Query 030707
Match_columns 173
No_of_seqs 36 out of 38
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 03:23:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030707.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030707hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1698 Mitochondrial/chloropl 99.5 1E-13 2.3E-18 116.4 7.1 115 41-171 5-125 (201)
2 TIGR01024 rplS_bact ribosomal 97.9 3.3E-05 7.1E-10 60.1 5.8 43 125-172 3-49 (113)
3 PRK05338 rplS 50S ribosomal pr 97.8 5E-05 1.1E-09 59.3 5.6 45 124-173 2-50 (116)
4 PF01245 Ribosomal_L19: Riboso 97.6 0.00011 2.4E-09 56.7 5.2 39 134-172 7-49 (113)
5 CHL00084 rpl19 ribosomal prote 97.6 0.00016 3.4E-09 56.7 6.0 46 122-172 4-53 (117)
6 COG0335 RplS Ribosomal protein 96.6 0.007 1.5E-07 47.9 6.0 44 124-172 4-51 (115)
7 PF09926 DUF2158: Uncharacteri 82.6 0.8 1.7E-05 31.5 1.5 11 146-156 1-11 (53)
8 PF12969 DUF3857: Domain of Un 76.9 1.9 4.2E-05 32.3 2.1 19 141-159 85-103 (177)
9 PF10447 EXOSC1: Exosome compo 71.8 0.73 1.6E-05 33.9 -1.2 33 124-156 45-79 (82)
10 KOG3409 Exosomal 3'-5' exoribo 69.8 2.1 4.6E-05 36.7 0.9 35 125-159 100-136 (193)
11 TIGR01352 tonB_Cterm TonB fami 68.6 12 0.00026 24.4 4.2 33 127-159 36-68 (74)
12 cd05791 S1_CSL4 S1_CSL4: CSL4, 51.9 11 0.00025 27.4 1.9 34 126-159 39-74 (92)
13 COG1499 NMD3 NMD protein affec 51.6 8.8 0.00019 35.0 1.6 15 142-156 243-257 (355)
14 PF00122 E1-E2_ATPase: E1-E2 A 51.2 9.1 0.0002 30.1 1.5 14 142-155 48-61 (230)
15 KOG0628 Aromatic-L-amino-acid/ 51.1 8.6 0.00019 37.2 1.5 41 119-160 6-48 (511)
16 PF02765 POT1: Telomeric singl 50.0 22 0.00048 27.4 3.4 26 144-169 71-98 (146)
17 PF06107 DUF951: Bacterial pro 47.7 12 0.00026 26.6 1.4 15 145-159 1-15 (57)
18 KOG3572 Uncharacterized conser 47.1 11 0.00025 40.5 1.8 18 141-158 123-140 (1701)
19 PF13550 Phage-tail_3: Putativ 45.8 24 0.00052 26.1 2.9 22 144-167 138-159 (164)
20 KOG3047 Predicted transcriptio 45.3 35 0.00075 28.5 4.0 47 121-172 51-97 (157)
21 PF01472 PUA: PUA domain; Int 45.3 32 0.0007 23.7 3.3 39 129-169 5-52 (74)
22 PHA03171 UL37 tegument protein 44.9 14 0.0003 35.5 1.9 42 97-139 96-137 (499)
23 PF14326 DUF4384: Domain of un 44.9 28 0.0006 24.4 3.0 22 144-165 1-22 (83)
24 cd03440 hot_dog The hotdog fol 44.1 55 0.0012 19.1 3.8 43 121-163 19-75 (100)
25 COG0250 NusG Transcription ant 43.1 19 0.00042 29.6 2.2 27 125-155 107-133 (178)
26 COG0810 TonB Periplasmic prote 42.7 30 0.00064 28.8 3.3 33 127-159 206-238 (244)
27 KOG3416 Predicted nucleic acid 40.4 16 0.00035 30.0 1.3 11 145-155 61-71 (134)
28 COG0361 InfA Translation initi 40.1 20 0.00043 26.5 1.7 12 145-156 46-57 (75)
29 cd04459 Rho_CSD Rho_CSD: Rho p 39.3 29 0.00064 24.8 2.4 23 145-167 40-62 (68)
30 PRK09521 exosome complex RNA-b 38.3 13 0.00029 29.9 0.6 36 125-160 98-133 (189)
31 PF08605 Rad9_Rad53_bind: Fung 38.0 24 0.00051 28.1 1.9 13 144-156 58-70 (131)
32 PF05697 Trigger_N: Bacterial 37.6 26 0.00057 26.6 2.1 23 128-150 26-48 (145)
33 TIGR02266 gmx_TIGR02266 Myxoco 36.1 63 0.0014 22.1 3.6 19 144-162 35-53 (96)
34 cd05829 Sortase_E Sortase E (S 35.1 44 0.00096 25.9 3.0 25 142-167 69-93 (144)
35 PRK11507 ribosome-associated p 34.2 26 0.00056 25.6 1.5 10 145-154 52-61 (70)
36 cd00164 S1_like S1_like: Ribos 34.1 32 0.0007 20.8 1.7 15 145-159 41-55 (65)
37 PF02563 Poly_export: Polysacc 33.9 29 0.00063 24.3 1.7 12 145-156 12-23 (82)
38 cd05702 S1_Rrp5_repeat_hs11_sc 33.4 41 0.00088 22.4 2.3 26 141-166 42-67 (70)
39 PF11720 Inhibitor_I78: Peptid 32.9 40 0.00086 23.0 2.2 24 146-169 29-59 (60)
40 cd04454 S1_Rrp4_like S1_Rrp4_l 32.2 27 0.00058 23.9 1.2 38 125-162 30-67 (82)
41 cd01288 FabZ FabZ is a 17kD be 32.1 82 0.0018 22.3 3.8 21 142-162 84-104 (131)
42 cd05830 Sortase_D_5 Sortase D 31.6 53 0.0012 25.0 2.9 37 122-168 50-86 (137)
43 cd04497 hPOT1_OB1_like hPOT1_O 31.5 38 0.00082 26.0 2.1 15 141-155 64-78 (138)
44 PF01191 RNA_pol_Rpb5_C: RNA p 31.2 30 0.00065 25.3 1.4 16 145-160 48-63 (74)
45 KOG0494 Transcription factor C 31.0 12 0.00026 34.3 -0.8 45 118-162 140-184 (332)
46 TIGR01076 sortase_fam LPXTG-si 31.0 55 0.0012 24.9 2.9 26 141-168 59-84 (136)
47 cd06165 Sortase_A_1 Sortase A 29.3 57 0.0012 24.3 2.7 38 122-168 47-84 (127)
48 PF13275 S4_2: S4 domain; PDB: 29.3 30 0.00064 24.7 1.1 10 145-154 48-57 (65)
49 PF03544 TonB_C: Gram-negative 28.6 38 0.00083 22.2 1.5 32 128-159 43-74 (79)
50 cd03692 mtIF2_IVc mtIF2_IVc: t 28.5 35 0.00075 24.1 1.3 11 143-153 73-83 (84)
51 cd06166 Sortase_D_5 Sortase D 28.1 65 0.0014 24.1 2.8 28 139-168 58-85 (126)
52 cd05692 S1_RPS1_repeat_hs4 S1_ 27.0 1.1E+02 0.0023 19.0 3.3 16 145-160 44-59 (69)
53 smart00739 KOW KOW (Kyprides, 26.9 55 0.0012 17.9 1.7 12 145-156 1-12 (28)
54 PF07497 Rho_RNA_bind: Rho ter 26.6 56 0.0012 24.1 2.2 21 145-165 42-62 (78)
55 PF09874 DUF2101: Predicted me 26.3 55 0.0012 28.5 2.4 16 142-157 178-193 (206)
56 COG1096 Predicted RNA-binding 26.2 45 0.00098 28.6 1.8 15 144-158 117-131 (188)
57 PF11213 DUF3006: Protein of u 26.2 67 0.0015 22.4 2.4 17 143-159 31-51 (71)
58 PF14801 GCD14_N: tRNA methylt 25.9 46 0.00099 23.6 1.5 11 145-155 5-15 (54)
59 TIGR00451 unchar_dom_2 unchara 25.7 78 0.0017 23.1 2.8 14 144-157 59-72 (107)
60 cd05828 Sortase_D_4 Sortase D 25.4 79 0.0017 23.7 2.9 34 122-168 49-82 (127)
61 smart00357 CSP Cold shock prot 24.9 1.6E+02 0.0034 18.2 3.8 17 143-159 34-50 (64)
62 cd00493 FabA_FabZ FabA/Z, beta 24.5 1.1E+02 0.0024 21.5 3.3 22 141-162 84-105 (131)
63 PRK09570 rpoH DNA-directed RNA 24.4 56 0.0012 24.3 1.8 15 145-159 51-65 (79)
64 PRK08559 nusG transcription an 23.8 68 0.0015 25.2 2.3 12 144-155 93-104 (153)
65 PRK04424 fatty acid biosynthes 23.8 1.3E+02 0.0027 24.4 3.9 46 117-162 101-155 (185)
66 smart00359 PUA Putative RNA-bi 23.7 1.9E+02 0.004 18.9 4.1 23 144-168 29-51 (77)
67 cd05687 S1_RPS1_repeat_ec1_hs1 23.6 46 0.001 21.7 1.2 16 145-160 44-59 (70)
68 smart00333 TUDOR Tudor domain. 22.7 2E+02 0.0042 18.0 3.9 25 145-172 2-26 (57)
69 PF01835 A2M_N: MG2 domain; I 22.5 75 0.0016 22.1 2.1 14 146-159 11-24 (99)
70 cd05708 S1_Rrp5_repeat_sc12 S1 22.4 66 0.0014 20.9 1.7 15 145-159 47-61 (77)
71 COG5475 Uncharacterized small 22.4 51 0.0011 23.9 1.2 12 145-156 4-15 (60)
72 cd04491 SoSSB_OBF SoSSB_OBF: A 22.3 1.3E+02 0.0029 20.4 3.3 20 143-162 46-66 (82)
