 Sum_probs=14.1
Q ss_pred CceEEEEECCCCcccH
Q 032980 97 QWGYVVITTPDGVLDH 112 (129)
Q Consensus 97 ~~Gi~IlSTs~Gimt~ 112 (129)
=+|..|+||+.||++.
T Consensus 106 y~GTTIvS~PGGIlDE 121 (153)
T PF09879_consen 106 YFGTTIVSHPGGILDE 121 (153)
T ss_pred cccceEecCCChhHHH
Confidence 4799999999999874
No 16
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=34.07 E-value=55 Score=20.48 Aligned_cols=31 Identities=13% Similarity=0.290 Sum_probs=25.2
Q ss_pred ceEEeecchHHHHHHHHhhccCCcccceEEEe
Q 032980 22 ATVELQPISTVMSSFLNIMKYRGYVKDFQVYD 53 (129)
Q Consensus 22 ~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~~ 53 (129)
-.+.+ .......++|+.|.++|+|.+|+...
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 45666 56667799999999999999998754
No 17
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=32.74 E-value=95 Score=22.61 Aligned_cols=56 Identities=13% Similarity=0.140 Sum_probs=36.3
Q ss_pred chHHHHHHHHhhccCCccc------c------eEEEeCCCcceEEEEEecccCCccccccceeecccchhhhhc
Q 032980 29 ISTVMSSFLNIMKYRGYVK------D------FQVYDPHRVGKIKVELLGRVNDCRALTYRQDIKASEIEGYTV 90 (129)
Q Consensus 29 ~Sk~~~~il~iL~~eGyI~------~------~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy~~~~~l~~~~~ 90 (129)
-|..=.++.++|+++||=- + --++..+..-.+.|+.|++-.. ++|++.+++.++..
T Consensus 6 G~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~~------kiYl~~e~ve~L~~ 73 (137)
T COG1591 6 GSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRET------KIYLDKEQVEKLVE 73 (137)
T ss_pred cchHHHHHHHHHHhcCceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccCC------cEEEcHHHHHHHHH
Confidence 3566678999999999842 1 0011112234688999986421 67999988877654
No 18
>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=31.49 E-value=35 Score=22.73 Aligned_cols=22 Identities=14% Similarity=0.383 Sum_probs=17.7
Q ss_pred cchHHHHHHHHhhccCCcccce
Q 032980 28 PISTVMSSFLNIMKYRGYVKDF 49 (129)
Q Consensus 28 p~Sk~~~~il~iL~~eGyI~~~ 49 (129)
|++|-+-++|..|.+||.+.+=
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 8899999999999999999854
No 19
>PHA02943 hypothetical protein; Provisional
Probab=27.70 E-value=80 Score=23.64 Aligned_cols=24 Identities=13% Similarity=0.131 Sum_probs=19.9
Q ss_pred chHHHHHHHHhhccCCcccceEEE
Q 032980 29 ISTVMSSFLNIMKYRGYVKDFQVY 52 (129)
Q Consensus 29 ~Sk~~~~il~iL~~eGyI~~~~~~ 52 (129)
+-.....+|.+|.+||+|+.++++
T Consensus 37 S~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 37 SHSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred CHHHHHHHHHHHHHcCceEEEeec
Confidence 345678899999999999998764
No 20
>COG4037 Predicted membrane protein [Function unknown]
Probab=23.59 E-value=38 Score=24.78 Aligned_cols=18 Identities=33% Similarity=0.787 Sum_probs=14.9
Q ss_pred CCceEEEEECCCCcccHH
Q 032980 96 RQWGYVVITTPDGVLDHE 113 (129)
Q Consensus 96 ~~~Gi~IlSTs~Gimt~~ 113 (129)
.-+|..|+|++.|+++.-
T Consensus 109 ~yfGTtIvS~PGGilDEI 126 (163)
T COG4037 109 RYFGTTIVSHPGGILDEI 126 (163)
T ss_pred EEcccEEecCCChhHHHH
Confidence 357999999999998753
No 21
>PRK15453 phosphoribulokinase; Provisional
Probab=22.92 E-value=95 Score=25.32 Aligned_cols=34 Identities=15% Similarity=0.070 Sum_probs=29.0
Q ss_pred HHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhh
Q 032980 6 LNNALRAIVNAERRGKATVELQPISTVMSSFLNIM 40 (129)
Q Consensus 6 lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL 40 (129)
..-+|+-|.++++++...+.+ |-.|+-++.--||
T Consensus 242 ~~yl~~~~~~~~~s~~~~~v~-~g~~~~~a~~~i~ 275 (290)
T PRK15453 242 FPYLLSMIQGSFMSRANTIVV-PGGKMGLAMELIL 275 (290)
T ss_pred HHHHHHHhccchhcCCCcEEe-cCchHHHHHHHHH
Confidence 346899999999999999998 9999988765554
No 22
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=22.56 E-value=1.1e+02 Score=19.52 Aligned_cols=24 Identities=17% Similarity=0.286 Sum_probs=15.6
Q ss_pred chHHHHHHHHhhccCCcccceEEEe
Q 032980 29 ISTVMSSFLNIMKYRGYVKDFQVYD 53 (129)
Q Consensus 29 ~Sk~~~~il~iL~~eGyI~~~~~~~ 53 (129)
.+++. .-|+.|.++|||+.-....
