Query 029551
Match_columns 191
No_of_seqs 35 out of 37
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 14:43:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029551.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029551hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1698 Mitochondrial/chloropl 99.8 1.5E-19 3.3E-24 153.1 8.3 129 40-184 4-138 (201)
2 TIGR01024 rplS_bact ribosomal 99.1 1.5E-10 3.4E-15 90.7 6.5 55 125-184 3-61 (113)
3 PRK05338 rplS 50S ribosomal pr 99.1 3.1E-10 6.7E-15 89.3 6.9 56 124-184 2-61 (116)
4 CHL00084 rpl19 ribosomal prote 99.0 2.1E-09 4.5E-14 84.9 7.1 58 122-184 4-65 (117)
5 PF01245 Ribosomal_L19: Riboso 98.9 1.9E-09 4.2E-14 84.0 6.5 51 134-184 7-61 (113)
6 COG0335 RplS Ribosomal protein 98.3 1.8E-06 4E-11 68.7 7.0 56 124-184 4-63 (115)
7 PF09926 DUF2158: Uncharacteri 79.3 1.2 2.6E-05 31.0 1.5 28 146-173 1-35 (53)
8 PF12969 DUF3857: Domain of Un 74.9 2.4 5.1E-05 32.3 2.1 22 141-162 85-106 (177)
9 PF05641 Agenet: Agenet domain 67.3 17 0.00036 25.3 4.9 42 146-189 1-42 (68)
10 TIGR01352 tonB_Cterm TonB fami 65.8 15 0.00033 24.2 4.3 33 127-159 36-68 (74)
11 PF10447 EXOSC1: Exosome compo 64.9 4.6 9.9E-05 30.2 1.8 32 125-156 46-79 (82)
12 KOG3409 Exosomal 3'-5' exoribo 62.4 3.5 7.6E-05 35.9 0.9 34 125-158 100-135 (193)
13 cd01288 FabZ FabZ is a 17kD be 58.9 21 0.00046 25.8 4.3 29 142-170 84-112 (131)
14 PHA03171 UL37 tegument protein 53.1 8.7 0.00019 37.3 1.9 41 97-138 96-136 (499)
15 cd03440 hot_dog The hotdog fol 52.4 42 0.0009 19.9 4.3 46 120-165 18-77 (100)
16 cd00493 FabA_FabZ FabA/Z, beta 51.7 31 0.00068 24.7 4.2 33 141-173 84-116 (131)
17 KOG0628 Aromatic-L-amino-acid/ 49.6 9.4 0.0002 37.4 1.5 34 119-153 6-40 (511)
18 COG1499 NMD3 NMD protein affec 47.2 11 0.00025 34.8 1.6 15 142-156 243-257 (355)
19 PF01472 PUA: PUA domain; Int 46.9 32 0.00069 24.1 3.5 29 129-157 5-42 (74)
20 PF00122 E1-E2_ATPase: E1-E2 A 46.8 12 0.00025 29.9 1.5 26 142-171 48-73 (230)
21 cd05791 S1_CSL4 S1_CSL4: CSL4, 45.4 16 0.00035 26.9 2.0 34 126-159 39-74 (92)
22 PRK04424 fatty acid biosynthes 45.3 42 0.00092 27.5 4.5 56 117-172 101-165 (185)
23 cd04454 S1_Rrp4_like S1_Rrp4_l 45.2 18 0.0004 25.0 2.1 39 125-163 30-68 (82)
24 PF06107 DUF951: Bacterial pro 44.5 14 0.00031 26.6 1.5 17 145-161 1-17 (57)
25 PF08605 Rad9_Rad53_bind: Fung 43.3 16 0.00035 29.5 1.8 13 144-156 58-70 (131)
26 PF13550 Phage-tail_3: Putativ 42.9 30 0.00065 26.0 3.1 14 144-157 138-151 (164)
27 KOG3572 Uncharacterized conser 41.4 16 0.00034 40.0 1.8 19 140-158 122-140 (1701)
28 smart00359 PUA Putative RNA-bi 39.0 78 0.0017 21.1 4.4 25 144-173 29-53 (77)
29 PRK00006 fabZ (3R)-hydroxymyri 38.3 64 0.0014 24.5 4.3 20 145-164 101-120 (147)
30 COG0810 TonB Periplasmic prote 36.9 43 0.00093 28.3 3.4 33 127-159 206-238 (244)
31 KOG3416 Predicted nucleic acid 35.6 21 0.00046 29.7 1.3 11 145-155 61-71 (134)
32 TIGR01750 fabZ beta-hydroxyacy 35.5 83 0.0018 23.5 4.5 23 141-163 93-115 (140)
33 COG0250 NusG Transcription ant 34.8 33 0.00071 28.7 2.4 38 124-165 106-153 (178)
34 TIGR02266 gmx_TIGR02266 Myxoco 34.6 1.4E+02 0.003 20.7 5.2 19 144-162 35-53 (96)
35 COG0361 InfA Translation initi 34.5 27 0.00059 26.2 1.7 13 145-157 46-58 (75)
36 PF04970 LRAT: Lecithin retino 33.6 57 0.0012 24.5 3.3 28 143-177 4-31 (125)
37 PF02765 POT1: Telomeric singl 32.9 40 0.00086 26.4 2.4 21 144-164 71-93 (146)
38 PRK13692 (3R)-hydroxyacyl-ACP 32.8 59 0.0013 26.0 3.5 20 142-161 93-112 (159)
39 PF05697 Trigger_N: Bacterial 31.4 38 0.00082 26.1 2.1 22 129-150 27-48 (145)
40 PRK09521 exosome complex RNA-b 30.9 20 0.00043 29.3 0.5 36 125-160 98-133 (189)
41 cd05702 S1_Rrp5_repeat_hs11_sc 30.7 59 0.0013 21.9 2.7 17 141-157 42-58 (70)
42 cd04491 SoSSB_OBF SoSSB_OBF: A 29.6 79 0.0017 21.9 3.3 23 143-165 46-69 (82)
43 PF02563 Poly_export: Polysacc 29.6 38 0.00081 24.1 1.7 13 145-157 12-24 (82)
44 PRK11507 ribosome-associated p 29.6 34 0.00074 25.3 1.5 9 146-154 53-61 (70)
45 cd00164 S1_like S1_like: Ribos 29.4 43 0.00094 20.5 1.8 15 145-159 41-55 (65)
46 PRK04163 exosome complex RNA-b 29.0 51 0.0011 28.1 2.7 37 125-161 87-127 (235)
47 COG1566 EmrA Multidrug resista 28.9 74 0.0016 29.4 3.8 59 123-182 234-294 (352)
48 cd03442 BFIT_BACH Brown fat-in 28.7 1.1E+02 0.0023 21.4 3.9 25 145-169 63-87 (123)
49 TIGR00451 unchar_dom_2 unchara 28.7 64 0.0014 23.9 2.9 29 129-157 35-72 (107)
50 smart00357 CSP Cold shock prot 28.5 89 0.0019 19.7 3.1 18 143-160 34-51 (64)
51 COG2030 MaoC Acyl dehydratase 28.1 90 0.002 24.7 3.8 29 138-166 99-127 (159)
52 PF07238 PilZ: PilZ domain; I 27.9 1.4E+02 0.003 19.9 4.2 20 145-164 44-63 (102)
53 cd04497 hPOT1_OB1_like hPOT1_O 27.7 48 0.001 25.8 2.1 15 141-155 64-78 (138)
54 KOG0494 Transcription factor C 27.6 14 0.0003 34.3 -1.0 45 118-162 140-184 (332)
55 cd03451 FkbR2 FkbR2 is a Strep 26.5 1.1E+02 0.0025 22.6 3.9 21 143-163 89-109 (146)
56 cd03692 mtIF2_IVc mtIF2_IVc: t 25.6 42 0.00091 24.0 1.3 11 143-153 73-83 (84)
57 PF03544 TonB_C: Gram-negative 25.3 53 0.0012 21.8 1.7 32 128-159 43-74 (79)
58 TIGR02219 phage_NlpC_fam putat 25.3 1.5E+02 0.0033 22.9 4.5 27 144-174 75-101 (134)
59 TIGR03684 arCOG00985 arCOG0415 25.2 1.2E+02 0.0026 23.9 4.0 14 144-157 98-111 (150)
60 PF12945 YcgR_2: Flagellar pro 25.1 68 0.0015 21.9 2.3 25 146-170 1-27 (87)
61 PF01191 RNA_pol_Rpb5_C: RNA p 25.1 44 0.00096 24.8 1.4 11 145-155 48-58 (74)
62 PF13275 S4_2: S4 domain; PDB: 25.0 40 0.00086 24.4 1.1 10 145-154 48-57 (65)
63 PF07703 A2M_N_2: Alpha-2-macr 24.7 1.4E+02 0.003 21.9 4.0 17 145-161 9-25 (136)
64 PF09874 DUF2101: Predicted me 24.6 61 0.0013 28.6 2.4 16 142-157 178-193 (206)
65 PF11213 DUF3006: Protein of u 24.4 76 0.0016 22.5 2.5 12 143-154 31-42 (71)
66 PF12238 MSA-2c: Merozoite sur 23.6 35 0.00076 29.8 0.7 12 178-191 194-205 (205)
67 cd03452 MaoC_C MaoC_C The C-t 23.5 1.1E+02 0.0023 23.5 3.3 22 141-162 84-105 (142)
68 smart00739 KOW KOW (Kyprides, 23.4 70 0.0015 17.8 1.8 12 145-156 1-12 (28)
69 COG1096 Predicted RNA-binding 22.2 59 0.0013 28.2 1.8 14 144-157 117-130 (188)
70 COG0186 RpsQ Ribosomal protein 22.0 1.6E+02 0.0034 22.8 3.9 30 145-174 55-84 (87)
71 PF14801 GCD14_N: tRNA methylt 21.8 61 0.0013 23.3 1.5 35 145-188 5-39 (54)
72 PF13437 HlyD_3: HlyD family s 21.7 2.3E+02 0.005 19.9 4.5 44 140-185 44-91 (105)
73 PF02752 Arrestin_C: Arrestin 21.3 1.7E+02 0.0036 20.7 3.7 22 146-167 16-37 (136)
74 PF01835 A2M_N: MG2 domain; I 21.3 82 0.0018 22.2 2.1 17 145-161 10-26 (99)
75 PF15493 YrpD: Domain of unkno 20.9 93 0.002 27.6 2.8 33 142-174 92-126 (208)
76 COG1813 Predicted transcriptio 20.8 29 0.00063 29.5 -0.3 48 108-155 113-163 (165)
77 PTZ00274 cytochrome b5 reducta 20.8 1E+02 0.0022 27.6 3.0 11 145-155 136-146 (325)
78 PRK08916 flagellar motor switc 20.7 89 0.0019 24.9 2.4 32 142-173 62-99 (116)
79 PRK08559 nusG transcription an 20.6 82 0.0018 25.1 2.2 12 144-155 93-104 (153)
80 cd04460 S1_RpoE S1_RpoE: RpoE, 20.4 1.5E+02 0.0032 21.5 3.3 33 146-178 54-89 (99)
81 cd03711 Tet_C Tet_C: C-terminu 20.4 26 0.00055 24.4 -0.6 61 121-188 14-74 (78)
82 cd05692 S1_RPS1_repeat_hs4 S1_ 20.3 1.4E+02 0.0031 18.7 2.9 20 145-164 44-63 (69)
