Query psy12657
Match_columns 260
No_of_seqs 153 out of 932
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 16:11:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12657.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12657hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00084 rpl19 ribosomal prote 100.0 4.8E-39 1E-43 263.3 10.9 93 6-98 16-109 (117)
2 TIGR01024 rplS_bact ribosomal 100.0 8.5E-39 1.8E-43 260.5 10.8 93 6-98 12-105 (113)
3 PRK05338 rplS 50S ribosomal pr 100.0 7.5E-39 1.6E-43 261.8 10.5 92 7-98 13-105 (116)
4 PF01245 Ribosomal_L19: Riboso 100.0 1.4E-38 3E-43 258.5 11.4 95 4-98 10-105 (113)
5 COG0335 RplS Ribosomal protein 100.0 2.7E-38 6E-43 258.2 9.7 93 6-98 14-107 (115)
6 KOG1698|consensus 100.0 1.5E-37 3.2E-42 273.3 8.5 117 1-160 85-201 (201)
7 KOG1698|consensus 98.2 4E-07 8.8E-12 81.4 1.6 37 69-115 153-189 (201)
8 PF01245 Ribosomal_L19: Riboso 98.0 3.8E-06 8.3E-11 68.9 3.3 43 98-140 62-104 (113)
9 TIGR01024 rplS_bact ribosomal 97.9 5.4E-06 1.2E-10 68.4 2.4 43 99-141 63-105 (113)
10 PRK05338 rplS 50S ribosomal pr 97.7 1.5E-05 3.3E-10 66.0 2.0 44 99-142 63-106 (116)
11 CHL00084 rpl19 ribosomal prote 97.6 2.7E-05 5.9E-10 64.6 2.3 44 98-141 66-109 (117)
12 COG0335 RplS Ribosomal protein 96.8 0.00066 1.4E-08 56.6 1.7 41 98-138 64-104 (115)
13 PF05641 Agenet: Agenet domain 78.5 7.2 0.00016 28.7 5.5 38 13-55 1-38 (68)
14 smart00743 Agenet Tudor-like d 71.1 26 0.00055 24.6 6.6 49 11-67 1-49 (61)
15 TIGR03170 flgA_cterm flagella 57.7 30 0.00066 27.3 5.4 50 9-63 62-111 (122)
16 PF13144 SAF_2: SAF-like 52.8 40 0.00086 28.8 5.7 52 6-62 133-184 (196)
17 cd04497 hPOT1_OB1_like hPOT1_O 52.7 22 0.00048 29.3 4.0 52 5-63 61-112 (138)
18 PF12969 DUF3857: Domain of Un 50.7 18 0.00039 29.4 3.2 21 7-27 84-104 (177)
19 PF02765 POT1: Telomeric singl 42.9 12 0.00027 31.0 1.1 51 5-63 65-117 (146)
20 PRK04183 glutamyl-tRNA(Gln) am 42.6 39 0.00085 33.5 4.6 57 12-83 2-58 (419)
21 PF14462 Prok-E2_E: Prokaryoti 42.3 21 0.00046 30.1 2.4 55 139-194 51-113 (122)
22 COG2139 RPL21A Ribosomal prote 37.9 33 0.00071 28.4 2.8 43 10-52 30-76 (98)
23 COG3269 Predicted RNA-binding 37.8 2E+02 0.0043 22.6 7.1 52 2-53 2-54 (73)
24 smart00739 KOW KOW (Kyprides, 36.6 87 0.0019 18.3 3.9 27 12-44 1-27 (28)
25 cd08544 Reeler Reeler, the N-t 36.5 82 0.0018 25.4 4.9 31 12-46 29-59 (135)
26 PRK01191 rpl24p 50S ribosomal 36.1 74 0.0016 26.9 4.7 60 12-79 45-106 (120)
27 PRK07018 flgA flagellar basal 35.4 89 0.0019 28.1 5.4 51 8-63 172-222 (235)
28 cd01737 LSm16_N LSm16 belongs 35.3 67 0.0014 24.7 3.9 34 15-55 5-38 (62)
29 PF03888 MucB_RseB: MucB/RseB 34.6 1.5E+02 0.0033 27.5 6.9 49 31-82 9-57 (285)
30 PF12701 LSM14: Scd6-like Sm d 34.1 1.3E+02 0.0029 24.2 5.7 39 14-60 6-45 (96)
31 PRK03999 translation initiatio 33.4 71 0.0015 26.7 4.2 58 7-69 5-62 (129)
32 cd06462 Peptidase_S24_S26 The 33.3 1.1E+02 0.0023 21.6 4.6 43 10-60 11-53 (84)
33 TIGR00405 L26e_arch ribosomal 30.9 2.8E+02 0.0061 22.7 7.3 37 11-53 85-121 (145)
34 cd01288 FabZ FabZ is a 17kD be 29.7 87 0.0019 24.1 3.9 27 13-39 88-114 (131)
35 PF02211 NHase_beta: Nitrile h 28.6 62 0.0013 29.7 3.3 39 6-44 128-170 (222)
36 TIGR01080 rplX_A_E ribosomal p 28.0 1.2E+02 0.0026 25.3 4.6 59 12-78 41-101 (114)
37 PF07238 PilZ: PilZ domain; I 27.9 1.3E+02 0.0028 21.4 4.3 32 12-45 44-75 (102)
38 COG1566 EmrA Multidrug resista 27.3 2E+02 0.0043 28.2 6.6 59 6-67 252-319 (352)
39 PRK08559 nusG transcription an 27.0 3.3E+02 0.0072 22.9 7.2 41 11-59 93-133 (153)
40 KOG3409|consensus 26.7 1.1E+02 0.0023 28.1 4.4 38 8-64 118-155 (193)
41 PRK06005 flgA flagellar basal 25.8 1.7E+02 0.0037 25.3 5.3 51 9-64 97-147 (160)
42 PF08776 VASP_tetra: VASP tetr 25.1 65 0.0014 22.8 2.1 15 226-240 9-23 (40)
43 PF12961 DUF3850: Domain of Un 24.4 1E+02 0.0023 24.0 3.4 26 12-43 28-53 (72)
44 TIGR01750 fabZ beta-hydroxyacy 23.7 1.2E+02 0.0025 24.2 3.7 28 12-39 97-124 (140)
45 cd00493 FabA_FabZ FabA/Z, beta 23.5 1.3E+02 0.0028 22.9 3.9 30 12-41 88-117 (131)
46 PRK00006 fabZ (3R)-hydroxymyri 23.4 1.3E+02 0.0028 24.3 4.0 27 13-39 102-128 (147)
47 PRK08515 flgA flagellar basal 22.9 1.9E+02 0.0041 26.1 5.2 50 8-63 161-210 (222)
48 PRK15136 multidrug efflux syst 22.6 1.6E+02 0.0035 28.2 5.1 33 8-43 261-293 (390)
49 PF11302 DUF3104: Protein of u 22.2 3.3E+02 0.0072 21.5 5.8 51 10-60 3-58 (75)
50 PRK04306 50S ribosomal protein 22.1 1E+02 0.0022 25.3 3.1 44 10-53 32-79 (98)
51 PF02014 Reeler: Reeler domain 22.0 79 0.0017 25.5 2.5 32 11-46 28-59 (132)
52 PRK12786 flgA flagellar basal 21.7 2.4E+02 0.0052 27.3 6.0 50 10-64 256-305 (338)
53 PF07313 DUF1460: Protein of u 21.0 2.8E+02 0.0061 25.3 6.0 43 10-61 151-194 (216)
54 PRK09455 rseB anti-sigma E fac 20.9 3.8E+02 0.0082 25.6 7.1 51 28-81 37-87 (319)
55 PF14438 SM-ATX: Ataxin 2 SM d 20.5 2.6E+02 0.0056 20.7 4.8 36 14-55 10-45 (77)
56 PF07703 A2M_N_2: Alpha-2-macr 20.4 4.2E+02 0.0091 20.6 7.2 73 10-98 7-79 (136)
57 TIGR00922 nusG transcription t 20.1 3.7E+02 0.0079 22.5 6.2 29 11-45 118-146 (172)
No 1
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00 E-value=4.8e-39 Score=263.35 Aligned_cols=93 Identities=26% Similarity=0.442 Sum_probs=91.0
Q ss_pred cCCCCCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeeccc
Q psy12657 6 SVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKR 84 (260)