73 PF05093 CIAPIN1: Cytokine-ind 22.3 42 0.00092 26.1 0.9 14 141-154 87-100 (100)
74 cd05707 S1_Rrp5_repeat_sc11 S1 21.9 33 0.00071 22.5 0.2 38 124-161 23-60 (68)
75 PF05641 Agenet: Agenet domain 21.7 1.7E+02 0.0037 19.9 3.8 16 146-161 1-16 (68)
76 PF01336 tRNA_anti-codon: OB-f 21.5 1.3E+02 0.0027 19.2 2.9 27 145-171 44-71 (75)
77 cd05688 S1_RPS1_repeat_ec3 S1_ 21.4 76 0.0016 19.9 1.8 15 146-160 45-59 (68)
78 COG1813 Predicted transcriptio 21.3 29 0.00062 29.1 -0.2 48 108-155 113-163 (165)
79 COG1188 Ribosome-associated he 21.3 70 0.0015 24.9 1.9 17 141-157 44-60 (100)
80 cd03451 FkbR2 FkbR2 is a Strep 21.1 92 0.002 22.7 2.4 23 140-162 86-108 (146)
81 cd05703 S1_Rrp5_repeat_hs12_sc 20.6 1.4E+02 0.003 20.4 3.1 42 124-165 23-68 (73)
82 smart00326 SH3 Src homology 3 20.4 77 0.0017 18.7 1.6 14 145-158 20-33 (58)
83 smart00316 S1 Ribosomal protei 20.2 80 0.0017 19.3 1.7 16 145-160 46-61 (72)
84 TIGR03784 marine_sortase sorta 20.1 1.3E+02 0.0027 24.6 3.3 26 140-167 103-129 (174)
No 1
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=99.47 E-value=1e-13 Score=116.36 Aligned_cols=115 Identities=17% Similarity=0.179 Sum_probs=84.9
Q ss_pred ceeeecc---CCCccccceecccccceeEEeeccchhhhhchhhHHHhHHHHhhccccchhhccccchhhhhhhccCCCC
Q 030707 41 GVSVSAK---PIGWNLGFFVNAQVKDSFVVRAEANEEAEANESIEEEQNEAVQAQGDVVVAVEAESEDKVEEEEVKAPRK 117 (173)
Q Consensus 41 rls~s~~---~~s~~~~~~~~~~~~~~fVvrAea~~ea~~~~~~~e~~~E~~~~~~d~v~~~Ege~~~v~eeee~~pprk 117 (173)
|+++++. +..|++.+.+.....++|++.+|....+...... ..++..+...-.+..+..++
T Consensus 5 r~~~~r~~~~~~a~~~~v~l~~~~~~~~~~~~e~~~~a~~~~~~----------------~~~~~~~~~~~~~~~~~f~~ 68 (201)
T KOG1698|consen 5 RLGFDRFPMFRAASYRNVSLKGKWFSSFIAISEERCFAPTKRPS----------------VNEPSPESPCVVEQYPEFLP 68 (201)
T ss_pred eeeeecccccchhhhheeecccceeeeeccccccccccCCCCcc----------------cccCCCCCccccccCccccc
Confidence 4444444 4577777888888889999988774443322220 12333333333344566677
Q ss_pred CccchhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccc---eeeeeEeee
Q 030707 118 PRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFD---YLYNVLCYS 171 (173)
Q Consensus 118 krkk~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnk---r~~~~~c~~ 171 (173)
-++..++||++||+++|++.++.|.+|.|++||||+|+.++|+|+ -+|-|+||.
T Consensus 69 ~~~~~~~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~ 125 (201)
T KOG1698|consen 69 LRKVAKRIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIR 125 (201)
T ss_pred chhHHHHHHHhhCHHHHHHHHhcccCCccccccEEEEEecCCccCCceeEEEEEEEE
Confidence 777799999999999999999999999999999999999999999 467789986
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=97.87 E-value=3.3e-05 Score=60.12 Aligned_cols=43 Identities=14% Similarity=0.356 Sum_probs=35.0
Q ss_pred HHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecc-cce---eeeeEeeec
Q 030707 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAV-FDY---LYNVLCYSF 172 (173)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPE-nkr---~~~~~c~~~ 172 (173)
+|+.++++++ .+.+|+|++||+|++.+.++| |+. .|.|+||.-
T Consensus 3 ~i~~~e~~~~-----~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~ 49 (113)
T TIGR01024 3 LIKQIEQEQL-----KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIAR 49 (113)
T ss_pred HHHHHHHHHh-----hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEE
Confidence 5666666655 578999999999999999998 553 589999974
No 3
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=97.79 E-value=5e-05 Score=59.34 Aligned_cols=45 Identities=13% Similarity=0.321 Sum_probs=36.1
Q ss_pred hHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeccc-c---eeeeeEeeecC
Q 030707 124 DIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVF-D---YLYNVLCYSFK 173 (173)
Q Consensus 124 ~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEn-k---r~~~~~c~~~~ 173 (173)
.||+.++.+.+ .+.+|+|++||+|++.+.+.|. + -.|.|+||+.+
T Consensus 2 ~~i~~~~~~~~-----~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~ 50 (116)
T PRK05338 2 NLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARR 50 (116)
T ss_pred cHHHHHHHHHh-----hcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEe
Confidence 36677777766 3779999999999999999974 3 36999999853
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=97.62 E-value=0.00011 Score=56.73 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=31.5
Q ss_pred HHHhhhcCCCCCCCCCcEEEEEEeecccc----eeeeeEeeec
Q 030707 134 VEASESERPIPDIRTGDVVEIKLVNAVFD----YLYNVLCYSF 172 (173)
Q Consensus 134 vee~~~~R~iPdiRpGdIVelkvEVPEnk----r~~~~~c~~~ 172 (173)
+|.......+|+|++||+|+|.+.++|.. ..|.|+|++.
T Consensus 7 ~e~~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~ 49 (113)
T PF01245_consen 7 VEREQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIAR 49 (113)
T ss_dssp HHHTTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEE
T ss_pred HHHHHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEE
Confidence 44444469999999999999999999543 4689999975
No 5
>CHL00084 rpl19 ribosomal protein L19
Probab=97.61 E-value=0.00016 Score=56.70 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=35.6
Q ss_pred hhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccc--e--eeeeEeeec
Q 030707 122 LGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFD--Y--LYNVLCYSF 172 (173)
Q Consensus 122 ~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnk--r--~~~~~c~~~ 172 (173)
+..||+-++++++ ...+|+|++||+|.+.+.+.|.. | .|.|+||+.
T Consensus 4 ~~~~i~~~~~~~~-----~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~ 53 (117)
T CHL00084 4 LQQLVKEIESEFL-----KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAK 53 (117)
T ss_pred HHHHHHHHHHHHh-----hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEE
Confidence 3456666666655 35899999999999999999754 2 689999975
No 6
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=96.56 E-value=0.007 Score=47.92 Aligned_cols=44 Identities=18% Similarity=0.306 Sum_probs=34.9
Q ss_pred hHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccc----eeeeeEeeec
Q 030707 124 DIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFD----YLYNVLCYSF 172 (173)
Q Consensus 124 ~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnk----r~~~~~c~~~ 172 (173)
.|++-|+++++..- +|+|+|||.|.+.+-+=|.. -.|-|+|++.
