Query 025088
Match_columns 258
No_of_seqs 133 out of 1131
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 02:35:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025088.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025088hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00731 ctc_TL5 ribosomal pr 100.0 8E-56 1.7E-60 381.4 22.3 175 54-247 1-175 (176)
2 PRK05618 50S ribosomal protein 100.0 4.5E-55 9.8E-60 382.6 25.1 189 49-253 1-189 (197)
3 PRK05943 50S ribosomal protein 100.0 1.8E-28 3.8E-33 191.6 12.7 93 52-160 2-94 (94)
4 PF14693 Ribosomal_TL5_C: Ribo 99.9 7.6E-28 1.6E-32 186.0 9.1 88 164-253 1-88 (88)
5 cd00495 Ribosomal_L25_TL5_CTC 99.9 2.9E-27 6.2E-32 183.3 11.4 90 53-159 2-91 (91)
6 PF01386 Ribosomal_L25p: Ribos 99.9 3.1E-27 6.8E-32 182.5 11.4 87 54-157 1-88 (88)
7 COG1825 RplY Ribosomal protein 99.9 6E-25 1.3E-29 171.7 9.4 92 52-160 2-93 (93)
8 PF01000 RNA_pol_A_bac: RNA po 59.9 15 0.00033 28.9 4.1 28 222-250 64-92 (112)
9 CHL00013 rpoA RNA polymerase a 49.3 29 0.00064 33.0 4.8 39 207-249 96-134 (327)
10 COG4856 Uncharacterized protei 48.5 50 0.0011 32.4 6.2 96 149-250 208-316 (403)
11 TIGR01764 excise DNA binding d 47.3 57 0.0012 20.6 4.7 37 61-107 12-48 (49)
12 PF12000 Glyco_trans_4_3: Gkyc 44.4 16 0.00034 31.6 2.0 26 59-84 49-74 (171)
13 PF11113 Phage_head_chap: Head 41.0 77 0.0017 22.8 4.7 29 134-165 13-41 (56)
14 cd06928 RNAP_alpha_NTD N-termi 37.9 72 0.0016 28.4 5.3 30 220-250 96-125 (215)
15 PRK14751 tetracycline resistan 37.8 26 0.00056 21.4 1.6 23 138-160 3-25 (28)
16 PRK00051 hisI phosphoribosyl-A 37.1 93 0.002 25.8 5.4 72 72-153 11-83 (125)
17 PF06434 Aconitase_2_N: Aconit 36.4 48 0.001 29.6 3.8 36 208-247 116-151 (204)
18 PF13028 DUF3889: Protein of u 36.2 1.1E+02 0.0023 24.4 5.3 37 116-159 60-96 (97)
19 PRK05182 DNA-directed RNA poly 33.7 61 0.0013 30.6 4.3 39 208-250 96-134 (310)
20 TIGR02027 rpoA DNA-directed RN 30.3 91 0.002 29.2 4.8 30 220-250 86-116 (297)
21 KOG3493 Ubiquitin-like protein 27.0 20 0.00044 26.7 -0.1 42 194-235 12-68 (73)
22 PF03100 CcmE: CcmE; InterPro 20.7 3.8E+02 0.0083 21.8 6.3 58 142-207 63-130 (131)
No 1
>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=8e-56 Score=381.40 Aligned_cols=175 Identities=24% Similarity=0.490 Sum_probs=166.8
Q ss_pred EEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCCcc
Q 025088 54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLI 133 (258)
Q Consensus 54 L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~~~ 133 (258)
|+|++|+.+||+++|+||++|+|||||||+ |.++++|++++++|.+++++.+. +++|+|+++|+
T Consensus 1 l~a~~R~~~gk~~~r~LR~~G~VPaVvYG~-----~~~~~~i~v~~~el~k~l~~~~~----~~~i~L~v~g~------- 64 (176)
T TIGR00731 1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGK-----GKENVNLELKSKEFIKYLRKGAT----STVLTLEIGGK------- 64 (176)
T ss_pred CeEEEeCCCCChHHHHHHHCCCccEEEECC-----CCCCEEEEECHHHHHHHHhccCC----cEEEEEEECCE-------
Confidence 579999999999999999999999999998 45799999999999999987653 79999999974
Q ss_pred ceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCeEEEEc
