Query 026232
Match_columns 241
No_of_seqs 126 out of 1097
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 05:22:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026232hhsearch_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 2.2E-55 4.8E-60 379.6 25.3 192 23-238 1-192 (197)
2 TIGR00731 ctc_TL5 ribosomal pr 100.0 1E-55 2.2E-60 375.8 22.0 175 29-229 1-175 (176)
3 PRK05943 50S ribosomal protein 100.0 2.9E-29 6.3E-34 193.4 12.8 93 27-141 2-94 (94)
4 PF01386 Ribosomal_L25p: Ribos 99.9 9.9E-28 2.2E-32 182.7 10.9 87 29-138 1-88 (88)
5 cd00495 Ribosomal_L25_TL5_CTC 99.9 1.9E-27 4.2E-32 181.9 11.1 90 28-140 2-91 (91)
6 PF14693 Ribosomal_TL5_C: Ribo 99.9 1.5E-27 3.2E-32 181.9 9.2 88 145-235 1-88 (88)
7 COG1825 RplY Ribosomal protein 99.9 3.2E-25 7E-30 170.7 9.0 92 27-141 2-93 (93)
8 TIGR01764 excise DNA binding d 69.8 15 0.00032 23.1 4.9 37 36-88 12-48 (49)
9 PF12000 Glyco_trans_4_3: Gkyc 68.6 3.4 7.4E-05 35.2 2.0 26 34-59 49-74 (171)
10 PF11113 Phage_head_chap: Head 60.3 24 0.00053 24.8 4.6 29 115-146 13-41 (56)
11 CHL00013 rpoA RNA polymerase a 58.7 19 0.0004 33.9 5.1 51 175-231 84-134 (327)
12 PF01000 RNA_pol_A_bac: RNA po 52.0 17 0.00036 28.2 3.1 27 203-231 64-91 (112)
13 cd06928 RNAP_alpha_NTD N-termi 46.6 46 0.001 29.1 5.4 39 188-231 86-124 (215)
14 PF12728 HTH_17: Helix-turn-he 42.1 88 0.0019 20.3 5.1 37 37-89 13-49 (51)
15 PRK14751 tetracycline resistan 41.0 25 0.00054 21.0 1.8 23 119-141 3-25 (28)
16 PF13028 DUF3889: Protein of u 36.7 1.2E+02 0.0026 23.7 5.6 36 98-140 61-96 (97)
17 TIGR02027 rpoA DNA-directed RN 36.5 66 0.0014 29.7 4.9 38 189-231 77-115 (297)
18 COG4856 Uncharacterized protei 35.6 95 0.0021 30.0 5.9 86 144-232 218-316 (403)
19 PRK05182 DNA-directed RNA poly 34.0 65 0.0014 29.9 4.5 38 189-231 96-133 (310)
20 TIGR00150 HI0065_YjeE ATPase, 30.9 56 0.0012 26.6 3.1 25 119-145 58-82 (133)
21 PF06434 Aconitase_2_N: Aconit 23.1 56 0.0012 28.8 1.9 36 189-229 116-151 (204)
22 PRK10646 ADP-binding protein; 22.9 73 0.0016 26.6 2.5 26 118-145 63-88 (153)
23 PF13670 PepSY_2: Peptidase pr 21.7 2.3E+02 0.005 20.5 4.8 51 73-135 24-81 (83)
24 PRK14979 DNA-directed RNA poly 21.6 1.9E+02 0.004 25.2 4.8 27 202-231 91-117 (195)
No 1
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=100.00 E-value=2.2e-55 Score=379.56 Aligned_cols=192 Identities=33% Similarity=0.487 Sum_probs=174.9
Q ss_pred CCcceEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEE
Q 026232 23 TSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPL 102 (241)
Q Consensus 23 ms~~~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L 102 (241)
|. ..+|+|.+|+..||+++||||++|+|||||||++ .++++++++.++|.+++++.. +.+++|+|
T Consensus 1 m~-~~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~~-----------~~~~~i~v~~~~l~k~l~~~~---~~~~~i~L 65 (197)
T PRK05618 1 ME-TITLEAEVREEFGKGAARRLRRAGKVPAVIYGKG-----------KEPVSISVDEKELIKALKKGA---FLSTLLDL 65 (197)
T ss_pred CC-eEEEEEEEcCcCCChHHHHHHHCCCCcEEEECCC-----------CCCEEEEECHHHHHHHHhcCC---ceeEEEEE
Confidence 44 4789999999999999999999999999999993 469999999999999995432 24789999
Q ss_pred EEcCCCCccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEee
Q 026232 103 QIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCP 182 (241)
Q Consensus 103 ~i~~g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~l 182 (241)
+++ | +++.||+||+|+||++++++|+|||+++++++|+++|||+|+|++.+++.|+||+|++.+++|+|+|+
T Consensus 66 ~i~-g-------~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k~GG~l~~~~~~v~v~~~ 137 (197)
T PRK05618 66 EVG-G-------KKQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECL 137 (197)
T ss_pred EEC-C-------EEEEEEEeeeeeccCCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccccceEEEEEEEEEEEEEc
Confidence 996 6 57899999999999999999999999999999999999999999865666669999999999999999
Q ss_pred cCCCCCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcCCCCCCCC
Q 026232 183 AEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEP 238 (241)
Q Consensus 183 P~~IPe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~~~e~~~~ 238 (241)
|.+||++|+||||+|++||+|+|+||++|+|+++++ +++.+||+|.+|+.++++.
T Consensus 138 p~~IP~~I~VDVs~L~~Gd~i~v~Dl~lp~~v~i~~-~~~~~v~~V~~~~~~~~~e 192 (197)
T PRK05618 138 PEDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVKLLD-DPDEVVATVVAPRGEEEEE 192 (197)
T ss_pred HHHCCccEEEEcccCCCCCEEEeeeecCCCCcEEcC-CCCcEEEEEEcCCcccccc
Confidence 999999999999999999999999999999999985 8899999999988865554
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=1e-55 Score=375.77 Aligned_cols=175 Identities=27% Similarity=0.467 Sum_probs=165.0
Q ss_pred EEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCCC
Q 026232 29 IQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGS 108 (241)
Q Consensus 29 L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g~ 108 (241)
|+|++|+.+||+++|||||+|+||||+||++ .++++++++.++|.+++++.+. +++|+|+++ |
T Consensus 1 l~a~~R~~~gk~~~r~LR~~G~VPaVvYG~~-----------~~~~~i~v~~~el~k~l~~~~~----~~~i~L~v~-g- 63 (176)
T TIGR00731 1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKG-----------KENVNLELKSKEFIKYLRKGAT----STVLTLEIG-G- 63 (176)
T ss_pred CeEEEeCCCCChHHHHHHHCCCccEEEECCC-----------CCCEEEEECHHHHHHHHhccCC----cEEEEEEEC-C-
Confidence 5799999999999999999999999999993 4699999999999999987653 689999998 6
Q ss_pred CccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEeecCCCCC
Q 026232 109 GSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISP 188 (241)
Q Consensus 109 ~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~lP~~IPe 188 (241)
++++||+||+|+||++++++|+|||+++++++|+++|||+|+|+ ++|+|+||+|++.+++|+|+|+|.+||+
T Consensus 64 ------~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~v~v~~~p~~IPe 135 (176)
T TIGR00731 64 ------KEFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVKNGGILTQVKRRIEVECKPKDIPD 135 (176)
T ss_pred ------EEEEEEEehhhhccCCCCeEEEEeEEeCCCCEEEEEeeEEEecc--cccccCCcEEEEEEEEEEEEECHHHCCc
Confidence 46799999999999999999999999999999999999999998 5799999999999999999999999999
Q ss_pred eEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEE
Q 026232 189 KIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKIS 229 (241)
Q Consensus 189 ~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~ 229 (241)
+|+||||+|++||+||++||++|+|+++++ +++.+||+|.
