Query gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 116
No_of_seqs 112 out of 1084
Neff 5.9
Searched_HMMs 39220
Date Sun May 29 19:49:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780712.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3419 consensus 100.0 5.9E-39 1.5E-43 258.9 8.0 104 1-104 1-104 (112)
2 CHL00005 rps16 ribosomal prote 100.0 6.5E-36 1.7E-40 240.3 7.2 80 2-86 1-80 (82)
3 COG0228 RpsP Ribosomal protein 100.0 8.1E-36 2.1E-40 239.7 7.1 78 2-81 1-78 (87)
4 PRK00040 rpsP 30S ribosomal pr 100.0 3.7E-35 9.5E-40 235.7 7.5 75 2-79 1-75 (75)
5 TIGR00002 S16 ribosomal protei 100.0 1.5E-32 3.9E-37 219.8 7.2 81 3-83 1-81 (81)
6 pfam00886 Ribosomal_S16 Riboso 99.9 2.6E-26 6.6E-31 181.9 6.7 58 9-70 1-58 (58)
7 KOG0135 consensus 67.9 6.5 0.00016 21.1 3.3 36 28-68 168-206 (661)
8 pfam08755 YccV-like Hemimethyl 52.2 10 0.00026 19.9 2.1 16 12-27 45-60 (100)
9 TIGR02097 yccV hemimethylated 39.5 20 0.00052 18.1 2.0 15 13-27 47-61 (103)
10 pfam11875 DUF3395 Domain of un 38.4 18 0.00046 18.4 1.6 20 32-53 102-121 (144)
11 TIGR01132 pgm phosphoglucomuta 36.1 23 0.0006 17.7 1.9 43 17-67 142-189 (553)
12 KOG2321 consensus 29.0 16 0.00041 18.7 0.0 33 27-59 59-91 (703)
13 pfam09086 DUF1924 Domain of un 27.6 50 0.0013 15.7 2.4 34 28-68 46-79 (98)
14 TIGR00625 tfb2 Transcription f 26.3 47 0.0012 15.8 2.1 28 67-94 154-182 (507)
15 TIGR01249 pro_imino_pep_1 prol 25.1 39 0.001 16.3 1.5 43 16-65 52-94 (310)
16 KOG3471 consensus 23.9 67 0.0017 14.9 2.9 64 10-87 120-186 (465)
17 KOG3423 consensus 22.9 64 0.0016 15.0 2.2 39 32-80 75-115 (176)
18 TIGR00845 caca sodium/calcium 21.5 20 0.00052 18.1 -0.6 13 10-22 399-411 (1067)
19 cd06364 PBP1_CaSR Ligand-bindi 21.1 76 0.0019 14.6 3.8 41 16-59 467-508 (510)
20 COG3785 Uncharacterized conser 20.8 58 0.0015 15.3 1.6 17 12-28 56-72 (116)
21 KOG2806 consensus 20.7 78 0.002 14.5 3.6 61 15-77 234-295 (432)
22 COG5162 Transcription initiati 20.5 78 0.002 14.5 2.4 40 32-81 77-118 (197)
No 1
>KOG3419 consensus
Probab=100.00 E-value=5.9e-39 Score=258.86 Aligned_cols=104 Identities=43% Similarity=0.674 Sum_probs=97.3
Q ss_pred CCCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 93014123066878882799992067877684102221215678788864479739999999841983568999999972
Q gi|254780712|r 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKA 80 (116)
Q Consensus 1 M~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~ 80 (116)
|+|+|||+|+||||||||||||||+|++|||++||+||||||++++++.+.|.||+|||+|||++|||||++|..||+++
T Consensus 1 ~~vkIRLar~GcknRPfY~Ivva~~r~~rdgk~iE~lG~ydPlp~~~~~~~v~Ln~dRikyWl~~GAqpS~tv~~Ll~~a 80 (112)
T KOG3419 1 MVVKIRLARFGCKNRPFYRIVVADSRKRRDGKPIEQLGTYDPLPNQDNEKLVALNFDRIKYWLGVGAQPSDTVEELLGKA 80 (112)
T ss_pred CEEEEEEHHCCCCCCCEEEEEEEECCCCCCCCCHHHEECCCCCCCCCCCCCEEECHHHHHHHHHCCCCCCHHHHHHHHHC
T ss_conf 91788623118667872699983044566688653223345788878873146318999999854884686899998754
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 986668000511225428898899
Q gi|254780712|r 81 GLIKRSPQNNPKKSQPKKKALERL 104 (116)
Q Consensus 81 Gl~~~~~~~~~~~~~~~kk~~e~~ 104 (116)
|+++.+|..+......++...+..