T Consensus 4 ~~i~~le~~q~~~~-----iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~ 51 (115)
T COG0335 4 PIIQQLEQEQIKKD-----IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIAR 51 (115)
T ss_pred HHHHHHHHHHHHhh-----CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEE
Confidence 47788888877665 99999999999888777544 4578899875
No 7
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=82.57 E-value=0.8 Score=31.50 Aligned_cols=11 Identities=45% Similarity=0.812 Sum_probs=9.6
Q ss_pred CCCCcEEEEEE
Q 030707 146 IRTGDVVEIKL 156 (173)
Q Consensus 146 iRpGdIVelkv 156 (173)
|++||||+||=
T Consensus 1 f~~GDvV~LKS 11 (53)
T PF09926_consen 1 FKIGDVVQLKS 11 (53)
T ss_pred CCCCCEEEEcc
Confidence 68999999983
No 8
>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=76.92 E-value=1.9 Score=32.31 Aligned_cols=19 Identities=32% Similarity=0.623 Sum_probs=12.0
Q ss_pred CCCCCCCCCcEEEEEEeec
Q 030707 141 RPIPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 141 R~iPdiRpGdIVelkvEVP 159 (173)
=.+|++++||||++...+=
T Consensus 85 ~~~p~v~~GdiIe~~y~~~ 103 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIK 103 (177)
T ss_dssp EE--S--TT-EEEEEEEEE
T ss_pred EEcCCCCCCcEEEEEEEEE
Confidence 4689999999999998884
No 9
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=71.77 E-value=0.73 Score=33.94 Aligned_cols=33 Identities=30% Similarity=0.561 Sum_probs=18.6
Q ss_pred hHHhHhhHHHHHHhhhcCC--CCCCCCCcEEEEEE
Q 030707 124 DIMGILNKRAVEASESERP--IPDIRTGDVVEIKL 156 (173)
Q Consensus 124 ~IM~ILnkeavee~~~~R~--iPdiRpGdIVelkv 156 (173)
...|+|.++.|...++.+. -=-|||||||.=||
T Consensus 45 ~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 45 PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV 79 (82)
T ss_dssp SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred ccEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence 3467777777776665554 45699999998776
No 10
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=69.78 E-value=2.1 Score=36.72 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=28.2
Q ss_pred HHhHhhHHHHHHhhhcCC--CCCCCCCcEEEEEEeec
Q 030707 125 IMGILNKRAVEASESERP--IPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 125 IM~ILnkeavee~~~~R~--iPdiRpGdIVelkvEVP 159 (173)
.-|+|.||.|.+.++.|. +--|||||||.-||---
T Consensus 100 FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~ 136 (193)
T KOG3409|consen 100 FRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISL 136 (193)
T ss_pred hcceeehhhccccccchhhhhhccCCCcEEEEEEeec
Confidence 357899999998887764 56899999999887553
No 11
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=68.59 E-value=12 Score=24.39 Aligned_cols=33 Identities=24% Similarity=0.247 Sum_probs=28.0
Q ss_pred hHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeec
Q 030707 127 GILNKRAVEASESERPIPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 127 ~ILnkeavee~~~~R~iPdiRpGdIVelkvEVP 159 (173)
..||+.+++.+++-+..|....|.-+..++.+|
T Consensus 36 ~~ld~~a~~av~~~~~~p~~~~g~~~~~~~~~~ 68 (74)
T TIGR01352 36 EALDRAALEAVRKARFEPPPPNGGPVAQSVTIP 68 (74)
T ss_pred hhHHHHHHHHHHhCCCCCCCCCCCceeEEEEEe
Confidence 579999999999999999998887666777666
No 12
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=51.87 E-value=11 Score=27.35 Aligned_cols=34 Identities=26% Similarity=0.517 Sum_probs=19.9
Q ss_pred HhHhhHHHHHHhhhc--CCCCCCCCCcEEEEEEeec
Q 030707 126 MGILNKRAVEASESE--RPIPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 126 M~ILnkeavee~~~~--R~iPdiRpGdIVelkvEVP 159 (173)
.++|..+.+...+.. .--=-|||||+|.-||.=-
T Consensus 39 ~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~ 74 (92)
T cd05791 39 RGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISL 74 (92)
T ss_pred ccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEc
Confidence 455665554322221 1123489999999998644
No 13
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=51.64 E-value=8.8 Score=35.03 Aligned_cols=15 Identities=40% Similarity=0.857 Sum_probs=13.0
Q ss_pred CCCCCCCCcEEEEEE
Q 030707 142 PIPDIRTGDVVEIKL 156 (173)
Q Consensus 142 ~iPdiRpGdIVelkv 156 (173)
-||+|||||||.++=
T Consensus 243 rip~~~~gDiV~~~~ 257 (355)
T COG1499 243 RIPEFRPGDIVSVRG 257 (355)
T ss_pred ECCCCCCCCEEEECC
Confidence 599999999998753
No 14
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=51.18 E-value=9.1 Score=30.09 Aligned_cols=14 Identities=29% Similarity=0.729 Sum_probs=10.6
Q ss_pred CCCCCCCCcEEEEE
Q 030707 142 PIPDIRTGDVVEIK 155 (173)
Q Consensus 142 ~iPdiRpGdIVelk 155 (173)
+.=+++|||||.|+
T Consensus 48 ~~~~L~~GDiI~l~ 61 (230)
T PF00122_consen 48 PSSELVPGDIIILK 61 (230)
T ss_dssp EGGGT-TTSEEEEE
T ss_pred hHhhccceeeeecc
Confidence 44579999999996
No 15
>KOG0628 consensus Aromatic-L-amino-acid/L-histidine decarboxylase [Amino acid transport and metabolism]
Probab=51.11 E-value=8.6 Score=37.16 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=26.1
Q ss_pred ccchhhHH-hHhhHHHHHHhhhcCCCCCCCCCcEEEE-EEeecc
Q 030707 119 RVKLGDIM-GILNKRAVEASESERPIPDIRTGDVVEI-KLVNAV 160 (173)
Q Consensus 119 rkk~g~IM-~ILnkeavee~~~~R~iPdiRpGdIVel-kvEVPE 160 (173)
+++.|+.| +++. .-.+.+++.|++|+++|||.=.+ -...||
T Consensus 6 fR~~gk~mVD~Ia-dY~e~ir~r~v~P~v~PGYl~~llP~~aPe 48 (511)
T KOG0628|consen 6 FREEGKEMVDYIA-DYLENIRKRRVLPDVKPGYLRDLLPSKAPE 48 (511)
T ss_pred HHHHHHHHHHHHH-HHHHhhhccCCCCCCCcchhhhhCCCCCCC
Confidence 44444433 3333 35688999999999999997532 334443
No 16
>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=50.02 E-value=22 Score=27.40 Aligned_cols=26 Identities=15% Similarity=0.473 Sum_probs=17.1
Q ss_pred CCCCC-CcEEEEE-EeecccceeeeeEe
Q 030707 144 PDIRT-GDVVEIK-LVNAVFDYLYNVLC 169 (173)
Q Consensus 144 PdiRp-GdIVelk-vEVPEnkr~~~~~c 169 (173)
|.++. ||||.|+ +.|=.-+....++|
T Consensus 71 P~v~~~GDii~l~r~kv~~~~~~~~~~~ 98 (146)
T PF02765_consen 71 PNVKSVGDIIRLRRVKVQSYNGKPQGLS 98 (146)
T ss_dssp CTTCSTTHEEEEEEEEEEEETTEEEEEE
T ss_pred CCCCCCCCEEEEEEEEEEEECCEEEEEe
Confidence 99999 9999877 65544333333443
No 17
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=47.71 E-value=12 Score=26.63 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=13.0
Q ss_pred CCCCCcEEEEEEeec
Q 030707 145 DIRTGDVVEIKLVNA 159 (173)
Q Consensus 145 diRpGdIVelkvEVP 159 (173)
++..||||++|=.=|
T Consensus 1 ~~~vgDiV~mKK~HP 15 (57)
T PF06107_consen 1 EYEVGDIVEMKKPHP 15 (57)
T ss_pred CccCCCEEEEcCCCC
Confidence 578999999998777
No 18
>KOG3572 consensus Uncharacterized conserved protein, contains DEP domain [Signal transduction mechanisms]
Probab=47.15 E-value=11 Score=40.52 Aligned_cols=18 Identities=44% Similarity=0.744 Sum_probs=15.0
Q ss_pred CCCCCCCCCcEEEEEEee
Q 030707 141 RPIPDIRTGDVVEIKLVN 158 (173)
Q Consensus 141 R~iPdiRpGdIVelkvEV 158 (173)
...|+|+|||||||+-..
