Query psy7634
Match_columns 206
No_of_seqs 281 out of 1360
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 23:22:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7634hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4600|consensus 100.0 2.4E-41 5.1E-46 275.2 10.6 129 3-156 5-134 (144)
2 COG0211 RpmA Ribosomal protein 100.0 2.9E-41 6.2E-46 255.3 9.2 86 25-137 1-86 (87)
3 CHL00121 rpl27 ribosomal prote 100.0 9E-40 2E-44 247.8 9.4 85 25-136 1-85 (86)
4 PF01016 Ribosomal_L27: Riboso 100.0 1.4E-39 3E-44 244.7 8.3 81 26-133 1-81 (81)
5 PRK05435 rpmA 50S ribosomal pr 100.0 4.5E-39 9.7E-44 242.3 9.7 72 25-102 1-72 (82)
6 TIGR00062 L27 ribosomal protei 100.0 7.5E-39 1.6E-43 241.6 8.9 72 25-102 1-72 (83)
7 COG0211 RpmA Ribosomal protein 99.9 1.3E-23 2.9E-28 159.3 4.5 50 151-206 1-50 (87)
8 PRK05435 rpmA 50S ribosomal pr 99.9 5E-23 1.1E-27 155.4 4.5 50 151-206 1-50 (82)
9 CHL00121 rpl27 ribosomal prote 99.9 5.3E-23 1.1E-27 156.4 4.4 50 151-206 1-50 (86)
10 TIGR00062 L27 ribosomal protei 99.9 5.9E-23 1.3E-27 155.3 4.3 50 151-206 1-50 (83)
11 KOG4600|consensus 99.9 6.1E-23 1.3E-27 167.6 3.7 56 145-206 22-77 (144)
12 PF01016 Ribosomal_L27: Riboso 99.9 1.3E-22 2.9E-27 152.9 2.9 49 152-206 1-49 (81)
13 PF14382 ECR1_N: Exosome compl 95.9 0.015 3.3E-07 38.4 4.0 38 58-100 1-38 (39)
14 COG1096 Predicted RNA-binding 94.1 0.13 2.9E-06 44.6 6.0 45 53-102 2-46 (188)
15 PRK09521 exosome complex RNA-b 92.9 0.2 4.4E-06 42.0 5.0 43 55-102 4-46 (189)
16 PRK04163 exosome complex RNA-b 81.1 2.7 5.8E-05 36.8 4.6 44 52-101 4-47 (235)
17 PF01551 Peptidase_M23: Peptid 78.5 2.6 5.6E-05 30.8 3.2 29 74-102 1-29 (96)
18 PRK14844 bifunctional DNA-dire 75.1 5.9 0.00013 46.0 6.0 48 51-99 2526-2584(2836)
19 PF03961 DUF342: Protein of un 72.1 8.1 0.00018 36.5 5.4 48 57-104 107-176 (451)
20 PRK09603 bifunctional DNA-dire 72.0 9.9 0.00021 44.4 6.9 51 51-102 2616-2679(2890)
21 PF13533 Biotin_lipoyl_2: Biot 72.0 3.4 7.4E-05 27.8 2.2 18 51-68 16-33 (50)
22 cd00210 PTS_IIA_glc PTS_IIA, P 66.9 23 0.00051 28.6 6.3 18 176-193 83-100 (124)
23 PF13533 Biotin_lipoyl_2: Biot 62.3 6.9 0.00015 26.3 2.1 19 176-194 15-33 (50)
24 TIGR00830 PTBA PTS system, glu 61.9 35 0.00075 27.5 6.5 18 176-193 83-100 (121)
25 PRK09439 PTS system glucose-sp 60.8 37 0.0008 28.9 6.7 18 176-193 105-122 (169)
26 COG1097 RRP4 RNA-binding prote 59.2 23 0.00049 32.1 5.4 46 52-102 4-49 (239)
27 cd06850 biotinyl_domain The bi 57.0 17 0.00037 23.9 3.4 39 51-101 13-51 (67)
28 PRK05889 putative acetyl-CoA c 51.9 21 0.00045 25.2 3.3 39 50-100 15-53 (71)
29 PF00364 Biotin_lipoyl: Biotin 49.0 14 0.00031 26.3 2.1 38 51-100 20-57 (74)
30 TIGR02994 ectoine_eutE ectoine 45.8 26 0.00057 32.2 3.8 42 52-102 269-311 (325)
31 PRK14844 bifunctional DNA-dire 42.5 1.3E+02 0.0027 36.0 8.9 24 170-193 2517-2542(2836)
32 COG1315 Uncharacterized conser 41.7 34 0.00075 34.2 4.1 32 73-105 219-251 (543)
33 cd06663 Biotinyl_lipoyl_domain 41.6 42 0.00091 23.1 3.5 39 51-101 19-57 (73)
34 COG4770 Acetyl/propionyl-CoA c 40.4 41 0.00089 34.3 4.4 59 25-98 566-624 (645)
35 PRK14875 acetoin dehydrogenase 40.3 34 0.00073 29.6 3.4 38 49-98 20-57 (371)
36 PF13375 RnfC_N: RnfC Barrel s 38.9 62 0.0013 25.1 4.4 43 52-107 45-87 (101)
37 PF00358 PTS_EIIA_1: phosphoen 38.6 69 0.0015 26.1 4.8 18 176-193 87-104 (132)
38 cd06253 M14_ASTE_ASPA_like_3 A 38.0 43 0.00092 30.2 3.8 41 53-102 244-284 (298)
39 TIGR01995 PTS-II-ABC-beta PTS 34.4 1.3E+02 0.0027 30.2 6.8 18 176-193 547-564 (610)
40 PRK06549 acetyl-CoA carboxylas 32.5 61 0.0013 26.4 3.6 39 49-99 73-111 (130)
41 PRK10255 PTS system N-acetyl g 32.0 1.6E+02 0.0034 30.2 7.0 18 176-193 583-600 (648)
42 PRK09824 PTS system beta-gluco 28.6 1.8E+02 0.0039 29.5 6.8 18 176-193 563-580 (627)
43 PF07596 SBP_bac_10: Protein o 28.4 38 0.00082 28.5 1.8 18 89-106 247-264 (265)
44 PF13540 RCC1_2: Regulator of 27.7 89 0.0019 18.8 2.9 19 81-99 4-22 (30)
45 PRK00566 DNA-directed RNA poly 27.3 89 0.0019 34.1 4.6 18 85-102 926-943 (1156)
46 cd06251 M14_ASTE_ASPA_like_1 A 25.1 97 0.0021 27.6 3.8 41 52-102 233-273 (287)
47 cd06254 M14_ASTE_ASPA_like_4 A 23.4 96 0.0021 27.5 3.5 42 51-102 236-277 (288)
48 PRK05641 putative acetyl-CoA c 23.3 1.2E+02 0.0026 25.2 3.9 44 42-100 92-135 (153)
49 TIGR02386 rpoC_TIGR DNA-direct 22.3 1.7E+02 0.0036 32.0 5.5 52 49-100 858-938 (1140)
50 PRK08225 acetyl-CoA carboxylas 21.8 1.4E+02 0.003 20.6 3.4 38 50-99 14-51 (70)
51 PF02749 QRPTase_N: Quinolinat 21.3 77 0.0017 23.4 2.1 21 177-197 49-69 (88)
52 TIGR02971 heterocyst_DevB ABC 21.2 67 0.0015 28.3 2.0 20 49-68 28-47 (327)
53 cd06252 M14_ASTE_ASPA_like_2 A 20.7 1.4E+02 0.0031 26.9 4.1 43 52-102 258-300 (316)
No 1
>KOG4600|consensus
Probab=100.00 E-value=2.4e-41 Score=275.22 Aligned_cols=129 Identities=31% Similarity=0.365 Sum_probs=112.4
Q ss_pred chhhhhhhhcccCCcc-cceeeeeeecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCe
Q psy7634 3 LSLVNSFKNLLTTSQP-VCMSVRNAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNV 81 (206)
Q Consensus 3 ~sl~~~~~~l~~~~~~-~~~~vr~A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NV 81 (206)
.+|+++-..+...++. ...++|+|+||++|||+| +|||+|+| ||||+++||+|.||+||||| |||+||||+||
T Consensus 5 l~l~tas~~~~~~ss~~~~l~vR~AtKk~aGStKN-~~dS~grr---lGvKk~egq~V~~G~IIvrQ--RgtkfHPG~nV 78 (144)