T Consensus 81 Gl~p~~p~~~~~a~~~rr~~a~~~ 104 (112)
T KOG3419 81 GLFPIHPMTFMNAKRNRRLTAEQV 104 (112)
T ss_pred CCCCCCHHHHHCCCCCHHHHHHHC
T ss_conf 788886366512312235565530
No 2
>CHL00005 rps16 ribosomal protein S16
Probab=100.00 E-value=6.5e-36 Score=240.34 Aligned_cols=80 Identities=35% Similarity=0.530 Sum_probs=75.5
Q ss_pred CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 30141230668788827999920678776841022212156787888644797399999998419835689999999729
Q gi|254780712|r 2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG 81 (116)
Q Consensus 2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G 81 (116)
||+|||+|+|+||+|||||||+|||+||||+|||+||||||+. +.+.||.||++|||++||||||||.+||+++|
T Consensus 1 MVkIRL~R~G~kk~P~YrIVv~dsr~~RdGk~iE~lG~YnP~~-----~~~~l~~eri~~Wl~~GAqpT~tV~~Llk~~g 75 (82)
T CHL00005 1 MVKLRLKRCGRKQQAVYRIVAIDVRSRREGRDLRKVGFYDPIK-----NQTYLNVPAILYFLEKGAQPTGTVYDILKKAE 75 (82)
T ss_pred CEEEECCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCC-----CCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCC
T ss_conf 9178301289888982689987357778998536777757999-----86533899999999976988899999999837
Q ss_pred CCCCC
Q ss_conf 86668
Q gi|254780712|r 82 LIKRS 86 (116)
Q Consensus 82 l~~~~ 86 (116)
+++..
T Consensus 76 i~~~~ 80 (82)
T CHL00005 76 VFKEL 80 (82)
T ss_pred CHHHH
T ss_conf 37765
No 3
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.1e-36 Score=239.73 Aligned_cols=78 Identities=60% Similarity=0.961 Sum_probs=75.6
Q ss_pred CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 30141230668788827999920678776841022212156787888644797399999998419835689999999729
Q gi|254780712|r 2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG 81 (116)
Q Consensus 2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G 81 (116)
||+|||+|+|+||+|||||||||||+||||+|||.||||||++ +.++.|.||.||+.|||++||||||||.+||+++|
T Consensus 1 ~vkIRL~R~G~kk~P~YrIVVaDsrs~RDGr~IE~lG~ynP~~--~~~~~v~l~~eri~~Wl~~GAqpSdtV~~ll~~~g 78 (87)
T COG0228 1 MVKIRLARGGSKKRPFYRIVVADSRSPRDGRFIERLGTYNPLL--GKEERVKLDEERILYWLSQGAQPSDTVRRLLKKAG 78 (87)
T ss_pred CEEEEHHHCCCCCCCEEEEEEECCCCCCCCCCHHHHCCCCCCC--CCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 9078530178766984799984168888986445400237887--87634788699999999859974489999999852
No 4
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=100.00 E-value=3.7e-35 Score=235.71 Aligned_cols=75 Identities=53% Similarity=0.925 Sum_probs=71.8
Q ss_pred CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 301412306687888279999206787768410222121567878886447973999999984198356899999997
Q gi|254780712|r 2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDK 79 (116)
Q Consensus 2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~ 79 (116)
||+|||+|+||||+|||||||+|+|+||||+|||+||||||+. +++.+.||.|||+|||++|||||++|.+||++
T Consensus 1 mvkIRL~R~G~k~~P~YrIVv~d~r~~RdGk~iE~lG~ydP~~---~~~~~~l~~eri~~Wl~~GAqpS~~V~~Llkk 75 (75)
T PRK00040 1 MVKIRLARGGAKKRPFYRIVVADSRSPRDGRFIERVGFYNPLA---KPAEVKLDEERVLYWLGQGAQPTDTVARLLKK 75 (75)
