Query psy8562
Match_columns 205
No_of_seqs 126 out of 1111
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 22:01:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8562.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8562hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05618 50S ribosomal protein 100.0 5.5E-60 1.2E-64 395.6 25.4 191 1-194 4-194 (197)
2 TIGR00731 ctc_TL5 ribosomal pr 100.0 1.5E-59 3.3E-64 386.9 22.8 175 3-183 1-175 (176)
3 PRK05943 50S ribosomal protein 100.0 1.8E-33 4E-38 210.1 13.2 93 1-93 2-94 (94)
4 PF01386 Ribosomal_L25p: Ribos 100.0 1.6E-31 3.5E-36 197.3 10.7 88 3-90 1-88 (88)
5 cd00495 Ribosomal_L25_TL5_CTC 100.0 6.1E-31 1.3E-35 195.1 11.8 91 1-92 1-91 (91)
6 COG1825 RplY Ribosomal protein 100.0 3.2E-29 6.9E-34 186.8 9.6 92 1-93 2-93 (93)
7 PF14693 Ribosomal_TL5_C: Ribo 99.9 1.2E-27 2.5E-32 176.8 9.4 88 97-189 1-88 (88)
8 TIGR01764 excise DNA binding d 75.0 10 0.00022 23.2 4.9 37 10-51 12-48 (49)
9 PF11113 Phage_head_chap: Head 71.4 8.6 0.00019 26.1 4.0 31 65-98 11-41 (56)
10 PF12000 Glyco_trans_4_3: Gkyc 71.1 2.9 6.2E-05 34.5 2.0 21 13-33 54-74 (171)
11 CHL00013 rpoA RNA polymerase a 69.0 11 0.00024 34.3 5.4 52 128-186 84-135 (327)
12 PF01000 RNA_pol_A_bac: RNA po 64.2 8.6 0.00019 28.9 3.2 28 156-186 64-92 (112)
13 PRK14751 tetracycline resistan 63.7 6.4 0.00014 22.6 1.8 23 71-93 3-25 (28)
14 PF13028 DUF3889: Protein of u 60.4 35 0.00076 25.7 5.9 35 58-92 61-96 (97)
15 cd06928 RNAP_alpha_NTD N-termi 57.2 30 0.00066 29.3 5.7 40 140-185 85-124 (215)
16 PF12728 HTH_17: Helix-turn-he 56.7 25 0.00054 22.2 4.0 37 11-52 13-49 (51)
17 TIGR02027 rpoA DNA-directed RN 47.4 41 0.0009 30.0 5.2 52 128-186 64-116 (297)
18 PRK05182 DNA-directed RNA poly 43.2 42 0.00091 30.1 4.6 40 141-186 95-134 (310)
19 PRK10646 ADP-binding protein; 41.3 25 0.00054 28.4 2.6 26 70-97 63-88 (153)
20 TIGR00150 HI0065_YjeE ATPase, 33.8 26 0.00057 27.6 1.6 26 70-97 57-82 (133)
21 PF13670 PepSY_2: Peptidase pr 33.5 1.7E+02 0.0036 20.5 5.8 50 36-87 24-81 (83)
22 PF06434 Aconitase_2_N: Aconit 32.3 31 0.00068 29.3 1.9 38 142-185 116-153 (204)
23 COG3603 Uncharacterized conser 31.4 78 0.0017 24.9 3.8 28 119-146 31-60 (128)
24 COG4856 Uncharacterized protei 31.1 61 0.0013 30.2 3.7 60 123-186 253-316 (403)
25 PF12920 TcdA_TcdB_pore: TcdA/ 28.9 4.4E+02 0.0095 26.5 9.4 120 5-160 401-520 (663)
26 PF02367 UPF0079: Uncharacteri 27.4 19 0.0004 28.1 -0.3 27 71-99 51-77 (123)
27 PF14467 DUF4426: Domain of un 25.8 3.2E+02 0.007 21.3 8.4 57 54-111 33-95 (122)
28 PRK08652 acetylornithine deace 24.0 57 0.0012 28.5 2.2 24 10-34 291-314 (347)
29 PRK08737 acetylornithine deace 23.0 59 0.0013 29.3 2.1 21 13-34 314-334 (364)
30 PRK14979 DNA-directed RNA poly 22.9 1.7E+02 0.0037 24.6 4.7 27 155-185 91-117 (195)
31 PF07708 Tash_PEST: Tash prote 21.8 65 0.0014 17.2 1.3 10 140-149 5-14 (19)
32 PF08038 Tom7: TOM7 family; I 21.3 11 0.00025 24.0 -2.0 12 20-31 15-26 (42)
33 PRK00783 DNA-directed RNA poly 21.2 1.6E+02 0.0034 25.4 4.4 29 155-186 103-132 (263)
34 smart00662 RPOLD RNA polymeras 20.9 2.1E+02 0.0045 24.2 4.9 28 155-185 91-120 (224)
35 PRK08554 peptidase; Reviewed 20.7 72 0.0016 29.6 2.2 45 5-50 379-426 (438)
36 cd04762 HTH_MerR-trunc Helix-T 20.4 1.7E+02 0.0036 17.2 3.3 36 11-50 12-47 (49)
No 1
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=100.00 E-value=5.5e-60 Score=395.60 Aligned_cols=191 Identities=39% Similarity=0.724 Sum_probs=178.4
Q ss_pred CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8562 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA 80 (205)
Q Consensus 1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p 80 (205)
++|+|++|+.+||+++||||++|+||||+||++.+|++++++.++|.+++++..+.+++|+|+++|++++||+|++|+||
T Consensus 4 ~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~~~~~~~i~v~~~~l~k~l~~~~~~~~~i~L~i~g~~~~vlikevQ~~p 83 (197)
T PRK05618 4 ITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGAFLSTLLDLEVGGKKQKVLVKDVQRHP 83 (197)
T ss_pred EEEEEEEcCcCCChHHHHHHHCCCCcEEEECCCCCCEEEEECHHHHHHHHhcCCceeEEEEEEECCEEEEEEEeeeeecc
Confidence 37999999999999999999999999999999999999999999999999765556889999999999999999999999
Q ss_pred cCCceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEec
Q psy8562 81 YKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSD 160 (205)
Q Consensus 81 v~~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~D 160 (205)
++++++|+|||+++++++|+++|||+|+|++.+++.| .||+|++.+++|+|+|+|.+||++|+||||+|++||+|||+|
T Consensus 84 v~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k-~GG~l~~~~~~v~v~~~p~~IP~~I~VDVs~L~~Gd~i~v~D 162 (197)
T PRK05618 84 VKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVK-LGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHVSD 162 (197)
T ss_pred CCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccc-cceEEEEEEEEEEEEEcHHHCCccEEEEcccCCCCCEEEeee
Confidence 9999999999999999999999999999988777766 599999999999999999999999999999999999999999
Q ss_pred cCCCCCeEEeccCCCCceEEEEECccccccCCCC
Q psy8562 161 IKLPRGVSVIHSTEEDPTIATAIIPVNTLESDNN 194 (205)
Q Consensus 161 l~lp~gv~~~~~~d~~~vV~sv~~~~~~~~~~~~ 194 (205)
|++|+|+++.. +++++||+|.+|+.+++++++
T Consensus 163 l~lp~~v~i~~--~~~~~v~~V~~~~~~~~~e~~ 194 (197)
T PRK05618 163 LKLPEGVKLLD--DPDEVVATVVAPRGEEEEEEE 194 (197)
T ss_pred ecCCCCcEEcC--CCCcEEEEEEcCCcccccccc
Confidence 99999999763 899999999999876655443
No 2
>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology.