T Consensus 28 ~g~Ls-~hL~~Le~~GyV~~~k~~~ 51 (80)
T PF13601_consen 28 DGNLS-KHLKKLEEAGYVEVEKEFE 51 (80)
T ss_dssp HHHHH-HHHHHHHHTTSEEEEEE-S
T ss_pred HHHHH-HHHHHHHHCCCEEEEEecc
Confidence 34444 4467799999999765443
No 23
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=22.04 E-value=1e+02 Score=25.04 Aligned_cols=34 Identities=12% Similarity=0.074 Sum_probs=29.4
Q ss_pred HHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhh
Q 032980 6 LNNALRAIVNAERRGKATVELQPISTVMSSFLNIM 40 (129)
Q Consensus 6 lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL 40 (129)
..-+|+-|.++++++...+.+ |-.|+-++.--||
T Consensus 236 ~~~~~~~~~~~~~s~~~~~v~-~g~~~~~a~~~i~ 269 (277)
T cd02029 236 FPYLLNMLHDSFMSRPNTIVV-PGGKMGLAMELIL 269 (277)
T ss_pred HHHHHHhhccchhcCCCcEEe-cCchHHHHHHHHH
Confidence 456899999999999999998 9999988876554
No 24
>PF08643 DUF1776: Fungal family of unknown function (DUF1776); InterPro: IPR013952 This is a fungal protein of unknown function. One of the proteins P32792 from SWISSPROT has been localised to the mitochondria [].
Probab=21.76 E-value=73 Score=26.02 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=26.4
Q ss_pred cCCceEEe--ecchHHHHHHHHhhccCCcccceEE
Q 032980 19 RGKATVEL--QPISTVMSSFLNIMKYRGYVKDFQV 51 (129)
Q Consensus 19 a~~~~v~i--~p~Sk~~~~il~iL~~eGyI~~~~~ 51 (129)
|+++-|.| .|+..++..++.=|++.|||==...
T Consensus 1 aR~evVvI~Gs~~~PltR~la~DLeRRGFIV~v~~ 35 (299)
T PF08643_consen 1 ARKEVVVIAGSPHDPLTRSLALDLERRGFIVYVTV 35 (299)
T ss_pred CceeEEEEECCCCCccHHHHHHHHhhCCeEEEEEe
Confidence 45666766 6889999999999999999964433
No 25
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=21.40 E-value=1.3e+02 Score=24.09 Aligned_cols=44 Identities=9% Similarity=0.140 Sum_probs=28.4
Q ss_pred hHHHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceE
Q 032980 5 ILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQ 50 (129)
Q Consensus 5 ~lad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~ 50 (129)
+..+++..|.++..... .|.| |--....+|++.|.+++.++.-.
T Consensus 55 S~~eil~~L~~g~~~~~-~vTI-pEG~t~~~i~~~l~~~~~~~~~~ 98 (297)
T PF02618_consen 55 SYKEILSILTSGKVAQV-RVTI-PEGFTLEQIAQRLAEKGGISKED 98 (297)
T ss_dssp -HHHHHHHHHH-----E-EEEE--TT--HHHHHHHHHCSTTEE---
T ss_pred CHHHHHHHHHhccccee-EEEe-cCCCcHHHHHHHHHhccCCCHHH
Confidence 56788999988877764 8887 99999999999999999995443
No 26
>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=21.15 E-value=1.7e+02 Score=19.28 Aligned_cols=41 Identities=10% Similarity=0.094 Sum_probs=26.5
Q ss_pred HHHHHHhhhhhhcCCceEEeecchHHHHHHHHhhccCCcccceEEE
Q 032980 7 NNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVY 52 (129)
Q Consensus 7 ad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eGyI~~~~~~ 52 (129)
+++...|++-. .....+ .......+|+-|.++|+|......
T Consensus 21 Yei~~~l~~~~---~~~~~i--~~gtlY~~L~rLe~~GlI~~~~~~ 61 (100)
T TIGR03433 21 YGIAQRIQQIS---EDVLQV--EEGSLYPALHRLERRGWIAAEWGE 61 (100)
T ss_pred HHHHHHHHHHc---CCcccc--CCCcHHHHHHHHHHCCCeEEEeee
Confidence 34555555532 223444 445677889999999999986443
No 27
>cd08788 CARD_NOD2_2_CARD15 Caspase activation and recruitment domain of NOD2, repeat 2. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 2. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=21.06 E-value=56 Score=21.71 Aligned_cols=22 Identities=14% Similarity=0.421 Sum_probs=18.8
Q ss_pred hHHHHHHHHhhccCCcccceEE
Q 032980 30 STVMSSFLNIMKYRGYVKDFQV 51 (129)
Q Consensus 30 Sk~~~~il~iL~~eGyI~~~~~ 51 (129)
+.....+|+.|++.|+|+.++-
T Consensus 13 ~~~V~~~Ld~ll~~G~is~~Ec 34 (81)
T cd08788 13 QHHVDGALELLLTRGFFSSYDC 34 (81)
T ss_pred HHHHHHHHHHHHHcCCccHhhc
Confidence 3567899999999999998864
Done!