83 COG1107 Archaea-specific RecJ- 20.2 97 0.0021 31.7 3.1 25 136-160 249-273 (715)
84 PRK14560 putative RNA-binding 20.0 1.7E+02 0.0036 23.4 3.9 26 144-173 105-130 (160)
No 1
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=1.5e-19 Score=153.11 Aligned_cols=129 Identities=17% Similarity=0.107 Sum_probs=100.0
Q ss_pred cceeeecc---CCCccccceecccccceeEEeeccchhhhcchhhHHHhHHHHhhccccchhhccccchhhhhhhcCCCC
Q 029551 40 HGVSVSAK---PIGWNLGFFVNAQVKDSFVVRAEANEEAEANESIEEEQNEAVQAQGDVVVAVEAESEDKVEEEEVKAPR 116 (191)
Q Consensus 40 srlsls~~---~~s~~~~~~~~~~~k~~fVvrAea~~ea~~~~~~~e~~~E~~~~~~d~v~~~Ege~~~v~eeeE~~~pr 116 (191)
||+++++. +..|++.+.+.....++|++.+|....+.....+ ..++.-+...-.+..+..+
T Consensus 4 sr~~~~r~~~~~~a~~~~v~l~~~~~~~~~~~~e~~~~a~~~~~~----------------~~~~~~~~~~~~~~~~~f~ 67 (201)
T KOG1698|consen 4 SRLGFDRFPMFRAASYRNVSLKGKWFSSFIAISEERCFAPTKRPS----------------VNEPSPESPCVVEQYPEFL 67 (201)
T ss_pred ceeeeecccccchhhhheeecccceeeeeccccccccccCCCCcc----------------cccCCCCCccccccCcccc
Confidence 34555554 4567777777778889999988774443322220 1233333333344556777
Q ss_pred CCccchhhHHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeecCCCCcceeeEEEee---ccCCceeEEe
Q 029551 117 KPRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKIGVGCPFTKVLLCQG---KMLGSTLQFE 184 (191)
Q Consensus 117 kkrkk~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPEnkRR~~t~~~ic~~---~glgstf~~~ 184 (191)
+-++..++||++||+++|++.++.|.+|.|++||||+|+.++|+|+|+++.++||||. +|+++||+.-
T Consensus 68 ~~~~~~~~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~atf~LR 138 (201)
T KOG1698|consen 68 PLRKVAKRIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLNATFLLR 138 (201)
T ss_pred cchhHHHHHHHhhCHHHHHHHHhcccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCCcceEEee
Confidence 7788899999999999999999999999999999999999999999999999999996 9999999863
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=99.11 E-value=1.5e-10 Score=90.69 Aligned_cols=55 Identities=15% Similarity=0.238 Sum_probs=48.2
Q ss_pred HHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeec-CCCCcceeeEEEee---ccCCceeEEe
Q 029551 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKI-GVGCPFTKVLLCQG---KMLGSTLQFE 184 (191)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPE-nkRR~~t~~~ic~~---~glgstf~~~ 184 (191)
+|+.++++.+ .+.+|+|++||+|++.+.++| ||.|.+.|.|+||+ +|++||||.-
T Consensus 3 ~i~~~e~~~~-----~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR 61 (113)
T TIGR01024 3 LIKQIEQEQL-----KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVR 61 (113)
T ss_pred HHHHHHHHHh-----hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEE
Confidence 5666666655 578999999999999999999 89999999999997 9999999974
No 3
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=99.08 E-value=3.1e-10 Score=89.35 Aligned_cols=56 Identities=14% Similarity=0.221 Sum_probs=48.6
Q ss_pred hHHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeec-CCCCcceeeEEEee---ccCCceeEEe
Q 029551 124 DIMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKI-GVGCPFTKVLLCQG---KMLGSTLQFE 184 (191)
Q Consensus 124 ~IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPE-nkRR~~t~~~ic~~---~glgstf~~~ 184 (191)
.||+.++.+.+ .+.+|+|++||+|++.+.+.| ||.|.+.|.|+||+ +|++||||.-
T Consensus 2 ~~i~~~~~~~~-----~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR 61 (116)
T PRK05338 2 NLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVR 61 (116)
T ss_pred cHHHHHHHHHh-----hcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEE
Confidence 36677777766 377999999999999999998 68899999999997 9999999974
No 4
>CHL00084 rpl19 ribosomal protein L19
Probab=98.95 E-value=2.1e-09 Score=84.91 Aligned_cols=58 Identities=16% Similarity=0.234 Sum_probs=47.7
Q ss_pred hhhHHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeec-CCCCcceeeEEEee---ccCCceeEEe
Q 029551 122 LGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKI-GVGCPFTKVLLCQG---KMLGSTLQFE 184 (191)
Q Consensus 122 ~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPE-nkRR~~t~~~ic~~---~glgstf~~~ 184 (191)
+..+++-++++.+ ...+|+|++||+|++.+.+.| ||.|.+.|.|+||+ +|+++|||.-
T Consensus 4 ~~~~i~~~~~~~~-----~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvR 65 (117)
T CHL00084 4 LQQLVKEIESEFL-----KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVR 65 (117)
T ss_pred HHHHHHHHHHHHh-----hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEE
Confidence 3456666666555 458999999999999999998 57789999999997 9999999963
No 5
>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=98.94 E-value=1.9e-09 Score=83.97 Aligned_cols=51 Identities=20% Similarity=0.249 Sum_probs=44.0
Q ss_pred HHHhhhcCCCCCCCCCcEEEEEEeeec-CCCCcceeeEEEee---ccCCceeEEe
Q 029551 134 VEASESERPIPDIRTGDVVEIKLFLKI-GVGCPFTKVLLCQG---KMLGSTLQFE 184 (191)
Q Consensus 134 vee~~~~R~iPdiRpGdIVelklEVPE-nkRR~~t~~~ic~~---~glgstf~~~ 184 (191)
+|.......+|+|+|||+|++.+.++| +|.|.+.|.|+||+ +|++|||++-
T Consensus 7 ~e~~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR 61 (113)
T PF01245_consen 7 VEREQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLR 61 (113)
T ss_dssp HHHTTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEE
T ss_pred HHHHHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEE
Confidence 444444699999999999999999995 57888999999997 8999999974
No 6
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=98.32 E-value=1.8e-06 Score=68.72 Aligned_cols=56 Identities=18% Similarity=0.266 Sum_probs=46.1
Q ss_pred hHHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeecCCC-CcceeeEEEee---ccCCceeEEe
Q 029551 124 DIMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKIGVG-CPFTKVLLCQG---KMLGSTLQFE 184 (191)
Q Consensus 124 ~IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPEnkR-R~~t~~~ic~~---~glgstf~~~ 184 (191)
.|++-|+++.+..- +|+|+|||.|.+.+-+-|..+ |.+.|.|+||+ +|+++||+.-
T Consensus 4 ~~i~~le~~q~~~~-----iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvR 63 (115)
T COG0335 4 PIIQQLEQEQIKKD-----IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVR 63 (115)
T ss_pred HHHHHHHHHHHHhh-----CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEE
Confidence 47788888877665 999999999999999887665 46788888875 9999999863
No 7
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=79.26 E-value=1.2 Score=31.05 Aligned_cols=28 Identities=25% Similarity=0.292 Sum_probs=17.2
Q ss_pred CCCCcEEEEE-----EeeecCCC--CcceeeEEEe
Q 029551 146 IRTGDVVEIK-----LFLKIGVG--CPFTKVLLCQ 173 (191)
Q Consensus 146 iRpGdIVelk-----lEVPEnkR--R~~t~~~ic~ 173 (191)
|++||||+|| |-|-+-.. ........|+
T Consensus 1 f~~GDvV~LKSGGp~MTV~~v~~~~~~~~~~v~C~ 35 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPRMTVTEVGPNAGASGGWVECQ 35 (53)
T ss_pred CCCCCEEEEccCCCCeEEEEccccccCCCCeEEEE
Confidence 6899999997 44432222 2344566776
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=74.90 E-value=2.4 Score=32.32 Aligned_cols=22 Identities=32% Similarity=0.567 Sum_probs=13.2
Q ss_pred CCCCCCCCCcEEEEEEeeecCC
Q 029551 141 RPIPDIRTGDVVEIKLFLKIGV 162 (191)
Q Consensus 141 R~iPdiRpGdIVelklEVPEnk 162 (191)
=.+|++++||||++...+=...