T Consensus 123 ~~fP~IKpGDIVEI~~~n 140 (1701)
T KOG3572|consen 123 AKFPEIKPGDIVEILSKN 140 (1701)
T ss_pred hhCCCCCCCceEEEeccC
Confidence 357999999999998653
No 19
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=45.82 E-value=24 Score=26.08 Aligned_cols=22 Identities=18% Similarity=0.286 Sum_probs=15.8
Q ss_pred CCCCCCcEEEEEEeecccceeeee
Q 030707 144 PDIRTGDVVEIKLVNAVFDYLYNV 167 (173)
Q Consensus 144 PdiRpGdIVelkvEVPEnkr~~~~ 167 (173)
-.++|||+|+|.-. .+...+++
T Consensus 138 ~~l~pGDvi~l~~~--~~~~~~RI 159 (164)
T PF13550_consen 138 LALEPGDVIALSDD--GRDMRFRI 159 (164)
T ss_pred ccCCCCCEEEEEeC--CCceEEEE
Confidence 56899999998766 44555554
No 20
>KOG3047 consensus Predicted transcriptional regulator UXT [Transcription]
Probab=45.34 E-value=35 Score=28.54 Aligned_cols=47 Identities=19% Similarity=0.097 Sum_probs=39.1
Q ss_pred chhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccceeeeeEeeec
Q 030707 121 KLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFDYLYNVLCYSF 172 (173)
Q Consensus 121 k~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnkr~~~~~c~~~ 172 (173)
++++..+-|-.++=.+.+..-. -|+-+-+..+||..+++|-.+||.|
T Consensus 51 kLk~t~eRL~eaahkel~~ktd-----LGcnfFmdi~VpDTk~i~VaL~~~f 97 (157)
T KOG3047|consen 51 KLKFTCERLLEAAHKELEGKTD-----LGCNFFMDIEVPDTKHIVVALCDDF 97 (157)
T ss_pred HHHHHHHHHHHhchhhhhcccc-----ccceeeEeeecCCcceEEEEeecce
Confidence 3778888887777777766544 4999999999999999999999987
No 21
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=45.32 E-value=32 Score=23.68 Aligned_cols=39 Identities=26% Similarity=0.103 Sum_probs=23.3
Q ss_pred hhHHHHHHhhhcCC---------CCCCCCCcEEEEEEeecccceeeeeEe
Q 030707 129 LNKRAVEASESERP---------IPDIRTGDVVEIKLVNAVFDYLYNVLC 169 (173)
Q Consensus 129 Lnkeavee~~~~R~---------iPdiRpGdIVelkvEVPEnkr~~~~~c 169 (173)
+|+.|++.+..-+. -.+|++||+|.|.-+ +++.+..|.|
T Consensus 5 Vd~~a~~~i~~Ga~L~~~GV~~~~~~f~~gd~V~i~~~--~g~~ia~G~a 52 (74)
T PF01472_consen 5 VDDGAVEAILNGASLFAPGVVEVDGDFRKGDEVAIVDE--DGEVIAVGRA 52 (74)
T ss_dssp E-HHHHHHHHTTSEEEGGGEEEEETT--TTSEEEEEET--TSSEEEEEEE
T ss_pred ECccHHHHHHcCCCcchHHhEECCCCcCCCCEEEEEcC--CCeEEEEEEE
Confidence 45566666555433 367999999998765 5666666654
No 22
>PHA03171 UL37 tegument protein; Provisional
Probab=44.92 E-value=14 Score=35.49 Aligned_cols=42 Identities=29% Similarity=0.302 Sum_probs=20.5
Q ss_pred hhhccccchhhhhhhccCCCCCccchhhHHhHhhHHHHHHhhh
Q 030707 97 VAVEAESEDKVEEEEVKAPRKPRVKLGDIMGILNKRAVEASES 139 (173)
Q Consensus 97 ~~~Ege~~~v~eeee~~pprkkrkk~g~IM~ILnkeavee~~~ 139 (173)
+++|+|+++.+||.|.+-|-....-+--+- =|-+||-++++|
T Consensus 96 ~d~~~~~~~~eee~e~~~pevnp~daegl~-glarea~~alkk 137 (499)
T PHA03171 96 PDTEAEEEDEEEEIEAPDPEVNPLDAEGLS-GLAREACDALKK 137 (499)
T ss_pred CchhhhhhhhhhhccCCCCCCCCcchhhhh-hhHHHHHHHHHH
Confidence 344555555555555555544443332222 255666666554
No 23
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=44.92 E-value=28 Score=24.45 Aligned_cols=22 Identities=27% Similarity=0.480 Sum_probs=18.0
Q ss_pred CCCCCCcEEEEEEeecccceee
Q 030707 144 PDIRTGDVVEIKLVNAVFDYLY 165 (173)
Q Consensus 144 PdiRpGdIVelkvEVPEnkr~~ 165 (173)
+.+|.||.|+++++....-++|
T Consensus 1 ~~~~~Ge~v~~~~~~~~~~Yl~ 22 (83)
T PF14326_consen 1 TVYRVGERVRFRVTSNRDGYLY 22 (83)
T ss_pred CcccCCCEEEEEEEeCCCeEEE
Confidence 4689999999999997666655
No 24
>cd03440 hot_dog The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold. These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis.
Probab=44.05 E-value=55 Score=19.08 Aligned_cols=43 Identities=16% Similarity=0.214 Sum_probs=27.7
Q ss_pred chhhHHhHhhHHHHHHhhhc--------------CCCCCCCCCcEEEEEEeecccce
Q 030707 121 KLGDIMGILNKRAVEASESE--------------RPIPDIRTGDVVEIKLVNAVFDY 163 (173)
Q Consensus 121 k~g~IM~ILnkeavee~~~~--------------R~iPdiRpGdIVelkvEVPEnkr 163 (173)
..++++.+++.-...-...- +=.-.+++||.|.+++++-...+
T Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~~~~~ 75 (100)
T cd03440 19 HGGLLLALADEAAGAAAARLGGRGLGAVTLSLDVRFLRPVRPGDTLTVEAEVVRVGR 75 (100)
T ss_pred chHHHHHHHHHHHHHHHHHhccCCCeEEEEEEEeEEecCCCCCCEEEEEEEEEeccc
Confidence 35566666666655555432 12235677999999999986653
No 25
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=43.09 E-value=19 Score=29.59 Aligned_cols=27 Identities=37% Similarity=0.673 Sum_probs=20.3
Q ss_pred HHhHhhHHHHHHhhhcCCCCCCCCCcEEEEE
Q 030707 125 IMGILNKRAVEASESERPIPDIRTGDVVEIK 155 (173)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelk 155 (173)
||+.|+.. ....++..+|.+||.|+|.
T Consensus 107 ~l~~~~~~----~~~~~~~~~~e~Gd~VrI~ 133 (178)
T COG0250 107 ILGFLEEE----VAPKKPKVDFEPGDVVRII 133 (178)
T ss_pred HHhhcccc----ccCCcccccCCCCCEEEEe
Confidence 55555544 5567788999999999983
No 26
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=42.73 E-value=30 Score=28.83 Aligned_cols=33 Identities=30% Similarity=0.280 Sum_probs=28.1
Q ss_pred hHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeec
Q 030707 127 GILNKRAVEASESERPIPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 127 ~ILnkeavee~~~~R~iPdiRpGdIVelkvEVP 159 (173)
..||++|++.+++.+..|.+.-|.-+.+++.+|
T Consensus 206 ~~lD~aal~air~~~~~p~~p~~~~~~~~i~~~ 238 (244)
T COG0810 206 PALDRAALEAIRKWRFKPPKPGGKKVGIKITIP 238 (244)
T ss_pred HHHHHHHHHHHHHhccCCCCCCCCccceeEEEE
Confidence 369999999999999999999876667777665
No 27
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=40.44 E-value=16 Score=29.96 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=9.3
Q ss_pred CCCCCcEEEEE
Q 030707 145 DIRTGDVVEIK 155 (173)
Q Consensus 145 diRpGdIVelk 155 (173)
-|.|||||.|+
T Consensus 61 ~~~PGDIirLt 71 (134)
T KOG3416|consen 61 LIQPGDIIRLT 71 (134)
T ss_pred ccCCccEEEec
Confidence 38999999885
No 28
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=40.10 E-value=20 Score=26.55 Aligned_cols=12 Identities=50% Similarity=0.700 Sum_probs=10.3
Q ss_pred CCCCCcEEEEEE
Q 030707 145 DIRTGDVVEIKL 156 (173)
Q Consensus 145 diRpGdIVelkv 156 (173)
-|+|||+|.+.+
T Consensus 46 ~I~~GD~V~Ve~ 57 (75)
T COG0361 46 RILPGDVVLVEL 57 (75)
T ss_pred EeCCCCEEEEEe
Confidence 489999998876
No 29
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=39.27 E-value=29 Score=24.81 Aligned_cols=23 Identities=26% Similarity=0.242 Sum_probs=17.5
Q ss_pred CCCCCcEEEEEEeecccceeeee
Q 030707 145 DIRTGDVVEIKLVNAVFDYLYNV 167 (173)
Q Consensus 145 diRpGdIVelkvEVPEnkr~~~~ 167 (173)
.+|+||+|.=.+..|...-+|..
T Consensus 40 ~LR~GD~V~G~vr~p~~~ek~~~ 62 (68)
T cd04459 40 NLRTGDTVVGQIRPPKEGERYFA 62 (68)
T ss_pred CCCCCCEEEEEEeCCCCCCCcce
Confidence 48999999999999855444443
No 30
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=38.33 E-value=13 Score=29.87 Aligned_cols=36 Identities=17% Similarity=0.268 Sum_probs=23.5
Q ss_pred HHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecc
Q 030707 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAV 160 (173)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPE 160 (173)
+.++|....+..-........|++||+|..||.--+
T Consensus 98 ~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 98 KLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred ceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 445566555543333334566999999999987665
No 31
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=37.95 E-value=24 Score=28.13 Aligned_cols=13 Identities=38% Similarity=0.626 Sum_probs=11.8
Q ss_pred CCCCCCcEEEEEE
Q 030707 144 PDIRTGDVVEIKL 156 (173)
Q Consensus 144 PdiRpGdIVelkv 156 (173)
=|||-||+|.++.
T Consensus 58 LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 58 LDLRIGDTVKVDG 70 (131)
T ss_pred eeeecCCEEEECC
Confidence 3899999999998
No 32
>PF05697 Trigger_N: Bacterial trigger factor protein (TF); InterPro: IPR008881 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This group of sequences contain the ribosomal subunit association domain.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 2D3O_1 1W26_A 1P9Y_A 1OMS_C 1T11_A 3GU0_A 2NSB_A 2NSC_A 3GTY_X.
