Query 021720
Match_columns 308
No_of_seqs 132 out of 877
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 05:09:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021720.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021720hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0335 RplS Ribosomal protein 99.9 2.6E-25 5.7E-30 185.2 9.4 72 232-308 5-77 (115)
2 CHL00084 rpl19 ribosomal prote 99.9 3.3E-25 7.1E-30 184.5 9.5 62 247-308 17-79 (117)
3 TIGR01024 rplS_bact ribosomal 99.9 3.6E-25 7.7E-30 183.2 9.3 73 231-308 2-75 (113)
4 PRK05338 rplS 50S ribosomal pr 99.9 3.8E-25 8.3E-30 183.7 9.3 73 231-308 2-75 (116)
5 PF01245 Ribosomal_L19: Riboso 99.9 2.1E-24 4.5E-29 177.8 10.8 68 241-308 7-75 (113)
6 KOG1698 Mitochondrial/chloropl 99.9 1.1E-21 2.3E-26 176.0 11.4 114 193-308 39-152 (201)
7 PF05641 Agenet: Agenet domain 78.0 7.1 0.00015 29.2 5.4 38 253-295 1-38 (68)
8 smart00743 Agenet Tudor-like d 74.6 19 0.00041 25.7 6.6 49 251-307 1-49 (61)
9 cd00493 FabA_FabZ FabA/Z, beta 44.0 36 0.00079 26.3 3.8 30 252-281 88-117 (131)
10 KOG0494 Transcription factor C 43.7 3.9 8.4E-05 40.1 -2.0 53 220-274 135-187 (332)
11 PF02211 NHase_beta: Nitrile h 43.1 21 0.00045 33.2 2.7 36 249-284 131-170 (222)
12 TIGR02266 gmx_TIGR02266 Myxoco 42.8 1E+02 0.0022 23.1 5.9 35 251-286 35-69 (96)
13 TIGR03170 flgA_cterm flagella 40.0 1E+02 0.0023 24.6 6.0 47 249-300 62-108 (122)
14 PF02765 POT1: Telomeric singl 39.5 28 0.0006 29.3 2.7 38 250-294 70-109 (146)
15 cd01288 FabZ FabZ is a 17kD be 39.0 44 0.00094 26.0 3.6 28 252-279 87-114 (131)
16 TIGR01750 fabZ beta-hydroxyacy 38.8 47 0.001 26.8 3.8 28 252-279 97-124 (140)
17 cd04497 hPOT1_OB1_like hPOT1_O 36.7 60 0.0013 27.2 4.3 41 249-296 65-105 (138)
18 PF12969 DUF3857: Domain of Un 36.2 29 0.00062 28.5 2.2 20 248-267 85-104 (177)
19 cd08544 Reeler Reeler, the N-t 35.9 67 0.0015 26.2 4.3 31 252-286 29-59 (135)
20 PF02752 Arrestin_C: Arrestin 35.2 53 0.0011 25.2 3.4 32 252-283 15-47 (136)
21 KOG1403 Predicted alanine-glyo 34.8 10 0.00022 38.4 -0.7 15 11-25 217-231 (452)
22 PRK00006 fabZ (3R)-hydroxymyri 32.6 62 0.0013 26.4 3.6 28 253-280 102-129 (147)
23 COG2139 RPL21A Ribosomal prote 31.9 42 0.00092 28.4 2.6 39 249-287 29-71 (98)
24 cd03451 FkbR2 FkbR2 is a Strep 31.3 69 0.0015 25.6 3.7 16 252-267 91-106 (146)
25 PF13144 SAF_2: SAF-like 31.0 1.8E+02 0.004 25.0 6.4 45 250-299 137-181 (196)
26 COG2030 MaoC Acyl dehydratase 30.0 64 0.0014 27.5 3.4 17 251-267 105-121 (159)
27 smart00739 KOW KOW (Kyprides, 29.6 1.3E+02 0.0027 18.0 3.8 27 252-284 1-27 (28)
28 TIGR00405 L26e_arch ribosomal 28.7 1.9E+02 0.0042 24.0 6.0 43 251-301 85-127 (145)
29 PF00238 Ribosomal_L14: Riboso 28.7 1E+02 0.0022 26.1 4.4 36 249-284 29-67 (122)
30 PF07977 FabA: FabA-like domai 28.5 54 0.0012 26.6 2.6 30 251-280 95-128 (138)
31 PF07238 PilZ: PilZ domain; I 27.6 2E+02 0.0043 20.7 5.2 32 252-285 44-75 (102)
32 PRK08571 rpl14p 50S ribosomal 27.4 1.5E+02 0.0032 26.0 5.2 36 249-284 43-78 (132)
33 PF09926 DUF2158: Uncharacteri 25.7 44 0.00096 24.9 1.5 10 253-262 1-10 (53)
34 PF02014 Reeler: Reeler domain 25.2 67 0.0014 26.3 2.6 34 251-288 28-61 (132)
35 TIGR01955 RfaH transcriptional 25.2 1.3E+02 0.0028 25.0 4.4 29 251-285 107-135 (159)
36 cd05690 S1_RPS1_repeat_ec5 S1_ 24.9 68 0.0015 22.6 2.3 21 252-272 45-66 (69)
37 cd03440 hot_dog The hotdog fol 24.8 1.8E+02 0.0039 18.5 4.2 30 251-280 56-85 (100)
38 COG0250 NusG Transcription ant 24.7 75 0.0016 28.5 3.0 49 226-284 101-149 (178)
39 PRK08559 nusG transcription an 24.4 2.8E+02 0.006 23.8 6.3 41 251-299 93-133 (153)
40 cd05708 S1_Rrp5_repeat_sc12 S1 24.3 79 0.0017 22.5 2.6 21 252-272 47-68 (77)
41 cd00164 S1_like S1_like: Ribos 24.3 83 0.0018 20.8 2.5 16 252-267 41-56 (65)
42 TIGR03673 rpl14p_arch 50S ribo 24.2 1.7E+02 0.0038 25.5 5.1 35 250-284 43-77 (131)
43 PRK05483 rplN 50S ribosomal pr 24.1 1.4E+02 0.0031 25.6 4.4 34 251-284 31-67 (122)
44 cd04455 S1_NusA S1_NusA: N-uti 24.0 1E+02 0.0022 22.4 3.2 16 252-267 40-55 (67)
45 PRK03999 translation initiatio 23.8 1.9E+02 0.0041 24.6 5.2 54 249-307 7-60 (129)
46 cd03450 NodN NodN (nodulation 23.5 1.5E+02 0.0033 25.2 4.5 33 253-285 98-134 (149)
47 cd04471 S1_RNase_R S1_RNase_R: 23.3 76 0.0017 23.0 2.4 22 251-272 56-78 (83)
48 cd04491 SoSSB_OBF SoSSB_OBF: A 23.1 1E+02 0.0022 23.0 3.0 25 250-274 46-71 (82)
49 cd05688 S1_RPS1_repeat_ec3 S1_ 23.1 78 0.0017 21.8 2.3 16 252-267 44-59 (68)
50 PTZ00054 60S ribosomal protein 23.0 1.7E+02 0.0036 26.0 4.8 35 249-283 50-84 (139)
51 PF12148 DUF3590: Protein of u 22.9 53 0.0012 27.0 1.6 22 250-271 63-84 (85)
52 PF01835 A2M_N: MG2 domain; I 22.4 3.1E+02 0.0068 20.8 5.7 19 249-267 7-25 (99)
53 PF08207 EFP_N: Elongation fac 22.0 3.3E+02 0.0071 20.0 5.8 49 252-307 4-53 (58)
54 PF14085 DUF4265: Domain of un 21.8 2E+02 0.0043 23.8 4.8 34 251-293 24-57 (117)
55 cd05703 S1_Rrp5_repeat_hs12_sc 21.7 1E+02 0.0022 23.0 2.8 22 252-273 46-68 (73)
56 COG1566 EmrA Multidrug resista 21.5 2.4E+02 0.0051 28.1 6.0 59 245-306 251-318 (352)
57 PRK04424 fatty acid biosynthes 21.4 1.3E+02 0.0029 26.5 3.9 30 251-280 137-166 (185)
58 cd03441 R_hydratase_like (R)-h 21.1 2.6E+02 0.0057 21.2 5.1 17 251-267 79-95 (127)
59 cd06462 Peptidase_S24_S26 The 21.1 1.7E+02 0.0036 20.8 3.7 43 250-300 11-53 (84)
60 cd03452 MaoC_C MaoC_C The C-t 21.0 1.2E+02 0.0026 25.0 3.4 17 252-268 88-104 (142)
61 PRK07018 flgA flagellar basal 21.0 2.9E+02 0.0063 25.2 6.1 47 249-300 173-219 (235)
62 TIGR00922 nusG transcription t 21.0 5.2E+02 0.011 21.9 7.6 28 251-284 118-145 (172)
63 TIGR01067 rplN_bact ribosomal 20.7 2E+02 0.0043 24.7 4.7 34 251-284 31-67 (122)
64 cd04452 S1_IF2_alpha S1_IF2_al 20.7 1.1E+02 0.0023 22.0 2.6 16 252-267 49-64 (76)
65 cd05705 S1_Rrp5_repeat_hs14 S1 20.6 1E+02 0.0022 23.2 2.6 22 252-273 50-72 (74)
66 cd05685 S1_Tex S1_Tex: The C-t 20.5 1.1E+02 0.0024 20.9 2.6 21 252-272 44-65 (68)
67 PF00717 Peptidase_S24: Peptid 20.4 61 0.0013 22.9 1.3 40 250-297 8-47 (70)
68 cd05706 S1_Rrp5_repeat_sc10 S1 20.4 1.2E+02 0.0025 21.8 2.8 16 252-267 47-62 (73)
No 1
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.6e-25 Score=185.21 Aligned_cols=72 Identities=49% Similarity=0.880 Sum_probs=66.4
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEeeC
Q 021720 232 IMQILDKEAVENVKSQREIPDIKPGYIVQLKVVIPE-NKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFPL 308 (308)
Q Consensus 232 LM~iLEKeemEe~r~KrdIPeFkpGDTVrV~~kI~E-nKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFPL 308 (308)