T KOG4600|consen 5 LRLSTASSSLDGSSSGLSFLAVRWATKKGAGSTKN-GRDSAGRR---LGVKKYEGQSVIPGNIIVRQ--RGTKFHPGDNV 78 (144)
T ss_pred eecchhhhhhcCCCCcceeeeeeeecccccCcccc-CCCCCccc---ccceecCCeeeecccEEEEe--cccccCCCccc
Confidence 4566666666655555 488999999999999999 99999999 99999999999999999999 99999999999
Q ss_pred eecCCceEEEeeceEEEEEEeeccCCccchhhhhhccCCCCCCCCeeEEEeeecCccccccccchhhhhhhhccc
Q psy7634 82 GFGARGTLFAMEKGKVKITVEKCNLNWKHTWVIANYSGQEGLPIYKKHIHVLPEEQHSRFRLVDEPRVRNAAKKT 156 (206)
Q Consensus 82 g~GkD~TLfAl~~G~V~f~~~~~~p~~~~~w~~~~~~grkg~~~~Kk~VnViP~~~~~~FkLvDe~~vR~a~kk~ 156 (206)
|||+|||||||++|+|+|++++++| .|++|+|.|..........+++.||--.|.-
T Consensus 79 GiGKDhtifaL~eG~Vrf~k~~~~~-------------------~Rk~i~V~~~~~~~l~~~~~k~~vr~~~k~~ 134 (144)
T KOG4600|consen 79 GIGKDHTIFALEEGRVRFEKSKITP-------------------PRKWIGVDPRGGLPLPPPYYKATVRRVTKLP 134 (144)
T ss_pred ccCCcceEEEeeccEEEEEEccCCC-------------------CcceEEEeecCCccCCCccchhhhhhhcccc
Confidence 9999999999999999999997644 3799999999888777778888887655443
No 2
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-41 Score=255.33 Aligned_cols=86 Identities=41% Similarity=0.584 Sum_probs=82.1
Q ss_pred eeecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEeec
Q psy7634 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVEKC 104 (206)
Q Consensus 25 ~A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~~~ 104 (206)
|||||++|||+| ||||++|| ||+|++|||+|.+|+||||| |||+||||+|||||+||||||++||+|+|+..
T Consensus 1 mA~KKg~GSt~N-gRDS~~kr---LGvK~~~Gq~v~aG~IivRQ--RGTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~k-- 72 (87)
T COG0211 1 MAHKKGGGSTRN-GRDSESKR---LGVKKFGGQFVKAGSIIVRQ--RGTKFHPGVNVGRGKDHTLFALVDGVVKFETK-- 72 (87)
T ss_pred Cccccccccccc-Cccccccc---cceeeeCCeEEecccEEEEe--ccccccCCcccccCCCceEEEeeccEEEEEEc--
Confidence 899999999999 99999999 99999999999999999999 99999999999999999999999999999986
Q ss_pred cCCccchhhhhhccCCCCCCCCeeEEEeeecCc
Q psy7634 105 NLNWKHTWVIANYSGQEGLPIYKKHIHVLPEEQ 137 (206)
Q Consensus 105 ~p~~~~~w~~~~~~grkg~~~~Kk~VnViP~~~ 137 (206)
+ ..|+||+|+|+++
T Consensus 73 -----------------~--~~rk~vsV~~~~~ 86 (87)
T COG0211 73 -----------------G--KNRKYVSVVPEAE 86 (87)
T ss_pred -----------------c--CCccEEEEEeecc
Confidence 1 2689999999865
No 3
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=100.00 E-value=9e-40 Score=247.80 Aligned_cols=85 Identities=35% Similarity=0.434 Sum_probs=80.6
Q ss_pred eeecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEeec
Q psy7634 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVEKC 104 (206)
Q Consensus 25 ~A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~~~ 104 (206)
|||||++|||+| ||||+||| ||+|++|||+|.||+||||| |||+||||+||+||+||||||+++|+|+|++.
T Consensus 1 mA~KK~~GStkN-grdS~~Kr---LGvK~~~gq~V~~G~IivRQ--RGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~-- 72 (86)
T CHL00121 1 MAHKKGAGSTKN-GRDSNAKR---LGVKRFGGEKVSAGNILIRQ--RGTKFKPGLNVGCGKDFTLYALIDGFVKFKKK-- 72 (86)
T ss_pred CCcccccCcCCC-CCCCCccc---ceeEEcCCEEEcCCcEEEEc--CCCeECCCCcccccCCceEEEccceEEEEEEe--
Confidence 899999999999 99999999 99999999999999999999 99999999999999999999999999999976
Q ss_pred cCCccchhhhhhccCCCCCCCCeeEEEeeecC
Q psy7634 105 NLNWKHTWVIANYSGQEGLPIYKKHIHVLPEE 136 (206)
Q Consensus 105 ~p~~~~~w~~~~~~grkg~~~~Kk~VnViP~~ 136 (206)
...+++|+|+|..
T Consensus 73 -------------------~~~~~~vsv~~~~ 85 (86)
T CHL00121 73 -------------------NKKQKSINVINIV 85 (86)
T ss_pred -------------------CCCCEEEEEeecc
Confidence 2367899999964
No 4
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 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 [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....
Probab=100.00 E-value=1.4e-39 Score=244.71 Aligned_cols=81 Identities=40% Similarity=0.568 Sum_probs=72.5
Q ss_pred eecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEeecc
Q psy7634 26 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVEKCN 105 (206)
Q Consensus 26 A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~~~~ 105 (206)
||||++|||+| +|||+||| ||||++|||+|.||+||||| |||+||||+||+||+||||||++||+|+|+++
T Consensus 1 A~KK~~GSt~N-grdS~~kr---lGvK~~~G~~V~~G~IivRQ--Rgtk~hPG~NVg~GrD~TLfAl~~G~V~f~~~--- 71 (81)
T PF01016_consen 1 AHKKGGGSTKN-GRDSNPKR---LGVKKFGGQFVKAGNIIVRQ--RGTKFHPGENVGMGRDHTLFALVDGRVKFTKE--- 71 (81)
T ss_dssp --SSSSSSSS---S-STTTT---SEESSSTTCEESSTSEEEEB--SSSSSEEBTTEEEETTSEEEESSSCEEEEEEE---
T ss_pred CCccccccccC-CCCCCCcc---cEEEEeCCEEEcCCCEEEEe--CCCcCcCCCCEEECCCCcEEEecCEEEEEEEe---
Confidence 89999999999 99999999 99999999999999999999 99999999999999999999999999999998
Q ss_pred CCccchhhhhhccCCCCCCCCeeEEEee
Q psy7634 106 LNWKHTWVIANYSGQEGLPIYKKHIHVL 133 (206)
Q Consensus 106 p~~~~~w~~~~~~grkg~~~~Kk~VnVi 133 (206)
...|+||+|+
T Consensus 72 ------------------~~~rk~v~V~ 81 (81)
T PF01016_consen 72 ------------------KRNRKYVSVV 81 (81)
T ss_dssp ------------------TTTEEEEEE-
T ss_pred ------------------CCCCEEEEeC
Confidence 2368999996
No 5
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=100.00 E-value=4.5e-39 Score=242.27 Aligned_cols=72 Identities=39% Similarity=0.552 Sum_probs=71.0
Q ss_pred eeecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 25 ~A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
|||||++|||+| +|||+||| ||||+++||+|.||+||||| |||+||||+||+||+||||||+++|+|+|++.
