Query gi|254780318|ref|YP_003064731.1| ribosomal protein L20 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 123
No_of_seqs 121 out of 1268
Neff 4.5
Searched_HMMs 39220
Date Sun May 29 16:19:20 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780318.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01032 rplT_bact ribosomal 100.0 0 0 375.5 9.4 114 1-114 1-114 (114)
2 COG0292 RplT Ribosomal protein 100.0 0 0 340.0 14.5 118 1-118 1-118 (118)
3 CHL00068 rpl20 ribosomal prote 100.0 0 0 326.2 14.6 114 1-114 1-116 (117)
4 PRK05185 rplT 50S ribosomal pr 100.0 0 0 323.0 13.9 114 2-115 1-114 (114)
5 pfam00453 Ribosomal_L20 Riboso 100.0 0 0 308.1 12.8 107 3-109 1-107 (107)
6 PTZ00030 60S ribosomal protein 100.0 0 0 305.8 14.1 111 11-121 2-112 (121)
7 KOG4707 consensus 100.0 6.2E-36 1.6E-40 230.9 7.5 117 1-117 8-124 (147)
8 COG3514 Uncharacterized protei 74.4 1.8 4.6E-05 23.4 1.7 14 59-72 75-88 (93)
9 PRK03573 transcriptional regul 72.0 8.7 0.00022 19.4 7.0 58 57-114 12-71 (144)
10 PRK07080 hypothetical protein; 44.6 11 0.00029 18.8 1.3 46 33-78 170-215 (318)
11 TIGR01326 OAH_OAS_sulfhy O-ace 40.6 6.2 0.00016 20.3 -0.5 42 67-113 101-143 (434)
12 pfam08809 DUF1799 Phage relate 37.8 34 0.00086 16.0 2.9 38 71-108 43-82 (83)
13 pfam03050 Transposase_25 Trans 37.0 36 0.00091 15.8 5.4 50 71-120 59-108 (178)
14 pfam01777 Ribosomal_L27e Ribos 36.5 13 0.00033 18.4 0.6 48 73-120 23-70 (85)
15 TIGR02111 PQQ_syn_pqqC coenzym 36.0 21 0.00052 17.2 1.5 12 55-66 66-77 (239)
16 pfam11333 DUF3135 Protein of u 31.4 44 0.0011 15.3 3.7 27 93-119 7-33 (83)
17 KOG3955 consensus 26.3 51 0.0013 14.9 2.2 44 72-117 212-264 (361)
18 KOG0942 consensus 23.9 61 0.0015 14.5 3.9 27 39-65 34-60 (1001)
19 pfam05225 HTH_psq helix-turn-h 23.9 56 0.0014 14.7 2.1 21 64-84 18-38 (45)
20 pfam11537 DUF3227 Protein of u 21.0 53 0.0013 14.8 1.5 47 63-113 10-56 (102)
21 cd07751 PolyPPase_VTC4_like Po 20.7 34 0.00087 15.9 0.5 26 60-85 251-277 (290)
22 TIGR02677 TIGR02677 conserved 20.6 53 0.0014 14.8 1.4 28 94-121 436-463 (514)
No 1
>TIGR01032 rplT_bact ribosomal protein L20; InterPro: IPR005812 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 , . This family covers bacterial ribosomal protein L20 and its chloroplast equivalent.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00 E-value=0 Score=375.50 Aligned_cols=114 Identities=61% Similarity=0.919 Sum_probs=113.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf 98775665556899899997413156452369999999999999987469988999999999867799997189999999
Q gi|254780318|r 1 MTRVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQFI 80 (123)
Q Consensus 1 M~Rvk~g~~~~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~fi 80 (123)
|+|||+|++++.|||||||+||||||+++++||+|+|+|++|++|||+|||++|||||+|||+|||||+|+||||||+||
T Consensus 1 M~RvK~g~~~r~RRKkiLK~AKGf~G~~~~~yr~Ak~~v~ka~~YaYrdRr~rKRdFR~LWI~RINAA~R~~GlsYS~fi 80 (114)
T TIGR01032 1 MMRVKRGVVARKRRKKILKLAKGFRGTRKKHYRVAKQTVIKAMAYAYRDRRQRKRDFRSLWITRINAAAREHGLSYSRFI 80 (114)
T ss_pred CCCCCCCCCCEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 93234675110011024330255401223550368999999886002455310034578899999999874588489987
Q ss_pred HHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 9999629864689999997419899999999999
Q gi|254780318|r 81 NGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSR 114 (123)
Q Consensus 81 ~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak 114 (123)
|||+++||+|||||||||||+||++|++||+.+|
T Consensus 81 n~LK~A~I~iNRKvLselAi~D~~aF~~~v~~~K 114 (114)