+++.|+++++ ++++|+|+|||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 5 ~i~~le~~q~-----~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~ 77 (115)
T COG0335 5 IIQQLEQEQI-----KKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPL 77 (115)
T ss_pred HHHHHHHHHH-----HhhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeec
Confidence 6667766655 456999999999999999999 89999999999999999999999999999999999999997
No 2
>CHL00084 rpl19 ribosomal protein L19
Probab=99.92 E-value=3.3e-25 Score=184.46 Aligned_cols=62 Identities=42% Similarity=0.772 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEeeC
Q 021720 247 QREIPDIKPGYIVQLKVVIPE-NKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFPL 308 (308)
Q Consensus 247 KrdIPeFkpGDTVrV~~kI~E-nKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFPL 308 (308)
+.++|+|+|||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 17 ~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl 79 (117)
T CHL00084 17 KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLL 79 (117)
T ss_pred hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEec
Confidence 679999999999999999999 89999999999999999999999999999999999999997
No 3
>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=99.92 E-value=3.6e-25 Score=183.20 Aligned_cols=73 Identities=40% Similarity=0.819 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEeeC
Q 021720 231 HIMQILDKEAVENVKSQREIPDIKPGYIVQLKVVIPE-NKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFPL 308 (308)
Q Consensus 231 nLM~iLEKeemEe~r~KrdIPeFkpGDTVrV~~kI~E-nKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFPL 308 (308)
++|+.++++++ ++++|+|+|||+|+|++++.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 2 ~~i~~~e~~~~-----~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl 75 (113)
T TIGR01024 2 NLIKQIEQEQL-----KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPL 75 (113)
T ss_pred cHHHHHHHHHh-----hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEc
Confidence 35555555433 679999999999999999999 89999999999999999999999999999999999999997
No 4
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=99.92 E-value=3.8e-25 Score=183.71 Aligned_cols=73 Identities=40% Similarity=0.831 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEeeC
Q 021720 231 HIMQILDKEAVENVKSQREIPDIKPGYIVQLKVVIPE-NKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFPL 308 (308)
Q Consensus 231 nLM~iLEKeemEe~r~KrdIPeFkpGDTVrV~~kI~E-nKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFPL 308 (308)
++|+.++++++ ++++|+|++||+|+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 2 ~~i~~~~~~~~-----~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl 75 (116)
T PRK05338 2 NLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPL 75 (116)
T ss_pred cHHHHHHHHHh-----hcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecC
Confidence 35566555444 578999999999999999999 89999999999999999999999999999999999999997
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=99.91 E-value=2.1e-24 Score=177.77 Aligned_cols=68 Identities=43% Similarity=0.809 Sum_probs=63.4
Q ss_pred HHHhhcCCCCCCCCCCCEEEEEEEecC-CCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEeeC
Q 021720 241 VENVKSQREIPDIKPGYIVQLKVVIPE-NKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFPL 308 (308)
Q Consensus 241 mEe~r~KrdIPeFkpGDTVrV~~kI~E-nKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFPL 308 (308)
+|+.+.+.++|+|+|||+|+|++++.| +|+|+|.|+|+||+++|+|+++||||||+++|+|||++|||
T Consensus 7 ~e~~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l 75 (113)
T PF01245_consen 7 VEREQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPL 75 (113)
T ss_dssp HHHTTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEET
T ss_pred HHHHHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEc
Confidence 334444789999999999999999999 89999999999999999999999999999999999999997
No 6
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.1e-21 Score=176.01 Aligned_cols=114 Identities=44% Similarity=0.724 Sum_probs=96.7
Q ss_pred ceeecccCcccccCCCCCCCCCCCCcccccccchHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCEEEEEEEecCCCccc
Q 021720 193 RCISTSESSVESASYPPAAASSDLAPRIKFKRLDKTARHIMQILDKEAVENVKSQREIPDIKPGYIVQLKVVIPENKRRV 272 (308)
Q Consensus 193 R~~sTt~~~v~~s~~~stap~pp~ppriK~K~l~Kra~nLM~iLEKeemEe~r~KrdIPeFkpGDTVrV~~kI~EnKeRi 272 (308)
|+++++..+ + ...+.--+..++....++...++.+.++|++||+++|++.+..+++|+|++||+|+|++.++++|.|+
T Consensus 39 ~~~a~~~~~-~-~~~~~~~~~~~~~~~~~f~~~~~~~~~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~ 116 (201)
T KOG1698|consen 39 RCFAPTKRP-S-VNEPSPESPCVVEQYPEFLPLRKVAKRIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPENKRKV 116 (201)
T ss_pred ccccCCCCc-c-cccCCCCCccccccCcccccchhHHHHHHHhhCHHHHHHHHhcccCCccccccEEEEEecCCccCCce
Confidence 777777765 2 22222111112334556678889999999999999999999999999999999999999999999999
Q ss_pred ceEEEEEEEEecCCCcceEEEEeccCCeeeEEEeeC
Q 021720 273 STLKGIVIARRNAGISTTFRLRRLVAGVGVESLFPL 308 (308)
Q Consensus 273 Q~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFPL 308 (308)
..|.||||+|+|+|+++||+|||+++|+|||-+|||
T Consensus 117 s~f~Gi~I~R~~~Gl~atf~LRnvIagvGVEi~~pL 152 (201)
T KOG1698|consen 117 SRFKGICIRRRNAGLNATFLLRNVIAGVGVEIVFPL 152 (201)
T ss_pred eEEEEEEEEecccCCcceEEeeehhhCceeEEEEec
Confidence 999999999999999999999999999999999997
No 7
>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=77.97 E-value=7.1 Score=29.19 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=25.6
Q ss_pred CCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEe
Q 021720 253 IKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRR 295 (308)
Q Consensus 253 FkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRK 295 (308)
|++||.|+|... |+.-|-.=|.|+|++..+.+ ++.|+-
T Consensus 1 F~~G~~VEV~s~--e~g~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSD--EDGFRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE---SBTT--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEc--CCCCCcEEEEEEEEEeCCCc---EEEEEE
Confidence 789999999753 34458899999999999876 787775
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=74.65 E-value=19 Score=25.69 Aligned_cols=49 Identities=16% Similarity=0.114 Sum_probs=36.0
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEee
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFP 307 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFP 307 (308)
+.|++||.|.|.... .-.=|+|+|++..+ +..|.|+=...+.|-+-.++