Q 025088 134 EKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDL 213 (258)
Q Consensus 134 ~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~IeVDv 213 (258)
+++|++||+|+||++++++|||||+++++++|+++|||+|+|+ ++|+|+||+|++.+++|+|+|+|++||++|+|||
T Consensus 65 -~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~v~v~~~p~~IPe~I~VDv 141 (176)
T TIGR00731 65 -EFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVKNGGILTQVKRRIEVECKPKDIPDFLELDV 141 (176)
T ss_pred -EEEEEEehhhhccCCCCeEEEEeEEeCCCCEEEEEeeEEEecc--cccccCCcEEEEEEEEEEEEECHHHCCccEEEEC
Confidence 6799999999999999999999999999999999999999998 6899999999999999999999999999999999
Q ss_pred CCCCCCCeEEEeccCCCCCeEEecCCCccEEEEE
Q 025088 214 SELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247 (258)
Q Consensus 214 S~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~ 247 (258)
|+|++||+||++||++|+|+++++|+|++||+|.
T Consensus 142 s~L~iGd~i~v~Dl~lp~gv~~~~d~~~~v~~V~ 175 (176)
T TIGR00731 142 SSLGVGESLKLSDLELPAGVSFITDDDEVVVTVI 175 (176)
T ss_pred ccCCCCCEEEEeeccCCCCcEEccCCCcEEEEEe
Confidence 9999999999999999999999999999999985
No 2
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=100.00 E-value=4.5e-55 Score=382.57 Aligned_cols=189 Identities=32% Similarity=0.518 Sum_probs=175.1
Q ss_pred CCceeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccC
Q 025088 49 RYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFG 128 (258)
Q Consensus 49 m~~~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~ 128 (258)
|...+|+|++|+.+||+++|+||++|+|||||||+ |.++++|+++.++|.+++++.. +.+++|+|+++|+
T Consensus 1 m~~~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~-----~~~~~~i~v~~~~l~k~l~~~~---~~~~~i~L~i~g~-- 70 (197)
T PRK05618 1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGK-----GKEPVSISVDEKELIKALKKGA---FLSTLLDLEVGGK-- 70 (197)
T ss_pred CCeEEEEEEEcCcCCChHHHHHHHCCCCcEEEECC-----CCCCEEEEECHHHHHHHHhcCC---ceeEEEEEEECCE--
Confidence 55689999999999999999999999999999998 3579999999999999995321 3488999999763
Q ss_pred CCCccceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCe
Q 025088 129 SGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPY 208 (258)
Q Consensus 129 ~~~~~~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~ 208 (258)
+++|++||||+||++++++|||||+++++++|+++|||.|+|++.+++.|+||+|++.+++|+|+|+|++||++
T Consensus 71 ------~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k~GG~l~~~~~~v~v~~~p~~IP~~ 144 (197)
T PRK05618 71 ------KQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEF 144 (197)
T ss_pred ------EEEEEEeeeeeccCCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccccceEEEEEEEEEEEEEcHHHCCcc
Confidence 78999999999999999999999999999999999999999998766677799999999999999999999999
Q ss_pred EEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEcccccc
Q 025088 209 IDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASD 253 (258)
Q Consensus 209 IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r~~~ 253 (258)
|+||||+|++||+|+++||++|+|+++++|+|++||+|.+++.+.