Probab=100.00 E-value=1.5e-59 Score=386.86 Aligned_cols=175 Identities=34% Similarity=0.618 Sum_probs=168.0
Q ss_pred EEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecccC
Q psy8562 3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYK 82 (205)
Q Consensus 3 l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~pv~ 82 (205)
|+|+.|+.+||+++|||||+|+||||+||++.+++++++++++|.+++++.+ .+++|+|+++|++++||+||+|+||++
T Consensus 1 l~a~~R~~~gk~~~r~LR~~G~VPaVvYG~~~~~~~i~v~~~el~k~l~~~~-~~~~i~L~v~g~~~~vlikevQ~~pv~ 79 (176)
T TIGR00731 1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRKGA-TSTVLTLEIGGKEFKVLVKDYQYNPVT 79 (176)
T ss_pred CeEEEeCCCCChHHHHHHHCCCccEEEECCCCCCEEEEECHHHHHHHHhccC-CcEEEEEEECCEEEEEEEehhhhccCC
Confidence 5799999999999999999999999999999999999999999999998765 588999999999999999999999999
Q ss_pred CceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEeccC
Q psy8562 83 KLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIK 162 (205)
Q Consensus 83 ~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~Dl~ 162 (205)
++++|+|||+++++++|+++|||+|+|+ ++|+| .||+|++.+++|+|+|+|.+||++|+||||+|++||+||++||+
T Consensus 80 ~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk-~GG~l~~~~~~v~v~~~p~~IPe~I~VDvs~L~iGd~i~v~Dl~ 156 (176)
T TIGR00731 80 NEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVK-NGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLE 156 (176)
T ss_pred CCeEEEEeEEeCCCCEEEEEeeEEEecc--ccccc-CCcEEEEEEEEEEEEECHHHCCccEEEECccCCCCCEEEEeecc
Confidence 9999999999999999999999999996 57999 89999999999999999999999999999999999999999999
Q ss_pred CCCCeEEeccCCCCceEEEEE
Q psy8562 163 LPRGVSVIHSTEEDPTIATAI 183 (205)
Q Consensus 163 lp~gv~~~~~~d~~~vV~sv~ 183 (205)
+|+|+++.. +++++||+|.
T Consensus 157 lp~gv~~~~--d~~~~v~~V~ 175 (176)
T TIGR00731 157 LPAGVSFIT--DDDEVVVTVI 175 (176)
T ss_pred CCCCcEEcc--CCCcEEEEEe
Confidence 999999763 8999999984
No 3
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=100.00 E-value=1.8e-33 Score=210.11 Aligned_cols=93 Identities=38% Similarity=0.580 Sum_probs=88.7
Q ss_pred CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8562 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA 80 (205)
Q Consensus 1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p 80 (205)
++|+|++|+.+||+++|+||++|+|||||||++.+|++++++.++|.+++++.++.+++|+|+++|++++|++||+|+||
T Consensus 2 ~~l~a~~R~~~gk~~~r~lR~~G~vPaViYG~~~~~~~i~v~~~el~k~l~~~~~~~~~i~L~v~g~~~~v~ikevQ~~p 81 (94)
T PRK05943 2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVITLVIDGKEVKVKVQAVQRHP 81 (94)
T ss_pred eEEEEEEeCcCCChHHHHHHHCCCCCEEEECCCCCcEEEEEcHHHHHHHHhcCCCcceEEEEEECCEEEEEEEeeeecCc
Confidence 47999999999999999999999999999999999999999999999999877656789999999999999999999999
Q ss_pred cCCceeEEEEEEe
Q psy8562 81 YKKLVLHADFQRV 93 (205)
Q Consensus 81 v~~~i~HvDF~~v 93 (205)
+|++++|||||+|
T Consensus 82 v~~~i~HvDF~~v 94 (94)
T PRK05943 82 FKPKLEHIDFVRA 94 (94)
T ss_pred CCCCeEeEeeeeC
Confidence 9999999999985
No 4
>PF01386 Ribosomal_L25p: Ribosomal L25p family; InterPro: IPR020055 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 [, ]. This entry models the short-form of the ribosomal L25 protein. The long-form has homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and Haemophilus influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA.; GO: 0003735 structural constituent of ribosome, 0008097 5S rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z 3KIY_Z ....
