Query psy2553
Match_columns 134
No_of_seqs 107 out of 340
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 19:11:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00159 60S ribosomal protein 100.0 1.3E-70 2.9E-75 415.4 10.3 133 2-134 1-133 (133)
2 KOG0878|consensus 100.0 5.9E-68 1.3E-72 393.7 2.8 124 1-124 1-124 (124)
3 PF01655 Ribosomal_L32e: Ribos 100.0 1.6E-62 3.6E-67 361.4 6.5 110 15-124 1-110 (110)
4 cd00513 Ribosomal_L32_L32e Rib 100.0 2E-61 4.3E-66 354.2 8.7 107 17-123 1-107 (107)
5 PRK08562 rpl32e 50S ribosomal 100.0 9.8E-61 2.1E-65 358.5 8.8 113 11-125 12-124 (125)
6 PRK12766 50S ribosomal protein 100.0 1.9E-55 4.1E-60 357.7 8.8 112 13-126 113-224 (232)
7 COG1717 RPL32 Ribosomal protei 100.0 8.8E-55 1.9E-59 327.7 0.0 123 4-128 9-132 (133)
8 COG1458 Predicted DNA-binding 68.0 3.6 7.9E-05 34.0 1.9 42 78-125 159-200 (221)
9 PF09894 DUF2121: Uncharacteri 61.2 8.1 0.00018 31.5 2.7 31 81-122 31-61 (194)
10 PF01248 Ribosomal_L7Ae: Ribos 47.9 62 0.0013 21.8 5.1 49 77-125 16-65 (95)
11 PTZ00106 60S ribosomal protein 42.7 60 0.0013 23.6 4.6 39 84-123 34-72 (108)
12 PRK12360 4-hydroxy-3-methylbut 39.9 54 0.0012 27.8 4.5 48 77-128 40-101 (281)
13 PRK01045 ispH 4-hydroxy-3-meth 39.7 59 0.0013 27.8 4.7 47 77-127 39-97 (298)
14 PF08745 UPF0278: UPF0278 fami 39.2 16 0.00035 30.0 1.2 46 75-126 149-194 (205)
15 PRK01018 50S ribosomal protein 37.6 91 0.002 22.0 4.8 39 84-123 25-63 (99)
16 PRK13602 putative ribosomal pr 36.7 1E+02 0.0022 21.1 4.7 37 89-125 24-60 (82)
17 PF12431 CitT: Transcriptional 33.0 18 0.0004 20.7 0.5 9 34-42 21-29 (30)
18 TIGR01019 sucCoAalpha succinyl 32.4 89 0.0019 26.3 4.6 34 93-126 89-122 (286)
19 PF01408 GFO_IDH_MocA: Oxidore 31.6 90 0.002 21.2 3.9 37 84-122 54-90 (120)
20 COG1609 PurR Transcriptional r 31.2 19 0.00042 30.0 0.5 27 101-128 26-52 (333)
21 PRK10727 DNA-binding transcrip 28.2 24 0.00053 28.4 0.6 27 101-128 27-53 (343)
22 PF07988 LMSTEN: LMSTEN motif; 28.0 34 0.00074 22.1 1.1 12 80-91 29-40 (48)
23 PRK05678 succinyl-CoA syntheta 27.6 1.2E+02 0.0025 25.7 4.6 34 93-126 91-124 (291)
24 PRK06683 hypothetical protein; 27.4 1.8E+02 0.0039 20.0 4.8 41 83-124 19-59 (82)
25 PRK06091 membrane protein FdrA 27.3 1E+02 0.0022 28.8 4.5 67 58-126 104-175 (555)
26 TIGR00431 TruB tRNA pseudourid 26.9 1.3E+02 0.0029 24.4 4.6 58 35-99 8-71 (209)
27 TIGR03677 rpl7ae 50S ribosomal 26.9 1.9E+02 0.0042 21.0 5.1 48 77-124 27-75 (117)
28 PF00356 LacI: Bacterial regul 26.4 45 0.00098 20.7 1.5 21 100-120 24-44 (46)
29 PRK10014 DNA-binding transcrip 26.3 31 0.00066 27.6 0.8 28 100-128 31-58 (342)
30 PF13727 CoA_binding_3: CoA-bi 26.3 95 0.0021 22.1 3.4 45 77-121 126-171 (175)
31 PRK11303 DNA-binding transcrip 25.7 27 0.00059 27.7 0.4 26 101-127 29-54 (328)
32 COG4075 Uncharacterized conser 25.5 56 0.0012 24.4 2.0 51 65-117 36-89 (110)
33 COG4412 Uncharacterized protei 25.4 40 0.00086 32.1 1.5 29 44-74 364-399 (760)
34 PF04760 IF2_N: Translation in 25.4 34 0.00074 21.2 0.8 28 105-132 15-43 (54)
35 TIGR01481 ccpA catabolite cont 25.2 28 0.0006 27.7 0.4 27 101-128 27-53 (329)
36 PF10126 Nit_Regul_Hom: Unchar 25.2 64 0.0014 24.2 2.3 51 64-116 35-88 (110)
37 PRK09526 lacI lac repressor; R 24.6 29 0.00064 27.7 0.4 27 100-127 30-56 (342)
38 COG1671 Uncharacterized protei 24.5 53 0.0012 25.8 1.8 45 82-133 56-100 (150)
39 PF07750 GcrA: GcrA cell cycle 24.4 23 0.00049 27.5 -0.2 39 81-120 8-46 (162)
40 PF08189 Meleagrin: Meleagrin/ 24.2 32 0.00069 21.3 0.4 12 54-65 6-17 (39)
41 PRK13601 putative L7Ae-like ri 23.8 2.3E+02 0.0051 19.6 4.8 42 83-125 16-57 (82)
42 PF05171 HemS: Haemin-degradin 23.7 1.4E+02 0.0031 21.7 3.9 42 80-126 1-46 (129)
43 PRK10339 DNA-binding transcrip 23.7 41 0.0009 26.9 1.1 28 101-129 29-56 (327)
44 PRK10401 DNA-binding transcrip 23.2 35 0.00075 27.6 0.6 27 100-127 26-52 (346)
45 PRK13371 4-hydroxy-3-methylbut 22.9 1.5E+02 0.0032 26.6 4.4 26 99-128 117-142 (387)
46 TIGR00216 ispH_lytB (E)-4-hydr 22.8 1.7E+02 0.0037 24.8 4.6 48 77-128 38-98 (280)
47 PRK09492 treR trehalose repres 22.4 35 0.00077 26.9 0.5 27 100-127 29-55 (315)
48 PRK14987 gluconate operon tran 22.2 37 0.0008 27.2 0.6 27 100-127 30-56 (331)
49 PRK10423 transcriptional repre 22.2 41 0.00088 26.6 0.8 26 101-127 24-49 (327)
50 TIGR02405 trehalos_R_Ecol treh 21.7 37 0.0008 27.0 0.5 27 100-127 26-52 (311)
51 PRK02193 truB tRNA pseudouridi 21.6 1.6E+02 0.0035 25.0 4.3 58 35-99 6-69 (279)
52 PRK14124 tRNA pseudouridine sy 21.3 1.9E+02 0.004 25.0 4.7 58 35-99 9-72 (308)
53 PRK01528 truB tRNA pseudouridi 21.3 1.8E+02 0.004 24.8 4.6 58 35-99 9-72 (292)
54 PTZ00222 60S ribosomal protein 20.6 2.1E+02 0.0046 24.4 4.7 51 73-123 129-180 (263)
55 PRK10703 DNA-binding transcrip 20.4 40 0.00086 27.0 0.4 26 101-127 27-52 (341)
56 PRK14846 truB tRNA pseudouridi 20.3 2E+02 0.0042 25.5 4.7 57 35-98 9-71 (345)
No 1
>PTZ00159 60S ribosomal protein L32; Provisional
Probab=100.00 E-value=1.3e-70 Score=415.40 Aligned_cols=133 Identities=62% Similarity=1.008 Sum_probs=131.7
Q ss_pred CCCCCCCCcccccCCCCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEech
Q psy2553 2 SIKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHNV 81 (134)
Q Consensus 2 ~~~pl~~~kivkkr~~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n~ 81 (134)
|+.|+.+++|+||++++|.|||||+|++|++|||||+||||+||++|+|+++||+||||||++|||||||||++|+|||+
T Consensus 1 m~~p~~~~~ivkkr~~kF~R~~s~ry~rl~~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tR~l~PsG~~~vlV~N~ 80 (133)
T PTZ00159 1 MVKPKVKKKIVKKRTKKFTRFQSERFPRVKPSWRKPRGIDNRVRRRFKGTRLMPKIGYGSDKKTRYLLPSGFYKFPVRNV 80 (133)
T ss_pred CCCCccccccccccCCcccccchhhccccccccCCCCCcccchhccccCccCCCcCccCCChhhcccCCCCCeeEEecCH
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCCcceeecccC
Q psy2553 82 KELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNARIRTEENE 134 (134)
