Query 028816
Match_columns 203
No_of_seqs 141 out of 1092
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 02:59:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028816.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028816hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00205 ribisomal protein L13 100.0 1.4E-75 3E-80 494.7 14.6 190 14-203 1-191 (191)
2 CHL00159 rpl13 ribosomal prote 100.0 3.3E-59 7.2E-64 380.2 12.5 133 24-156 10-142 (143)
3 PRK09216 rplM 50S ribosomal pr 100.0 9.1E-59 2E-63 378.0 12.4 131 27-157 12-142 (144)
4 TIGR01066 rplM_bact ribosomal 100.0 1.8E-58 3.9E-63 374.7 12.0 131 26-156 9-139 (140)
5 COG0102 RplM Ribosomal protein 100.0 2E-56 4.4E-61 365.0 11.2 132 26-157 11-143 (148)
6 PF00572 Ribosomal_L13: Riboso 100.0 1.2E-55 2.6E-60 353.1 7.7 127 30-156 1-127 (128)
7 KOG3203 Mitochondrial/chloropl 100.0 7.9E-54 1.7E-58 351.6 8.5 137 4-149 6-142 (165)
8 cd00392 Ribosomal_L13 Ribosoma 100.0 3.9E-53 8.6E-58 332.9 10.3 114 30-143 1-114 (114)
9 TIGR01077 L13_A_E ribosomal pr 100.0 3.9E-43 8.4E-48 285.6 9.1 131 31-177 1-132 (142)
10 PTZ00068 60S ribosomal protein 100.0 4.3E-43 9.4E-48 299.3 8.9 129 29-177 4-138 (202)
11 PRK06394 rpl13p 50S ribosomal 100.0 1.1E-40 2.5E-45 272.3 9.5 130 29-178 3-137 (146)
12 KOG3204 60S ribosomal protein 99.9 4.2E-24 9.2E-29 181.4 3.4 127 29-177 6-133 (197)
13 PF04989 CmcI: Cephalosporin h 53.2 15 0.00033 32.0 3.3 47 18-80 101-151 (206)
14 KOG3974 Predicted sugar kinase 51.1 11 0.00024 34.8 2.1 51 12-64 116-166 (306)
15 PF12396 DUF3659: Protein of u 41.4 8.7 0.00019 27.7 -0.0 24 31-54 14-37 (64)
16 cd04195 GT2_AmsE_like GT2_AmsE 39.4 1.2E+02 0.0026 23.7 6.2 67 12-80 14-95 (201)
17 cd01856 YlqF YlqF. Proteins o 35.9 65 0.0014 25.7 4.3 56 9-77 2-58 (171)
18 PRK03759 isopentenyl-diphospha 35.6 51 0.0011 27.1 3.7 44 28-79 6-50 (184)
19 PF00436 SSB: Single-strand bi 31.9 44 0.00096 24.1 2.5 23 39-73 54-76 (104)
20 cd02885 IPP_Isomerase Isopente 30.7 55 0.0012 26.3 3.0 46 29-82 3-48 (165)
21 PRK10026 arsenate reductase; P 30.4 71 0.0015 26.1 3.7 59 14-76 79-137 (141)
22 PRK11397 dacD D-alanyl-D-alani 28.5 53 0.0011 31.0 2.9 37 5-41 8-51 (388)
23 cd04196 GT_2_like_d Subfamily 27.8 99 0.0022 24.1 4.0 68 11-81 11-95 (214)
24 TIGR02150 IPP_isom_1 isopenten 27.2 36 0.00078 27.3 1.4 41 31-79 2-43 (158)
25 cd04496 SSB_OBF SSB_OBF: A sub 26.5 68 0.0015 22.8 2.7 30 28-73 43-72 (100)
26 COG0629 Ssb Single-stranded DN 26.4 66 0.0014 26.4 2.9 22 39-72 57-78 (167)
27 KOG0023 Alcohol dehydrogenase, 25.4 1.4E+02 0.003 28.4 5.0 42 19-75 173-214 (360)
28 PRK05853 hypothetical protein; 24.9 68 0.0015 26.9 2.7 23 39-73 49-71 (161)
29 TIGR03707 PPK2_P_aer polyphosp 24.6 88 0.0019 27.5 3.4 31 14-44 182-212 (230)
30 PRK09880 L-idonate 5-dehydroge 24.3 2E+02 0.0043 25.3 5.6 42 9-51 151-192 (343)
31 PRK07772 single-stranded DNA-b 24.0 69 0.0015 27.4 2.6 23 39-73 59-81 (186)
32 PHA02754 hypothetical protein; 23.9 52 0.0011 23.9 1.5 16 65-80 43-58 (67)
33 PRK15393 NUDIX hydrolase YfcD; 23.9 93 0.002 25.6 3.3 38 29-75 11-48 (180)
34 COG3499 Phage protein U [Gener 23.7 44 0.00095 28.0 1.3 25 17-41 67-91 (147)
35 PRK06752 single-stranded DNA-b 23.4 72 0.0016 24.4 2.4 29 29-73 47-75 (112)
36 cd08284 FDH_like_2 Glutathione 22.7 2.2E+02 0.0048 24.5 5.6 43 8-51 148-190 (344)
37 PRK07274 single-stranded DNA-b 22.1 1.2E+02 0.0026 24.1 3.5 29 29-73 47-75 (131)
38 PRK06863 single-stranded DNA-b 21.7 1.1E+02 0.0023 25.8 3.2 29 29-73 52-80 (168)
39 PRK08182 single-stranded DNA-b 21.3 88 0.0019 25.6 2.6 23 39-73 60-82 (148)
40 PRK09010 single-stranded DNA-b 21.1 1.1E+02 0.0023 26.1 3.1 29 29-73 54-82 (177)
41 TIGR00621 ssb single stranded 20.6 82 0.0018 25.9 2.3 29 29-73 51-79 (164)
42 PF03447 NAD_binding_3: Homose 20.5 1.6E+02 0.0035 21.9 3.8 37 28-78 59-95 (117)
43 TIGR00292 thiazole biosynthesi 20.3 35 0.00076 29.9 0.1 48 29-81 159-207 (254)
44 PRK08763 single-stranded DNA-b 20.2 87 0.0019 26.2 2.4 28 29-72 52-79 (164)
45 PF03621 MbtH: MbtH-like prote 20.1 71 0.0015 22.2 1.6 13 64-76 9-21 (54)
46 PRK05733 single-stranded DNA-b 20.1 1.4E+02 0.0031 25.1 3.7 28 29-72 53-80 (172)
No 1
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=1.4e-75 Score=494.70 Aligned_cols=190 Identities=83% Similarity=1.316 Sum_probs=184.6
Q ss_pred HHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeec
Q 028816 14 KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHT 93 (203)
Q Consensus 14 ~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~ht 93 (203)
++|+|||+++|+++++||||||+||+||||||.||++|+|||||+|||++||||+||||||++|+|||+||.+|.|++||
T Consensus 1 ~~~~~~~~~~~~~~r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVINAekI~lTG~K~~~K~Y~~ht 80 (191)
T PLN00205 1 KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFYRWHT 80 (191)
T ss_pred CcccccccccccCCCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccEEEEeCChhhcceEEEec
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCccccChhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhH
Q 028816 94 GYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAM 173 (203)
Q Consensus 94 gYpGglk~~~~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~ 173 (203)
|||||+++++++++++++|++||++||+||||+|++|+.++++|+||+|++|||++|+|+++++||+++|++||+++|+|
T Consensus 81 gypGglk~~~~~~~~~r~P~~Il~kAVrGMLPkn~lr~~~~krLkVY~G~~hp~~~q~p~~~~~p~~~~~~~~~~~~~~~ 160 (191)
T PLN00205 81 GYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGDKPLEPFVMPPRQVREMRPRARRAM 160 (191)
T ss_pred CCCCCcccccHHHHhccCHHHHHHHHHHhcCCCCchHHHHHhCCEEECCCCCChhccCCeEecCChHHhhccCchhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhh-HHHhhhhhhhhhhhhcC
Q 028816 174 IREQKKAEMQQSN-KDMRKNRKKEVEAEVTA 203 (203)
Q Consensus 174 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 203 (203)
|+||+|+||+++. +.++++++++++.|++|
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (191)
T PLN00205 161 IRAQKKAEQREQAANEKRKGKKKEVEVEVTA 191 (191)
T ss_pred HHHHHHHHHHHHHHhhhccccccccccccCC
Confidence 9999999999988 77888888888888764
No 2
