Query 029787
Match_columns 188
No_of_seqs 114 out of 1062
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:39:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029787hhsearch_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 1.2E-35 2.5E-40 244.4 14.6 116 54-188 1-116 (176)
2 PRK05618 50S ribosomal protein 100.0 2.5E-34 5.3E-39 240.0 16.8 122 51-188 3-124 (197)
3 PRK05943 50S ribosomal protein 100.0 5E-30 1.1E-34 191.6 12.9 93 52-160 2-94 (94)
4 PF01386 Ribosomal_L25p: Ribos 100.0 7.8E-29 1.7E-33 183.0 9.9 88 54-157 1-88 (88)
5 cd00495 Ribosomal_L25_TL5_CTC 100.0 2.5E-28 5.5E-33 180.7 11.3 90 53-159 2-91 (91)
6 COG1825 RplY Ribosomal protein 99.9 2.6E-25 5.6E-30 166.8 9.5 92 52-160 2-93 (93)
7 TIGR01764 excise DNA binding d 58.9 34 0.00073 20.7 4.8 37 61-107 12-48 (49)
8 PF12000 Glyco_trans_4_3: Gkyc 58.2 7.9 0.00017 32.0 2.2 26 59-84 49-74 (171)
9 PF13028 DUF3889: Protein of u 57.0 31 0.00068 26.2 5.1 38 115-159 59-96 (97)
10 PRK14751 tetracycline resistan 40.5 23 0.00049 21.0 1.6 23 138-160 3-25 (28)
11 PF11113 Phage_head_chap: Head 34.5 1.1E+02 0.0024 21.1 4.6 29 134-165 13-41 (56)
12 PF14467 DUF4426: Domain of un 23.6 2.9E+02 0.0063 21.8 5.9 62 114-178 34-95 (122)
13 cd04920 ACT_AKiii-DAPDC_2 ACT 23.4 1.8E+02 0.0039 19.3 4.1 37 67-109 21-57 (63)
14 PF12728 HTH_17: Helix-turn-he 23.2 2E+02 0.0043 17.9 4.9 37 62-108 13-49 (51)
15 PLN03132 NADH dehydrogenase (u 22.5 36 0.00079 32.5 0.7 14 18-31 2-17 (461)
16 PRK10646 ADP-binding protein; 20.8 57 0.0012 26.5 1.4 25 137-163 63-87 (153)
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=1.2e-35 Score=244.36 Aligned_cols=116 Identities=23% Similarity=0.420 Sum_probs=108.8
Q ss_pred EEEEEcCCCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhhCCCcceeEEEEEEECCccCCCCCc
Q 029787 54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLI 133 (188)
Q Consensus 54 L~a~~R~~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~~~~~~~s~v~~L~v~g~~~~g~~~ 133 (188)
|+|++|+..||+++|||||+|+|||||||+ +.++++|++++++|.+++++ .+.+++|+|+++|+
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-----GKENVNLELKSKEFIKYLRK----GATSTVLTLEIGGK------- 64 (176)
T ss_pred CeEEEeCCCCChHHHHHHHCCCccEEEECC-----CCCCEEEEECHHHHHHHHhc----cCCcEEEEEEECCE-------
Confidence 579999999999999999999999999998 67899999999999999974 23689999999985
Q ss_pred ceEeEEEeeeeccCCCCCceeEEeEEeCCCCeEEEEEeEEEEecCCCccccCCCC
Q 029787 134 EKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGME 188 (188)
Q Consensus 134 e~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~V~v~VPV~f~Ged~s~GvK~GG~ 188 (188)
+++|++||||+||++++++||||++++++++|+++|||+|+|+ ++|+|+||+
T Consensus 65 -~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk~GG~ 116 (176)
T TIGR00731 65 -EFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVKNGGI 116 (176)
T ss_pred -EEEEEEehhhhccCCCCeEEEEeEEeCCCCEEEEEeeEEEecc--cccccCCcE
Confidence 7899999999999999999999999999999999999999999 679999995
No 2
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=100.00 E-value=2.5e-34 Score=239.97 Aligned_cols=122 Identities=32% Similarity=0.489 Sum_probs=111.9
Q ss_pred ceEEEEEEcCCCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhhCCCcceeEEEEEEECCccCCC
Q 029787 51 DETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSG 130 (188)
Q Consensus 51 ~~~L~a~~R~~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~~~~~~~s~v~~L~v~g~~~~g 130 (188)