T Consensus 145 I~VDVs~L~~Gd~i~v~Dl~lp~~v~i~~~~~~~v~~V~~~~~~~ 189 (197)
T PRK05618 145 IEVDVSGLEIGDSIHVSDLKLPEGVKLLDDPDEVVATVVAPRGEE 189 (197)
T ss_pred EEEEcccCCCCCEEEeeeecCCCCcEEcCCCCcEEEEEEcCCccc
Confidence 999999999999999999999999999999999999999998653
No 3
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=99.96 E-value=1.8e-28 Score=191.64 Aligned_cols=93 Identities=24% Similarity=0.334 Sum_probs=84.5
Q ss_pred eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088 52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD 131 (258)
Q Consensus 52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~ 131 (258)
.+|+|++|+.+||+++|+||++|+|||||||+ |.++++|++++++|.+++++.+ +.+++|+|+++|+
T Consensus 2 ~~l~a~~R~~~gk~~~r~lR~~G~vPaViYG~-----~~~~~~i~v~~~el~k~l~~~~---~~~~~i~L~v~g~----- 68 (94)
T PRK05943 2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGG-----NEAPVSIVLDHKDVINLQAKAE---FYKEVITLVIDGK----- 68 (94)
T ss_pred eEEEEEEeCcCCChHHHHHHHCCCCCEEEECC-----CCCcEEEEEcHHHHHHHHhcCC---CcceEEEEEECCE-----
Confidence 46899999999999999999999999999998 4578999999999999998644 3478999999874
Q ss_pred ccceEeEEEeeeeeccCCCCceEEEEEEe
Q 025088 132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA 160 (258)
Q Consensus 132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v 160 (258)
+++|++||||+||+|++++|||||+|
T Consensus 69 ---~~~v~ikevQ~~pv~~~i~HvDF~~v 94 (94)
T PRK05943 69 ---EVKVKVQAVQRHPFKPKLEHIDFVRA 94 (94)
T ss_pred ---EEEEEEeeeecCcCCCCeEeEeeeeC
Confidence 67999999999999999999999986
No 4
>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=7.6e-28 Score=186.04 Aligned_cols=88 Identities=32% Similarity=0.620 Sum_probs=78.3
Q ss_pred CeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCeEEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccE
Q 025088 164 ALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPV 243 (258)
Q Consensus 164 ~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vV 243 (258)
++|+++|||+|+|+ |+|+|+||+|++.+++|+|+|+|++||++|+||||+|++||+|+++||++|+|+++++|+|++|
T Consensus 1 e~v~~~VPv~~~G~--~~gvk~Gg~l~~~~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~~d~~~vV 78 (88)
T PF14693_consen 1 EKVKVEVPVHFVGE--SPGVKKGGILQQVLREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEILDDPETVV 78 (88)
T ss_dssp S-EEEEEEEEEESS--SHHHCTTSEEEESTSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEESS-TTSEE
T ss_pred CeEEEEEeEEEEcc--cccCcCCcEEEEEEeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEcCCCCcEE
Confidence 58999999999997 7999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcccccc
Q 025088 244 CKIAGGRASD 253 (258)
Q Consensus 244 vsV~~~r~~~ 253 (258)
|+|.++|+++
T Consensus 79 ~~v~~~~~ee 88 (88)
T PF14693_consen 79 ASVVAPRVEE 88 (88)
T ss_dssp EEEE-SCSS-