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=3.3e-59 Score=380.24 Aligned_cols=133 Identities=40% Similarity=0.640 Sum_probs=128.7
Q ss_pred ccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccC
Q 028816 24 NLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT 103 (203)
Q Consensus 24 ~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~ 103 (203)
+.-.|+|+||||+||+||||||.||++|+|||||+|||++||||+||||||++|+|||+||.+|.|++|||||||+++++
T Consensus 10 ~~~~r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~kv~~TG~K~~~K~y~~htg~pGg~k~~~ 89 (143)
T CHL00159 10 DYKNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFYVRHSGRPGGLKIET 89 (143)
T ss_pred hhcCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEecceeEEeCchhhheEEEecCCCCCCccccc
Confidence 34468999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816 104 LKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 156 (203)
Q Consensus 104 ~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~ 156 (203)
++++++++|++||++||+||||+|.+|+.+|++|+||+|++|||++|+|++++
T Consensus 90 ~~~~~~r~P~~il~~aV~gMLPkn~lgr~~~~rLkvy~G~~hph~aq~p~~~~ 142 (143)
T CHL00159 90 FEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHPHVAQKPIKIN 142 (143)
T ss_pred HHHHhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCccccCCeecC
Confidence 99999999999999999999999999999999999999999999999997665
No 3
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=9.1e-59 Score=378.00 Aligned_cols=131 Identities=46% Similarity=0.812 Sum_probs=128.5
Q ss_pred CceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhH
Q 028816 27 GLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKE 106 (203)
Q Consensus 27 ~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~ 106 (203)
.++|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||+||.+|.||+|||||||++++++++
T Consensus 12 ~~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pGglk~~~~~~ 91 (144)
T PRK09216 12 ERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYRHSGYPGGLKEITFGE 91 (144)
T ss_pred CCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCceeEEcCchHhheeeEEecccCCCCEEecHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816 107 QMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM 157 (203)
Q Consensus 107 ~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~ 157 (203)
+++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.+++
T Consensus 92 ~~~r~P~~il~~aVrgMLPkn~lgr~~~~rLkvy~G~~hp~~~q~p~~~~~ 142 (144)
T PRK09216 92 LLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHPHAAQQPEVLEI 142 (144)
T ss_pred HhhhCHHHHHHHHHHhcCCCCccHHHHHhCcEEeCCCCCCccccCCEeccc
Confidence 999999999999999999999999999999999999999999999988775
No 4
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=100.00 E-value=1.8e-58 Score=374.72 Aligned_cols=131 Identities=46% Similarity=0.781 Sum_probs=127.6
Q ss_pred CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816 26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK 105 (203)
Q Consensus 26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~ 105 (203)
-.|+|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||++|++|.||+|||||||+++++++
T Consensus 9 ~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pgg~k~~~~~ 88 (140)
T TIGR01066 9 KKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTFE 88 (140)
T ss_pred hcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEEEEeCchhhceeeEEEcccCCccccccHH
Confidence 35899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816 106 EQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 156 (203)
Q Consensus 106 ~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~ 156 (203)
++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.++
T Consensus 89 ~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkvy~G~~hp~~~q~p~~~~ 139 (140)
T TIGR01066 89 EMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPHEAQKPIVLD 139 (140)
T ss_pred HhhhcCHHHHHHHHHHhcCCCCccHHHHHhCeEEeCCCCCChhhcCCeecC
Confidence 999999999999999999999999999999999999999999999987665
No 5
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-56 Score=365.05 Aligned_cols=132 Identities=42% Similarity=0.747 Sum_probs=126.3
Q ss_pred CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816 26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK 105 (203)
Q Consensus 26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~ 105 (203)
..++|+||||+|++||||||.||+.|+|||||+||||+||||+|||||||+|+|||+|..+|.||+|||||||+++.+++
T Consensus 11 ~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~hs~~~gglk~~t~~ 90 (148)
T COG0102 11 VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYRHSGYPGGLKNPTRG 90 (148)
T ss_pred ccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceeeEEecccccceEEEEeeccCCcccccccc
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred HHhh-cChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816 106 EQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM 157 (203)
Q Consensus 106 ~~~~-r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~ 157 (203)
.+.+ +.|++||++||+||||+|.+++++|++|+||.|++|||.+|+|+.+.+
T Consensus 91 ~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~aq~p~~l~~ 143 (148)
T COG0102 91 GPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHEAQKPEALEL 143 (148)
T ss_pred cccccCCHHHHHHHHHhccCCCChhHHHHHhCceEecCCCCccccccchhhhh
Confidence 6666 999999999999999999999999999999999999999998876553
No 6
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 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 L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=100.00 E-value=1.2e-55 Score=353.07 Aligned_cols=127 Identities=48% Similarity=0.834 Sum_probs=124.4
Q ss_pred EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhh
Q 028816 30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQME 109 (203)
Q Consensus 30 W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~ 109 (203)
|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||++|.+|.|++|||||||++..+++.+++