Q Consensus 6 ~~~diPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrgKV 84 (260)
.+.++|+|+|||+|+|++.+.| +|+|+|.|+|+||+++++|+++||||||+++|+|||++||+|||.|++|+|+++|++
T Consensus 16 ~~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~gkv 95 (117)
T CHL00084 16 LKKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLLHSPKLASIEVLRRSKV 95 (117)
T ss_pred hhcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEecCCCccceEEEEEeCcc
Confidence 3578999999999999999998 899999999999999999999999999999999999999999999999999999999
Q ss_pred cccceehhhccCcc
Q psy12657 85 LDDDLLYLRDALPN 98 (260)
Q Consensus 85 RRAKLYYLRdr~gK 98 (260)
|||||||||++.||
T Consensus 96 RRAKLyYLR~~~gK 109 (117)
T CHL00084 96 RRAKLYYLRNRVGK 109 (117)
T ss_pred chheeEEeccCcCh
Confidence 99999999999999
No 2
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=100.00 E-value=8.5e-39 Score=260.48 Aligned_cols=93 Identities=28% Similarity=0.461 Sum_probs=91.2
Q ss_pred cCCCCCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeeccc
Q psy12657 6 SVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKR 84 (260)
Q Consensus 6 ~~~diPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrgKV 84 (260)
.+.++|+|+|||+|+|++.+.| +|+|+|.|+|+||+++++|+++||||||+++|+|||++||||||.|++|+|+++|++
T Consensus 12 ~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl~~~kv 91 (113)
T TIGR01024 12 LKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPLHSPNIDSIEVVRRGKV 91 (113)
T ss_pred hhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEcCCCccceEEEEEeCcc
Confidence 3678999999999999999999 899999999999999999999999999999999999999999999999999999999
Q ss_pred cccceehhhccCcc
Q psy12657 85 LDDDLLYLRDALPN 98 (260)
Q Consensus 85 RRAKLYYLRdr~gK 98 (260)
|||||||||++.||
T Consensus 92 rRaKLyYLR~~~gK 105 (113)
T TIGR01024 92 RRAKLYYLRERRGK 105 (113)
T ss_pred chhheeeeccCcch
Confidence 99999999999999
No 3
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00 E-value=7.5e-39 Score=261.82 Aligned_cols=92 Identities=29% Similarity=0.479 Sum_probs=90.5
Q ss_pred CCCCCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeecccc
Q psy12657 7 VIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKRL 85 (260)
Q Consensus 7 ~~diPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrgKVR 85 (260)
+.++|+|+|||+|+|++.+.| +|+|+|.|+|+||+++++|+++||||||+++|+|||++||||||.|++|+|+++|++|
T Consensus 13 ~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~gkvR 92 (116)
T PRK05338 13 RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLHSPRIDSIEVVRRGKVR 92 (116)
T ss_pred hcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCCCCcccEEEEEEecccc
Confidence 478999999999999999998 8999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceehhhccCcc
Q psy12657 86 DDDLLYLRDALPN 98 (260)
Q Consensus 86 RAKLYYLRdr~gK 98 (260)
||||||||++.||
T Consensus 93 RAKLyYLR~~~gK 105 (116)
T PRK05338 93 RAKLYYLRELRGK 105 (116)
T ss_pred hhheeeeccCcch
Confidence 9999999999999
No 4
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=100.00 E-value=1.4e-38 Score=258.47 Aligned_cols=95 Identities=36% Similarity=0.574 Sum_probs=92.1
Q ss_pred cccCCCCCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeec
Q psy12657 4 RRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLE 82 (260)
Q Consensus 4 Rr~~~diPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrg 82 (260)
...+.++|+|+|||+|+|++.+.| +++|+|.|+|+||+++++|++|||||||+++|+|||++||||||.|++|+|++++
T Consensus 10 ~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~~ 89 (113)
T PF01245_consen 10 EQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRG 89 (113)
T ss_dssp TTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEB
T ss_pred HHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEec
Confidence 345689999999999999999997 8999999999999999999999999999999999999999999999999999999
Q ss_pred cccccceehhhccCcc
Q psy12657 83 KRLDDDLLYLRDALPN 98 (260)
Q Consensus 83 KVRRAKLYYLRdr~gK 98 (260)
++|||||||||++.||
T Consensus 90 kvrRaKLyYLR~~~gK 105 (113)
T PF01245_consen 90 KVRRAKLYYLRDRKGK 105 (113)
T ss_dssp ECSSSSTGGGGCTTSH
T ss_pred ccchhhhhhhhcCccc
Confidence 9999999999999998
No 5
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-38 Score=258.23 Aligned_cols=93 Identities=29% Similarity=0.459 Sum_probs=90.9
Q ss_pred cCCCCCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeeccc
Q psy12657 6 SVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKR 84 (260)
Q Consensus 6 ~~~diPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrgKV 84 (260)
...++|+|+|||+|+|++.+.| +|+|+|.|+|+|||++|+|+++|||||++++|+|||++||+|||.|++|+|+++|+|
T Consensus 14 ~~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~rrGkV 93 (115)
T COG0335 14 IKKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPLHSPLIESIEVVRRGKV 93 (115)
T ss_pred HHhhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeecCCCceeEEEEEecCce
Confidence 3567999999999999999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred cccceehhhccCcc
Q psy12657 85 LDDDLLYLRDALPN 98 (260)
Q Consensus 85 RRAKLYYLRdr~gK 98 (260)
|||||||||++.||
T Consensus 94 RRAKLYYLR~~~GK 107 (115)
T COG0335 94 RRAKLYYLRERRGK 107 (115)
T ss_pred eeeeeEeeeccccc
Confidence 99999999999999
No 6
>KOG1698|consensus