T ss_pred EEEeccccCC
Confidence 9999999874
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=2.9e-27 Score=183.33 Aligned_cols=90 Identities=36% Similarity=0.560 Sum_probs=83.5
Q ss_pred eEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCCc
Q 025088 53 TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDL 132 (258)
Q Consensus 53 ~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~~ 132 (258)
+|+|.+|+.+||+++|+||++|+|||||||+ |.++++|++++++|.+++++.|. +++|+|+++|+
T Consensus 2 ~l~a~~R~~~gk~~~r~lR~~G~iPavvYG~-----~~~~~~i~v~~~~l~k~l~~~~~----~~~~~L~i~g~------ 66 (91)
T cd00495 2 TLKAEKREETGKGASRRLRRAGKVPAVIYGK-----GKEPISISVDEKELEKLLRKEGR----STLIELNIDGK------ 66 (91)
T ss_pred eEEEEEcccCCChHHHHHHHCCCCCEEEECC-----CCCCEEEEEcHHHHHHHHhhcCC----ceEEEEEECCE------
Confidence 6899999999999999999999999999997 35799999999999999998774 79999999864
Q ss_pred cceEeEEEeeeeeccCCCCceEEEEEE
Q 025088 133 IEKVRVLPRKVHLHSGTDAPLNVTFLR 159 (258)
Q Consensus 133 ~~~~~vliKeVQ~hpvt~~ilHVDF~~ 159 (258)
+++|++||||+||++++++||||++
T Consensus 67 --~~~~~ikevQ~~pv~~~i~HvDF~~ 91 (91)
T cd00495 67 --KENVLIKDVQRHPVKDKILHVDFLR 91 (91)
T ss_pred --EEEEEEehhhhccCCCCEEEEeccC
Confidence 7899999999999999999999984
No 6
>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=3.1e-27 Score=182.47 Aligned_cols=87 Identities=26% Similarity=0.494 Sum_probs=80.9
Q ss_pred EEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHH-hhcCcccceeEEEEEEECCccCCCCc
Q 025088 54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLV-GHLGRSFFVSRLFDLEVRSEFGSGDL 132 (258)
Q Consensus 54 L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l-~~~g~~~f~s~l~~L~v~g~~~~~~~ 132 (258)
|+|++|+.+||+++|+||++|+|||||||+ |.++++|+|+.++|.+++ +..+. +++|+|+++|+
T Consensus 1 L~a~~R~~~gk~~~r~LR~~G~iPaviYG~-----~~~~~~i~v~~~~l~k~~~~~~~~----~~~i~L~i~g~------ 65 (88)
T PF01386_consen 1 LKAEKREETGKSAARRLRREGKIPAVIYGK-----GKESIPISVDEKELEKLLRRKHGE----NSVIELNIDGK------ 65 (88)
T ss_dssp EEEEESSSTSSSHHHHHHHTTEEEEEEEES-----SEEEEEEEEEHHHHHHHHTHHHTT----TSEEEEEETTE------
T ss_pred CeEEEcCcCCCHHHHHHHHcCCceEEEECC-----CCCCEEEEEeHHHHHHHHHhcCCc----eEEEEEEECCE------
Confidence 689999999999999999999999999998 457899999999999999 55554 79999999984
Q ss_pred cceEeEEEeeeeeccCCCCceEEEE
Q 025088 133 IEKVRVLPRKVHLHSGTDAPLNVTF 157 (258)
Q Consensus 133 ~~~~~vliKeVQ~hpvt~~ilHVDF 157 (258)
+++|++||||+||++++++||||
T Consensus 66 --~~~vlikevQ~~p~~~~i~HvDF 88 (88)
T PF01386_consen 66 --KYNVLIKEVQRDPVTDKILHVDF 88 (88)
T ss_dssp --EEEEEEEEEEEESSSSSEEEEEE
T ss_pred --EEEEEEEeeeeCCCCCCeEeccC
Confidence 89999999999999999999999
No 7
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=6e-25 Score=171.71 Aligned_cols=92 Identities=30% Similarity=0.498 Sum_probs=86.2