T Consensus 1 W~viDA~~~~lGRLAs~iAk~L~GKhk~~y~p~~d~Gd~VvViNae~i~~tG~k~~~k~y~~h~~~~g~~~~~~~~~~~~ 80 (128)
T PF00572_consen 1 WYVIDAKGQILGRLASKIAKLLLGKHKPTYTPNVDCGDHVVVINAEKIVLTGKKWRQKVYYRHTGYPGGLKNPTAKGLHE 80 (128)
T ss_dssp EEEEETTTBBHHHHHHHHHHHHCTTSSTSSBTTSSTTEEEEEECGGGBEESSHHHHHHHHHHEHSSSTSCEEEECHHHHC
T ss_pred CEEEeCCCCchHHHHHHHHHHHhCCCCCccCcCccCCCEEEEEcCeeeEecCCeecceEEEeecccchhhcccchhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816 110 RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 156 (203)
Q Consensus 110 r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~ 156 (203)
++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+++.++
T Consensus 81 ~~P~~i~~~aVrgMLP~n~~g~~~l~rL~vy~g~~hp~~~~~~~~~~ 127 (128)
T PF00572_consen 81 KDPSRILKRAVRGMLPKNKLGREALKRLKVYPGEPHPHAAQKPVVLE 127 (128)
T ss_dssp SSHHHHHHHHHHTTSTTSHHHHHHHTTEEEESSSSCSTTSSSCBEEE
T ss_pred cCHHHHHHHHHHHHCCCChhhhHHhhceEEECCCCCChhccCCEeCC
Confidence 99999999999999999999999999999999999999999987654
No 7
>KOG3203 consensus Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.9e-54 Score=351.57 Aligned_cols=137 Identities=47% Similarity=0.749 Sum_probs=132.2
Q ss_pred hhhhHhhhchHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCccccccccc
Q 028816 4 QAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRK 83 (203)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K 83 (203)
+..++|.||...|+| |.|+||||++|+||||||+||..|+|||||+|||+.||||+|||+||++|.|||+|
T Consensus 6 a~~~~~~g~~~~afa---------RvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K 76 (165)
T KOG3203|consen 6 AVSRSFRGNQWLAFA---------RVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKK 76 (165)
T ss_pred hhhccccchHHHHHh---------hhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhheeccch
Confidence 456789999999999 77999999999999999999999999999999999999999999999999999999
Q ss_pred ccceeEeeecccCCCccccChhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCC
Q 028816 84 LKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149 (203)
Q Consensus 84 ~~~K~Y~~htgYpGglk~~~~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~ 149 (203)
|.+|+|++|||||||++..+...++.++|++|+++||+||||+|.+|++.+++|++|+|.+||+..
T Consensus 77 ~~qk~Y~~HsGyPG~lk~~~~~q~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p~~~ 142 (165)
T KOG3203|consen 77 WEQKIYRSHSGYPGGLKQTTADQLADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHPEKV 142 (165)
T ss_pred hhhhhhhhcCCCCCchhhhHHHHHhhhCHHHHHHHHHHhhCccchHHHHHhheeeccCCccCchhh
Confidence 999999999999999998889999999999999999999999999999999999999999999654
No 8
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=100.00 E-value=3.9e-53 Score=332.88 Aligned_cols=114 Identities=50% Similarity=0.849 Sum_probs=112.9
Q ss_pred EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhh
Q 028816 30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQME 109 (203)
Q Consensus 30 W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~ 109 (203)
|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||++|.+|.||+|||||||+++.+++++++
T Consensus 1 w~viDA~~~~lGRlAs~iA~~L~gKhKp~y~p~~d~Gd~VvViNa~~i~~tG~k~~~k~y~~~~~~~g~~~~~~~~~~~~ 80 (114)
T cd00392 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYYRHTGYPGGLKNPTAGPLHP 80 (114)
T ss_pred CEEEeCCCCchHHHHHHHHHHHcCCCCCCcCCCccCCCEEEEEeccEEEEeCchhhccceEEeccCCCCCccCCcchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cChhHHHHHHHhccCCCCCchhhhhcCceecCCC
Q 028816 110 RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 143 (203)
Q Consensus 110 r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~ 143 (203)
++|++||++||+||||+|.+|+++|+||+||+|+
T Consensus 81 ~~P~~il~~aV~gMLPkn~~g~~~l~rLkvy~g~ 114 (114)
T cd00392 81 RAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 114 (114)
T ss_pred hCHHHHHHHHHHhcCCCChhHHHHHhCcEEeCCC
Confidence 9999999999999999999999999999999985
No 9
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=100.00 E-value=3.9e-43 Score=285.58 Aligned_cols=131 Identities=27% Similarity=0.398 Sum_probs=117.3
Q ss_pred EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhhc
Q 028816 31 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMER 110 (203)
Q Consensus 31 ~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~r 110 (203)
+||||+||+||||||.||++|+ |||+|||||||+|.|||+|+.+|.||+||+++|.....++++++++
T Consensus 1 ivIDA~~~vlGRLAs~IA~~L~------------~Gd~VvViNaeki~~TG~k~~~k~~y~~~~~~g~~~~~~~~~~~~r 68 (142)
T TIGR01077 1 TVIDGSGHILGRLASVVAKQLL------------NGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNPRRGPFFPR 68 (142)
T ss_pred CEEeCCCCchHHHHHHHHHHHh------------cCCEEEEEechHheecCchhhheeEEEEECCCCCcccCCHHHhhhc
Confidence 5899999999999999999998 9999999999999999999999999999976555555589999999
Q ss_pred ChhHHHHHHHhccCCCC-CchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHH
Q 028816 111 DPTEAIRKAVLRMLPRN-KLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ 177 (203)
Q Consensus 111 ~P~~Ii~rAVrGMLPkn-~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~ 177 (203)
+|++||++||+||||+| .+++.+|+||+||+|+||||++|++ .++| .++ ..|+.+.|++|++-
T Consensus 69 ~P~~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~~h~~~~qk~--~~~~-~a~-~~~~~~~~~~~~lg 132 (142)
T TIGR01077 69 APSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKR--VVVP-EAL-VSRLSPTRKYVTLG 132 (142)
T ss_pred CHHHHHHHHHHHhCCCCChhHHHHHhCcEEecCCCCCccccCc--cccC-hhh-hhccCCCCceEEHH
Confidence 99999999999999998 5667899999999999999999987 4554 555 78899998887654
No 10
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=4.3e-43 Score=299.26 Aligned_cols=129 Identities=30% Similarity=0.456 Sum_probs=118.5
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccC-----
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT----- 103 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~----- 103 (203)
+|+||||+||+||||||.||+.|+ |||+|||||||+|+|||+++++|.||+| +++.++
T Consensus 4 ~w~vIDA~g~vLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iTG~k~~~K~~y~~-----~lk~~~~~nP~ 66 (202)