T Consensus 1 ~~~~~G~~Ve~~~~~-----~~~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v~ 49 (61)
T smart00743 1 SDFKKGDRVEVFSKE-----EDSWWEAVVTKVLG---DGKYLVRYLTESEPLKETVD 49 (61)
T ss_pred CCcCCCCEEEEEECC-----CCEEEEEEEEEECC---CCEEEEEECCCCcccEEEEe
Confidence 368999999999652 55789999999887 45688887664466555543
No 9
>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=43.99 E-value=36 Score=26.27 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=24.1
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEEEE
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIVIA 281 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVVIA 281 (308)
...|||+|.+.+++.+.+.+.-.|.+.+..
T Consensus 88 ~v~pgd~l~i~~~i~~~~~~~~~~~~~~~~ 117 (131)
T cd00493 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAYV 117 (131)
T ss_pred CcCCCCEEEEEEEEEEeeCCEEEEEEEEEE
Confidence 467999999999999866677888877653
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=43.66 E-value=3.9 Score=40.12 Aligned_cols=53 Identities=23% Similarity=0.317 Sum_probs=38.4
Q ss_pred cccccchHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCEEEEEEEecCCCcccce
Q 021720 220 IKFKRLDKTARHIMQILDKEAVENVKSQREIPDIKPGYIVQLKVVIPENKRRVST 274 (308)
Q Consensus 220 iK~K~l~Kra~nLM~iLEKeemEe~r~KrdIPeFkpGDTVrV~~kI~EnKeRiQ~ 274 (308)
.|.|+.+++-+.+...+..+++|+.+++...|++++-..+.++.+++| .|||+
T Consensus 135 ~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpE--DRIqV 187 (332)
T KOG0494|consen 135 AKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPE--DRIQV 187 (332)
T ss_pred cccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCch--hhhhH
Confidence 333333344445666777778888887778999999999999988888 56665
No 11
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=43.09 E-value=21 Score=33.20 Aligned_cols=36 Identities=17% Similarity=0.287 Sum_probs=19.8
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceE----EEEEEEEec
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTL----KGIVIARRN 284 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~F----eGVVIARRN 284 (308)
.-|.|++||.|+|.-.-+..-.|+..| +|+|.+..+
T Consensus 131 ~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 131 APPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp SS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEec
Confidence 468999999999997766677777766 788887665
No 12
>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=42.81 E-value=1e+02 Score=23.14 Aligned_cols=35 Identities=34% Similarity=0.479 Sum_probs=26.4
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCC
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAG 286 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrG 286 (308)
..+.+|+.|.|.+.++.+... -...|.|+..+..+
T Consensus 35 ~~~~~g~~v~l~l~l~~~~~~-i~~~g~Vv~~~~~~ 69 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGGERP-VELKGVVAWVRPAA 69 (96)
T ss_pred CCcCCCCEEEEEEEcCCCCeE-EEEEEEEEEeCCCC
Confidence 457899999999999875333 34679999887644
No 13
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=40.05 E-value=1e+02 Score=24.60 Aligned_cols=47 Identities=17% Similarity=0.085 Sum_probs=34.7
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCCe
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAGV 300 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GV 300 (308)
..|-++-||.|.|.+...- =..+-..+|..+..++.+++|||...|-
T Consensus 62 ~~~~V~~G~~V~i~~~~~~-----~~i~~~g~Al~~g~~G~~I~V~N~~s~k 108 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGG-----LSVTTEGKALEDGAVGDQIRVRNLSSGK 108 (122)
T ss_pred CccEEcCCCEEEEEEecCC-----EEEEEEEEEccccCCCCEEEEEECCCCC
Confidence 4578999999999986432 1223344688899999999999976553
No 14
>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=39.54 E-value=28 Score=29.30 Aligned_cols=38 Identities=21% Similarity=0.458 Sum_probs=24.9
Q ss_pred CCCCCC-CCEEEEE-EEecCCCcccceEEEEEEEEecCCCcceEEEE
Q 021720 250 IPDIKP-GYIVQLK-VVIPENKRRVSTLKGIVIARRNAGISTTFRLR 294 (308)
Q Consensus 250 IPeFkp-GDTVrV~-~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLR 294 (308)
+|.+.. ||+|.++ ++| |.|.|-..+..+.+-+++|.|=
T Consensus 70 LP~v~~~GDii~l~r~kv-------~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 70 LPNVKSVGDIIRLRRVKV-------QSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp SCTTCSTTHEEEEEEEEE-------EEETTEEEEEEECECTEEEEEE
T ss_pred CCCCCCCCCEEEEEEEEE-------EEECCEEEEEecCCCcEEEEEE
Confidence 599888 9999998 554 4444444454454455666654
No 15
>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=39.02 E-value=44 Score=26.01 Aligned_cols=28 Identities=25% Similarity=0.421 Sum_probs=22.8
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEE
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIV 279 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVV 279 (308)
...|||+|++.+++.+.+.+.-.|++.+
T Consensus 87 pv~pgd~l~i~~~v~~~~~~~~~~~~~~ 114 (131)
T cd01288 87 PVVPGDQLILEVELLKLRRGIGKFKGKA 114 (131)
T ss_pred ccCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 4568999999999998667777777775
No 16
>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=38.80 E-value=47 Score=26.82 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=22.1
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEE
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIV 279 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVV 279 (308)
..+|||+|++++++.+..++.-.|++.+
T Consensus 97 ~v~pGd~l~i~~~i~~~~~~~~~~~~~~ 124 (140)
T TIGR01750 97 PVVPGDQLILHAEFLKKRRKIGKFKGEA 124 (140)
T ss_pred ccCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 4678999999999988656667777765
No 17
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=36.73 E-value=60 Score=27.17 Aligned_cols=41 Identities=20% Similarity=0.300 Sum_probs=30.7
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEec
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRL 296 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKI 296 (308)
.+|.+.+||+|.++= =++|.|.|-..+..+. -.++|-|=+-
T Consensus 65 ~LP~v~~GDVIll~~------~kv~~~~g~~~~~~~~-~~ss~avf~~ 105 (138)
T cd04497 65 SLPIVKVGDIILLRR------VKIQSYNGKPQGISND-RGSSWAVFRG 105 (138)
T ss_pred hCCCCCCCCEEEEEE------EEEEEECCceEEEECC-CceeEEEEcC
Confidence 589889999999972 5788888888888776 3466665443
No 18
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=36.18 E-value=29 Score=28.46 Aligned_cols=20 Identities=25% Similarity=0.489 Sum_probs=13.3
Q ss_pred CCCCCCCCCCEEEEEEEecC
Q 021720 248 REIPDIKPGYIVQLKVVIPE 267 (308)
Q Consensus 248 rdIPeFkpGDTVrV~~kI~E 267 (308)
-.+|++++||+|+..+.+..