Probab=100.00 E-value=1.5e-37 Score=273.32 Aligned_cols=117 Identities=49% Similarity=0.842 Sum_probs=110.4
Q ss_pred CcccccCCCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEee
Q psy12657 1 MIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLR 80 (260)
Q Consensus 1 m~~Rr~~~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlr 80 (260)
|+.|+...++|+|+|||+|+|++.+++++.++..|.||||+++++|+++||+|||++.|+|||.+
T Consensus 85 ~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~atf~LRnvIagvGVEi~--------------- 149 (201)
T KOG1698|consen 85 VLERRKVRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLNATFLLRNVIAGVGVEIV--------------- 149 (201)
T ss_pred HHHHHhcccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCCcceEEeeehhhCceeEEE---------------
Confidence 67899999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccccccceehhhccCcccccccceeeEEeecCCCCcceeEEEeeeecccchhHhHhhCCCCCCccCCCcccccCCCCCc
Q psy12657 81 LEKRLDDDLLYLRDALPNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPV 160 (260)
Q Consensus 81 rgKVRRAKLYYLRdr~gK~v~g~gv~iky~~y~p~i~~i~vl~lekrld~~l~ylrda~~~~~t~~~~m~p~~~~~~~~v 160 (260)
|++|||+|++|+||++||++|+.|.|||||+|+||||+++|+|..+++|++|
T Consensus 150 ----------------------------~pLYsP~IkeI~Vlk~~k~rra~LyYLRd~lp~lstfd~~m~~~~~~~~~~~ 201 (201)
T KOG1698|consen 150 ----------------------------FPLYSPNIKEIKVLKLEKRRRAKLYYLRDALPELSTFDANMRPKKEENGHKV 201 (201)
T ss_pred ----------------------------EeccCCCeeEEEEechhhcccchhhhhhccccccCchhhccccccccCCCCC
Confidence 5566667777888899999999999999999999999999999999999885
No 7
>KOG1698|consensus
Probab=98.23 E-value=4e-07 Score=81.39 Aligned_cols=37 Identities=51% Similarity=0.899 Sum_probs=34.0
Q ss_pred cCCccceEEEeeeccccccceehhhccCcccccccceeeEEeecCCC
Q psy12657 69 YDPTIHNITVLRLEKRLDDDLLYLRDALPNVVDNLGIEIAYDMYDPT 115 (260)
Q Consensus 69 ySP~I~sIeVlrrgKVRRAKLYYLRdr~gK~v~g~gv~iky~~y~p~ 115 (260)
|||+|++|+|++..+++||+||||||..+. |..|+-+
T Consensus 153 YsP~IkeI~Vlk~~k~rra~LyYLRd~lp~----------lstfd~~ 189 (201)
T KOG1698|consen 153 YSPNIKEIKVLKLEKRRRAKLYYLRDALPE----------LSTFDAN 189 (201)
T ss_pred cCCCeeEEEEechhhcccchhhhhhccccc----------cCchhhc
Confidence 899999999999999999999999999998 8777543
No 8
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=98.03 E-value=3.8e-06 Score=68.92 Aligned_cols=43 Identities=37% Similarity=0.621 Sum_probs=40.5
Q ss_pred ccccccceeeEEeecCCCCcceeEEEeeeecccchhHhHhhCC
Q psy12657 98 NVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALP 140 (260)
Q Consensus 98 K~v~g~gv~iky~~y~p~i~~i~vl~lekrld~~l~ylrda~~ 140 (260)
+++.|+|||..|.+|||.|++|+|++..+..+..|.||||+..
T Consensus 62 ~~~~g~gVE~~f~l~SP~I~~IeV~~~~kvrRaKLyYLR~~~g 104 (113)
T PF01245_consen 62 NISQGVGVERVFPLYSPLIKSIEVLRRGKVRRAKLYYLRDRKG 104 (113)
T ss_dssp EEETTEEEEEEEETTSTTEEEEEEEEEBECSSSSTGGGGCTTS
T ss_pred EEecCccEEEEEEcCCCCeEEEEEEEecccchhhhhhhhcCcc
Confidence 3689999999999999999999999999999999999999764
No 9
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=97.92 E-value=5.4e-06 Score=68.39 Aligned_cols=43 Identities=28% Similarity=0.470 Sum_probs=40.6
Q ss_pred cccccceeeEEeecCCCCcceeEEEeeeecccchhHhHhhCCC
Q psy12657 99 VVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQ 141 (260)
Q Consensus 99 ~v~g~gv~iky~~y~p~i~~i~vl~lekrld~~l~ylrda~~~ 141 (260)
++.|.|+|..|.+|||.|++|+|++..|..+..|.||||+...
T Consensus 63 i~~gvGVEr~fpl~SP~I~~IeVl~~~kvrRaKLyYLR~~~gK 105 (113)
T TIGR01024 63 ISYGVGVERIFPLHSPNIDSIEVVRRGKVRRAKLYYLRERRGK 105 (113)
T ss_pred eccCccEEEEEEcCCCccceEEEEEeCccchhheeeeccCcch
Confidence 5899999999999999999999999999999999999998654
No 10
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=97.73 E-value=1.5e-05 Score=66.04 Aligned_cols=44 Identities=27% Similarity=0.443 Sum_probs=40.9
Q ss_pred cccccceeeEEeecCCCCcceeEEEeeeecccchhHhHhhCCCC
Q psy12657 99 VVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQY 142 (260)
Q Consensus 99 ~v~g~gv~iky~~y~p~i~~i~vl~lekrld~~l~ylrda~~~~ 142 (260)
++.|.|+|-.|.+|||.|.+|+|++..|..+..|.||||+...-
T Consensus 63 i~~gvGVEr~fpl~SP~I~~IeV~r~gkvRRAKLyYLR~~~gK~ 106 (116)
T PRK05338 63 ISYGVGVERTFPLHSPRIDSIEVVRRGKVRRAKLYYLRELRGKA 106 (116)
T ss_pred cccCccEEEEecCCCCcccEEEEEEecccchhheeeeccCcchh
Confidence 58899999999999999999999999999999999999976543
No 11
>CHL00084 rpl19 ribosomal protein L19
Probab=97.64 E-value=2.7e-05 Score=64.65 Aligned_cols=44 Identities=30% Similarity=0.523 Sum_probs=40.9
Q ss_pred ccccccceeeEEeecCCCCcceeEEEeeeecccchhHhHhhCCC
Q psy12657 98 NVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQ 141 (260)
Q Consensus 98 K~v~g~gv~iky~~y~p~i~~i~vl~lekrld~~l~ylrda~~~ 141 (260)
+++.|.|+|-.|.+|||.|.+|+|++..|.-+..|.||||+...
T Consensus 66 ki~~gvGVEr~fpl~SP~I~~IeV~r~gkvRRAKLyYLR~~~gK 109 (117)
T CHL00084 66 KVFQGIGVERVFLLHSPKLASIEVLRRSKVRRAKLYYLRNRVGK 109 (117)
T ss_pred EeccCccEEEEEecCCCccceEEEEEeCccchheeEEeccCcCh
Confidence 35899999999999999999999999999999999999998654
No 12
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=96.77 E-value=0.00066 Score=56.58 Aligned_cols=41 Identities=29% Similarity=0.511 Sum_probs=38.9
Q ss_pred ccccccceeeEEeecCCCCcceeEEEeeeecccchhHhHhh
Q psy12657 98 NVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDA 138 (260)
Q Consensus 98 K~v~g~gv~iky~~y~p~i~~i~vl~lekrld~~l~ylrda 138 (260)
|++.|.|+|..|.+|||.|.+|+|++-=|--...|.|||+.
