Query gi|254780646|ref|YP_003065059.1| 50S ribosomal protein L21 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs 103 out of 1616
Neff 5.4
Searched_HMMs 39220
Date Sun May 29 20:50:10 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780646.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00075 rpl21 ribosomal prote 100.0 1.2E-42 0 258.7 13.1 102 1-102 3-104 (110)
2 PRK05573 rplU 50S ribosomal pr 100.0 1.5E-42 0 258.3 13.1 103 1-103 1-103 (103)
3 PRK12278 50S ribosomal protein 100.0 2.2E-42 0 257.3 12.9 102 1-103 1-103 (216)
4 COG0261 RplU Ribosomal protein 100.0 4.4E-42 0 255.7 12.1 103 1-103 1-103 (103)
5 TIGR00061 L21 ribosomal protei 100.0 5.3E-41 1.4E-45 249.6 11.4 101 2-102 1-101 (101)
6 pfam00829 Ribosomal_L21p Ribos 100.0 2.4E-40 5.6E-45 245.9 11.2 96 1-96 1-96 (96)
7 KOG1686 consensus 99.9 9.8E-24 2.5E-28 153.2 9.9 102 1-102 26-128 (151)
8 pfam02563 Poly_export Polysacc 58.4 12 0.00031 18.7 3.3 54 6-66 6-59 (83)
9 pfam05896 NQRA Na(+)-transloca 57.2 12 0.0003 18.7 3.1 59 9-73 26-86 (257)
10 PRK06748 hypothetical protein; 47.2 25 0.00065 16.9 3.7 47 1-47 33-79 (84)
11 COG0662 {ManC} Mannose-6-phosp 43.9 29 0.00073 16.6 3.8 23 3-25 68-90 (127)
12 COG3168 PilP Tfp pilus assembl 41.8 28 0.0007 16.7 3.0 49 2-52 111-161 (170)
13 pfam07883 Cupin_2 Cupin domain 39.9 33 0.00084 16.2 3.6 22 3-24 29-50 (70)
14 pfam04351 PilP Pilus assembly 39.6 26 0.00066 16.8 2.5 42 1-42 90-134 (148)
15 TIGR03027 pepcterm_export puta 37.9 35 0.00089 16.1 3.0 47 12-65 1-47 (165)
16 PRK10531 putative pectinestera 37.1 24 0.00061 17.0 2.0 37 29-65 236-286 (427)
17 PRK10572 DNA-binding transcrip 35.9 39 0.00098 15.9 3.8 21 3-23 60-80 (290)
18 PRK12784 hypothetical protein; 34.5 41 0.001 15.7 3.6 50 1-50 33-82 (84)
19 cd05792 S1_eIF1AD_like S1_eIF1 30.3 19 0.00048 17.6 0.6 39 34-73 32-70 (78)
20 pfam06249 EutQ Ethanolamine ut 29.7 49 0.0013 15.3 3.4 31 11-41 40-71 (152)
21 KOG0126 consensus 27.8 53 0.0014 15.1 5.9 29 3-34 36-64 (219)
22 TIGR02213 lolE_release lipopro 25.2 24 0.0006 17.1 0.3 34 24-61 158-192 (416)
23 KOG1119 consensus 21.4 49 0.0013 15.3 1.4 30 8-37 125-155 (199)
24 TIGR02351 thiH thiazole biosyn 20.4 25 0.00063 17.0 -0.3 26 32-57 119-145 (378)
No 1
>CHL00075 rpl21 ribosomal protein L21
Probab=100.00 E-value=1.2e-42 Score=258.70 Aligned_cols=102 Identities=33% Similarity=0.546 Sum_probs=101.0
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEEECCC
Q ss_conf 96799999888897699899982446789972130421453068851226743378679999996345673899996388
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFKKRRR 80 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~krR 80 (103)
|||||++||+||||++||+|.+|++++++|++++|++|||+++++++.+|+|+|+||+|+|+|++|+||+||++||||||
T Consensus 3 ~yAIi~~gGkQykV~~G~~l~v~~l~~~~G~~i~~~~VLl~~~~~~~~iG~P~l~~a~V~a~V~~~~kg~Ki~vfK~KrR 82 (110)
T CHL00075 3 TYAIIEAGGKQLWVEPGRFYDINHFPLEPGTKIILYRVLLIRNESEILIGKPWLENAKVKGRILHHLRGKKITVYKMRSK 82 (110)
T ss_pred EEEEEEECCEEEEECCCCEEEEEECCCCCCCEEEEEEEEEEECCCCEEECCCCCCCCEEEEEEEEECCCCCEEEEEECCC
T ss_conf 29999989999999589999998548899999999578999789977999832168799999984158980999994798
Q ss_pred CCCEEECCCCCCCEEEEEEEEE
Q ss_conf 8716642745760099996761
Q gi|254780646|r 81 QNYRRTHGHRQEMTVVRITSIV 102 (103)
Q Consensus 81 K~yrr~~GhRq~~T~ikI~~I~ 102 (103)
|+|||++||||+||+|+|++|.