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~~~ 106 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKSKN 106 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE-T
T ss_pred EEcCCCCCCcEEEEEEEEEecC
Confidence 4689999999999999985444
No 9
>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=67.30 E-value=17 Score=25.33 Aligned_cols=42 Identities=14% Similarity=-0.082 Sum_probs=23.2
Q ss_pred CCCCcEEEEEEeeecCCCCcceeeEEEeeccCCceeEEeeccee
Q 029551 146 IRTGDVVEIKLFLKIGVGCPFTKVLLCQGKMLGSTLQFEFGGLL 189 (191)
Q Consensus 146 iRpGdIVelklEVPEnkRR~~t~~~ic~~~glgstf~~~~~~~~ 189 (191)
|++||.||++-+...- |...+-++.+..-..++|..+|-.++
T Consensus 1 F~~G~~VEV~s~e~g~--~gaWf~a~V~~~~~~~~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGF--RGAWFPATVLKENGDDKYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT----EEEEEEEEEEETT-EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCC--CcEEEEEEEEEeCCCcEEEEEECCcc
Confidence 7899999999876444 55566666654333339998886543
No 10
>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=65.82 E-value=15 Score=24.21 Aligned_cols=33 Identities=24% Similarity=0.272 Sum_probs=27.7
Q ss_pred HHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeee
Q 029551 127 GILNKRAVEASESERPIPDIRTGDVVEIKLFLK 159 (191)
Q Consensus 127 ~ILnkeavee~~~~R~iPdiRpGdIVelklEVP 159 (191)
..||+.+++.+++-+..|....|.-+..++.+|
T Consensus 36 ~~ld~~a~~av~~~~~~p~~~~g~~~~~~~~~~ 68 (74)
T TIGR01352 36 EALDRAALEAVRKARFEPPPPNGGPVAQSVTIP 68 (74)
T ss_pred hhHHHHHHHHHHhCCCCCCCCCCCceeEEEEEe
Confidence 579999999999999999988887666666665
No 11
>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=64.89 E-value=4.6 Score=30.19 Aligned_cols=32 Identities=31% Similarity=0.586 Sum_probs=17.2
Q ss_pred HHHHhhHHHHHHhhhcCC--CCCCCCCcEEEEEE
Q 029551 125 IMGILNKRAVEASESERP--IPDIRTGDVVEIKL 156 (191)
Q Consensus 125 IM~ILnkeavee~~~~R~--iPdiRpGdIVelkl 156 (191)
..|+|.++.|...++.+. -=-|||||||.=||
T Consensus 46 f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 46 FQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV 79 (82)
T ss_dssp S-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred cEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence 456676766666555543 45699999998776
No 12
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=62.44 E-value=3.5 Score=35.88 Aligned_cols=34 Identities=32% Similarity=0.553 Sum_probs=27.1
Q ss_pred HHHHhhHHHHHHhhhcC--CCCCCCCCcEEEEEEee
Q 029551 125 IMGILNKRAVEASESER--PIPDIRTGDVVEIKLFL 158 (191)
Q Consensus 125 IM~ILnkeavee~~~~R--~iPdiRpGdIVelklEV 158 (191)
.-++|.||.+.+.++.| ++--|||||||.-||==
T Consensus 100 FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis 135 (193)
T KOG3409|consen 100 FRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVIS 135 (193)
T ss_pred hcceeehhhccccccchhhhhhccCCCcEEEEEEee
Confidence 34788999998888776 45689999999888643
No 13
>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=58.91 E-value=21 Score=25.76 Aligned_cols=29 Identities=10% Similarity=-0.252 Sum_probs=20.2
Q ss_pred CCCCCCCCcEEEEEEeeecCCCCcceeeE
Q 029551 142 PIPDIRTGDVVEIKLFLKIGVGCPFTKVL 170 (191)
Q Consensus 142 ~iPdiRpGdIVelklEVPEnkRR~~t~~~ 170 (191)
=.=.++|||.+++++++-+..++..++.+
T Consensus 84 f~~pv~pgd~l~i~~~v~~~~~~~~~~~~ 112 (131)
T cd01288 84 FRKPVVPGDQLILEVELLKLRRGIGKFKG 112 (131)
T ss_pred EccccCCCCEEEEEEEEEEeeCCEEEEEE
Confidence 33456789999999999877655433333
No 14
>PHA03171 UL37 tegument protein; Provisional
Probab=53.08 E-value=8.7 Score=37.32 Aligned_cols=41 Identities=32% Similarity=0.399 Sum_probs=19.7
Q ss_pred hhhccccchhhhhhhcCCCCCCccchhhHHHHhhHHHHHHhh
Q 029551 97 VAVEAESEDKVEEEEVKAPRKPRVKLGDIMGILNKRAVEASE 138 (191)
Q Consensus 97 ~~~Ege~~~v~eeeE~~~prkkrkk~g~IM~ILnkeavee~~ 138 (191)
+++|+|+++.+||.|++.|-....-+--+-| |-+||-++++
T Consensus 96 ~d~~~~~~~~eee~e~~~pevnp~daegl~g-larea~~alk 136 (499)
T PHA03171 96 PDTEAEEEDEEEEIEAPDPEVNPLDAEGLSG-LAREACDALK 136 (499)
T ss_pred CchhhhhhhhhhhccCCCCCCCCcchhhhhh-hHHHHHHHHH
Confidence 3455555555566666555544443222222 4445544443
No 15
>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=52.42 E-value=42 Score=19.92 Aligned_cols=46 Identities=17% Similarity=0.184 Sum_probs=30.0
Q ss_pred cchhhHHHHhhHHHHHHhhhc--------------CCCCCCCCCcEEEEEEeeecCCCCc
Q 029551 120 VKLGDIMGILNKRAVEASESE--------------RPIPDIRTGDVVEIKLFLKIGVGCP 165 (191)
Q Consensus 120 kk~g~IM~ILnkeavee~~~~--------------R~iPdiRpGdIVelklEVPEnkRR~ 165 (191)
...++++..++.-...-...- +=.-.+++||.|.+++++....++.
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~ 77 (100)
T cd03440 18 VHGGLLLALADEAAGAAAARLGGRGLGAVTLSLDVRFLRPVRPGDTLTVEAEVVRVGRSS 77 (100)
T ss_pred cchHHHHHHHHHHHHHHHHHhccCCCeEEEEEEEeEEecCCCCCCEEEEEEEEEeccccE
Confidence 335566666666555555431 1223567799999999998877663
No 16
>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=51.73 E-value=31 Score=24.68 Aligned_cols=33 Identities=9% Similarity=-0.197 Sum_probs=22.1
Q ss_pred CCCCCCCCCcEEEEEEeeecCCCCcceeeEEEe
Q 029551 141 RPIPDIRTGDVVEIKLFLKIGVGCPFTKVLLCQ 173 (191)
Q Consensus 141 R~iPdiRpGdIVelklEVPEnkRR~~t~~~ic~ 173 (191)
+=.=+++|||.+.+++++-+.+....++.+.+.
T Consensus 84 kf~~~v~pgd~l~i~~~i~~~~~~~~~~~~~~~ 116 (131)
T cd00493 84 KFRGPVLPGDTLTLEVELLKVRRGLGKFDGRAY 116 (131)
T ss_pred EECCCcCCCCEEEEEEEEEEeeCCEEEEEEEEE
Confidence 334467899999999999877664444444333
No 17
>KOG0628 consensus Aromatic-L-amino-acid/L-histidine decarboxylase [Amino acid transport and metabolism]
Probab=49.60 E-value=9.4 Score=37.40 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=23.4
Q ss_pred ccchhhHH-HHhhHHHHHHhhhcCCCCCCCCCcEEE
Q 029551 119 RVKLGDIM-GILNKRAVEASESERPIPDIRTGDVVE 153 (191)
Q Consensus 119 rkk~g~IM-~ILnkeavee~~~~R~iPdiRpGdIVe 153 (191)
+++.|+.| +++. .-.+.+++.|++||++|||.=.