T TIGR01032 81 NGLKKANIEINRKVLSELAINDPEAFKEIVEQAK 114 (114)
T ss_pred HHHHHCCCCCCHHHHHHHHHHCHHHHHHHHHHHC
T ss_conf 5798748231437768986215789999998619
No 2
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=340.01 Aligned_cols=118 Identities=59% Similarity=0.898 Sum_probs=116.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf 98775665556899899997413156452369999999999999987469988999999999867799997189999999
Q gi|254780318|r 1 MTRVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQFI 80 (123)
Q Consensus 1 M~Rvk~g~~~~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~fi 80 (123)
|+|||+|+++++|||+|||+||||||+++++|++|+|+|++|++|+|+||+++|||||+|||+|||||+|++|+|||+||
T Consensus 1 M~RvK~gv~~r~RrKkiLK~AKG~~G~r~~~~r~Akq~v~ka~~yaYrdRr~rKRdFR~LWI~RINAA~R~~GlsYS~fi 80 (118)
T COG0292 1 MARVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQRKRDFRKLWIARINAAARENGLSYSRFI 80 (118)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 97420117889999999999520353421499999999999999999878988627999999999999998289599999
Q ss_pred HHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf 99996298646899999974198999999999999855
Q gi|254780318|r 81 NGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRSRLL 118 (123)
Q Consensus 81 ~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak~~l~ 118 (123)
+||++++|+|||||||||||+||.+|..||+.+|.+|+
T Consensus 81 ~gLkkA~I~inRKvLadlAi~dp~aF~~lv~~aK~al~ 118 (118)
T COG0292 81 NGLKKAGIEIDRKVLADLAINDPAAFAALVEKAKAALA 118 (118)
T ss_pred HHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
T ss_conf 89998165100999999980289999999999987539
No 3
>CHL00068 rpl20 ribosomal protein L20
Probab=100.00 E-value=0 Score=326.23 Aligned_cols=114 Identities=45% Similarity=0.703 Sum_probs=112.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHH
Q ss_conf 98775665556899899997413156452369999999999999987469988999999999867799997189--9999
Q gi|254780318|r 1 MTRVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDL--NYSQ 78 (123)
Q Consensus 1 M~Rvk~g~~~~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~--sYS~ 78 (123)
|||||+|+++++||++||++|+||+|++++||++|+|+|+|||+|||+||+.|||+||+|||+|||||+|++|+ +||+
T Consensus 1 M~Rvk~g~~~~~rrkkilk~akGfrG~~~~~~r~A~~~v~kAl~yayr~Rk~kKr~fR~LWI~RINAa~r~~gl~~sYS~ 80 (117)
T CHL00068 1 MTRVKRGYIARKRRKKILLFASGFRGAHSRLFRTANQQKMKALVSSYRDRKKKKRDFRRLWITRINAAIREYGVSYSYSK 80 (117)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf 99865749999999999998061476765416999999999999998739888679999999999999998388154999
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 999999629864689999997419899999999999
Q gi|254780318|r 79 FINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSR 114 (123)
Q Consensus 79 fi~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak 114 (123)
||+||+++||+|||||||||||+||.+|++||+.++
T Consensus 81 fi~~L~~~~I~LnRKvLs~LAi~dp~~F~~lv~~v~ 116 (117)
T CHL00068 81 FIHNLYKNQILLNRKILAQIAILDRNCFYMISNEII 116 (117)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 999999918848499999999709899999999871
No 4
>PRK05185 rplT 50S ribosomal protein L20; Provisional
Probab=100.00 E-value=0 Score=322.98 Aligned_cols=114 Identities=60% Similarity=0.910 Sum_probs=112.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf 87756655568998999974131564523699999999999999874699889999999998677999971899999999
Q gi|254780318|r 2 TRVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQFIN 81 (123)
Q Consensus 2 ~Rvk~g~~~~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~fi~ 81 (123)