T ss_pred CEEEEHHCCCCCCCCEEEEEEEECCCCCCCCCHHEEEEECCCC---CCCEEEECHHHHHHHHHCCCCCCHHHHHHHCC
T ss_conf 9388120089989985899996266678886100004777989---98669984999999998789868999998639
No 5
>TIGR00002 S16 ribosomal protein S16; InterPro: IPR000307 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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups: Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.97 E-value=1.5e-32 Score=219.80 Aligned_cols=81 Identities=56% Similarity=0.948 Sum_probs=78.3
Q ss_pred CHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCCC
Q ss_conf 01412306687888279999206787768410222121567878886447973999999984198356899999997298
Q gi|254780712|r 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAGL 82 (116)
Q Consensus 3 vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~Gl 82 (116)
|+|||+|+|||++|||||||+|++++|||+|||+||+|||++..++.+++.||.|||.|||++||||||||.+||.++|+
T Consensus 1 vkiRL~r~G~k~~p~Yrivv~d~~~~RdG~~ie~lG~y~P~~~~~~~~~~~l~~~~~~~wl~~Ga~pt~tv~~ll~~~g~ 80 (81)
T TIGR00002 1 VKIRLKRGGRKKRPFYRIVVADSRSPRDGRYIEELGFYNPLLKEDDEERVKLDVERIKYWLSKGAQPTDTVRNLLKKAGV 80 (81)
T ss_pred CEEECCCCCCCCCCEEEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf 91110237765686157886247897454123331544788889875246636799999986699857788999886147
Q ss_pred C
Q ss_conf 6
Q gi|254780712|r 83 I 83 (116)
Q Consensus 83 ~ 83 (116)
+
T Consensus 81 ~ 81 (81)
T TIGR00002 81 F 81 (81)
T ss_pred C
T ss_conf 9
No 6
>pfam00886 Ribosomal_S16 Ribosomal protein S16.
Probab=99.93 E-value=2.6e-26 Score=181.86 Aligned_cols=58 Identities=60% Similarity=1.021 Sum_probs=55.3
Q ss_pred HCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCC
Q ss_conf 06687888279999206787768410222121567878886447973999999984198356
Q gi|254780712|r 9 CGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPT 70 (116)
Q Consensus 9 r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS 70 (116)
|+||||+|||||||+|||++|||+|||+||+|||+++ +.+.||.|||+|||++|||||
T Consensus 1 R~G~k~~P~YrIVv~d~r~~RdGk~iE~lG~YdP~~~----~~~~l~~eri~~Wl~~GAqPs 58 (58)
T pfam00886 1 RGGRKKRPFYRIVVADSRSPRDGRFIEELGTYNPIAN----GEVKLDVERIKYWLGKGAQPT 58 (58)
T ss_pred CCCCCCCCEEEEEEEECCCCCCCCCHHEEEEECCCCC----CEEEEEHHHHHHHHHCCCCCC
T ss_conf 9887789868999974777889976103545659998----558982899999998749993
No 7
>KOG0135 consensus
Probab=67.88 E-value=6.5 Score=21.11 Aligned_cols=36 Identities=28% Similarity=0.577 Sum_probs=26.9
Q ss_pred CCCCCCEEEEEEECCCCCCCCCCEEEE---CHHHHHHHHHCCCC
Q ss_conf 776841022212156787888644797---39999999841983
Q gi|254780712|r 28 PRDGKFIEKLGTWNPTLPKENPLRFTM---NFERIQHWMSKGAQ 68 (116)
Q Consensus 28 ~Rdgk~iE~lG~YnP~~~k~~~~~i~l---~~eRi~yWL~~GAq 68 (116)
--+-+-|+-.-||||.+ ++..| |++.+++|+|+-|.
T Consensus 168 GSNt~~I~TtatyDP~t-----~EfVinTP~~~A~K~WiGn~a~ 206 (661)
T KOG0135 168 GSNTKGIQTTATYDPTT-----EEFVINTPDFSAIKCWIGNAAK 206 (661)
T ss_pred CCCCCCEEEEEEECCCC-----CEEEECCCCHHHHHHHHCCCCC
T ss_conf 76645314554126987-----7267548968888887503223
No 8
>pfam08755 YccV-like Hemimethylated DNA-binding protein YccV like. YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.
