Query 029588
Match_columns 191
No_of_seqs 146 out of 1092
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 15:19:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029588hhsearch_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 1.2E-76 2.5E-81 496.2 14.9 190 2-191 1-191 (191)
2 CHL00159 rpl13 ribosomal prote 100.0 1.4E-59 3E-64 378.7 12.2 134 11-144 9-142 (143)
3 PRK09216 rplM 50S ribosomal pr 100.0 2.9E-59 6.4E-64 377.1 12.4 133 13-145 10-142 (144)
4 TIGR01066 rplM_bact ribosomal 100.0 4E-59 8.7E-64 374.8 11.7 133 12-144 7-139 (140)
5 COG0102 RplM Ribosomal protein 100.0 8.9E-57 1.9E-61 363.4 11.5 133 12-144 9-142 (148)
6 PF00572 Ribosomal_L13: Riboso 100.0 2.6E-56 5.6E-61 353.5 8.2 127 18-144 1-127 (128)
7 cd00392 Ribosomal_L13 Ribosoma 100.0 1.1E-53 2.4E-58 332.8 10.3 114 18-131 1-114 (114)
8 KOG3203 Mitochondrial/chloropl 100.0 5.2E-52 1.1E-56 337.3 6.8 128 10-137 15-142 (165)
9 PTZ00068 60S ribosomal protein 100.0 7.2E-44 1.6E-48 301.0 9.4 129 17-165 4-138 (202)
10 TIGR01077 L13_A_E ribosomal pr 100.0 7.5E-44 1.6E-48 286.9 9.0 131 19-165 1-132 (142)
11 PRK06394 rpl13p 50S ribosomal 100.0 4.6E-41 1E-45 271.9 9.6 130 17-166 3-137 (146)
12 KOG3204 60S ribosomal protein 99.9 2.2E-25 4.8E-30 187.2 3.7 128 16-165 5-133 (197)
13 PF04989 CmcI: Cephalosporin h 54.0 16 0.00035 31.5 3.5 44 9-68 104-151 (206)
14 PF12396 DUF3659: Protein of u 42.7 8 0.00017 27.5 -0.0 25 18-42 13-37 (64)
15 cd02885 IPP_Isomerase Isopente 38.5 37 0.0008 27.0 3.2 46 16-69 2-47 (165)
16 KOG3974 Predicted sugar kinase 35.3 18 0.00039 33.0 1.0 46 5-52 121-166 (306)
17 PRK03759 isopentenyl-diphospha 32.5 95 0.0021 25.2 4.8 44 16-67 6-50 (184)
18 PF00436 SSB: Single-strand bi 30.8 48 0.001 23.7 2.5 23 27-61 54-76 (104)
19 COG3499 Phage protein U [Gener 29.3 25 0.00054 29.0 0.8 26 4-29 66-91 (147)
20 PRK10026 arsenate reductase; P 26.3 1.2E+02 0.0025 24.6 4.2 57 4-64 81-137 (141)
21 COG0629 Ssb Single-stranded DN 26.0 69 0.0015 26.0 2.9 22 27-60 57-78 (167)
22 cd04496 SSB_OBF SSB_OBF: A sub 25.7 72 0.0016 22.4 2.6 31 15-61 42-72 (100)
23 PRK15393 NUDIX hydrolase YfcD; 25.6 88 0.0019 25.5 3.4 39 16-63 10-48 (180)
24 PRK05853 hypothetical protein; 25.0 67 0.0015 26.6 2.6 23 27-61 49-71 (161)
25 TIGR02150 IPP_isom_1 isopenten 24.8 51 0.0011 26.1 1.9 41 19-67 2-43 (158)
26 PHA02754 hypothetical protein; 24.6 51 0.0011 23.7 1.6 16 53-68 43-58 (67)
27 cd04195 GT2_AmsE_like GT2_AmsE 24.5 1.9E+02 0.0042 22.3 5.1 65 2-68 16-95 (201)
28 PRK07772 single-stranded DNA-b 23.7 71 0.0015 27.1 2.6 23 27-61 59-81 (186)
29 PF06088 TLP-20: Nucleopolyhed 23.6 50 0.0011 27.8 1.6 15 50-64 64-78 (169)
30 PF03447 NAD_binding_3: Homose 23.6 1.3E+02 0.0028 22.2 3.8 35 16-64 59-93 (117)
31 PRK06752 single-stranded DNA-b 23.3 72 0.0016 24.1 2.4 29 17-61 47-75 (112)
32 TIGR00292 thiazole biosynthesi 22.0 30 0.00065 30.0 -0.0 50 17-71 159-209 (254)
33 PRK09010 single-stranded DNA-b 22.0 1E+02 0.0022 25.9 3.1 30 16-61 53-82 (177)
34 PRK07274 single-stranded DNA-b 21.8 1.2E+02 0.0027 23.7 3.5 30 16-61 46-75 (131)
35 PRK06863 single-stranded DNA-b 21.7 1.1E+02 0.0024 25.4 3.3 30 16-61 51-80 (168)
36 KOG0422 Ubiquitin-protein liga 21.6 65 0.0014 26.8 1.9 19 46-64 74-94 (153)
37 PRK08182 single-stranded DNA-b 21.5 87 0.0019 25.3 2.6 23 27-61 60-82 (148)
38 PF04379 DUF525: Protein of un 21.3 41 0.0009 25.1 0.7 17 10-26 27-43 (90)
39 KOG0023 Alcohol dehydrogenase, 21.2 1.6E+02 0.0035 27.7 4.5 43 6-63 172-214 (360)
40 PRK05733 single-stranded DNA-b 21.0 1.4E+02 0.003 25.0 3.7 29 16-60 52-80 (172)
41 PF03621 MbtH: MbtH-like prote 20.9 68 0.0015 22.1 1.6 13 52-64 9-21 (54)
42 PRK09880 L-idonate 5-dehydroge 20.4 1.7E+02 0.0038 25.4 4.5 31 8-39 162-192 (343)
43 PRK08763 single-stranded DNA-b 20.3 87 0.0019 25.9 2.4 28 17-60 52-79 (164)
44 TIGR00621 ssb single stranded 20.1 86 0.0019 25.5 2.3 29 17-61 51-79 (164)
No 1
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=1.2e-76 Score=496.22 Aligned_cols=190 Identities=82% Similarity=1.313 Sum_probs=185.4
Q ss_pred hhhhhhhcccccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeec
Q 029588 2 QKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHT 81 (191)
Q Consensus 2 ~~~~~~~~~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hs 81 (191)
++|+|||.++++++++||||||+||+||||||.||++|+|||||+|||++||||+||||||++|.|||+||.+|.|++||
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCcceeccchhhhhcChHHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceecCCcchhccccccchhH
Q 029588 82 GYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAM 161 (191)
Q Consensus 82 gypgglk~~~~~~~~~r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~ 161 (191)
|||||+++++++++++++|++||++||+||||+|++|+.+|++|+||+|++|||++|+++++++||+.+|+|||+++|+|
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 029588 162 IREQKKAEMQQSN-KDMRKNRKKEVEAEVTA 191 (191)
Q Consensus 162 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 191 (191)
|+||+|+||+++. +.+++|++++++.|++|
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (191)
T PLN00205 161 IRAQKKAEQREQAANEKRKGKKKEVEVEVTA 191 (191)
T ss_pred HHHHHHHHHHHHHHhhhccccccccccccCC
Confidence 9999999999988 78888999988888765
No 2
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=1.4e-59 Score=378.73 Aligned_cols=134 Identities=40% Similarity=0.630 Sum_probs=129.5