T Consensus 64 kis~G~GVEr~Fp~~SP~Ie~IeV~rrGkVRRAKLYYLR~~ 104 (115)
T COG0335 64 KISYGVGVERVFPLHSPLIESIEVVRRGKVRRAKLYYLRER 104 (115)
T ss_pred EeecCceEEEEeecCCCceeEEEEEecCceeeeeeEeeecc
Confidence 57999999999999999999999999999999999999975
No 13
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=78.52 E-value=7.2 Score=28.66 Aligned_cols=38 Identities=13% Similarity=0.212 Sum_probs=25.5
Q ss_pred cCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEE
Q psy12657 13 FFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 55 (260)
Q Consensus 13 F~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRn 55 (260)
|++||.|+|..... .-+-.=|.|.|++..+.+ ++.|+-
T Consensus 1 F~~G~~VEV~s~e~--g~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDED--GFRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-SB--TT--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEcCC--CCCcEEEEEEEEEeCCCc---EEEEEE
Confidence 78999999987554 347889999999999876 777775
No 14
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=71.07 E-value=26 Score=24.61 Aligned_cols=49 Identities=12% Similarity=0.200 Sum_probs=35.5
Q ss_pred CCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEe
Q psy12657 11 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYD 67 (260)
Q Consensus 11 PeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~Fp 67 (260)
..|.+||.|.|.... .-.=|.|+|++..+ +..+.|+=.-.+.|-+..|+
T Consensus 1 ~~~~~G~~Ve~~~~~-----~~~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v~ 49 (61)
T smart00743 1 SDFKKGDRVEVFSKE-----EDSWWEAVVTKVLG---DGKYLVRYLTESEPLKETVD 49 (61)
T ss_pred CCcCCCCEEEEEECC-----CCEEEEEEEEEECC---CCEEEEEECCCCcccEEEEe
Confidence 368999999999864 23679999999987 44577776544466666654
No 15
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=57.69 E-value=30 Score=27.34 Aligned_cols=50 Identities=10% Similarity=-0.061 Sum_probs=37.8
Q ss_pred CCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEE
Q psy12657 9 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 63 (260)
Q Consensus 9 diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVE 63 (260)
.-|-++-||.|.|.+.... =...--..|..+.+++.++.+||...|-=+.
T Consensus 62 ~~~~V~~G~~V~i~~~~~~-----~~i~~~g~Al~~g~~G~~I~V~N~~s~k~i~ 111 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGG-----LSVTTEGKALEDGAVGDQIRVRNLSSGKIIS 111 (122)
T ss_pred CccEEcCCCEEEEEEecCC-----EEEEEEEEEccccCCCCEEEEEECCCCCEEE
Confidence 3467899999999998764 1245566777888999999999976654443
No 16
>PF13144 SAF_2: SAF-like
Probab=52.75 E-value=40 Score=28.78 Aligned_cols=52 Identities=12% Similarity=0.033 Sum_probs=39.2
Q ss_pred cCCCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeE
Q psy12657 6 SVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGI 62 (260)
Q Consensus 6 ~~~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGV 62 (260)
.....|-++-||.|.|.+.... -...--.+|..++.+|.++.|||...|-=|
T Consensus 133 ~l~~~~~V~~G~~V~v~~~~g~-----i~i~~~g~Al~~G~~G~~I~V~N~~S~k~v 184 (196)
T PF13144_consen 133 DLEPPPLVKRGDIVTVIARSGG-----ISISTEGKALEDGALGDTIRVKNLSSGKIV 184 (196)
T ss_pred ccccceecCCCCEEEEEEEeCC-----EEEEEEEEEccCCCCCCEEEEEECCCCCEE
Confidence 3445688999999999988764 234556677888899999999997655333
No 17
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=52.67 E-value=22 Score=29.34 Aligned_cols=52 Identities=13% Similarity=0.055 Sum_probs=36.2
Q ss_pred ccCCCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEE
Q psy12657 5 RSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 63 (260)
Q Consensus 5 r~~~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVE 63 (260)
.....+|.+.+||+|.++=. ++|.|.|-..+..+. -.+++-|=+-..+..++
T Consensus 61 ~~~~~LP~v~~GDVIll~~~------kv~~~~g~~~~~~~~-~~ss~avf~~~~~~~~~ 112 (138)
T cd04497 61 PNEESLPIVKVGDIILLRRV------KIQSYNGKPQGISND-RGSSWAVFRGDDGVVPI 112 (138)
T ss_pred CChhhCCCCCCCCEEEEEEE------EEEEECCceEEEECC-CceeEEEEcCCCCCCcC
Confidence 34567998899999999743 457888888888766 45777665544444443
No 18
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=50.66 E-value=18 Score=29.37 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=13.8
Q ss_pred CCCCCCcCCCCEEEEEEEecC
Q psy12657 7 VIDIPSFFVGSILSVTSADKH 27 (260)
Q Consensus 7 ~~diPeF~vGDiV~V~~~i~E 27 (260)
...+|.+++||+|...+.+..
T Consensus 84 ~~~~p~v~~GdiIe~~y~~~~ 104 (177)
T PF12969_consen 84 VFAFPDVRVGDIIEYSYTIKS 104 (177)
T ss_dssp EEE--S--TT-EEEEEEEEEE
T ss_pred EEEcCCCCCCcEEEEEEEEEe
Confidence 367999999999999999865
No 19
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=42.88 E-value=12 Score=30.98 Aligned_cols=51 Identities=10% Similarity=0.110 Sum_probs=34.0
Q ss_pred ccCCCCCCcCC-CCEEEEE-EEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEE
Q psy12657 5 RSVIDIPSFFV-GSILSVT-SADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 63 (260)
Q Consensus 5 r~~~diPeF~v-GDiV~V~-~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVE 63 (260)
.....+|.+.. ||+|.++ +. +|.|.|-..+..+.+-++++.|= ..++.|..
T Consensus 65 ~~~~~LP~v~~~GDii~l~r~k-------v~~~~~~~~~~~~~~~~ss~~vf-~~~~~~~~ 117 (146)
T PF02765_consen 65 PHKESLPNVKSVGDIIRLRRVK-------VQSYNGKPQGLSNSTSNSSWAVF-SSGGSGAP 117 (146)
T ss_dssp SSHHHSCTTCSTTHEEEEEEEE-------EEEETTEEEEEEECECTEEEEEE-CTSSTTTC
T ss_pred CCHHHCCCCCCCCCEEEEEEEE-------EEEECCEEEEEecCCCcEEEEEE-ecCCCCCC
Confidence 33456899988 9999998 44 45666766677666666777765 33444443
No 20
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=42.60 E-value=39 Score=33.54 Aligned_cols=57 Identities=26% Similarity=0.303 Sum_probs=37.5
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeecc
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEK 83 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrgK 83 (260)
.+.+||.|+|.... ..|+|++|-... +-.-.+.|.|= .++|+..- .|.+|+++.++.
T Consensus 2 ~~~~gd~v~~~~~~-------~~~~g~~~p~~~-~~~~~~kl~~g-yn~g~~~~------~~~~~~~~~~~~ 58 (419)
T PRK04183 2 GMEVGDRVRVEKDD-------VVYEGILMPSYE-DDHIVIKLDNG-YNIGIDID------KIAEIELLEKGE 58 (419)
T ss_pred CCCCCCEEEEEECC-------eEEEEEEecCCC-CCEEEEEcCCC-ceeeeccc------cccceEEccccc
Confidence 36789999997543 689999997665 11222333332 34777654 678889888763
No 21
>PF14462 Prok-E2_E: Prokaryotic E2 family E
Probab=42.26 E-value=21 Score=30.15 Aligned_cols=55 Identities=36% Similarity=0.790 Sum_probs=40.7
Q ss_pred CCCCCCccCCCc----ccccCCCCCcc-ccceeeeecCCCccccccccC---CCCccccccccc
Q psy12657 139 LPQYSTFPFDME----PEYLLDGAPVP-INDIKVKLKPRPWVGRWERKG---YKGIDDVDQHIT 194 (260)
Q Consensus 139 ~~~~~t~~~~m~----p~~~~~~~~vp-vn~~kvk~~p~pw~~~we~~~---~~gi~~~~~~~~ 194 (260)
++-|-.-+.||- +-.+.+|.++| -...--.+.-++| .||.|++ -.|+|++..||.