T Consensus 83 K~yrR~~GHRQ~~T~ikI~~I~ 104 (110)
T CHL00075 83 KKTRKKQGHRQKLTRFLIDSIS 104 (110)
T ss_pred CCCCCCCCCCCCCEEEEEEEEE
T ss_conf 8876787558883699998995
No 2
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=100.00 E-value=1.5e-42 Score=258.30 Aligned_cols=103 Identities=55% Similarity=0.837 Sum_probs=101.5
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEEECCC
Q ss_conf 96799999888897699899982446789972130421453068851226743378679999996345673899996388
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFKKRRR 80 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~krR 80 (103)
|||||++||+||||++||.|.||++++++||.++|++|||+++++++.+|+|+|+||+|+|+|++|++|+|+++||||||
T Consensus 1 MyAVi~~gGkQykV~~gd~i~v~~l~~~~G~~i~~~~VLlv~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~krR 80 (103)
T PRK05573 1 MYAIIKTGGKQYKVEEGDVIKVEKLDAEVGDTVEFDEVLLVGGGEEVKIGAPYVEGAKVTAEVLEHGRGKKVIVFKKKRR 80 (103)
T ss_pred CEEEEEECCEEEEECCCCEEEECCCCCCCCCEEEEEEEEEECCCCCEEECCCCCCCCEEEEEEEEECCCCCEEEEEECCC
T ss_conf 98999979999999699999992316789999998688998499868868976887599999984237884999996598
Q ss_pred CCCEEECCCCCCCEEEEEEEEEC
Q ss_conf 87166427457600999967619
Q gi|254780646|r 81 QNYRRTHGHRQEMTVVRITSIVT 103 (103)
Q Consensus 81 K~yrr~~GhRq~~T~ikI~~I~s 103 (103)
|+|||++||||+||+|+|++|..
T Consensus 81 K~yrr~~GHRQ~~T~i~I~~I~~ 103 (103)
T PRK05573 81 KNYRKKQGHRQPYTKVKITSINA 103 (103)
T ss_pred CCCCCCCCCCCCCEEEEEEEEEC
T ss_conf 88525774478717999988889
No 3
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=100.00 E-value=2.2e-42 Score=257.30 Aligned_cols=102 Identities=51% Similarity=0.876 Sum_probs=95.9
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEE-ECC
Q ss_conf 9679999988889769989998244678997213042145306885122674337867999999634567389999-638
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFK-KRR 79 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK-~kr 79 (103)
|||||++|||||+|++||.|.||+|++++||+|+|++|||+++ +.+.+|+|+|+||+|+|+|++|.||+||++|+ +||
T Consensus 1 MyAII~tGGKQYkV~~Gd~l~Vekl~~e~G~~v~fd~VLlv~~-~~~~vG~P~v~gA~V~A~Vle~~kg~KvivfkKkRR 79 (216)
T PRK12278 1 MFAVIKTGGKQYKVAAGDTLRVEKLAAEAGETVQFNDVLMLGG-ENVTVGAPFVDGAAVQAEVVEQIKGRKVIHFVKRRR 79 (216)
T ss_pred CEEEEEECCEEEEECCCCEEEEEECCCCCCCEEEEEEEEEECC-CCCEECCCCCCCCEEEEEEEEECCCCEEEEEEEECC
T ss_conf 9799996998999848999999602789999988606799869-983589642468789999985036855999998227
Q ss_pred CCCCEEECCCCCCCEEEEEEEEEC
Q ss_conf 887166427457600999967619
Q gi|254780646|r 80 RQNYRRTHGHRQEMTVVRITSIVT 103 (103)
Q Consensus 80 RK~yrr~~GhRq~~T~ikI~~I~s 103 (103)
|+||||++||||+||+|+|++|+.