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~ 104 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKS 104 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE
T ss_pred EEcCCCCCCcEEEEEEEEEe
Confidence 46899999999999999976
No 19
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=35.88 E-value=67 Score=26.23 Aligned_cols=31 Identities=19% Similarity=0.366 Sum_probs=26.6
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEEEEEecCC
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAG 286 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrG 286 (308)
.+.||+.++|++.-.+. ..|+|..|.-|+.+
T Consensus 29 ~y~pG~~~~Vtl~~~~~----~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSSP----SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCCC----CceeEEEEEEEcCC
Confidence 78999999999886544 89999999988865
No 20
>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=35.18 E-value=53 Score=25.16 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=22.3
Q ss_pred CCCCCCEEEEEEEecC-CCcccceEEEEEEEEe
Q 021720 252 DIKPGYIVQLKVVIPE-NKRRVSTLKGIVIARR 283 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E-nKeRiQ~FeGVVIARR 283 (308)
.|.+||+|.|.++|.. .+.+++..+--++.+.
T Consensus 15 ~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~~~ 47 (136)
T PF02752_consen 15 AYVPGETIPVNVEIDNQSKKKIKKIKVSLVERI 47 (136)
T ss_dssp EEETT--EEEEEEEEE-SSSEEEEEEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCCCEEEEEEEEEEEEE
Confidence 4889999999999986 5667776666665543
No 21
>KOG1403 consensus Predicted alanine-glyoxylate aminotransferase [General function prediction only]
Probab=34.76 E-value=10 Score=38.42 Aligned_cols=15 Identities=67% Similarity=1.032 Sum_probs=12.6
Q ss_pred eeeccCceeeeeEEe
Q 021720 11 NLQSCGGQLIDVAFY 25 (308)
Q Consensus 11 ~~~~~~~~~~~~~~~ 25 (308)
.|||||||+|--|=|
T Consensus 217 slQSCGGQiiPPagY 231 (452)
T KOG1403|consen 217 SLQSCGGQIIPPAGY 231 (452)
T ss_pred HHHhcCCcccCchhH
Confidence 489999999987755
No 22
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=32.58 E-value=62 Score=26.43 Aligned_cols=28 Identities=25% Similarity=0.484 Sum_probs=22.1
Q ss_pred CCCCCEEEEEEEecCCCcccceEEEEEE
Q 021720 253 IKPGYIVQLKVVIPENKRRVSTLKGIVI 280 (308)
Q Consensus 253 FkpGDTVrV~~kI~EnKeRiQ~FeGVVI 280 (308)
.+|||+|++.+++.+.++++-.+++.+.
T Consensus 102 v~pGd~l~i~~~i~~~~~~~v~~~~~~~ 129 (147)
T PRK00006 102 VVPGDQLILEVELLKQRRGIWKFKGVAT 129 (147)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEEE
Confidence 3589999999999886666677777763
No 23
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=31.88 E-value=42 Score=28.41 Aligned_cols=39 Identities=18% Similarity=0.216 Sum_probs=29.9
Q ss_pred CCCCCCCCCEEEEEEEecC----CCcccceEEEEEEEEecCCC
Q 021720 249 EIPDIKPGYIVQLKVVIPE----NKRRVSTLKGIVIARRNAGI 287 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~E----nKeRiQ~FeGVVIARRNrGL 287 (308)
-+-+|++||.|-+.+.=.= --.|.|=..|+|+.++++-.
T Consensus 29 ~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay 71 (98)
T COG2139 29 YLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAY 71 (98)
T ss_pred HHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEE
Confidence 4678999999877654321 35799999999999998654
No 24
>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=31.31 E-value=69 Score=25.61 Aligned_cols=16 Identities=6% Similarity=-0.010 Sum_probs=14.1
Q ss_pred CCCCCCEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPE 267 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E 267 (308)
..+|||+|.+..+|.+
T Consensus 91 pv~~GDtl~~~~~v~~ 106 (146)
T cd03451 91 PVFHGDTLYAESEVLS 106 (146)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4689999999999987
No 25
>PF13144 SAF_2: SAF-like
Probab=31.05 E-value=1.8e+02 Score=25.03 Aligned_cols=45 Identities=22% Similarity=0.263 Sum_probs=34.0
Q ss_pred CCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCC
Q 021720 250 IPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAG 299 (308)
Q Consensus 250 IPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~G 299 (308)
.|.++-||.|.|.+.... =..+--.+|..+..++..+.|||...|
T Consensus 137 ~~~V~~G~~V~v~~~~g~-----i~i~~~g~Al~~G~~G~~I~V~N~~S~ 181 (196)
T PF13144_consen 137 PPLVKRGDIVTVIARSGG-----ISISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred ceecCCCCEEEEEEEeCC-----EEEEEEEEEccCCCCCCEEEEEECCCC
Confidence 478999999999876432 223344578889999999999997654
No 26
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=30.01 E-value=64 Score=27.50 Aligned_cols=17 Identities=18% Similarity=0.376 Sum_probs=15.1
Q ss_pred CCCCCCCEEEEEEEecC
Q 021720 251 PDIKPGYIVQLKVVIPE 267 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~E 267 (308)
-.+.+||+|++..++.+
T Consensus 105 ~PV~~Gdtl~~~~~v~~ 121 (159)
T COG2030 105 KPVFPGDTLRARVEVLD 121 (159)
T ss_pred CCCCCCCEEEEEEEEEE
Confidence 46899999999999987
No 27
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=29.60 E-value=1.3e+02 Score=18.00 Aligned_cols=27 Identities=15% Similarity=0.138 Sum_probs=18.1
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEEEEEec
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIVIARRN 284 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRN 284 (308)
.|.+||.|+|.- -...-++|++++..+
T Consensus 1 ~~~~G~~V~I~~------G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIA------GPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeE------CCCCCcEEEEEEEcC
Confidence 378999999873 334445777777653
No 28
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=28.71 E-value=1.9e+02 Score=24.03 Aligned_cols=43 Identities=23% Similarity=0.204 Sum_probs=28.0
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCCee
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVG 301 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVG 301 (308)
..|.+||.|+|. ..=.+-|+|+|+...+... ..+|.=+..+.-
T Consensus 85 ~~~~~Gd~V~I~------~GPf~G~~g~v~~~d~~k~--~v~v~l~~~~~~ 127 (145)
T TIGR00405 85 ESIKKGDIVEII------SGPFKGERAKVIRVDESKE--EVTLELIEAAVP 127 (145)
T ss_pred cccCCCCEEEEe------ecCCCCCeEEEEEEcCCCC--EEEEEEEEcCcc
Confidence 459999999996 2456778899988875433 344433333433
No 29
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=28.69 E-value=1e+02 Score=26.13 Aligned_cols=36 Identities=11% Similarity=0.184 Sum_probs=27.3
Q ss_pred CCCCCCCCCEEEEEEEec--C-CCcccceEEEEEEEEec
Q 021720 249 EIPDIKPGYIVQLKVVIP--E-NKRRVSTLKGIVIARRN 284 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~--E-nKeRiQ~FeGVVIARRN 284 (308)
..+.-.+||+|.|.++-. . .-++=|.+.|+|+..+.