+|||+|+++++||++||++|+||+|++++||++|+|+|+|||+|||+||+.+|||||+|||+|||||+|++|++||+||+
T Consensus 1 ~Rvk~g~~~r~rrkkilk~akGfrG~~~~~~r~A~~~v~kAl~yayr~Rk~kKr~fR~LWI~RINAa~r~~g~sYs~fi~ 80 (114)
T PRK05185 1 ARVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQKKRDFRKLWIARINAAARQNGLSYSRFIN 80 (114)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 97655178899999999980303556454159999999999999996799998899999999999999994987999998
Q ss_pred HHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf 9996298646899999974198999999999999
Q gi|254780318|r 82 GLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRS 115 (123)
Q Consensus 82 ~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak~ 115 (123)
+|+++||.||||||||||++||++|++||+++|+
T Consensus 81 ~L~~~~I~LNRKvLs~LAi~ep~sF~~lv~~~k~ 114 (114)
T PRK05185 81 GLKKAGIEIDRKVLADLAVNDPAAFAALVEKAKA 114 (114)
T ss_pred HHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHCC
T ss_conf 9999098766899999985188999999998709
No 5
>pfam00453 Ribosomal_L20 Ribosomal protein L20.
Probab=100.00 E-value=0 Score=308.15 Aligned_cols=107 Identities=60% Similarity=0.912 Sum_probs=105.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 77566555689989999741315645236999999999999998746998899999999986779999718999999999
Q gi|254780318|r 3 RVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQFING 82 (123)
Q Consensus 3 Rvk~g~~~~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~fi~~ 82 (123)
|||+|+++++||++||++|+||+|++++||++|+|+|+|||+|||+||+++||+||+|||+|||||+|++|+|||+||+|
T Consensus 1 Rvkrg~~~r~rrkkilk~akGf~G~~~~~~r~A~~~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~sYs~fi~~ 80 (107)
T pfam00453 1 RVKRGVVARKRRKKILKLAKGFRGARSKLFRTAKQQVMKALQYAYRDRKKKKRDFRRLWITRINAAAREHGLSYSRFING 80 (107)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 98761899999999999816466675441899999999999999956999999999999999999999919879999989
Q ss_pred HHHCCCCCCHHHHHHHHHCCHHHHHHH
Q ss_conf 996298646899999974198999999
Q gi|254780318|r 83 LHKAGIVLDRKVLSDLAITQLDSFKKI 109 (123)
Q Consensus 83 L~~~~i~LnRKvLa~LAi~dp~~F~~l 109 (123)
|++++|+|||||||||||+||.+|++|
T Consensus 81 L~~~~I~LnRKvLa~LAi~dp~~F~~l 107 (107)
T pfam00453 81 LKKANIELNRKVLAQLAINDPEAFKAL 107 (107)
T ss_pred HHHHCCCCCHHHHHHHHHCCHHHHHCC
T ss_conf 989188766899999984198855209
No 6
>PTZ00030 60S ribosomal protein L20; Provisional
Probab=100.00 E-value=0 Score=305.82 Aligned_cols=111 Identities=35% Similarity=0.533 Sum_probs=107.6
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
Q ss_conf 68998999974131564523699999999999999874699889999999998677999971899999999999629864
Q gi|254780318|r 11 SAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQFINGLHKAGIVL 90 (123)
Q Consensus 11 ~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~fi~~L~~~~i~L 90 (123)
+-+|++||++||||+|++++||++|+|+|+||++|||+||+.+||+||+|||+|||||+|++|+|||+||+||+++||+|
T Consensus 2 k~~Rkkilk~AkGfrG~~~~~~r~A~~~v~kAl~yayr~Rk~kKR~fR~LWI~RINAA~r~~g~sYS~fi~gLk~~~I~L 81 (121)
T PTZ00030 2 KIPREIVFQVAKGFRGRSKGCKKLARERAAKALLYSYVSRRKRHRDFRKHWIATINRAAREWEMTYSRFQGSLINSNCEL 81 (121)
T ss_pred CCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCC
T ss_conf 76199999980667677666189999999999999995689998789999999999999884998999999999929847
Q ss_pred CHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 6899999974198999999999999855653
Q gi|254780318|r 91 DRKVLSDLAITQLDSFKKIVELSRSRLLVDV 121 (123)
Q Consensus 91 nRKvLa~LAi~dp~~F~~lv~~ak~~l~~~~ 121 (123)
||||||||||+||++|++||+++|.+|.+..