Probab=37.57 E-value=26 Score=26.59 Aligned_cols=23 Identities=22% Similarity=0.375 Sum_probs=16.9
Q ss_pred HhhHHHHHHhhhcCCCCCCCCCc
Q 030707 128 ILNKRAVEASESERPIPDIRTGD 150 (173)
Q Consensus 128 ILnkeavee~~~~R~iPdiRpGd 150 (173)
-.-.+++.++++.=.||.||+|=
T Consensus 26 ~~~~~~l~~~~k~~~ipGFRkGK 48 (145)
T PF05697_consen 26 KAYEKALKELAKKVKIPGFRKGK 48 (145)
T ss_dssp HHHHHHHHHHHTTTTBTTS-TTS
T ss_pred HHHHHHHHHHHhhCCCCCCCCCC
Confidence 33456778888888999999995
No 33
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=36.11 E-value=63 Score=22.13 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=16.0
Q ss_pred CCCCCCcEEEEEEeecccc
Q 030707 144 PDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 144 PdiRpGdIVelkvEVPEnk 162 (173)
.++.+|+.|+|++..|.+.
T Consensus 35 ~~~~~g~~v~l~l~l~~~~ 53 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGGE 53 (96)
T ss_pred CCcCCCCEEEEEEEcCCCC
Confidence 3578899999999999754
No 34
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=35.09 E-value=44 Score=25.88 Aligned_cols=25 Identities=28% Similarity=0.393 Sum_probs=16.1
Q ss_pred CCCCCCCCcEEEEEEeecccceeeee
Q 030707 142 PIPDIRTGDVVEIKLVNAVFDYLYNV 167 (173)
Q Consensus 142 ~iPdiRpGdIVelkvEVPEnkr~~~~ 167 (173)
.+.++++||+|.|.-. -.+.+.|+|
T Consensus 69 ~L~~l~~GD~I~v~~~-~g~~~~Y~V 93 (144)
T cd05829 69 RLGDLRKGDKVEVTRA-DGQTATFRV 93 (144)
T ss_pred chhcCCCCCEEEEEEC-CCCEEEEEE
Confidence 4457899999988662 222355554
No 35
>PRK11507 ribosome-associated protein; Provisional
Probab=34.22 E-value=26 Score=25.61 Aligned_cols=10 Identities=30% Similarity=0.508 Sum_probs=8.4
Q ss_pred CCCCCcEEEE
Q 030707 145 DIRTGDVVEI 154 (173)
Q Consensus 145 diRpGdIVel 154 (173)
-||+||+|++
T Consensus 52 Kl~~GD~V~~ 61 (70)
T PRK11507 52 KIVAGQTVSF 61 (70)
T ss_pred CCCCCCEEEE
Confidence 3789999987
No 36
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=34.14 E-value=32 Score=20.77 Aligned_cols=15 Identities=33% Similarity=0.625 Sum_probs=12.5
Q ss_pred CCCCCcEEEEEEeec
Q 030707 145 DIRTGDVVEIKLVNA 159 (173)
Q Consensus 145 diRpGdIVelkvEVP 159 (173)
.+++||+|++++---
T Consensus 41 ~~~~G~~v~~~v~~~ 55 (65)
T cd00164 41 VFKVGDEVEVKVLEV 55 (65)
T ss_pred EeCCCCEEEEEEEEE
Confidence 489999999998654
No 37
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=33.86 E-value=29 Score=24.29 Aligned_cols=12 Identities=33% Similarity=0.678 Sum_probs=7.4
Q ss_pred CCCCCcEEEEEE
Q 030707 145 DIRTGDVVEIKL 156 (173)
Q Consensus 145 diRpGdIVelkv 156 (173)
-|.|||+|+|++
T Consensus 12 ~l~pGD~l~i~v 23 (82)
T PF02563_consen 12 RLGPGDVLRISV 23 (82)
T ss_dssp ---TT-EEEEEE
T ss_pred EECCCCEEEEEE
Confidence 478999999987
No 38
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=33.43 E-value=41 Score=22.36 Aligned_cols=26 Identities=8% Similarity=0.263 Sum_probs=17.7
Q ss_pred CCCCCCCCCcEEEEEEeecccceeee
Q 030707 141 RPIPDIRTGDVVEIKLVNAVFDYLYN 166 (173)
Q Consensus 141 R~iPdiRpGdIVelkvEVPEnkr~~~ 166 (173)
.+.--|++||+|+.|+---...+.+|
T Consensus 42 ~~~~~~~~Gd~i~~kVl~~d~~~~~~ 67 (70)
T cd05702 42 NPLSKFKIGQKIKARVIGGHDAKTHR 67 (70)
T ss_pred ChhHhCCCCCEEEEEEEEEeCccccc
Confidence 33444899999999986555444444
No 39
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=32.90 E-value=40 Score=22.99 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=18.7
Q ss_pred CCCCcEE-------EEEEeecccceeeeeEe
Q 030707 146 IRTGDVV-------EIKLVNAVFDYLYNVLC 169 (173)
Q Consensus 146 iRpGdIV-------elkvEVPEnkr~~~~~c 169 (173)
|+|||.| +|.+++=++.+++++-|
T Consensus 29 i~Pg~~vTmDyr~dRLnv~~D~~g~I~~v~C 59 (60)
T PF11720_consen 29 IRPGDAVTMDYRPDRLNVEVDDDGVITRVRC 59 (60)
T ss_pred eCCCCcCcccCCCCcEEEEECCCCcEEEEec
Confidence 4577776 56778888889999888
No 40
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=32.24 E-value=27 Score=23.88 Aligned_cols=38 Identities=13% Similarity=0.181 Sum_probs=22.9
Q ss_pred HHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccc
Q 030707 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnk 162 (173)
..++|...++........-.-|++||+|..++.--.+.
T Consensus 30 ~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 30 GTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred ceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 34444444443222222334489999999999877654
No 41
>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=32.10 E-value=82 Score=22.33 Aligned_cols=21 Identities=10% Similarity=0.039 Sum_probs=16.0
Q ss_pred CCCCCCCCcEEEEEEeecccc
Q 030707 142 PIPDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 142 ~iPdiRpGdIVelkvEVPEnk 162 (173)
=.=.++|||.+++++++-+.+
T Consensus 84 f~~pv~pgd~l~i~~~v~~~~ 104 (131)
T cd01288 84 FRKPVVPGDQLILEVELLKLR 104 (131)
T ss_pred EccccCCCCEEEEEEEEEEee
Confidence 334566899999999988654
No 42
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=31.61 E-value=53 Score=25.02 Aligned_cols=37 Identities=22% Similarity=0.205 Sum_probs=26.5
Q ss_pred hhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccceeeeeE
Q 030707 122 LGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFDYLYNVL 168 (173)
Q Consensus 122 ~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnkr~~~~~ 168 (173)
+||-|.. . ..-+.+..++.||.|.|.- +.+.+.|.|.
T Consensus 50 aGH~~~~---~-----~~F~~L~~l~~Gd~i~v~~--~~~~~~Y~V~ 86 (137)
T cd05830 50 AGHRTTY---G-----APFNDLDKLRPGDKIVVET--ADGWYTYVVR 86 (137)
T ss_pred EecCCCC---C-----cccccHhhCCCCCEEEEEE--CCeEEEEEEe
Confidence 8898853 1 2357788999999877753 6667777664
No 43
>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=31.47 E-value=38 Score=26.00 Aligned_cols=15 Identities=20% Similarity=0.742 Sum_probs=12.3
Q ss_pred CCCCCCCCCcEEEEE
Q 030707 141 RPIPDIRTGDVVEIK 155 (173)
Q Consensus 141 R~iPdiRpGdIVelk 155 (173)
..+|.+..||||.||
T Consensus 64 ~~LP~v~~GDVIll~ 78 (138)
T cd04497 64 ESLPIVKVGDIILLR 78 (138)
T ss_pred hhCCCCCCCCEEEEE
Confidence 348888999999875
No 44
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=31.16 E-value=30 Score=25.32 Aligned_cols=16 Identities=31% Similarity=0.424 Sum_probs=10.9
Q ss_pred CCCCCcEEEEEEeecc
Q 030707 145 DIRTGDVVEIKLVNAV 160 (173)
Q Consensus 145 diRpGdIVelkvEVPE 160 (173)
++++||||+|.=.=+.
T Consensus 48 g~k~GdVvkI~R~S~t 63 (74)
T PF01191_consen 48 GAKPGDVVKIIRKSET 63 (74)
T ss_dssp T--TTSEEEEEEEETT
T ss_pred CCCCCCEEEEEecCCC
Confidence 7899999998755553
No 45
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=31.05 E-value=12 Score=34.27 Aligned_cols=45 Identities=16% Similarity=0.113 Sum_probs=39.7
Q ss_pred CccchhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccc
Q 030707 118 PRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 118 krkk~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnk 162 (173)
||.+++-|.--+--+.+|++=++.-.||+..-..+-+|.++||.+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDR 184 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDR 184 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhh
Confidence 444478888888889999999999999999999999999999977
No 46
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=31.01 E-value=55 Score=24.90 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=18.8
Q ss_pred CCCCCCCCCcEEEEEEeecccceeeeeE
Q 030707 141 RPIPDIRTGDVVEIKLVNAVFDYLYNVL 168 (173)
Q Consensus 141 R~iPdiRpGdIVelkvEVPEnkr~~~~~ 168 (173)
+.+..+++||.|.|. .+...+.|.|.