T PTZ00068 4 KVIVIDCKGHLLGRLASVVAKELL------------LGQKIVVVRCEDLNISGSLFRNKVKYEE-----FLRKRMNTNPR 66 (202)
T ss_pred ceEEEECCCCcHHHHHHHHHHHHh------------CCCEEEEEecceeEeecchhhheeeeEe-----eeEeeccCCCC
Confidence 799999999999999999999999 9999999999999999999999999998 466666
Q ss_pred hhHHhhcChhHHHHHHHhccCCC-CCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHH
Q 028816 104 LKEQMERDPTEAIRKAVLRMLPR-NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ 177 (203)
Q Consensus 104 ~~~~~~r~P~~Ii~rAVrGMLPk-n~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~ 177 (203)
.+++|++.|++||++||+||||+ +.+|+++|+||+||+|+||||++++. ++ .|.++|++|+.|.|.||+.-
T Consensus 67 ~g~~~~r~P~~Il~raVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~--~v-vp~A~r~~rl~~~~ky~~lg 138 (202)
T PTZ00068 67 RGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKR--VV-IPSALRVLRLKPERPYTVLG 138 (202)
T ss_pred cchhcccCHHHHHHHHHhhhCCCCChhHHHHHhCCEEecCCCCchhccCc--cc-ccchhhhhccCCCCceeeHH
Confidence 48999999999999999999998 55777899999999999999999975 44 47999999999999888653
No 11
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00 E-value=1.1e-40 Score=272.26 Aligned_cols=130 Identities=21% Similarity=0.295 Sum_probs=111.0
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCcccc----Ch
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKER----TL 104 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~----~~ 104 (203)
+-+||||+||+||||||.||++|+ +||+||||||++|++||+|+.+ |++|++|+ +++.. ++
T Consensus 3 ~~~viDA~~~vlGRLAs~IA~~L~------------~Gd~VVViNa~kv~~tG~K~~~--~~~y~~~~-~~k~~~np~~~ 67 (146)
T PRK06394 3 AMVVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGNRERV--IEKYKQRR-ERGSHYNPYRN 67 (146)
T ss_pred ccEEEECCCCchHHHHHHHHHHHh------------CCCEEEEEechheEecCchhhh--eeeEeCCC-CCcccCCCCCh
Confidence 468999999999999999999999 7999999999999999999877 55566676 46666 78
Q ss_pred hHHhhcChhHHHHHHHhccCC-CCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHHH
Q 028816 105 KEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQK 178 (203)
Q Consensus 105 ~~~~~r~P~~Ii~rAVrGMLP-kn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~ 178 (203)
+++++++|++||++||+|||| +|.+++.+|+||+||+|+||||++|+|+.+.+ +.+ .++. .|.+|+.-+
T Consensus 68 ~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~~rLkvy~G~~h~~~~qkp~~~~~---a~~-~~~~-~~k~~~lge 137 (146)
T PRK06394 68 GPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDE---ADL-SRLS-TIKYVTLGE 137 (146)
T ss_pred HHhhhcCHHHHHHHHHHhcCCCCChhHHHHHhCcEEecCCCCCcccCCCEEecH---HHH-hccC-CCCcEEHHH
Confidence 999999999999999999999 78888899999999999999999998854443 333 3555 577877644
No 12
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=4.2e-24 Score=181.39 Aligned_cols=127 Identities=26% Similarity=0.393 Sum_probs=111.8
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHh
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQM 108 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~ 108 (203)
+-.+||+.||++||||+.||+.|+ .|+.||||.||.|.|||+.+++|.|-.+ .-. ..+++|
T Consensus 6 ~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~lrk------~~~-~ng~~h 66 (197)
T KOG3204|consen 6 KLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLFLRK------RLN-RNGPFH 66 (197)
T ss_pred EEeeccchhhhhhhHHHHHHHHHh------------cCCeEEEEEEeEEEEecceecchHHHhh------hhc-ccCcch
Confidence 567999999999999999999999 9999999999999999999999844222 111 238999
Q ss_pred hcChhHHHHHHHhccCCCCCchh-hhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHH
Q 028816 109 ERDPTEAIRKAVLRMLPRNKLRD-DRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ 177 (203)
Q Consensus 109 ~r~P~~Ii~rAVrGMLPkn~lr~-~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~ 177 (203)
++-|++|++++|+||+|+++.++ ..+++|++|+|.|+|++.+++ ++ .|.+++++|+.+.|++|..=
T Consensus 67 fr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r--~v-~p~a~~v~~lk~~~K~c~lG 133 (197)
T KOG3204|consen 67 FRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKR--LV-VPVAFQVLRLKPYKKYCLLG 133 (197)
T ss_pred hhhHHHHHHHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCC--cc-CCcceeeecccCCceeEEec
Confidence 99999999999999999998877 579999999999999999987 44 57999999999999998654
No 13
>PF04989 CmcI: Cephalosporin hydroxylase; InterPro: IPR007072 This entry contains Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) []. Members of this family are about 220 amino acids long. It also includes the CmcI protein O85726 from SWISSPROT, which is presumed to represent the cephalosporin-7--hydroxylase []. However this has not been experimentally verified.; GO: 0008168 methyltransferase activity, 0008610 lipid biosynthetic process; PDB: 2BR4_B 2BR3_E 2BR5_E 2BM8_J 2BM9_E.
Probab=53.23 E-value=15 Score=31.97 Aligned_cols=47 Identities=23% Similarity=0.260 Sum_probs=26.6
Q ss_pred hhhhhcccCCceEEEEeCC----CCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccc
Q 028816 18 AGLRRINLEGLRWRVFDAK----GQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVT 80 (203)
Q Consensus 18 ~~~~~~~~~~r~W~vIDA~----gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iT 80 (203)
.-+..+......|+|||-. .++++-|.. .+.++. .||++|| |+..+.
T Consensus 101 ~~v~~~~~~~~~vlVilDs~H~~~hvl~eL~~-y~plv~------------~G~Y~IV---eDt~~~ 151 (206)
T PF04989_consen 101 DQVRELASPPHPVLVILDSSHTHEHVLAELEA-YAPLVS------------PGSYLIV---EDTIIE 151 (206)
T ss_dssp HTSGSS----SSEEEEESS----SSHHHHHHH-HHHT--------------TT-EEEE---TSHHHH
T ss_pred HHHHHhhccCCceEEEECCCccHHHHHHHHHH-hCccCC------------CCCEEEE---Eecccc
Confidence 3334444456789888844 577777776 666666 9999998 444443
No 14
>KOG3974 consensus Predicted sugar kinase [Carbohydrate transport and metabolism]
Probab=51.13 E-value=11 Score=34.77 Aligned_cols=51 Identities=22% Similarity=0.132 Sum_probs=39.7
Q ss_pred chHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCC
Q 028816 12 NMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRD 64 (203)
Q Consensus 12 ~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d 64 (203)
+|-+-++.+..........+||||+|--| ++....+.+.|-++.+-|||+.