T Consensus 82 nRKvLseLAi~dP~sFk~lv~~aK~~l~~~~ 112 (121)
T PTZ00030 82 NRKSLFELALNEPISFKCLVDESKYLLSELH 112 (121)
T ss_pred CHHHHHHHHHCCHHHHHHHHHHHHHHHHHCC
T ss_conf 5899999995188999999999999987467
No 7
>KOG4707 consensus
Probab=100.00 E-value=6.2e-36 Score=230.93 Aligned_cols=117 Identities=42% Similarity=0.614 Sum_probs=114.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf 98775665556899899997413156452369999999999999987469988999999999867799997189999999
Q gi|254780318|r 1 MTRVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQFI 80 (123)
Q Consensus 1 M~Rvk~g~~~~~rrkkilk~akGfrG~r~~~~r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~fi 80 (123)
|.++++|+....|+++++++|+||||+.++|||.|.++|+|||+|+++||.+||++||.|||+||||++.|+|+.||.|+
T Consensus 8 l~~~~r~~d~~~rr~~l~k~Aa~frgr~~~~~r~A~r~v~rAlvy~~k~R~~kK~~mr~lwieRv~A~~~e~gv~y~~F~ 87 (147)
T KOG4707 8 LWLRNRGPDRYMRRQELFKFAAHFRGRKRRCYRLAVRTVIRALVYATKDRYLKKRDMRTLWIERVNAGAAEHGVRYSPFK 87 (147)
T ss_pred CEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 02252661799989999999999887332489999999999999998888888776888888888877877356512234
Q ss_pred HHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 9999629864689999997419899999999999985
Q gi|254780318|r 81 NGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRSRL 117 (123)
Q Consensus 81 ~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak~~l 117 (123)
++|.+.+|.||+|+|||||++||.+|.+||+.++.+-
T Consensus 88 ~~L~k~~ilLn~k~Lsqlai~eP~sf~~lv~~~k~r~ 124 (147)
T KOG4707 88 HGLHKSPILLNRKVLSQLAIVEPRSFCALVVLSKERH 124 (147)
T ss_pred CCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCHHHC
T ss_conf 7765243522377753566507401256751557447
No 8
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.45 E-value=1.8 Score=23.42 Aligned_cols=14 Identities=57% Similarity=0.907 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99998677999971
Q gi|254780318|r 59 SLWIQRINAAVRVY 72 (123)
Q Consensus 59 ~LWI~RINAa~r~~ 72 (123)
.=|.+|||+++|++
T Consensus 75 kGwQtRiN~aLR~~ 88 (93)
T COG3514 75 KGWQTRINAALRQY 88 (93)
T ss_pred CHHHHHHHHHHHHH
T ss_conf 60889999999999
No 9
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=72.02 E-value=8.7 Score=19.42 Aligned_cols=58 Identities=10% Similarity=0.192 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHH--HHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 99999986779999718999999999--99629864689999997419899999999999
Q gi|254780318|r 57 FRSLWIQRINAAVRVYDLNYSQFING--LHKAGIVLDRKVLSDLAITQLDSFKKIVELSR 114 (123)
Q Consensus 57 fR~LWI~RINAa~r~~g~sYS~fi~~--L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak 114 (123)
.-++|-..+|....++|+++++|.-- |...+-.+.-+-||+..--||.+...+++..-
T Consensus 12 ~~r~~r~~~~~~L~~~gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE 71 (144)
T PRK03573 12 LVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999999886699825999999999739898999999997987836999999999
No 10
>PRK07080 hypothetical protein; Validated
Probab=44.62 E-value=11 Score=18.76 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf 9999999999999874699889999999998677999971899999
Q gi|254780318|r 33 RAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQ 78 (123)
Q Consensus 33 r~A~~~v~kAl~yayrdRk~kKr~fR~LWI~RINAa~r~~g~sYS~ 78 (123)
-.+..+.-+--.|...+-...-.+||..||.|..+-.++.|+++..