T Consensus 1 mA~KK~~GStkN-grdS~~kr---LGvK~~~g~~V~~G~IivRQ--RGtk~~PG~nVg~GrD~TlfA~~~G~V~f~~~ 72 (82)
T PRK05435 1 MAHKKGGGSTRN-GRDSESKR---LGVKRFGGQFVKAGNIIVRQ--RGTKFHPGVNVGRGKDHTLFALVDGVVKFERK 72 (82)
T ss_pred CCcccccCcCCC-CCCCCccc---ceeEecCCEEEcCCcEEEEe--CCCeECCCCCEeecCCceEEEecceEEEEEEc
Confidence 899999999999 99999999 99999999999999999999 99999999999999999999999999999975
No 6
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=100.00 E-value=7.5e-39 Score=241.58 Aligned_cols=72 Identities=36% Similarity=0.523 Sum_probs=71.1
Q ss_pred eeecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 25 ~A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
|||||++|||+| +|||+||| ||+|+++||+|.||+||||| |||+||||+||+||+||||||+++|+|+|++.
T Consensus 1 ~A~Kk~~GSt~N-grdS~~kr---LGvK~~~gq~V~~G~IivRQ--RGtk~hPG~nVg~GrD~TlfAl~~G~V~f~~~ 72 (83)
T TIGR00062 1 MATKKGVGSTKN-GRDSEAKR---LGVKRAGGQFVRAGSIIVRQ--RGTKFHPGNNVGMGKDHTLFALSDGVVKFEKK 72 (83)
T ss_pred CCcccccCcCCC-CCCCCCcc---ceeEecCCEEEcCCcEEEEc--CCceECCCCcccccCCCeEEEecceEEEEEEc
Confidence 899999999999 99999999 99999999999999999999 99999999999999999999999999999986
No 7
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.3e-23 Score=159.33 Aligned_cols=50 Identities=42% Similarity=0.634 Sum_probs=49.3
Q ss_pred hhhcccCccccCCCCCCCCCcCCCCCeeeeCCeEEeeCcEEEEeecCcccccCCCC
Q psy7634 151 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLN 206 (206)
Q Consensus 151 ~a~kk~~gst~N~~~r~s~~~rl~~G~k~~~g~~v~~G~Ii~rQrgt~~~~hpG~n 206 (206)
|||||++|||+|+ |||.++|| |+|++|||+|.||+||||||||+ ||||.|
T Consensus 1 mA~KKg~GSt~Ng--RDS~~krL--GvK~~~Gq~v~aG~IivRQRGTk--~hpG~N 50 (87)
T COG0211 1 MAHKKGGGSTRNG--RDSESKRL--GVKKFGGQFVKAGSIIVRQRGTK--FHPGVN 50 (87)
T ss_pred CcccccccccccC--cccccccc--ceeeeCCeEEecccEEEEecccc--ccCCcc
Confidence 7999999999999 89999999 99999999999999999999999 999998
No 8
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=99.87 E-value=5e-23 Score=155.41 Aligned_cols=50 Identities=38% Similarity=0.622 Sum_probs=49.2
Q ss_pred hhhcccCccccCCCCCCCCCcCCCCCeeeeCCeEEeeCcEEEEeecCcccccCCCC
Q psy7634 151 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLN 206 (206)
Q Consensus 151 ~a~kk~~gst~N~~~r~s~~~rl~~G~k~~~g~~v~~G~Ii~rQrgt~~~~hpG~n 206 (206)
|||||++|||+|+ |||+++|| |||+++||+|.||+||||||||+ ||||+|
T Consensus 1 mA~KK~~GStkNg--rdS~~krL--GvK~~~g~~V~~G~IivRQRGtk--~~PG~n 50 (82)
T PRK05435 1 MAHKKGGGSTRNG--RDSESKRL--GVKRFGGQFVKAGNIIVRQRGTK--FHPGVN 50 (82)
T ss_pred CCcccccCcCCCC--CCCCcccc--eeEecCCEEEcCCcEEEEeCCCe--ECCCCC
Confidence 7999999999999 89999999 99999999999999999999999 999998
No 9
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=99.87 E-value=5.3e-23 Score=156.40 Aligned_cols=50 Identities=38% Similarity=0.557 Sum_probs=49.2
Q ss_pred hhhcccCccccCCCCCCCCCcCCCCCeeeeCCeEEeeCcEEEEeecCcccccCCCC
Q psy7634 151 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLN 206 (206)
Q Consensus 151 ~a~kk~~gst~N~~~r~s~~~rl~~G~k~~~g~~v~~G~Ii~rQrgt~~~~hpG~n 206 (206)
|||||++|||+|+ |||+++|| |||++|||+|.||+||||||||+ ||||+|
T Consensus 1 mA~KK~~GStkNg--rdS~~KrL--GvK~~~gq~V~~G~IivRQRGtk--~hPG~N 50 (86)
T CHL00121 1 MAHKKGAGSTKNG--RDSNAKRL--GVKRFGGEKVSAGNILIRQRGTK--FKPGLN 50 (86)
T ss_pred CCcccccCcCCCC--CCCCcccc--eeEEcCCEEEcCCcEEEEcCCCe--ECCCCc
Confidence 7999999999999 89999999 99999999999999999999999 999998
No 10
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=99.87 E-value=5.9e-23 Score=155.34 Aligned_cols=50 Identities=36% Similarity=0.540 Sum_probs=49.2
Q ss_pred hhhcccCccccCCCCCCCCCcCCCCCeeeeCCeEEeeCcEEEEeecCcccccCCCC
Q psy7634 151 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLN 206 (206)
Q Consensus 151 ~a~kk~~gst~N~~~r~s~~~rl~~G~k~~~g~~v~~G~Ii~rQrgt~~~~hpG~n 206 (206)
|||||++|||+|+ |||+++|| |||+++||+|.||+||||||||+ ||||+|
T Consensus 1 ~A~Kk~~GSt~Ng--rdS~~krL--GvK~~~gq~V~~G~IivRQRGtk--~hPG~n 50 (83)
T TIGR00062 1 MATKKGVGSTKNG--RDSEAKRL--GVKRAGGQFVRAGSIIVRQRGTK--FHPGNN 50 (83)
T ss_pred CCcccccCcCCCC--CCCCCccc--eeEecCCEEEcCCcEEEEcCCce--ECCCCc
Confidence 7999999999999 89999999 99999999999999999999999 999998
No 11
>KOG4600|consensus
Probab=99.87 E-value=6.1e-23 Score=167.64 Aligned_cols=56 Identities=39% Similarity=0.530 Sum_probs=53.9
Q ss_pred chhhhhhhhcccCccccCCCCCCCCCcCCCCCeeeeCCeEEeeCcEEEEeecCcccccCCCC
Q psy7634 145 DEPRVRNAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLN 206 (206)
Q Consensus 145 De~~vR~a~kk~~gst~N~~~r~s~~~rl~~G~k~~~g~~v~~G~Ii~rQrgt~~~~hpG~n 206 (206)
..++||+|+||++|||+|+ +||+|+|| |+|+++||+|.||+||+|||||| ||||.|
T Consensus 22 ~~l~vR~AtKk~aGStKN~--~dS~grrl--GvKk~egq~V~~G~IIvrQRgtk--fHPG~n 77 (144)
T KOG4600|consen 22 SFLAVRWATKKGAGSTKNG--RDSAGRRL--GVKKYEGQSVIPGNIIVRQRGTK--FHPGDN 77 (144)
T ss_pred eeeeeeeecccccCccccC--CCCCcccc--cceecCCeeeecccEEEEecccc--cCCCcc
Confidence 4568999999999999999 89999999 99999999999999999999999 999987
No 12
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 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 [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....