T Consensus 80 kk~yrRk~GHRQ~~T~ikI~~Ila 103 (216)
T PRK12278 80 KHSSRRTKGHRQKLTLVRITEILA 103 (216)
T ss_pred CCCCCCCCCCCCCCCEEEEEEEEC
T ss_conf 877647777578864799988635
No 4
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.4e-42 Score=255.66 Aligned_cols=103 Identities=54% Similarity=0.845 Sum_probs=101.5
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEEECCC
Q ss_conf 96799999888897699899982446789972130421453068851226743378679999996345673899996388
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFKKRRR 80 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~krR 80 (103)
|||||++|||||+|++||.+.+|+|++++|++++||+|||+++++.+.+|.|+++||+|+|+|++|+|++||++||||||
T Consensus 1 mYAii~tGGKQykV~~G~~i~vEkl~~e~g~~v~f~~VL~v~~~~~v~iG~P~v~ga~V~aeV~~hgr~kKV~i~K~k~r 80 (103)
T COG0261 1 MYAIIKTGGKQYKVEEGDVIKVEKLDAEPGDKVEFDEVLMVGGGEEVKIGAPYVEGAKVTAEVVEHGRGKKVIIFKYKRR 80 (103)
T ss_pred CEEEEEECCEEEEEECCCEEEEEECCCCCCCEEEEEEEEEECCCCCEEECCCEECCCEEEEEEHHHCCCCEEEEEEECCC
T ss_conf 93899979989999569899999827788999999899998189746888840068699999912278766999994157
Q ss_pred CCCEEECCCCCCCEEEEEEEEEC
Q ss_conf 87166427457600999967619
Q gi|254780646|r 81 QNYRRTHGHRQEMTVVRITSIVT 103 (103)
Q Consensus 81 K~yrr~~GhRq~~T~ikI~~I~s 103 (103)
|||+|++||||+||+|+|++|..
T Consensus 81 K~~~rk~GHRQ~yT~vkI~~I~~ 103 (103)
T COG0261 81 KNYRKKQGHRQPYTRVKITGIVA 103 (103)
T ss_pred CCCCCCCCCCCCEEEEEEEEEEC
T ss_conf 67322447666447999998619
No 5
>TIGR00061 L21 ribosomal protein L21; InterPro: IPR001787 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00 E-value=5.3e-41 Score=249.58 Aligned_cols=101 Identities=50% Similarity=0.771 Sum_probs=100.1
Q ss_pred EEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEEECCCC
Q ss_conf 67999998888976998999824467899721304214530688512267433786799999963456738999963888
Q gi|254780646|r 2 FAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFKKRRRQ 81 (103)
Q Consensus 2 yAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~krRK 81 (103)
||||++|||||+|+|||.+.+|+|++++|+.++||+|||++++++..||+|||+||+|+|+|++|.|++||.+|||+|||
T Consensus 1 YAi~~~GGKQy~V~EG~~~~~eKL~~~~~~~~~~~~vL~v~~g~~vkiG~P~V~gA~v~a~v~~~gr~~KV~~~k~rrrK 80 (101)
T TIGR00061 1 YAIVEIGGKQYKVEEGQTVKIEKLDAAPGDTVEFDKVLLVKKGDDVKIGKPYVEGAKVEAEVEKHGRGKKVIVYKYRRRK 80 (101)
T ss_pred CEEEEECCEEEEECCCCEEEEECCCCCCCCEEEEEEEEEEECCCCEEECCCEECCCEEEEEEEECCCCCCEEEEEEECCC
T ss_conf 94885489788821996799972474559778887778884599346178483397899999863577856988814178
Q ss_pred CCEEECCCCCCCEEEEEEEEE
Q ss_conf 716642745760099996761
Q gi|254780646|r 82 NYRRTHGHRQEMTVVRITSIV 102 (103)
Q Consensus 82 ~yrr~~GhRq~~T~ikI~~I~ 102 (103)
+++++.||||+||+|+|++|.
T Consensus 81 ~~~kk~GHRQ~yT~v~v~~I~ 101 (101)
T TIGR00061 81 HSRKKQGHRQPYTKVKVTKIV 101 (101)
T ss_pred CCCCCCCEECCCCEEEEEEEC
T ss_conf 865420114045559898859
No 6
>pfam00829 Ribosomal_L21p Ribosomal prokaryotic L21 protein.