T Consensus 170 dp~Rmq~FRMrEyV~iGt~e~v~a~R~~W~~r~~~~~~~L~L~~~v 215 (318)
T PRK07080 170 DPARMQLFRMREYVRIGTPEQILAFRQRWIERGTRMADALGLPVEI 215 (318)
T ss_pred CHHHHHHHHCEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 8588886440445771799999999999999999999975998523
No 11
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235 This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=40.59 E-value=6.2 Score=20.26 Aligned_cols=42 Identities=17% Similarity=0.297 Sum_probs=34.7
Q ss_pred HHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHCC-HHHHHHHHHHH
Q ss_conf 999971899999999999629864689999997419-89999999999
Q gi|254780318|r 67 AAVRVYDLNYSQFINGLHKAGIVLDRKVLSDLAITQ-LDSFKKIVELS 113 (123)
Q Consensus 67 Aa~r~~g~sYS~fi~~L~~~~i~LnRKvLa~LAi~d-p~~F~~lv~~a 113 (123)
+.++.||=||+-|-+.|++-+|+. .-....| |+.|.++++.=
T Consensus 101 sS~~LYGGTynLF~~TlkrlGIev-----rFvd~dd~pe~~~k~id~n 143 (434)
T TIGR01326 101 SSSYLYGGTYNLFKHTLKRLGIEV-----RFVDGDDDPEELEKAIDEN 143 (434)
T ss_pred ECCCCCCHHHHHHHHHHHHCCEEE-----EEECCCCCHHHHHHHCCCC
T ss_conf 806444225789999555448148-----8727888878999760667
No 12
>pfam08809 DUF1799 Phage related hypothetical protein (DUF1799). Members of this family are about 100 amino acids in length and are uncharacterized.
Probab=37.82 E-value=34 Score=15.98 Aligned_cols=38 Identities=24% Similarity=0.360 Sum_probs=31.3
Q ss_pred HHCCCHHHHHHHHHHCCCC--CCHHHHHHHHHCCHHHHHH
Q ss_conf 7189999999999962986--4689999997419899999
Q gi|254780318|r 71 VYDLNYSQFINGLHKAGIV--LDRKVLSDLAITQLDSFKK 108 (123)
Q Consensus 71 ~~g~sYS~fi~~L~~~~i~--LnRKvLa~LAi~dp~~F~~ 108 (123)
-.|+.|+.+-+.+...+|. --+.++.+|-|-|..+...
T Consensus 43 ~~GLDY~~l~~~~~~~gi~~e~~~~~f~~lrvME~~AL~~ 82 (83)
T pfam08809 43 ATGLDYSVLFAVLRRYGIDAEERDDVFDDLRVMERAALEM 82 (83)
T ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6403099999999881897765999999999999999973
No 13
>pfam03050 Transposase_25 Transposase IS66 family. Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens.
Probab=36.97 E-value=36 Score=15.83 Aligned_cols=50 Identities=18% Similarity=0.218 Sum_probs=44.7
Q ss_pred HHCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf 71899999999999629864689999997419899999999999985565
Q gi|254780318|r 71 VYDLNYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRSRLLVD 120 (123)
Q Consensus 71 ~~g~sYS~fi~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak~~l~~~ 120 (123)
.+++++.+...-|...++.|.+..|+++...--+.+..+++..++.+...
T Consensus 59 ~~~lP~~R~~~~~~~~G~~IS~~ti~~~~~~~a~~l~p~~~~i~~~l~~~ 108 (178)
T pfam03050 59 ADHLPLYRQAEILARFGIEISRGTLANWVGRAAELLEPLYDALRAHLLAS 108 (178)
T ss_pred CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 54688999999999839973899999999999998414999999999849
No 14
>pfam01777 Ribosomal_L27e Ribosomal L27e protein family. The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family.