Probab=99.86 E-value=1.3e-22 Score=152.88 Aligned_cols=49 Identities=39% Similarity=0.599 Sum_probs=43.6
Q ss_pred hhcccCccccCCCCCCCCCcCCCCCeeeeCCeEEeeCcEEEEeecCcccccCCCC
Q psy7634 152 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLN 206 (206)
Q Consensus 152 a~kk~~gst~N~~~r~s~~~rl~~G~k~~~g~~v~~G~Ii~rQrgt~~~~hpG~n 206 (206)
||||++|||+|+ |||+++|| |||++|||+|.||+||||||||+ ||||+|
T Consensus 1 A~KK~~GSt~Ng--rdS~~krl--GvK~~~G~~V~~G~IivRQRgtk--~hPG~N 49 (81)
T PF01016_consen 1 AHKKGGGSTKNG--RDSNPKRL--GVKKFGGQFVKAGNIIVRQRGTK--FHPGEN 49 (81)
T ss_dssp --SSSSSSSS----S-STTTTS--EESSSTTCEESSTSEEEEBSSSS--SEEBTT
T ss_pred CCccccccccCC--CCCCCccc--EEEEeCCEEEcCCCEEEEeCCCc--CcCCCC
Confidence 899999999998 89999999 99999999999999999999999 999998
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=95.87 E-value=0.015 Score=38.43 Aligned_cols=38 Identities=34% Similarity=0.478 Sum_probs=32.4
Q ss_pred EEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEE
Q psy7634 58 VVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKIT 100 (206)
Q Consensus 58 ~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~ 100 (206)
.|.||+.|... ..|.||.++.+ +|..|||.+-|.|+..
T Consensus 1 iV~PG~~l~~~----~e~~~G~GTY~-~~g~I~asv~G~v~~~ 38 (39)
T PF14382_consen 1 IVVPGDRLGSS----EEYMPGHGTYV-RDGNIYASVAGTVKID 38 (39)
T ss_dssp EE-TT-EEEET----TTSEESTTEEE-ETTEEEESSSEEEEEE
T ss_pred CCCCCCEeecC----CCEecCCCEEE-eCCEEEEEeeEEEEEc
Confidence 48899999987 58999999999 8999999999999864
No 14
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.11 E-value=0.13 Score=44.64 Aligned_cols=45 Identities=22% Similarity=0.316 Sum_probs=40.3
Q ss_pred eeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 53 KQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 53 ~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
..+|.+|.||+.|..+ -.|.||+++.-- |+.|+|...|.+.+...
T Consensus 2 ~~~g~~v~PGd~~a~~----EE~~~G~gt~~~-~g~i~Aa~~G~~~~d~~ 46 (188)
T COG1096 2 VKDGTFVLPGDVLAVI----EEFLPGEGTYEE-GGEIRAAATGVVRRDDK 46 (188)
T ss_pred cccCcEEcCcceeeee----eeeecCCCeEeE-CCEEEEeecccEEEccc
Confidence 3578999999999999 799999999876 99999999999998754
No 15
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=92.91 E-value=0.2 Score=42.04 Aligned_cols=43 Identities=30% Similarity=0.397 Sum_probs=36.9
Q ss_pred CCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 55 EGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 55 ~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
+++.|.||+.|.-. ..|.||.|+.. .|.+|||.+-|.+.+..+
T Consensus 4 ~~~~V~PGe~l~~~----~e~~~G~Gty~-~~~~i~as~~G~~~id~~ 46 (189)
T PRK09521 4 QGDLVLPGDYLAVI----EEYLPGEGTYE-DNGEVYASVVGKVFIDDI 46 (189)
T ss_pred cCCEECCCCccccc----cceEcCCCEEe-eCCEEEEEeeEEEEEcCC
Confidence 67899999999765 46999999987 578899999999998643
No 16
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=81.09 E-value=2.7 Score=36.76 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=37.5
Q ss_pred EeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEE
Q psy7634 52 RKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITV 101 (206)
Q Consensus 52 K~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~ 101 (206)
-..++..|.||+.|.-+ .|.||.|+.. .|..|+|.+-|.+.+..