Q Consensus 82 keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~arl~~~e~e 134 (134)
+|||.|+|||++|||||||+||++||++|+|+|+||||+|+||+|||++||+|
T Consensus 81 keLe~L~m~~~~~aa~Ia~~Vg~rKR~~I~~rA~eL~ikV~N~~arl~~ee~e 133 (133)
T PTZ00159 81 KDLEMLLMHNRKYAAEIAHNVSARKRKAIVERAKELNVRVLNGNARLRKEEKE 133 (133)
T ss_pred HHHHHHhcCCcceEEEEecccccchHHHHHHHHHHhCCcccCCCcccchhhcC
Confidence 99999999999999999999999999999999999999999999999999997
No 2
>KOG0878|consensus
Probab=100.00 E-value=5.9e-68 Score=393.72 Aligned_cols=124 Identities=72% Similarity=1.161 Sum_probs=122.4
Q ss_pred CCCCCCCCCcccccCCCCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEec
Q psy2553 1 MSIKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHN 80 (134)
Q Consensus 1 ~~~~pl~~~kivkkr~~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n 80 (134)
++++||++|+|+||++++|+|||||+|+++++|||||+||||+|||||||+++||+||||||++||||+||||++|+|||
T Consensus 1 ~~~~pl~~~kivkkr~kkFirh~sdry~~v~~~WrkPrGiDnrVrRRFkgqilMPnIgYgsnKkTrh~lP~G~~kflv~n 80 (124)
T KOG0878|consen 1 ATMRPLVKPKIVKKRTKKFIRHQSDRYVRVKESWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTRHMLPNGFKKFLVHN 80 (124)
T ss_pred CCCccccccHHHHHhcccccccccchhhhhhhhccCCCcchhHHHHHhccceeccccccCCCccceecCChhhhHHhhhh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecC
Q psy2553 81 VKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNG 124 (134)
Q Consensus 81 ~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~ 124 (134)
|+|||+|+|||++|||||||+||++||++|+|||+||||+|||+
T Consensus 81 vkele~Llm~nk~YcaEIAhnVsak~r~~Ivera~qL~i~vtn~ 124 (124)
T KOG0878|consen 81 VKELEVLLMHNKTYCAEIAHNVSAKKRKAIVERAAQLGIRVTNR 124 (124)
T ss_pred hhHHHHHHHhhHHHHHHHhhccccccHHHHHHHHHhhceeccCC
Confidence 99999999999999999999999999999999999999999996
No 3
>PF01655 Ribosomal_L32e: Ribosomal protein L32; InterPro: IPR001515 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 [, ]. The L32e family consists of proteins that have 135 to 240 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3O58_b 3IZS_h 1S1I 3O5H_b 2ZKR_y 1Q7Y_Z 1VQ7_Y 3CCQ_Y 3CCV_Y 3CC7_Y ....
Probab=100.00 E-value=1.6e-62 Score=361.38 Aligned_cols=110 Identities=67% Similarity=1.087 Sum_probs=86.5
Q ss_pred CCCCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEechhhhHHHhhcCccc
Q psy2553 15 RRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHNVKELEVLMMQNRKY 94 (134)
Q Consensus 15 r~~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n~keLe~L~~~~~~~ 94 (134)
+|++|+|||||+|++|++|||||+||||++|++|+|+++||+||||||++|||||||||++|+|||++|||.|+|||++|
T Consensus 1 k~~~F~R~~s~r~~rl~~sWRKPrGiDnk~Rrr~kG~~~mp~iGYgs~k~tR~l~PsG~~~~lV~n~~eLe~L~m~~~~~ 80 (110)
T PF01655_consen 1 KTKKFIRHQSDRYKRLKDSWRKPRGIDNKVRRRFKGKPLMPNIGYGSPKKTRGLHPSGFRKVLVHNVKELEVLLMDNKSY 80 (110)
T ss_dssp --S--B-TTTTTSTTS-SS-----SSS-TCCHT-TTS---S-GCGS--TTTTTB-TTSSEEEEESSHHHHHHCHHHTTTE
T ss_pred CCCcccccccccccccccccCCCCcccCcceeeecCccCccccccCCCccccccCCCCCeEEEEeccchHHHHhcCCcce
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeeccCCcccHHHHHHHHHhcCCceecC
Q psy2553 95 CAEIGHAVSSKKRRDIVQRAQQLSIRLTNG 124 (134)
Q Consensus 95 ~~~Ia~~Vg~kkr~~I~erA~el~irV~N~ 124 (134)
||||||+||++||++|+|+|+||||+|+||
T Consensus 81 ~~~Ia~~Vg~kkr~~I~erA~el~ikV~N~ 110 (110)
T PF01655_consen 81 AAEIAHNVGSKKRKEIVERAAELGIKVLNP 110 (110)
T ss_dssp EEEE-TTS-HHHHHHHHHHHHHHT-EBSSH
T ss_pred EEEEecCcccccHHHHHHHHHHhCCcccCC
Confidence 999999999999999999999999999996
No 4
>cd00513 Ribosomal_L32_L32e Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.
Probab=100.00 E-value=2e-61 Score=354.20 Aligned_cols=107 Identities=64% Similarity=1.047 Sum_probs=106.1
Q ss_pred CCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEechhhhHHHhhcCccceE
Q psy2553 17 KVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCA 96 (134)
Q Consensus 17 ~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n~keLe~L~~~~~~~~~ 96 (134)
++|.|||||+|++|++|||||+||||+||++|+|+++||+||||||++|||||||||++|+|||++|||+|+|||++|||
T Consensus 1 ~kF~R~~s~r~~rl~~sWRkPrGiDnkvRrr~kg~~~mp~iGYgS~k~tR~l~PsG~~~~lV~N~~eLe~l~~~n~~~~a 80 (107)
T cd00513 1 KKFKRHQSDRYKRLGDSWRKPRGIDNKVRRRFKGKPAMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLDMHNRTYAA 80 (107)
T ss_pred CCccccchhcccccccccCCCCCcccchhccccCCCCCCcccCCCChhhcccCCCCCeEEEecCHHHHHHHhccCCeeEE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeccCCcccHHHHHHHHHhcCCceec
Q psy2553 97 EIGHAVSSKKRRDIVQRAQQLSIRLTN 123 (134)
Q Consensus 97 ~Ia~~Vg~kkr~~I~erA~el~irV~N 123 (134)
||||+||++||++|+|+|+||||+|+|
T Consensus 81 ~Ia~~Vg~rKR~~I~~rA~el~ikV~N 107 (107)
T cd00513 81 RIAHTVGARKRKEIVERAKELGIKVLN 107 (107)
T ss_pred EEecccccchHHHHHHHHHHhCCcccC
Confidence 999999999999999999999999998
No 5
>PRK08562 rpl32e 50S ribosomal protein L32e; Validated
Probab=100.00 E-value=9.8e-61 Score=358.52 Aligned_cols=113 Identities=36% Similarity=0.685 Sum_probs=111.0
Q ss_pred ccccCCCCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEechhhhHHHhhc
Q psy2553 11 IVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHNVKELEVLMMQ 90 (134)
Q Consensus 11 ivkkr~~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n~keLe~L~~~ 90 (134)
.+||++++|+|||||+|++|++|||||+||||+||++|+|+++||+||||||++|||||||||++|+|||++|||+| |
T Consensus 12 ~~kkk~~kF~R~~s~r~~rl~~sWRKPrGiDnkvRrr~kg~~~mp~iGYgS~k~tR~l~PsG~~~vlV~N~keLe~l--~ 89 (125)
T PRK08562 12 KLKRKKPEFKRQDWHRYKRLGDKWRRPRGLDSKMRLKLKGKPAIVEVGYRSPKAVRGLHPSGYEEVLVHNVKELEKL--D 89 (125)
T ss_pred HhhccCCCcccccccccccccccCCCCCCcccchhccccCCCCCCcCCcCCChhhcccCCCCCeeEEecCHHHhhhc--c
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred CccceEEeeccCCcccHHHHHHHHHhcCCceecCC
Q psy2553 91 NRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGN 125 (134)
Q Consensus 91 ~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~ 125 (134)
|++|||||||+||++||++|+|+|+||||+|+||.