T Consensus 6 fR~~gk~mVD~Ia-dY~e~ir~r~v~P~v~PGYl~~ 40 (511)
T KOG0628|consen 6 FREEGKEMVDYIA-DYLENIRKRRVLPDVKPGYLRD 40 (511)
T ss_pred HHHHHHHHHHHHH-HHHHhhhccCCCCCCCcchhhh
Confidence 34444433 3333 4568899999999999999643
No 18
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=47.16 E-value=11 Score=34.82 Aligned_cols=15 Identities=40% Similarity=0.857 Sum_probs=13.0
Q ss_pred CCCCCCCCcEEEEEE
Q 029551 142 PIPDIRTGDVVEIKL 156 (191)
Q Consensus 142 ~iPdiRpGdIVelkl 156 (191)
.||++||||||.++=
T Consensus 243 rip~~~~gDiV~~~~ 257 (355)
T COG1499 243 RIPEFRPGDIVSVRG 257 (355)
T ss_pred ECCCCCCCCEEEECC
Confidence 599999999998753
No 19
>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=46.85 E-value=32 Score=24.07 Aligned_cols=29 Identities=34% Similarity=0.341 Sum_probs=18.8
Q ss_pred hhHHHHHHhhhcCCC---------CCCCCCcEEEEEEe
Q 029551 129 LNKRAVEASESERPI---------PDIRTGDVVEIKLF 157 (191)
Q Consensus 129 Lnkeavee~~~~R~i---------PdiRpGdIVelklE 157 (191)
+|+.|++.+...+.+ ++|++||+|.|.-+
T Consensus 5 Vd~~a~~~i~~Ga~L~~~GV~~~~~~f~~gd~V~i~~~ 42 (74)
T PF01472_consen 5 VDDGAVEAILNGASLFAPGVVEVDGDFRKGDEVAIVDE 42 (74)
T ss_dssp E-HHHHHHHHTTSEEEGGGEEEEETT--TTSEEEEEET
T ss_pred ECccHHHHHHcCCCcchHHhEECCCCcCCCCEEEEEcC
Confidence 566677766665443 67999999998766
No 20
>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=46.79 E-value=12 Score=29.91 Aligned_cols=26 Identities=31% Similarity=0.569 Sum_probs=16.4
Q ss_pred CCCCCCCCcEEEEEEeeecCCCCcceeeEE
Q 029551 142 PIPDIRTGDVVEIKLFLKIGVGCPFTKVLL 171 (191)
Q Consensus 142 ~iPdiRpGdIVelklEVPEnkRR~~t~~~i 171 (191)
+.=+++|||||.|+ .+.+-+.+.+.+
T Consensus 48 ~~~~L~~GDiI~l~----~g~~vPaD~~ll 73 (230)
T PF00122_consen 48 PSSELVPGDIIILK----AGDIVPADGILL 73 (230)
T ss_dssp EGGGT-TTSEEEEE----TTEBESSEEEEE
T ss_pred hHhhccceeeeecc----cccccccCccce
Confidence 44589999999984 455555554444
No 21
>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=45.41 E-value=16 Score=26.91 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=19.2
Q ss_pred HHHhhHHHHHHhhhc--CCCCCCCCCcEEEEEEeee
Q 029551 126 MGILNKRAVEASESE--RPIPDIRTGDVVEIKLFLK 159 (191)
Q Consensus 126 M~ILnkeavee~~~~--R~iPdiRpGdIVelklEVP 159 (191)
.++|..+.+...+.. .--=-|||||+|.-|+-=-
T Consensus 39 ~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~ 74 (92)
T cd05791 39 RGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISL 74 (92)
T ss_pred ccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEc
Confidence 455555554322221 1113489999999988643
No 22
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=45.29 E-value=42 Score=27.50 Aligned_cols=56 Identities=14% Similarity=0.043 Sum_probs=33.3
Q ss_pred CCccchhhHHHHhhHHHHHHh---------hhcCCCCCCCCCcEEEEEEeeecCCCCcceeeEEE
Q 029551 117 KPRVKLGDIMGILNKRAVEAS---------ESERPIPDIRTGDVVEIKLFLKIGVGCPFTKVLLC 172 (191)
Q Consensus 117 kkrkk~g~IM~ILnkeavee~---------~~~R~iPdiRpGdIVelklEVPEnkRR~~t~~~ic 172 (191)
.+...-+++|...+-=++... .+.|=.=+++|||.+.++.++-..+++...+.+-+
T Consensus 101 ~~i~hG~f~~aqa~~la~~~~~~~~~~~~i~~irF~kPV~pGD~L~~ea~v~~~~~~~~~v~~~~ 165 (185)
T PRK04424 101 TGIARGHHLFAQANSLAVAVIDAELALTGVANIRFKRPVKLGERVVAKAEVVRKKGNKYIVEVKS 165 (185)
T ss_pred CCeecHHHHHHHHHHHHHHhcCCcEEEEEeeeEEEccCCCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 344455666766555222211 22233446899999999999997776644444333
No 23
>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=45.23 E-value=18 Score=25.05 Aligned_cols=39 Identities=10% Similarity=0.060 Sum_probs=23.1
Q ss_pred HHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeecCCC
Q 029551 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKIGVG 163 (191)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPEnkR 163 (191)
..++|...++..-.....-.-+++||+|..++.--.+.+
T Consensus 30 ~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~ 68 (82)
T cd04454 30 GTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDM 68 (82)
T ss_pred ceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCC
Confidence 334444444432222222334899999999998877653
No 24
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=44.47 E-value=14 Score=26.61 Aligned_cols=17 Identities=35% Similarity=0.522 Sum_probs=13.9
Q ss_pred CCCCCcEEEEEEeeecC
Q 029551 145 DIRTGDVVEIKLFLKIG 161 (191)
Q Consensus 145 diRpGdIVelklEVPEn 161 (191)
++..||||++|=.=|=.
T Consensus 1 ~~~vgDiV~mKK~HPCG 17 (57)
T PF06107_consen 1 EYEVGDIVEMKKPHPCG 17 (57)
T ss_pred CccCCCEEEEcCCCCCC
Confidence 57899999999877743
No 25
>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=43.26 E-value=16 Score=29.49 Aligned_cols=13 Identities=38% Similarity=0.626 Sum_probs=11.8
Q ss_pred CCCCCCcEEEEEE
Q 029551 144 PDIRTGDVVEIKL 156 (191)
Q Consensus 144 PdiRpGdIVelkl 156 (191)
=|||-||+|.++.
T Consensus 58 LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 58 LDLRIGDTVKVDG 70 (131)
T ss_pred eeeecCCEEEECC
Confidence 4899999999998
No 26
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=42.93 E-value=30 Score=25.96 Aligned_cols=14 Identities=21% Similarity=0.309 Sum_probs=11.8
Q ss_pred CCCCCCcEEEEEEe
Q 029551 144 PDIRTGDVVEIKLF 157 (191)
Q Consensus 144 PdiRpGdIVelklE 157 (191)
..++|||+|+|.-.
T Consensus 138 ~~l~pGDvi~l~~~ 151 (164)
T PF13550_consen 138 LALEPGDVIALSDD 151 (164)
T ss_pred ccCCCCCEEEEEeC
Confidence 56899999998766
No 27
>KOG3572 consensus Uncharacterized conserved protein, contains DEP domain [Signal transduction mechanisms]
Probab=41.44 E-value=16 Score=40.04 Aligned_cols=19 Identities=37% Similarity=0.565 Sum_probs=15.5
Q ss_pred cCCCCCCCCCcEEEEEEee
Q 029551 140 ERPIPDIRTGDVVEIKLFL 158 (191)
Q Consensus 140 ~R~iPdiRpGdIVelklEV 158 (191)
-...|+|+|||||||+-.-
T Consensus 122 ~~~fP~IKpGDIVEI~~~n 140 (1701)
T KOG3572|consen 122 RAKFPEIKPGDIVEILSKN 140 (1701)
T ss_pred hhhCCCCCCCceEEEeccC
Confidence 3468999999999998643
No 28
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=39.05 E-value=78 Score=21.10 Aligned_cols=25 Identities=28% Similarity=0.133 Sum_probs=17.3
Q ss_pred CCCCCCcEEEEEEeeecCCCCcceeeEEEe
Q 029551 144 PDIRTGDVVEIKLFLKIGVGCPFTKVLLCQ 173 (191)
Q Consensus 144 PdiRpGdIVelklEVPEnkRR~~t~~~ic~ 173 (191)
.++++||+|.|.-+ ...+.++|++.
T Consensus 29 ~~~~~g~~V~v~~~-----~g~~vg~G~~~ 53 (77)
T smart00359 29 GGIKEGDVVVIVDE-----KGEPLGIGLAN 53 (77)
T ss_pred CCcCCCCEEEEEcC-----CCCEEEEEEEe
Confidence 57999999998744 34555666654
No 29
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=38.33 E-value=64 Score=24.45 Aligned_cols=20 Identities=15% Similarity=0.087 Sum_probs=15.6
Q ss_pred CCCCCcEEEEEEeeecCCCC
Q 029551 145 DIRTGDVVEIKLFLKIGVGC 164 (191)
Q Consensus 145 diRpGdIVelklEVPEnkRR 164 (191)
+++|||.|.+++++-+.++.
T Consensus 101 pv~pGd~l~i~~~i~~~~~~ 120 (147)
T PRK00006 101 PVVPGDQLILEVELLKQRRG 120 (147)
T ss_pred ccCCCCEEEEEEEEEEeeCC
Confidence 45699999999999765544
No 30
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=36.87 E-value=43 Score=28.29 Aligned_cols=33 Identities=30% Similarity=0.306 Sum_probs=27.7
Q ss_pred HHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeee
Q 029551 127 GILNKRAVEASESERPIPDIRTGDVVEIKLFLK 159 (191)
Q Consensus 127 ~ILnkeavee~~~~R~iPdiRpGdIVelklEVP 159 (191)
-.||++|++.+++-+..|.+.-|.-+.+++.+|
T Consensus 206 ~~lD~aal~air~~~~~p~~p~~~~~~~~i~~~ 238 (244)
T COG0810 206 PALDRAALEAIRKWRFKPPKPGGKKVGIKITIP 238 (244)
T ss_pred HHHHHHHHHHHHHhccCCCCCCCCccceeEEEE
Confidence 369999999999999999998876657776665
No 31
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=35.60 E-value=21 Score=29.68 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=9.4
Q ss_pred CCCCCcEEEEE
Q 029551 145 DIRTGDVVEIK 155 (191)
Q Consensus 145 diRpGdIVelk 155 (191)
-|+|||||+|+
T Consensus 61 ~~~PGDIirLt 71 (134)
T KOG3416|consen 61 LIQPGDIIRLT 71 (134)
T ss_pred ccCCccEEEec
Confidence 48999999985
No 32
>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=35.49 E-value=83 Score=23.54 Aligned_cols=23 Identities=9% Similarity=-0.041 Sum_probs=16.9
Q ss_pred CCCCCCCCCcEEEEEEeeecCCC
Q 029551 141 RPIPDIRTGDVVEIKLFLKIGVG 163 (191)
Q Consensus 141 R~iPdiRpGdIVelklEVPEnkR 163 (191)
|=.=.++|||.+++++++-...+
T Consensus 93 kF~~~v~pGd~l~i~~~i~~~~~ 115 (140)
T TIGR01750 93 KFRRPVVPGDQLILHAEFLKKRR 115 (140)
T ss_pred EECCccCCCCEEEEEEEEEEccC
Confidence 33446788999999999875443
No 33
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=34.82 E-value=33 Score=28.69 Aligned_cols=38 Identities=29% Similarity=0.382 Sum_probs=26.8
Q ss_pred hHHHHhhHHHHHHhhhcCCCCCCCCCcEEEE----------EEeeecCCCCc
Q 029551 124 DIMGILNKRAVEASESERPIPDIRTGDVVEI----------KLFLKIGVGCP 165 (191)
Q Consensus 124 ~IM~ILnkeavee~~~~R~iPdiRpGdIVel----------klEVPEnkRR~ 165 (191)
+||+.|+.. ....++..+|.+||.|+| +++-....|..