Probab=52.25 E-value=10 Score=19.91 Aligned_cols=16 Identities=19% Similarity=0.540 Sum_probs=13.0
Q ss_pred CCCCCEEEEEEEECCC
Q ss_conf 8788827999920678
Q gi|254780712|r 12 SKSRHHYRIVVANSRS 27 (116)
Q Consensus 12 ~k~rp~yrIVvadsr~ 27 (116)
.|+.|||||.|-|..+
T Consensus 45 ~k~QPfYhvLv~~~~~ 60 (100)
T pfam08755 45 ARDQPFYHVLVEDDDS 60 (100)
T ss_pred CCCCCCEEEEEECCCC
T ss_conf 5679836999966986
No 9
>TIGR02097 yccV hemimethylated DNA binding domain; InterPro: IPR011722 This entry describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein . The model entry describes a domain in longer eukaryotic proteins..
Probab=39.53 E-value=20 Score=18.08 Aligned_cols=15 Identities=20% Similarity=0.538 Sum_probs=11.6
Q ss_pred CCCCEEEEEEEECCC
Q ss_conf 788827999920678
Q gi|254780712|r 13 KSRHHYRIVVANSRS 27 (116)
Q Consensus 13 k~rp~yrIVvadsr~ 27 (116)
++.|||+|+|=|...
T Consensus 47 ~~qPfY~vl~e~~~~ 61 (103)
T TIGR02097 47 KDQPFYHVLVEDDEG 61 (103)
T ss_pred CCCCCEEEEEECCCC
T ss_conf 578972688864899
No 10
>pfam11875 DUF3395 Domain of unknown function (DUF3395). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 147 to 176 amino acids in length. This domain is found associated with pfam00226.
Probab=38.39 E-value=18 Score=18.38 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=13.0
Q ss_pred CCEEEEEEECCCCCCCCCCEEE
Q ss_conf 4102221215678788864479
Q gi|254780712|r 32 KFIEKLGTWNPTLPKENPLRFT 53 (116)
Q Consensus 32 k~iE~lG~YnP~~~k~~~~~i~ 53 (116)
..-..+|||||.+. .++.+.
T Consensus 102 ~Ks~L~GF~DPcpg--~~K~L~ 121 (144)
T pfam11875 102 SKSNLLGFYDPCPG--EPKVLY 121 (144)
T ss_pred CHHCCCCCCCCCCC--CCCEEE
T ss_conf 35217765699989--986799
No 11
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific; InterPro: IPR005852 Phosphoglucomutase, alpha-D-glucose phosphate-specific () links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose . Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.; GO: 0004614 phosphoglucomutase activity, 0005975 carbohydrate metabolic process.
Probab=36.11 E-value=23 Score=17.70 Aligned_cols=43 Identities=30% Similarity=0.539 Sum_probs=26.2
Q ss_pred EEEEEEEECCC-CCCCCCEEEEEE-ECCCCCCCCCCE---EEECHHHHHHHHHCCC
Q ss_conf 27999920678-776841022212-156787888644---7973999999984198
Q gi|254780712|r 17 HYRIVVANSRS-PRDGKFIEKLGT-WNPTLPKENPLR---FTMNFERIQHWMSKGA 67 (116)
Q Consensus 17 ~yrIVvadsr~-~Rdgk~iE~lG~-YnP~~~k~~~~~---i~l~~eRi~yWL~~GA 67 (116)
-==||++-|.. |.|| |. ||| |..+|.+ .+.=.+|+...|..|-
T Consensus 142 ADGIviTPSHNPP~DG------GiKYNP--P~GGPA~~~~T~~i~~RAN~~l~~~~ 189 (553)
T TIGR01132 142 ADGIVITPSHNPPEDG------GIKYNP--PNGGPADTEATQAIEDRANELLKAGL 189 (553)
T ss_pred CCEEEECCCCCCCCCC------CEECCC--CCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 5614775877747886------764077--44588866888999999999997223
No 12
>KOG2321 consensus
Probab=29.03 E-value=16 Score=18.71 Aligned_cols=33 Identities=24% Similarity=0.539 Sum_probs=16.9
Q ss_pred CCCCCCCEEEEEEECCCCCCCCCCEEEECHHHH
Q ss_conf 877684102221215678788864479739999
Q gi|254780712|r 27 SPRDGKFIEKLGTWNPTLPKENPLRFTMNFERI 59 (116)
Q Consensus 27 ~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi 59 (116)
..+||+||=-.|+|-|...=-+-..+.|++||-
T Consensus 59 ~s~DGqY~lAtG~YKP~ikvydlanLSLKFERh 91 (703)
T KOG2321 59 VSPDGQYLLATGTYKPQIKVYDLANLSLKFERH 91 (703)
T ss_pred ECCCCCEEEEECCCCCCEEEEECCCCEEEEEEC
T ss_conf 668886798743668724898701142432331
No 13
>pfam09086 DUF1924 Domain of unknown function (DUF1924). This domain is found in a set of bacterial proteins, including Cytochrome c-type protein. It is functionally uncharacterized.