T Consensus 90 ~~~~aa~Ia~~Vg~rKR~~I~~rA~el~ikV~N~~ 124 (125)
T PRK08562 90 PETQAARIASTVGKRKRLEILKKARELGIKVLNPG 124 (125)
T ss_pred CCceEEEEeccccchhHHHHHHHHHHhCCcccCCC
Confidence 99999999999999999999999999999999996
No 6
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=100.00 E-value=1.9e-55 Score=357.66 Aligned_cols=112 Identities=28% Similarity=0.433 Sum_probs=109.5
Q ss_pred ccCCCCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEechhhhHHHhhcCc
Q psy2553 13 KKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHNVKELEVLMMQNR 92 (134)
Q Consensus 13 kkr~~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n~keLe~L~~~~~ 92 (134)
++++|+|+|||||+|+||++|||||+||||||||+|+|+++||+||||||++|||||||||++|+|||++|||+| ||+
T Consensus 113 ~~~~p~F~R~~~~r~~r~~~sWRkPrGidnk~Rr~~kg~~~mp~iGYgS~k~~R~l~PsG~~~vlV~N~~eLe~l--~~~ 190 (232)
T PRK12766 113 REGKPQFNRQDYHKKKRTPTSWRRPRGGLSKQRRGIKGKGDTVEAGFRTPTAVRGKHPSGFEEVRVHNTDDLEGV--DGD 190 (232)
T ss_pred hccCCCeecccccccccccccCCCCCCCccchhcccCCCCCCCcCCCCCChhhcccCCCCCeeEEecCHHHHhhc--cCc
Confidence 567899999999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred cceEEeeccCCcccHHHHHHHHHhcCCceecCCc
Q psy2553 93 KYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNA 126 (134)
Q Consensus 93 ~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~a 126 (134)
+|||+|||+||+|||++|+++|+||||+|+||+-
T Consensus 191 ~~aa~Ia~~Vg~rKR~~I~erA~el~ikV~N~~~ 224 (232)
T PRK12766 191 TEAVRIASKVGARKRERIEEVAEEQGIRVLNPTY 224 (232)
T ss_pred ceEEEeeccccchhHHHHHHHHHHhCCcccCCCc
Confidence 9999999999999999999999999999999984
No 7
>COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.8e-55 Score=327.70 Aligned_cols=123 Identities=41% Similarity=0.723 Sum_probs=115.0
Q ss_pred CCCCCCccccc-CCCCcccccccccccccccccCCCcCCchhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEechh
Q psy2553 4 KPVYRPKIVKK-RRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHNVK 82 (134)
Q Consensus 4 ~pl~~~kivkk-r~~~F~R~~sdr~~rik~sWRKPrGiDnkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n~k 82 (134)
++|++++++.| ++|+|+||+||+|+|++++||+|+||||++|++++|.+.||+||||||+++||||||||++|+|||++
T Consensus 9 ~rLl~ir~~~k~kKp~F~R~~~~Rykrl~~~WRrPrG~dsK~Rr~~kg~p~~v~iGyrsPk~vRglhPSG~~~VlV~Nv~ 88 (133)
T COG1717 9 KRLLKIRRVLKRKKPEFKRQESDRYKRLGEKWRRPRGIDSKMRRKLKGKPPMVKIGYRSPKAVRGLHPSGYEEVLVHNVK 88 (133)
T ss_pred HHHHHHHHHHHhccchhhhHHHHHHhhhhhhccCCCCchHHHHHHhcCCCCCcccCCCCcHhhcccCCCccceeeeecHH
Confidence 35666775544 57789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 83 ELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 83 eLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
|||.| ++.++||+|||+||++||.+|+++|.||||+|+||++|+
T Consensus 89 dLe~l--dp~~~aarIAs~VG~rKR~eI~~rA~elGikVlN~~~r~ 132 (133)
T COG1717 89 DLEKL--DPETQAARIASTVGARKRIEILERARELGIKVLNPGGRV 132 (133)
T ss_pred HHhhc--CchhHHHHHHHhhhHHHHHHHHHHHHHhCcEEeCCcccc
Confidence 99999 566889999999999999999999999999999999986
No 8
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=67.97 E-value=3.6 Score=33.96 Aligned_cols=42 Identities=19% Similarity=0.344 Sum_probs=36.0
Q ss_pred EechhhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCC
Q psy2553 78 VHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGN 125 (134)
Q Consensus 78 V~n~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~ 125 (134)
..+..||++|+..-+-.|+..|+..| |..-|.+||+++.++.
T Consensus 159 LDSapDlDvLLLAkELdaavVssD~G------ir~WAe~LGlrfv~a~ 200 (221)
T COG1458 159 LDSAPDLDVLLLAKELDAAVVSSDEG------IRTWAEKLGLRFVDAF 200 (221)
T ss_pred ccccchhHHHHHHHHhCceEEecchh------HHHHHHHhCCeeeCHh
Confidence 36789999999877778999999988 6678999999999875
No 9
>PF09894 DUF2121: Uncharacterized protein conserved in archaea (DUF2121); InterPro: IPR016754 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. They do show distant similarity to NTPases and to nucleic acid binding enzymes.
Probab=61.24 E-value=8.1 Score=31.46 Aligned_cols=31 Identities=23% Similarity=0.576 Sum_probs=25.6
Q ss_pred hhhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCcee
Q psy2553 81 VKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLT 122 (134)
Q Consensus 81 ~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~ 122 (134)
-+.||.+| |+.+| +...++.++|.|||+.|.
T Consensus 31 re~LEeeL-----YsG~I------ktdeEL~kkA~Elgv~i~ 61 (194)
T PF09894_consen 31 REKLEEEL-----YSGKI------KTDEELLKKAEELGVKIK 61 (194)
T ss_pred HHHHHHHH-----hCCcc------CCHHHHHHHHHHcCCEEE
Confidence 46788775 88888 678999999999999754
No 10
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 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 family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=47.89 E-value=62 Score=21.85 Aligned_cols=49 Identities=10% Similarity=0.112 Sum_probs=39.9
Q ss_pred EEechhhhHHHhhcCccceEEeeccCCcccHHH-HHHHHHhcCCceecCC
Q psy2553 77 VVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRD-IVQRAQQLSIRLTNGN 125 (134)
Q Consensus 77 lV~n~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~-I~erA~el~irV~N~~ 125 (134)
+|.-.++....+...+...+-||.+++...... |..-|.+.+|.+..-.