T Consensus 29 ~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~ 67 (122)
T PF00238_consen 29 RRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKK 67 (122)
T ss_dssp TTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSS
T ss_pred CccccccceEEEEEEeecccCccccccceEEEEEEEEeE
Confidence 356678999999999876 3 34556999999998765
No 30
>PF07977 FabA: FabA-like domain; InterPro: IPR013114 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes []. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. 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. This enzyme domain has a HotDog fold.; PDB: 3D6X_F 2GLV_J 2GLM_E 2GLP_E 2GLL_C 1U1Z_F 3ESI_A 3AZB_T 3AZA_M 3AZ9_U ....
Probab=28.48 E-value=54 Score=26.62 Aligned_cols=30 Identities=17% Similarity=0.361 Sum_probs=23.0
Q ss_pred CCCCCCC-EEEEEEEecC---CCcccceEEEEEE
Q 021720 251 PDIKPGY-IVQLKVVIPE---NKRRVSTLKGIVI 280 (308)
Q Consensus 251 PeFkpGD-TVrV~~kI~E---nKeRiQ~FeGVVI 280 (308)
=.+.||| ++++.+.+.+ .......|+|.+.
T Consensus 95 ~~v~Pg~~~l~~~v~i~~~~~~~~~~~~~~~~~~ 128 (138)
T PF07977_consen 95 GPVYPGDKTLRIEVEIKKIRRREGGMAIFDGTAY 128 (138)
T ss_dssp S-B-TTE-EEEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred ccEeCCCcEEEEEEEEEEeecccCCEEEEEEEEE
Confidence 4578999 9999999988 6777888887654
No 31
>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=27.57 E-value=2e+02 Score=20.65 Aligned_cols=32 Identities=22% Similarity=0.417 Sum_probs=23.9
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNA 285 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNr 285 (308)
.+.+||.|.|.+.+.....-. +.|.|+..++.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~~--~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFPI--VTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSCEE--EEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCeeE--EEEEEEEEECC
Confidence 789999999998777644332 99999998876
No 32
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=27.35 E-value=1.5e+02 Score=25.99 Aligned_cols=36 Identities=22% Similarity=0.377 Sum_probs=28.3
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEec
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRN 284 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRN 284 (308)
.+|.-.+||+|.|.++-.....|-|++.+||+..+.
T Consensus 43 r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 78 (132)
T PRK08571 43 RLPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQRK 78 (132)
T ss_pred cCCccccCCEEEEEEEECCCcccCCEeEEEEEEecc
Confidence 357789999999998865534456999999998663
No 33
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=25.73 E-value=44 Score=24.94 Aligned_cols=10 Identities=60% Similarity=0.727 Sum_probs=8.8
Q ss_pred CCCCCEEEEE
Q 021720 253 IKPGYIVQLK 262 (308)
Q Consensus 253 FkpGDTVrV~ 262 (308)
|++||+|+++
T Consensus 1 f~~GDvV~LK 10 (53)
T PF09926_consen 1 FKIGDVVQLK 10 (53)
T ss_pred CCCCCEEEEc
Confidence 7899999886
No 34
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=25.23 E-value=67 Score=26.29 Aligned_cols=34 Identities=21% Similarity=0.429 Sum_probs=25.5
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCc
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGIS 288 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLn 288 (308)
..+.||+.++|++ +....+.|+|..|.-|...-.
T Consensus 28 ~~y~pg~~~~Vtl----~~~~~~~F~GFllqAr~~~~~ 61 (132)
T PF02014_consen 28 SSYEPGQTYTVTL----SSSGSSSFRGFLLQARDANNS 61 (132)
T ss_dssp SSB-TTBEEEEEE----EETTTEEBSEEEEEEEETT--
T ss_pred CeEcCCCEEEEEE----ECCCCCceeEEEEEEEeCCCC
Confidence 4689999999998 556678899999988865443
No 35
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=25.19 E-value=1.3e+02 Score=24.99 Aligned_cols=29 Identities=10% Similarity=0.107 Sum_probs=22.7
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecC
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNA 285 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNr 285 (308)
..|.+||.|+|. ..=.+-|+|+|....++
T Consensus 107 ~~~~~G~~V~V~------~GPf~g~~g~v~~~~~~ 135 (159)
T TIGR01955 107 TLPYKGDKVRIT------DGAFAGFEAIFLEPDGE 135 (159)
T ss_pred cCCCCCCEEEEe------ccCCCCcEEEEEEECCC
Confidence 469999999886 24477899999998743
No 36
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: 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 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=24.92 E-value=68 Score=22.57 Aligned_cols=21 Identities=24% Similarity=0.268 Sum_probs=15.3
Q ss_pred CCCCCCEEEEEEEecC-CCccc
Q 021720 252 DIKPGYIVQLKVVIPE-NKRRV 272 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E-nKeRi 272 (308)
.|++||.|+|.+.-.. .++|+
T Consensus 45 ~~~~G~~v~v~v~~id~~~~~i 66 (69)
T cd05690 45 IYKKGQEVEAVVLNIDVERERI 66 (69)
T ss_pred EECCCCEEEEEEEEEECCcCEE
Confidence 4899999999965443 55554
No 37
>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=24.81 E-value=1.8e+02 Score=18.54 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=19.9
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEE
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVI 280 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVI 280 (308)
-...+||.|.+..++.+..++.-.++..+.
T Consensus 56 ~~~~~g~~v~~~~~~~~~~~~~~~~~~~~~ 85 (100)
T cd03440 56 RPVRPGDTLTVEAEVVRVGRSSVTVEVEVR 85 (100)
T ss_pred cCCCCCCEEEEEEEEEeccccEEEEEEEEE
Confidence 456779999999999884444344444433
No 38
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=24.68 E-value=75 Score=28.50 Aligned_cols=49 Identities=22% Similarity=0.383 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEec
Q 021720 226 DKTARHIMQILDKEAVENVKSQREIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRN 284 (308)
Q Consensus 226 ~Kra~nLM~iLEKeemEe~r~KrdIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRN 284 (308)
.+.+.++|+.++.. ....+...+|.+||.|+|.- -=..-|+|.|+..-.