T Consensus 4 ~~~~~~~V~PGd~l~~~-----~~~~G~Gty~-~~g~i~As~~G~~~~~~ 47 (235)
T PRK04163 4 FVEDRKIVVPGDLLAEG-----EFKAGRGTYK-ENGKIYSTVVGLVDIKD 47 (235)
T ss_pred eeeCCcEECCCCCcCcC-----CeecCCceEE-eCCEEEEEEeEEEEEEC
Confidence 35678899999999644 6999999987 78999999999999874
No 17
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=78.48 E-value=2.6 Score=30.82 Aligned_cols=29 Identities=24% Similarity=0.419 Sum_probs=23.3
Q ss_pred eeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 74 DYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 74 k~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
+||.|.-+.......++|+++|+|.|..+
T Consensus 1 r~h~Gid~~~~~g~~V~A~~~G~V~~~~~ 29 (96)
T PF01551_consen 1 RFHNGIDFAAPEGTPVYAPADGKVVFVGE 29 (96)
T ss_dssp -EE-SEEEEETTT-EEEESSSEEEEEEEE
T ss_pred CCeeeEEeCCCCCCEEEeCccEEEEEEEe
Confidence 57888888888888899999999999886
No 18
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=75.08 E-value=5.9 Score=46.02 Aligned_cols=48 Identities=19% Similarity=0.255 Sum_probs=34.2
Q ss_pred eEeeCCeEEeeCcEEEEeecCCc----eeecCCC-------eeecCCceEEEeeceEEEE
Q psy7634 51 FRKQEGEVVEKGSILYISYVQRL----DYHPGLN-------VGFGARGTLFAMEKGKVKI 99 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ~~Rgt----k~hPG~N-------Vg~GkD~TLfAl~~G~V~f 99 (206)
+-+.+||.|++|+||+|=- |-+ .+--|.- ...-+++.+.|.+||+|.|
T Consensus 2526 l~v~~g~~v~~Gdilakip-r~~~~t~DIT~GLpRv~eLFEar~pk~~a~isei~G~V~~ 2584 (2836)
T PRK14844 2526 LNVQDGQKVHAGDVITRTP-RESVKTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAF 2584 (2836)
T ss_pred EeeccCceecccceeeccc-ccccccCccCCCCccchheeeeecCCCceEEecCCcEEEe
Confidence 5678999999999999941 211 1222221 2355689999999999998
No 19
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=72.10 E-value=8.1 Score=36.47 Aligned_cols=48 Identities=21% Similarity=0.269 Sum_probs=37.8
Q ss_pred eEEeeCcEEEEee--------------------cCCceeecCCCeeec-CC-ceEEEeeceEEEEEEeec
Q psy7634 57 EVVEKGSILYISY--------------------VQRLDYHPGLNVGFG-AR-GTLFAMEKGKVKITVEKC 104 (206)
Q Consensus 57 q~V~~G~IivRQ~--------------------~Rgtk~hPG~NVg~G-kD-~TLfAl~~G~V~f~~~~~ 104 (206)
..|.+|+.|++-- -+-..|.+|+||.+- .| .+|+|.++|.+.|....+
T Consensus 107 ~~V~~G~~la~~~p~~~G~~G~~V~G~~I~~~~~~~~~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~~~i 176 (451)
T PF03961_consen 107 PSVKKGDVLAEKIPPTPGEPGRDVFGEPIPAKPGKDIPLKAGKNTEVSEEDGNKLYAAIDGRPVFENGKI 176 (451)
T ss_pred eEECCCCEEEEEccCCCCCCCcccCCCCcCCCCCCccceeCCCCEEEEcCCCCEEEEecCCEEEEECCEE
Confidence 3489999999853 223567889999998 66 589999999999997543
No 20
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=72.04 E-value=9.9 Score=44.41 Aligned_cols=51 Identities=18% Similarity=0.162 Sum_probs=34.8
Q ss_pred eEeeCCeEEeeCcEEEEeecCCc----eeecCCC-------ee--ecCCceEEEeeceEEEEEEe
Q psy7634 51 FRKQEGEVVEKGSILYISYVQRL----DYHPGLN-------VG--FGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ~~Rgt----k~hPG~N-------Vg--~GkD~TLfAl~~G~V~f~~~ 102 (206)
+-+.+|+.|.+|+||+|=- |-+ .+--|.- +. .-+|..+.|.+||+|.|.++
T Consensus 2616 l~v~~g~~v~~gdilak~p-~~~~~t~DITgGLprv~eLfear~~~pk~~a~i~ei~G~v~~~~~ 2679 (2890)
T PRK09603 2616 IAISDGSSVEQAEVLAKIP-KATVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKP 2679 (2890)
T ss_pred EEecCCCEecccceEeecc-ccccccccccCCcccchhheEeecCCCCCceEEeccceEEEeccc
Confidence 5678999999999999931 221 1222210 12 35689999999999999543
No 21
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=72.02 E-value=3.4 Score=27.79 Aligned_cols=18 Identities=33% Similarity=0.584 Sum_probs=15.7
Q ss_pred eEeeCCeEEeeCcEEEEe
Q psy7634 51 FRKQEGEVVEKGSILYIS 68 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ 68 (206)
+.+.+|+.|++|++|++=
T Consensus 16 v~V~~G~~VkkGd~L~~l 33 (50)
T PF13533_consen 16 VYVKEGQQVKKGDVLLVL 33 (50)
T ss_pred EEecCCCEEcCCCEEEEE
Confidence 567799999999999974
No 22
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=66.86 E-value=23 Score=28.57 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=15.2
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=++...|+.|++|+.|++
T Consensus 83 ~~~vk~Gd~V~~G~~l~~ 100 (124)
T cd00210 83 TSHVEEGQRVKQGDKLLE 100 (124)
T ss_pred EEEecCCCEEcCCCEEEE
Confidence 456679999999999986
No 23
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=62.28 E-value=6.9 Score=26.28 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=16.1
Q ss_pred CeeeeCCeEEeeCcEEEEe
Q psy7634 176 GFRKQEGEVVEKGSILYIS 194 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~rQ 194 (206)
-|-..+|++|++|.+|++=
T Consensus 15 ~v~V~~G~~VkkGd~L~~l 33 (50)
T PF13533_consen 15 SVYVKEGQQVKKGDVLLVL 33 (50)
T ss_pred EEEecCCCEEcCCCEEEEE
Confidence 4567799999999999974
No 24
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=61.92 E-value=35 Score=27.51 Aligned_cols=18 Identities=33% Similarity=0.375 Sum_probs=15.4
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=++...||.|++|..|++
T Consensus 83 ~~~v~~Gd~V~~G~~l~~ 100 (121)
T TIGR00830 83 TSHVEEGQRVKKGDPLLE 100 (121)
T ss_pred EEEecCCCEEcCCCEEEE
Confidence 456778999999999986
No 25
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=60.82 E-value=37 Score=28.86 Aligned_cols=18 Identities=22% Similarity=0.211 Sum_probs=15.2
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=+....||.|++|+.|++
T Consensus 105 ~~~Vk~Gd~Vk~G~~L~~ 122 (169)
T PRK09439 105 KRIAEEGQRVKVGDPIIE 122 (169)
T ss_pred EEEecCCCEEeCCCEEEE
Confidence 456779999999999986
No 26
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=59.24 E-value=23 Score=32.05 Aligned_cols=46 Identities=15% Similarity=0.281 Sum_probs=37.2
Q ss_pred EeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 52 RKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 52 K~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
.....+.|.||++|.-+ ..|..|.++.+ .|.-+||.+-|.|.++-.
T Consensus 4 ~~~~~~iV~PGd~vl~~----~~~~~G~Gty~-~~~~iyssv~G~~~~~~~ 49 (239)
T COG1097 4 SVSMRKIVLPGDLVLAE----GSYKLGHGTYF-EGGKIYSSVVGLLDVKGK 49 (239)
T ss_pred eccccceecCCCccCCC----CCEecCCCcEe-cCCEEEEEEEeEEEEeCC
Confidence 34567899999976555 56777877777 899999999999999865
No 27
>cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
Probab=57.03 E-value=17 Score=23.90 Aligned_cols=39 Identities=26% Similarity=0.280 Sum_probs=29.5
Q ss_pred eEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEE
Q psy7634 51 FRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITV 101 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~ 101 (206)
+.+..|+.|.+|+.|+.= ... ..+.+|.|.++|+|....
T Consensus 13 ~~v~~G~~v~~g~~l~~i--~~~----------~~~~~i~ap~~G~v~~~~ 51 (67)
T cd06850 13 VLVKEGDKVEAGQPLAVL--EAM----------KMENEVTAPVAGVVKEIL 51 (67)
T ss_pred EEeCCCCEECCCCEEEEE--Ecc----------cEEEEEeCCCCEEEEEEE
Confidence 566789999999999974 211 125689999999997654
No 28
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=51.93 E-value=21 Score=25.15 Aligned_cols=39 Identities=21% Similarity=0.287 Sum_probs=29.4
Q ss_pred ceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEE
Q psy7634 50 GFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKIT 100 (206)
Q Consensus 50 GiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~ 100 (206)
=+.+..|+.|.+|+.|+-= --.+ .++.|.|.++|+|.-.