T Consensus 136 ~I~VDvs~L~iGd~i~v~Dl~lp~gv~~~~-d~~~~v~~V~ 175 (176)
T TIGR00731 136 FLELDVSSLGVGESLKLSDLELPAGVSFIT-DDDEVVVTVI 175 (176)
T ss_pred cEEEECccCCCCCEEEEeeccCCCCcEEcc-CCCcEEEEEe
Confidence 999999999999999999999999999985 8889999984
No 3
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=99.96 E-value=2.9e-29 Score=193.42 Aligned_cols=93 Identities=26% Similarity=0.356 Sum_probs=84.1
Q ss_pred eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232 27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA 106 (241)
Q Consensus 27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~ 106 (241)
++|+|++|+..||+++|+||++|+|||||||++ .++++++++.++|.+++++.+ +.+++|+|+++
T Consensus 2 ~~l~a~~R~~~gk~~~r~lR~~G~vPaViYG~~-----------~~~~~i~v~~~el~k~l~~~~---~~~~~i~L~v~- 66 (94)
T PRK05943 2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGGN-----------EAPVSIVLDHKDVINLQAKAE---FYKEVITLVID- 66 (94)
T ss_pred eEEEEEEeCcCCChHHHHHHHCCCCCEEEECCC-----------CCcEEEEEcHHHHHHHHhcCC---CcceEEEEEEC-
Confidence 579999999999999999999999999999993 468999999999999998654 23689999998
Q ss_pred CCCccccccceeeeeeeeeeccCCCceeEEEEEEe
Q 026232 107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA 141 (241)
Q Consensus 107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v 141 (241)
| ++++||+||+|+||++++++|||||+|
T Consensus 67 g-------~~~~v~ikevQ~~pv~~~i~HvDF~~v 94 (94)
T PRK05943 67 G-------KEVKVKVQAVQRHPFKPKLEHIDFVRA 94 (94)
T ss_pred C-------EEEEEEEeeeecCcCCCCeEeEeeeeC
Confidence 6 467999999999999999999999985
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=99.95 E-value=9.9e-28 Score=182.74 Aligned_cols=87 Identities=31% Similarity=0.498 Sum_probs=80.4
Q ss_pred EEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHH-HhcCCCceeeeEEEEEEcCC
Q 026232 29 IQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSIL-KSVELPFFCSTTFPLQIRAG 107 (241)
Q Consensus 29 L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll-~~~g~~~~~~~v~~L~i~~g 107 (241)
|+|++|+.+||+++|+||++|+|||||||++ .++++|+++.++|.+++ +..+. +++|+|+++ |
T Consensus 1 L~a~~R~~~gk~~~r~LR~~G~iPaviYG~~-----------~~~~~i~v~~~~l~k~~~~~~~~----~~~i~L~i~-g 64 (88)
T PF01386_consen 1 LKAEKREETGKSAARRLRREGKIPAVIYGKG-----------KESIPISVDEKELEKLLRRKHGE----NSVIELNID-G 64 (88)
T ss_dssp EEEEESSSTSSSHHHHHHHTTEEEEEEEESS-----------EEEEEEEEEHHHHHHHHTHHHTT----TSEEEEEET-T
T ss_pred CeEEEcCcCCCHHHHHHHHcCCceEEEECCC-----------CCCEEEEEeHHHHHHHHHhcCCc----eEEEEEEEC-C
Confidence 7899999999999999999999999999993 46899999999999999 55554 689999998 6
Q ss_pred CCccccccceeeeeeeeeeccCCCceeEEEE
Q 026232 108 SGSSVLLDSGKVLPIKVHRDEETGRILNLVF 138 (241)
Q Consensus 108 ~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF 138 (241)
+++.||+||+|+||++++++||||
T Consensus 65 -------~~~~vlikevQ~~p~~~~i~HvDF 88 (88)
T PF01386_consen 65 -------KKYNVLIKEVQRDPVTDKILHVDF 88 (88)
T ss_dssp -------EEEEEEEEEEEEESSSSSEEEEEE
T ss_pred -------EEEEEEEEeeeeCCCCCCeEeccC
Confidence 578999999999999999999999
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=99.95 E-value=1.9e-27 Score=181.85 Aligned_cols=90 Identities=31% Similarity=0.474 Sum_probs=83.0
Q ss_pred EEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCC
Q 026232 28 TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAG 107 (241)