T Consensus 59 ~~L~~l~~GD~i~v~--~~~~~~~Y~V~ 84 (136)
T TIGR01076 59 TNLDKLKKGDMLYLH--VGNEVLTYQVT 84 (136)
T ss_pred CCHHHCCCCCEEEEE--ECCcEEEEEEE
Confidence 455568999988665 47777777764
No 47
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=29.32 E-value=57 Score=24.28 Aligned_cols=38 Identities=21% Similarity=0.225 Sum_probs=24.9
Q ss_pred hhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccceeeeeE
Q 030707 122 LGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFDYLYNVL 168 (173)
Q Consensus 122 ~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnkr~~~~~ 168 (173)
+||-|.. + -.--+.+.+++.||.|.|.. +...+.|.+.
T Consensus 47 aGH~~~~-~------~~~F~~L~~l~~Gd~I~l~~--~~~~~~Y~V~ 84 (127)
T cd06165 47 AGHNMRN-K------GVLFSPLYKVKVGDKIYLTD--KDNVYEYKVT 84 (127)
T ss_pred EcccCCC-C------CcccCCHHHCcCCCEEEEEE--CCEEEEEEEe
Confidence 7777642 1 12345566778999988866 6677777764
No 48
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=29.28 E-value=30 Score=24.68 Aligned_cols=10 Identities=70% Similarity=1.125 Sum_probs=6.4
Q ss_pred CCCCCcEEEE
Q 030707 145 DIRTGDVVEI 154 (173)
Q Consensus 145 diRpGdIVel 154 (173)
-||+||+|++
T Consensus 48 Kl~~GD~V~~ 57 (65)
T PF13275_consen 48 KLRPGDVVEI 57 (65)
T ss_dssp ---SSEEEEE
T ss_pred cCCCCCEEEE
Confidence 3789999987
No 49
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=28.64 E-value=38 Score=22.23 Aligned_cols=32 Identities=25% Similarity=0.332 Sum_probs=24.1
Q ss_pred HhhHHHHHHhhhcCCCCCCCCCcEEEEEEeec
Q 030707 128 ILNKRAVEASESERPIPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 128 ILnkeavee~~~~R~iPdiRpGdIVelkvEVP 159 (173)
+||+++++.+++.+-.|...-|.-+.+++.+|
T Consensus 43 ~l~~~a~~~v~~~~~~p~~~~g~~~~~~~~~~ 74 (79)
T PF03544_consen 43 ILDEAALRAVKKWRFKPAPKNGKPVKVTYTVP 74 (79)
T ss_dssp CSHHHHHHHHCC-EE-TT--CCEECEEEEEEE
T ss_pred HHHHHHHHHHHhCCCCCCCcCCEEEEEEEEEE
Confidence 79999999999988888777788888887666
No 50
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=28.51 E-value=35 Score=24.08 Aligned_cols=11 Identities=45% Similarity=0.987 Sum_probs=9.1
Q ss_pred CCCCCCCcEEE
Q 030707 143 IPDIRTGDVVE 153 (173)
Q Consensus 143 iPdiRpGdIVe 153 (173)
+.||++||+||
T Consensus 73 ~~d~~~Gdvi~ 83 (84)
T cd03692 73 FNDIKVGDIIE 83 (84)
T ss_pred cccCCCCCEEE
Confidence 44899999987
No 51
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=28.11 E-value=65 Score=24.15 Aligned_cols=28 Identities=14% Similarity=0.296 Sum_probs=20.8
Q ss_pred hcCCCCCCCCCcEEEEEEeecccceeeeeE
Q 030707 139 SERPIPDIRTGDVVEIKLVNAVFDYLYNVL 168 (173)
Q Consensus 139 ~~R~iPdiRpGdIVelkvEVPEnkr~~~~~ 168 (173)
--+.+.++++||.|.|.-. ...+.|.|.
T Consensus 58 ~F~~L~~l~~Gd~v~v~~~--~~~~~Y~V~ 85 (126)
T cd06166 58 IFNRLDEVEKGDEIKVTTK--NGTYKYKIT 85 (126)
T ss_pred ccCChHHCCCCCEEEEEEC--CEEEEEEEE
Confidence 3467778899999988764 666777764
No 52
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=27.00 E-value=1.1e+02 Score=19.02 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=12.4
Q ss_pred CCCCCcEEEEEEeecc
Q 030707 145 DIRTGDVVEIKLVNAV 160 (173)
Q Consensus 145 diRpGdIVelkvEVPE 160 (173)
-++.||.|++++.--+
T Consensus 44 ~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 44 VLKEGDKVKVKVLSID 59 (69)
T ss_pred ccCCCCEEEEEEEEEC
Confidence 3799999999984433
No 53
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=26.86 E-value=55 Score=17.92 Aligned_cols=12 Identities=25% Similarity=0.468 Sum_probs=9.5
Q ss_pred CCCCCcEEEEEE
Q 030707 145 DIRTGDVVEIKL 156 (173)
Q Consensus 145 diRpGdIVelkv 156 (173)
.|++||.|+|.-
T Consensus 1 ~~~~G~~V~I~~ 12 (28)
T smart00739 1 KFEVGDTVRVIA 12 (28)
T ss_pred CCCCCCEEEEeE
Confidence 478999998864
No 54
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=26.60 E-value=56 Score=24.07 Aligned_cols=21 Identities=33% Similarity=0.376 Sum_probs=12.9
Q ss_pred CCCCCcEEEEEEeecccceee
Q 030707 145 DIRTGDVVEIKLVNAVFDYLY 165 (173)
Q Consensus 145 diRpGdIVelkvEVPEnkr~~ 165 (173)
.+|+||.|+=.+.-|.+.-+|
T Consensus 42 ~LR~GD~V~G~vr~p~~~ek~ 62 (78)
T PF07497_consen 42 GLRTGDLVEGQVRPPREGEKY 62 (78)
T ss_dssp T--TTEEEEEEEE--STTSSS
T ss_pred CCCCCCEEEEEEeCCCCCCcc
Confidence 479999999999998554444
No 55
>PF09874 DUF2101: Predicted membrane protein (DUF2101); InterPro: IPR018663 This family of conserved hypothetical proteins has no known function.
Probab=26.28 E-value=55 Score=28.50 Aligned_cols=16 Identities=38% Similarity=0.812 Sum_probs=13.9
Q ss_pred CCCCCCCCcEEEEEEe
Q 030707 142 PIPDIRTGDVVEIKLV 157 (173)
Q Consensus 142 ~iPdiRpGdIVelkvE 157 (173)
..||..+||+|.|.||
T Consensus 178 ~~~d~~~G~vVKl~VE 193 (206)
T PF09874_consen 178 AVPDVEEGDVVKLLVE 193 (206)
T ss_pred CCCCCCCCceEEEEEe
Confidence 3579999999999987
No 56
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=26.17 E-value=45 Score=28.56 Aligned_cols=15 Identities=27% Similarity=0.667 Sum_probs=12.3
Q ss_pred CCCCCCcEEEEEEee
Q 030707 144 PDIRTGDVVEIKLVN 158 (173)
Q Consensus 144 PdiRpGdIVelkvEV 158 (173)
=.||+||||+-||--
T Consensus 117 d~f~~GDivrA~Vis 131 (188)
T COG1096 117 DAFRIGDIVRARVIS 131 (188)
T ss_pred cccccccEEEEEEEe
Confidence 579999999987743
No 57
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=26.17 E-value=67 Score=22.43 Aligned_cols=17 Identities=29% Similarity=0.409 Sum_probs=12.9
Q ss_pred CCCCCCCcEEEE----EEeec
Q 030707 143 IPDIRTGDVVEI----KLVNA 159 (173)
Q Consensus 143 iPdiRpGdIVel----kvEVP 159 (173)
-+++|.|||+++ .+++-
T Consensus 31 P~~~keGDvl~i~~~~~~~~d 51 (71)
T PF11213_consen 31 PEGAKEGDVLEIGEDGSIEID 51 (71)
T ss_pred CCCCCcccEEEECCCceEEEC
Confidence 357999999999 55543
No 58
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=25.90 E-value=46 Score=23.57 Aligned_cols=11 Identities=36% Similarity=0.694 Sum_probs=6.9
Q ss_pred CCCCCcEEEEE
Q 030707 145 DIRTGDVVEIK 155 (173)
Q Consensus 145 diRpGdIVelk 155 (173)
+||.||-|||.