Probab=100.00 E-value=2.4e-40 Score=245.89 Aligned_cols=96 Identities=56% Similarity=0.839 Sum_probs=95.0
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEEECCC
Q ss_conf 96799999888897699899982446789972130421453068851226743378679999996345673899996388
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFKKRRR 80 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~krR 80 (103)
|||||++||+||||++||.|.||++++++||.++|++|||+++++++.+|+|+|++|+|+|+|++|.||+||++||||||
T Consensus 1 MyAVi~~gGkQykV~~G~~i~v~~l~~~~G~~i~~~~VLl~~~~~~~~iG~P~l~~a~V~a~V~~~~r~~Ki~vfK~krR 80 (96)
T pfam00829 1 MYAIIETGGKQYKVEEGDVIFVEKLDAEVGDKIEFDKVLLVGGDGKVKIGKPYVEGAKVKAEVLEHGRGKKVIVFKYKRR 80 (96)
T ss_pred CEEEEEECCEEEEECCCCEEEECCCCCCCCCEEEEEEEEEEECCCCEEECCCCCCCCEEEEEEEEECCCCCEEEEEECCC
T ss_conf 98999979999998599999987647789999996486998489968839871357699999983148883999994598
Q ss_pred CCCEEECCCCCCCEEE
Q ss_conf 8716642745760099
Q gi|254780646|r 81 QNYRRTHGHRQEMTVV 96 (103)
Q Consensus 81 K~yrr~~GhRq~~T~i 96 (103)
|||||++||||+||+|
T Consensus 81 K~yrr~~GHRQ~~T~i 96 (96)
T pfam00829 81 KNYRKKQGHRQPYTRV 96 (96)
T ss_pred CCCCCCCCCCCCEEEC
T ss_conf 8864677547760709
No 7
>KOG1686 consensus
Probab=99.90 E-value=9.8e-24 Score=153.19 Aligned_cols=102 Identities=39% Similarity=0.459 Sum_probs=98.8
Q ss_pred CEEEEEECCEEEEECCCCEEEEECC-CCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEEEEEECC
Q ss_conf 9679999988889769989998244-678997213042145306885122674337867999999634567389999638
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKI-VAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVVVFKKRR 79 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l-~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~vfK~kr 79 (103)
.||++..||+||+|..||.+..+++ ...++|++.+++|||++.-+.+.+|+|.+++|+|.|.|+++++..|+.+|++|+
T Consensus 26 ~favv~v~srq~kvs~gd~iy~eg~~p~nv~d~i~l~kVlLvg~~~~T~~grpvv~~vtv~aVv~e~g~~~kvvhfk~k~ 105 (151)
T KOG1686 26 GFAVVSVGSRQRKVSSGDTIYTEGLKPKNVLDSIPLPKVLLVGPVEETRIGRPVVKKVTVHAVVEEYGLLFKVVHFKSKQ 105 (151)
T ss_pred CCEEEEECCEEEEECCCCEEEECCCCCCCCCCCCCCCEEEEECCCCEEEECCCCCCCCEEEEEEEECCCCCCEEEEEECC
T ss_conf 52799985616886599746404753566566656404787667410475673346522787743004455079998612
Q ss_pred CCCCEEECCCCCCCEEEEEEEEE
Q ss_conf 88716642745760099996761
Q gi|254780646|r 80 RQNYRRTHGHRQEMTVVRITSIV 102 (103)
Q Consensus 80 RK~yrr~~GhRq~~T~ikI~~I~ 102 (103)
+|.|+|..||||..|+|+|++|-
T Consensus 106 ~k~tr~~~~~~qe~t~LrIt~it 128 (151)
T KOG1686 106 WKVTRRDLGHRQEATELRITCIT 128 (151)
T ss_pred HHHHHHHHCCCCCCCEEEEEEEE
T ss_conf 23433542025766179886500
No 8
>pfam02563 Poly_export Polysaccharide biosynthesis/export protein. This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.
Probab=58.42 E-value=12 Score=18.66 Aligned_cols=54 Identities=15% Similarity=0.219 Sum_probs=36.9
Q ss_pred EECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEEC
Q ss_conf 9998888976998999824467899721304214530688512267433786799999963
Q gi|254780646|r 6 EHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQ 66 (103)
Q Consensus 6 ~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~ 66 (103)
......|++.+||.+.+.-...+. ++.-+.++.++.+.+ |++-...|.+.=+++
T Consensus 6 ~~~~~~Y~lgpGD~l~i~v~g~~~-----~~~~~~V~~dG~I~l--P~vG~v~v~GlT~~e 59 (83)
T pfam02563 6 AAASPDYRLGPGDVLRITVFGEPE-----LSGEVRVDPDGTISL--PLVGPVKVAGLTPEE 59 (83)
T ss_pred CCCCCCCEECCCCEEEEEEECCCC-----CEEEEEECCCCCEEC--CCCCEEEECCCCHHH
T ss_conf 679998888799999999947766-----407899999972965--766459980799999
No 9
>pfam05896 NQRA Na(+)-translocating NADH-quinone reductase subunit A (NQRA). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration.