T Consensus 16 lv~G~~~v~k~l~~~~~~lvilA~d~~~~~~~~~l~~~c~~~~Ip~~~~~ 65 (95)
T PF01248_consen 16 LVKGIKEVLKALKKGKAKLVILAEDCSPDSIKKHLPALCEEKNIPYVFVP 65 (95)
T ss_dssp EEESHHHHHHHHHTTCESEEEEETTSSSGHHHHHHHHHHHHTTEEEEEES
T ss_pred EEEchHHHHHHHHcCCCcEEEEcCCCChhhhcccchhheeccceeEEEEC
Confidence 455566666666677899999999999999999 8899999999876543
No 11
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=42.74 E-value=60 Score=23.58 Aligned_cols=39 Identities=15% Similarity=0.141 Sum_probs=33.5
Q ss_pred hHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceec
Q psy2553 84 LEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTN 123 (134)
Q Consensus 84 Le~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N 123 (134)
+..|- ..+-..+-||.+.+...++.|...|.+.+|.|.+
T Consensus 34 lkalk-~gkaklViiA~D~~~~~kkki~~~~~~~~Vpv~~ 72 (108)
T PTZ00106 34 LKALR-NGKAKLVIISNNCPPIRRSEIEYYAMLSKTGVHH 72 (108)
T ss_pred HHHHH-cCCeeEEEEeCCCCHHHHHHHHHHHhhcCCCEEE
Confidence 44443 4678999999999999999999999999999875
No 12
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=39.94 E-value=54 Score=27.80 Aligned_cols=48 Identities=15% Similarity=0.270 Sum_probs=31.8
Q ss_pred EEechhhhHHHhhcC-------------ccceEEe-eccCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 77 VVHNVKELEVLMMQN-------------RKYCAEI-GHAVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 77 lV~n~keLe~L~~~~-------------~~~~~~I-a~~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
+|||+..++.|--.. ....+-| ||.|+ .++.++|++.|+.|.+.++=+
T Consensus 40 iVHN~~Vv~~L~~~Gv~~v~~~~~~~v~~~~~ViirAHGv~----~~~~~~~~~~g~~viDaTCP~ 101 (281)
T PRK12360 40 LIHNNQVVSDLEEKGVKTIEESEIDSLKEGDVVIIRSHGVS----KKVYKDLKDKGLEIIDATCPF 101 (281)
T ss_pred CcCCHHHHHHHHHCcCEEECcCchhhCCCCCEEEEeCCCCC----HHHHHHHHHCCCeEEeCCCcc
Confidence 688888887773110 0111222 78876 567888999999999887643
No 13
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=39.75 E-value=59 Score=27.79 Aligned_cols=47 Identities=19% Similarity=0.240 Sum_probs=32.1
Q ss_pred EEechhhhHHHhhc-----------CccceEEe-eccCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 77 VVHNVKELEVLMMQ-----------NRKYCAEI-GHAVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 77 lV~n~keLe~L~~~-----------~~~~~~~I-a~~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
+|||+..++.|--. ++.-.+-| ||.++ .++.+.|++.|+.|++.++=
T Consensus 39 iIHN~~vv~~L~~~GV~~v~~~~~v~~~~~ViirAHGv~----~~~~~~~~~~g~~viDaTCP 97 (298)
T PRK01045 39 IVHNRYVVERLEKKGAIFVEELDEVPDGAIVIFSAHGVS----PAVREEAKERGLTVIDATCP 97 (298)
T ss_pred CccCHHHHHHHHHCCCEEecCcccCCCCCEEEEeCCCCC----HHHHHHHHHCCCeEEeCCCc
Confidence 78999888887311 10112222 88877 46777899999999998763
No 14
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=39.19 E-value=16 Score=29.97 Aligned_cols=46 Identities=17% Similarity=0.309 Sum_probs=24.5
Q ss_pred EEEEechhhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCCc
Q psy2553 75 KVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNA 126 (134)
Q Consensus 75 ~~lV~n~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~a 126 (134)
.-.+-+..|+++|+..-+-.|+-++.--| |..-|.+|||+++||..
T Consensus 149 ~G~ldS~~D~dvl~LA~El~a~lvt~D~g------i~~~A~~lGi~~i~~~~ 194 (205)
T PF08745_consen 149 KGILDSREDIDVLLLALELDAVLVTDDYG------IQNWAEKLGIRFIDARD 194 (205)
T ss_dssp ------HHHHHHHHHHHHHT--EE---HH------HHHHHHHTT--EE----
T ss_pred cccCCChHhHHHHHHHHHcCCEEEeCCHh------HHHHHHHCCCEEEeccc
Confidence 34456899999998766667777776644 88899999999999863
No 15
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=37.63 E-value=91 Score=22.00 Aligned_cols=39 Identities=10% Similarity=0.116 Sum_probs=32.9
Q ss_pred hHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceec
Q psy2553 84 LEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTN 123 (134)
Q Consensus 84 Le~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N 123 (134)
++.| -..+-..+-||...+...++.|...|.+.+|.+.+
T Consensus 25 ~kai-~~gkaklViiA~D~~~~~~~~i~~~c~~~~Ip~~~ 63 (99)
T PRK01018 25 IKAI-KLGKAKLVIVASNCPKDIKEDIEYYAKLSGIPVYE 63 (99)
T ss_pred HHHH-HcCCceEEEEeCCCCHHHHHHHHHHHHHcCCCEEE
Confidence 3444 34678899999999999999999999999998765
No 16
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=36.74 E-value=1e+02 Score=21.14 Aligned_cols=37 Identities=3% Similarity=0.046 Sum_probs=32.2
Q ss_pred hcCccceEEeeccCCcccHHHHHHHHHhcCCceecCC
Q psy2553 89 MQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGN 125 (134)
Q Consensus 89 ~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~ 125 (134)
-..+-..+-||.+++..-++.|...|.+.+|.+..-.
T Consensus 24 ~~gkaklViiA~D~~~~~~~~i~~~c~~~~Vp~~~~~ 60 (82)
T PRK13602 24 KRGSVKEVVVAEDADPRLTEKVEALANEKGVPVSKVD 60 (82)
T ss_pred HcCCeeEEEEECCCCHHHHHHHHHHHHHcCCCEEEEC
Confidence 3578889999999999999999999999999876543
No 17
>PF12431 CitT: Transcriptional regulator
Probab=33.02 E-value=18 Score=20.74 Aligned_cols=9 Identities=67% Similarity=0.937 Sum_probs=7.0
Q ss_pred ccCCCcCCc
Q psy2553 34 WRKPKGIDN 42 (134)
Q Consensus 34 WRKPrGiDn 42 (134)
=+=|+|||.
T Consensus 21 ~~LPKGID~ 29 (30)
T PF12431_consen 21 ERLPKGIDE 29 (30)
T ss_pred cCCCCCccc
Confidence 457999995
No 18
>TIGR01019 sucCoAalpha succinyl-CoA synthetase, alpha subunit. ATP citrate lyases appear to form an outgroup.
Probab=32.37 E-value=89 Score=26.34 Aligned_cols=34 Identities=12% Similarity=0.138 Sum_probs=27.7
Q ss_pred cceEEeeccCCcccHHHHHHHHHhcCCceecCCc
Q psy2553 93 KYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNA 126 (134)
Q Consensus 93 ~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~a 126 (134)
..++-|++.++..-..+|.+.|.+.|++|+=||+
T Consensus 89 k~avIis~Gf~e~~~~~l~~~a~~~girilGPNc 122 (286)
T TIGR01019 89 ELIVCITEGIPVHDMLKVKRYMEESGTRLIGPNC 122 (286)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHcCCEEECCCC
Confidence 4566778888766568999999999999998875
No 19
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=31.56 E-value=90 Score=21.17 Aligned_cols=37 Identities=19% Similarity=0.213 Sum_probs=29.4
Q ss_pred hHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCcee
Q psy2553 84 LEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLT 122 (134)
Q Consensus 84 Le~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~ 122 (134)
++.|+.++.-.++-|+..-+ .+.+++..|.+.|+.|+
T Consensus 54 ~~~ll~~~~~D~V~I~tp~~--~h~~~~~~~l~~g~~v~ 90 (120)
T PF01408_consen 54 LEELLADEDVDAVIIATPPS--SHAEIAKKALEAGKHVL 90 (120)
T ss_dssp HHHHHHHTTESEEEEESSGG--GHHHHHHHHHHTTSEEE
T ss_pred HHHHHHhhcCCEEEEecCCc--chHHHHHHHHHcCCEEE
Confidence 55666666788899988765 59999999999999764
No 20
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=31.21 E-value=19 Score=30.03 Aligned_cols=27 Identities=30% Similarity=0.407 Sum_probs=24.1
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
.|+...|+.|.+-|+|||.+ -|..||-
T Consensus 26 ~Vs~eTr~kV~~a~~elgY~-pN~~Ar~ 52 (333)
T COG1609 26 YVSEETREKVLAAIKELGYR-PNAVARS 52 (333)
T ss_pred CCCHHHHHHHHHHHHHHCCC-CCHHHHH
Confidence 79999999999999999996 8887763
No 21
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=28.21 E-value=24 Score=28.43 Aligned_cols=27 Identities=30% Similarity=0.298 Sum_probs=23.2
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
.|+.+.|+.|.+-|+|||. +.|..||-
T Consensus 27 ~Vs~~tr~rV~~~a~elgY-~pn~~ar~ 53 (343)
T PRK10727 27 KASEASRLAVHSAMESLSY-HPNANARA 53 (343)
T ss_pred CCCHHHHHHHHHHHHHHCC-CCCHHHHh
Confidence 5899999999999999999 57776653
No 22
>PF07988 LMSTEN: LMSTEN motif; InterPro: IPR012642 Proteins containing the Wos2 domain are involved in the regulation of the cell cycle [] and are Myb-related transcriptional activators. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2AGH_A 1SB0_B.