T Consensus 5 pf~~GdrVQlT 15 (54)
T PF14801_consen 5 PFRAGDRVQLT 15 (54)
T ss_dssp S--TT-EEEEE
T ss_pred CCCCCCEEEEc
Confidence 68999999986
No 59
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=25.70 E-value=78 Score=23.11 Aligned_cols=14 Identities=36% Similarity=0.387 Sum_probs=11.8
Q ss_pred CCCCCCcEEEEEEe
Q 030707 144 PDIRTGDVVEIKLV 157 (173)
Q Consensus 144 PdiRpGdIVelkvE 157 (173)
.+|++||+|.|..+
T Consensus 59 ~~~~~gd~V~I~~~ 72 (107)
T TIGR00451 59 EDIKEGDDVVVVDE 72 (107)
T ss_pred CCcCCCCEEEEEEC
Confidence 58999999998754
No 60
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=25.37 E-value=79 Score=23.71 Aligned_cols=34 Identities=21% Similarity=0.332 Sum_probs=25.1
Q ss_pred hhhHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeecccceeeeeE
Q 030707 122 LGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVFDYLYNVL 168 (173)
Q Consensus 122 ~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEnkr~~~~~ 168 (173)
+||-|. --+.+..+++||.|.|.-. ...+.|.+.
T Consensus 49 aGH~~~-----------~F~~L~~l~~Gd~i~v~~~--~~~~~Y~V~ 82 (127)
T cd05828 49 AGHRDT-----------HFRFLGELEPGDIITLQTL--GGTYTYRVT 82 (127)
T ss_pred EEeCch-----------hhhChhcCCCCCEEEEEEC--CEEEEEEEe
Confidence 888872 3567888999999888654 666777664
No 61
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=24.90 E-value=1.6e+02 Score=18.21 Aligned_cols=17 Identities=41% Similarity=0.728 Sum_probs=14.7
Q ss_pred CCCCCCCcEEEEEEeec
Q 030707 143 IPDIRTGDVVEIKLVNA 159 (173)
Q Consensus 143 iPdiRpGdIVelkvEVP 159 (173)
...++.||.|.+++.-+
T Consensus 34 ~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 34 LKSLREGDEVEFKVVSP 50 (64)
T ss_pred CCcCCCCCEEEEEEEEc
Confidence 56789999999999875
No 62
>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=24.52 E-value=1.1e+02 Score=21.48 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=16.9
Q ss_pred CCCCCCCCCcEEEEEEeecccc
Q 030707 141 RPIPDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 141 R~iPdiRpGdIVelkvEVPEnk 162 (173)
+=.=+++|||.+.+++++=+.+
T Consensus 84 kf~~~v~pgd~l~i~~~i~~~~ 105 (131)
T cd00493 84 KFRGPVLPGDTLTLEVELLKVR 105 (131)
T ss_pred EECCCcCCCCEEEEEEEEEEee
Confidence 3344678999999999988655
No 63
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=24.39 E-value=56 Score=24.32 Aligned_cols=15 Identities=27% Similarity=0.461 Sum_probs=11.8
Q ss_pred CCCCCcEEEEEEeec
Q 030707 145 DIRTGDVVEIKLVNA 159 (173)
Q Consensus 145 diRpGdIVelkvEVP 159 (173)
++++||||+|.=.=+
T Consensus 51 g~k~GdVvkI~R~S~ 65 (79)
T PRK09570 51 GAKPGDVIKIVRKSP 65 (79)
T ss_pred CCCCCCEEEEEECCC
Confidence 789999999865444
No 64
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=23.76 E-value=68 Score=25.22 Aligned_cols=12 Identities=42% Similarity=0.786 Sum_probs=10.5
Q ss_pred CCCCCCcEEEEE
Q 030707 144 PDIRTGDVVEIK 155 (173)
Q Consensus 144 PdiRpGdIVelk 155 (173)
-+|++||.|+|+
T Consensus 93 ~~~~~G~~V~I~ 104 (153)
T PRK08559 93 EGIKEGDIVELI 104 (153)
T ss_pred cCCCCCCEEEEe
Confidence 579999999986
No 65
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=23.75 E-value=1.3e+02 Score=24.37 Aligned_cols=46 Identities=15% Similarity=0.018 Sum_probs=27.9
Q ss_pred CCccchhhHHhHhhHHHHHHh---------hhcCCCCCCCCCcEEEEEEeecccc
Q 030707 117 KPRVKLGDIMGILNKRAVEAS---------ESERPIPDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 117 kkrkk~g~IM~ILnkeavee~---------~~~R~iPdiRpGdIVelkvEVPEnk 162 (173)
......+++|...+-=++... ...|=.=+++|||.+.+++++-..+
T Consensus 101 ~~i~hG~f~~aqa~~la~~~~~~~~~~~~i~~irF~kPV~pGD~L~~ea~v~~~~ 155 (185)
T PRK04424 101 TGIARGHHLFAQANSLAVAVIDAELALTGVANIRFKRPVKLGERVVAKAEVVRKK 155 (185)
T ss_pred CCeecHHHHHHHHHHHHHHhcCCcEEEEEeeeEEEccCCCCCCEEEEEEEEEEcc
Confidence 334445666655554222211 2233344678999999999999755
No 66
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=23.72 E-value=1.9e+02 Score=18.93 Aligned_cols=23 Identities=35% Similarity=0.122 Sum_probs=14.9
Q ss_pred CCCCCCcEEEEEEeecccceeeeeE
Q 030707 144 PDIRTGDVVEIKLVNAVFDYLYNVL 168 (173)
Q Consensus 144 PdiRpGdIVelkvEVPEnkr~~~~~ 168 (173)
.+|++||+|.|.-+ ..+.+..|+
T Consensus 29 ~~~~~g~~V~v~~~--~g~~vg~G~ 51 (77)
T smart00359 29 GGIKEGDVVVIVDE--KGEPLGIGL 51 (77)
T ss_pred CCcCCCCEEEEEcC--CCCEEEEEE
Confidence 57999999988754 234444443
No 67
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=23.65 E-value=46 Score=21.70 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=13.4
Q ss_pred CCCCCcEEEEEEeecc
Q 030707 145 DIRTGDVVEIKLVNAV 160 (173)
Q Consensus 145 diRpGdIVelkvEVPE 160 (173)
.+++||+|++++.--+
T Consensus 44 ~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 44 EVKVGDEVEVYVLRVE 59 (70)
T ss_pred cCCCCCEEEEEEEEEE
Confidence 3899999999987654
No 68
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=22.74 E-value=2e+02 Score=18.05 Aligned_cols=25 Identities=16% Similarity=0.170 Sum_probs=18.7
Q ss_pred CCCCCcEEEEEEeecccceeeeeEeeec
Q 030707 145 DIRTGDVVEIKLVNAVFDYLYNVLCYSF 172 (173)
Q Consensus 145 diRpGdIVelkvEVPEnkr~~~~~c~~~ 172 (173)
.++.|+++..+. ++..-|++.+.+.
T Consensus 2 ~~~~G~~~~a~~---~d~~wyra~I~~~ 26 (57)
T smart00333 2 TFKVGDKVAARW---EDGEWYRARIIKV 26 (57)
T ss_pred CCCCCCEEEEEe---CCCCEEEEEEEEE
Confidence 578999999887 4667777776653
No 69
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=22.51 E-value=75 Score=22.10 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=10.9
Q ss_pred CCCCcEEEEEEeec
Q 030707 146 IRTGDVVEIKLVNA 159 (173)
Q Consensus 146 iRpGdIVelkvEVP 159 (173)
.||||.|.+|+-+=
T Consensus 11 YrPGetV~~~~~~~ 24 (99)
T PF01835_consen 11 YRPGETVHFRAIVR 24 (99)
T ss_dssp E-TTSEEEEEEEEE
T ss_pred cCCCCEEEEEEEEe
Confidence 69999999998843
No 70
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.41 E-value=66 Score=20.88 Aligned_cols=15 Identities=33% Similarity=0.470 Sum_probs=12.3
Q ss_pred CCCCCcEEEEEEeec
Q 030707 145 DIRTGDVVEIKLVNA 159 (173)
Q Consensus 145 diRpGdIVelkvEVP 159 (173)
-++.||+|++++.--
T Consensus 47 ~~~~Gd~v~v~i~~v 61 (77)
T cd05708 47 LFRVGDKVRAKVLKI 61 (77)
T ss_pred eecCCCEEEEEEEEE
Confidence 379999999997654
No 71
>COG5475 Uncharacterized small protein [Function unknown]
Probab=22.39 E-value=51 Score=23.90 Aligned_cols=12 Identities=50% Similarity=0.714 Sum_probs=9.9
Q ss_pred CCCCCcEEEEEE
Q 030707 145 DIRTGDVVEIKL 156 (173)
Q Consensus 145 diRpGdIVelkv 156 (173)
-|.+||+|+||=
T Consensus 4 ~FstgdvV~lKs 15 (60)
T COG5475 4 SFSTGDVVTLKS 15 (60)
T ss_pred eeecCcEEEeec
Confidence 378999999973
No 72
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=22.30 E-value=1.3e+02 Score=20.44 Aligned_cols=20 Identities=35% Similarity=0.541 Sum_probs=16.0
Q ss_pred CCCCCCCcEEEEE-Eeecccc
Q 030707 143 IPDIRTGDVVEIK-LVNAVFD 162 (173)
Q Consensus 143 iPdiRpGdIVelk-vEVPEnk 162 (173)
.+.|.+||+|.|+ ..+=+.+
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~ 66 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFN 66 (82)
T ss_pred cccCCCCCEEEEEeEEEEecC
Confidence 6779999999999 7775544
No 73
>PF05093 CIAPIN1: Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis; InterPro: IPR007785 Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS) []. CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis []. In addition, it has also anti-apoptotic effects in the cell. It is involved in negative control of cell death upon cytokine withdrawal and promotes development of hematopoietic cells [].