T Consensus 116 ~~~k~i~~iley~~~~dvP~VIDaDGL~L--v~q~~e~l~~~~~~viLTPNvv 166 (306)
T KOG3974|consen 116 AILKEIAKILEYLRGKDVPLVIDADGLWL--VEQLPERLIGGYPKVILTPNVV 166 (306)
T ss_pred HHHHHHHHHHHHHhcCCCcEEEcCCceEe--hhhchhhhhccCceeeeCCcHH
Confidence 45555666666777778899999999543 5666677999999999999974
No 15
>PF12396 DUF3659: Protein of unknown function (DUF3659) ; InterPro: IPR022124 This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
Probab=41.37 E-value=8.7 Score=27.70 Aligned_cols=24 Identities=33% Similarity=0.549 Sum_probs=22.4
Q ss_pred EEEeCCCCcchhhHHHHHHHHhCC
Q 028816 31 RVFDAKGQVLGRLASQVATVVQGK 54 (203)
Q Consensus 31 ~vIDA~gqvLGRLAS~VAk~L~GK 54 (203)
.|+|.+|.++|||..--++.|.|+
T Consensus 14 ~V~d~~G~~vG~vveGd~k~L~G~ 37 (64)
T PF12396_consen 14 NVVDDDGNVVGRVVEGDPKKLVGK 37 (64)
T ss_pred eEECCCCCEEEEEecCCHHHhcCC
Confidence 689999999999999999999987
No 16
>cd04195 GT2_AmsE_like GT2_AmsE_like is involved in exopolysaccharide amylovora biosynthesis. AmsE is a glycosyltransferase involved in exopolysaccharide amylovora biosynthesis in Erwinia amylovora. Amylovara is one of the three exopolysaccharide produced by E. amylovora. Amylovara-deficient mutants are non-pathogenic. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds.
Probab=39.44 E-value=1.2e+02 Score=23.73 Aligned_cols=67 Identities=15% Similarity=0.135 Sum_probs=40.8
Q ss_pred chHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCC-CCCC--------------CCCCEEEEEeCcc
Q 028816 12 NMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTY-APNR--------------DDGDMCIVLNAKD 76 (203)
Q Consensus 12 ~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~y-tP~~--------------d~Gd~VVVVNaek 76 (203)
.+.+++.++..+.+....++|||- |..-......+..+.. +....+ +... ..||+|++++++.
T Consensus 14 ~l~~~l~Sl~~q~~~~~eiiivdd-~ss~d~t~~~~~~~~~-~~~i~~i~~~~n~G~~~a~N~g~~~a~gd~i~~lD~Dd 91 (201)
T cd04195 14 FLREALESILKQTLPPDEVVLVKD-GPVTQSLNEVLEEFKR-KLPLKVVPLEKNRGLGKALNEGLKHCTYDWVARMDTDD 91 (201)
T ss_pred HHHHHHHHHHhcCCCCcEEEEEEC-CCCchhHHHHHHHHHh-cCCeEEEEcCccccHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 588999999999888778888874 3322344444443322 221222 1111 1479999999888
Q ss_pred cccc
Q 028816 77 ICVT 80 (203)
Q Consensus 77 I~iT 80 (203)
+...
T Consensus 92 ~~~~ 95 (201)
T cd04195 92 ISLP 95 (201)
T ss_pred ccCc
Confidence 7654
No 17
>cd01856 YlqF YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.
Probab=35.87 E-value=65 Score=25.72 Aligned_cols=56 Identities=25% Similarity=0.235 Sum_probs=34.6
Q ss_pred hhhchHHHhhhhhhcccCCce-EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCccc
Q 028816 9 FSGNMKKALAGLRRINLEGLR-WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDI 77 (203)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~r~-W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI 77 (203)
|-|+|++++--+...--+..- .+|+||.... +.....+...+.+ -..++|+|=-+.
T Consensus 2 ~~~~~~~~~~~~~~~i~~aD~il~v~D~~~~~-~~~~~~i~~~~~~------------k~~ilVlNK~Dl 58 (171)
T cd01856 2 FPGHMAKALRQIKEKLKLVDLVIEVRDARIPL-SSRNPLLEKILGN------------KPRIIVLNKADL 58 (171)
T ss_pred CchHHHHHHHHHHHHHhhCCEEEEEeeccCcc-CcCChhhHhHhcC------------CCEEEEEehhhc
Confidence 788999988877665555444 7899997433 2222234555542 246888885444
No 18
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=35.62 E-value=51 Score=27.08 Aligned_cols=44 Identities=16% Similarity=0.192 Sum_probs=29.4
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCc-cccc
Q 028816 28 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK-DICV 79 (203)
Q Consensus 28 r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNae-kI~i 79 (203)
..|.++|..|..+|+.....+....|. |++.+ .|+|+|.+ +|.+
T Consensus 6 E~~~~vd~~~~~~g~~~r~~~~~~~~~----~h~av----~v~i~~~~g~vLL 50 (184)
T PRK03759 6 ELVVLLDEQGVPTGTAEKAAAHTADTP----LHLAF----SCYLFDADGRLLV 50 (184)
T ss_pred eeEEEECCCCCCcccccHHHHHhcCCC----eeeEE----EEEEEcCCCeEEE
Confidence 469999999999999888777544443 33322 36677754 3444
No 19
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=31.93 E-value=44 Score=24.14 Aligned_cols=23 Identities=35% Similarity=0.498 Sum_probs=16.5
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 39 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 39 vLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
+.|.+|..++..|. .||.|.|.-
T Consensus 54 ~~g~~A~~~~~~l~------------kG~~V~V~G 76 (104)
T PF00436_consen 54 AWGKLAENVAEYLK------------KGDRVYVEG 76 (104)
T ss_dssp EEHHHHHHHHHH--------------TT-EEEEEE
T ss_pred eeeecccccceEEc------------CCCEEEEEE
Confidence 35889999999999 999887753
No 20
>cd02885 IPP_Isomerase Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mamm
Probab=30.66 E-value=55 Score=26.25 Aligned_cols=46 Identities=13% Similarity=0.062 Sum_probs=26.0
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccc
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGR 82 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~ 82 (203)
.|-|+|..|+++|.-.-..+....+- |+ ..-.|+|+|.+.=++-+.
T Consensus 3 ~~~~~d~~~~~~g~~~r~~~~~~~~~----~~----~~v~v~i~~~~~~iLl~k 48 (165)
T cd02885 3 LVILVDEDDNPIGTAEKLEAHLKGTL----LH----RAFSVFLFNSKGRLLLQR 48 (165)
T ss_pred EEEEECCCCCCccccCHHHHhhcCCc----ce----eEEEEEEEcCCCcEEEEe
Confidence 68899999999996444444322211 11 112377788754333333
No 21
>PRK10026 arsenate reductase; Provisional
Probab=30.45 E-value=71 Score=26.12 Aligned_cols=59 Identities=15% Similarity=0.113 Sum_probs=40.6
Q ss_pred HHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcc
Q 028816 14 KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKD 76 (203)
Q Consensus 14 ~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaek 76 (203)
+.+++-|...-.==++.+|+|..|.++||=...|-.+| ++. |.-.-..+.|..+ +|+..