..+|+|++|+..||+++||||++|+|||||||+ +.++++|+++.++|.+++++ ..+.+.+|+|+++|+
T Consensus 3 ~~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~-----~~~~~~i~v~~~~l~k~l~~---~~~~~~~i~L~i~g~---- 70 (197)
T PRK05618 3 TITLEAEVREEFGKGAARRLRRAGKVPAVIYGK-----GKEPVSISVDEKELIKALKK---GAFLSTLLDLEVGGK---- 70 (197)
T ss_pred eEEEEEEEcCcCCChHHHHHHHCCCCcEEEECC-----CCCCEEEEECHHHHHHHHhc---CCceeEEEEEEECCE----
Confidence 478999999999999999999999999999998 57899999999999999964 446789999999764
Q ss_pred CCcceEeEEEeeeeccCCCCCceeEEeEEeCCCCeEEEEEeEEEEecCCCccccCCCC
Q 029787 131 DLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGME 188 (188)
Q Consensus 131 ~~~e~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~V~v~VPV~f~Ged~s~GvK~GG~ 188 (188)
+++|++|+||+||++++++||||++++++++|+++|||+|+|++.+++.|+||+
T Consensus 71 ----~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k~GG~ 124 (197)
T PRK05618 71 ----KQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGV 124 (197)
T ss_pred ----EEEEEEeeeeeccCCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccccceE
Confidence 889999999999999999999999999999999999999999977666666984
No 3
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=99.97 E-value=5e-30 Score=191.62 Aligned_cols=93 Identities=24% Similarity=0.331 Sum_probs=85.8
Q ss_pred eEEEEEEcCCCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhhCCCcceeEEEEEEECCccCCCC
Q 029787 52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD 131 (188)
Q Consensus 52 ~~L~a~~R~~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~~~~~~~s~v~~L~v~g~~~~g~ 131 (188)
.+|+|++|+..||+++|+||++|+|||||||+ |.++++|++++++|.+++++ .++.+++|+|+++|+
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-----NEAPVSIVLDHKDVINLQAK---AEFYKEVITLVIDGK----- 68 (94)
T ss_pred eEEEEEEeCcCCChHHHHHHHCCCCCEEEECC-----CCCcEEEEEcHHHHHHHHhc---CCCcceEEEEEECCE-----
Confidence 57999999999999999999999999999998 67899999999999999974 334678999999985
Q ss_pred CcceEeEEEeeeeccCCCCCceeEEeEEe
Q 029787 132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA 160 (188)
Q Consensus 132 ~~e~~~vliKeVQ~hpvt~~ilHVDF~~v 160 (188)
++.|++||||+||++++++||||++|
T Consensus 69 ---~~~v~ikevQ~~pv~~~i~HvDF~~v 94 (94)
T PRK05943 69 ---EVKVKVQAVQRHPFKPKLEHIDFVRA 94 (94)
T ss_pred ---EEEEEEeeeecCcCCCCeEeEeeeeC
Confidence 78999999999999999999999985
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=99.96 E-value=7.8e-29 Score=183.04 Aligned_cols=88 Identities=25% Similarity=0.443 Sum_probs=82.2
Q ss_pred EEEEEcCCCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhhCCCcceeEEEEEEECCccCCCCCc
Q 029787 54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLI 133 (188)
Q Consensus 54 L~a~~R~~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~~~~~~~s~v~~L~v~g~~~~g~~~ 133 (188)
|+|++|+.+||+++++||++|+|||||||+ +.++++|+|++++|.+++++ ..+.+++|+|+++|+
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-----GKESIPISVDEKELEKLLRR---KHGENSVIELNIDGK------- 65 (88)
T ss_dssp EEEEESSSTSSSHHHHHHHTTEEEEEEEES-----SEEEEEEEEEHHHHHHHHTH---HHTTTSEEEEEETTE-------
T ss_pred CeEEEcCcCCCHHHHHHHHcCCceEEEECC-----CCCCEEEEEeHHHHHHHHHh---cCCceEEEEEEECCE-------
Confidence 789999999999999999999999999998 67899999999999999942 356789999999995
Q ss_pred ceEeEEEeeeeccCCCCCceeEEe
Q 029787 134 EKVRVLPRKVHLHSGTDAPLNVTF 157 (188)
Q Consensus 134 e~~~vliKeVQ~hpvt~~ilHVDF 157 (188)
++.|++||||+||++++++||||
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 99999999999999999999999