Probab=99.97 E-value=1.6e-31 Score=197.34 Aligned_cols=88 Identities=33% Similarity=0.567 Sum_probs=83.3
Q ss_pred EEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecccC
Q psy8562 3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYK 82 (205)
Q Consensus 3 l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~pv~ 82 (205)
|+|++|+.+||+++|+||++|+|||||||++.+|++|+++.++|.+++++..+.+++|+|+++|++++||+||+|+||++
T Consensus 1 L~a~~R~~~gk~~~r~LR~~G~iPaviYG~~~~~~~i~v~~~~l~k~~~~~~~~~~~i~L~i~g~~~~vlikevQ~~p~~ 80 (88)
T PF01386_consen 1 LKAEKREETGKSAARRLRREGKIPAVIYGKGKESIPISVDEKELEKLLRRKHGENSVIELNIDGKKYNVLIKEVQRDPVT 80 (88)
T ss_dssp EEEEESSSTSSSHHHHHHHTTEEEEEEEESSEEEEEEEEEHHHHHHHHTHHHTTTSEEEEEETTEEEEEEEEEEEEESSS
T ss_pred CeEEEcCcCCCHHHHHHHHcCCceEEEECCCCCCEEEEEeHHHHHHHHHhcCCceEEEEEEECCEEEEEEEEeeeeCCCC
Confidence 78999999999999999999999999999999999999999999999953334578999999999999999999999999
Q ss_pred CceeEEEE
Q psy8562 83 KLVLHADF 90 (205)
Q Consensus 83 ~~i~HvDF 90 (205)
++++||||
T Consensus 81 ~~i~HvDF 88 (88)
T PF01386_consen 81 DKILHVDF 88 (88)
T ss_dssp SSEEEEEE
T ss_pred CCeEeccC
Confidence 99999999
No 5
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=99.97 E-value=6.1e-31 Score=195.11 Aligned_cols=91 Identities=41% Similarity=0.693 Sum_probs=87.0
Q ss_pred CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8562 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA 80 (205)
Q Consensus 1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p 80 (205)
.+|+|.+|+.+||+++|+||++|+|||||||++.+|++|+++.++|.+++++.+ .+++|+|+++|+++.|++||+|+||
T Consensus 1 ~~l~a~~R~~~gk~~~r~lR~~G~iPavvYG~~~~~~~i~v~~~~l~k~l~~~~-~~~~~~L~i~g~~~~~~ikevQ~~p 79 (91)
T cd00495 1 LTLKAEKREETGKGASRRLRRAGKVPAVIYGKGKEPISISVDEKELEKLLRKEG-RSTLIELNIDGKKENVLIKDVQRHP 79 (91)
T ss_pred CeEEEEEcccCCChHHHHHHHCCCCCEEEECCCCCCEEEEEcHHHHHHHHhhcC-CceEEEEEECCEEEEEEEehhhhcc
Confidence 479999999999999999999999999999999999999999999999998776 5789999999999999999999999
Q ss_pred cCCceeEEEEEE
Q psy8562 81 YKKLVLHADFQR 92 (205)
Q Consensus 81 v~~~i~HvDF~~ 92 (205)
++++++|||||+
T Consensus 80 v~~~i~HvDF~~ 91 (91)
T cd00495 80 VKDKILHVDFLR 91 (91)
T ss_pred CCCCEEEEeccC
Confidence 999999999985
No 6
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.2e-29 Score=186.85 Aligned_cols=92 Identities=39% Similarity=0.643 Sum_probs=89.0
Q ss_pred CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8562 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA 80 (205)
Q Consensus 1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p 80 (205)
+.|+|+.|+..||+++|+||++|++|||+||++.+|+++++++++|.+++++.+ .|++|+|+++|++..|++|++|+||
T Consensus 2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~g~~~v~i~l~~~~~~k~~~~~~-~~~v~~l~v~g~~~~Vlvkd~Q~~p 80 (93)
T COG1825 2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGGGKEPVNIALDHHEFAKALRKLG-YSTVITLEVDGKEIKVLVKDVQRHP 80 (93)
T ss_pred ceeceeEecccCcchhHhHHhcCCCCEEEECCCCCCceEEEcHHHHHHHHhhcc-cceEEEEEECCeEEEEEehhhhhCc
Confidence 578999999999999999999999999999999999999999999999999887 7899999999999999999999999
Q ss_pred cCCceeEEEEEEe
Q psy8562 81 YKKLVLHADFQRV 93 (205)
Q Consensus 81 v~~~i~HvDF~~v 93 (205)
+++.++|+||+++
T Consensus 81 ~~~~~~HvDf~~v 93 (93)
T COG1825 81 LTDEVQHIDFLRV 93 (93)
T ss_pred ccCceeecccccC
Confidence 9999999999975
No 7
>PF14693 Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal domain; PDB: 1FEU_D 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z ....
Probab=99.95 E-value=1.2e-27 Score=176.84 Aligned_cols=88 Identities=35% Similarity=0.776 Sum_probs=76.6
Q ss_pred CeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCC
Q psy8562 97 KKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEED 176 (205)
Q Consensus 97 ~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~ 176 (205)
++|+++|||+|+|+ ++|+| .||+|++.+++|+|+|+|++||++|++|||+|++||+||++||++|+|+++.. |+|
T Consensus 1 e~v~~~VPv~~~G~--~~gvk-~Gg~l~~~~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~~--d~~ 75 (88)
T PF14693_consen 1 EKVKVEVPVHFVGE--SPGVK-KGGILQQVLREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEILD--DPE 75 (88)
T ss_dssp S-EEEEEEEEEESS--SHHHC-TTSEEEESTSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEESS---TT
T ss_pred CeEEEEEeEEEEcc--cccCc-CCcEEEEEEeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEcC--CCC
Confidence 68999999999996 79999 89999999999999999999999999999999999999999999999999874 899
Q ss_pred ceEEEEECccccc
Q psy8562 177 PTIATAIIPVNTL 189 (205)
Q Consensus 177 ~vV~sv~~~~~~~ 189 (205)
++||+|..|++++
T Consensus 76 ~vV~~v~~~~~ee 88 (88)
T PF14693_consen 76 TVVASVVAPRVEE 88 (88)
T ss_dssp SEEEEEE-SCSS-
T ss_pred cEEEEEeccccCC
Confidence 9999999999764
No 8
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=75.04 E-value=10 Score=23.16 Aligned_cols=37 Identities=14% Similarity=0.143 Sum_probs=29.2
Q ss_pred CCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhh
Q psy8562 10 KKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALK 51 (205)
Q Consensus 10 ~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~ 51 (205)
..+.+..+++.++|.+|++.-|+ ...++..+|.+.++
T Consensus 12 gis~~ti~~~~~~g~i~~~~~g~-----~~~~~~~~l~~~~~ 48 (49)
T TIGR01764 12 GVSKDTVYRLIHEGELPAYRVGR-----HYRIPREDVDEYLE 48 (49)
T ss_pred CCCHHHHHHHHHcCCCCeEEeCC-----eEEEeHHHHHHHHh
Confidence 35667788999999999986542 46789999998875
No 9
>PF11113 Phage_head_chap: Head assembly gene product; InterPro: IPR021049 This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex [].