Probab=57.20 E-value=12 Score=18.73 Aligned_cols=59 Identities=22% Similarity=0.309 Sum_probs=43.5
Q ss_pred CEEEEECCCCEEEE-ECCCCCCCCCEEHHHEEEEEC-CCCCEECCCCCCCCEEEEEEEECCCCCCEE
Q ss_conf 88889769989998-244678997213042145306-885122674337867999999634567389
Q gi|254780646|r 9 GKQSRVSATDTITV-EKIVAKDGDNIRFDNVLAVGK-DEHLSVGTPRVEGAYVEAEVVKQLRTKKVV 73 (103)
Q Consensus 9 GkQykV~~Gd~l~v-~~l~~~~G~~i~l~~VL~~~~-~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~ 73 (103)
-+.|-+.+.|+.-+ ++|-.++||++.....|+... ...+.+-+| |.++|.+-.||+|=.
T Consensus 26 ~~~~ai~p~Df~glkPkl~VkeGD~Vk~G~pLF~dK~np~i~f~SP------vsG~V~~I~RG~kR~ 86 (257)
T pfam05896 26 VRTVALLGEDYVGMKPKMLVKEGDKVKAGQPLFEDKKNPGVKFTAP------ASGTVVAINRGAKRV 86 (257)
T ss_pred CCEEEECCCCCCCCCEEEEEECCCEEECCCEEEEEECCCCCEEECC------CCEEEEEECCCCCCC
T ss_conf 7579984601488732699834999855875799736988468567------873895010567510
No 10
>PRK06748 hypothetical protein; Validated
Probab=47.16 E-value=25 Score=16.89 Aligned_cols=47 Identities=15% Similarity=0.170 Sum_probs=38.6
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCC
Q ss_conf 96799999888897699899982446789972130421453068851
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHL 47 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~ 47 (103)
+++|=..+|+--+|+.|=-=.++.++.++|+++.-+.+|+.-.++-.
T Consensus 33 L~~I~~~dg~le~v~vGisG~I~~v~Ve~Gq~i~~~~lL~~vedDll 79 (84)
T PRK06748 33 LALIETIDKQKVEIKVGISGYIESLEVVEGQAIADQKLLITVRDDLL 79 (84)
T ss_pred EEEEEECCCCEEEEEEEEEEEEEEEEEECCCEECCCCEEEEEECCEE
T ss_conf 45775069828999982142788988622846537738999871478
No 11
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=43.89 E-value=29 Score=16.59 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=20.6
Q ss_pred EEEEECCEEEEECCCCEEEEECC
Q ss_conf 79999988889769989998244
Q gi|254780646|r 3 AIIEHGGKQSRVSATDTITVEKI 25 (103)
Q Consensus 3 AIi~~gGkQykV~~Gd~l~v~~l 25 (103)
|.+.++|+++-|.+||.+.|+.=
T Consensus 68 g~v~~~~~~~~v~~gd~~~iP~g 90 (127)
T COG0662 68 GKVTIGGEEVEVKAGDSVYIPAG 90 (127)
T ss_pred EEEEECCEEEEECCCCEEEECCC
T ss_conf 99999999999748999998999
No 12
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=41.83 E-value=28 Score=16.68 Aligned_cols=49 Identities=20% Similarity=0.236 Sum_probs=31.2
Q ss_pred EEEEEECCEEEEECCCCEEEEEC--CCCCCCCCEEHHHEEEEECCCCCEECCC
Q ss_conf 67999998888976998999824--4678997213042145306885122674
Q gi|254780646|r 2 FAIIEHGGKQSRVSATDTITVEK--IVAKDGDNIRFDNVLAVGKDEHLSVGTP 52 (103)
Q Consensus 2 yAIi~~gGkQykV~~Gd~l~v~~--l~~~~G~~i~l~~VL~~~~~~~~~iG~P 52 (103)
.|+|+..|+-|+|..|+++-.+. +-.-.-+.|.+.+.+ .|+..-+.-+|
T Consensus 111 ~A~i~~~~~v~~V~vG~YlGqN~GrV~rI~d~~i~l~Elv--~dG~g~W~eR~ 161 (170)
T COG3168 111 SALIEAPGGVYRVRVGQYLGQNYGRVVRITDDSIVLNELV--PDGTGNWLERP 161 (170)
T ss_pred EEEEECCCCEEEEEECCEEECCCCEEEEECCCEEEEEEEC--CCCCCCHHHCC
T ss_conf 8999738926998501075024766888538727724224--67666443243
No 13
>pfam07883 Cupin_2 Cupin domain. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).