T Consensus 15 ~~~v~~Gd~V~~g~~l~~v--e~~K----------~~~~I~a~~~G~V~~i 53 (71)
T PRK05889 15 EVVVNEGDQIGKGDTLVLL--ESMK----------MEIPVLAEVAGTVSKV 53 (71)
T ss_pred EEEeCCCCEECCCCEEEEE--Eecc----------ceeEEeCCCCEEEEEE
Confidence 3677899999999999853 2222 4778999999998644
No 29
>PF00364 Biotin_lipoyl: Biotin-requiring enzyme; InterPro: IPR000089 The biotin / lipoyl attachment domain has a conserved lysine residue that binds biotin or lipoic acid. Biotin plays a catalytic role in some carboxyl transfer reactions and is covalently attached, via an amide bond, to a lysine residue in enzymes requiring this coenzyme []. E2 acyltransferases have an essential cofactor, lipoic acid, which is covalently bound via an amide linkage to a lysine group []. The lipoic acid cofactor is found in a variety of proteins that include, H-protein of the glycine cleavage system (GCS), mammalian and yeast pyruvate dehydrogenases and fast migrating protein (FMP) (gene acoC) from Ralstonia eutropha (Alcaligenes eutrophus).; PDB: 2EJG_D 2D5D_A 2EJF_C 2EVB_A 1IYV_A 1IYU_A 1LAC_A 1LAB_A 1DCZ_A 1DD2_A ....
Probab=49.00 E-value=14 Score=26.33 Aligned_cols=38 Identities=24% Similarity=0.172 Sum_probs=28.5
Q ss_pred eEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEE
Q psy7634 51 FRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKIT 100 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~ 100 (206)
+.+..|+.|.+|+.|+-= --+.-...+.|..+|+|+--
T Consensus 20 ~~v~~G~~V~~G~~l~~i------------et~K~~~~v~a~~~G~i~~i 57 (74)
T PF00364_consen 20 WLVEEGDKVKKGDPLAEI------------ETMKMEMEVEAPVSGIIKEI 57 (74)
T ss_dssp ESSSTTEEESTTSEEEEE------------ESSSEEEEEEBSSSEEEEEE
T ss_pred EEECCCCEEEcCceEEEE------------EcCccceEEECCCCEEEEEE
Confidence 667789999999998874 12334578999999998643
No 30
>TIGR02994 ectoine_eutE ectoine utilization protein EutE. Members of this family, part of the succinylglutamate desuccinylase / aspartoacylase family (pfam04952), belong to ectoine utilization operons, as found in Sinorhizobium meliloti 1021 (where it the operon is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida.
Probab=45.82 E-value=26 Score=32.15 Aligned_cols=42 Identities=17% Similarity=0.094 Sum_probs=31.2
Q ss_pred EeeCCeEEeeCcEEEEeecCCceee-cCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 52 RKQEGEVVEKGSILYISYVQRLDYH-PGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 52 K~~~Gq~V~~G~IivRQ~~Rgtk~h-PG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
.+.-|+.|++|++|... .- +. +|.-+ +++.|++||+|-+...
T Consensus 269 ~v~~G~~V~~G~~lg~I--~d--~~~~G~~~-----~~i~Ap~dGiV~~~~~ 311 (325)
T TIGR02994 269 MIDLGDPVSKGDVIARV--YP--VGRTGVAP-----VEYRAKRDGLLAARHF 311 (325)
T ss_pred ecCCCCEeCCCCEEEEE--EC--CCCCCCce-----EEEEeCCCcEEEEEeC
Confidence 34558999999999999 21 22 34322 7999999999998764
No 31
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=42.55 E-value=1.3e+02 Score=36.01 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=18.9
Q ss_pred CcCCCCC--eeeeCCeEEeeCcEEEE
Q psy7634 170 GFRFPKG--FRKQEGEVVEKGSILYI 193 (206)
Q Consensus 170 ~~rl~~G--~k~~~g~~v~~G~Ii~r 193 (206)
-..||.| +-+.||+.|++|.||+|
T Consensus 2517 ~y~lp~ga~l~v~~g~~v~~Gdilak 2542 (2836)
T PRK14844 2517 CYFIPIGAVLNVQDGQKVHAGDVITR 2542 (2836)
T ss_pred eeecCCCceEeeccCceecccceeec
Confidence 3445654 46789999999999998
No 32
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=41.71 E-value=34 Score=34.24 Aligned_cols=32 Identities=19% Similarity=0.230 Sum_probs=25.9
Q ss_pred ceeecCCCeeecCC-ceEEEeeceEEEEEEeecc
Q psy7634 73 LDYHPGLNVGFGAR-GTLFAMEKGKVKITVEKCN 105 (206)
Q Consensus 73 tk~hPG~NVg~GkD-~TLfAl~~G~V~f~~~~~~ 105 (206)
..+++|.|+- -+| .||.|.++|..-+.+..++
T Consensus 219 ~~l~lG~nt~-~kd~~tlvA~~~G~~~~s~~tI~ 251 (543)
T COG1315 219 IKLNLGKNTA-FKDNNTLVAKRDGQPIVSKNTIS 251 (543)
T ss_pred eeeecCCCCc-cCCCCEEEEeeCCeEEecCCeeE
Confidence 5788999998 555 8999999999988865543
No 33
>cd06663 Biotinyl_lipoyl_domains Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue.
Probab=41.56 E-value=42 Score=23.10 Aligned_cols=39 Identities=28% Similarity=0.352 Sum_probs=27.5
Q ss_pred eEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEE
Q psy7634 51 FRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITV 101 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~ 101 (206)
+.+..|+.|.+|+.|..= -.+-....|.|+++|+|.-..
T Consensus 19 ~~v~~G~~v~~g~~l~~i------------e~~k~~~~i~ap~~G~v~~~~ 57 (73)
T cd06663 19 WLKKVGDKVKKGDVLAEI------------EAMKATSDVEAPKSGTVKKVL 57 (73)
T ss_pred EEcCCcCEECCCCEEEEE------------EeCCeEEEEEcCCCEEEEEEE
Confidence 456688888888888873 112225679999999986543
No 34
>COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]
Probab=40.40 E-value=41 Score=34.32 Aligned_cols=59 Identities=22% Similarity=0.213 Sum_probs=43.1
Q ss_pred eeecccCCCcCCCCCCCCCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEE
Q psy7634 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVK 98 (206)
Q Consensus 25 ~A~Kk~~gSt~N~grds~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~ 98 (206)
+.++....|+.-.--.=+|.= .-|...+||.|.+|+.||-- =-|-..|+|-|..||+|.
T Consensus 566 ~~~~~~~~~~~~l~aPMpG~v---~~v~V~~G~~V~~G~~lvvl------------EAMKME~~l~A~~dG~V~ 624 (645)
T COG4770 566 GGAKVAAASSGELLAPMPGTV---VSVAVKEGQEVSAGDLLVVL------------EAMKMENTLRAPRDGVVA 624 (645)
T ss_pred ccccccCCCCCceecCCCceE---EEEEecCCCEecCCCeEEEe------------EehhcccceecCcCcEEE
Confidence 344444444443223334555 66899999999999999987 567788999999999997
No 35
>PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
Probab=40.34 E-value=34 Score=29.64 Aligned_cols=38 Identities=29% Similarity=0.289 Sum_probs=30.5
Q ss_pred cceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEE
Q psy7634 49 KGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVK 98 (206)
Q Consensus 49 lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~ 98 (206)
.-+.+..|+.|.+|++|+.- =.+--.+.+-|+.+|+|.