Probab=71.39 E-value=8.6 Score=26.12 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=27.4
Q ss_pred CCeEEEEEEEeEeecccCCceeEEEEEEeCCCCe
Q psy8562 65 YGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKK 98 (205)
Q Consensus 65 ~G~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~ 98 (205)
||+.+.|.|.+++++ +-=+++||-..+.+++
T Consensus 11 dG~~hiVYi~~~~~~---~G~l~vdfsT~~e~~k 41 (56)
T PF11113_consen 11 DGESHIVYITELHYD---DGKLKVDFSTPSEDRK 41 (56)
T ss_pred CCCEEEEEEEEEEEc---CCeEEEEEeCCCcchh
Confidence 899999999999999 5568999999998764
No 10
>PF12000 Glyco_trans_4_3: Gkycosyl transferase family 4 group; InterPro: IPR022623 This presumed domain is functionally uncharacterised and found in bacteria. This region is about 170 amino acids in length and is found N-terminal to PF00534 from PFAM. There is a single completely conserved residue G that may be functionally important.
Probab=71.14 E-value=2.9 Score=34.48 Aligned_cols=21 Identities=33% Similarity=0.477 Sum_probs=18.8
Q ss_pred chHHHHHHHcCCeeEEEecCC
Q psy8562 13 TSFSRNLRKIGKVPGIIYGGN 33 (205)
Q Consensus 13 k~~ar~LRr~G~IPaViYG~~ 33 (205)
-+++++||++|++|-+|+|+.
T Consensus 54 ~~a~~~L~~~Gf~PDvI~~H~ 74 (171)
T PF12000_consen 54 ARAARQLRAQGFVPDVIIAHP 74 (171)
T ss_pred HHHHHHHHHcCCCCCEEEEcC
Confidence 457889999999999999986
No 11
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=69.04 E-value=11 Score=34.25 Aligned_cols=52 Identities=21% Similarity=0.317 Sum_probs=38.2
Q ss_pred cEEEEEEeCCCCCceEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCCceEEEEECcc
Q psy8562 128 SDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPV 186 (205)
Q Consensus 128 ~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~~vV~sv~~~~ 186 (205)
..|.++..+. =|..+.+.+.+ ...++.+||.+|.++++. +|++.||++....
T Consensus 84 K~I~~k~~~~-~~~~~~l~~~G---p~~vtA~Di~~p~~ieiv---npd~~Iatl~~~~ 135 (327)
T CHL00013 84 KEIVLKSNLY-GPQKASICVQG---PKYVTAQDIILPPSVEIV---DPTQHIATITEPI 135 (327)
T ss_pred hcCeEEccCC-CcEEEEEEEeC---CeEEEeeeeccCCCeEEe---CCCeEEEEeCCCC
Confidence 4555554442 35566776664 358999999999999987 6999999998653
No 12
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....
Probab=64.21 E-value=8.6 Score=28.85 Aligned_cols=28 Identities=36% Similarity=0.502 Sum_probs=25.0
Q ss_pred EEEeccCC-CCCeEEeccCCCCceEEEEECcc
Q psy8562 156 IHLSDIKL-PRGVSVIHSTEEDPTIATAIIPV 186 (205)
Q Consensus 156 i~v~Dl~l-p~gv~~~~~~d~~~vV~sv~~~~ 186 (205)
|+.+||.+ |.++++. +|+..||++....
T Consensus 64 V~a~di~~~~~~i~iv---n~d~~I~tl~~~~ 92 (112)
T PF01000_consen 64 VTAGDIKLEPSGIEIV---NPDIYIATLSEGQ 92 (112)
T ss_dssp EEGGGSEESBTTEEES---STTSEEEEEESST
T ss_pred cccceeEecCCceEEe---cCCeEEEEECCCC
Confidence 99999999 9999987 6999999997654
No 13
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=63.72 E-value=6.4 Score=22.61 Aligned_cols=23 Identities=17% Similarity=0.222 Sum_probs=19.1
Q ss_pred EEEEeEeecccCCceeEEEEEEe
Q psy8562 71 VLLRNFQLHAYKKLVLHADFQRV 93 (205)
Q Consensus 71 vlikevQ~~pv~~~i~HvDF~~v 93 (205)
|++-=++.+|-...|.|-||+++
T Consensus 3 cm~mi~h~~psdksi~hwdf~~l 25 (28)
T PRK14751 3 CMPMVMHKNPSDKSIYHWDFYAL 25 (28)
T ss_pred ceeeeeecCCCcCceeeeeehhh
Confidence 45556788999999999999975
No 14
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=60.39 E-value=35 Score=25.67 Aligned_cols=35 Identities=9% Similarity=0.186 Sum_probs=27.6
Q ss_pred EEEEEEE-CCeEEEEEEEeEeecccCCceeEEEEEE
Q psy8562 58 SILNLEI-YGKVELVLLRNFQLHAYKKLVLHADFQR 92 (205)
Q Consensus 58 ~vi~L~i-~G~~~~vlikevQ~~pv~~~i~HvDF~~ 92 (205)
-.|.|.+ +|.+...+.-+|-+||.|++++-|.|++
T Consensus 61 e~Fkl~l~~~~kefgV~v~V~f~p~T~ki~~I~~~e 96 (97)
T PF13028_consen 61 EKFKLWLREGGKEFGVFVTVSFNPKTEKIISINVEE 96 (97)
T ss_pred EEEEEEEEcCCeEEEEEEEEEEeCCCCcEEEEEEEe
Confidence 3677777 4555666777899999999999999875
No 15
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=57.22 E-value=30 Score=29.29 Aligned_cols=40 Identities=28% Similarity=0.505 Sum_probs=30.8
Q ss_pred CceEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCCceEEEEECc
Q psy8562 140 PKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185 (205)
Q Consensus 140 Pe~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~~vV~sv~~~ 185 (205)
+-.+.+++++= ..++.+||.+|.++++. +|+..+|++...