T Consensus 51 P~gYP~~~~DmfY~~P~L~~~~G~~iP~~~~~~~~~~G~~w-QrWSRH~~~W~P~~D~l~T~l~ 113 (122)
T PF14462_consen 51 PPGYPDAPLDMFYVYPPLKLADGGPIPNAAEVTQTFDGRTW-QRWSRHNNPWRPGVDDLWTHLA 113 (122)
T ss_pred CCCCCCCCCCcEEECCceEccCCCcCCchhcchhhcCCeee-eeecCCCCCCCCCCCcHHHHHH
Confidence 566777777773 34778889999 6666667778999 8999984 358888876653
No 22
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=37.94 E-value=33 Score=28.37 Aligned_cols=43 Identities=12% Similarity=0.131 Sum_probs=32.1
Q ss_pred CCCcCCCCEEEEEEEecC----CCcccceEEEEEEEEecCCcCeeEE
Q psy12657 10 IPSFFVGSILSVTSADKH----DPNKTRKFVGICIQKRYCGLRHEFV 52 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E----~K~R~Q~F~GIVIarr~~Gl~sTFt 52 (260)
+-+|.+||.|.+.+.-+- --.|.|-..|+|+..+++...-.+.
T Consensus 30 l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~ 76 (98)
T COG2139 30 LQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVY 76 (98)
T ss_pred HhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEe
Confidence 568999999988765432 3678999999999999865443333
No 23
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=37.83 E-value=2e+02 Score=22.62 Aligned_cols=52 Identities=15% Similarity=0.148 Sum_probs=41.1
Q ss_pred cccccCCCCCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEE
Q psy12657 2 IKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVL 53 (260)
Q Consensus 2 ~~Rr~~~diPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtL 53 (260)
..+++...-|.+..||+-.|++.... .-.-+..++|.|+-.-+...+-+.++
T Consensus 2 ~~~~~~~~~~PVeeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a~~Gd~V~v 54 (73)
T COG3269 2 AHRREEQRTPPVEEGETYEVEIEDVGDQGDGIARVEGFVVFVPGAEVGDEVKV 54 (73)
T ss_pred ccccccCCCCCcccCCEEEEEEEEeccCCCceEEEEEEEEEeCCCCCCCeeeE
Confidence 34667777889999999999998876 55677889999999988766665544
No 24
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=36.60 E-value=87 Score=18.32 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=18.6
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEec
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRY 44 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~ 44 (260)
.|.+||.|.|.-=. ..-+.|+++++.+
T Consensus 1 ~~~~G~~V~I~~G~------~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGP------FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECC------CCCcEEEEEEEcC
Confidence 37899999998532 2346788877654
No 25
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=36.48 E-value=82 Score=25.39 Aligned_cols=31 Identities=26% Similarity=0.385 Sum_probs=26.7
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEecCC
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCG 46 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~G 46 (260)
.+.||+.+.|++..... ..|.|..|.-+..+
T Consensus 29 ~y~pG~~~~Vtl~~~~~----~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSSP----SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCCC----CceeEEEEEEEcCC
Confidence 67899999999998754 78999999998865
No 26
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=36.11 E-value=74 Score=26.94 Aligned_cols=60 Identities=12% Similarity=0.068 Sum_probs=37.0
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEe--ecceeEEEEEeecCCccceEEEe
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV--VDNLGIEIAYDLYDPTIHNITVL 79 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRni--i~GvGVEr~FpLySP~I~sIeVl 79 (260)
.++.||.|.|..=. .|. =+|.|+++.... ..++|-++ ....|+|+-+|+|.-+|.=+...
T Consensus 45 ~IkkGD~V~VisG~--~KG----k~GkV~~V~~~~--~~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l~ 106 (120)
T PRK01191 45 PVRKGDTVKVMRGD--FKG----EEGKVVEVDLKR--GRIYVEGVTVKKADGTEVPRPIHPSNVMITKLD 106 (120)
T ss_pred eEeCCCEEEEeecC--CCC----ceEEEEEEEcCC--CEEEEeCcEEECCCCeEEEcccchhHeEEEeCc
Confidence 57899999996432 222 348888885432 13333322 33456899999998776654443
No 27
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=35.36 E-value=89 Score=28.12 Aligned_cols=51 Identities=8% Similarity=-0.022 Sum_probs=37.4
Q ss_pred CCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEE
Q psy12657 8 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 63 (260)
Q Consensus 8 ~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVE 63 (260)
..-|-++-||.|.|.+.... =...--..|..+.++|.++.|||...|-=|.
T Consensus 172 ~~~~~V~~G~~V~i~~~~g~-----~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~i~ 222 (235)
T PRK07018 172 RQAWVVCKGQTVSIIARGDG-----FSVKTEGEALNDGAVGQQIRVRNMASGQVVS 222 (235)
T ss_pred cCccEeCCCCEEEEEEecCC-----EEEEEEEEEcCCCCCCCeEEEEECCCCCEEE
Confidence 34567899999999988763 1244555677888999999999986664443
No 28
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=35.34 E-value=67 Score=24.66 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=22.9
Q ss_pred CCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEE
Q psy12657 15 VGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 55 (260)
Q Consensus 15 vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRn 55 (260)
.|+.|.++-- +-+-.|+|.|.++...- -|+.+|+
T Consensus 5 iGs~VSI~C~-----~~lGVyQG~i~~V~~~~--qTI~l~~ 38 (62)
T cd01737 5 LGSIVSINCG-----ETLGVYQGLVSAVDQES--QTISLAF 38 (62)
T ss_pred cceEEEEecC-----CceEEEEEEEEEeCccc--eEEEEee
Confidence 5777777653 34678999999987643 3454444
No 29
>PF03888 MucB_RseB: MucB/RseB family; InterPro: IPR005588 The members of this family are regulators of the anti-sigma E protein RseD.; PDB: 2P4B_B 2V42_B 2V43_A 3M4W_A.
Probab=34.61 E-value=1.5e+02 Score=27.54 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=37.1
Q ss_pred ccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeec
Q psy12657 31 KTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLE 82 (260)
Q Consensus 31 R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrg 82 (260)
+.++|+|+.+-.++..+.|.=.+..+.+|.-.|+...|..|. .||+|++
T Consensus 9 ~~lnY~g~fv~~~~~~~~s~ri~H~~~~~~e~ErL~~LdG~~---reviR~~ 57 (285)
T PF03888_consen 9 RQLNYEGTFVYQRGGQMESMRIRHAVDDGGEYERLESLDGPP---REVIRRG 57 (285)
T ss_dssp HHSEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEE-SSS-----EEEEET
T ss_pred HhCCeEEEEEEEeCCeEEEEEEEEEeeCCEEEEEEEecCCCc---EEEEEEC
Confidence 568999999999988776666666668888899999999985 4566654
No 30
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=34.11 E-value=1.3e+02 Score=24.24 Aligned_cols=39 Identities=23% Similarity=0.316 Sum_probs=30.0
Q ss_pred CCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEe-ecce
Q psy12657 14 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV-VDNL 60 (260)
Q Consensus 14 ~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRni-i~Gv 60 (260)
..|+.|.+..... -+|+|++..+.. -++|++|+|+ ..|+
T Consensus 6 ~IGs~ISlisk~~------iRYeG~L~~Id~--~~sTItL~nVr~~Gt 45 (96)
T PF12701_consen 6 YIGSKISLISKSD------IRYEGILYSIDT--EDSTITLKNVRSFGT 45 (96)
T ss_dssp CTTCEEEEEETTT------EEEEEEEEEEET--TTTEEEEEEEEETTE
T ss_pred ccCCEEEEEECCC------cEEEEEEEEEcC--CCCEEEeeeeeecCc
Confidence 3688888775543 579999999986 4699999998 5555
No 31
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=33.37 E-value=71 Score=26.72 Aligned_cols=58 Identities=12% Similarity=0.127 Sum_probs=34.0
Q ss_pred CCCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeec
Q psy12657 7 VIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLY 69 (260)
Q Consensus 7 ~~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLy 69 (260)
....++|+.|++|... .....+..++-.--+++ ++-...+.+||+..|.=+|.+|+-.