T Consensus 106 ~~l~~~~~~----~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~ 153 (178)
T COG0250 106 HILGFLEEE----VAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGK 153 (178)
T ss_pred HHHhhcccc----ccCCcccccCCCCCEEEEeccCCCCccEEEEEEcCcCcE
Confidence 366666544 556788899999999998 56666555543
No 34
>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=34.60 E-value=1.4e+02 Score=20.74 Aligned_cols=19 Identities=37% Similarity=0.420 Sum_probs=16.3
Q ss_pred CCCCCCcEEEEEEeeecCC
Q 029551 144 PDIRTGDVVEIKLFLKIGV 162 (191)
Q Consensus 144 PdiRpGdIVelklEVPEnk 162 (191)
.++.+|+.|+|++.+|.+.
T Consensus 35 ~~~~~g~~v~l~l~l~~~~ 53 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGGE 53 (96)
T ss_pred CCcCCCCEEEEEEEcCCCC
Confidence 3578999999999999874
No 35
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=34.48 E-value=27 Score=26.19 Aligned_cols=13 Identities=46% Similarity=0.575 Sum_probs=10.7
Q ss_pred CCCCCcEEEEEEe
Q 029551 145 DIRTGDVVEIKLF 157 (191)
Q Consensus 145 diRpGdIVelklE 157 (191)
-|+|||+|.+.+-
T Consensus 46 ~I~~GD~V~Ve~~ 58 (75)
T COG0361 46 RILPGDVVLVELS 58 (75)
T ss_pred EeCCCCEEEEEec
Confidence 4899999998763
No 36
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=33.56 E-value=57 Score=24.50 Aligned_cols=28 Identities=14% Similarity=0.140 Sum_probs=17.4
Q ss_pred CCCCCCCcEEEEEEeeecCCCCcceeeEEEeeccC
Q 029551 143 IPDIRTGDVVEIKLFLKIGVGCPFTKVLLCQGKML 177 (191)
Q Consensus 143 iPdiRpGdIVelklEVPEnkRR~~t~~~ic~~~gl 177 (191)
.+.++|||+|++... ..+=-||.++.|.
T Consensus 4 ~~~~~~GD~I~~~r~-------~y~H~gIYvG~~~ 31 (125)
T PF04970_consen 4 KKRLKPGDHIEVPRG-------LYEHWGIYVGDGE 31 (125)
T ss_dssp --S--TT-EEEEEET-------TEEEEEEEEETTE
T ss_pred ccCCCCCCEEEEecC-------CccEEEEEecCCe
Confidence 356899999998755 6777788887553
No 37
>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=32.85 E-value=40 Score=26.39 Aligned_cols=21 Identities=19% Similarity=0.605 Sum_probs=15.9
Q ss_pred CCCCC-CcEEEEE-EeeecCCCC
Q 029551 144 PDIRT-GDVVEIK-LFLKIGVGC 164 (191)
Q Consensus 144 PdiRp-GdIVelk-lEVPEnkRR 164 (191)
|.++. ||||.|+ +.|-.=+++
T Consensus 71 P~v~~~GDii~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 71 PNVKSVGDIIRLRRVKVQSYNGK 93 (146)
T ss_dssp CTTCSTTHEEEEEEEEEEEETTE
T ss_pred CCCCCCCCEEEEEEEEEEEECCE
Confidence 99999 9999887 666544444
No 38
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=32.78 E-value=59 Score=26.04 Aligned_cols=20 Identities=15% Similarity=0.119 Sum_probs=15.8
Q ss_pred CCCCCCCCcEEEEEEeeecC
Q 029551 142 PIPDIRTGDVVEIKLFLKIG 161 (191)
Q Consensus 142 ~iPdiRpGdIVelklEVPEn 161 (191)
=+=++++||.|..+++|-+-
T Consensus 93 f~~PV~~GDtL~~~~eV~~~ 112 (159)
T PRK13692 93 FEKPIVAGDKLYCDVYVDSV 112 (159)
T ss_pred EeCCccCCCEEEEEEEEEEE
Confidence 33468999999999999654
No 39
>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=31.36 E-value=38 Score=26.08 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=16.6
Q ss_pred hhHHHHHHhhhcCCCCCCCCCc
Q 029551 129 LNKRAVEASESERPIPDIRTGD 150 (191)
Q Consensus 129 Lnkeavee~~~~R~iPdiRpGd 150 (191)
.-.+++.++.+.=.||.||+|=
T Consensus 27 ~~~~~l~~~~k~~~ipGFRkGK 48 (145)
T PF05697_consen 27 AYEKALKELAKKVKIPGFRKGK 48 (145)
T ss_dssp HHHHHHHHHHTTTTBTTS-TTS
T ss_pred HHHHHHHHHHhhCCCCCCCCCC
Confidence 3456778888888999999994
No 40
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=30.90 E-value=20 Score=29.28 Aligned_cols=36 Identities=17% Similarity=0.217 Sum_probs=23.1
Q ss_pred HHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeec
Q 029551 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKI 160 (191)
Q Consensus 125 IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPE 160 (191)
+.++|....+..-........|++||+|..|+.--+
T Consensus 98 ~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 98 KLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred ceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 445555555433222334556999999999987666
No 41
>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=30.73 E-value=59 Score=21.89 Aligned_cols=17 Identities=12% Similarity=0.579 Sum_probs=12.8
Q ss_pred CCCCCCCCCcEEEEEEe
Q 029551 141 RPIPDIRTGDVVEIKLF 157 (191)
Q Consensus 141 R~iPdiRpGdIVelklE 157 (191)
.+.--+++||+|+.|+-
T Consensus 42 ~~~~~~~~Gd~i~~kVl 58 (70)
T cd05702 42 NPLSKFKIGQKIKARVI 58 (70)
T ss_pred ChhHhCCCCCEEEEEEE
Confidence 33344899999999963
No 42
>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=29.65 E-value=79 Score=21.92 Aligned_cols=23 Identities=30% Similarity=0.444 Sum_probs=18.6
Q ss_pred CCCCCCCcEEEEE-EeeecCCCCc
Q 029551 143 IPDIRTGDVVEIK-LFLKIGVGCP 165 (191)
Q Consensus 143 iPdiRpGdIVelk-lEVPEnkRR~ 165 (191)
.+.+.+||+|.++ ..+=+.+.+.
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~g~~ 69 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFNGRL 69 (82)
T ss_pred cccCCCCCEEEEEeEEEEecCCcE
Confidence 6779999999999 8887766554
No 43
>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=29.61 E-value=38 Score=24.08 Aligned_cols=13 Identities=38% Similarity=0.805 Sum_probs=7.9
Q ss_pred CCCCCcEEEEEEe
Q 029551 145 DIRTGDVVEIKLF 157 (191)
Q Consensus 145 diRpGdIVelklE 157 (191)
-|.|||+|+|++-
T Consensus 12 ~l~pGD~l~i~v~ 24 (82)
T PF02563_consen 12 RLGPGDVLRISVF 24 (82)
T ss_dssp ---TT-EEEEEET
T ss_pred EECCCCEEEEEEe
Confidence 4789999999883
No 44
>PRK11507 ribosome-associated protein; Provisional
Probab=29.58 E-value=34 Score=25.34 Aligned_cols=9 Identities=33% Similarity=0.545 Sum_probs=7.9
Q ss_pred CCCCcEEEE
Q 029551 146 IRTGDVVEI 154 (191)
Q Consensus 146 iRpGdIVel 154 (191)
+||||+|++
T Consensus 53 l~~GD~V~~ 61 (70)
T PRK11507 53 IVAGQTVSF 61 (70)
T ss_pred CCCCCEEEE
Confidence 789999987
No 45
>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=29.39 E-value=43 Score=20.51 Aligned_cols=15 Identities=33% Similarity=0.507 Sum_probs=12.4
Q ss_pred CCCCCcEEEEEEeee
Q 029551 145 DIRTGDVVEIKLFLK 159 (191)
Q Consensus 145 diRpGdIVelklEVP 159 (191)
.+++||+|++++-=-
T Consensus 41 ~~~~G~~v~~~v~~~ 55 (65)
T cd00164 41 VFKVGDEVEVKVLEV 55 (65)
T ss_pred EeCCCCEEEEEEEEE
Confidence 489999999998644
No 46
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=28.96 E-value=51 Score=28.14 Aligned_cols=37 Identities=14% Similarity=-0.050 Sum_probs=23.8
Q ss_pred HHHHhhHHHHHHhh----hcCCCCCCCCCcEEEEEEeeecC
Q 029551 125 IMGILNKRAVEASE----SERPIPDIRTGDVVEIKLFLKIG 161 (191)
Q Consensus 125 IM~ILnkeavee~~----~~R~iPdiRpGdIVelklEVPEn 161 (191)
.-++|....+...+ ..+.-+-|++||+|..||.--..
T Consensus 87 ~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~ 127 (235)
T PRK04163 87 YKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR 127 (235)
T ss_pred ceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC
Confidence 44566666654432 23445569999999999975543
No 47
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=28.89 E-value=74 Score=29.44 Aligned_cols=59 Identities=19% Similarity=0.190 Sum_probs=42.5
Q ss_pred hhHHHHhhHHHHH--HhhhcCCCCCCCCCcEEEEEEeeecCCCCcceeeEEEeeccCCceeE
Q 029551 123 GDIMGILNKRAVE--ASESERPIPDIRTGDVVEIKLFLKIGVGCPFTKVLLCQGKMLGSTLQ 182 (191)
Q Consensus 123 g~IM~ILnkeave--e~~~~R~iPdiRpGdIVelklEVPEnkRR~~t~~~ic~~~glgstf~ 182 (191)
.-+|.+.+.+.+- .-=+|-.+..+|+|+-++|++.--... -.+.+++--|+-|-|++|.