T Consensus 85 ~~~~~l~~~gp---~~V~a~Di~~~~~i~iv---np~~~IatL~~~ 124 (215)
T cd06928 85 PQVLRLKVKGP---GVVTAADIELPSGVEIV---NPDQYIATLTED 124 (215)
T ss_pred eEEEEEEEecC---eEEEhHhcCcCCCcEEe---CCCcEEEEECCC
Confidence 44555555531 46999999999999976 699999999765
No 16
>PF12728 HTH_17: Helix-turn-helix domain
Probab=56.73 E-value=25 Score=22.21 Aligned_cols=37 Identities=16% Similarity=0.112 Sum_probs=29.0
Q ss_pred CCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhc
Q psy8562 11 KGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKK 52 (205)
Q Consensus 11 ~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~ 52 (205)
.+.+..+++.++|.+|+. +.| -..-++..+|.+++..
T Consensus 13 is~~tv~~~~~~g~i~~~--~~g---~~~~~~~~~l~~~~~~ 49 (51)
T PF12728_consen 13 ISRSTVYRWIRQGKIPPF--KIG---RKWRIPKSDLDRWLER 49 (51)
T ss_pred cCHHHHHHHHHcCCCCeE--EeC---CEEEEeHHHHHHHHHh
Confidence 345668899999999999 222 3488999999999874
No 17
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=47.44 E-value=41 Score=29.98 Aligned_cols=52 Identities=21% Similarity=0.277 Sum_probs=35.8
Q ss_pred cEEEEEEeCCCCCceEEEeccCCCCCCeEEEeccC-CCCCeEEeccCCCCceEEEEECcc
Q psy8562 128 SDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIK-LPRGVSVIHSTEEDPTIATAIIPV 186 (205)
Q Consensus 128 ~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~Dl~-lp~gv~~~~~~d~~~vV~sv~~~~ 186 (205)
+.|.++.... =+..+.+++.+ ...++.+||. +|.++++. +||..||++....
T Consensus 64 K~i~~~~~~~-~~~~~~l~~~g---p~~VtA~Di~~~p~~ieiv---npd~~IatL~~~~ 116 (297)
T TIGR02027 64 KQLVVKSEGD-GERTMTLSKKG---PGVVTAGDIKAPPGDVEIV---NPDLVIATLTEPA 116 (297)
T ss_pred hceEEeccCC-CcEEEEEEEeC---CEEEEhhhcccCCCCcEEe---CCCeEEEEECCCC
Confidence 3444444332 23456666553 2679999999 89999977 6999999997653
No 18
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=43.16 E-value=42 Score=30.14 Aligned_cols=40 Identities=18% Similarity=0.170 Sum_probs=31.0
Q ss_pred ceEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCCceEEEEECcc
Q psy8562 141 KFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPV 186 (205)
Q Consensus 141 e~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~~vV~sv~~~~ 186 (205)
..+.+++.+ . ..++.+||.+|+++++. +|+..||++....
T Consensus 95 ~~~~l~~~g--p-~~VtA~Di~~~~~v~iv---n~d~~IatL~~~~ 134 (310)
T PRK05182 95 VTLTLSKKG--P-GEVTAGDIETDGDVEIV---NPDLVIATLNEGA 134 (310)
T ss_pred EEEEEEecC--C-eEEEHHHcCCCCCcEEe---CCCeEEEEECCCC
Confidence 355666553 2 38999999999999976 5999999997643
No 19
>PRK10646 ADP-binding protein; Provisional
Probab=41.31 E-value=25 Score=28.45 Aligned_cols=26 Identities=23% Similarity=0.453 Sum_probs=19.1
Q ss_pred EEEEEeEeecccCCceeEEEEEEeCCCC
Q psy8562 70 LVLLRNFQLHAYKKLVLHADFQRVDTEK 97 (205)
Q Consensus 70 ~vlikevQ~~pv~~~i~HvDF~~v~~~~ 97 (205)
-.++++++.. ...+.|+|+||+...+
T Consensus 63 Ftlv~~Y~~~--~~~l~H~DlYRL~~~~ 88 (153)
T PRK10646 63 YTLVEPYTLD--NLMVYHFDLYRLADPE 88 (153)
T ss_pred EeeEEEeeCC--CCCEEEEeeccCCCHH
Confidence 4678888633 3469999999997544
No 20
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=33.84 E-value=26 Score=27.56 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=18.5
Q ss_pred EEEEEeEeecccCCceeEEEEEEeCCCC
Q psy8562 70 LVLLRNFQLHAYKKLVLHADFQRVDTEK 97 (205)
Q Consensus 70 ~vlikevQ~~pv~~~i~HvDF~~v~~~~ 97 (205)
-.++.+++.. ...+.|+||||++..+
T Consensus 57 f~lv~~Y~~~--~~~l~H~DlYRl~~~~ 82 (133)
T TIGR00150 57 FTLVNEYNEG--NLMVYHFDLYRLADPE 82 (133)
T ss_pred eeeeeecccC--CCcEEEechhhcCChh
Confidence 4677777633 2469999999997543
No 21
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=33.55 E-value=1.7e+02 Score=20.46 Aligned_cols=50 Identities=10% Similarity=0.031 Sum_probs=35.5
Q ss_pred ceEEEEeHHHHHHHhhcCCcceEEEEEEE-CCeEEEEE-------EEeEeecccCCceeE
Q psy8562 36 PVKISMNHNMIYHALKKETFHSSILNLEI-YGKVELVL-------LRNFQLHAYKKLVLH 87 (205)
Q Consensus 36 ~~~i~v~~~e~~k~~~~~~~~~~vi~L~i-~G~~~~vl-------ikevQ~~pv~~~i~H 87 (205)
|..-.++..++.+.+...|. .+-++++ ++..+.+- --++..||.|+++++
T Consensus 24 p~~~~~~~~~~~~~l~~~G~--~v~~ve~~~~g~yev~~~~~dG~~~ev~vD~~tG~V~~ 81 (83)
T PF13670_consen 24 PPADWLSIEQAVAKLEAQGY--QVREVEFDDDGCYEVEARDKDGKKVEVYVDPATGEVVK 81 (83)
T ss_pred CccccCCHHHHHHHHHhcCC--ceEEEEEcCCCEEEEEEEECCCCEEEEEEcCCCCeEee
Confidence 34444578888888888764 6888888 54344432 347899999999876