Q ss_pred eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088 52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD 131 (258)
Q Consensus 52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~ 131 (258)
.+|+|+.|+..||+++|+||++|+|||||||. |.++++|+++.++|.+++++.+. +++|+|+++|+
T Consensus 2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~-----g~~~v~i~l~~~~~~k~~~~~~~----~~v~~l~v~g~----- 67 (93)
T COG1825 2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGG-----GKEPVNIALDHHEFAKALRKLGY----STVITLEVDGK----- 67 (93)
T ss_pred ceeceeEecccCcchhHhHHhcCCCCEEEECC-----CCCCceEEEcHHHHHHHHhhccc----ceEEEEEECCe-----
Confidence 56899999999999999999999999999997 56889999999999999998774 89999999984
Q ss_pred ccceEeEEEeeeeeccCCCCceEEEEEEe
Q 025088 132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA 160 (258)
Q Consensus 132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v 160 (258)
+..|++|++|+||+++.++|+||+++
T Consensus 68 ---~~~Vlvkd~Q~~p~~~~~~HvDf~~v 93 (93)
T COG1825 68 ---EIKVLVKDVQRHPLTDEVQHIDFLRV 93 (93)
T ss_pred ---EEEEEehhhhhCcccCceeecccccC
Confidence 78999999999999999999999975
No 8
>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=59.90 E-value=15 Score=28.89 Aligned_cols=28 Identities=21% Similarity=0.546 Sum_probs=25.3
Q ss_pred EEEeccCC-CCCeEEecCCCccEEEEEccc
Q 025088 222 ILAGDLKV-HPALKLLRSKDEPVCKIAGGR 250 (258)
Q Consensus 222 I~v~DL~l-p~gv~ll~d~e~vVvsV~~~r 250 (258)
|+.+||.+ |++++++ ++|..+|++....
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 9999999 6889999998664
No 9
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=49.29 E-value=29 Score=33.05 Aligned_cols=39 Identities=10% Similarity=0.253 Sum_probs=29.7
Q ss_pred CeEEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEcc
Q 025088 207 PYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGG 249 (258)
Q Consensus 207 e~IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~ 249 (258)
....+++.+ ...++.+||.+|++++++ +||..+|++...
T Consensus 96 ~~~~l~~~G---p~~vtA~Di~~p~~ieiv-npd~~Iatl~~~ 134 (327)
T CHL00013 96 QKASICVQG---PKYVTAQDIILPPSVEIV-DPTQHIATITEP 134 (327)
T ss_pred EEEEEEEeC---CeEEEeeeeccCCCeEEe-CCCeEEEEeCCC
Confidence 344455443 357999999999999998 678888999764
No 10
>COG4856 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.50 E-value=50 Score=32.37 Aligned_cols=96 Identities=18% Similarity=0.262 Sum_probs=62.1
Q ss_pred CCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeE---------EEEEeeEEEEEeeCCCCCC----eEEEEcCC
Q 025088 149 TDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGY---------LNTIKRTVKFLCPADIVPP----YIDVDLSE 215 (258)
Q Consensus 149 t~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~---------L~~~~~~V~V~~~p~~IPe----~IeVDvS~ 215 (258)
.+++|.++. ...++.++||++=.+...+.-+++-|. +..-..+++|.+.-+.+=+ .++||+|.