Probab=36.52 E-value=13 Score=18.41 Aligned_cols=48 Identities=15% Similarity=0.119 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999999629864689999997419899999999999985565
Q gi|254780318|r 73 DLNYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRSRLLVD 120 (123)
Q Consensus 73 g~sYS~fi~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~ak~~l~~~ 120 (123)
-++|+++|-.=..-++.++..+++.-++.||..=...-.+++..+++.
T Consensus 23 vvNyNHlMPTRY~vd~~~~K~~v~~d~~~d~~~k~~a~~~~k~~feer 70 (85)
T pfam01777 23 VVNYNHLMPTRYSVDVEDLKKVVSKDALKDPSKRKEARKEVKKKFEER 70 (85)
T ss_pred EEECCCCCCCCEEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHH
T ss_conf 764144455523641502103117888749578899999999999999
No 15
>TIGR02111 PQQ_syn_pqqC coenzyme PQQ biosynthesis protein C; InterPro: IPR011845 This entry describes the coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein PqqC. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes, including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria . PQQC has been found to be required in the synthesis of PQQ but its function is unclear. This entry does not include related proteins likely to be functionally distinct from PqqC, such as homologs found in the Chlamydias.; GO: 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=35.96 E-value=21 Score=17.24 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999998677
Q gi|254780318|r 55 RDFRSLWIQRIN 66 (123)
Q Consensus 55 r~fR~LWI~RIN 66 (123)
.++|+.||+||-
T Consensus 66 ~~~Rr~W~qRi~ 77 (239)
T TIGR02111 66 PELRRIWRQRIL 77 (239)
T ss_pred HHHHHHHHHHHH
T ss_conf 888999987442
No 16
>pfam11333 DUF3135 Protein of unknown function (DUF3135). This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=31.44 E-value=44 Score=15.29 Aligned_cols=27 Identities=11% Similarity=0.107 Sum_probs=20.2
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999741989999999999998556
Q gi|254780318|r 93 KVLSDLAITQLDSFKKIVELSRSRLLV 119 (123)
Q Consensus 93 KvLa~LAi~dp~~F~~lv~~ak~~l~~ 119 (123)
.-|-+||-+||+.|..+-...-+.+-+
T Consensus 7 DeL~~LA~~dPeafe~lr~~l~~e~I~ 33 (83)
T pfam11333 7 DELKALAKNDPEALEQLRHELIEEAIE 33 (83)
T ss_pred HHHHHHHHHCHHHHHHHHHHHHHHHHH
T ss_conf 999999987999999999999999998
No 17
>KOG3955 consensus
Probab=26.30 E-value=51 Score=14.92 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=29.7
Q ss_pred HCCCHHHHHHHHHHCCCCCCHHHHHHHHHC---------CHHHHHHHHHHHHHHH
Q ss_conf 189999999999962986468999999741---------9899999999999985
Q gi|254780318|r 72 YDLNYSQFINGLHKAGIVLDRKVLSDLAIT---------QLDSFKKIVELSRSRL 117 (123)
Q Consensus 72 ~g~sYS~fi~~L~~~~i~LnRKvLa~LAi~---------dp~~F~~lv~~ak~~l 117 (123)
.|.+--.||..-. |..-||.|||||..- |-+-=+-+.+-||..|
T Consensus 212 sGctLqEFmdCPY--NLAnNRQMLadLSLVGCYnlsfiPegkraqlllESAKkNL 264 (361)
T KOG3955 212 SGCPLKEFMDCPY--NLANNRQMLADLSLVGCYNLSFIPEGKRAQLLLESAKKNL 264 (361)
T ss_pred CCCCHHHHHCCCH--HHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 7864999855850--1220687865331101100010676217789999988644
No 18
>KOG0942 consensus
Probab=23.89 E-value=61 Score=14.49 Aligned_cols=27 Identities=22% Similarity=0.075 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999987469988999999999867
Q gi|254780318|r 39 VDRSQQYAYRDRRVKKRDFRSLWIQRI 65 (123)
Q Consensus 39 v~kAl~yayrdRk~kKr~fR~LWI~RI 65 (123)
++.++.-.|++|++.|+.||.-|+.--
T Consensus 34 ~vQs~~Rg~~~r~~~~~~~R~~fd~~~ 60 (1001)
T KOG0942 34 KVQSFWRGFRVRHNQKLLFREEFDAVS 60 (1001)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 799998889999999999999989988
No 19
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=23.86 E-value=56 Score=14.69 Aligned_cols=21 Identities=24% Similarity=0.355 Sum_probs=16.2
Q ss_pred HHHHHHHHHCCCHHHHHHHHH
Q ss_conf 677999971899999999999
Q gi|254780318|r 64 RINAAVRVYDLNYSQFINGLH 84 (123)
Q Consensus 64 RINAa~r~~g~sYS~fi~~L~ 84 (123)
-|+-|++.+|+++|.+-.-++
T Consensus 18 S~~kAa~~ygIP~sTL~~r~~ 38 (45)
T pfam05225 18 SLRKAARKYGIPRSTLWRRLR 38 (45)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
T ss_conf 799999997898589999975
No 20
>pfam11537 DUF3227 Protein of unknown function (DUF3227). This archaeal family of proteins has no known function.