No 22
>PF06434 Aconitase_2_N: Aconitate hydratase 2 N-terminus; InterPro: IPR015929 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal region of bacterial aconitase B (AcnB), which consists of both a HEAT-like domain and a 'swivel' domain. HEAT-like domains are usually implicated in protein-protein interactions, while the 'swivel' domain is usually a mobile unit in proteins that carry it. In AcnB, this N-terminal region was shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=32.29 E-value=31 Score=29.26 Aligned_cols=38 Identities=18% Similarity=0.251 Sum_probs=17.3
Q ss_pred eEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCCceEEEEECc
Q psy8562 142 FIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185 (205)
Q Consensus 142 ~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~~vV~sv~~~ 185 (205)
-|++||++|..||.|.+. |..-++.. +..+++++..-+
T Consensus 116 PIe~dv~~l~~Gdvi~I~----p~~gki~~--~~gev~~~f~l~ 153 (204)
T PF06434_consen 116 PIECDVSSLNTGDVITIY----PYEGKIYK--ENGEVISTFELK 153 (204)
T ss_dssp EEE---TT--TT-EEEEE----TTTTEEEE--TT--EEEE---S
T ss_pred eEEEeccccCCCcEEEEe----cCCcEEEC--CCCCEEEEeecC
Confidence 699999999999999874 33333331 345677766543
No 23
>COG3603 Uncharacterized conserved protein [Function unknown]
Probab=31.36 E-value=78 Score=24.91 Aligned_cols=28 Identities=25% Similarity=0.469 Sum_probs=23.1
Q ss_pred CCeEEEEEe--cEEEEEEeCCCCCceEEEe
Q psy8562 119 NSCIISNVI--SDLYISCLPKNLPKFIEIN 146 (205)
Q Consensus 119 ~GG~l~~~~--~~i~V~~~p~~IPe~I~vD 146 (205)
.+|+.++.. .++.+-|+++++|+.+++|
T Consensus 31 ~~~F~sIt~t~eelsivc~~~~vp~~V~~~ 60 (128)
T COG3603 31 GPGFWSITRTPEELSIVCLADRVPDVVQIE 60 (128)
T ss_pred CCceEEEEcCCceEEEEeecccCCcceEec
Confidence 356766665 6899999999999999985
No 24
>COG4856 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.13 E-value=61 Score=30.25 Aligned_cols=60 Identities=15% Similarity=0.173 Sum_probs=41.8
Q ss_pred EEEEecEEEEEEeCCCCCc----eEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCCceEEEEECcc
Q psy8562 123 ISNVISDLYISCLPKNLPK----FIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPV 186 (205)
Q Consensus 123 l~~~~~~i~V~~~p~~IPe----~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~~vV~sv~~~~ 186 (205)
+.....++.|.+.-..+=+ .+.||+|....+..+++ +|++|+|++.. .|..+=+++..-+
T Consensus 253 it~s~~tv~I~Gs~dvLd~lseId~~vDlskI~~~t~~tv-~lpvPegv~sv---~Ps~i~v~l~t~k 316 (403)
T COG4856 253 ITPSKNTVTIVGSQDVLDNLSEIDAPVDLSKISKDTTKTV-KLPVPEGVKSV---SPSSIEVRLDTDK 316 (403)
T ss_pred eecCCceEEEEcchHhhcchheeeeeeehhhccCCceEEE-EeeCCCcceec---CCceEEEEEeech
Confidence 3444567777765433211 16899999999999998 59999999955 3777667776433
No 25
>PF12920 TcdA_TcdB_pore: TcdA/TcdB pore forming domain; InterPro: IPR024769 Toxins A (TcdA) and B (TcdB) of Clostridium difficile belong to the family of clostridial glucosylating toxins. These toxins glucosylate small GTPases of Rho and Ras families, inhibiting the signalling and regulatory functions of these switch proteins. After receptor-binding, the toxins are endocytosed to reach acidic endosomal compartments from where the toxins are translocated into the cytosol []. TcdB has been shown to consist of a N-terminal glucosyltransferase domain (GTD), responsible for the biological effects of the toxin, a cysteine protease domain (CPD), responsible for autocatalytic cleavage, a hydrophobic region (HR), which has been suggested to be involved in toxin translocation, and a C-terminal repetitive domain involved in receptor binding. The pore-forming region of toxin B has been described to be in a region in the middle of the protein, within amino acid residues 830 and 990 []. This entry represents the pore forming domain of TcdA and TcdB. It is also found in other toxins. ; GO: 0009405 pathogenesis
Probab=28.92 E-value=4.4e+02 Score=26.46 Aligned_cols=120 Identities=13% Similarity=0.097 Sum_probs=73.6
Q ss_pred EEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecccCCc
Q psy8562 5 AFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKL 84 (205)
Q Consensus 5 a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~pv~~~ 84 (205)
+..|...|-...|||+..+.-+=-.|.-. .+..+.++ +..- ..|-+++.+|...+..++-.+-.+- .+.