T Consensus 101 ~~ei~~~l~~~~~~----~~~~~~~~~~e~Gd~VrI~~------GpFa~f~g~V~evd~ 149 (178)
T COG0250 101 EEEIEHILGFLEEE----VAPKKPKVDFEPGDVVRIID------GPFAGFKAKVEEVDE 149 (178)
T ss_pred HHHHHHHHhhcccc----ccCCcccccCCCCCEEEEec------cCCCCccEEEEEEcC
Confidence 34455666666543 22245668999999999852 233346666666554
No 39
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=24.38 E-value=2.8e+02 Score=23.80 Aligned_cols=41 Identities=24% Similarity=0.210 Sum_probs=28.0
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCC
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAG 299 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~G 299 (308)
-.|.+||.|+|. ..-.+-|+|.|+...+.- ...+|.=+-+.
T Consensus 93 ~~~~~G~~V~I~------~Gpf~g~~g~V~~vd~~k--~~v~v~ll~~~ 133 (153)
T PRK08559 93 EGIKEGDIVELI------AGPFKGEKARVVRVDESK--EEVTVELLEAA 133 (153)
T ss_pred cCCCCCCEEEEe------ccCCCCceEEEEEEcCCC--CEEEEEEECCc
Confidence 359999999996 245677899999987642 22555444444
No 40
>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=24.33 E-value=79 Score=22.47 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=15.1
Q ss_pred CCCCCCEEEEEEEecC-CCccc
Q 021720 252 DIKPGYIVQLKVVIPE-NKRRV 272 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E-nKeRi 272 (308)
.|++||.|+|.+.-.+ ++.|+
T Consensus 47 ~~~~Gd~v~v~i~~vd~~~~~i 68 (77)
T cd05708 47 LFRVGDKVRAKVLKIDAEKKRI 68 (77)
T ss_pred eecCCCEEEEEEEEEeCCCCEE
Confidence 4899999999875544 45554
No 41
>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=24.28 E-value=83 Score=20.77 Aligned_cols=16 Identities=31% Similarity=0.295 Sum_probs=13.0
Q ss_pred CCCCCCEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPE 267 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E 267 (308)
.|++||+|++.+.-..
T Consensus 41 ~~~~G~~v~~~v~~~d 56 (65)
T cd00164 41 VFKVGDEVEVKVLEVD 56 (65)
T ss_pred EeCCCCEEEEEEEEEc
Confidence 4899999999976543
No 42
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=24.25 E-value=1.7e+02 Score=25.53 Aligned_cols=35 Identities=23% Similarity=0.335 Sum_probs=27.5
Q ss_pred CCCCCCCCEEEEEEEecCCCcccceEEEEEEEEec
Q 021720 250 IPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRN 284 (308)
Q Consensus 250 IPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRN 284 (308)
+|.-.+||+|.|.++-.....|-|++.+||+..+.
T Consensus 43 ~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 77 (131)
T TIGR03673 43 LPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRK 77 (131)
T ss_pred CCccccCCEEEEEEEECCccccCCEeEEEEEEeCc
Confidence 47778999999998865533455999999998764
No 43
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=24.12 E-value=1.4e+02 Score=25.58 Aligned_cols=34 Identities=12% Similarity=0.189 Sum_probs=26.4
Q ss_pred CCCCCCCEEEEEEEecC--C-CcccceEEEEEEEEec
Q 021720 251 PDIKPGYIVQLKVVIPE--N-KRRVSTLKGIVIARRN 284 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~E--n-KeRiQ~FeGVVIARRN 284 (308)
+.-.+||+|.|.++-.. . -+|-|++.+||+..+.
T Consensus 31 ~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T PRK05483 31 RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEecc
Confidence 56789999999987533 2 3567999999998763
No 44
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=24.02 E-value=1e+02 Score=22.42 Aligned_cols=16 Identities=19% Similarity=0.291 Sum_probs=13.7
Q ss_pred CCCCCCEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPE 267 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E 267 (308)
.|++||.|+|.+.-.+
T Consensus 40 ~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 40 SYRPGDRIKAYVLEVR 55 (67)
T ss_pred cCCCCCEEEEEEEEEe
Confidence 5899999999987665
No 45
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=23.85 E-value=1.9e+02 Score=24.63 Aligned_cols=54 Identities=11% Similarity=0.145 Sum_probs=31.2
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCCeeeEEEee
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAGVGVESLFP 307 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GVGVERiFP 307 (308)
..++|+.|++|.+.=. -=++..++-.--.++| +-.-.+.+|++..|.=+|.+|+
T Consensus 7 ~~~~lrkG~~i~~~g~----p~~V~~~~~~kpGkhg-~a~vr~k~knL~tG~~~e~~~~ 60 (129)
T PRK03999 7 EVGELKEGSYVVIDGE----PCKIVEISKSKPGKHG-SAKARIVAIGIFDGQKRSLVQP 60 (129)
T ss_pred cHHHccCCCEEEECCE----EEEEEEEEeecCCCCC-cEEEEEEEEECCCCCEEEEEec
Confidence 4689999999976410 1111122211111212 2245677999999988888885
No 46
>cd03450 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear.
Probab=23.49 E-value=1.5e+02 Score=25.23 Aligned_cols=33 Identities=9% Similarity=0.118 Sum_probs=22.9
Q ss_pred CCCCCEEEEEEEecC--CCc--ccceEEEEEEEEecC
Q 021720 253 IKPGYIVQLKVVIPE--NKR--RVSTLKGIVIARRNA 285 (308)
Q Consensus 253 FkpGDTVrV~~kI~E--nKe--RiQ~FeGVVIARRNr 285 (308)
..+||+|.+..+|.+ .++ |++...=..|.+++.
T Consensus 98 V~~GDtl~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~ 134 (149)
T cd03450 98 VPVGSRVRGRFTLLSVEELKGGGVQVTLEVTVEIEGE 134 (149)
T ss_pred eeCCcEEEEEEEEEEEEEcCCCeEEEEEEEEEEEeCC
Confidence 679999999999987 222 245555556666654
No 47
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=23.29 E-value=76 Score=22.97 Aligned_cols=22 Identities=23% Similarity=0.451 Sum_probs=15.7
Q ss_pred CCCCCCCEEEEEEEecC-CCccc
Q 021720 251 PDIKPGYIVQLKVVIPE-NKRRV 272 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~E-nKeRi 272 (308)
-.|++||.|+|.+.-.. .+.++
T Consensus 56 ~~~~~gd~v~v~v~~vd~~~~~i 78 (83)
T cd04471 56 KVFRLGDKVKVRVVRVDLDRRKI 78 (83)
T ss_pred CEEcCCCEEEEEEEEeccccCEE
Confidence 46899999999976554 34443
No 48
>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=23.09 E-value=1e+02 Score=23.05 Aligned_cols=25 Identities=24% Similarity=0.501 Sum_probs=19.3
Q ss_pred CCCCCCCCEEEEE-EEecCCCcccce
Q 021720 250 IPDIKPGYIVQLK-VVIPENKRRVST 274 (308)
Q Consensus 250 IPeFkpGDTVrV~-~kI~EnKeRiQ~ 274 (308)
.+.+.+||+|++. .++.+-+.+.|.