Probab=27.99 E-value=34 Score=22.05 Aligned_cols=12 Identities=50% Similarity=0.850 Sum_probs=10.0
Q ss_pred chhhhHHHhhcC
Q psy2553 80 NVKELEVLMMQN 91 (134)
Q Consensus 80 n~keLe~L~~~~ 91 (134)
.++|||.|+|..
T Consensus 29 rikelelllms~ 40 (48)
T PF07988_consen 29 RIKELELLLMSA 40 (48)
T ss_dssp HHHHHHHHHHCH
T ss_pred HHHHHHHHHHhh
Confidence 478999999964
No 23
>PRK05678 succinyl-CoA synthetase subunit alpha; Validated
Probab=27.58 E-value=1.2e+02 Score=25.69 Aligned_cols=34 Identities=12% Similarity=0.100 Sum_probs=26.2
Q ss_pred cceEEeeccCCcccHHHHHHHHHhcCCceecCCc
Q psy2553 93 KYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNA 126 (134)
Q Consensus 93 ~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~a 126 (134)
..++-|++.++.....+|++.|.+.|++|+=||+
T Consensus 91 k~avI~s~Gf~~~~~~~l~~~a~~~girvlGPNc 124 (291)
T PRK05678 91 DLIVCITEGIPVLDMLEVKAYLERKKTRLIGPNC 124 (291)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHcCCEEECCCC
Confidence 4456667777654445999999999999998875
No 24
>PRK06683 hypothetical protein; Provisional
Probab=27.37 E-value=1.8e+02 Score=19.99 Aligned_cols=41 Identities=20% Similarity=0.147 Sum_probs=33.7
Q ss_pred hhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecC
Q psy2553 83 ELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNG 124 (134)
Q Consensus 83 eLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~ 124 (134)
-++.|- .++-..+-||...+..-++.|...|.+.+|.|..-
T Consensus 19 v~kaik-~gkaklViiA~Da~~~~~~~i~~~~~~~~Vpv~~~ 59 (82)
T PRK06683 19 TLEAIK-NGIVKEVVIAEDADMRLTHVIIRTALQHNIPITKV 59 (82)
T ss_pred HHHHHH-cCCeeEEEEECCCCHHHHHHHHHHHHhcCCCEEEE
Confidence 344443 46778899999999999999999999999987653
No 25
>PRK06091 membrane protein FdrA; Validated
Probab=27.31 E-value=1e+02 Score=28.80 Aligned_cols=67 Identities=10% Similarity=0.083 Sum_probs=48.1
Q ss_pred CCCCCccccccCCCCceEEEEech-----hhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCCc
Q psy2553 58 GYGSAKKTRHMLPNHFLKVVVHNV-----KELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNA 126 (134)
Q Consensus 58 GYgS~k~tr~l~PsGf~~~lV~n~-----keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~a 126 (134)
+|.+=+.....+|.. .-.+|.-+ ..++..+-.. ..++-|+.++|..-..+|.+.|.+.|++|+=||+
T Consensus 104 ~~~t~~~a~~~lpe~-DLAvIsVPa~~v~~al~ea~~~G-~~viI~S~gfg~~~E~~L~e~Ar~~GlrvmGPNC 175 (555)
T PRK06091 104 QVRRWDSACQKLPDA-NLALISVAGEYAAELAEQALDRN-LNVMMFSDNVTLEDEIRLKTRAREKGLLVMGPDC 175 (555)
T ss_pred ccccHHHHHhcCCCC-CEEEEecCHHHHHHHHHHHHHcC-CeEEEEcCCCCHHHHHHHHHHHHHcCCEEECCCC
Confidence 566655555667765 44455433 3444444333 5688889999988889999999999999999987
No 26
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=26.93 E-value=1.3e+02 Score=24.41 Aligned_cols=58 Identities=26% Similarity=0.380 Sum_probs=42.1
Q ss_pred cCCCcCC-----chhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEec-hhhhHHHhhcCccceEEee
Q psy2553 35 RKPKGID-----NRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHN-VKELEVLMMQNRKYCAEIG 99 (134)
Q Consensus 35 RKPrGiD-----nkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n-~keLe~L~~~~~~~~~~Ia 99 (134)
-||.|+. +++|+-++- .+||.+..=. -+.+|.=-+.|.. .+-++.++.++++|-+.+-
T Consensus 8 ~KP~g~tS~~vv~~vkk~~~~----kKvGH~GTLD---P~AsGvLiv~vG~~Tkl~~~~~~~~K~Y~~~~~ 71 (209)
T TIGR00431 8 DKPQGMTSFDALAKVRRLLNV----KKVGHTGTLD---PFATGVLPILVGKATKLSPYLTDLDKEYRAEIR 71 (209)
T ss_pred ECCCCCCHHHHHHHHHHHhCC----CcCCCCCCCC---CcCceEEEEEEChHhhhhHHHcCCCCeEEEEEE
Confidence 4899998 678887753 4788876433 3567777787774 6677777667999988773
No 27
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=26.85 E-value=1.9e+02 Score=20.98 Aligned_cols=48 Identities=8% Similarity=0.015 Sum_probs=36.0
Q ss_pred EEechhhhHHHhhcCccceEEeeccCCcc-cHHHHHHHHHhcCCceecC
Q psy2553 77 VVHNVKELEVLMMQNRKYCAEIGHAVSSK-KRRDIVQRAQQLSIRLTNG 124 (134)
Q Consensus 77 lV~n~keLe~L~~~~~~~~~~Ia~~Vg~k-kr~~I~erA~el~irV~N~ 124 (134)
++.-.++....+-..+.+.+-||..++.. .++.+...|.+.+|.+...
T Consensus 27 l~~G~~~v~kaikkgka~LVilA~D~s~~~~~~~i~~lc~~~~Ip~~~~ 75 (117)
T TIGR03677 27 IKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYVYV 75 (117)
T ss_pred EeEcHHHHHHHHHcCCccEEEEeCCCCcHHHHHHHHHHHHHcCCCEEEe
Confidence 34444554444445778999999999987 5899999999999976543
No 28
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=26.39 E-value=45 Score=20.69 Aligned_cols=21 Identities=33% Similarity=0.498 Sum_probs=18.7
Q ss_pred ccCCcccHHHHHHHHHhcCCc
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIR 120 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~ir 120 (134)
..|+...|+.|.+-|++||..
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYR 44 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-
T ss_pred CCCCHHHHHHHHHHHHHHCCC
Confidence 678999999999999999984
No 29
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=26.32 E-value=31 Score=27.62 Aligned_cols=28 Identities=18% Similarity=0.253 Sum_probs=23.9
Q ss_pred ccCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
..||.+.|+.|.+-|+|||. +.|..||.