T Consensus 234 ~~l~alVp~~~~yV~AnFkETqL~~~r~Gq~a~I~~da~~~~-~~~~G~v~~i~~~tg~~fs 294 (352)
T COG1566 234 TPLMALVPLDSFYVVANFKETQLARVRPGQPAEITLDAYPGN-GVVEGIVEGIAPATGSAFS 294 (352)
T ss_pred CceEEEecccceEEEeeeeeeecCcccCCCeEEEEEEcCCCc-eEEEEEEEEecCCcccccc
Confidence 3678887766654 344677899999999999999875443 4556666666677788764
No 48
>cd03442 BFIT_BACH Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis, and brown adipose tissues. The archeal and eukaryotic members of this family have two tandem copies of the conserved hot dog fold, while most bacterial members have only one copy.
Probab=28.75 E-value=1.1e+02 Score=21.42 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=19.5
Q ss_pred CCCCCcEEEEEEeeecCCCCcceee
Q 029551 145 DIRTGDVVEIKLFLKIGVGCPFTKV 169 (191)
Q Consensus 145 diRpGdIVelklEVPEnkRR~~t~~ 169 (191)
++++||.|+++..+-.-.|+..+..
T Consensus 63 p~~~gd~l~i~~~v~~~g~~~~~~~ 87 (123)
T cd03442 63 PVRVGDVVELSARVVYTGRTSMEVG 87 (123)
T ss_pred ccccCcEEEEEEEEEEecCCeEEEE
Confidence 4679999999999988777654443
No 49
>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=28.70 E-value=64 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.274 Sum_probs=19.3
Q ss_pred hhHHHHHHhhhcCCC---------CCCCCCcEEEEEEe
Q 029551 129 LNKRAVEASESERPI---------PDIRTGDVVEIKLF 157 (191)
Q Consensus 129 Lnkeavee~~~~R~i---------PdiRpGdIVelklE 157 (191)
+|+.+++.+..-..+ .+|++||+|.|..+
T Consensus 35 vd~~a~~~l~~Ga~L~~pGV~~~~~~~~~gd~V~I~~~ 72 (107)
T TIGR00451 35 VDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDE 72 (107)
T ss_pred EChhHHHHHHCCccccCCeeEeCCCCcCCCCEEEEEEC
Confidence 455566655443332 58999999999864
No 50
>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=28.45 E-value=89 Score=19.67 Aligned_cols=18 Identities=33% Similarity=0.510 Sum_probs=15.2
Q ss_pred CCCCCCCcEEEEEEeeec
Q 029551 143 IPDIRTGDVVEIKLFLKI 160 (191)
Q Consensus 143 iPdiRpGdIVelklEVPE 160 (191)
...+++||.|..++.-++
T Consensus 34 ~~~~~~Gd~V~~~i~~~~ 51 (64)
T smart00357 34 LKSLREGDEVEFKVVSPR 51 (64)
T ss_pred CCcCCCCCEEEEEEEEcc
Confidence 567899999999998764
No 51
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=28.10 E-value=90 Score=24.72 Aligned_cols=29 Identities=10% Similarity=0.059 Sum_probs=23.1
Q ss_pred hhcCCCCCCCCCcEEEEEEeeecCCCCcc
Q 029551 138 ESERPIPDIRTGDVVEIKLFLKIGVGCPF 166 (191)
Q Consensus 138 ~~~R~iPdiRpGdIVelklEVPEnkRR~~ 166 (191)
.+.|=+=++++||.|..+++|-+.+.+.+
T Consensus 99 ~~vRF~~PV~~Gdtl~~~~~v~~~~~~~~ 127 (159)
T COG2030 99 DEVRFVKPVFPGDTLRARVEVLDKRPSKS 127 (159)
T ss_pred cceEecCCCCCCCEEEEEEEEEEeeecCC
Confidence 45566778999999999999987765554
No 52
>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=27.88 E-value=1.4e+02 Score=19.86 Aligned_cols=20 Identities=25% Similarity=0.197 Sum_probs=14.8
Q ss_pred CCCCCcEEEEEEeeecCCCC
Q 029551 145 DIRTGDVVEIKLFLKIGVGC 164 (191)
Q Consensus 145 diRpGdIVelklEVPEnkRR 164 (191)
++.+|+.|+|++..+....-
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~ 63 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFP 63 (102)
T ss_dssp G--TTSEEEEEEECTTTSCE
T ss_pred CCCCCCEEEEEEEeCCCCee
Confidence 68899999999988876654
No 53
>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=27.73 E-value=48 Score=25.83 Aligned_cols=15 Identities=20% Similarity=0.742 Sum_probs=12.4
Q ss_pred CCCCCCCCCcEEEEE
Q 029551 141 RPIPDIRTGDVVEIK 155 (191)
Q Consensus 141 R~iPdiRpGdIVelk 155 (191)
..+|.+..||||.||
T Consensus 64 ~~LP~v~~GDVIll~ 78 (138)
T cd04497 64 ESLPIVKVGDIILLR 78 (138)
T ss_pred hhCCCCCCCCEEEEE
Confidence 348888999999875
No 54
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=27.61 E-value=14 Score=34.31 Aligned_cols=45 Identities=18% Similarity=0.159 Sum_probs=39.2
Q ss_pred CccchhhHHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeecCC
Q 029551 118 PRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKIGV 162 (191)
Q Consensus 118 krkk~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPEnk 162 (191)
||..++-|.--+--+.+|++-++.-.||+..-..+-+|.|+||.+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDR 184 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDR 184 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhh
Confidence 444478888888889999999999999999999999999999853
No 55
>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=26.51 E-value=1.1e+02 Score=22.59 Aligned_cols=21 Identities=10% Similarity=-0.070 Sum_probs=16.5
Q ss_pred CCCCCCCcEEEEEEeeecCCC
Q 029551 143 IPDIRTGDVVEIKLFLKIGVG 163 (191)
Q Consensus 143 iPdiRpGdIVelklEVPEnkR 163 (191)
.=+++|||.|.++++|=+.++
T Consensus 89 ~~pv~~GDtl~~~~~v~~~~~ 109 (146)
T cd03451 89 PAPVFHGDTLYAESEVLSKRE 109 (146)
T ss_pred cCCCCCCCEEEEEEEEEEEec
Confidence 345789999999999976543
No 56
>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=25.57 E-value=42 Score=24.01 Aligned_cols=11 Identities=45% Similarity=0.987 Sum_probs=9.1
Q ss_pred CCCCCCCcEEE
Q 029551 143 IPDIRTGDVVE 153 (191)
Q Consensus 143 iPdiRpGdIVe 153 (191)
+.||++||++|
T Consensus 73 ~~d~~~Gdvi~ 83 (84)
T cd03692 73 FNDIKVGDIIE 83 (84)
T ss_pred cccCCCCCEEE
Confidence 44999999987
No 57
>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=25.32 E-value=53 Score=21.85 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=23.8
Q ss_pred HhhHHHHHHhhhcCCCCCCCCCcEEEEEEeee
Q 029551 128 ILNKRAVEASESERPIPDIRTGDVVEIKLFLK 159 (191)
Q Consensus 128 ILnkeavee~~~~R~iPdiRpGdIVelklEVP 159 (191)
+||+++++.+++.+-.|...-|.-+.+++.+|
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 79999999999988888777788888877666
No 58
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=25.31 E-value=1.5e+02 Score=22.88 Aligned_cols=27 Identities=15% Similarity=0.283 Sum_probs=19.2
Q ss_pred CCCCCCcEEEEEEeeecCCCCcceeeEEEee
Q 029551 144 PDIRTGDVVEIKLFLKIGVGCPFTKVLLCQG 174 (191)
Q Consensus 144 PdiRpGdIVelklEVPEnkRR~~t~~~ic~~ 174 (191)
-+++|||+|-.+. +..+...=+||.++
T Consensus 75 ~~~qpGDlvff~~----~~~~~~~HvGIy~G 101 (134)
T TIGR02219 75 DAAQPGDVLVFRW----RPGAAAKHAAIAAS 101 (134)
T ss_pred hcCCCCCEEEEee----CCCCCCcEEEEEeC
Confidence 3799999999874 22333457888875
No 59
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=25.25 E-value=1.2e+02 Score=23.89 Aligned_cols=14 Identities=36% Similarity=0.527 Sum_probs=12.5
Q ss_pred CCCCCCcEEEEEEe
Q 029551 144 PDIRTGDVVEIKLF 157 (191)
Q Consensus 144 PdiRpGdIVelklE 157 (191)
++|++||+|.|..+
T Consensus 98 ~~~~~Gd~V~I~~~ 111 (150)
T TIGR03684 98 PSIKEGDIVFVVDE 111 (150)
T ss_pred CCCCCCCEEEEEEC
Confidence 68999999999875
No 60
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=25.14 E-value=68 Score=21.90 Aligned_cols=25 Identities=16% Similarity=0.208 Sum_probs=13.4
Q ss_pred CCCCcEEEEEEeeecCCC--CcceeeE
Q 029551 146 IRTGDVVEIKLFLKIGVG--CPFTKVL 170 (191)
Q Consensus 146 iRpGdIVelklEVPEnkR--R~~t~~~ 170 (191)
|++|+.|+|.+.=|.+.+ -.+.+++
T Consensus 1 L~iG~~i~i~i~~~~~~~~~y~S~v~g 27 (87)
T PF12945_consen 1 LKIGQKIEIEITNPTGEKGRYKSRVIG 27 (87)
T ss_dssp --TT-EEEEEEE-TTS-EEEEEEEEEE
T ss_pred CCCCCEEEEEEECCCCceEEEEEEEEE
Confidence 589999999887776433 3444444
No 61
>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=25.14 E-value=44 Score=24.80 Aligned_cols=11 Identities=45% Similarity=0.706 Sum_probs=8.0
Q ss_pred CCCCCcEEEEE
Q 029551 145 DIRTGDVVEIK 155 (191)
Q Consensus 145 diRpGdIVelk 155 (191)
++++||||+|.