Probab=27.63 E-value=50 Score=15.72 Aligned_cols=34 Identities=35% Similarity=0.770 Sum_probs=26.3
Q ss_pred CCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCC
Q ss_conf 77684102221215678788864479739999999841983
Q gi|254780712|r 28 PRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQ 68 (116)
Q Consensus 28 ~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAq 68 (116)
.+.||.|| ||.|.-||+++. |..+|..|+...+.
T Consensus 46 ~~TgK~I~------PmAps~Np~Rft-D~akvEKwF~RNC~ 79 (98)
T pfam09086 46 VKTGKPIE------PMAPSVNPERFT-DAAKVEKWFTRNCN 79 (98)
T ss_pred CCCCCCCC------CCCCCCCHHHHC-CHHHHHHHHHCCCH
T ss_conf 65788646------768766856406-98999999971055
No 14
>TIGR00625 tfb2 Transcription factor tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0003702 RNA polymerase II transcription factor activity, 0006281 DNA repair, 0006355 regulation of transcription DNA-dependent, 0005634 nucleus.
Probab=26.28 E-value=47 Score=15.84 Aligned_cols=28 Identities=29% Similarity=0.539 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHHCCCCCCC-CCCCCHHH
Q ss_conf 83568999999972986668-00051122
Q gi|254780712|r 67 AQPTDRILFFLDKAGLIKRS-PQNNPKKS 94 (116)
Q Consensus 67 AqpS~~V~~LL~~~Gl~~~~-~~~~~~~~ 94 (116)
+-||+.|..||+++||+... +.+..+.+
T Consensus 154 k~p~e~vl~LLk~~gLM~~~~~~~~~~IT 182 (507)
T TIGR00625 154 KVPSEDVLSLLKRAGLMKEVESKEELKIT 182 (507)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCCCCEEC
T ss_conf 47857999997404777888888884136
No 15
>TIGR01249 pro_imino_pep_1 proline iminopeptidase; InterPro: IPR005944 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidase belong to MEROPS peptidase family S33 (clan SC). They are proline iminopeptidase (Prolyl aminopeptidase, 3.4.11.5 from EC), which catalyzes the removal of the N-terminal proline from peptides. This family represents one of two related families of proline iminopeptidase containing the alpha/beta fold. The fine specificities of the various members, including both the range of short peptides from which proline can be removed and whether other amino acids such as alanine can be also removed, may vary among members. ; GO: 0016804 prolyl aminopeptidase activity, 0005737 cytoplasm.
Probab=25.11 E-value=39 Score=16.34 Aligned_cols=43 Identities=14% Similarity=0.203 Sum_probs=23.6
Q ss_pred CEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC
Q ss_conf 82799992067877684102221215678788864479739999999841
Q gi|254780712|r 16 HHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK 65 (116)
Q Consensus 16 p~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~ 65 (116)
=+||||..|+|-.=..+. |+=..+ .+.--+.=|+|.++.=|+-
T Consensus 52 e~~rIvL~DQRGcGkS~p------~a~~~e-NtTWdLV~DiEkLR~~L~I 94 (310)
T TIGR01249 52 ETYRIVLLDQRGCGKSTP------HACLEE-NTTWDLVADIEKLREKLGI 94 (310)
T ss_pred CCEEEEEEEECCCCCCCC------CCCCCC-CCCHHHHHHHHHHHHHCCC
T ss_conf 635899983078889862------433224-7705667439999986289
No 16
>KOG3471 consensus
Probab=23.91 E-value=67 Score=14.93 Aligned_cols=64 Identities=28% Similarity=0.527 Sum_probs=39.3
Q ss_pred CCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC---CCCCCHHHHHHHHHCCCCCCC
Q ss_conf 66878882799992067877684102221215678788864479739999999841---983568999999972986668
Q gi|254780712|r 10 GGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK---GAQPTDRILFFLDKAGLIKRS 86 (116)
Q Consensus 10 ~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~---GAqpS~~V~~LL~~~Gl~~~~ 86 (116)
+|.+.++|=-.|+-+...+||+.++|. |.- =.-|-|.|.+-- -.-||+.|.+||+++|++...