Q ss_pred cccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceec
Q 029588 11 INLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKER 90 (191)
Q Consensus 11 ~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~ 90 (191)
.+...++|+||||+||+||||||.||++|+|||||+|||++||||+||||||++|.|||+||.+|.|++|||||||++++
T Consensus 9 ~~~~~r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~kv~~TG~K~~~K~y~~htg~pGg~k~~ 88 (143)
T CHL00159 9 KDYKNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFYVRHSGRPGGLKIE 88 (143)
T ss_pred chhcCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEecceeEEeCchhhheEEEecCCCCCCcccc
Confidence 34557899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhcChHHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 029588 91 TLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 144 (191)
Q Consensus 91 ~~~~~~~r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~ 144 (191)
+++++++++|++||++||+||||+|.+|+.+|++|+||+|++|||++|+|++++
T Consensus 89 ~~~~~~~r~P~~il~~aV~gMLPkn~lgr~~~~rLkvy~G~~hph~aq~p~~~~ 142 (143)
T CHL00159 89 TFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHPHVAQKPIKIN 142 (143)
T ss_pred cHHHHhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCccccCCeecC
Confidence 999999999999999999999999999999999999999999999999997665
No 3
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=2.9e-59 Score=377.14 Aligned_cols=133 Identities=45% Similarity=0.788 Sum_probs=129.3
Q ss_pred cCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceeccc
Q 029588 13 LEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTL 92 (191)
Q Consensus 13 ~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~~ 92 (191)
..+++|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|.|||++|.+|.||+|||||||++++++
T Consensus 10 ~~~~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pGglk~~~~ 89 (144)
T PRK09216 10 EVERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYRHSGYPGGLKEITF 89 (144)
T ss_pred hcCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCceeEEcCchHhheeeEEecccCCCCEEecH
Confidence 34689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhcChHHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 029588 93 KEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM 145 (191)
Q Consensus 93 ~~~~~r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~~ 145 (191)
+++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.+++
T Consensus 90 ~~~~~r~P~~il~~aVrgMLPkn~lgr~~~~rLkvy~G~~hp~~~q~p~~~~~ 142 (144)
T PRK09216 90 GELLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHPHAAQQPEVLEI 142 (144)
T ss_pred HHHhhhCHHHHHHHHHHhcCCCCccHHHHHhCcEEeCCCCCCccccCCEeccc
Confidence 99999999999999999999999999999999999999999999999987774
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=4e-59 Score=374.83 Aligned_cols=133 Identities=45% Similarity=0.765 Sum_probs=128.9
Q ss_pred ccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceecc
Q 029588 12 NLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT 91 (191)
Q Consensus 12 ~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~ 91 (191)
++..++|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|.|||++|++|.||+|||||||+++++
T Consensus 7 ~~~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pgg~k~~~ 86 (140)
T TIGR01066 7 DDKKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYRHSGYPGGLKSRT 86 (140)
T ss_pred hhhcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEEEEeCchhhceeeEEEcccCCcccccc
Confidence 44578999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhhcChHHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 029588 92 LKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 144 (191)
Q Consensus 92 ~~~~~~r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~ 144 (191)
++++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.++
T Consensus 87 ~~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkvy~G~~hp~~~q~p~~~~ 139 (140)
T TIGR01066 87 FEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPHEAQKPIVLD 139 (140)
T ss_pred HHHhhhcCHHHHHHHHHHhcCCCCccHHHHHhCeEEeCCCCCChhhcCCeecC
Confidence 99999999999999999999999999999999999999999999999987665
No 5
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-57 Score=363.38 Aligned_cols=133 Identities=42% Similarity=0.730 Sum_probs=126.6
Q ss_pred ccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceecc
Q 029588 12 NLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT 91 (191)
Q Consensus 12 ~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~ 91 (191)
....++|+||||+|++||||||.||+.|+|||||+||||+||||+|||||||+|+|||+|..+|.||+|||||||+++.+
T Consensus 9 ~~~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~hs~~~gglk~~t 88 (148)
T COG0102 9 SEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYRHSGYPGGLKNPT 88 (148)
T ss_pred ccccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceeeEEecccccceEEEEeeccCCcccccc
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhh-cChHHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 029588 92 LKEQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 144 (191)
Q Consensus 92 ~~~~~~-r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~ 144 (191)
++.+.. +.|++||++||+||||+|.+++++|++|+||.|+||||.+|+|+.+.