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=99.96 E-value=2.5e-28 Score=180.74 Aligned_cols=90 Identities=33% Similarity=0.488 Sum_probs=83.9
Q ss_pred EEEEEEcCCCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhhCCCcceeEEEEEEECCccCCCCC
Q 029787 53 TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDL 132 (188)
Q Consensus 53 ~L~a~~R~~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~~~~~~~s~v~~L~v~g~~~~g~~ 132 (188)
+|+|++|+.+||+++|+||++|+|||||||+ +.++++|+++.++|.+++++ .+.+++|+|+++|+
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-----GKEPISISVDEKELEKLLRK----EGRSTLIELNIDGK------ 66 (91)
T ss_pred eEEEEEcccCCChHHHHHHHCCCCCEEEECC-----CCCCEEEEEcHHHHHHHHhh----cCCceEEEEEECCE------
Confidence 6899999999999999999999999999998 67899999999999999985 33689999999975
Q ss_pred cceEeEEEeeeeccCCCCCceeEEeEE
Q 029787 133 IEKVRVLPRKVHLHSGTDAPLNVTFLR 159 (188)
Q Consensus 133 ~e~~~vliKeVQ~hpvt~~ilHVDF~~ 159 (188)
++.|++||||+||++++++||||++
T Consensus 67 --~~~~~ikevQ~~pv~~~i~HvDF~~ 91 (91)
T cd00495 67 --KENVLIKDVQRHPVKDKILHVDFLR 91 (91)
T ss_pred --EEEEEEehhhhccCCCCEEEEeccC
Confidence 8899999999999999999999984
No 6
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.6e-25 Score=166.79 Aligned_cols=92 Identities=28% Similarity=0.450 Sum_probs=86.5
Q ss_pred eEEEEEEcCCCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhhCCCcceeEEEEEEECCccCCCC
Q 029787 52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD 131 (188)
Q Consensus 52 ~~L~a~~R~~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~~~~~~~s~v~~L~v~g~~~~g~ 131 (188)
.+|+|+.|++.||+++|+||++|+||||+||. |.++++|.++.+++.|.+++ .+.|++|+|+|+|+
T Consensus 2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~-----g~~~v~i~l~~~~~~k~~~~----~~~~~v~~l~v~g~----- 67 (93)
T COG1825 2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGG-----GKEPVNIALDHHEFAKALRK----LGYSTVITLEVDGK----- 67 (93)
T ss_pred ceeceeEecccCcchhHhHHhcCCCCEEEECC-----CCCCceEEEcHHHHHHHHhh----cccceEEEEEECCe-----
Confidence 57999999999999999999999999999998 68899999999999999986 23789999999996
Q ss_pred CcceEeEEEeeeeccCCCCCceeEEeEEe
Q 029787 132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA 160 (188)
Q Consensus 132 ~~e~~~vliKeVQ~hpvt~~ilHVDF~~v 160 (188)
+..|++|++|+||+++.++|+||+++
T Consensus 68 ---~~~Vlvkd~Q~~p~~~~~~HvDf~~v 93 (93)
T COG1825 68 ---EIKVLVKDVQRHPLTDEVQHIDFLRV 93 (93)
T ss_pred ---EEEEEehhhhhCcccCceeecccccC
Confidence 99999999999999999999999975
No 7
>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=58.86 E-value=34 Score=20.67 Aligned_cols=37 Identities=5% Similarity=0.156 Sum_probs=28.3
Q ss_pred CCCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHh
Q 029787 61 SPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVG 107 (188)
Q Consensus 61 ~~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk 107 (188)
..+.+...++.++|.+|++.-|. ...++..++++.++
T Consensus 12 gis~~ti~~~~~~g~i~~~~~g~----------~~~~~~~~l~~~~~ 48 (49)
T TIGR01764 12 GVSKDTVYRLIHEGELPAYRVGR----------HYRIPREDVDEYLE 48 (49)
T ss_pred CCCHHHHHHHHHcCCCCeEEeCC----------eEEEeHHHHHHHHh
Confidence 35667788999999999976542 35689999998874
No 8
>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=58.21 E-value=7.9 Score=32.01 Aligned_cols=26 Identities=23% Similarity=0.418 Sum_probs=20.9
Q ss_pred cCCCCChHhHHHHHCCCCcEEEecCC
Q 029787 59 RASPGTRVSVKERKAGRVPSIVFEQE 84 (188)
Q Consensus 59 R~~~Gk~~arrLRr~G~VPgVvYG~~ 84 (188)
|...--+++.+||++|++|=||+|+.