T Consensus 20 ~~~~~~~g~~v~~~~~~~~~------------e~~k~~~~~~a~~~g~~~ 57 (371)
T PRK14875 20 AGWLVQEGDEVEKGDELLDV------------ETDKITNEVEAPAAGTLR 57 (371)
T ss_pred EEEEcCCCCEeCCCCEEEEE------------EecceeEEEecCCCeEEE
Confidence 44677899999999999985 234446889999999996
No 36
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=38.93 E-value=62 Score=25.11 Aligned_cols=43 Identities=16% Similarity=0.238 Sum_probs=29.7
Q ss_pred EeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEeeccCC
Q psy7634 52 RKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVEKCNLN 107 (206)
Q Consensus 52 K~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~~~~p~ 107 (206)
-+.-||.|..|++|.+- .+. + .-.|+|.++|+|.=-.+..+|+
T Consensus 45 ~V~~Gd~V~~GQ~Ia~~--~~~-------~----sa~iHAsvSG~V~~I~~~~~~~ 87 (101)
T PF13375_consen 45 VVKVGDKVKKGQLIAEA--EGF-------L----SAPIHASVSGTVTAIEKRPIPH 87 (101)
T ss_pred EEcCCCEEcCCCEEEec--CCC-------c----EeeEEcCCCeEEEEEeeeEcCC
Confidence 34568999999999987 221 1 1268999999997655544444
No 37
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=38.61 E-value=69 Score=26.10 Aligned_cols=18 Identities=28% Similarity=0.276 Sum_probs=13.1
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=++...|+.|++|..|+.
T Consensus 87 ~~~v~~G~~V~~G~~L~~ 104 (132)
T PF00358_consen 87 ETLVKEGDKVKAGQPLIE 104 (132)
T ss_dssp EESS-TTSEE-TTEEEEE
T ss_pred EEEEeCCCEEECCCEEEE
Confidence 356678999999999985
No 38
>cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=37.99 E-value=43 Score=30.19 Aligned_cols=41 Identities=20% Similarity=0.163 Sum_probs=29.9
Q ss_pred eeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 53 KQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 53 ~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
+.-|+.|++|++|... .- .++|+- -.++.|+.||.|-+.+.
T Consensus 244 ~~~G~~V~~Gq~lg~i--~d--p~~g~~-----~~~v~Ap~dGiv~~~~~ 284 (298)
T cd06253 244 KHLGDIVKRGDVIGEI--VD--PLEGEV-----IEEVIAPCDGILFTLRE 284 (298)
T ss_pred cCCCCEECCCCEEEEE--eC--CCCCCe-----eEEEEcCCCeEEEEeec
Confidence 3458999999999998 22 122222 25899999999999875
No 39
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component. This model represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (Hydroquinone-O-beta-D-glucopyranoside). These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.
Probab=34.36 E-value=1.3e+02 Score=30.23 Aligned_cols=18 Identities=22% Similarity=0.379 Sum_probs=15.3
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=....+||.|++|+.|++
T Consensus 547 ~~~v~~g~~V~~G~~l~~ 564 (610)
T TIGR01995 547 EILVKVGDHVKAGQLLLT 564 (610)
T ss_pred EEEecCcCEEcCCCEEEE
Confidence 456779999999999986
No 40
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=32.46 E-value=61 Score=26.41 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=30.8
Q ss_pred cceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEE
Q psy7634 49 KGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKI 99 (206)
Q Consensus 49 lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f 99 (206)
+=|....|+.|.+|+.|+.= .-++ -...|.|.++|+|.-
T Consensus 73 ~~i~V~~Gd~V~~Gq~L~~l--EamK----------me~eI~Ap~~G~V~~ 111 (130)
T PRK06549 73 LKVLVAVGDQVTENQPLLIL--EAMK----------MENEIVASSAGTVTA 111 (130)
T ss_pred EEEEeCCCCEECCCCEEEEE--eccC----------ccEEEEcCCCeEEEE
Confidence 45788999999999999985 3232 367899999999964
No 41
>PRK10255 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional
Probab=32.02 E-value=1.6e+02 Score=30.16 Aligned_cols=18 Identities=22% Similarity=0.182 Sum_probs=15.3
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=..+.+||.|++|+.|++
T Consensus 583 ~~~Vk~Gd~V~~G~~l~~ 600 (648)
T PRK10255 583 KRLVEEGAQVSAGQPILE 600 (648)
T ss_pred eEEecCCCEEcCCCEEEE
Confidence 456779999999999986
No 42
>PRK09824 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional
Probab=28.64 E-value=1.8e+02 Score=29.53 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=15.2
Q ss_pred CeeeeCCeEEeeCcEEEE
Q psy7634 176 GFRKQEGEVVEKGSILYI 193 (206)
Q Consensus 176 G~k~~~g~~v~~G~Ii~r 193 (206)
=+...+||.|++|+.|++
T Consensus 563 ~~~v~~Gd~V~~G~~l~~ 580 (627)
T PRK09824 563 TAHVNVGDKVNTGDLLIE 580 (627)
T ss_pred eEEecCCCEEcCCCEEEE
Confidence 456778999999999986
No 43
>PF07596 SBP_bac_10: Protein of unknown function (DUF1559); InterPro: IPR011453 This is a large family of paralogous proteins apparently unique to planctomycetes.
Probab=28.45 E-value=38 Score=28.54 Aligned_cols=18 Identities=33% Similarity=0.530 Sum_probs=14.9
Q ss_pred EEEeeceEEEEEEeeccC
Q psy7634 89 LFAMEKGKVKITVEKCNL 106 (206)
Q Consensus 89 LfAl~~G~V~f~~~~~~p 106 (206)
-|+++||-|+|-.|-+|+
T Consensus 247 n~~~~DGSVrfis~tId~ 264 (265)
T PF07596_consen 247 NFLMADGSVRFISETIDL 264 (265)
T ss_pred eEEEecceEEecccccCC
Confidence 568899999999986654
No 44
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=27.68 E-value=89 Score=18.79 Aligned_cols=19 Identities=21% Similarity=0.218 Sum_probs=15.6
Q ss_pred eeecCCceEEEeeceEEEE
Q psy7634 81 VGFGARGTLFAMEKGKVKI 99 (206)
Q Consensus 81 Vg~GkD~TLfAl~~G~V~f 99 (206)
|-.|.+||+.=+.||.|.-
T Consensus 4 ia~G~~ht~al~~~g~v~~ 22 (30)
T PF13540_consen 4 IACGGYHTCALTSDGEVYC 22 (30)
T ss_dssp EEEESSEEEEEE-TTEEEE
T ss_pred EEecCCEEEEEEcCCCEEE
Confidence 7789999999999999853
No 45
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=27.28 E-value=89 Score=34.10 Aligned_cols=18 Identities=22% Similarity=0.217 Sum_probs=14.7
Q ss_pred CCceEEEeeceEEEEEEe
Q psy7634 85 ARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 85 kD~TLfAl~~G~V~f~~~ 102 (206)
++..+.|.+||+|.|..+
T Consensus 926 k~~a~ise~~G~v~~~~~ 943 (1156)
T PRK00566 926 KGPAIIAEIDGTVSFGKE 943 (1156)
T ss_pred CCceEEEecCCEEEeccc
Confidence 467899999999998643
No 46
>cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=25.13 E-value=97 Score=27.56 Aligned_cols=41 Identities=22% Similarity=0.098 Sum_probs=28.8
Q ss_pred EeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 52 RKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 52 K~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
.+.-|+.|.+|++|.+. .- |=. ..-.++.|++||.|.+...