Q Consensus 28 ~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g 107 (241)
+|+|.+|+.+||+++|+||++|+|||||||++ .++++|+++.++|.+++++.+. +++|+|+++ |
T Consensus 2 ~l~a~~R~~~gk~~~r~lR~~G~iPavvYG~~-----------~~~~~i~v~~~~l~k~l~~~~~----~~~~~L~i~-g 65 (91)
T cd00495 2 TLKAEKREETGKGASRRLRRAGKVPAVIYGKG-----------KEPISISVDEKELEKLLRKEGR----STLIELNID-G 65 (91)
T ss_pred eEEEEEcccCCChHHHHHHHCCCCCEEEECCC-----------CCCEEEEEcHHHHHHHHhhcCC----ceEEEEEEC-C
Confidence 68999999999999999999999999999992 4799999999999999988763 689999998 6
Q ss_pred CCccccccceeeeeeeeeeccCCCceeEEEEEE
Q 026232 108 SGSSVLLDSGKVLPIKVHRDEETGRILNLVFVW 140 (241)
Q Consensus 108 ~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~ 140 (241)
+++.|++||+|+||++++++||||++
T Consensus 66 -------~~~~~~ikevQ~~pv~~~i~HvDF~~ 91 (91)
T cd00495 66 -------KKENVLIKDVQRHPVKDKILHVDFLR 91 (91)
T ss_pred -------EEEEEEEehhhhccCCCCEEEEeccC
Confidence 56799999999999999999999984
No 6
>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=1.5e-27 Score=181.89 Aligned_cols=88 Identities=35% Similarity=0.649 Sum_probs=77.6
Q ss_pred CEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEeecCCCCCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCcc
Q 026232 145 TELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMP 224 (241)
Q Consensus 145 ~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~lP~~IPe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~v 224 (241)
|+|+++|||+|+|+ |+|+|+||+|++.+++|+|+|+|.+||++|+||||+|++||+||++||++|+|++++ +|++.+
T Consensus 1 e~v~~~VPv~~~G~--~~gvk~Gg~l~~~~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~-~d~~~v 77 (88)
T PF14693_consen 1 EKVKVEVPVHFVGE--SPGVKKGGILQQVLREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEIL-DDPETV 77 (88)
T ss_dssp S-EEEEEEEEEESS--SHHHCTTSEEEESTSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEES-S-TTSE
T ss_pred CeEEEEEeEEEEcc--cccCcCCcEEEEEEeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEc-CCCCcE
Confidence 68999999999998 689999999999999999999999999999999999999999999999999999999 489999
Q ss_pred EEEEEcCCCCC
Q 026232 225 LCKISATKLEN 235 (241)
Q Consensus 225 V~~V~~~~~e~ 235 (241)
||+|.++|+|+
T Consensus 78 V~~v~~~~~ee 88 (88)
T PF14693_consen 78 VASVVAPRVEE 88 (88)
T ss_dssp EEEEE-SCSS-
T ss_pred EEEEeccccCC
Confidence 99999999875
No 7
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=3.2e-25 Score=170.71 Aligned_cols=92 Identities=26% Similarity=0.392 Sum_probs=85.5
Q ss_pred eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232 27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA 106 (241)
Q Consensus 27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~ 106 (241)
.+|+++.|+..||+++|+||++|+||||+||. +.++++++++.++|.+.+++.+. +++|+|+++
T Consensus 2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~-----------g~~~v~i~l~~~~~~k~~~~~~~----~~v~~l~v~- 65 (93)
T COG1825 2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGG-----------GKEPVNIALDHHEFAKALRKLGY----STVITLEVD- 65 (93)
T ss_pred ceeceeEecccCcchhHhHHhcCCCCEEEECC-----------CCCCceEEEcHHHHHHHHhhccc----ceEEEEEEC-
Confidence 47999999999999999999999999999999 35789999999999999998773 799999998
Q ss_pred CCCccccccceeeeeeeeeeccCCCceeEEEEEEe