T Consensus 208 ~Gn~L~v~I----~P~evn~tV~vek~sksVpv~Vk~tGslpdg~si~sit~s~~tv~I~Gs~dvLd~lseId~~vDlsk 283 (403)
T COG4856 208 KGNVLPVAI----DPQEVNLTVPVEKPSKSVPVNVKRTGSLPDGVSISSITPSKNTVTIVGSQDVLDNLSEIDAPVDLSK 283 (403)
T ss_pred CCCCccccc----CCceEEEEEeeeccCcccceeeeecccCCCCcceeeeecCCceEEEEcchHhhcchheeeeeeehhh
Confidence 466665443 245677888877666544333443332 3444567888776553321 16799999
Q ss_pred CCCCCeEEEeccCCCCCeEEecCCCccEEEEEccc
Q 025088 216 LDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGR 250 (258)
Q Consensus 216 L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r 250 (258)
...+..+++ +|++|+|++...+. .+=+.+..-+
T Consensus 284 I~~~t~~tv-~lpvPegv~sv~Ps-~i~v~l~t~k 316 (403)
T COG4856 284 ISKDTTKTV-KLPVPEGVKSVSPS-SIEVRLDTDK 316 (403)
T ss_pred ccCCceEEE-EeeCCCcceecCCc-eEEEEEeech
Confidence 999999988 58999999988655 5556665443
No 11
>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=47.33 E-value=57 Score=20.63 Aligned_cols=37 Identities=5% Similarity=0.134 Sum_probs=28.1
Q ss_pred CCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHh
Q 025088 61 SPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVG 107 (258)
Q Consensus 61 ~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~ 107 (258)
..+.+..+++.++|.+|++.-| . ...++..+|++.++
T Consensus 12 gis~~ti~~~~~~g~i~~~~~g-------~---~~~~~~~~l~~~~~ 48 (49)
T TIGR01764 12 GVSKDTVYRLIHEGELPAYRVG-------R---HYRIPREDVDEYLE 48 (49)
T ss_pred CCCHHHHHHHHHcCCCCeEEeC-------C---eEEEeHHHHHHHHh
Confidence 3456678899999999997653 1 24589999998875
No 12
>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=44.40 E-value=16 Score=31.64 Aligned_cols=26 Identities=23% Similarity=0.418 Sum_probs=20.7
Q ss_pred cCCCCchHhHHHHHcCCccEEEecCc
Q 025088 59 RASPGTRVSVKERKAGRVPSIVFEQE 84 (258)
Q Consensus 59 R~~~Gk~~arkLRr~G~VPaVIYG~~ 84 (258)
|-..--+++++||++|++|-||+|+.
T Consensus 49 rg~av~~a~~~L~~~Gf~PDvI~~H~ 74 (171)
T PF12000_consen 49 RGQAVARAARQLRAQGFVPDVIIAHP 74 (171)
T ss_pred HHHHHHHHHHHHHHcCCCCCEEEEcC
Confidence 44444567899999999999999863
No 13
>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=41.04 E-value=77 Score=22.77 Aligned_cols=29 Identities=24% Similarity=0.312 Sum_probs=24.9
Q ss_pred ceEeEEEeeeeeccCCCCceEEEEEEeCCCCe
Q 025088 134 EKVRVLPRKVHLHSGTDAPLNVTFLRAPPEAL 165 (258)
Q Consensus 134 ~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~ 165 (258)
+.+-|.+-+++++ +-=+++||-..+++++
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 4899999999999 5568999999998764
No 14
>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=37.86 E-value=72 Score=28.38 Aligned_cols=30 Identities=10% Similarity=0.327 Sum_probs=25.2
Q ss_pred CeEEEeccCCCCCeEEecCCCccEEEEEccc
Q 025088 220 QKILAGDLKVHPALKLLRSKDEPVCKIAGGR 250 (258)
Q Consensus 220 d~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r 250 (258)
..++.+||.+|++++++ +++..+|++....