T Consensus 31 ~~vs~~tr~~V~~~a~elgY-~p~~~a~~ 58 (342)
T PRK10014 31 GRISTATGERVNQAIEELGF-VRNRQASA 58 (342)
T ss_pred CCCCHHHHHHHHHHHHHhCC-CcCHHHHh
Confidence 36999999999999999998 67877753
No 30
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=26.27 E-value=95 Score=22.07 Aligned_cols=45 Identities=13% Similarity=0.228 Sum_probs=28.2
Q ss_pred EEechhhhHHHhhcCccceEEeeccC-CcccHHHHHHHHHhcCCce
Q psy2553 77 VVHNVKELEVLMMQNRKYCAEIGHAV-SSKKRRDIVQRAQQLSIRL 121 (134)
Q Consensus 77 lV~n~keLe~L~~~~~~~~~~Ia~~V-g~kkr~~I~erA~el~irV 121 (134)
.+.+.+||..++..+.-+-+-||=.- ....-++|++.+.+.++.|
T Consensus 126 ~lg~~~~l~~~~~~~~id~v~ial~~~~~~~i~~ii~~~~~~~v~v 171 (175)
T PF13727_consen 126 VLGDLDDLPELVREHDIDEVIIALPWSEEEQIKRIIEELENHGVRV 171 (175)
T ss_dssp EE--GGGHHHHHHHHT--EEEE--TTS-HHHHHHHHHHHHTTT-EE
T ss_pred eEcCHHHHHHHHHhCCCCEEEEEcCccCHHHHHHHHHHHHhCCCEE
Confidence 56799999999877666666666333 3455568899999999875
No 31
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=25.74 E-value=27 Score=27.73 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=22.4
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
.|+...|+.|.+.|+|||. +.|..||
T Consensus 29 ~Vs~~tr~rV~~~a~elgY-~pn~~a~ 54 (328)
T PRK11303 29 RVSDKTVEKVMAVVREHNY-HPNAVAA 54 (328)
T ss_pred CcCHHHHHHHHHHHHHhCC-CCCHHHH
Confidence 5899999999999999998 5676665
No 32
>COG4075 Uncharacterized conserved protein, homolog of nitrogen regulatory protein PII [Function unknown]
Probab=25.51 E-value=56 Score=24.37 Aligned_cols=51 Identities=16% Similarity=0.173 Sum_probs=39.5
Q ss_pred ccccCCCCceEEEEechhhhHHHh---hcCccceEEeeccCCcccHHHHHHHHHhc
Q psy2553 65 TRHMLPNHFLKVVVHNVKELEVLM---MQNRKYCAEIGHAVSSKKRRDIVQRAQQL 117 (134)
Q Consensus 65 tr~l~PsGf~~~lV~n~keLe~L~---~~~~~~~~~Ia~~Vg~kkr~~I~erA~el 117 (134)
-||+-|.-|+-|.+. +|.|... .+-...|+-|..-|.-.+-+.|.+.++|.
T Consensus 36 YrGvsPd~wkgf~~~--EDpE~aik~i~D~s~~AVlI~tVV~Ee~vekie~~~~Ek 89 (110)
T COG4075 36 YRGVSPDKWKGFSKE--EDPESAIKAIRDLSDKAVLIGTVVKEEKVEKIEELLKEK 89 (110)
T ss_pred ecCcChhHhcCcccc--cCHHHHHHHHHHhhhceEEEEEecCHHHHHHHHHHHHHH
Confidence 478899988888887 6666432 23345688999999999999999998874
No 33
>COG4412 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.41 E-value=40 Score=32.09 Aligned_cols=29 Identities=34% Similarity=0.555 Sum_probs=21.7
Q ss_pred hhhhccCCCCCCCCCCCCC-------ccccccCCCCce
Q psy2553 44 VRRRFKGQYLMPNIGYGSA-------KKTRHMLPNHFL 74 (134)
Q Consensus 44 vRrr~kG~~~mp~iGYgS~-------k~tr~l~PsGf~ 74 (134)
.--+++|+.- | +||+|- -++.|++|+||.
T Consensus 364 ydtqy~GtgE-P-VgYwsImssGsWaGki~Gt~p~gFs 399 (760)
T COG4412 364 YDTQYKGTGE-P-VGYWSIMSSGSWAGKIKGTLPGGFS 399 (760)
T ss_pred cccccccCCC-c-ccceeeecccccccccCCcCCcccc
Confidence 3356788664 5 899873 578999999985
No 34
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=25.41 E-value=34 Score=21.20 Aligned_cols=28 Identities=21% Similarity=0.424 Sum_probs=18.5
Q ss_pred ccHHHHHHHH-HhcCCceecCCcceeecc
Q psy2553 105 KKRRDIVQRA-QQLSIRLTNGNARIRTEE 132 (134)
Q Consensus 105 kkr~~I~erA-~el~irV~N~~arl~~~e 132 (134)
..-++|++.+ .++|+.+.|++.-|-.++
T Consensus 15 v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~ 43 (54)
T PF04760_consen 15 VPSKEIIKKLFKELGIMVKSINSSLDEEE 43 (54)
T ss_dssp SSHHHHHHHH-HHHTS---SSSS-EETTG
T ss_pred cCHHHHHHHHHHhCCcCcCCCCCcCCHHH
Confidence 4678899999 669999899888775544
No 35
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=25.21 E-value=28 Score=27.70 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=23.3
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
.|+.+.|+.|.+-|+|||. +.|+.||-
T Consensus 27 ~vs~~tr~rV~~~a~~lgY-~pn~~a~~ 53 (329)
T TIGR01481 27 NVKPATRKKVLEVIKRLDY-RPNAVARG 53 (329)
T ss_pred CCCHHHHHHHHHHHHHHCC-CCCHHHHH
Confidence 6999999999999999999 56776653
No 36
>PF10126 Nit_Regul_Hom: Uncharacterized protein, homolog of nitrogen regulatory protein PII; InterPro: IPR019296 This family consists of various hypothetical archaeal proteins. It includes a putative nitrogen regulatory protein PII homolog.
Probab=25.21 E-value=64 Score=24.19 Aligned_cols=51 Identities=16% Similarity=0.255 Sum_probs=37.7
Q ss_pred cccccCCCCceEEEEechhhhHHHh---hcCccceEEeeccCCcccHHHHHHHHHh
Q psy2553 64 KTRHMLPNHFLKVVVHNVKELEVLM---MQNRKYCAEIGHAVSSKKRRDIVQRAQQ 116 (134)
Q Consensus 64 ~tr~l~PsGf~~~lV~n~keLe~L~---~~~~~~~~~Ia~~Vg~kkr~~I~erA~e 116 (134)
+-|||-|.-|+.|++. +|.|.-. -+-...|+-|..-|+.++...|.+..+|
T Consensus 35 eYkGmSP~~wkgf~l~--EDpe~ai~~I~d~s~~aV~I~TVV~~~~~~~i~~~i~e 88 (110)
T PF10126_consen 35 EYKGMSPQDWKGFLLD--EDPEMAIKAINDLSENAVLIGTVVDEEKVEKIEKLIKE 88 (110)
T ss_pred eecCCChHHhcCcccc--cCHHHHHHHHHHhccCcEEEEEEECHHHHHHHHHHHHH
Confidence 4588999999999877 6666542 2223468888888898888888887766
No 37
>PRK09526 lacI lac repressor; Reviewed
Probab=24.57 E-value=29 Score=27.72 Aligned_cols=27 Identities=26% Similarity=0.327 Sum_probs=23.6
Q ss_pred ccCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
..||.+.|+.|.+-|+|||. +.|..||
T Consensus 30 ~~vs~~tr~rV~~~a~elgY-~pn~~a~ 56 (342)
T PRK09526 30 SHVSAKTREKVEAAMAELNY-VPNRVAQ 56 (342)
T ss_pred CCCCHHHHHHHHHHHHHHCC-CcCHHHH
Confidence 46999999999999999998 6777776
No 38
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.45 E-value=53 Score=25.76 Aligned_cols=45 Identities=16% Similarity=0.085 Sum_probs=33.7
Q ss_pred hhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCCcceeeccc
Q psy2553 82 KELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGNARIRTEEN 133 (134)
Q Consensus 82 keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~arl~~~e~ 133 (134)
.|...+- ..+...+.|-+-+| +..++-+.|..|+||++|+-.++|
T Consensus 56 aD~~Iv~-~a~~gDlVVT~Di~------LA~~ll~kg~~v~~prGr~y~~~n 100 (150)
T COG1671 56 ADDWIVN-LAEKGDLVVTADIP------LASLLLDKGAAVLNPRGRLYTEEN 100 (150)
T ss_pred HHHHHHH-hCCCCCEEEECchH------HHHHHHhcCCEEECCCCcccCHhH
Confidence 3444333 34667777777766 677888999999999999998876
No 39
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=24.39 E-value=23 Score=27.53 Aligned_cols=39 Identities=18% Similarity=0.348 Sum_probs=30.5
Q ss_pred hhhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCc
Q psy2553 81 VKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIR 120 (134)
Q Consensus 81 ~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~ir 120 (134)
++.|..|..+ .--+.+||..+|.-.|.+++.+|.-||+.