T Consensus 48 g~k~GdVvkI~ 58 (74)
T PF01191_consen 48 GAKPGDVVKII 58 (74)
T ss_dssp T--TTSEEEEE
T ss_pred CCCCCCEEEEE
Confidence 78999999985
No 62
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=24.96 E-value=40 Score=24.40 Aligned_cols=10 Identities=70% Similarity=1.125 Sum_probs=6.2
Q ss_pred CCCCCcEEEE
Q 029551 145 DIRTGDVVEI 154 (191)
Q Consensus 145 diRpGdIVel 154 (191)
-+|+||+|++
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 63
>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=24.74 E-value=1.4e+02 Score=21.90 Aligned_cols=17 Identities=6% Similarity=0.243 Sum_probs=14.8
Q ss_pred CCCCCcEEEEEEeeecC
Q 029551 145 DIRTGDVVEIKLFLKIG 161 (191)
Q Consensus 145 diRpGdIVelklEVPEn 161 (191)
.++|||.+++.+.-|..
T Consensus 9 ~~~~Ge~~~v~v~~~~~ 25 (136)
T PF07703_consen 9 SYKPGETAKVTVQSPFP 25 (136)
T ss_dssp SB-TTSEEEEEEEEESC
T ss_pred CcCCCCEEEEEEEcCCC
Confidence 57899999999999988
No 64
>PF09874 DUF2101: Predicted membrane protein (DUF2101); InterPro: IPR018663 This family of conserved hypothetical proteins has no known function.
Probab=24.62 E-value=61 Score=28.62 Aligned_cols=16 Identities=38% Similarity=0.771 Sum_probs=14.0
Q ss_pred CCCCCCCCcEEEEEEe
Q 029551 142 PIPDIRTGDVVEIKLF 157 (191)
Q Consensus 142 ~iPdiRpGdIVelklE 157 (191)
..||+.+||+|.|.||
T Consensus 178 ~~~d~~~G~vVKl~VE 193 (206)
T PF09874_consen 178 AVPDVEEGDVVKLLVE 193 (206)
T ss_pred CCCCCCCCceEEEEEe
Confidence 3679999999999987
No 65
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=24.38 E-value=76 Score=22.50 Aligned_cols=12 Identities=42% Similarity=0.637 Sum_probs=10.3
Q ss_pred CCCCCCCcEEEE
Q 029551 143 IPDIRTGDVVEI 154 (191)
Q Consensus 143 iPdiRpGdIVel 154 (191)
-+++|.|||+++
T Consensus 31 P~~~keGDvl~i 42 (71)
T PF11213_consen 31 PEGAKEGDVLEI 42 (71)
T ss_pred CCCCCcccEEEE
Confidence 357999999999
No 66
>PF12238 MSA-2c: Merozoite surface antigen 2c; InterPro: IPR021060 This family of proteins are restricted to the apicomplexan Babesia bovis. Proteins in this entry are typically between 263 and 318 amino acids in length and plasma membrane glycoproteins. These antigens present on the merozoite surface (MSA) and are involved in the parasite invasion of the bovine erythrocyte. MSA-2c has been suggested as a possible antigen for a vaccine candidate [].
Probab=23.64 E-value=35 Score=29.80 Aligned_cols=12 Identities=58% Similarity=1.093 Sum_probs=9.7
Q ss_pred CceeEEeecceecC
Q 029551 178 GSTLQFEFGGLLLA 191 (191)
Q Consensus 178 gstf~~~~~~~~~~ 191 (191)
||+||| |||-.|
T Consensus 194 gsSFTf--GGLTVA 205 (205)
T PF12238_consen 194 GSSFTF--GGLTVA 205 (205)
T ss_pred CCceec--CCcccC
Confidence 999885 998765
No 67
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=23.52 E-value=1.1e+02 Score=23.47 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=16.5
Q ss_pred CCCCCCCCCcEEEEEEeeecCC
Q 029551 141 RPIPDIRTGDVVEIKLFLKIGV 162 (191)
Q Consensus 141 R~iPdiRpGdIVelklEVPEnk 162 (191)
|=.=++++||.|.++++|-+-+
T Consensus 84 rf~~PV~~GDtl~~~~~V~~~~ 105 (142)
T cd03452 84 RFLEPVYPGDTIQVRLTCKRKI 105 (142)
T ss_pred EECCCCCCCCEEEEEEEEEEEe
Confidence 3344578999999999997553
No 68
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=23.38 E-value=70 Score=17.76 Aligned_cols=12 Identities=25% Similarity=0.468 Sum_probs=8.9
Q ss_pred CCCCCcEEEEEE
Q 029551 145 DIRTGDVVEIKL 156 (191)
Q Consensus 145 diRpGdIVelkl 156 (191)
.+++||.|+|.-
T Consensus 1 ~~~~G~~V~I~~ 12 (28)
T smart00739 1 KFEVGDTVRVIA 12 (28)
T ss_pred CCCCCCEEEEeE
Confidence 368899888753
No 69
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.20 E-value=59 Score=28.24 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=11.9
Q ss_pred CCCCCCcEEEEEEe
Q 029551 144 PDIRTGDVVEIKLF 157 (191)
Q Consensus 144 PdiRpGdIVelklE 157 (191)
=.|||||||+-||=
T Consensus 117 d~f~~GDivrA~Vi 130 (188)
T COG1096 117 DAFRIGDIVRARVI 130 (188)
T ss_pred cccccccEEEEEEE
Confidence 57999999998764
No 70
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=22.00 E-value=1.6e+02 Score=22.80 Aligned_cols=30 Identities=20% Similarity=0.275 Sum_probs=25.9
Q ss_pred CCCCCcEEEEEEeeecCCCCcceeeEEEee
Q 029551 145 DIRTGDVVEIKLFLKIGVGCPFTKVLLCQG 174 (191)
Q Consensus 145 diRpGdIVelklEVPEnkRR~~t~~~ic~~ 174 (191)
+.+.||+|+|.=-.|-.|.--|..+.|.-.
T Consensus 55 ~~k~GD~V~I~EtRPLSKtK~~~vv~i~~~ 84 (87)
T COG0186 55 EAKVGDIVRIAETRPLSKTKRFVVVEIVEK 84 (87)
T ss_pred cCCCCCEEEEEEccccCCcceEEEEEEeee
Confidence 478999999999999999988888887654
No 71
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=21.79 E-value=61 Score=23.28 Aligned_cols=35 Identities=26% Similarity=0.316 Sum_probs=17.9
Q ss_pred CCCCCcEEEEEEeeecCCCCcceeeEEEeeccCCceeEEeecce
Q 029551 145 DIRTGDVVEIKLFLKIGVGCPFTKVLLCQGKMLGSTLQFEFGGL 188 (191)
Q Consensus 145 diRpGdIVelklEVPEnkRR~~t~~~ic~~~glgstf~~~~~~~ 188 (191)
+||.||-|||. ..|+|-.|+++.- |-.|+...|.+
T Consensus 5 pf~~GdrVQlT----D~Kgr~~Ti~L~~-----G~~fhThrG~i 39 (54)
T PF14801_consen 5 PFRAGDRVQLT----DPKGRKHTITLEP-----GGEFHTHRGAI 39 (54)
T ss_dssp S--TT-EEEEE----ETT--EEEEE--T-----T-EEEETTEEE
T ss_pred CCCCCCEEEEc----cCCCCeeeEEECC-----CCeEEcCcccc
Confidence 68999988875 6788888877653 44555555443
No 72
>PF13437 HlyD_3: HlyD family secretion protein
Probab=21.70 E-value=2.3e+02 Score=19.94 Aligned_cols=44 Identities=23% Similarity=0.305 Sum_probs=28.6
Q ss_pred cCCCCCCC-CCcEEEEEEeeecCCCCcceeeEEEeecc---CCceeEEee
Q 029551 140 ERPIPDIR-TGDVVEIKLFLKIGVGCPFTKVLLCQGKM---LGSTLQFEF 185 (191)
Q Consensus 140 ~R~iPdiR-pGdIVelklEVPEnkRR~~t~~~ic~~~g---lgstf~~~~ 185 (191)
++.+.-|+ +|+-|.+++. + +......++..-|... -+.+|++++
T Consensus 44 ~~~~~~i~~~g~~v~v~~~-~-~~~~~~~g~V~~I~~~~~~~~~~~~v~~ 91 (105)
T PF13437_consen 44 EKDIARIKDPGQKVTVRLD-P-GPEKTIEGKVSSISPSPDPQGGTYRVEI 91 (105)
T ss_pred hHhhcceEeCCCEEEEEEC-C-CCCcEEEEEEEEEeCcccCCCcEEEEEE
Confidence 45566777 9999999998 3 3333777777777532 233666654
No 73
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=21.32 E-value=1.7e+02 Score=20.74 Aligned_cols=22 Identities=5% Similarity=0.096 Sum_probs=14.5
Q ss_pred CCCCcEEEEEEeeecCCCCcce
Q 029551 146 IRTGDVVEIKLFLKIGVGCPFT 167 (191)
Q Consensus 146 iRpGdIVelklEVPEnkRR~~t 167 (191)
+.|||.|.+.+++-++..+...