Probab=22.27 E-value=42 Score=26.07 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=11.3
Q ss_pred CCCCCCCCCcEEEE
Q 030707 141 RPIPDIRTGDVVEI 154 (173)
Q Consensus 141 R~iPdiRpGdIVel 154 (173)
+=+|.|+||+-|+|
T Consensus 87 lGlPaFkpGe~V~l 100 (100)
T PF05093_consen 87 LGLPAFKPGEKVKL 100 (100)
T ss_pred CCCCCCCCCCeecC
Confidence 34799999998875
No 74
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.93 E-value=33 Score=22.45 Aligned_cols=38 Identities=13% Similarity=0.058 Sum_probs=23.6
Q ss_pred hHHhHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeccc
Q 030707 124 DIMGILNKRAVEASESERPIPDIRTGDVVEIKLVNAVF 161 (173)
Q Consensus 124 ~IM~ILnkeavee~~~~R~iPdiRpGdIVelkvEVPEn 161 (173)
.+.+.|....+..-...++-=.++.||.|++++.--..
T Consensus 23 ~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 23 GVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred CCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence 35666665555332233343449999999999876543
No 75
>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=21.74 E-value=1.7e+02 Score=19.89 Aligned_cols=16 Identities=31% Similarity=0.474 Sum_probs=9.4
Q ss_pred CCCCcEEEEEEeeccc
Q 030707 146 IRTGDVVEIKLVNAVF 161 (173)
Q Consensus 146 iRpGdIVelkvEVPEn 161 (173)
|++||.|||+-+....
T Consensus 1 F~~G~~VEV~s~e~g~ 16 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGF 16 (68)
T ss_dssp --TT-EEEEEE-SBTT
T ss_pred CCCCCEEEEEEcCCCC
Confidence 7899999998765443
No 76
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=21.55 E-value=1.3e+02 Score=19.20 Aligned_cols=27 Identities=11% Similarity=0.256 Sum_probs=17.0
Q ss_pred CCCCCcEEEEEEeeccccee-eeeEeee
Q 030707 145 DIRTGDVVEIKLVNAVFDYL-YNVLCYS 171 (173)
Q Consensus 145 diRpGdIVelkvEVPEnkr~-~~~~c~~ 171 (173)
.|++||+|.++=.+=..+.. ....+.+
T Consensus 44 ~l~~g~~v~v~G~v~~~~~~~~~l~~~~ 71 (75)
T PF01336_consen 44 KLKEGDIVRVRGKVKRYNGGELELIVPK 71 (75)
T ss_dssp TS-TTSEEEEEEEEEEETTSSEEEEEEE
T ss_pred cCCCCeEEEEEEEEEEECCccEEEEECE
Confidence 48899999998666544443 4444443
No 77
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.39 E-value=76 Score=19.93 Aligned_cols=15 Identities=33% Similarity=0.596 Sum_probs=12.2
Q ss_pred CCCCcEEEEEEeecc
Q 030707 146 IRTGDVVEIKLVNAV 160 (173)
Q Consensus 146 iRpGdIVelkvEVPE 160 (173)
|++||.|++++.=-+
T Consensus 45 ~~~Gd~v~v~i~~vd 59 (68)
T cd05688 45 VNVGDEVEVKVLKID 59 (68)
T ss_pred ECCCCEEEEEEEEEE
Confidence 799999999976543
No 78
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=21.32 E-value=29 Score=29.08 Aligned_cols=48 Identities=31% Similarity=0.373 Sum_probs=38.2
Q ss_pred hhhhccCCCCCccchhhHHhHhhHHHHHHhhhcCCCCC---CCCCcEEEEE
Q 030707 108 EEEEVKAPRKPRVKLGDIMGILNKRAVEASESERPIPD---IRTGDVVEIK 155 (173)
Q Consensus 108 eeee~~pprkkrkk~g~IM~ILnkeavee~~~~R~iPd---iRpGdIVelk 155 (173)
|-.+.+|--+-.++|-.+.+|+-.|.+++....-.-.+ +-=||||.||
T Consensus 113 E~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~~~~~~~~~~TLGdiv~ik 163 (165)
T COG1813 113 ERGEATPNIKVAKKLEKLLGIKLVEKVDEEEEGPKGKDDDGLTLGDIVRIK 163 (165)
T ss_pred HhcccCccHHHHHHHHHHhCceeeeeccccccccccCCcCCCcccceEEec
Confidence 66777888888888999999999999988877734444 4459999997
No 79
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=21.32 E-value=70 Score=24.92 Aligned_cols=17 Identities=24% Similarity=0.743 Sum_probs=13.7
Q ss_pred CCCCCCCCCcEEEEEEe
Q 030707 141 RPIPDIRTGDVVEIKLV 157 (173)
Q Consensus 141 R~iPdiRpGdIVelkvE 157 (173)
+|==++++||+|.|++.
T Consensus 44 KpS~~VK~GD~l~i~~~ 60 (100)
T COG1188 44 KPSKEVKVGDILTIRFG 60 (100)
T ss_pred ccccccCCCCEEEEEeC
Confidence 56668999999998763
No 80
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=21.13 E-value=92 Score=22.75 Aligned_cols=23 Identities=13% Similarity=-0.078 Sum_probs=16.9
Q ss_pred cCCCCCCCCCcEEEEEEeecccc
Q 030707 140 ERPIPDIRTGDVVEIKLVNAVFD 162 (173)
Q Consensus 140 ~R~iPdiRpGdIVelkvEVPEnk 162 (173)
.|=.=+++|||.|.++++|=+.+
T Consensus 86 ~~f~~pv~~GDtl~~~~~v~~~~ 108 (146)
T cd03451 86 VRFPAPVFHGDTLYAESEVLSKR 108 (146)
T ss_pred EEecCCCCCCCEEEEEEEEEEEe
Confidence 33335578999999999987544
No 81
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.60 E-value=1.4e+02 Score=20.40 Aligned_cols=42 Identities=19% Similarity=0.267 Sum_probs=24.2
Q ss_pred hHHhHhhHHHHHHh--hhcCCCCCCCCCcEEEEEEee--cccceee
Q 030707 124 DIMGILNKRAVEAS--ESERPIPDIRTGDVVEIKLVN--AVFDYLY 165 (173)
Q Consensus 124 ~IM~ILnkeavee~--~~~R~iPdiRpGdIVelkvEV--PEnkr~~ 165 (173)
+|++.|....+-.- ....+.=-|++||.|+.|+-- +++++++
T Consensus 23 ~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~ 68 (73)
T cd05703 23 DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLR 68 (73)
T ss_pred CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEE
Confidence 46666665555321 112233339999999999543 4555543
No 82
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=20.41 E-value=77 Score=18.68 Aligned_cols=14 Identities=14% Similarity=0.456 Sum_probs=11.6
Q ss_pred CCCCCcEEEEEEee
Q 030707 145 DIRTGDVVEIKLVN 158 (173)
Q Consensus 145 diRpGdIVelkvEV 158 (173)
.|+.||+|.+.=+.
T Consensus 20 ~~~~Gd~v~v~~~~ 33 (58)
T smart00326 20 SFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCEEEEEEcC
Confidence 58999999987665
No 83
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=20.18 E-value=80 Score=19.31 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=13.1
Q ss_pred CCCCCcEEEEEEeecc
Q 030707 145 DIRTGDVVEIKLVNAV 160 (173)
Q Consensus 145 diRpGdIVelkvEVPE 160 (173)
-+++||.|.+++.--.
T Consensus 46 ~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 46 VLKVGDEVKVKVLSVD 61 (72)
T ss_pred eecCCCEEEEEEEEEe
Confidence 3899999999987553
No 84
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=20.11 E-value=1.3e+02 Score=24.61 Aligned_cols=26 Identities=23% Similarity=0.347 Sum_probs=18.3
Q ss_pred cCCCCCCCCCcEEEEEEeecccc-eeeee
Q 030707 140 ERPIPDIRTGDVVEIKLVNAVFD-YLYNV 167 (173)
Q Consensus 140 ~R~iPdiRpGdIVelkvEVPEnk-r~~~~ 167 (173)
-+.+.++++||.|.|.- ..++ ++|+|
T Consensus 103 F~~L~~L~~GD~I~v~~--~~g~~~~Y~V 129 (174)
T TIGR03784 103 FAFLQELRPGDVIRLQT--PDGQWQSYQV 129 (174)
T ss_pred CCChhhCCCCCEEEEEE--CCCeEEEEEE
Confidence 67899999999988753 3443 34554
Done!