T Consensus 79 ~e~l~ll~~~P~LIKRPIi~~~~~a~i~Rp~e~v~~~l-~~~-~~~~~~~~~~~~~--~~~~~ 137 (141)
T PRK10026 79 DQLIDFMLQHPILINRPIVVTPLGTRLCRPSEVVLEIL-PDA-QKGAFTKEDGEKV--VDEAG 137 (141)
T ss_pred HHHHHHHHhCccceeCcEEEcCCCeEEECCHHHHHHHh-ccc-ccccccccCCeEe--ecCCC
Confidence 34444444443334678999999999999777776666 765 6666677788776 77653
No 22
>PRK11397 dacD D-alanyl-D-alanine carboxypeptidase; Provisional
Probab=28.48 E-value=53 Score=31.05 Aligned_cols=37 Identities=30% Similarity=0.458 Sum_probs=27.5
Q ss_pred hhhHhhhchHHHhhhhh------hcccCCceEEEEeC-CCCcch
Q 028816 5 AATAFSGNMKKALAGLR------RINLEGLRWRVFDA-KGQVLG 41 (203)
Q Consensus 5 ~~~~~~~~~~~~~~~~~------~~~~~~r~W~vIDA-~gqvLG 41 (203)
+++-|.=|++-|++.-+ ......+.|+|||+ +|++|-
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~p~i~A~sail~D~~tG~vL~ 51 (388)
T PRK11397 8 AASLFAFNLSSAFAAENIPFSPQPPAIDAGSWVLMDYTTGQILT 51 (388)
T ss_pred HHHHHHHHHhhhhcccccccCCCCCCccceEEEEEECCCCcChh
Confidence 45667779999987543 34467889999997 788764
No 23
>cd04196 GT_2_like_d Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=27.81 E-value=99 Score=24.13 Aligned_cols=68 Identities=16% Similarity=0.162 Sum_probs=38.8
Q ss_pred hchHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCC--CCCCC---------------CCCCCEEEEEe
Q 028816 11 GNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKP--TYAPN---------------RDDGDMCIVLN 73 (203)
Q Consensus 11 ~~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp--~ytP~---------------~d~Gd~VVVVN 73 (203)
..+..|+..+..+....-.++|||-...- + ..+. +..+..++.+ .+.++ ...||+|++++
T Consensus 11 ~~l~~~l~sl~~q~~~~~eiiVvddgS~d-~-t~~~-~~~~~~~~~~~~~~~~~~~~~G~~~~~n~g~~~~~g~~v~~ld 87 (214)
T cd04196 11 KYLREQLDSILAQTYKNDELIISDDGSTD-G-TVEI-IKEYIDKDPFIIILIRNGKNLGVARNFESLLQAADGDYVFFCD 87 (214)
T ss_pred HHHHHHHHHHHhCcCCCeEEEEEeCCCCC-C-cHHH-HHHHHhcCCceEEEEeCCCCccHHHHHHHHHHhCCCCEEEEEC
Confidence 35788999998887776788999842221 1 1111 2222222211 11111 12589999999
Q ss_pred Cccccccc
Q 028816 74 AKDICVTG 81 (203)
Q Consensus 74 aekI~iTG 81 (203)
++.+...+
T Consensus 88 ~Dd~~~~~ 95 (214)
T cd04196 88 QDDIWLPD 95 (214)
T ss_pred CCcccChh
Confidence 98776644
No 24
>TIGR02150 IPP_isom_1 isopentenyl-diphosphate delta-isomerase, type 1. This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate.
Probab=27.24 E-value=36 Score=27.29 Aligned_cols=41 Identities=7% Similarity=0.148 Sum_probs=27.1
Q ss_pred EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCc-cccc
Q 028816 31 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK-DICV 79 (203)
Q Consensus 31 ~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNae-kI~i 79 (203)
.|+|..|+.+|+.....+....|- ||. +-.|+|+|.+ +|-+
T Consensus 2 ~~~d~~~~~~g~~~r~~~~~~~g~----~h~----~v~v~v~~~~g~vLl 43 (158)
T TIGR02150 2 ILVDENDNPIGTASKAEVHLQETP----LHR----AFSVFLFNEEGQLLL 43 (158)
T ss_pred EEECCCCCEeeeeeHHHhhhcCCC----eEE----EEEEEEEcCCCeEEE
Confidence 589999999999877777544332 221 2348888875 4444
No 25
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=26.52 E-value=68 Score=22.81 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=23.1
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 28 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 28 r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
-.|+-|-+ -|.+|..+++.|. .||.|+|.-
T Consensus 43 ~~~~~v~~----~g~~a~~~~~~~~------------kG~~V~v~G 72 (100)
T cd04496 43 TDWIRVVA----FGKLAENAAKYLK------------KGDLVYVEG 72 (100)
T ss_pred cEEEEEEE----EhHHHHHHHHHhC------------CCCEEEEEE
Confidence 45666654 4569999999999 999998764
No 26
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=26.43 E-value=66 Score=26.36 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=19.5
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEE
Q 028816 39 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 72 (203)
Q Consensus 39 vLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVV 72 (203)
+.|++|..++.+|. .|+.|+|.
T Consensus 57 ~wgk~Ae~~~~yl~------------KG~~V~Ve 78 (167)
T COG0629 57 IWGKLAENAAEYLK------------KGSLVYVE 78 (167)
T ss_pred EehHHHHHHHHHhc------------CCCEEEEE
Confidence 57899999999999 89998875
No 27
>KOG0023 consensus Alcohol dehydrogenase, class V [Secondary metabolites biosynthesis, transport and catabolism]
Probab=25.38 E-value=1.4e+02 Score=28.42 Aligned_cols=42 Identities=29% Similarity=0.359 Sum_probs=35.3
Q ss_pred hhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCc
Q 028816 19 GLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK 75 (203)
Q Consensus 19 ~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNae 75 (203)
-|.+.+....+|+-|-+-|= ||.||.++|+- .|-+|+||-..
T Consensus 173 pLk~~g~~pG~~vgI~GlGG-LGh~aVq~AKA--------------MG~rV~vis~~ 214 (360)
T KOG0023|consen 173 PLKRSGLGPGKWVGIVGLGG-LGHMAVQYAKA--------------MGMRVTVISTS 214 (360)
T ss_pred hhHHcCCCCCcEEEEecCcc-cchHHHHHHHH--------------hCcEEEEEeCC
Confidence 46777888899999998887 99999999994 47789998754
No 28
>PRK05853 hypothetical protein; Validated
Probab=24.90 E-value=68 Score=26.89 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=20.3
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 39 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 39 vLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
+.|+||..++++|. .|+.|+|.-
T Consensus 49 ~wg~lAe~v~~~L~------------KG~~V~V~G 71 (161)
T PRK05853 49 CWGRLVTGVGAALG------------KGAPVIVVG 71 (161)
T ss_pred EEhHHHHHHHHHcC------------CCCEEEEEE
Confidence 67889999999999 899998864
No 29
>TIGR03707 PPK2_P_aer polyphosphate kinase 2, PA0141 family. Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterized protein in Pseudomonas aeruginosa. This family comprises one of three well-separated clades in the larger family described by Pfam model pfam03976. PA0141 from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate residue from polyphosphate. Most species with a member of this family also encode a polyphosphate kinase 1 (PPK1).