Probab=39.93 E-value=33 Score=16.24 Aligned_cols=22 Identities=14% Similarity=0.228 Sum_probs=18.8
Q ss_pred EEEEECCEEEEECCCCEEEEEC
Q ss_conf 7999998888976998999824
Q gi|254780646|r 3 AIIEHGGKQSRVSATDTITVEK 24 (103)
Q Consensus 3 AIi~~gGkQykV~~Gd~l~v~~ 24 (103)
+.+..+|+.+.+.+||.+.++.
T Consensus 29 ~~~~~~g~~~~l~~Gd~~~ip~ 50 (70)
T pfam07883 29 GELTVDGEEVVLKAGDSVYFPA 50 (70)
T ss_pred EEEEECCEEEECCCCCEEEECC
T ss_conf 9999988899868999999899
No 14
>pfam04351 PilP Pilus assembly protein, PilP. The PilP family are periplasmic proteins involved in the biogenesis of type IV pili.
Probab=39.57 E-value=26 Score=16.82 Aligned_cols=42 Identities=17% Similarity=0.309 Sum_probs=27.6
Q ss_pred CEEEEEE-CCEEEEECCCCEEEEEC--CCCCCCCCEEHHHEEEEE
Q ss_conf 9679999-98888976998999824--467899721304214530
Q gi|254780646|r 1 MFAIIEH-GGKQSRVSATDTITVEK--IVAKDGDNIRFDNVLAVG 42 (103)
Q Consensus 1 MyAIi~~-gGkQykV~~Gd~l~v~~--l~~~~G~~i~l~~VL~~~ 42 (103)
++|.|+. .|.-|+|..|+.+=.+. +-.-.-+.|.+.+++-=+
T Consensus 90 ~~ALv~~pdg~v~~V~~G~ylG~n~G~I~~I~~~~i~l~E~v~Dg 134 (148)
T pfam04351 90 LWALVRTPDGSVYRVKVGNYLGQNYGRITKITETEIELIEIVPDG 134 (148)
T ss_pred EEEEEECCCCCEEEEECCCEECCCCCEEEEEECCEEEEEEEEECC
T ss_conf 999999699988997028760446868999948939999980879
No 15
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=37.86 E-value=35 Score=16.12 Aligned_cols=47 Identities=13% Similarity=0.211 Sum_probs=31.1
Q ss_pred EEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEECCCCCCCCEEEEEEEE
Q ss_conf 897699899982446789972130421453068851226743378679999996
Q gi|254780646|r 12 SRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVK 65 (103)
Q Consensus 12 ykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~ 65 (103)
|++.+||.|.|.-+..+. |+..+.++.++. |--|++-..+|.+.=++
T Consensus 1 Y~lgpGD~l~I~v~~~~~-----l~~~~~V~~dG~--I~lP~vG~v~v~GlT~~ 47 (165)
T TIGR03027 1 YVIGPGDSLNINVWRNPE-----LSGSVPVRPDGK--ITTPLVGDLVASGKTPT 47 (165)
T ss_pred CCCCCCCEEEEEEECCCC-----CEEEEEECCCCE--EECCCCCEEEEECCCHH
T ss_conf 978899889999937877-----416689899972--96578727999368899
No 16
>PRK10531 putative pectinesterase; Provisional
Probab=37.08 E-value=24 Score=17.04 Aligned_cols=37 Identities=30% Similarity=0.537 Sum_probs=28.8
Q ss_pred CCCCEEHHHEEEEECCCCCEEC--------------CCCCCCCEEEEEEEE
Q ss_conf 9972130421453068851226--------------743378679999996
Q gi|254780646|r 29 DGDNIRFDNVLAVGKDEHLSVG--------------TPRVEGAYVEAEVVK 65 (103)
Q Consensus 29 ~G~~i~l~~VL~~~~~~~~~iG--------------~P~l~~a~V~a~V~~ 65 (103)
.||++.|++|.++|+-+...++ +-|+.+..|++.|-=
T Consensus 236 ~gDkv~~~nv~~lG~QDTL~v~~~~~~n~~~~~~~~R~Y~~nsYIEGDVDF 286 (427)
T PRK10531 236 DGDKVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLVTNSYIEGDVDF 286 (427)
T ss_pred CCCCEEEECCEEECCCCEEEECCCCCCCCCCCCCCCCEEEEEEEEEECCEE
T ss_conf 176125662578603643886156654422235545168870388742138
No 17
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=35.85 E-value=39 Score=15.87 Aligned_cols=21 Identities=19% Similarity=0.308 Sum_probs=19.0
Q ss_pred EEEEECCEEEEECCCCEEEEE
Q ss_conf 799999888897699899982
Q gi|254780646|r 3 AIIEHGGKQSRVSATDTITVE 23 (103)
Q Consensus 3 AIi~~gGkQykV~~Gd~l~v~ 23 (103)
.+++.+|++|.|++||.+.+.