T Consensus 5 ~~~~~~lrkG~~i~~~----g~p~~V~~~~~~kpGkh-g~a~vr~k~knL~tG~~~e~~~~s~ 62 (129)
T PRK03999 5 QVEVGELKEGSYVVID----GEPCKIVEISKSKPGKH-GSAKARIVAIGIFDGQKRSLVQPVD 62 (129)
T ss_pred cccHHHccCCCEEEEC----CEEEEEEEEEeecCCCC-CcEEEEEEEEECCCCCEEEEEecCC
Confidence 3456899999999652 11111111111111111 1235678899999999999998843
No 32
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=33.32 E-value=1.1e+02 Score=21.60 Aligned_cols=43 Identities=19% Similarity=0.206 Sum_probs=29.0
Q ss_pred CCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecce
Q psy12657 10 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNL 60 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~Gv 60 (260)
.|.|..||+|-|.-... ..-.|-+++.+..| ..+++|++....
T Consensus 11 ~P~i~~gd~v~i~~~~~------~~~~G~iv~~~~~~--~~~~ikrl~~~~ 53 (84)
T cd06462 11 EPTIPDGDLVLVDKSSY------EPKRGDIVVFRLPG--GELTVKRVIGLP 53 (84)
T ss_pred cCcccCCCEEEEEecCC------CCcCCEEEEEEcCC--CcEEEEEEEEEC
Confidence 58899999999885433 23345555555444 678888887665
No 33
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=30.91 E-value=2.8e+02 Score=22.72 Aligned_cols=37 Identities=16% Similarity=0.062 Sum_probs=25.6
Q ss_pred CCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEE
Q psy12657 11 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVL 53 (260)
Q Consensus 11 PeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtL 53 (260)
..|.+||.|+|.- .=.+-|+|.++...+.....++.+
T Consensus 85 ~~~~~Gd~V~I~~------GPf~G~~g~v~~~d~~k~~v~v~l 121 (145)
T TIGR00405 85 ESIKKGDIVEIIS------GPFKGERAKVIRVDESKEEVTLEL 121 (145)
T ss_pred cccCCCCEEEEee------cCCCCCeEEEEEEcCCCCEEEEEE
Confidence 4599999999973 224569999999876544333333
No 34
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=29.67 E-value=87 Score=24.07 Aligned_cols=27 Identities=19% Similarity=0.091 Sum_probs=20.5
Q ss_pred cCCCCEEEEEEEecCCCcccceEEEEE
Q psy12657 13 FFVGSILSVTSADKHDPNKTRKFVGIC 39 (260)
Q Consensus 13 F~vGDiV~V~~~i~E~K~R~Q~F~GIV 39 (260)
..|||+|.+...+.+...+.-.|.+.+
T Consensus 88 v~pgd~l~i~~~v~~~~~~~~~~~~~~ 114 (131)
T cd01288 88 VVPGDQLILEVELLKLRRGIGKFKGKA 114 (131)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 468999999999887556666666665
No 35
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=28.64 E-value=62 Score=29.68 Aligned_cols=39 Identities=18% Similarity=0.222 Sum_probs=20.9
Q ss_pred cCCCCCCcCCCCEEEEEEEecCCCcccceE----EEEEEEEec
Q psy12657 6 SVIDIPSFFVGSILSVTSADKHDPNKTRKF----VGICIQKRY 44 (260)
Q Consensus 6 ~~~diPeF~vGDiV~V~~~i~E~K~R~Q~F----~GIVIarr~ 44 (260)
....-|.|.+||.|+|.-..+..-+|+..| .|+|.+..+
T Consensus 128 ~~~~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 128 PVDAPPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp TTSSS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEec
Confidence 344578999999999998777666676655 688887664
No 36
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=28.03 E-value=1.2e+02 Score=25.29 Aligned_cols=59 Identities=10% Similarity=0.076 Sum_probs=35.3
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEe--ecceeEEEEEeecCCccceEEE
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV--VDNLGIEIAYDLYDPTIHNITV 78 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRni--i~GvGVEr~FpLySP~I~sIeV 78 (260)
.++.||.|.|..=-. + --+|.|+.+..... .++|-.+ ....|+|.-.|+|.-+|.=+..
T Consensus 41 ~IkkGD~V~Vi~Gk~--K----Gk~GkV~~V~~~~~--~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l 101 (114)
T TIGR01080 41 PVRKGDKVRIMRGDF--K----GHEGKVSKVDLKRY--RIYVEGVTKEKVNGTEVPVPIHPSNVMITKL 101 (114)
T ss_pred eeecCCEEEEecCCC--C----CCEEEEEEEEcCCC--EEEEcCeEEECCCCeEEEeeechHHeEEEec
Confidence 689999999973221 2 24588888864432 2333222 1223578888888776665544
No 37
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=27.93 E-value=1.3e+02 Score=21.43 Aligned_cols=32 Identities=6% Similarity=-0.041 Sum_probs=23.4
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEecC
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 45 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~ 45 (260)
.+.+||.|.|.+.......-. +.|.|+...+.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~~--~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFPI--VTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSCEE--EEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCeeE--EEEEEEEEECC
Confidence 688999999999887643322 99999998876
No 38
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=27.30 E-value=2e+02 Score=28.18 Aligned_cols=59 Identities=15% Similarity=0.076 Sum_probs=44.1
Q ss_pred cCCCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecC-C--------cCeeEEEEEeecceeEEEEEe
Q psy12657 6 SVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC-G--------LRHEFVLRNVVDNLGIEIAYD 67 (260)
Q Consensus 6 ~~~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~-G--------l~sTFtLRnii~GvGVEr~Fp 67 (260)
+...+..+++|+-++|++..-... ..|.|++-++... | .+.|+.-=++++++.|...|.
T Consensus 252 kETqL~~~r~Gq~a~I~~da~~~~---~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~ld 319 (352)
T COG1566 252 KETQLARVRPGQPAEITLDAYPGN---GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIELD 319 (352)
T ss_pred eeeecCcccCCCeEEEEEEcCCCc---eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEec
Confidence 456789999999999999877533 8899999999642 2 244555567788888876654
No 39
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=26.96 E-value=3.3e+02 Score=22.95 Aligned_cols=41 Identities=7% Similarity=0.037 Sum_probs=27.3
Q ss_pred CCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecc
Q psy12657 11 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDN 59 (260)
Q Consensus 11 PeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~G 59 (260)
-.|.+||.|+|+- .-.+-|.|.|+...+.. ...+|.-+-..
T Consensus 93 ~~~~~G~~V~I~~------Gpf~g~~g~V~~vd~~k--~~v~v~ll~~~ 133 (153)
T PRK08559 93 EGIKEGDIVELIA------GPFKGEKARVVRVDESK--EEVTVELLEAA 133 (153)
T ss_pred cCCCCCCEEEEec------cCCCCceEEEEEEcCCC--CEEEEEEECCc
Confidence 3599999999973 33466999999997642 22444443333
No 40
>KOG3409|consensus
Probab=26.69 E-value=1.1e+02 Score=28.06 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=24.1
Q ss_pred CCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEE
Q psy12657 8 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEI 64 (260)
Q Consensus 8 ~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr 64 (260)
.-+-.|+|||+|.-.+ |+ .|.+++|.|=..-+..||-.