Probab=24.56 E-value=88 Score=27.55 Aligned_cols=31 Identities=16% Similarity=0.247 Sum_probs=25.3
Q ss_pred HHHhhhhhhcccCCceEEEEeCCCCcchhhH
Q 028816 14 KKALAGLRRINLEGLRWRVFDAKGQVLGRLA 44 (203)
Q Consensus 14 ~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLA 44 (203)
+-+...|.+.++..--|+||||++.-..+|.
T Consensus 182 ~a~e~~l~~T~t~~APW~iI~a~dk~~a~l~ 212 (230)
T TIGR03707 182 RAKDEMFARTDTPEAPWTVVRSDDKKRARLN 212 (230)
T ss_pred HHHHHHHHhcCCCCCCeEEEcCCCHHHHHHH
Confidence 3345567888888889999999999988875
No 30
>PRK09880 L-idonate 5-dehydrogenase; Provisional
Probab=24.32 E-value=2e+02 Score=25.31 Aligned_cols=42 Identities=12% Similarity=0.121 Sum_probs=30.1
Q ss_pred hhhchHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHH
Q 028816 9 FSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVV 51 (203)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L 51 (203)
|...+.-|..++.+......++++|-+.| .+|.+|.++|+.+
T Consensus 151 ~~~~~~~a~~al~~~~~~~g~~VlV~G~G-~vG~~aiqlak~~ 192 (343)
T PRK09880 151 FAEPLAVAIHAAHQAGDLQGKRVFVSGVG-PIGCLIVAAVKTL 192 (343)
T ss_pred hhcHHHHHHHHHHhcCCCCCCEEEEECCC-HHHHHHHHHHHHc
Confidence 44444455666666555456788888876 8999999999965
No 31
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=23.97 E-value=69 Score=27.44 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=20.1
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 39 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 39 vLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
+.|.+|..||..|. .||.|+|.=
T Consensus 59 ~Wg~~Ae~va~~L~------------KGd~V~V~G 81 (186)
T PRK07772 59 IWRQAAENVAESLT------------KGMRVIVTG 81 (186)
T ss_pred EecHHHHHHHHhcC------------CCCEEEEEE
Confidence 67889999999999 899998863
No 32
>PHA02754 hypothetical protein; Provisional
Probab=23.91 E-value=52 Score=23.93 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=13.6
Q ss_pred CCCEEEEEeCcccccc
Q 028816 65 DGDMCIVLNAKDICVT 80 (203)
Q Consensus 65 ~Gd~VVVVNaekI~iT 80 (203)
.||++|||-|+.|++.
T Consensus 43 SGdkIVVi~aD~I~i~ 58 (67)
T PHA02754 43 SGDKIVVITADAIKIE 58 (67)
T ss_pred cCCEEEEEEcceEEEE
Confidence 6999999999988763
No 33
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=23.91 E-value=93 Score=25.60 Aligned_cols=38 Identities=8% Similarity=0.107 Sum_probs=25.6
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCc
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK 75 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNae 75 (203)
-|.|+|..|+++|......+.. .|- ++ .+-.|+|+|.+
T Consensus 11 ~~~~~d~~~~~~g~~~~~~~~~-~~~----~h----~~~~v~v~~~~ 48 (180)
T PRK15393 11 WVDIVNENNEVIAQASREQMRA-QCL----RH----RATYIVVHDGM 48 (180)
T ss_pred EEEEECCCCCEeeEEEHHHHhh-CCC----ce----EEEEEEEECCC
Confidence 5999999999999985544442 221 12 34468888864
No 34
>COG3499 Phage protein U [General function prediction only]
Probab=23.70 E-value=44 Score=27.99 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=21.5
Q ss_pred hhhhhhcccCCceEEEEeCCCCcch
Q 028816 17 LAGLRRINLEGLRWRVFDAKGQVLG 41 (203)
Q Consensus 17 ~~~~~~~~~~~r~W~vIDA~gqvLG 41 (203)
+.+|.+.-..+..|.+||..|++.|
T Consensus 67 L~aL~a~A~~G~p~~Li~G~G~i~G 91 (147)
T COG3499 67 LDALRALAETGTPLPLIDGDGAIYG 91 (147)
T ss_pred HHHHHHHHhcCCceEEEcCCceEEE
Confidence 5678888888999999999999855
No 35
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=23.37 E-value=72 Score=24.42 Aligned_cols=29 Identities=14% Similarity=0.134 Sum_probs=22.5
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
.|+-+- +.|++|..++.+|. .||.|+|.-
T Consensus 47 ~~~~v~----~wg~~Ae~~~~~l~------------KG~~V~V~G 75 (112)
T PRK06752 47 DFINCV----VWRKSAENVTEYCT------------KGSLVGITG 75 (112)
T ss_pred EEEEEE----EehHHHHHHHHhcC------------CCCEEEEEE
Confidence 465553 57789999999998 899987753
No 36
>cd08284 FDH_like_2 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 2. Glutathione-dependent formaldehyde dehydrogenases (FDHs) are members of the zinc-dependent/medium chain alcohol dehydrogenase family. Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD to formate and NADH. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. These tetrameric FDHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains and a structural zinc in a lobe of the catalytic domain. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typical
Probab=22.67 E-value=2.2e+02 Score=24.48 Aligned_cols=43 Identities=16% Similarity=0.096 Sum_probs=30.1
Q ss_pred HhhhchHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHH
Q 028816 8 AFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVV 51 (203)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L 51 (203)
.|.-+.--|...+..........++|.+.| .+|.++.++|+.+
T Consensus 148 ~l~~~~~ta~~~~~~~~~~~~~~vlI~g~g-~vg~~~~~~a~~~ 190 (344)
T cd08284 148 LLGDILPTGYFGAKRAQVRPGDTVAVIGCG-PVGLCAVLSAQVL 190 (344)
T ss_pred hhcCchHHHHhhhHhcCCccCCEEEEECCc-HHHHHHHHHHHHc
Confidence 344455556666655556666888888865 8999999998853
No 37
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=22.11 E-value=1.2e+02 Score=24.05 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=23.2
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
.|+-|- +.|++|..++.+|. .|+.|.|--
T Consensus 47 ~w~~v~----~fg~~Ae~v~~~l~------------KG~~V~V~G 75 (131)
T PRK07274 47 DFINVV----LWGKLAETLASYAS------------KGSLISIDG 75 (131)
T ss_pred EEEEEE----EehHHHHHHHHHcC------------CCCEEEEEE
Confidence 477665 45889999999999 899988753
No 38
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=21.66 E-value=1.1e+02 Score=25.85 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=24.0
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
.|+-|. +.|++|..++++|. .|+.|+|.-
T Consensus 52 ~w~~Vv----~fgk~AE~v~~~Lk------------KGs~V~VeG 80 (168)
T PRK06863 52 EWHRIV----FYRRQAEVAGEYLR------------KGSQVYVEG 80 (168)
T ss_pred eEEEEE----EEhHHHHHHHHHCC------------CCCEEEEEE
Confidence 488775 56889999999999 899998764
No 39
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=21.32 E-value=88 Score=25.55 Aligned_cols=23 Identities=26% Similarity=0.196 Sum_probs=20.0