T Consensus 120 gg~~~~s~~s~~l~~~~~~r~v~~ld~---ya~-----------~rwe~ILh~mvgt~~a~~~se~v~~ll~~a~lm~~~ 185 (465)
T KOG3471 120 GGGKQNSFGSLVLGEDKHNRDVDFLDK---YAS-----------ERWECILHFMVGTPEAKAVSEGVLNLLKHAGLMSRD 185 (465)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHH---HHH-----------HHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCC
T ss_conf 577766677754287757666315678---888-----------889999988717863135574299999854755789
Q ss_pred C
Q ss_conf 0
Q gi|254780712|r 87 P 87 (116)
Q Consensus 87 ~ 87 (116)
.
T Consensus 186 ~ 186 (465)
T KOG3471 186 E 186 (465)
T ss_pred C
T ss_conf 8
No 17
>KOG3423 consensus
Probab=22.88 E-value=64 Score=15.04 Aligned_cols=39 Identities=31% Similarity=0.617 Sum_probs=26.8
Q ss_pred CCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC-CCCCCH-HHHHHHHHC
Q ss_conf 4102221215678788864479739999999841-983568-999999972
Q gi|254780712|r 32 KFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK-GAQPTD-RILFFLDKA 80 (116)
Q Consensus 32 k~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~-GAqpS~-~V~~LL~~~ 80 (116)
-||++|-.|-|+.| ..=+.|+|.. |-|-+| +|.+|++.+
T Consensus 75 efl~qLddYtP~IP----------Davt~~yL~~aGf~~~D~rv~RLvsLa 115 (176)
T KOG3423 75 EFLAQLDDYTPTIP----------DAVTDHYLKKAGFQTSDPRVKRLVSLA 115 (176)
T ss_pred HHHHHHHCCCCCCC----------HHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 99998730799883----------899999998558776768799999999
No 18
>TIGR00845 caca sodium/calcium exchanger 1; InterPro: IPR004836 Na^+/Ca^2+ exchange proteins are involved in maintaining Ca^2+ homeostasis in a wide variety of cell types. They are found in both the plasma membrane and intracellular organellar membranes, where they exchange Na^+ for Ca^2+ in an electrogenic manner. When located in the plasma membrane, they generally utilise the transmembrane (TM) Na^+ concentration gradient in order to extrude Ca^2+ from cells. Three mammalian isoforms have been cloned to date (NCX1-3), which consist of 920-970 amino acid residues that are predicted to possess 11 or 12 TM domains. Interestingly, they possess a short motif (~30 residues) that is similar to the Na^+/K^+-ATPase, although its function is unknown , . NCX1 has been found to be predominantly expressed in the heart, where it plays an important role in excitation-contraction coupling, but it is also abundant in a variety of other tissues . NCX2 and NCX3 transcripts have been detected in the brain and skeletal muscle , . Homologous Na^+/Ca^2+ exchange proteins have also been found in Caenorhabditis elegans, Drosophila melanogaster and Loligo opalescens (California market squid). ; GO: 0005432 calcium:sodium antiporter activity, 0006816 calcium ion transport, 0016020 membrane.