T Consensus 96 ~~V~a~Di~~~~~i~iv-np~~~IatL~~~~ 125 (215)
T cd06928 96 GVVTAADIELPSGVEIV-NPDQYIATLTEDA 125 (215)
T ss_pred eEEEhHhcCcCCCcEEe-CCCcEEEEECCCC
Confidence 46999999999999987 5778999987653
No 15
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=37.84 E-value=26 Score=21.37 Aligned_cols=23 Identities=13% Similarity=0.252 Sum_probs=19.2
Q ss_pred EEEeeeeeccCCCCceEEEEEEe
Q 025088 138 VLPRKVHLHSGTDAPLNVTFLRA 160 (258)
Q Consensus 138 vliKeVQ~hpvt~~ilHVDF~~v 160 (258)
|++--++..|-...|.|-||+.+
T Consensus 3 cm~mi~h~~psdksi~hwdf~~l 25 (28)
T PRK14751 3 CMPMVMHKNPSDKSIYHWDFYAL 25 (28)
T ss_pred ceeeeeecCCCcCceeeeeehhh
Confidence 55666788999999999999875
No 16
>PRK00051 hisI phosphoribosyl-AMP cyclohydrolase; Reviewed
Probab=37.11 E-value=93 Score=25.83 Aligned_cols=72 Identities=25% Similarity=0.264 Sum_probs=42.2
Q ss_pred HcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeE-EEEEEECCccCCCCccceEeEEEeeeeeccCCC
Q 025088 72 KAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSR-LFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTD 150 (258)
Q Consensus 72 r~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~-l~~L~v~g~~~~~~~~~~~~vliKeVQ~hpvt~ 150 (258)
+.|+||+|+-.... |.--....+++..|.+.+.+ |...|.|+ .=.|=..|+.+ ...-.+++|..|--.+
T Consensus 11 ~~GLipaivqd~~t---g~VLMlaymn~eAl~~Tl~t-g~~~y~SRSR~~lW~KGetS------G~~q~v~~i~~DCD~D 80 (125)
T PRK00051 11 ADGLVPAIAQDAET---GEVLMVAWMNEEALAKTLET-GRAHYWSRSRQKLWRKGETS------GHVQKVHEVRLDCDGD 80 (125)
T ss_pred CCCcEEEEEEECCC---CCEEEEEEcCHHHHHHHHhc-CcEEEEeCccCcccCCCCCc------CCeEEEEEEEecCCCC
Confidence 37999999997543 33234567888889998875 43333333 22344555421 1223567777776555
Q ss_pred Cce
Q 025088 151 APL 153 (258)
Q Consensus 151 ~il 153 (258)
.++
T Consensus 81 ~Ll 83 (125)
T PRK00051 81 AVL 83 (125)
T ss_pred EEE
Confidence 443
No 17
>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=36.37 E-value=48 Score=29.64 Aligned_cols=36 Identities=19% Similarity=0.208 Sum_probs=18.9
Q ss_pred eEEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEE
Q 025088 208 YIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247 (258)
Q Consensus 208 ~IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~ 247 (258)
.|++|++.|+.||.|.+. |..-++..+..+++.+..
T Consensus 116 PIe~dv~~l~~Gdvi~I~----p~~gki~~~~gev~~~f~ 151 (204)
T PF06434_consen 116 PIECDVSSLNTGDVITIY----PYEGKIYKENGEVISTFE 151 (204)
T ss_dssp EEE---TT--TT-EEEEE----TTTTEEEETT--EEEE--
T ss_pred eEEEeccccCCCcEEEEe----cCCcEEECCCCCEEEEee
Confidence 799999999999999875 444456555666777654
No 18
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=36.17 E-value=1.1e+02 Score=24.37 Aligned_cols=37 Identities=16% Similarity=0.083 Sum_probs=28.3
Q ss_pred eEEEEEEECCccCCCCccceEeEEEeeeeeccCCCCceEEEEEE
Q 025088 116 SRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLR 159 (258)
Q Consensus 116 s~l~~L~v~g~~~~~~~~~~~~vliKeVQ~hpvt~~ilHVDF~~ 159 (258)
--.|.|-+..++ +.--+.=+|-+||.|++++-|.|++
T Consensus 60 ~e~Fkl~l~~~~-------kefgV~v~V~f~p~T~ki~~I~~~e 96 (97)
T PF13028_consen 60 VEKFKLWLREGG-------KEFGVFVTVSFNPKTEKIISINVEE 96 (97)
T ss_pred EEEEEEEEEcCC-------eEEEEEEEEEEeCCCCcEEEEEEEe
Confidence 356777777541 4556667899999999999999875
No 19
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=33.72 E-value=61 Score=30.59 Aligned_cols=39 Identities=13% Similarity=0.311 Sum_probs=29.6
Q ss_pred eEEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEccc
Q 025088 208 YIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGR 250 (258)
Q Consensus 208 ~IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r 250 (258)
.+.+++.+ . ..++.+||.+|++++++ +++..+|++....