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 39 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 39 vLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
+.|++|..++.+|. .||.|+|.-
T Consensus 60 ~wg~~Ae~v~~~l~------------KG~~V~V~G 82 (148)
T PRK08182 60 LWHRDAEHWARLYQ------------KGMRVLVEG 82 (148)
T ss_pred EEhHHHHHHHHhcC------------CCCEEEEEE
Confidence 67889999999999 899988764
No 40
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=21.13 E-value=1.1e+02 Score=26.09 Aligned_cols=29 Identities=17% Similarity=0.437 Sum_probs=23.2
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
.|+-|- +.|++|..++++|. .|+.|+|.-
T Consensus 54 ~w~~V~----~fgk~Ae~~~~~L~------------KGs~V~VeG 82 (177)
T PRK09010 54 EWHRVV----LFGKLAEVAGEYLR------------KGSQVYIEG 82 (177)
T ss_pred EEEEEE----EehhHHHHHHHhcC------------CCCEEEEEE
Confidence 476663 67789999999999 898888754
No 41
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.64 E-value=82 Score=25.93 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=23.0
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVN 73 (203)
.|+-|- +.|++|..++..|. .|+.|+|.-
T Consensus 51 ~~~~v~----~wg~~Ae~~~~~l~------------KG~~V~V~G 79 (164)
T TIGR00621 51 EWHDIV----IFGRLAEVAAQYLK------------KGSLVYVEG 79 (164)
T ss_pred eEEEEE----EehHHHHHHHHhCC------------CCCEEEEEE
Confidence 365554 67789999999999 999998754
No 42
>PF03447 NAD_binding_3: Homoserine dehydrogenase, NAD binding domain; InterPro: IPR005106 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Homoserine dehydrogenase (1.1.1.3 from EC) catalyses the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine [, ]. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116 from SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain []. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet. This entry represents the NAD(P)-binding domain of aspartate and homoserine dehydrogenase. Asparate dehydrogenase (1.4.1.21 from EC) is strictly specific for L-aspartate as substrate and catalyses the first step in NAD biosynthesis from aspartate. The enzyme has a higher affinity for NAD+ than NADP+ []. Note that the C terminus of the protein contributes a helix to this domain that is not covered by this model.; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 3ING_A 3MTJ_A 3DO5_A 3JSA_A 3C8M_A 1J5P_A 1H2H_A 2EJW_E 1TVE_A 1EBU_D ....
Probab=20.50 E-value=1.6e+02 Score=21.88 Aligned_cols=37 Identities=11% Similarity=0.096 Sum_probs=25.5
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccc
Q 028816 28 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDIC 78 (203)
Q Consensus 28 r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~ 78 (203)
+--+||||.+. .-++..+...|. .|-+||..|-.-+.
T Consensus 59 ~~dvvVE~t~~--~~~~~~~~~~L~------------~G~~VVt~nk~ala 95 (117)
T PF03447_consen 59 DIDVVVECTSS--EAVAEYYEKALE------------RGKHVVTANKGALA 95 (117)
T ss_dssp T-SEEEE-SSC--HHHHHHHHHHHH------------TTCEEEES-HHHHH
T ss_pred CCCEEEECCCc--hHHHHHHHHHHH------------CCCeEEEECHHHhh
Confidence 46799999665 556777888888 89899988855433
No 43
>TIGR00292 thiazole biosynthesis enzyme. This enzyme is involved in the biosynthesis of the thiamine precursor thiazole, and is repressed by thiamine.This family includes c-thi1, a Citrus gene induced during natural and ethylene induced fruit maturation and is highly homologous to plant and yeast thi genes involved in thiamine biosynthesis.
Probab=20.31 E-value=35 Score=29.87 Aligned_cols=48 Identities=19% Similarity=0.171 Sum_probs=29.4
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCE-EEEEeCccccccc
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDM-CIVLNAKDICVTG 81 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~-VVVVNaekI~iTG 81 (203)
--+||||+|+- +.+++.+++.+-.... +|.. .|.. .-+..+|+.++..
T Consensus 159 Ak~VVdATG~~-a~v~~~l~~~~~~~~~---~~~~-~g~~~~~~~~~e~~~~~~ 207 (254)
T TIGR00292 159 SRVVVDATGHD-AEIVAVCAKKIVLEDQ---VPKL-GGEKSMWAEVAEVAIHEN 207 (254)
T ss_pred cCEEEEeecCC-chHHHHHHHHcCcccC---Cccc-CCchhhhhhhhHHHHHhc
Confidence 35899999988 7999999988753321 1211 3332 2345556655543
No 44
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.21 E-value=87 Score=26.25 Aligned_cols=28 Identities=18% Similarity=0.577 Sum_probs=22.3
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEE
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 72 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVV 72 (203)
.||=|- +.|.+|..|+.+|. .|+.|+|-
T Consensus 52 ~w~~Vv----~fgk~Ae~v~~~L~------------KGs~V~Ve 79 (164)
T PRK08763 52 EWHRVK----FFGKLGEIAGEYLR------------KGSQCYIE 79 (164)
T ss_pred eEEEEE----EehHHHHHHHHhcC------------CCCEEEEE
Confidence 466554 56889999999999 89988774
No 45
>PF03621 MbtH: MbtH-like protein; InterPro: IPR005153 This domain is found in the MbtH protein O05821 from SWISSPROT as well as at the N terminus of the antibiotic synthesis protein NIKP1. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues. Many of the members of this family are found in known antibiotic synthesis gene clusters.; PDB: 2PST_X 2GPF_A 2LPD_A 2KHR_A.
Probab=20.13 E-value=71 Score=22.25 Aligned_cols=13 Identities=23% Similarity=0.657 Sum_probs=8.3
Q ss_pred CCCCEEEEEeCcc
Q 028816 64 DDGDMCIVLNAKD 76 (203)
Q Consensus 64 d~Gd~VVVVNaek 76 (203)
+.|.+.||||.+.
T Consensus 9 ~~~~f~VlvN~e~ 21 (54)
T PF03621_consen 9 EDGTFLVLVNDEG 21 (54)
T ss_dssp --S-EEEEEETT-
T ss_pred CCCeEEEEEcCCC
Confidence 4588999999875
No 46
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=20.10 E-value=1.4e+02 Score=25.14 Aligned_cols=28 Identities=14% Similarity=0.457 Sum_probs=23.3
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEE
Q 028816 29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 72 (203)
Q Consensus 29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVV 72 (203)
.|+-|. +.|++|..++.+|. .|+.|.|-
T Consensus 53 ~w~~Vv----~fgk~Ae~v~~~l~------------KGs~V~Ve 80 (172)
T PRK05733 53 EWHRVS----LFGKVAEIAGEYLR------------KGSQVYIE 80 (172)
T ss_pred eEEEEE----EehHHHHHHHHHhC------------CCCEEEEE
Confidence 588776 56789999999999 99998764
Done!