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~g~~ql 71 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFNGRLEL 71 (82)
T ss_pred cccCCCCCEEEEEeEEEEecCCcEEE
Confidence 5779999999999 888775555554
No 49
>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=23.08 E-value=78 Score=21.80 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=12.8
Q ss_pred CCCCCCEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPE 267 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E 267 (308)
.|++||.|+|.+.-..
T Consensus 44 ~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 44 VVNVGDEVEVKVLKID 59 (68)
T ss_pred EECCCCEEEEEEEEEE
Confidence 3899999999875544
No 50
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=23.00 E-value=1.7e+02 Score=25.95 Aligned_cols=35 Identities=23% Similarity=0.352 Sum_probs=28.1
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEe
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARR 283 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARR 283 (308)
.+|.-.+||+|.|.++-.....|-|++.+||+..+
T Consensus 50 r~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVRtK 84 (139)
T PTZ00054 50 RLPSASLGDMVLATVKKGKPELRKKVLNAVIIRQR 84 (139)
T ss_pred cCcccccCCEEEEEEEECCCcccCCEeeEEEEEEC
Confidence 34778899999999887654456699999999866
No 51
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=22.90 E-value=53 Score=26.98 Aligned_cols=22 Identities=27% Similarity=0.418 Sum_probs=14.8
Q ss_pred CCCCCCCCEEEEEEEecCCCcc
Q 021720 250 IPDIKPGYIVQLKVVIPENKRR 271 (308)
Q Consensus 250 IPeFkpGDTVrV~~kI~EnKeR 271 (308)
.-++.+|++|-|.|.+.+.|||
T Consensus 63 w~~L~VG~~VMvNYN~d~P~er 84 (85)
T PF12148_consen 63 WDELKVGQVVMVNYNVDEPKER 84 (85)
T ss_dssp GGG--TT-EEEEEE-TTSTTS-
T ss_pred HHhCCcccEEEEecCCCCcccC
Confidence 4578999999999999988877
No 52
>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=22.43 E-value=3.1e+02 Score=20.79 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=15.3
Q ss_pred CCCCCCCCCEEEEEEEecC
Q 021720 249 EIPDIKPGYIVQLKVVIPE 267 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~E 267 (308)
|-|-.+|||+|.+...+..
T Consensus 7 Dr~iYrPGetV~~~~~~~~ 25 (99)
T PF01835_consen 7 DRPIYRPGETVHFRAIVRD 25 (99)
T ss_dssp SSSEE-TTSEEEEEEEEEE
T ss_pred CccCcCCCCEEEEEEEEec
Confidence 5688999999999998765
No 53
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=22.05 E-value=3.3e+02 Score=20.00 Aligned_cols=49 Identities=20% Similarity=0.361 Sum_probs=27.3
Q ss_pred CCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCC-cceEEEEeccCCeeeEEEee
Q 021720 252 DIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGI-STTFRLRRLVAGVGVESLFP 307 (308)
Q Consensus 252 eFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGL-nSTFTLRKIs~GVGVERiFP 307 (308)
++++|.+|++.= .--++..++ -.+.++|- --...+|++..|.-+|++|.
T Consensus 4 dlr~G~~i~~~g----~~~~V~~~~---~~k~gkg~a~v~~klknl~tG~~~e~tf~ 53 (58)
T PF08207_consen 4 DLRKGMVIEIDG----EPYVVLDFQ---HVKPGKGGAFVRVKLKNLRTGSKVEKTFR 53 (58)
T ss_dssp G--TTSEEEETT----EEEEEEEEE---EECCTTSSSEEEEEEEETTTTEEEEEEEE
T ss_pred HccCCCEEEECC----EEEEEEEEE---EECCCCCCeEEEEEEEECCCCCEEEEEEC
Confidence 578888887630 112222232 22234441 12345999999999999985
No 54
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=21.82 E-value=2e+02 Score=23.80 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=21.7
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEE
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRL 293 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTL 293 (308)
+.+..||+|++... ...-.|.++|.+ +| |+|++|
T Consensus 24 ~glA~gDvV~~~~~-----~g~~~~~~~v~~---sG-nsTiRv 57 (117)
T PF14085_consen 24 YGLALGDVVRAEPD-----DGELWFQKVVES---SG-NSTIRV 57 (117)
T ss_pred CCCCCCCEEEEEeC-----CCeEEEEEEEec---CC-CEEEEE
Confidence 46788999999842 355667776543 34 555554
No 55
>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=21.66 E-value=1e+02 Score=22.99 Aligned_cols=22 Identities=18% Similarity=0.221 Sum_probs=16.0
Q ss_pred CCCCCCEEEEEEEecC-CCcccc
Q 021720 252 DIKPGYIVQLKVVIPE-NKRRVS 273 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E-nKeRiQ 273 (308)
.|++||.|++.+.-.. +++|+.
T Consensus 46 ~~~vG~~v~~kV~~id~~~~~i~ 68 (73)
T cd05703 46 KFPIGQALKAKVVGVDKEHKLLR 68 (73)
T ss_pred hCCCCCEEEEEEEEEeCCCCEEE
Confidence 4999999999965443 566654
No 56
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=21.46 E-value=2.4e+02 Score=28.10 Aligned_cols=59 Identities=17% Similarity=0.214 Sum_probs=40.8
Q ss_pred hcCCCCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCC---------CcceEEEEeccCCeeeEEEe
Q 021720 245 KSQREIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAG---------ISTTFRLRRLVAGVGVESLF 306 (308)
Q Consensus 245 r~KrdIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrG---------LnSTFTLRKIs~GVGVERiF 306 (308)
+++.++..+++|+-++|++-.-... ..|+|+|-++-..- .+.|..-=|+.+.+.|...+
T Consensus 251 FkETqL~~~r~Gq~a~I~~da~~~~---~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~l 318 (352)
T COG1566 251 FKETQLARVRPGQPAEITLDAYPGN---GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIEL 318 (352)
T ss_pred eeeeecCcccCCCeEEEEEEcCCCc---eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEe
Confidence 3456899999999999998766533 89999999987422 22333345666666665543
No 57
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=21.37 E-value=1.3e+02 Score=26.46 Aligned_cols=30 Identities=17% Similarity=0.032 Sum_probs=21.9
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEE
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVI 280 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVI 280 (308)
-...|||+|.+..++.+.+.+.-.+++.+-
T Consensus 137 kPV~pGD~L~~ea~v~~~~~~~~~v~~~~~ 166 (185)
T PRK04424 137 RPVKLGERVVAKAEVVRKKGNKYIVEVKSY 166 (185)
T ss_pred cCCCCCCEEEEEEEEEEccCCEEEEEEEEE
Confidence 357899999999999986655545555543
No 58
>cd03441 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.