T Consensus 60 G~~~~~~~~y~l~~Gd~fLi~ 80 (290)
T PRK10572 60 GVIFNGGRAFVCRPGDLLLFP 80 (290)
T ss_pred EEEEECCEEEEECCCCEEEEC
T ss_conf 999989999996699889988
No 18
>PRK12784 hypothetical protein; Provisional
Probab=34.49 E-value=41 Score=15.74 Aligned_cols=50 Identities=20% Similarity=0.288 Sum_probs=38.3
Q ss_pred CEEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEEECCCCCEEC
Q ss_conf 96799999888897699899982446789972130421453068851226
Q gi|254780646|r 1 MFAIIEHGGKQSRVSATDTITVEKIVAKDGDNIRFDNVLAVGKDEHLSVG 50 (103)
Q Consensus 1 MyAIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~l~~VL~~~~~~~~~iG 50 (103)
++.|=...|+--+|..|=-=.+..++.++|+.+.-+.+|+.-.++-..-|
T Consensus 33 L~~I~~~dg~le~v~vGiSG~I~~v~Ve~Gq~i~~~tlL~~~edDllitG 82 (84)
T PRK12784 33 LMMIRKNNGELEKVAVGISGNIRLVNVVVGQQIHTDTLLVRLEDDLLITG 82 (84)
T ss_pred EEEEEECCCCEEEEEEEEEEEEEEEEEECCCEECCCCEEEEEECCEEEEC
T ss_conf 45775069828999982011689998622854347718999860367735
No 19
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=30.26 E-value=19 Score=17.62 Aligned_cols=39 Identities=31% Similarity=0.452 Sum_probs=29.3
Q ss_pred EHHHEEEEECCCCCEECCCCCCCCEEEEEEEECCCCCCEE
Q ss_conf 3042145306885122674337867999999634567389
Q gi|254780646|r 34 RFDNVLAVGKDEHLSVGTPRVEGAYVEAEVVKQLRTKKVV 73 (103)
Q Consensus 34 ~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~ 73 (103)
.|-+-+-+.-++++.+. |.-+|.+|.|+|+.-...+.|.
T Consensus 32 KFRk~iWiKRG~fVlvd-~~~eg~Kv~geIv~Il~~e~vK 70 (78)
T cd05792 32 KFRKNIWIKRGDFVLVE-PIEEGDKVKAEIVKILTRDHVK 70 (78)
T ss_pred HHHCCEEEECCCEEEEE-ECCCCCEEEEEEEEEECHHHHH
T ss_conf 34316899718999997-6047980789999996578988
No 20
>pfam06249 EutQ Ethanolamine utilisation protein EutQ. The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear.
Probab=29.69 E-value=49 Score=15.28 Aligned_cols=31 Identities=3% Similarity=0.196 Sum_probs=17.7
Q ss_pred EEEECCCCEEEEECCC-CCCCCCEEHHHEEEE
Q ss_conf 8897699899982446-789972130421453
Q gi|254780646|r 11 QSRVSATDTITVEKIV-AKDGDNIRFDNVLAV 41 (103)
Q Consensus 11 QykV~~Gd~l~v~~l~-~~~G~~i~l~~VL~~ 41 (103)
--||..|+....++++ +++++.+.+.+++-.