T Consensus 49 rg~av~~a~~~L~~~Gf~PDvI~~H~ 74 (171)
T PF12000_consen 49 RGQAVARAARQLRAQGFVPDVIIAHP 74 (171)
T ss_pred HHHHHHHHHHHHHHcCCCCCEEEEcC
Confidence 34444567899999999999999984
No 9
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=56.96 E-value=31 Score=26.22 Aligned_cols=38 Identities=16% Similarity=0.120 Sum_probs=29.0
Q ss_pred eeEEEEEEECCccCCCCCcceEeEEEeeeeccCCCCCceeEEeEE
Q 029787 115 VSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLR 159 (188)
Q Consensus 115 ~s~v~~L~v~g~~~~g~~~e~~~vliKeVQ~hpvt~~ilHVDF~~ 159 (188)
.-..|.|.+..+ .+..-+.-+|-+||.|++++.|.|++
T Consensus 59 t~e~Fkl~l~~~-------~kefgV~v~V~f~p~T~ki~~I~~~e 96 (97)
T PF13028_consen 59 TVEKFKLWLREG-------GKEFGVFVTVSFNPKTEKIISINVEE 96 (97)
T ss_pred eEEEEEEEEEcC-------CeEEEEEEEEEEeCCCCcEEEEEEEe
Confidence 345788888543 24555666899999999999999875
No 10
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=40.53 E-value=23 Score=20.99 Aligned_cols=23 Identities=13% Similarity=0.252 Sum_probs=19.4
Q ss_pred EEEeeeeccCCCCCceeEEeEEe
Q 029787 138 VLPRKVHLHSGTDAPLNVTFLRA 160 (188)
Q Consensus 138 vliKeVQ~hpvt~~ilHVDF~~v 160 (188)
|++--++.+|-...|.|-||+.+
T Consensus 3 cm~mi~h~~psdksi~hwdf~~l 25 (28)
T PRK14751 3 CMPMVMHKNPSDKSIYHWDFYAL 25 (28)
T ss_pred ceeeeeecCCCcCceeeeeehhh
Confidence 56666889999999999999864
No 11
>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=34.47 E-value=1.1e+02 Score=21.12 Aligned_cols=29 Identities=24% Similarity=0.312 Sum_probs=24.8
Q ss_pred ceEeEEEeeeeccCCCCCceeEEeEEeCCCCe
Q 029787 134 EKVRVLPRKVHLHSGTDAPLNVTFLRAPPEAL 165 (188)
Q Consensus 134 e~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~ 165 (188)
+.+-|.+-+++++ +-=+++||-..+.+++
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 4999999999998 6668999999888654
No 12
>PF14467 DUF4426: Domain of unknown function (DUF4426); PDB: 3UC2_D.