Q 026232 107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA 141 (241)
Q Consensus 107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v 141 (241)
| ++..||+|++|+||+++.++|+||+++
T Consensus 66 g-------~~~~Vlvkd~Q~~p~~~~~~HvDf~~v 93 (93)
T COG1825 66 G-------KEIKVLVKDVQRHPLTDEVQHIDFLRV 93 (93)
T ss_pred C-------eEEEEEehhhhhCcccCceeecccccC
Confidence 6 578999999999999999999999975
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=69.80 E-value=15 Score=23.13 Aligned_cols=37 Identities=16% Similarity=0.228 Sum_probs=29.1
Q ss_pred CCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHH
Q 026232 36 CTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILK 88 (241)
Q Consensus 36 ~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~ 88 (241)
..+.+..+++.++|.+|++.-|. ...++..+|.+.++
T Consensus 12 gis~~ti~~~~~~g~i~~~~~g~----------------~~~~~~~~l~~~~~ 48 (49)
T TIGR01764 12 GVSKDTVYRLIHEGELPAYRVGR----------------HYRIPREDVDEYLE 48 (49)
T ss_pred CCCHHHHHHHHHcCCCCeEEeCC----------------eEEEeHHHHHHHHh
Confidence 45667789999999999986554 26789999988764
No 9
>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=68.59 E-value=3.4 Score=35.21 Aligned_cols=26 Identities=31% Similarity=0.455 Sum_probs=21.3
Q ss_pred cCCCCChHHHHHHHCCCccEEEeCCC
Q 026232 34 RECTGSRVSARDRSQGRIPAVVFAQD 59 (241)
Q Consensus 34 R~~~Gk~~~rrLRr~G~VPaViYG~~ 59 (241)
|...--+++++||++|++|-+|+||.
T Consensus 49 rg~av~~a~~~L~~~Gf~PDvI~~H~ 74 (171)
T PF12000_consen 49 RGQAVARAARQLRAQGFVPDVIIAHP 74 (171)
T ss_pred HHHHHHHHHHHHHHcCCCCCEEEEcC
Confidence 34444567899999999999999994
No 10
>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=60.32 E-value=24 Score=24.84 Aligned_cols=29 Identities=21% Similarity=0.247 Sum_probs=24.9
Q ss_pred cceeeeeeeeeeccCCCceeEEEEEEeCCCCE
Q 026232 115 DSGKVLPIKVHRDEETGRILNLVFVWADDGTE 146 (241)
Q Consensus 115 ~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~ 146 (241)
+.+-|.+.+++++ +-=+++||--.+.+++
T Consensus 13 ~~hiVYi~~~~~~---~G~l~vdfsT~~e~~k 41 (56)
T PF11113_consen 13 ESHIVYITELHYD---DGKLKVDFSTPSEDRK 41 (56)
T ss_pred CEEEEEEEEEEEc---CCeEEEEEeCCCcchh
Confidence 6899999999999 5568999999988664
No 11
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=58.74 E-value=19 Score=33.87 Aligned_cols=51 Identities=16% Similarity=0.152 Sum_probs=35.6
Q ss_pred cEEEEEeecCCCCCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcC
Q 026232 175 TSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISAT 231 (241)
Q Consensus 175 ~~I~V~~lP~~IPe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~ 231 (241)
+.|.++..+. =|..+.+++.+ ...++.+||.+|++++++ +++..||++...
T Consensus 84 K~I~~k~~~~-~~~~~~l~~~G---p~~vtA~Di~~p~~ieiv--npd~~Iatl~~~ 134 (327)
T CHL00013 84 KEIVLKSNLY-GPQKASICVQG---PKYVTAQDIILPPSVEIV--DPTQHIATITEP 134 (327)
T ss_pred hcCeEEccCC-CcEEEEEEEeC---CeEEEeeeeccCCCeEEe--CCCeEEEEeCCC
Confidence 3444444332 24466666654 348999999999999998 578999999754
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=51.96 E-value=17 Score=28.21 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=24.2
Q ss_pred EEEeccCC-CCCeEEeecCCCccEEEEEcC
Q 026232 203 VFMSDIEV-HPSWKLLSKNEKMPLCKISAT 231 (241)
Q Consensus 203 i~V~DL~l-p~gv~il~~~~~~vV~~V~~~ 231 (241)
|+.+||.+ |++++++ +++..||++...