T Consensus 118 ~v~ksFrPgDiVlAkV----------------is---~~~~~~y~LTtAeneLGVV~ 155 (193)
T KOG3409|consen 118 KVYKSFRPGDIVLAKV----------------IS---LGDGSNYLLTTAENELGVVF 155 (193)
T ss_pred hhhhccCCCcEEEEEE----------------ee---cCCCCcEEEEEecccceEEE
Confidence 3356799999886543 32 45666776666666666643
No 41
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.79 E-value=1.7e+02 Score=25.26 Aligned_cols=51 Identities=10% Similarity=-0.038 Sum_probs=36.4
Q ss_pred CCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEE
Q psy12657 9 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEI 64 (260)
Q Consensus 9 diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr 64 (260)
.-+-++-||.|.+.+.... =...-.-+|..+.+.+.++.+||...|-=|.-
T Consensus 97 ~p~~V~rG~~V~i~~~~~g-----~~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv~g 147 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAGG-----LTITAAGTPLQSGAAGDLIRVRNVDSGVIVSG 147 (160)
T ss_pred CCcEEeCCCEEEEEEecCC-----EEEEEEEEEcccCCCCCEEEEEECCCCCEEEE
Confidence 3456899999999998763 11233345667888999999999876655543
No 42
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=25.08 E-value=65 Score=22.79 Aligned_cols=15 Identities=40% Similarity=0.645 Sum_probs=12.4
Q ss_pred HHHHHHHHHHhhhhh
Q psy12657 226 QEEIFSEVFSELHQL 240 (260)
Q Consensus 226 ~~~i~~e~~~~~~~~ 240 (260)
++||+.||..|||++
T Consensus 9 KqEIL~EvrkEl~K~ 23 (40)
T PF08776_consen 9 KQEILEEVRKELQKV 23 (40)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 468999999999875
No 43
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=24.35 E-value=1e+02 Score=23.98 Aligned_cols=26 Identities=31% Similarity=0.487 Sum_probs=19.1
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEEEe
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQKR 43 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr 43 (260)
+|++||++...-.... .|.|-.+..+
T Consensus 28 df~VGD~L~L~E~~~~------~YTGr~~~~~ 53 (72)
T PF12961_consen 28 DFQVGDILVLREWDNG------EYTGREIEAE 53 (72)
T ss_pred CCCCCCEEEEEEecCC------CccccEEEEE
Confidence 6899999999876643 5777766543
No 44
>TIGR01750 fabZ beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ. This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains.
Probab=23.69 E-value=1.2e+02 Score=24.24 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=20.1
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEE
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGIC 39 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIV 39 (260)
.+.|||+|.++..+.....+.-.|.|.+
T Consensus 97 ~v~pGd~l~i~~~i~~~~~~~~~~~~~~ 124 (140)
T TIGR01750 97 PVVPGDQLILHAEFLKKRRKIGKFKGEA 124 (140)
T ss_pred ccCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 3568999999999886545555566654
No 45
>cd00493 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface.
Probab=23.53 E-value=1.3e+02 Score=22.93 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=22.0
Q ss_pred CcCCCCEEEEEEEecCCCcccceEEEEEEE
Q psy12657 12 SFFVGSILSVTSADKHDPNKTRKFVGICIQ 41 (260)
Q Consensus 12 eF~vGDiV~V~~~i~E~K~R~Q~F~GIVIa 41 (260)
...|||+|.+.+.+.+.......|.+.+..
T Consensus 88 ~v~pgd~l~i~~~i~~~~~~~~~~~~~~~~ 117 (131)
T cd00493 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAYV 117 (131)
T ss_pred CcCCCCEEEEEEEEEEeeCCEEEEEEEEEE
Confidence 456999999999998755566666666553
No 46
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=23.42 E-value=1.3e+02 Score=24.26 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=19.5
Q ss_pred cCCCCEEEEEEEecCCCcccceEEEEE
Q psy12657 13 FFVGSILSVTSADKHDPNKTRKFVGIC 39 (260)
Q Consensus 13 F~vGDiV~V~~~i~E~K~R~Q~F~GIV 39 (260)
..|||+|.+...+.+.+.+.-.|.+-+
T Consensus 102 v~pGd~l~i~~~i~~~~~~~v~~~~~~ 128 (147)
T PRK00006 102 VVPGDQLILEVELLKQRRGIWKFKGVA 128 (147)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 358999999999886545555565555
No 47
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.89 E-value=1.9e+02 Score=26.09 Aligned_cols=50 Identities=8% Similarity=-0.120 Sum_probs=34.9
Q ss_pred CCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEE
Q psy12657 8 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 63 (260)
Q Consensus 8 ~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVE 63 (260)
...|-++-||.|.|.+.... =...---.|..++.+|.++.||| ..|-=|+
T Consensus 161 ~~~~lV~rGd~V~i~~~~gg-----~~I~~~G~Al~~G~~Gd~IrVrN-~Sgkii~ 210 (222)
T PRK08515 161 KALILVRKNDIINGVLKEGG-----VSIEISLKALQDGNLGDIIQAKN-KSNKILK 210 (222)
T ss_pred CCcceEecCCEEEEEEECCC-----EEEEEEEEEcccCCCCCEEEEEe-CCCCEEE
Confidence 44567899999999988763 01222334667788999999999 6665454
No 48
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=22.63 E-value=1.6e+02 Score=28.20 Aligned_cols=33 Identities=15% Similarity=0.212 Sum_probs=24.7
Q ss_pred CCCCCcCCCCEEEEEEEecCCCcccceEEEEEEEEe
Q psy12657 8 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 43 (260)
Q Consensus 8 ~diPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr 43 (260)
.++..+++|+.|.|++..-.. -..|.|.|..+.