T Consensus 8 ~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hRlgL~ 46 (162)
T PF07750_consen 8 VERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHRLGLS 46 (162)
T ss_pred HHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhccccc
Confidence 4556666433 34577999999999999999999999974
No 40
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=24.22 E-value=32 Score=21.31 Aligned_cols=12 Identities=50% Similarity=0.808 Sum_probs=9.3
Q ss_pred CCCCCCCCCccc
Q psy2553 54 MPNIGYGSAKKT 65 (134)
Q Consensus 54 mp~iGYgS~k~t 65 (134)
-|+|||-|++=.
T Consensus 6 cpkiGYCS~~Cs 17 (39)
T PF08189_consen 6 CPKIGYCSSKCS 17 (39)
T ss_pred Ccccceeccccc
Confidence 489999998643
No 41
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=23.75 E-value=2.3e+02 Score=19.56 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=34.2
Q ss_pred hhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCCceecCC
Q psy2553 83 ELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNGN 125 (134)
Q Consensus 83 eLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~irV~N~~ 125 (134)
-|..|- .++-..+-||...+..-++.|...|.+.+|.|....
T Consensus 16 vlkaIk-~gkakLViiA~Da~~~~~k~i~~~c~~~~Vpv~~~~ 57 (82)
T PRK13601 16 TLKAIT-NCNVLQVYIAKDAEEHVTKKIKELCEEKSIKIVYID 57 (82)
T ss_pred HHHHHH-cCCeeEEEEeCCCCHHHHHHHHHHHHhCCCCEEEeC
Confidence 344443 467788999999999999999999999999886543
No 42
>PF05171 HemS: Haemin-degrading HemS.ChuX domain; InterPro: IPR007845 The Yersinia enterocolitica O:8 periplasmic binding protein-dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS. The structure for HemS has been solved and consists of a tandem repeat of the domain represented in this entry[].; GO: 0006826 iron ion transport; PDB: 2HQ2_A 2J0R_A 2J0P_A 1U9T_A.
Probab=23.71 E-value=1.4e+02 Score=21.68 Aligned_cols=42 Identities=17% Similarity=0.267 Sum_probs=29.7
Q ss_pred chhhhHHHhhcCccceEEeeccCCcccHHHHHHHHHhcCC----ceecCCc
Q psy2553 80 NVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSI----RLTNGNA 126 (134)
Q Consensus 80 n~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~I~erA~el~i----rV~N~~a 126 (134)
++.|++.|......+|.++... =.+|++.++++|+ -|-|+.|
T Consensus 1 ~vse~~~l~~~~~~~a~rl~~~-----~~~lL~~l~~~g~~vm~~vrN~g~ 46 (129)
T PF05171_consen 1 GVSEAELLAAAGGDFARRLDAD-----FPALLEALAELGLPVMAFVRNPGA 46 (129)
T ss_dssp TS-HHHHHHHSCTTTEEEE-TH-----HHHHHHHHHHHT-SEEEEEEESSE
T ss_pred CcCHHHHHHhcCCCCEEEhhHh-----HHHHHHHHHHcCCcEEEEECCCce
Confidence 4678888876777889998833 5899999999994 3456654
No 43
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=23.70 E-value=41 Score=26.89 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=24.1
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCccee
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNARIR 129 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~arl~ 129 (134)
.|+.+.|+.|.+.|+|||. +-|..+++.
T Consensus 29 ~vs~~tr~rV~~~a~~lgY-~pn~~~~~~ 56 (327)
T PRK10339 29 NVKEETKHRILEIAEKLEY-KTSSARKLQ 56 (327)
T ss_pred CcCHHHHHHHHHHHHHhCC-CCchhhhhh
Confidence 3899999999999999999 678877764
No 44
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=23.18 E-value=35 Score=27.58 Aligned_cols=27 Identities=26% Similarity=0.388 Sum_probs=23.2
Q ss_pred ccCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
..|+.+.|+.|.+.|+|||. +-|..||
T Consensus 26 ~~Vs~~tr~kV~~~a~elgY-~pn~~a~ 52 (346)
T PRK10401 26 ALVSADTREAVMKAVSELGY-RPNANAQ 52 (346)
T ss_pred CCCCHHHHHHHHHHHHHHCC-CCCHHHH
Confidence 36999999999999999997 6777665
No 45
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=22.90 E-value=1.5e+02 Score=26.56 Aligned_cols=26 Identities=4% Similarity=0.028 Sum_probs=21.3
Q ss_pred eccCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 99 GHAVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 99 a~~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
||.|+ .++.++|++.|+.|.+.++=+
T Consensus 117 AHGv~----~~v~~~~~~rgl~iiDATCP~ 142 (387)
T PRK13371 117 AFGAT----VQEMQLLNEKGCHIVDTTCPW 142 (387)
T ss_pred CCCCC----HHHHHHHHHCCCeEEecCCcc
Confidence 77776 578899999999999988643
No 46
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=22.81 E-value=1.7e+02 Score=24.81 Aligned_cols=48 Identities=17% Similarity=0.295 Sum_probs=31.9
Q ss_pred EEechhhhHHHhhcC------------ccceEEe-eccCCcccHHHHHHHHHhcCCceecCCcce
Q psy2553 77 VVHNVKELEVLMMQN------------RKYCAEI-GHAVSSKKRRDIVQRAQQLSIRLTNGNARI 128 (134)
Q Consensus 77 lV~n~keLe~L~~~~------------~~~~~~I-a~~Vg~kkr~~I~erA~el~irV~N~~arl 128 (134)
+|||+..++.|-... ..-.+-| ||.|+ .++.+.|++.|+.|.+.++=+
T Consensus 38 iIHN~~Vv~~L~~~Gv~~~v~~~~~v~~~~~ViirAHGv~----~~~~~~~~~~gl~viDaTCP~ 98 (280)
T TIGR00216 38 IVHNPQVVERLRERGVFFFLEDLDEVAAGDTVIIRAHGVP----PEVREELEKKGLEVIDATCPL 98 (280)
T ss_pred CccCHHHHHHHHHCCCEEeecCcccCCCCCEEEEeCCCCC----HHHHHHHHHCCCeEEeCCCcc
Confidence 678888777773211 0111222 78877 578889999999999988643
No 47
>PRK09492 treR trehalose repressor; Provisional
Probab=22.35 E-value=35 Score=26.91 Aligned_cols=27 Identities=22% Similarity=0.238 Sum_probs=23.1
Q ss_pred ccCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
..|+...|+.|.+.|.|||. +.|..||
T Consensus 29 ~~vs~~tr~rV~~~a~elgY-~pn~~a~ 55 (315)
T PRK09492 29 SGVSEETRERVEAVINQHGF-SPSKSAR 55 (315)
T ss_pred CCCCHHHHHHHHHHHHHHCC-CcCHHHH
Confidence 46899999999999999998 6776665
No 48
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=22.24 E-value=37 Score=27.18 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=23.1
Q ss_pred ccCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
..||...|+.|.+-|+|||. +-|..||
T Consensus 30 ~~vs~~tr~rV~~~a~elgY-~pn~~a~ 56 (331)
T PRK14987 30 EQVSVALRGKIAAALDELGY-IPNRAPD 56 (331)
T ss_pred CCCCHHHHHHHHHHHHHhCC-CccHHHH
Confidence 36899999999999999998 5777665
No 49