T Consensus 89 ~~~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~aq~p~~l~ 142 (148)
T COG0102 89 RGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHEAQKPEALE 142 (148)
T ss_pred cccccccCCHHHHHHHHHhccCCCChhHHHHHhCceEecCCCCccccccchhhh
Confidence 966665 99999999999999999999999999999999999999999886554
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=2.6e-56 Score=353.49 Aligned_cols=127 Identities=48% Similarity=0.834 Sum_probs=124.5
Q ss_pred EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceeccchhhhh
Q 029588 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQME 97 (191)
Q Consensus 18 W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~~~~~~~ 97 (191)
|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|.|||++|.+|.|++|||||||++..+++.+++
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 029588 98 RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV 144 (191)
Q Consensus 98 r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~ 144 (191)
++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+++.++
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 99999999999999999999999999999999999999999987665
No 7
>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=1.1e-53 Score=332.78 Aligned_cols=114 Identities=50% Similarity=0.849 Sum_probs=112.9
Q ss_pred EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceeccchhhhh
Q 029588 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQME 97 (191)
Q Consensus 18 W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~~~~~~~ 97 (191)
|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|.|||++|.+|.||+||||||++++.+++++++
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 029588 98 RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 131 (191)
Q Consensus 98 r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~ 131 (191)
++|++||++||+||||+|.+|+.+|+||+||+|+
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 8
>KOG3203 consensus Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-52 Score=337.27 Aligned_cols=128 Identities=47% Similarity=0.731 Sum_probs=122.9
Q ss_pred ccccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCccee
Q 029588 10 RINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKE 89 (191)
Q Consensus 10 ~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~ 89 (191)
.+...+|.|+||||++|+||||||+||..|+|||||+|||+.||||+|||+||++|.|||+||.+|+|++|||||||++.
T Consensus 15 ~~~afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K~~qk~Y~~HsGyPG~lk~ 94 (165)
T KOG3203|consen 15 QWLAFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWEQKIYRSHSGYPGGLKQ 94 (165)
T ss_pred HHHHHhhhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhheeccchhhhhhhhhcCCCCCchhh
Confidence 45556688999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccchhhhhcChHHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCC
Q 029588 90 RTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 137 (191)
Q Consensus 90 ~~~~~~~~r~P~~Il~rAVrGMLPkn~~r~~~l~rLkvy~G~~hp~~~ 137 (191)
.+...++.++|++|+++||+||||+|.+|+..|++|+||+|.+||+..