T Consensus 233 ~~~~Gd~V~~G~~ig~i--~d----~~~----~~~~~v~ap~~G~v~~~~~ 273 (287)
T cd06251 233 LVKLGDKVKKGQLLATI--TD----PFG----EEEAEVKAPFDGIVIGRNN 273 (287)
T ss_pred ecCCCCEECCCCEEEEE--EC----CCC----CceEEEECCCCeEEEEecC
Confidence 34568899999999888 11 111 1127899999999977664
No 47
>cd06254 M14_ASTE_ASPA_like_4 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=23.41 E-value=96 Score=27.54 Aligned_cols=42 Identities=24% Similarity=0.222 Sum_probs=30.9
Q ss_pred eEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 51 FRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 51 iK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
..+.-|+.|++|++|... .- .+ |+ ..+++.|+.||.|-+.+.
T Consensus 236 ~~~~~G~~V~~G~~lg~i--~d--p~-g~-----~~~~i~Ap~dG~v~~~~~ 277 (288)
T cd06254 236 PFVKAGDTVQKGALLGYV--TD--YF-GN-----VIAEYRAPFDGVVLYNTA 277 (288)
T ss_pred EecCCCCEecCCCEEEEE--EC--CC-CC-----ceEEEEcCCCcEEEEeeC
Confidence 344569999999999998 21 11 31 137899999999998875
No 48
>PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=23.33 E-value=1.2e+02 Score=25.21 Aligned_cols=44 Identities=23% Similarity=0.231 Sum_probs=32.8
Q ss_pred CCCCccCcceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEE
Q psy7634 42 NSGFRFPKGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKIT 100 (206)
Q Consensus 42 ~~kr~~~lGiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~ 100 (206)
.|+- +-|.+..||.|.+|+.|+.= --++ -+..|-|.++|+|.-.
T Consensus 92 ~G~I---~~~~V~~Gd~V~~Gq~l~~i--EamK----------me~eI~Ap~~G~V~~i 135 (153)
T PRK05641 92 PGKI---LRILVREGQQVKVGQGLLIL--EAMK----------MENEIPAPKDGVVKKI 135 (153)
T ss_pred CeEE---EEEEeCCCCEEcCCCEEEEE--eecc----------cceEEecCCCeEEEEE
Confidence 3555 66888999999999999874 2222 2458999999998754
No 49
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=22.26 E-value=1.7e+02 Score=32.05 Aligned_cols=52 Identities=23% Similarity=0.296 Sum_probs=33.6
Q ss_pred cceEeeCCeEEeeCc---EEEEee--cCCc-----eeecCCCeee-------------------cCCceEEEeeceEEEE
Q psy7634 49 KGFRKQEGEVVEKGS---ILYISY--VQRL-----DYHPGLNVGF-------------------GARGTLFAMEKGKVKI 99 (206)
Q Consensus 49 lGiK~~~Gq~V~~G~---IivRQ~--~Rgt-----k~hPG~NVg~-------------------GkD~TLfAl~~G~V~f 99 (206)
+|+-...|..|..|+ ||+=|- --|| .||-|==.+- -+|..+.|.+||+|+|
T Consensus 858 YG~~La~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHtGGv~~~~~DIT~GlpRv~elfear~p~~~a~iae~~G~v~~ 937 (1140)
T TIGR02386 858 YGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFEARTPKDKAVIAEVDGTVEI 937 (1140)
T ss_pred CCCcccCCcEecccccceeEeeeecCCCcchhehhheeeccccccccccccCchhhhhhhhcccCCCceEEEecCCEEEE
Confidence 555566678888775 677773 0133 4887632221 1356799999999998
Q ss_pred E
Q psy7634 100 T 100 (206)
Q Consensus 100 ~ 100 (206)
.
T Consensus 938 ~ 938 (1140)
T TIGR02386 938 I 938 (1140)
T ss_pred e
Confidence 5
No 50
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=21.84 E-value=1.4e+02 Score=20.62 Aligned_cols=38 Identities=26% Similarity=0.323 Sum_probs=27.7
Q ss_pred ceEeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEE
Q psy7634 50 GFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKI 99 (206)
Q Consensus 50 GiK~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f 99 (206)
-+.+..|+.|.+|+.|..= .-.+ ....+.|.++|+|.-
T Consensus 14 ~~~v~~G~~V~~g~~l~~v--e~~k----------~~~~v~s~~~G~v~~ 51 (70)
T PRK08225 14 KIVVKVGDTVEEGQDVVIL--ESMK----------MEIPIVAEEAGTVKK 51 (70)
T ss_pred EEEeCCCCEECCCCEEEEE--EcCC----------CcceEeCCCCEEEEE
Confidence 3667779999999999873 2222 367899999998853
No 51
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=21.33 E-value=77 Score=23.37 Aligned_cols=21 Identities=19% Similarity=0.317 Sum_probs=15.9
Q ss_pred eeeeCCeEEeeCcEEEEeecC
Q psy7634 177 FRKQEGEVVEKGSILYISYVQ 197 (206)
Q Consensus 177 ~k~~~g~~v~~G~Ii~rQrgt 197 (206)
+.+.||+.|.+|++|++=+|.
T Consensus 49 ~~~~dG~~v~~g~~i~~i~G~ 69 (88)
T PF02749_consen 49 WLVKDGDRVEPGDVILEIEGP 69 (88)
T ss_dssp ESS-TT-EEETTCEEEEEEEE
T ss_pred EEeCCCCCccCCcEEEEEEeC
Confidence 456899999999999987764
No 52
>TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. strain PCC 7120 is partially characterized as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter, required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. PCC 7120 has seven members.
Probab=21.18 E-value=67 Score=28.28 Aligned_cols=20 Identities=30% Similarity=0.376 Sum_probs=14.8
Q ss_pred cceEeeCCeEEeeCcEEEEe
Q psy7634 49 KGFRKQEGEVVEKGSILYIS 68 (206)
Q Consensus 49 lGiK~~~Gq~V~~G~IivRQ 68 (206)
.-|.+.+|+.|++|++|++=
T Consensus 28 ~~i~V~eG~~V~~G~~L~~l 47 (327)
T TIGR02971 28 KKLLVAEGDRVQAGQVLAEL 47 (327)
T ss_pred EEEEccCCCEecCCcEEEEe
Confidence 44667788888888888774
No 53
>cd06252 M14_ASTE_ASPA_like_2 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=20.71 E-value=1.4e+02 Score=26.88 Aligned_cols=43 Identities=16% Similarity=0.081 Sum_probs=29.4
Q ss_pred EeeCCeEEeeCcEEEEeecCCceeecCCCeeecCCceEEEeeceEEEEEEe
Q psy7634 52 RKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGKVKITVE 102 (206)
Q Consensus 52 K~~~Gq~V~~G~IivRQ~~Rgtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~ 102 (206)
.+.-|+.|++|++|... .- -|-+|+- .+++.|+.+|.|-....
T Consensus 258 ~~~~G~~V~~G~~lg~i--~d-~~~~g~~-----~~~v~Ap~~Giv~~~~~ 300 (316)
T cd06252 258 LVDLGDEVSAGQVAGRI--HF-PERPGRP-----PLEIRAPDGGVLAARRP 300 (316)
T ss_pred ecCCCCEEcCCCEEEEE--EC-CCCCCCc-----eEEEEcCCCeEEEEeeC
Confidence 34558999999999988 11 1112322 26899999999987764
Done!