T Consensus 16 ~~~Ge~i~v~v~i~n~s~~~i~ 37 (136)
T PF02752_consen 16 YVPGETIPVNVEIDNQSKKKIK 37 (136)
T ss_dssp EETT--EEEEEEEEE-SSSEEE
T ss_pred ECCCCEEEEEEEEEECCCCEEE
Confidence 5699999999999966665433
No 74
>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=21.32 E-value=82 Score=22.24 Aligned_cols=17 Identities=18% Similarity=0.261 Sum_probs=12.6
Q ss_pred CCCCCcEEEEEEeeecC
Q 029551 145 DIRTGDVVEIKLFLKIG 161 (191)
Q Consensus 145 diRpGdIVelklEVPEn 161 (191)
=.||||.|.+|+-+=..
T Consensus 10 iYrPGetV~~~~~~~~~ 26 (99)
T PF01835_consen 10 IYRPGETVHFRAIVRDL 26 (99)
T ss_dssp EE-TTSEEEEEEEEEEE
T ss_pred CcCCCCEEEEEEEEecc
Confidence 36999999999996533
No 75
>PF15493 YrpD: Domain of unknown function, YrpD
Probab=20.93 E-value=93 Score=27.61 Aligned_cols=33 Identities=12% Similarity=0.260 Sum_probs=25.6
Q ss_pred CCCCCCCCcEEEEEEeeec--CCCCcceeeEEEee
Q 029551 142 PIPDIRTGDVVEIKLFLKI--GVGCPFTKVLLCQG 174 (191)
Q Consensus 142 ~iPdiRpGdIVelklEVPE--nkRR~~t~~~ic~~ 174 (191)
=-+.|+||-.|||++-+|- |-|-...+..+|--
T Consensus 92 Y~ngf~pGqdVqm~~y~n~nGn~Rltl~Gta~c~d 126 (208)
T PF15493_consen 92 YKNGFKPGQDVQMTLYKNYNGNTRLTLWGTAICAD 126 (208)
T ss_pred ecCCCCCCCeEEEEEEEeCCCCEEEEEEeeeeccc
Confidence 3589999999999999993 44556777777753
No 76
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=20.83 E-value=29 Score=29.46 Aligned_cols=48 Identities=31% Similarity=0.327 Sum_probs=38.6
Q ss_pred hhhhcCCCCCCccchhhHHHHhhHHHHHHhhhcCCCCCC---CCCcEEEEE
Q 029551 108 EEEEVKAPRKPRVKLGDIMGILNKRAVEASESERPIPDI---RTGDVVEIK 155 (191)
Q Consensus 108 eeeE~~~prkkrkk~g~IM~ILnkeavee~~~~R~iPdi---RpGdIVelk 155 (191)
|-.+.+|--+-.+||-.+.+|+-.|.+++....-.-.+. -=||||.||
T Consensus 113 E~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~~~~~~~~~~TLGdiv~ik 163 (165)
T COG1813 113 ERGEATPNIKVAKKLEKLLGIKLVEKVDEEEEGPKGKDDDGLTLGDIVRIK 163 (165)
T ss_pred HhcccCccHHHHHHHHHHhCceeeeeccccccccccCCcCCCcccceEEec
Confidence 777778888888999999999999998888777444444 459999987
No 77
>PTZ00274 cytochrome b5 reductase; Provisional
Probab=20.77 E-value=1e+02 Score=27.60 Aligned_cols=11 Identities=18% Similarity=0.471 Sum_probs=9.5
Q ss_pred CCCCCcEEEEE
Q 029551 145 DIRTGDVVEIK 155 (191)
Q Consensus 145 diRpGdIVelk 155 (191)
++++||.|+|+
T Consensus 136 ~lk~Gd~v~v~ 146 (325)
T PTZ00274 136 GMHVGDKLLFR 146 (325)
T ss_pred cCCCCCEEEEe
Confidence 46999999997
No 78
>PRK08916 flagellar motor switch protein; Reviewed
Probab=20.72 E-value=89 Score=24.91 Aligned_cols=32 Identities=9% Similarity=0.137 Sum_probs=19.9
Q ss_pred CCCCCCCCcEEEEE------EeeecCCCCcceeeEEEe
Q 029551 142 PIPDIRTGDVVEIK------LFLKIGVGCPFTKVLLCQ 173 (191)
Q Consensus 142 ~iPdiRpGdIVelk------lEVPEnkRR~~t~~~ic~ 173 (191)
.+=.+++||||.|. +++=-|.+..+.+....+
T Consensus 62 ELL~L~~GDVI~Ld~~~~e~V~I~Vng~~~~~Gelg~~ 99 (116)
T PRK08916 62 QLLKLGPGSVLELDRKVGEAIDIYVNNRLVARGEVVLV 99 (116)
T ss_pred HHhcCCCCCEEEcCCCCCCCEEEEECCEEEEEEEEEEE
Confidence 34468999999996 444445555555444444
No 79
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=20.56 E-value=82 Score=25.14 Aligned_cols=12 Identities=42% Similarity=0.786 Sum_probs=10.6
Q ss_pred CCCCCCcEEEEE
Q 029551 144 PDIRTGDVVEIK 155 (191)
Q Consensus 144 PdiRpGdIVelk 155 (191)
-++++||.|+|+
T Consensus 93 ~~~~~G~~V~I~ 104 (153)
T PRK08559 93 EGIKEGDIVELI 104 (153)
T ss_pred cCCCCCCEEEEe
Confidence 579999999986
No 80
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=20.36 E-value=1.5e+02 Score=21.45 Aligned_cols=33 Identities=24% Similarity=0.220 Sum_probs=21.1
Q ss_pred CCCCcEEEEEEeeecCCCC--cceeeEEEee-ccCC
Q 029551 146 IRTGDVVEIKLFLKIGVGC--PFTKVLLCQG-KMLG 178 (191)
Q Consensus 146 iRpGdIVelklEVPEnkRR--~~t~~~ic~~-~glg 178 (191)
++.||.|++++.=-....| ....+.+.+. .++|
T Consensus 54 ~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~~~~g 89 (99)
T cd04460 54 LKVGDVVRARIVAVSLKERRPRESKIGLTMRQPGLG 89 (99)
T ss_pred ECCCCEEEEEEEEEeHHHCcCCCceEEEEEecCCCC
Confidence 7999999999976654322 2445555552 5554
No 81
>cd03711 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=20.36 E-value=26 Score=24.42 Aligned_cols=61 Identities=26% Similarity=0.365 Sum_probs=37.6
Q ss_pred chhhHHHHhhHHHHHHhhhcCCCCCCCCCcEEEEEEeeecCCCCcceeeEEEeeccCCceeEEeecce
Q 029551 121 KLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLFLKIGVGCPFTKVLLCQGKMLGSTLQFEFGGL 188 (191)
Q Consensus 121 k~g~IM~ILnkeavee~~~~R~iPdiRpGdIVelklEVPEnkRR~~t~~~ic~~~glgstf~~~~~~~ 188 (191)
-+|.||+.|+++.=+-.. ++.. ++.+.|+-++|-..=-.+.-.+..+++|-|+ |+++|.|.
T Consensus 14 ~~g~v~~~l~~rrg~i~~-----~~~~-~~~~~i~~~~P~~~~~g~~~~Lr~~T~G~~~-~~~~f~~y 74 (78)
T cd03711 14 ALGRAMSDLAKMGATFED-----PQIK-GDEVTLEGTIPVATSQDYQSELPSYTHGEGV-LETEFKGY 74 (78)
T ss_pred HHHHHHHHHHHcCCEeeC-----cEec-CCEEEEEEEECHHHHhhHHHHhHhhcCCeEE-EEEEeCCe
Confidence 378899999876533221 2223 3678899999954433333334444567664 88888764
No 82
>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=20.31 E-value=1.4e+02 Score=18.75 Aligned_cols=20 Identities=25% Similarity=0.363 Sum_probs=14.1
Q ss_pred CCCCCcEEEEEEeeecCCCC
Q 029551 145 DIRTGDVVEIKLFLKIGVGC 164 (191)
Q Consensus 145 diRpGdIVelklEVPEnkRR 164 (191)
-++.||.|++++.=-+.+++
T Consensus 44 ~~~~Gd~v~v~v~~~~~~~~ 63 (69)
T cd05692 44 VLKEGDKVKVKVLSIDARGR 63 (69)
T ss_pred ccCCCCEEEEEEEEECCCCc
Confidence 37999999999844443443
No 83
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=20.23 E-value=97 Score=31.72 Aligned_cols=25 Identities=28% Similarity=0.418 Sum_probs=21.2
Q ss_pred HhhhcCCCCCCCCCcEEEEEEeeec
Q 029551 136 ASESERPIPDIRTGDVVEIKLFLKI 160 (191)
Q Consensus 136 e~~~~R~iPdiRpGdIVelklEVPE 160 (191)
+....|.-|+|++||||++.=+|--
T Consensus 249 e~aGvRAyP~IevGdiV~ViG~V~~ 273 (715)
T COG1107 249 EEAGVRAYPEIEVGDIVEVIGEVTR 273 (715)
T ss_pred ccCCcccCCCCCCCceEEEEEEEee
Confidence 3468899999999999999887753
No 84
>PRK14560 putative RNA-binding protein; Provisional
Probab=20.03 E-value=1.7e+02 Score=23.45 Aligned_cols=26 Identities=23% Similarity=0.052 Sum_probs=18.1
Q ss_pred CCCCCCcEEEEEEeeecCCCCcceeeEEEe
Q 029551 144 PDIRTGDVVEIKLFLKIGVGCPFTKVLLCQ 173 (191)
Q Consensus 144 PdiRpGdIVelklEVPEnkRR~~t~~~ic~ 173 (191)
++|++||+|.|..+ ++ .....+|+|.
T Consensus 105 ~~~~~Gd~V~I~~~---~~-~~~vavG~~~ 130 (160)
T PRK14560 105 EDIKEGDIVFVVEE---TH-GKPLAVGRAL 130 (160)
T ss_pred CCCCCCCEEEEEEC---CC-CeEEEEEEEe
Confidence 69999999999874 22 3345666655
Done!