T Consensus 401 ~t~r~d~gfd~Lrrle~~~~F~~~fy~fp--------se~~I~~l-~~eY-~~T~I~V~LD~~~R~LVvP~l~~~~-~~k 469 (663)
T PF12920_consen 401 ATTRHDSGFDVLRRLEEDYRFDFDFYAFP--------SEYVIRRL-KPEY-VDTPIEVILDNQNRTLVVPTLPEEW-RGK 469 (663)
T ss_pred CcccCCcHHHHHHHHhhcCCCceEEeccc--------hHHHHhhc-eeee-ecceEEEEeCCCccEEEecCCChhH-hCc
Confidence 35688999999999999986332233211 12244443 3333 3578999999988777766665543 222
Q ss_pred eeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEec
Q psy8562 85 VLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSD 160 (205)
Q Consensus 85 i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~D 160 (205)
+ -=.|.|.+ |.- --.|+...-+|++.| .+-++.-.+|+|.+.-+++|++.+
T Consensus 470 L------------------sY~l~G~g---G~y--~l~L~~g~a~i~l~~--~~~~~~Wiida~~l~~~~~i~~~~ 520 (663)
T PF12920_consen 470 L------------------SYSLIGAG---GEY--QLSLNPGQASITLVS--NNKNSRWIIDASHLVKSSSIQVED 520 (663)
T ss_pred E------------------EEEEECCC---eEE--EEEEcccceEEEEec--cCCcceEEEehHHhcccCceeecc
Confidence 2 22455621 111 112333335677788 889999999999997666666553
No 26
>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.
Probab=27.35 E-value=19 Score=28.07 Aligned_cols=27 Identities=15% Similarity=0.312 Sum_probs=17.5
Q ss_pred EEEEeEeecccCCceeEEEEEEeCCCCeE
Q psy8562 71 VLLRNFQLHAYKKLVLHADFQRVDTEKKI 99 (205)
Q Consensus 71 vlikevQ~~pv~~~i~HvDF~~v~~~~~v 99 (205)
.++..+.. -...+.|+||||+...+..
T Consensus 51 ~l~~~Y~~--~~~~l~H~DLYRl~~~~e~ 77 (123)
T PF02367_consen 51 SLVNEYEG--GNIPLYHFDLYRLEDPEEL 77 (123)
T ss_dssp TSEEEEEE--TTEEEEEEE-TT-SSTHHH
T ss_pred EEEEEecC--CCceEEEeeccccCCHHHH
Confidence 34555544 6678999999999876653
No 27
>PF14467 DUF4426: Domain of unknown function (DUF4426); PDB: 3UC2_D.
Probab=25.75 E-value=3.2e+02 Score=21.28 Aligned_cols=57 Identities=12% Similarity=0.110 Sum_probs=37.6
Q ss_pred CcceEEEEEEE--CC----eEEEEEEEeEeecccCCceeEEEEEEeCCCCeEEEEEeEEEEecC
Q psy8562 54 TFHSSILNLEI--YG----KVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSE 111 (205)
Q Consensus 54 ~~~~~vi~L~i--~G----~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~ 111 (205)
+....++++.| .+ ....+-|+-.-+| +.++...++|.+|.+|..|--=-|+.|.+++
T Consensus 33 Sk~~gllNIsVl~~~~~~~~av~a~v~G~a~n-L~gq~~~L~FreI~Eg~AIYYlA~f~~~~~E 95 (122)
T PF14467_consen 33 SKYRGLLNISVLDKSDGGKPAVPAQVSGTARN-LLGQQRTLEFREIREGDAIYYLAEFPFRNEE 95 (122)
T ss_dssp -TTEEEEEEEEEETT----EE--EEEEEEEE--TT--EEEE--EEEEETTEEEEEEEEE--SSE
T ss_pred cCCeEEEEEEEecCCCccCCccceEEEEEEec-cccceeeeeEEEEecCCcEEEEEeeccCCCc
Confidence 33578999998 22 3456788888888 7788999999999999999887788777753
No 28
>PRK08652 acetylornithine deacetylase; Provisional
Probab=24.01 E-value=57 Score=28.45 Aligned_cols=24 Identities=17% Similarity=0.297 Sum_probs=19.3
Q ss_pred CCCchHHHHHHHcCCeeEEEecCCC
Q psy8562 10 KKGTSFSRNLRKIGKVPGIIYGGNK 34 (205)
Q Consensus 10 ~~Gk~~ar~LRr~G~IPaViYG~~~ 34 (205)
..|...++.+++.| +|+++||.+.
T Consensus 291 ~~g~tDa~~~~~~g-ip~v~~Gpg~ 314 (347)
T PRK08652 291 MRSWTDAINFRYNG-TKTVVWGPGE 314 (347)
T ss_pred CCccchhHHHHHCC-CCEEEECCCc
Confidence 34556789998887 8999999874
No 29
>PRK08737 acetylornithine deacetylase; Provisional
Probab=23.05 E-value=59 Score=29.27 Aligned_cols=21 Identities=14% Similarity=0.292 Sum_probs=17.0
Q ss_pred chHHHHHHHcCCeeEEEecCCC
Q psy8562 13 TSFSRNLRKIGKVPGIIYGGNK 34 (205)
Q Consensus 13 k~~ar~LRr~G~IPaViYG~~~ 34 (205)
...++.+++.| ||+|+||.|.
T Consensus 314 ~tDa~~~~~~G-ip~v~~GpG~ 334 (364)
T PRK08737 314 WTEASLFSAAG-YTALVYGPGD 334 (364)
T ss_pred ccCHHHHHHcC-CCEEEECCCC
Confidence 34577888887 8999999984
No 30
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=22.85 E-value=1.7e+02 Score=24.58 Aligned_cols=27 Identities=22% Similarity=0.190 Sum_probs=22.6
Q ss_pred eEEEeccCCCCCeEEeccCCCCceEEEEECc
Q psy8562 155 SIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185 (205)
Q Consensus 155 ~i~v~Dl~lp~gv~~~~~~d~~~vV~sv~~~ 185 (205)
.++.+||..+.+ ++. +||..||++...