T Consensus 64 V~a~di~~~~~~i~iv--n~d~~I~tl~~~ 91 (112)
T PF01000_consen 64 VTAGDIKLEPSGIEIV--NPDIYIATLSEG 91 (112)
T ss_dssp EEGGGSEESBTTEEES--STTSEEEEEESS
T ss_pred cccceeEecCCceEEe--cCCeEEEEECCC
Confidence 99999999 9999998 578999999754
No 13
>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=46.64 E-value=46 Score=29.15 Aligned_cols=39 Identities=15% Similarity=0.250 Sum_probs=29.1
Q ss_pred CeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcC
Q 026232 188 PKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISAT 231 (241)
Q Consensus 188 e~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~ 231 (241)
-.+.+++++ . ..++.+||..|.+++++ +++..||++...
T Consensus 86 ~~~~l~~~g--p-~~V~a~Di~~~~~i~iv--np~~~IatL~~~ 124 (215)
T cd06928 86 QVLRLKVKG--P-GVVTAADIELPSGVEIV--NPDQYIATLTED 124 (215)
T ss_pred EEEEEEEec--C-eEEEhHhcCcCCCcEEe--CCCcEEEEECCC
Confidence 344555442 1 46999999999999998 478999998754
No 14
>PF12728 HTH_17: Helix-turn-helix domain
Probab=42.11 E-value=88 Score=20.29 Aligned_cols=37 Identities=16% Similarity=0.220 Sum_probs=28.6
Q ss_pred CCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHh
Q 026232 37 TGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKS 89 (241)
Q Consensus 37 ~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~ 89 (241)
...+...++.++|.+|+.--|+ ...++..+|++.+++
T Consensus 13 is~~tv~~~~~~g~i~~~~~g~----------------~~~~~~~~l~~~~~~ 49 (51)
T PF12728_consen 13 ISRSTVYRWIRQGKIPPFKIGR----------------KWRIPKSDLDRWLER 49 (51)
T ss_pred cCHHHHHHHHHcCCCCeEEeCC----------------EEEEeHHHHHHHHHh
Confidence 3456688999999999993222 388999999998874
No 15
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=40.95 E-value=25 Score=21.02 Aligned_cols=23 Identities=17% Similarity=0.361 Sum_probs=18.4
Q ss_pred eeeeeeeeccCCCceeEEEEEEe
Q 026232 119 VLPIKVHRDEETGRILNLVFVWA 141 (241)
Q Consensus 119 vlikevQ~hpv~~~ilHvDF~~v 141 (241)
|++-=+..+|-...|.|-||+.+
T Consensus 3 cm~mi~h~~psdksi~hwdf~~l 25 (28)
T PRK14751 3 CMPMVMHKNPSDKSIYHWDFYAL 25 (28)
T ss_pred ceeeeeecCCCcCceeeeeehhh
Confidence 34445788899999999999875
No 16
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=36.71 E-value=1.2e+02 Score=23.68 Aligned_cols=36 Identities=19% Similarity=0.236 Sum_probs=26.7
Q ss_pred eEEEEEEcCCCCccccccceeeeeeeeeeccCCCceeEEEEEE
Q 026232 98 TTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVW 140 (241)
Q Consensus 98 ~v~~L~i~~g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~ 140 (241)
..|.|-+..| .+.--+.-+|-+||.|++++-|.|++
T Consensus 61 e~Fkl~l~~~-------~kefgV~v~V~f~p~T~ki~~I~~~e 96 (97)
T PF13028_consen 61 EKFKLWLREG-------GKEFGVFVTVSFNPKTEKIISINVEE 96 (97)
T ss_pred EEEEEEEEcC-------CeEEEEEEEEEEeCCCCcEEEEEEEe
Confidence 5778888633 12344555799999999999999875
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=36.50 E-value=66 Score=29.69 Aligned_cols=38 Identities=11% Similarity=0.201 Sum_probs=29.1
Q ss_pred eEEEEccCCCCCCeEEEeccC-CCCCeEEeecCCCccEEEEEcC
Q 026232 189 KIEVDVSNLDIGDRVFMSDIE-VHPSWKLLSKNEKMPLCKISAT 231 (241)
Q Consensus 189 ~I~VDVs~L~iGd~i~V~DL~-lp~gv~il~~~~~~vV~~V~~~ 231 (241)
.+.+++.+ ...++.+||. +|.+++++ +++..||++...