T Consensus 96 ~~~l~~~g--p-~~VtA~Di~~~~~v~iv-n~d~~IatL~~~~ 134 (310)
T PRK05182 96 TLTLSKKG--P-GEVTAGDIETDGDVEIV-NPDLVIATLNEGA 134 (310)
T ss_pred EEEEEecC--C-eEEEHHHcCCCCCcEEe-CCCeEEEEECCCC
Confidence 44555543 2 38999999999999987 5778999997654
No 20
>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=30.28 E-value=91 Score=29.21 Aligned_cols=30 Identities=17% Similarity=0.292 Sum_probs=25.2
Q ss_pred CeEEEeccC-CCCCeEEecCCCccEEEEEccc
Q 025088 220 QKILAGDLK-VHPALKLLRSKDEPVCKIAGGR 250 (258)
Q Consensus 220 d~I~v~DL~-lp~gv~ll~d~e~vVvsV~~~r 250 (258)
..++.+||. +|++++++ ++|..+|++....
T Consensus 86 ~~VtA~Di~~~p~~ieiv-npd~~IatL~~~~ 116 (297)
T TIGR02027 86 GVVTAGDIKAPPGDVEIV-NPDLVIATLTEPA 116 (297)
T ss_pred EEEEhhhcccCCCCcEEe-CCCeEEEEECCCC
Confidence 579999999 89999987 6678999997653
No 21
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=27.02 E-value=20 Score=26.67 Aligned_cols=42 Identities=21% Similarity=0.313 Sum_probs=28.8
Q ss_pred eEEEEEeeCCC---------------CCCeEEEEcCCCCCCCeEEEeccCCCCCeEE
Q 025088 194 RTVKFLCPADI---------------VPPYIDVDLSELDVEQKILAGDLKVHPALKL 235 (258)
Q Consensus 194 ~~V~V~~~p~~---------------IPe~IeVDvS~L~iGd~I~v~DL~lp~gv~l 235 (258)
..|.|+|.|+| .|+.|.+.=-.-=..|.|+++|..+++|..+
T Consensus 12 KKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~l 68 (73)
T KOG3493|consen 12 KKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNL 68 (73)
T ss_pred ceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccE
Confidence 46788888875 4666665522223468999999999887643
No 22
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=20.73 E-value=3.8e+02 Score=21.76 Aligned_cols=58 Identities=24% Similarity=0.460 Sum_probs=30.8
Q ss_pred eeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccC-eE-----E----EEEeeEEEEEeeCCCCCC
Q 025088 142 KVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKG-GY-----L----NTIKRTVKFLCPADIVPP 207 (258)
Q Consensus 142 eVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~G-G~-----L----~~~~~~V~V~~~p~~IPe 207 (258)
.++++| .-.++.|.-.+.+. ++||++.|. .+...+.| ++ + ...-++|-++|+-+..|+
T Consensus 63 Sv~~~~---~~~~~~F~i~D~~~----~i~V~Y~G~-~Pd~F~eg~~VVv~G~~~~~g~F~A~~lL~KcpskY~p~ 130 (131)
T PF03100_consen 63 SVEYDP---DGNTLTFTITDGGK----EIPVVYTGP-LPDLFREGQGVVVEGRLGEDGVFEATELLAKCPSKYMPP 130 (131)
T ss_dssp TEEE-T---TSSEEEEEEE-SS-----EEEEEEES---CTT--TTSEEEEEEEECCTSEEEEEEEEETS------H
T ss_pred CEEEcC---CCCEEEEEEEECCc----EEEEEECCC-CCccccCCCeEEEEEEECCCCEEEEEEEEeCCCCCCCCC
Confidence 677776 56778899988865 479999996 35555544 22 2 234567888887766654
Done!