T Consensus 91 ~Vta~Di~~~~~-~iv---npdi~I~tL~~g 117 (195)
T PRK14979 91 TVYSSDLKSENG-EVA---FKNIPIVKLAEG 117 (195)
T ss_pred eEEHHHcCCCCC-ccc---CCCcEEEEECCC
Confidence 699999999888 655 699999999754
No 31
>PF07708 Tash_PEST: Tash protein PEST motif; InterPro: IPR011695 The PEST motif is found in one or more copies in Tash AT-hook proteins from Theileria annulata. Tash proteins are transported to the host nucleus and are thought to be involved in pathogenesis []. The PEST motif is often found in conjunction with the (IPR007480 from INTERPRO), whose function is unknown. These repeats may be part of the PEST motif (a signal for rapid proteolytic degradation) [], though this is not proven. This motif is also found in other T. annulata proteins, which have no other known domains.
Probab=21.76 E-value=65 Score=17.15 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=7.8
Q ss_pred CceEEEeccC
Q psy8562 140 PKFIEINLEK 149 (205)
Q Consensus 140 Pe~I~vDvs~ 149 (205)
|+.|.|+|++
T Consensus 5 PEti~vEi~S 14 (19)
T PF07708_consen 5 PETIPVEIGS 14 (19)
T ss_pred CceEEEEecc
Confidence 7888888775
No 32
>PF08038 Tom7: TOM7 family; InterPro: IPR012621 This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=21.28 E-value=11 Score=23.99 Aligned_cols=12 Identities=33% Similarity=0.459 Sum_probs=9.4
Q ss_pred HHcCCeeEEEec
Q psy8562 20 RKIGKVPGIIYG 31 (205)
Q Consensus 20 Rr~G~IPaViYG 31 (205)
=.-|+||.|||=
T Consensus 15 ~HyGfIP~Ilyl 26 (42)
T PF08038_consen 15 FHYGFIPLILYL 26 (42)
T ss_pred EEeeehHHHHHH
Confidence 346999999994
No 33
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=21.24 E-value=1.6e+02 Score=25.40 Aligned_cols=29 Identities=14% Similarity=0.113 Sum_probs=23.8
Q ss_pred eEEEeccCC-CCCeEEeccCCCCceEEEEECcc
Q psy8562 155 SIHLSDIKL-PRGVSVIHSTEEDPTIATAIIPV 186 (205)
Q Consensus 155 ~i~v~Dl~l-p~gv~~~~~~d~~~vV~sv~~~~ 186 (205)
.++.+||.. |+++++. +|+..||++....
T Consensus 103 ~V~a~dl~~~~~~v~~v---~~~~~I~~L~~~~ 132 (263)
T PRK00783 103 TVYSGDLKSSDPDVKPV---DPNIPIVKLKEGQ 132 (263)
T ss_pred cEEccccccCCCCceec---CCCcEEEEeCCCC
Confidence 589999997 8899866 5899999997643
No 34
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=20.88 E-value=2.1e+02 Score=24.24 Aligned_cols=28 Identities=21% Similarity=0.252 Sum_probs=24.0
Q ss_pred eEEEeccCCCC--CeEEeccCCCCceEEEEECc
Q psy8562 155 SIHLSDIKLPR--GVSVIHSTEEDPTIATAIIP 185 (205)
Q Consensus 155 ~i~v~Dl~lp~--gv~~~~~~d~~~vV~sv~~~ 185 (205)
.++.+||..|. ++++. +|+..|+++...
T Consensus 91 ~V~a~Dl~~~~~~~v~~v---np~~~I~~L~~g 120 (224)
T smart00662 91 EVTAGDLKSDSDPDVEIV---NPDIPIAKLREG 120 (224)
T ss_pred cEEHHHcccCCCCCcEEe---CCCcEEEEECCC
Confidence 59999999997 88876 699999999854
No 35
>PRK08554 peptidase; Reviewed
Probab=20.74 E-value=72 Score=29.62 Aligned_cols=45 Identities=20% Similarity=0.181 Sum_probs=29.5
Q ss_pred EEEeCCCCchHHHHHHHcCCeeEEEecCCCCce---EEEEeHHHHHHHh
Q psy8562 5 AFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPV---KISMNHNMIYHAL 50 (205)
Q Consensus 5 a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~---~i~v~~~e~~k~~ 50 (205)
.......|-..++.++..| +|++.||.+.... .=.++-.+|.+..
T Consensus 379 ~~~~~~~GgtDa~~~~~~G-ip~v~~Gp~~~~~H~~~E~v~i~~l~~~~ 426 (438)
T PRK08554 379 AEPVEGPGASDSRYFTPYG-VKAIDFGPKGGNIHGPNEYVEIDSLKKMP 426 (438)
T ss_pred cEEEecCCchHHHHHHhcC-CCceEECCCCCCCCCCcceEEHHHHHHHH
Confidence 3445556778899999999 8999999964322 2234444554443
No 36
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.42 E-value=1.7e+02 Score=17.20 Aligned_cols=36 Identities=19% Similarity=0.054 Sum_probs=25.0
Q ss_pred CCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHh
Q psy8562 11 KGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHAL 50 (205)
Q Consensus 11 ~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~ 50 (205)
...+..+++.++|.+|+.-- .+-...++..++.+++
T Consensus 12 vs~~tl~~~~~~g~~~~~~~----~~~~~~~~~~ei~~~~ 47 (49)
T cd04762 12 VSPSTLRRWVKEGKLKAIRT----PGGHRRFPEEDLERLL 47 (49)
T ss_pred cCHHHHHHHHHcCCCCceeC----CCCceecCHHHHHHHH
Confidence 34566788899999997421 2244568888888765
Done!