T Consensus 77 ~~~l~~~g---p~~VtA~Di~~~p~~ieiv--npd~~IatL~~~ 115 (297)
T TIGR02027 77 TMTLSKKG---PGVVTAGDIKAPPGDVEIV--NPDLVIATLTEP 115 (297)
T ss_pred EEEEEEeC---CEEEEhhhcccCCCCcEEe--CCCeEEEEECCC
Confidence 45555543 2579999999 89999998 478999998754
No 18
>COG4856 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.61 E-value=95 Score=30.03 Aligned_cols=86 Identities=16% Similarity=0.205 Sum_probs=55.9
Q ss_pred CCEEEEEEeEEEEecCCCCccccCeEE---------EEEecEEEEEeecCCCCC----eEEEEccCCCCCCeEEEeccCC
Q 026232 144 GTELKVDVPVVFKGVESCPGLKKGGYL---------KSIRTSLKYLCPAEHISP----KIEVDVSNLDIGDRVFMSDIEV 210 (241)
Q Consensus 144 ~~~V~v~VPI~l~G~~~s~Gvk~GG~L---------~~~~~~I~V~~lP~~IPe----~I~VDVs~L~iGd~i~V~DL~l 210 (241)
...+.+.||++=.+...+.-+++-|.+ .....++.|.+.-+.+=+ .++||+|+...+..+++ +|++
T Consensus 218 P~evn~tV~vek~sksVpv~Vk~tGslpdg~si~sit~s~~tv~I~Gs~dvLd~lseId~~vDlskI~~~t~~tv-~lpv 296 (403)
T COG4856 218 PQEVNLTVPVEKPSKSVPVNVKRTGSLPDGVSISSITPSKNTVTIVGSQDVLDNLSEIDAPVDLSKISKDTTKTV-KLPV 296 (403)
T ss_pred CceEEEEEeeeccCcccceeeeecccCCCCcceeeeecCCceEEEEcchHhhcchheeeeeeehhhccCCceEEE-EeeC
Confidence 455677887776666543333443332 333457777775443321 16799999999999998 6999
Q ss_pred CCCeEEeecCCCccEEEEEcCC
Q 026232 211 HPSWKLLSKNEKMPLCKISATK 232 (241)
Q Consensus 211 p~gv~il~~~~~~vV~~V~~~~ 232 (241)
|+|++... |..+=+++...+
T Consensus 297 Pegv~sv~--Ps~i~v~l~t~k 316 (403)
T COG4856 297 PEGVKSVS--PSSIEVRLDTDK 316 (403)
T ss_pred CCcceecC--CceEEEEEeech
Confidence 99999973 556666665443
No 19
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=33.95 E-value=65 Score=29.94 Aligned_cols=38 Identities=13% Similarity=0.250 Sum_probs=29.6
Q ss_pred eEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcC
Q 026232 189 KIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISAT 231 (241)
Q Consensus 189 ~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~ 231 (241)
.+.+++.+ . ..++.+||.+|++++++ +++..||++...