Probab=21.15 E-value=2.6e+02 Score=21.20 Aligned_cols=17 Identities=18% Similarity=0.354 Sum_probs=15.0
Q ss_pred CCCCCCCEEEEEEEecC
Q 021720 251 PDIKPGYIVQLKVVIPE 267 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~E 267 (308)
-.+.+||+|.+..+|.+
T Consensus 79 ~Pv~~Gd~l~~~~~v~~ 95 (127)
T cd03441 79 APVFPGDTLRVEVEVLG 95 (127)
T ss_pred CCcCCCCEEEEEEEEEE
Confidence 35799999999999987
No 59
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=21.08 E-value=1.7e+02 Score=20.83 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=26.1
Q ss_pred CCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCCe
Q 021720 250 IPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAGV 300 (308)
Q Consensus 250 IPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GV 300 (308)
.|.|..||+|-|.-... ..-.|=+++.+..| ....+|++....
T Consensus 11 ~P~i~~gd~v~i~~~~~------~~~~G~iv~~~~~~--~~~~ikrl~~~~ 53 (84)
T cd06462 11 EPTIPDGDLVLVDKSSY------EPKRGDIVVFRLPG--GELTVKRVIGLP 53 (84)
T ss_pred cCcccCCCEEEEEecCC------CCcCCEEEEEEcCC--CcEEEEEEEEEC
Confidence 58899999998873211 23334333444334 568888876554
No 60
>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=21.02 E-value=1.2e+02 Score=24.96 Aligned_cols=17 Identities=18% Similarity=0.446 Sum_probs=14.5
Q ss_pred CCCCCCEEEEEEEecCC
Q 021720 252 DIKPGYIVQLKVVIPEN 268 (308)
Q Consensus 252 eFkpGDTVrV~~kI~En 268 (308)
..++||+|.+..+|.+.
T Consensus 88 PV~~GDtl~~~~~V~~~ 104 (142)
T cd03452 88 PVYPGDTIQVRLTCKRK 104 (142)
T ss_pred CCCCCCEEEEEEEEEEE
Confidence 46899999999999873
No 61
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.01 E-value=2.9e+02 Score=25.23 Aligned_cols=47 Identities=15% Similarity=0.101 Sum_probs=33.6
Q ss_pred CCCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEeccCCe
Q 021720 249 EIPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLVAGV 300 (308)
Q Consensus 249 dIPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs~GV 300 (308)
..|-++-||.|.|.+...- =+ .+--..|..+.+++..++|||...|-
T Consensus 173 ~~~~V~~G~~V~i~~~~g~--~~---i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGDG--FS---VKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred CccEeCCCCEEEEEEecCC--EE---EEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 3567999999999876322 11 22334588899999999999876553
No 62
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=20.99 E-value=5.2e+02 Score=21.88 Aligned_cols=28 Identities=18% Similarity=0.209 Sum_probs=22.4
Q ss_pred CCCCCCCEEEEEEEecCCCcccceEEEEEEEEec
Q 021720 251 PDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRN 284 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRN 284 (308)
..|.+||.|+|. ..=.+-|+|+|+...+
T Consensus 118 ~~~~~G~~V~I~------~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVN------DGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEe------ecCCCCcEEEEEEEcC
Confidence 558999999996 2457788999998764
No 63
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=20.74 E-value=2e+02 Score=24.65 Aligned_cols=34 Identities=9% Similarity=0.166 Sum_probs=26.5
Q ss_pred CCCCCCCEEEEEEEecC--C-CcccceEEEEEEEEec
Q 021720 251 PDIKPGYIVQLKVVIPE--N-KRRVSTLKGIVIARRN 284 (308)
Q Consensus 251 PeFkpGDTVrV~~kI~E--n-KeRiQ~FeGVVIARRN 284 (308)
+.-.+||+|.|.++-.. . -+|-|++.+||+..+.
T Consensus 31 ~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T TIGR01067 31 RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCccccccEEEEEEEEeec
Confidence 56889999999987533 2 3567999999998763
No 64
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=20.65 E-value=1.1e+02 Score=22.02 Aligned_cols=16 Identities=25% Similarity=0.206 Sum_probs=12.5
Q ss_pred CCCCCCEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPE 267 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E 267 (308)
.|++||+|+|.+.-.+
T Consensus 49 ~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 49 LVKVGRKEVVKVIRVD 64 (76)
T ss_pred eeCCCCEEEEEEEEEE
Confidence 3899999999865443
No 65
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: 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 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.58 E-value=1e+02 Score=23.24 Aligned_cols=22 Identities=23% Similarity=0.279 Sum_probs=16.5
Q ss_pred CCCCCCEEEEEEEecC-CCcccc
Q 021720 252 DIKPGYIVQLKVVIPE-NKRRVS 273 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E-nKeRiQ 273 (308)
.|++||.|++.+.-.+ ++.|+.
T Consensus 50 ~~~~G~~v~~kVl~id~~~~~i~ 72 (74)
T cd05705 50 YLPEGKLLTAKVLSVNSEKNLVE 72 (74)
T ss_pred ccCCCCEEEEEEEEEECCCCEEe
Confidence 5899999999987654 555553
No 66
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=20.49 E-value=1.1e+02 Score=20.88 Aligned_cols=21 Identities=29% Similarity=0.502 Sum_probs=14.7
Q ss_pred CCCCCCEEEEEEEecC-CCccc
Q 021720 252 DIKPGYIVQLKVVIPE-NKRRV 272 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E-nKeRi 272 (308)
.|++||.|+|.+.-.. .+.|+
T Consensus 44 ~~~~Gd~v~v~i~~vd~~~~~i 65 (68)
T cd05685 44 VVSVGDIVEVKVISIDEERGRI 65 (68)
T ss_pred hcCCCCEEEEEEEEEECCCCEE
Confidence 3799999999876544 34443
No 67
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=20.44 E-value=61 Score=22.87 Aligned_cols=40 Identities=25% Similarity=0.359 Sum_probs=21.8
Q ss_pred CCCCCCCCEEEEEEEecCCCcccceEEEEEEEEecCCCcceEEEEecc
Q 021720 250 IPDIKPGYIVQLKVVIPENKRRVSTLKGIVIARRNAGISTTFRLRRLV 297 (308)
Q Consensus 250 IPeFkpGDTVrV~~kI~EnKeRiQ~FeGVVIARRNrGLnSTFTLRKIs 297 (308)
-|.|+.||+|-|.-.. ..+.-. +|+.+...+ . ..+++++.
T Consensus 8 ~P~i~~Gd~v~v~~~~-----~~~~gd-ivv~~~~~~-~-~~~iKrv~ 47 (70)
T PF00717_consen 8 EPTIKDGDIVLVDPSS-----EPKDGD-IVVVKIDGD-E-ELYIKRVV 47 (70)
T ss_dssp GGTSSTTEEEEEEETS--------TTS-EEEEEETTE-E-SEEEEEEE
T ss_pred ccCeeCCCEEEEEEcC-----CCccCe-EEEEEECCc-e-eeEEEEEE
Confidence 4899999999887322 222222 333333322 1 47788775
No 68
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: 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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.35 E-value=1.2e+02 Score=21.84 Aligned_cols=16 Identities=25% Similarity=0.229 Sum_probs=12.8
Q ss_pred CCCCCCEEEEEEEecC
Q 021720 252 DIKPGYIVQLKVVIPE 267 (308)
Q Consensus 252 eFkpGDTVrV~~kI~E 267 (308)
.|++||+|++.+.-..
T Consensus 47 ~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 47 KFKKNDIVRACVLSVD 62 (73)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3899999999876544
Done!