T Consensus 40 ~ikv~~~~~~~~~~~dtGnp~~~v~~kdl~~~ 71 (152)
T pfam06249 40 SIKLPDVKVVKFGRLDTGNPHDVVYTKDLVTL 71 (152)
T ss_pred EEEECCCEEEECCCCCCCCCCCEEEEEECCCC
T ss_conf 48850000255032347897756874000051
No 21
>KOG0126 consensus
Probab=27.83 E-value=53 Score=15.09 Aligned_cols=29 Identities=24% Similarity=0.316 Sum_probs=22.8
Q ss_pred EEEEECCEEEEECCCCEEEEECCCCCCCCCEE
Q ss_conf 79999988889769989998244678997213
Q gi|254780646|r 3 AIIEHGGKQSRVSATDTITVEKIVAKDGDNIR 34 (103)
Q Consensus 3 AIi~~gGkQykV~~Gd~l~v~~l~~~~G~~i~ 34 (103)
|-|-+||-.|-.++||+|.|- ++-|+.+.
T Consensus 36 A~Iyiggl~~~LtEgDil~VF---SqyGe~vd 64 (219)
T KOG0126 36 AYIYIGGLPYELTEGDILCVF---SQYGEIVD 64 (219)
T ss_pred EEEEECCCCCCCCCCCEEEEE---ECCCCEEE
T ss_conf 379977876545578689985---23583477
No 22
>TIGR02213 lolE_release lipoprotein releasing system, transmembrane protein LolE; InterPro: IPR011926 This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in Escherichia coli and related species.; GO: 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=25.23 E-value=24 Score=17.07 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=18.3
Q ss_pred CCCCCCCCCEEHHHEEEEE-CCCCCEECCCCCCCCEEEE
Q ss_conf 4467899721304214530-6885122674337867999
Q gi|254780646|r 24 KIVAKDGDNIRFDNVLAVG-KDEHLSVGTPRVEGAYVEA 61 (103)
Q Consensus 24 ~l~~~~G~~i~l~~VL~~~-~~~~~~iG~P~l~~a~V~a 61 (103)
-|+.+.||=|+ ||+. .+++..+-+|.=.-++|++
T Consensus 158 eL~VkvGDwvt----llIpq~n~~~k~~qPkRvrv~Vtg 192 (416)
T TIGR02213 158 ELDVKVGDWVT----LLIPQSNEDEKLAQPKRVRVKVTG 192 (416)
T ss_pred HCCCCCCCEEE----EEECCCCCCCCCCCCCCEEEEEEE
T ss_conf 20866265799----971078974323588300378877
No 23
>KOG1119 consensus
Probab=21.39 E-value=49 Score=15.28 Aligned_cols=30 Identities=20% Similarity=0.433 Sum_probs=12.6
Q ss_pred CCEEEEECCCCEEEEE-CCCCCCCCCEEHHH
Q ss_conf 9888897699899982-44678997213042
Q gi|254780646|r 8 GGKQSRVSATDTITVE-KIVAKDGDNIRFDN 37 (103)
Q Consensus 8 gGkQykV~~Gd~l~v~-~l~~~~G~~i~l~~ 37 (103)
.|-||+.+-+..+.-| ++..+.|..+-.|.
T Consensus 125 sGFQYkf~LD~~in~dD~vf~e~~arVVvD~ 155 (199)
T KOG1119 125 SGFQYKFRLDNKINNDDRVFVENGARVVVDN 155 (199)
T ss_pred CCEEEEEEECCCCCCCCEEEEECCCEEEEEC
T ss_conf 3358888844777876657861880899853
No 24
>TIGR02351 thiH thiazole biosynthesis protein ThiH; InterPro: IPR012726 Members of this protein family are the ThiH proteins involved in thiamine biosynthesis. They are homologues of the BioB protein of biotin biosynthesis. Genes encoding these proteins are generally found in operons with other thiamin biosynthesis genes. ; GO: 0005506 iron ion binding, 0051539 4 iron 4 sulfur cluster binding, 0009228 thiamin biosynthetic process.
Probab=20.44 E-value=25 Score=16.97 Aligned_cols=26 Identities=23% Similarity=0.367 Sum_probs=22.1
Q ss_pred CEE-HHHEEEEECCCCCEECCCCCCCC
Q ss_conf 213-04214530688512267433786
Q gi|254780646|r 32 NIR-FDNVLAVGKDEHLSVGTPRVEGA 57 (103)
Q Consensus 32 ~i~-l~~VL~~~~~~~~~iG~P~l~~a 57 (103)
+.. |+.|||+.++.....|-+|+..+
T Consensus 119 k~gPf~~iLlvtGE~e~~~g~~Yi~~~ 145 (378)
T TIGR02351 119 KSGPFKEILLVTGESEKAAGVEYIEEA 145 (378)
T ss_pred HCCCCHHEEEECCCCCCCCCHHHHHHH
T ss_conf 207701300111577755883789999
Done!