T Consensus 95 ~~~~q~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p~~~ 142 (165)
T KOG3203|consen 95 TTADQLADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHPEKV 142 (165)
T ss_pred hHHHHHhhhCHHHHHHHHHHhhCccchHHHHHhheeeccCCccCchhh
Confidence 889999999999999999999999999999999999999999999765
No 9
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=7.2e-44 Score=301.00 Aligned_cols=129 Identities=30% Similarity=0.462 Sum_probs=118.7
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceecc-----
Q 029588 17 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT----- 91 (191)
Q Consensus 17 ~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~----- 91 (191)
+|+||||+||+||||||.||+.|+ |||+|||||||+|+|||+++++|.||+| +++.++
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 chhhhhcChHHHHHHHHhccCCC-CCchhhhhcCceecCCCCCCCCCCCCcceecCCcchhccccccchhHHHHH
Q 029588 92 LKEQMERDPTEAIRKAVLRMLPR-NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ 165 (191)
Q Consensus 92 ~~~~~~r~P~~Il~rAVrGMLPk-n~~r~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~ 165 (191)
.++++++.|++||++||+||||+ +.+|+.+|+||+||+|+||||++++. +..|.++|++|+.|+|.||+.-
T Consensus 67 ~g~~~~r~P~~Il~raVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~---~vvp~A~r~~rl~~~~ky~~lg 138 (202)
T PTZ00068 67 RGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKR---VVIPSALRVLRLKPERPYTVLG 138 (202)
T ss_pred cchhcccCHHHHHHHHHhhhCCCCChhHHHHHhCCEEecCCCCchhccCc---ccccchhhhhccCCCCceeeHH
Confidence 48999999999999999999998 55777899999999999999999965 4589999999999999888653
No 10
>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=7.5e-44 Score=286.91 Aligned_cols=131 Identities=27% Similarity=0.387 Sum_probs=117.6
Q ss_pred EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceeccchhhhhc
Q 029588 19 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMER 98 (191)
Q Consensus 19 ~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~~~~~~~r 98 (191)
+||||+||+||||||.||+.|+ |||+|||||||+|.|||+++.+|.||+||+++|.....++++++++
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 9999999999999999999999999999966555555588999999
Q ss_pred ChHHHHHHHHhccCCCC-CchhhhhcCceecCCCCCCCCCCCCcceecCCcchhccccccchhHHHHH
Q 029588 99 DPTEAIRKAVLRMLPRN-KLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ 165 (191)
Q Consensus 99 ~P~~Il~rAVrGMLPkn-~~r~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~ 165 (191)
+|++||++||+||||+| .+|+.+|+||+||+|+||||++|+++ + .|.++ ..|+.+.|++|.+-
T Consensus 69 ~P~~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~~h~~~~qk~~--~-~~~a~-~~~~~~~~~~~~lg 132 (142)
T TIGR01077 69 APSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRV--V-VPEAL-VSRLSPTRKYVTLG 132 (142)
T ss_pred CHHHHHHHHHHHhCCCCChhHHHHHhCcEEecCCCCCccccCcc--c-cChhh-hhccCCCCceEEHH
Confidence 99999999999999998 56678999999999999999999874 3 55666 78899999887654
No 11
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00 E-value=4.6e-41 Score=271.85 Aligned_cols=130 Identities=21% Similarity=0.295 Sum_probs=110.7
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceec----cc
Q 029588 17 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKER----TL 92 (191)
Q Consensus 17 ~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~----~~ 92 (191)
.-+||||+||+||||||.||++|+ +||+||||||++|.+||+|+.+ |++|++|+ +++.. ++
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 44555566 45555 78
Q ss_pred hhhhhcChHHHHHHHHhccCC-CCCchhhhhcCceecCCCCCCCCCCCCcceecCCcchhccccccchhHHHHHH
Q 029588 93 KEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQK 166 (191)
Q Consensus 93 ~~~~~r~P~~Il~rAVrGMLP-kn~~r~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~ 166 (191)
+++++++|++||++||+|||| +|.+++.+|+||+||+|+||||++|+++.+.+ +++ .++. .|.+|+.-+
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 78888899999999999999999998865543 444 3555 577877643
No 12
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=2.2e-25 Score=187.24 Aligned_cols=128 Identities=25% Similarity=0.403 Sum_probs=112.9
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccCccccceeEeeecccCCcceeccchhh
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQ 95 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG~K~~~K~Y~~hsgypgglk~~~~~~~ 95 (191)
..-.+||+.||++|||||.||+.|+ .|+.||||.||.|.+||+.|++|.| .+..-. ..+++
T Consensus 5 ~~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~------lrk~~~-~ng~~ 65 (197)
T KOG3204|consen 5 VKLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLF------LRKRLN-RNGPF 65 (197)
T ss_pred EEEeeccchhhhhhhHHHHHHHHHh------------cCCeEEEEEEeEEEEecceecchHH------Hhhhhc-ccCcc
Confidence 3568999999999999999999999 9999999999999999999999844 332211 23999
Q ss_pred hhcChHHHHHHHHhccCCCCCchh-hhhcCceecCCCCCCCCCCCCcceecCCcchhccccccchhHHHHH
Q 029588 96 MERDPTEAIRKAVLRMLPRNKLRD-DRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ 165 (191)
Q Consensus 96 ~~r~P~~Il~rAVrGMLPkn~~r~-~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~ 165 (191)
|++-|++||+++|+||+|+++.++ .++++|.+|+|.|+|++.+++ ...|.+++++|+.|.+++|..=
T Consensus 66 hfr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r---~v~p~a~~v~~lk~~~K~c~lG 133 (197)
T KOG3204|consen 66 HFRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKR---LVVPVAFQVLRLKPYKKYCLLG 133 (197)
T ss_pred hhhhHHHHHHHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCC---ccCCcceeeecccCCceeEEec
Confidence 999999999999999999998877 579999999999999999976 4589999999999999998654
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=54.03 E-value=16 Score=31.50 Aligned_cols=44 Identities=25% Similarity=0.274 Sum_probs=24.9
Q ss_pred cccccCCceEEEEeCC----CCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeccccccc
Q 029588 9 RRINLEGLRWRVFDAK----GQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVT 68 (191)
Q Consensus 9 ~~~~~~~r~W~vIDA~----gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vT 68 (191)
+.+......|+|||-. .++++-|.. .+.++. .|+|+|| |+..+.