T Consensus 261 ~~l~~v~~Gq~V~I~~da~p~---~~~~~G~V~~I~ 293 (390)
T PRK15136 261 TQLANMRIGQPATITSDIYGD---DVVYTGKVVGLD 293 (390)
T ss_pred HHHhcCCCCCEEEEEEecCCC---CceEEEEEEEEC
Confidence 356789999999998765322 136999999984
No 49
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=22.15 E-value=3.3e+02 Score=21.53 Aligned_cols=51 Identities=14% Similarity=0.138 Sum_probs=36.0
Q ss_pred CCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCC----cCeeEEEEEeecce
Q psy12657 10 IPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCG----LRHEFVLRNVVDNL 60 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~G----l~sTFtLRnii~Gv 60 (260)
+..+++||+|-|.-...- ......-..|-||...+.. ..|=|.+=++-.|+
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~ 58 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGV 58 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCe
Confidence 567899999999755522 3444567899999986543 45668888876553
No 50
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=22.12 E-value=1e+02 Score=25.26 Aligned_cols=44 Identities=14% Similarity=0.055 Sum_probs=31.7
Q ss_pred CCCcCCCCEEEEEEEecC----CCcccceEEEEEEEEecCCcCeeEEE
Q psy12657 10 IPSFFVGSILSVTSADKH----DPNKTRKFVGICIQKRYCGLRHEFVL 53 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E----~K~R~Q~F~GIVIarr~~Gl~sTFtL 53 (260)
+-+|++||+|.|...-.- --.+.+--.|.|+.++++..+-.+.+
T Consensus 32 l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~v 79 (98)
T PRK04306 32 LQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKD 79 (98)
T ss_pred HHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEE
Confidence 346999999998765443 34667777899999998766555533
No 51
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=21.97 E-value=79 Score=25.50 Aligned_cols=32 Identities=25% Similarity=0.368 Sum_probs=23.8
Q ss_pred CCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCC
Q psy12657 11 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCG 46 (260)
Q Consensus 11 PeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~G 46 (260)
..+.||+.+.|++. ....+.|.|..|.-+..+
T Consensus 28 ~~y~pg~~~~Vtl~----~~~~~~F~GFllqAr~~~ 59 (132)
T PF02014_consen 28 SSYEPGQTYTVTLS----SSGSSSFRGFLLQARDAN 59 (132)
T ss_dssp SSB-TTBEEEEEEE----ETTTEEBSEEEEEEEETT
T ss_pred CeEcCCCEEEEEEE----CCCCCceeEEEEEEEeCC
Confidence 35789999999992 334578999999887543
No 52
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.69 E-value=2.4e+02 Score=27.26 Aligned_cols=50 Identities=4% Similarity=-0.141 Sum_probs=37.5
Q ss_pred CCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEE
Q psy12657 10 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEI 64 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr 64 (260)
-+-++-||.|.|.+.... =....-..|..+.+.|.++.|||...|--|.-
T Consensus 256 p~lV~rGd~V~i~~~~gg-----l~v~~~G~ALe~G~~Gd~IrV~N~~S~kiv~g 305 (338)
T PRK12786 256 PDLVQRGQLVTLIYQTPG-----IYLTARGKALEDGAEGDVVRVLNLQSKRTVTG 305 (338)
T ss_pred ccEEcCCCEEEEEEEcCC-----EEEEEEEEEccccCCCCEEEEEECCCCCEEEE
Confidence 346789999999998874 12455566777888999999999866655543
No 53
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2P1G_B 2IM9_A.
Probab=21.02 E-value=2.8e+02 Score=25.34 Aligned_cols=43 Identities=23% Similarity=0.281 Sum_probs=31.1
Q ss_pred CCCcCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCcCeeEEEEEeeccee
Q psy12657 10 IPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLG 61 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E-~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvG 61 (260)
++.++.||+|.+...+.. + -+=.|+++...++ ..+||.+..-+
T Consensus 151 ~~~i~~GDiI~i~t~~~GLD----vsH~Giav~~~~~-----l~l~hASs~~~ 194 (216)
T PF07313_consen 151 LSQIKNGDIIAIVTNIKGLD----VSHVGIAVWKNDG-----LHLRHASSLHK 194 (216)
T ss_dssp HTTS-TT-EEEEEEECTTEC----EEEEEEEEEETTE-----EEEEEEETTTT
T ss_pred HhcCCCCCEEEEEeCCCCCc----eeeEEEEEEECCe-----EEEEeCCCCCC
Confidence 467899999999999876 3 4567888776654 78899876655
No 54
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=20.92 E-value=3.8e+02 Score=25.62 Aligned_cols=51 Identities=10% Similarity=0.104 Sum_probs=36.8
Q ss_pred CCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeee
Q psy12657 28 DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRL 81 (260)
Q Consensus 28 ~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrr 81 (260)
...+.++|+|+.+-.++..+.|.=....+.+|.=.|+.-.|..|. .||+|+
T Consensus 37 ~A~~~lnY~g~fV~~~~~~i~s~ri~H~~~~~~e~erL~~LdG~~---rEviR~ 87 (319)
T PRK09455 37 EASQSLNYELSFINITKQGIESLRYRHARLDNKPLAQLLQMDGPR---REIIQR 87 (319)
T ss_pred HHHHhCCeEEEEEEEeCCeEEEEEEEEEEeCCEEEEEEEecCCCc---eEEEEE
Confidence 356789999999999976665544444556677799998888874 455555
No 55
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=20.51 E-value=2.6e+02 Score=20.68 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=23.4
Q ss_pred CCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEE
Q psy12657 14 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 55 (260)
Q Consensus 14 ~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRn 55 (260)
-+|..|.|++... ..|+||.-+..-.+-+..+.|+.
T Consensus 10 lvG~~V~V~~~~G------~~yeGif~s~s~~~~~~~vvLk~ 45 (77)
T PF14438_consen 10 LVGQTVEVTTKNG------SVYEGIFHSASPESNEFDVVLKM 45 (77)
T ss_dssp TTTSEEEEEETTS-------EEEEEEEEE-T---T--EEEEE
T ss_pred CcCCEEEEEECCC------CEEEEEEEeCCCcccceeEEEEe
Confidence 4799999998876 46999999887654466676654
No 56
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=20.38 E-value=4.2e+02 Score=20.64 Aligned_cols=73 Identities=15% Similarity=0.136 Sum_probs=38.3
Q ss_pred CCCcCCCCEEEEEEEecCCCcccceEEEEEEEEecCCcCeeEEEEEeecceeEEEEEeecCCccceEEEeeeccccccce
Q psy12657 10 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKRLDDDL 89 (260)
Q Consensus 10 iPeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~sIeVlrrgKVRRAKL 89 (260)
-..+.+||.+.|.+..... ...|-=.| ..+.++-.+-.+. +.++.. ...|++-+=+.=+..|+ .
T Consensus 7 ~~~~~~Ge~~~v~v~~~~~---~~~~~~~v--~s~g~I~~~~~~~-~~~~~~-~~~~~v~~~~~P~~~v~---------~ 70 (136)
T PF07703_consen 7 KDSYKPGETAKVTVQSPFP---NGTFLYLV--ESRGKIVSTGSVE-LKNGST-TFEFPVTPDMAPNFYVL---------A 70 (136)
T ss_dssp SSSB-TTSEEEEEEEEESC---ESEEEEEE--EETTEEEEEEEEE-CTTTSS-EEEEEE-GGGTSEEEEE---------E
T ss_pred CCCcCCCCEEEEEEEcCCC---ccEEEEEE--EECCeEEEEEEEE-ecCCcE-EEEEecchhcCCcEEEE---------E
Confidence 3568899999999998864 22222222 3344555555555 333332 44555533333355555 5
Q ss_pred ehhhccCcc
Q psy12657 90 LYLRDALPN 98 (260)
Q Consensus 90 YYLRdr~gK 98 (260)
||++...|.
T Consensus 71 ~~v~~~~g~ 79 (136)
T PF07703_consen 71 YYVRPADGE 79 (136)
T ss_dssp EEETTCTCE
T ss_pred EEEcCCCCe
Confidence 677554444
No 57
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=20.07 E-value=3.7e+02 Score=22.46 Aligned_cols=29 Identities=24% Similarity=0.322 Sum_probs=21.7
Q ss_pred CCcCCCCEEEEEEEecCCCcccceEEEEEEEEecC
Q psy12657 11 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 45 (260)
Q Consensus 11 PeF~vGDiV~V~~~i~E~K~R~Q~F~GIVIarr~~ 45 (260)
..|.+||.|+|.- .=.+-|+|+++.+.+.
T Consensus 118 ~~~~~G~~V~I~~------Gpf~G~~g~v~~~~~~ 146 (172)
T TIGR00922 118 IDFEVGEQVRVND------GPFANFTGTVEEVDYE 146 (172)
T ss_pred cCCCCCCEEEEee------cCCCCcEEEEEEEcCC
Confidence 3488999999972 2345699999998653
Done!