T Consensus 96 ~~~l~~~g--p-~~VtA~Di~~~~~v~iv--n~d~~IatL~~~ 133 (310)
T PRK05182 96 TLTLSKKG--P-GEVTAGDIETDGDVEIV--NPDLVIATLNEG 133 (310)
T ss_pred EEEEEecC--C-eEEEHHHcCCCCCcEEe--CCCeEEEEECCC
Confidence 55566543 3 38999999999999998 478999998754
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=30.90 E-value=56 Score=26.60 Aligned_cols=25 Identities=8% Similarity=-0.000 Sum_probs=16.0
Q ss_pred eeeeeeeeccCCCceeEEEEEEeCCCC
Q 026232 119 VLPIKVHRDEETGRILNLVFVWADDGT 145 (241)
Q Consensus 119 vlikevQ~hpv~~~ilHvDF~~v~~~~ 145 (241)
.++++.... ...+.|+||||+...+
T Consensus 58 ~lv~~Y~~~--~~~l~H~DlYRl~~~~ 82 (133)
T TIGR00150 58 TLVNEYNEG--NLMVYHFDLYRLADPE 82 (133)
T ss_pred eeeeecccC--CCcEEEechhhcCChh
Confidence 344454322 3469999999997543
No 21
>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=23.06 E-value=56 Score=28.76 Aligned_cols=36 Identities=25% Similarity=0.314 Sum_probs=17.5
Q ss_pred eEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEE
Q 026232 189 KIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKIS 229 (241)
Q Consensus 189 ~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~ 229 (241)
-|++||+.|+.||.|.+. |..=++.. +..+++++..
T Consensus 116 PIe~dv~~l~~Gdvi~I~----p~~gki~~-~~gev~~~f~ 151 (204)
T PF06434_consen 116 PIECDVSSLNTGDVITIY----PYEGKIYK-ENGEVISTFE 151 (204)
T ss_dssp EEE---TT--TT-EEEEE----TTTTEEEE-TT--EEEE--
T ss_pred eEEEeccccCCCcEEEEe----cCCcEEEC-CCCCEEEEee
Confidence 699999999999999875 33345553 4456676654
No 22
>PRK10646 ADP-binding protein; Provisional
Probab=22.93 E-value=73 Score=26.64 Aligned_cols=26 Identities=12% Similarity=-0.042 Sum_probs=17.7
Q ss_pred eeeeeeeeeccCCCceeEEEEEEeCCCC
Q 026232 118 KVLPIKVHRDEETGRILNLVFVWADDGT 145 (241)
Q Consensus 118 ~vlikevQ~hpv~~~ilHvDF~~v~~~~ 145 (241)
-.|+++++.. ...+.|+|+||+...+
T Consensus 63 Ftlv~~Y~~~--~~~l~H~DlYRL~~~~ 88 (153)
T PRK10646 63 YTLVEPYTLD--NLMVYHFDLYRLADPE 88 (153)
T ss_pred EeeEEEeeCC--CCCEEEEeeccCCCHH
Confidence 3566666422 3469999999997544
No 23
>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=21.72 E-value=2.3e+02 Score=20.47 Aligned_cols=51 Identities=14% Similarity=0.085 Sum_probs=31.9
Q ss_pred ceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCCCCccccccceeee-------eeeeeeccCCCceeE
Q 026232 73 KQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVL-------PIKVHRDEETGRILN 135 (241)
Q Consensus 73 ~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g~~~~~~~~~~~vl-------ikevQ~hpv~~~ilH 135 (241)
+..-.++..++.+.+...|. .+-+++++++. .|.+- --|+..||.|+++++
T Consensus 24 p~~~~~~~~~~~~~l~~~G~-----~v~~ve~~~~g-------~yev~~~~~dG~~~ev~vD~~tG~V~~ 81 (83)
T PF13670_consen 24 PPADWLSIEQAVAKLEAQGY-----QVREVEFDDDG-------CYEVEARDKDGKKVEVYVDPATGEVVK 81 (83)
T ss_pred CccccCCHHHHHHHHHhcCC-----ceEEEEEcCCC-------EEEEEEEECCCCEEEEEEcCCCCeEee
Confidence 34444577888888887652 66777773121 12211 237899999999886
No 24
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=21.55 E-value=1.9e+02 Score=25.24 Aligned_cols=27 Identities=19% Similarity=0.449 Sum_probs=22.4
Q ss_pred eEEEeccCCCCCeEEeecCCCccEEEEEcC
Q 026232 202 RVFMSDIEVHPSWKLLSKNEKMPLCKISAT 231 (241)
Q Consensus 202 ~i~V~DL~lp~gv~il~~~~~~vV~~V~~~ 231 (241)
.++.+||..+.+ +++ +++.+||++...
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 776 578999999753
Done!