T Consensus 104 ~~~~~~~~~vlVilDs~H~~~hvl~eL~~-y~plv~------------~G~Y~IV---eDt~~~ 151 (206)
T PF04989_consen 104 RELASPPHPVLVILDSSHTHEHVLAELEA-YAPLVS------------PGSYLIV---EDTIIE 151 (206)
T ss_dssp GSS----SSEEEEESS----SSHHHHHHH-HHHT--------------TT-EEEE---TSHHHH
T ss_pred HHhhccCCceEEEECCCccHHHHHHHHHH-hCccCC------------CCCEEEE---Eecccc
Confidence 3344446788888754 567777766 566565 9999998 454444
No 14
>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=42.67 E-value=8 Score=27.54 Aligned_cols=25 Identities=32% Similarity=0.474 Sum_probs=22.9
Q ss_pred EEEEeCCCCcchhhHHHHHHHHhCC
Q 029588 18 WRVFDAKGQVLGRLASQVATVVQGK 42 (191)
Q Consensus 18 W~vIDA~gqiLGRLAS~VAk~L~GK 42 (191)
=.|+|.+|.++|||..--++.|.|+
T Consensus 13 G~V~d~~G~~vG~vveGd~k~L~G~ 37 (64)
T PF12396_consen 13 GNVVDDDGNVVGRVVEGDPKKLVGK 37 (64)
T ss_pred CeEECCCCCEEEEEecCCHHHhcCC
Confidence 3689999999999999999999987
No 15
>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=38.54 E-value=37 Score=26.95 Aligned_cols=46 Identities=11% Similarity=0.008 Sum_probs=26.6
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecccccccC
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTG 69 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaekI~vTG 69 (191)
..|-|+|..|+++|.-.-..+....+- |+ ..-.|+|+|.+.-++-+
T Consensus 2 e~~~~~d~~~~~~g~~~r~~~~~~~~~----~~----~~v~v~i~~~~~~iLl~ 47 (165)
T cd02885 2 ELVILVDEDDNPIGTAEKLEAHLKGTL----LH----RAFSVFLFNSKGRLLLQ 47 (165)
T ss_pred cEEEEECCCCCCccccCHHHHhhcCCc----ce----eEEEEEEEcCCCcEEEE
Confidence 468999999999996444444333321 11 12237778865333333
No 16
>KOG3974 consensus Predicted sugar kinase [Carbohydrate transport and metabolism]
Probab=35.31 E-value=18 Score=32.98 Aligned_cols=46 Identities=20% Similarity=0.077 Sum_probs=34.4
Q ss_pred hhhhcccccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCC
Q 029588 5 LAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRD 52 (191)
Q Consensus 5 ~~~~~~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d 52 (191)
++.+.........-+||||+|-- -++....+.+.|-++.+-|||+.
T Consensus 121 i~~iley~~~~dvP~VIDaDGL~--Lv~q~~e~l~~~~~~viLTPNvv 166 (306)
T KOG3974|consen 121 IAKILEYLRGKDVPLVIDADGLW--LVEQLPERLIGGYPKVILTPNVV 166 (306)
T ss_pred HHHHHHHHhcCCCcEEEcCCceE--ehhhchhhhhccCceeeeCCcHH
Confidence 44444444555778999999954 46666777999999999999974
No 17
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=32.53 E-value=95 Score=25.20 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=29.7
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecc-cccc
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK-DICV 67 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNae-kI~v 67 (191)
..|.|+|..|..+|+.....+....|. |++. -.|+|+|.+ +|.+
T Consensus 6 E~~~~vd~~~~~~g~~~r~~~~~~~~~----~h~a----v~v~i~~~~g~vLL 50 (184)
T PRK03759 6 ELVVLLDEQGVPTGTAEKAAAHTADTP----LHLA----FSCYLFDADGRLLV 50 (184)
T ss_pred eeEEEECCCCCCcccccHHHHHhcCCC----eeeE----EEEEEEcCCCeEEE
Confidence 569999999999999888877644444 3332 236677754 3444
No 18
>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=30.77 E-value=48 Score=23.71 Aligned_cols=23 Identities=35% Similarity=0.498 Sum_probs=16.3
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 27 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 27 iLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
+.|.+|..++..|. .||.|.|.-
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 899887753
No 19
>COG3499 Phage protein U [General function prediction only]
Probab=29.31 E-value=25 Score=29.05 Aligned_cols=26 Identities=27% Similarity=0.519 Sum_probs=22.1
Q ss_pred hhhhhcccccCCceEEEEeCCCCcch
Q 029588 4 ALAGLRRINLEGLRWRVFDAKGQVLG 29 (191)
Q Consensus 4 ~~~~~~~~~~~~r~W~vIDA~gqiLG 29 (191)
-+.+|++....+..|.+||+.|++.|
T Consensus 66 sL~aL~a~A~~G~p~~Li~G~G~i~G 91 (147)
T COG3499 66 SLDALRALAETGTPLPLIDGDGAIYG 91 (147)
T ss_pred HHHHHHHHHhcCCceEEEcCCceEEE
Confidence 36788888889999999999999844
No 20
>PRK10026 arsenate reductase; Provisional
Probab=26.33 E-value=1.2e+02 Score=24.57 Aligned_cols=57 Identities=16% Similarity=0.106 Sum_probs=37.7
Q ss_pred hhhhhcccccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeccc
Q 029588 4 ALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKD 64 (191)
Q Consensus 4 ~~~~~~~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaek 64 (191)
+++-|.....-=+.-+|+|..|.++||=...|-.+| ++. |.-.-..+.|..+ +|+..