Probab=21.53 E-value=20 Score=18.09 Aligned_cols=13 Identities=46% Similarity=0.577 Sum_probs=7.0
Q ss_pred CCCCCCCEEEEEE
Q ss_conf 6687888279999
Q gi|254780712|r 10 GGSKSRHHYRIVV 22 (116)
Q Consensus 10 ~G~k~rp~yrIVv 22 (116)
.|.|-|+||||.|
T Consensus 399 r~~KSRAFYRIQA 411 (1067)
T TIGR00845 399 RQQKSRAFYRIQA 411 (1067)
T ss_pred CCCCCCHHHHHHH
T ss_conf 4898400135345
No 19
>cd06364 PBP1_CaSR Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calci
Probab=21.14 E-value=76 Score=14.59 Aligned_cols=41 Identities=27% Similarity=0.412 Sum_probs=22.5
Q ss_pred CEEEEEEEECCCCCCCCC-EEEEEEECCCCCCCCCCEEEECHHHH
Q ss_conf 827999920678776841-02221215678788864479739999
Q gi|254780712|r 16 HHYRIVVANSRSPRDGKF-IEKLGTWNPTLPKENPLRFTMNFERI 59 (116)
Q Consensus 16 p~yrIVvadsr~~Rdgk~-iE~lG~YnP~~~k~~~~~i~l~~eRi 59 (116)
+.|-|+=- +..|-+|.+ ...||+|+|..+ ....+.||.+.|
T Consensus 467 ~~YdI~n~-q~~~~~g~~~~~~VG~~~~~~~--~~~~L~in~~~I 508 (510)
T cd06364 467 GNYSIINW-HLSPEDGSVVFKEVGYYNVYAK--KGERLFINESKI 508 (510)
T ss_pred CEEEEEEE-EECCCCCCEEEEEEEEEECCCC--CCCEEEEECCCC
T ss_conf 41669997-6659999589999679828678--888679850023
No 20
>COG3785 Uncharacterized conserved protein [Function unknown]
Probab=20.85 E-value=58 Score=15.31 Aligned_cols=17 Identities=12% Similarity=0.397 Sum_probs=10.9
Q ss_pred CCCCCEEEEEEEECCCC
Q ss_conf 87888279999206787
Q gi|254780712|r 12 SKSRHHYRIVVANSRSP 28 (116)
Q Consensus 12 ~k~rp~yrIVvadsr~~ 28 (116)
.+-.||||+++-|.-.+
T Consensus 56 ~rdqPfYHllaEnde~~ 72 (116)
T COG3785 56 LRDQPFYHLLAENDETE 72 (116)
T ss_pred CCCCCCEEEEEECCCCC
T ss_conf 44586101442068861
No 21
>KOG2806 consensus
Probab=20.66 E-value=78 Score=14.53 Aligned_cols=61 Identities=18% Similarity=0.212 Sum_probs=38.0
Q ss_pred CCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHH-HHHHHHHCCCCCCHHHHHHH
Q ss_conf 8827999920678776841022212156787888644797399-99999841983568999999
Q gi|254780712|r 15 RHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFE-RIQHWMSKGAQPTDRILFFL 77 (116)
Q Consensus 15 rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~e-Ri~yWL~~GAqpS~~V~~LL 77 (116)
-=|..|...|-..|.++. +..|.--|+..-.....-.+|.| .++||+.+|++|+.-|-.+=
T Consensus 234 ~DfiNi~syDf~gpw~~~--~~tGp~aPl~~~~~~~~~~~Nvd~~~ky~~~~~~~~~Kl~~gip 295 (432)
T KOG2806 234 VDFINIMSYDYYGPWSLP--CFTGPPSPLYKGPSMTNPKMNVDSLLKYWTEKGLPPSKLVLALP 295 (432)
T ss_pred CCEEEEEEEECCCCCCCC--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEEEC
T ss_conf 785888753015777778--75897776577655566654321344544205788733799964
No 22
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=20.52 E-value=78 Score=14.51 Aligned_cols=40 Identities=18% Similarity=0.430 Sum_probs=28.0
Q ss_pred CCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC-CCCCCH-HHHHHHHHCC
Q ss_conf 4102221215678788864479739999999841-983568-9999999729
Q gi|254780712|r 32 KFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK-GAQPTD-RILFFLDKAG 81 (116)
Q Consensus 32 k~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~-GAqpS~-~V~~LL~~~G 81 (116)
-+++.+-+|-|+.| ..-+.|+|.+ |-..+| +|.+||+...
T Consensus 77 e~l~~mDsy~PliP----------d~v~DYyl~k~Gf~~~D~rvKkLl~L~a 118 (197)
T COG5162 77 ELLQNMDSYTPLIP----------DSVTDYYLEKAGFVTSDQRVKKLLSLLA 118 (197)
T ss_pred HHHHHCCCCCCCCC----------HHHHHHHHHHCCCEECCHHHHHHHHHHH
T ss_conf 99986125788761----------7999999985484104489999999999
Done!