Probab=23.60 E-value=2.9e+02 Score=21.75 Aligned_cols=62 Identities=11% Similarity=0.091 Sum_probs=35.3
Q ss_pred ceeEEEEEEECCccCCCCCcceEeEEEeeeeccCCCCCceeEEeEEeCCCCeEEEEEeEEEEecC
Q 029787 114 FVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178 (188)
Q Consensus 114 ~~s~v~~L~v~g~~~~g~~~e~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~V~v~VPV~f~Ged 178 (188)
....++++.|-...+.|. ....+-+.-.-+| +.++...++|.+|..|.-|--=-++.|.+++
T Consensus 34 k~~gllNIsVl~~~~~~~--~av~a~v~G~a~n-L~gq~~~L~FreI~Eg~AIYYlA~f~~~~~E 95 (122)
T PF14467_consen 34 KYRGLLNISVLDKSDGGK--PAVPAQVSGTARN-LLGQQRTLEFREIREGDAIYYLAEFPFRNEE 95 (122)
T ss_dssp TTEEEEEEEEEETT------EE--EEEEEEEE--TT--EEEE--EEEEETTEEEEEEEEE--SSE
T ss_pred CCeEEEEEEEecCCCccC--CccceEEEEEEec-cccceeeeeEEEEecCCcEEEEEeeccCCCc
Confidence 457899999954321221 4566777777777 5688899999999888877666666665553
No 13
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.35 E-value=1.8e+02 Score=19.30 Aligned_cols=37 Identities=16% Similarity=0.017 Sum_probs=27.4
Q ss_pred hHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhhh
Q 029787 67 SVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHL 109 (188)
Q Consensus 67 arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~~ 109 (188)
.+.|-+. -|..+-||. ...++.+.+++++..+.++.+
T Consensus 21 ~~~L~~~-~i~~i~~~~-----s~~~is~vv~~~d~~~av~~L 57 (63)
T cd04920 21 LEVFGKK-PVHLVSQAA-----NDLNLTFVVDEDQADGLCARL 57 (63)
T ss_pred HHHHhcC-CceEEEEeC-----CCCeEEEEEeHHHHHHHHHHH
Confidence 3445444 477888886 355788999999999998864
No 14
>PF12728 HTH_17: Helix-turn-helix domain
Probab=23.23 E-value=2e+02 Score=17.95 Aligned_cols=37 Identities=11% Similarity=0.269 Sum_probs=28.3
Q ss_pred CCChHhHHHHHCCCCcEEEecCCCCCCCCceeeEEEeHHHHHHHHhh
Q 029787 62 PGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGH 108 (188)
Q Consensus 62 ~Gk~~arrLRr~G~VPgVvYG~~~~~~g~~~~~I~v~~~el~kllk~ 108 (188)
...+...++.++|.+|++- . | ....++..+|++.++.
T Consensus 13 is~~tv~~~~~~g~i~~~~--~-----g---~~~~~~~~~l~~~~~~ 49 (51)
T PF12728_consen 13 ISRSTVYRWIRQGKIPPFK--I-----G---RKWRIPKSDLDRWLER 49 (51)
T ss_pred cCHHHHHHHHHcCCCCeEE--e-----C---CEEEEeHHHHHHHHHh
Confidence 3456688999999999993 2 1 2377999999999874
No 15
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=22.53 E-value=36 Score=32.49 Aligned_cols=14 Identities=71% Similarity=0.883 Sum_probs=8.3
Q ss_pred hhhhh-hhhh-hcCCC
Q 029787 18 LRCFS-QAAA-AILPD 31 (188)
Q Consensus 18 ~~~~~-~~~~-~~~~~ 31 (188)
+|-|| |+|| |+.++
T Consensus 2 ~~~~~~~~~~~~~~~~ 17 (461)
T PLN03132 2 LRAFSTQAAATAATPQ 17 (461)
T ss_pred ccccccccccccCCCC
Confidence 68899 5554 44443
No 16
>PRK10646 ADP-binding protein; Provisional
Probab=20.85 E-value=57 Score=26.48 Aligned_cols=25 Identities=12% Similarity=0.044 Sum_probs=18.5
Q ss_pred eEEEeeeeccCCCCCceeEEeEEeCCC
Q 029787 137 RVLPRKVHLHSGTDAPLNVTFLRAPPE 163 (188)
Q Consensus 137 ~vliKeVQ~hpvt~~ilHVDF~~v~~~ 163 (188)
..++++++.. ...+.|+|+||+...
T Consensus 63 Ftlv~~Y~~~--~~~l~H~DlYRL~~~ 87 (153)
T PRK10646 63 YTLVEPYTLD--NLMVYHFDLYRLADP 87 (153)
T ss_pred EeeEEEeeCC--CCCEEEEeeccCCCH
Confidence 3588887632 457999999999743
Done!