T Consensus 81 ~l~ll~~~P~LIKRPIi~~~~~a~i~Rp~e~v~~~l-~~~-~~~~~~~~~~~~~--~~~~~ 137 (141)
T PRK10026 81 LIDFMLQHPILINRPIVVTPLGTRLCRPSEVVLEIL-PDA-QKGAFTKEDGEKV--VDEAG 137 (141)
T ss_pred HHHHHHhCccceeCcEEEcCCCeEEECCHHHHHHHh-ccc-ccccccccCCeEe--ecCCC
Confidence 333343333333567999999999999666666665 765 6666666778766 77654
No 21
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=26.02 E-value=69 Score=25.98 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=19.4
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEE
Q 029588 27 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 60 (191)
Q Consensus 27 iLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVV 60 (191)
+.|++|..++.+|. .|+.|+|.
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 79988875
No 22
>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=25.74 E-value=72 Score=22.44 Aligned_cols=31 Identities=29% Similarity=0.488 Sum_probs=23.3
Q ss_pred CceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 15 GLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 15 ~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
...|+=|-+ .|.+|..+++.|. .||.|+|.-
T Consensus 42 ~~~~~~v~~----~g~~a~~~~~~~~------------kG~~V~v~G 72 (100)
T cd04496 42 ETDWIRVVA----FGKLAENAAKYLK------------KGDLVYVEG 72 (100)
T ss_pred ccEEEEEEE----EhHHHHHHHHHhC------------CCCEEEEEE
Confidence 345665554 5569999999999 899998764
No 23
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=25.60 E-value=88 Score=25.45 Aligned_cols=39 Identities=8% Similarity=0.080 Sum_probs=26.7
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecc
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK 63 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNae 63 (191)
.-|.|+|..|+++|......+.. .|- ++ .+-.|+|+|.+
T Consensus 10 e~~~~~d~~~~~~g~~~~~~~~~-~~~----~h----~~~~v~v~~~~ 48 (180)
T PRK15393 10 EWVDIVNENNEVIAQASREQMRA-QCL----RH----RATYIVVHDGM 48 (180)
T ss_pred eEEEEECCCCCEeeEEEHHHHhh-CCC----ce----EEEEEEEECCC
Confidence 45999999999999986555542 221 22 24578888864
No 24
>PRK05853 hypothetical protein; Validated
Probab=24.99 E-value=67 Score=26.58 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=20.3
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 27 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 27 iLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
+.|++|..++++|. .|+.|+|.-
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 67889999999998 899998864
No 25
>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=24.80 E-value=51 Score=26.10 Aligned_cols=41 Identities=7% Similarity=0.148 Sum_probs=27.6
Q ss_pred EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecc-cccc
Q 029588 19 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK-DICV 67 (191)
Q Consensus 19 ~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNae-kI~v 67 (191)
.|+|..|+.+|+.....+....|- ||. +-.|+|+|.+ +|.+
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 222 3348888875 4444
No 26
>PHA02754 hypothetical protein; Provisional
Probab=24.57 E-value=51 Score=23.66 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=13.7
Q ss_pred CCCEEEEEeccccccc
Q 029588 53 DGDMCIVLNAKDICVT 68 (191)
Q Consensus 53 ~Gd~VVVVNaekI~vT 68 (191)
.||++|||-|+.|.+.
T Consensus 43 SGdkIVVi~aD~I~i~ 58 (67)
T PHA02754 43 SGDKIVVITADAIKIE 58 (67)
T ss_pred cCCEEEEEEcceEEEE
Confidence 5999999999988763
No 27
>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=24.50 E-value=1.9e+02 Score=22.26 Aligned_cols=65 Identities=15% Similarity=0.135 Sum_probs=35.9
Q ss_pred hhhhhhhcccccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCC-CCCC--------------CCCCEEEEEeccccc
Q 029588 2 QKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTY-APNR--------------DDGDMCIVLNAKDIC 66 (191)
Q Consensus 2 ~~~~~~~~~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y-~P~~--------------d~Gd~VVVVNaekI~ 66 (191)
.+++.++..+.+....++|||- |..-......+..+.. +....+ +... ..||+|++++++.+.
T Consensus 16 ~~~l~Sl~~q~~~~~eiiivdd-~ss~d~t~~~~~~~~~-~~~i~~i~~~~n~G~~~a~N~g~~~a~gd~i~~lD~Dd~~ 93 (201)
T cd04195 16 REALESILKQTLPPDEVVLVKD-GPVTQSLNEVLEEFKR-KLPLKVVPLEKNRGLGKALNEGLKHCTYDWVARMDTDDIS 93 (201)
T ss_pred HHHHHHHHhcCCCCcEEEEEEC-CCCchhHHHHHHHHHh-cCCeEEEEcCccccHHHHHHHHHHhcCCCEEEEeCCcccc
Confidence 4567777777766677888874 3222344444443322 222222 1111 147999999988875
Q ss_pred cc
Q 029588 67 VT 68 (191)
Q Consensus 67 vT 68 (191)
..