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.16 E-value=41 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.157 Sum_probs=23.0
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
.|+.+.|+.|.+.|+|||. +.|..||
T Consensus 24 ~vs~~tr~rV~~~a~~lgY-~pn~~a~ 49 (327)
T PRK10423 24 FVSEAITAKVEAAIKELNY-APSALAR 49 (327)
T ss_pred CCCHHHHHHHHHHHHHHCC-CccHHHH
Confidence 6999999999999999998 5777776
No 50
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=21.74 E-value=37 Score=27.05 Aligned_cols=27 Identities=30% Similarity=0.297 Sum_probs=23.1
Q ss_pred ccCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 100 HAVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 100 ~~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
..||...|+.|.+.|+|||. +.|..||
T Consensus 26 ~~vs~~tr~rV~~~a~~lgY-~pn~~a~ 52 (311)
T TIGR02405 26 PKVSIETRERVEQVIQQSGF-VPSKSAR 52 (311)
T ss_pred CCCCHHHHHHHHHHHHHHCC-CcCHHHH
Confidence 46899999999999999997 6777765
No 51
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=21.61 E-value=1.6e+02 Score=24.96 Aligned_cols=58 Identities=26% Similarity=0.352 Sum_probs=41.5
Q ss_pred cCCCcCC-----chhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEec-hhhhHHHhhcCccceEEee
Q psy2553 35 RKPKGID-----NRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHN-VKELEVLMMQNRKYCAEIG 99 (134)
Q Consensus 35 RKPrGiD-----nkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n-~keLe~L~~~~~~~~~~Ia 99 (134)
-||.|+. +++|+.++- .+||.+..=. -+.+|.=.+.|.. .+-++-|+..+++|.+++-
T Consensus 6 ~KP~G~tS~dvv~~vrr~~~~----kKvGH~GTLD---P~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~ 69 (279)
T PRK02193 6 YKPKGISSFKFIKNFAKTNNI----KKIGHTGTLD---PLASGLLLVATDEDTKLIDYLDQKDKTYIAKIK 69 (279)
T ss_pred ECCCCCCHHHHHHHHHHHcCC----CccccCccCC---CcCeeEEEEEEChhhhhhHHhccCCcEEEEEEE
Confidence 4899998 577776644 3788776433 3567777788874 6677777767899998874
No 52
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=21.30 E-value=1.9e+02 Score=24.96 Aligned_cols=58 Identities=26% Similarity=0.410 Sum_probs=41.3
Q ss_pred cCCCcCC-----chhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEec-hhhhHHHhhcCccceEEee
Q psy2553 35 RKPKGID-----NRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHN-VKELEVLMMQNRKYCAEIG 99 (134)
Q Consensus 35 RKPrGiD-----nkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n-~keLe~L~~~~~~~~~~Ia 99 (134)
-||.|+. +++|+.++ +.+||.+..=. -+.+|.=.+.|.+ .+-++.|+..+++|-+++-
T Consensus 9 ~KP~G~TS~dvv~~vrr~l~----~kKvGH~GTLD---P~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~ 72 (308)
T PRK14124 9 YKPKGPTSHDVVDEVRKKLK----TRKVGHAGTLD---PFATGVLIVGVNKATRLLEYLKNEKKVYYVKMR 72 (308)
T ss_pred ECCCCCCHHHHHHHHHHHcC----CCccCcCcCCC---CCCcEEEEEEEChHHhhhHHHhcCCceEEEEEE
Confidence 4899999 57888775 34788776433 2457777777775 5667777667899988873
No 53
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=21.25 E-value=1.8e+02 Score=24.80 Aligned_cols=58 Identities=21% Similarity=0.348 Sum_probs=42.2
Q ss_pred cCCCcCC-----chhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEec-hhhhHHHhhcCccceEEee
Q psy2553 35 RKPKGID-----NRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHN-VKELEVLMMQNRKYCAEIG 99 (134)
Q Consensus 35 RKPrGiD-----nkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n-~keLe~L~~~~~~~~~~Ia 99 (134)
-||.|+. +++|+-++ ..+||.+..=. -+.+|.=.+.|.. .+-++-|+..+++|.+++-
T Consensus 9 ~KP~G~TS~dvv~~vrk~~~----~kKvGH~GTLD---P~AtGvL~v~vG~aTKl~~~l~~~~K~Y~~~~~ 72 (292)
T PRK01528 9 YKPRGISSAKLVSIVKKILG----KVKIGHAGTLD---VEAEGVLPLAVGEATKLVQLLIDAKKTYIFTVK 72 (292)
T ss_pred eCCCCCCHHHHHHHHHHHcC----CCccCcCccCC---CcCceEEEEEEChHhhhhHHHhcCCceEEEEEE
Confidence 4899999 57887774 34788776432 3567777777774 6778888777999998874
No 54
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=20.57 E-value=2.1e+02 Score=24.43 Aligned_cols=51 Identities=12% Similarity=0.036 Sum_probs=42.9
Q ss_pred ceEEEEechhhhHHHhhcCccceEEeeccCCcccHHH-HHHHHHhcCCceec
Q psy2553 73 FLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRD-IVQRAQQLSIRLTN 123 (134)
Q Consensus 73 f~~~lV~n~keLe~L~~~~~~~~~~Ia~~Vg~kkr~~-I~erA~el~irV~N 123 (134)
-..++++-.++...++...+...+-|||.|+..--.. |-..|.+++|....
T Consensus 129 kp~~LvsG~n~VtkaIekkKAkLVIIA~DVsPie~vk~LpaLCrk~~VPY~i 180 (263)
T PTZ00222 129 APLAVVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAI 180 (263)
T ss_pred CCCeeccCHHHHHHHHHcCCceEEEEeCCCCHHHHHHHHHHHHHhcCCCEEE
Confidence 3467888888888888888999999999999888865 89999999986543
No 55
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=20.36 E-value=40 Score=27.03 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=22.3
Q ss_pred cCCcccHHHHHHHHHhcCCceecCCcc
Q psy2553 101 AVSSKKRRDIVQRAQQLSIRLTNGNAR 127 (134)
Q Consensus 101 ~Vg~kkr~~I~erA~el~irV~N~~ar 127 (134)
.||...|+.|.+.|+|||. +-|..||
T Consensus 27 ~vs~~tr~~V~~~a~elgY-~pn~~a~ 52 (341)
T PRK10703 27 FVAEETRNAVWAAIKELHY-SPSAVAR 52 (341)
T ss_pred CCCHHHHHHHHHHHHHHCC-CcCHHHH
Confidence 6899999999999999998 4676665
No 56
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=20.35 E-value=2e+02 Score=25.46 Aligned_cols=57 Identities=21% Similarity=0.364 Sum_probs=41.4
Q ss_pred cCCCcCC-----chhhhhccCCCCCCCCCCCCCccccccCCCCceEEEEec-hhhhHHHhhcCccceEEe
Q psy2553 35 RKPKGID-----NRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKVVVHN-VKELEVLMMQNRKYCAEI 98 (134)
Q Consensus 35 RKPrGiD-----nkvRrr~kG~~~mp~iGYgS~k~tr~l~PsGf~~~lV~n-~keLe~L~~~~~~~~~~I 98 (134)
-||.|+. +++|+.++- -+||.+..=. -+.+|.=.+.|.. .+-++-++.++++|-+++
T Consensus 9 dKP~G~TS~dvv~~vrk~l~~----kKVGH~GTLD---P~AtGVL~i~vG~aTKl~~~l~~~~K~Y~a~~ 71 (345)
T PRK14846 9 YKPRGISSAQLVSIVKKILGK----TKIGHAGTLD---VEAEGILPFAVGEATKLIHLLIDARKTYIFTV 71 (345)
T ss_pred eCCCCCCHHHHHHHHHHHhCC----CcCCcCccCC---CcCceEEEEEEChhhhhhHHHhcCCceEEEEE
Confidence 4899999 678877753 4788776432 2466766777764 677888877789998877
Done!