Probab=20.95 E-value=53 Score=14.83 Aligned_cols=47 Identities=17% Similarity=0.189 Sum_probs=23.8
Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf 867799997189999999999962986468999999741989999999999
Q gi|254780318|r 63 QRINAAVRVYDLNYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELS 113 (123)
Q Consensus 63 ~RINAa~r~~g~sYS~fi~~L~~~~i~LnRKvLa~LAi~dp~~F~~lv~~a 113 (123)
..+--+.|+.|-..-..+..--++. +|.- -+||..||.-|+..|+..
T Consensus 10 aTa~e~Lr~~~p~~e~~LeahL~a~--~n~g--iEia~eDP~kFkeav~~L 56 (102)
T pfam11537 10 ATAIEALKEFAPGFEATLEAHLNAK--LNAG--IEIAGEDPAKFKEAVEEL 56 (102)
T ss_pred HHHHHHHHHHCHHHHHHHHHHHHHH--HCCC--EEEHHCCHHHHHHHHHHH
T ss_conf 9999999985800799999999877--5666--110305989999999999
No 21
>cd07751 PolyPPase_VTC4_like Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) protein VTC4, and similar proteins. Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2,-3, and -4 contain polyP polymerase domains. S. cerevisiae VTC4 belongs to this subgroup. For VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. This activity is metal ion-dependent. The ATP gamma phosphate may be cleaved and then transferred to an acceptor phosphate to form polyP. PolyP is ubiquitous. In prokaryotes, it is a store of phosphate and energy. In eukaryotes, polyPs have roles in bone calcification, and osmoregulation, and in phosphate transport in the symbiosis of mycorrhizal fungi and plants. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel.
Probab=20.73 E-value=34 Score=15.93 Aligned_cols=26 Identities=19% Similarity=0.554 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHCC-CHHHHHHHHHH
Q ss_conf 999867799997189-99999999996
Q gi|254780318|r 60 LWIQRINAAVRVYDL-NYSQFINGLHK 85 (123)
Q Consensus 60 LWI~RINAa~r~~g~-sYS~fi~~L~~ 85 (123)
.||.-+....--.-+ .||+|+||+..
T Consensus 251 ~Wi~eL~~s~lv~evpkFSKf~hG~A~ 277 (290)
T cd07751 251 EWVEELLNSHLVEEVYKFSKFLHGCAT 277 (290)
T ss_pred HHHHHHHHCCCCEECCCCCHHHHHHHH
T ss_conf 899999756683786653478876788
No 22
>TIGR02677 TIGR02677 conserved hypothetical protein TIGR02677; InterPro: IPR013493 Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). .
Probab=20.63 E-value=53 Score=14.81 Aligned_cols=28 Identities=29% Similarity=0.255 Sum_probs=24.2
Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999974198999999999999855653
Q gi|254780318|r 94 VLSDLAITQLDSFKKIVELSRSRLLVDV 121 (123)
Q Consensus 94 vLa~LAi~dp~~F~~lv~~ak~~l~~~~ 121 (123)
.||+|-..||..|..|..+.-.+|.+..
T Consensus 436 ~Ls~~~~l~P~~f~llL~LLg~AL~~~~ 463 (514)
T TIGR02677 436 RLSDLGALDPRVFKLLLGLLGKALTAQG 463 (514)
T ss_pred EECCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 0024567688899999999999961568
Done!