T Consensus 94 ~~ 95 (201)
T cd04195 94 LP 95 (201)
T ss_pred Cc
Confidence 54
No 28
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=23.73 E-value=71 Score=27.07 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=20.1
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 27 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 27 iLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
+.|.+|..||..|. .||.|+|.=
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 29
>PF06088 TLP-20: Nucleopolyhedrovirus telokin-like protein-20 (TLP20); InterPro: IPR009092 The baculovirus, Autographa californica nuclear polyhedrosis virus (AcMNPV), telokin-like protein (Tlp20) lies in a region of the baculoviral genome that is expressed late in the viral replication cycle, however its function is unknown. Tlp20 was discovered using anti-telokin antibodies, telokin being the C-terminal domain of smooth-muscle myosin light-chain kinase []. Both Tlp20 and telokin display a seven-stranded antiparallel beta-barrel structure, although the 3-dimensional structures of the beta-barrels are different and there is no sequence homology between the two. Tlp20 is structurally similar to dUTPase in its fold and trimeric assembly [].; PDB: 1TUL_A.
Probab=23.56 E-value=50 Score=27.84 Aligned_cols=15 Identities=27% Similarity=0.344 Sum_probs=10.9
Q ss_pred CCCCCCEEEEEeccc
Q 029588 50 NRDDGDMCIVLNAKD 64 (191)
Q Consensus 50 ~~d~Gd~VVVVNaek 64 (191)
.+.||||||+.|+-.
T Consensus 64 ~v~~gdY~V~~N~~~ 78 (169)
T PF06088_consen 64 TVTCGDYVVVYNFVE 78 (169)
T ss_dssp EEESSSEEEEEE--S
T ss_pred EEecCCEEEEEEeec
Confidence 456999999999766
No 30
>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=23.55 E-value=1.3e+02 Score=22.16 Aligned_cols=35 Identities=11% Similarity=0.070 Sum_probs=24.1
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeccc
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKD 64 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNaek 64 (191)
..-+||||.+. .-++..+...|. .|-+||..|-.=
T Consensus 59 ~~dvvVE~t~~--~~~~~~~~~~L~------------~G~~VVt~nk~a 93 (117)
T PF03447_consen 59 DIDVVVECTSS--EAVAEYYEKALE------------RGKHVVTANKGA 93 (117)
T ss_dssp T-SEEEE-SSC--HHHHHHHHHHHH------------TTCEEEES-HHH
T ss_pred CCCEEEECCCc--hHHHHHHHHHHH------------CCCeEEEECHHH
Confidence 45699999665 456677788888 898999888543
No 31
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=23.31 E-value=72 Score=24.12 Aligned_cols=29 Identities=14% Similarity=0.134 Sum_probs=22.4
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 17 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 17 ~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
.|+-+- +.|++|..++.+|. .||.|.|.-
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 465543 67789999999988 899988753
No 32
>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=22.01 E-value=30 Score=29.97 Aligned_cols=50 Identities=18% Similarity=0.181 Sum_probs=30.7
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCE-EEEEecccccccCcc
Q 029588 17 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDM-CIVLNAKDICVTGRK 71 (191)
Q Consensus 17 ~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~-VVVVNaekI~vTG~K 71 (191)
--+||||+|+- +.+++.+++.+-.... +|.. .|.. .-...+|+.++...+
T Consensus 159 Ak~VVdATG~~-a~v~~~l~~~~~~~~~---~~~~-~g~~~~~~~~~e~~~~~~t~ 209 (254)
T TIGR00292 159 SRVVVDATGHD-AEIVAVCAKKIVLEDQ---VPKL-GGEKSMWAEVAEVAIHENTR 209 (254)
T ss_pred cCEEEEeecCC-chHHHHHHHHcCcccC---Cccc-CCchhhhhhhhHHHHHhccC
Confidence 35899999987 7999999998753332 1111 3333 334556666664443
No 33
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=21.99 E-value=1e+02 Score=25.94 Aligned_cols=30 Identities=17% Similarity=0.408 Sum_probs=23.6
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
-.|+-|- +.|++|..++.+|. .|+.|.|.-
T Consensus 53 t~w~~V~----~fgk~Ae~~~~~L~------------KGs~V~VeG 82 (177)
T PRK09010 53 TEWHRVV----LFGKLAEVAGEYLR------------KGSQVYIEG 82 (177)
T ss_pred eEEEEEE----EehhHHHHHHHhcC------------CCCEEEEEE
Confidence 3576663 67789999999999 899888754
No 34
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=21.84 E-value=1.2e+02 Score=23.70 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=23.5
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
-.|+-|- +.|++|..++.+|. .|+.|.|--
T Consensus 46 t~w~~v~----~fg~~Ae~v~~~l~------------KG~~V~V~G 75 (131)
T PRK07274 46 ADFINVV----LWGKLAETLASYAS------------KGSLISIDG 75 (131)
T ss_pred EEEEEEE----EehHHHHHHHHHcC------------CCCEEEEEE
Confidence 3577665 45889999999999 899988753
No 35
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=21.72 E-value=1.1e+02 Score=25.44 Aligned_cols=30 Identities=17% Similarity=0.256 Sum_probs=24.3
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
-.|+-|. +.|++|..++++|. .|+.|+|.-
T Consensus 51 t~w~~Vv----~fgk~AE~v~~~Lk------------KGs~V~VeG 80 (168)
T PRK06863 51 TEWHRIV----FYRRQAEVAGEYLR------------KGSQVYVEG 80 (168)
T ss_pred ceEEEEE----EEhHHHHHHHHHCC------------CCCEEEEEE
Confidence 3588775 57889999999998 899998854
No 36
>KOG0422 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.62 E-value=65 Score=26.76 Aligned_cols=19 Identities=37% Similarity=1.038 Sum_probs=13.9
Q ss_pred CCCCCCCC-CCEEE-EEeccc
Q 029588 46 TYAPNRDD-GDMCI-VLNAKD 64 (191)
Q Consensus 46 ~y~P~~d~-Gd~VV-VVNaek 64 (191)
+||||+|. |+.++ ||-+|+
T Consensus 74 iYHpNVDe~gqvClPiis~En 94 (153)
T KOG0422|consen 74 IYHPNVDEKGQVCLPIISAEN 94 (153)
T ss_pred eccCCCCCCCceeeeeeeccc
Confidence 79999987 77765 555554
No 37
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=21.48 E-value=87 Score=25.28 Aligned_cols=23 Identities=26% Similarity=0.196 Sum_probs=19.9
Q ss_pred cchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 27 VLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 27 iLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
+.|++|..++.+|. .||.|.|.-
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 899998764
No 38
>PF04379 DUF525: Protein of unknown function (DUF525); InterPro: IPR007474 This domain is found in the bacterial protein ApaG and at the C termini of some F-box proteins (IPR001810 from INTERPRO). F-box proteins contain a carboxy-terminal domain that interacts with protein substrates []. The ApaG domain is ~125 amino acids in length, and is named after the bacterial ApaG protein, of which it forms the core. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several beta-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [, , ].; PDB: 2F1E_A 1XVS_A 1TZA_A 1XQ4_D.
Probab=21.34 E-value=41 Score=25.15 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=12.8
Q ss_pred ccccCCceEEEEeCCCC
Q 029588 10 RINLEGLRWRVFDAKGQ 26 (191)
Q Consensus 10 ~~~~~~r~W~vIDA~gq 26 (191)
.+.+-+|.|.|.|+.|+
T Consensus 27 ~vqL~sR~W~I~d~~g~ 43 (90)
T PF04379_consen 27 SVQLLSRHWIITDADGH 43 (90)
T ss_dssp -EEEEEEEEEEEETTS-
T ss_pred CEEEEccEEEEEeCCCC
Confidence 45567899999999985
No 39
>KOG0023 consensus Alcohol dehydrogenase, class V [Secondary metabolites biosynthesis, transport and catabolism]
Probab=21.17 E-value=1.6e+02 Score=27.72 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=35.1
Q ss_pred hhhcccccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEecc
Q 029588 6 AGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAK 63 (191)
Q Consensus 6 ~~~~~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVNae 63 (191)
+.|.+.+....+|+-|-+-|= ||.+|.+.|+. .|-+|++|-..
T Consensus 172 spLk~~g~~pG~~vgI~GlGG-LGh~aVq~AKA--------------MG~rV~vis~~ 214 (360)
T KOG0023|consen 172 SPLKRSGLGPGKWVGIVGLGG-LGHMAVQYAKA--------------MGMRVTVISTS 214 (360)
T ss_pred ehhHHcCCCCCcEEEEecCcc-cchHHHHHHHH--------------hCcEEEEEeCC
Confidence 346677777889999998887 99999999994 47889998743
No 40
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=20.98 E-value=1.4e+02 Score=24.99 Aligned_cols=29 Identities=14% Similarity=0.426 Sum_probs=23.6
Q ss_pred ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEE
Q 029588 16 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 60 (191)
Q Consensus 16 r~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVV 60 (191)
-.|+-|. +.|++|..++.+|. .|+.|.|-
T Consensus 52 T~w~~Vv----~fgk~Ae~v~~~l~------------KGs~V~Ve 80 (172)
T PRK05733 52 TEWHRVS----LFGKVAEIAGEYLR------------KGSQVYIE 80 (172)
T ss_pred ceEEEEE----EehHHHHHHHHHhC------------CCCEEEEE
Confidence 3577776 56789999999999 89998774
No 41
>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=20.87 E-value=68 Score=22.06 Aligned_cols=13 Identities=23% Similarity=0.657 Sum_probs=8.4
Q ss_pred CCCCEEEEEeccc
Q 029588 52 DDGDMCIVLNAKD 64 (191)
Q Consensus 52 d~Gd~VVVVNaek 64 (191)
+.|.+.||||.+.
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 4589999999875
No 42
>PRK09880 L-idonate 5-dehydrogenase; Provisional
Probab=20.39 E-value=1.7e+02 Score=25.39 Aligned_cols=31 Identities=10% Similarity=0.035 Sum_probs=22.5
Q ss_pred hcccccCCceEEEEeCCCCcchhhHHHHHHHH
Q 029588 8 LRRINLEGLRWRVFDAKGQVLGRLASQVATVV 39 (191)
Q Consensus 8 ~~~~~~~~r~W~vIDA~gqiLGRLAS~VAk~L 39 (191)
+.+......++++|-+.| .+|.+|.++|+.+
T Consensus 162 l~~~~~~~g~~VlV~G~G-~vG~~aiqlak~~ 192 (343)
T PRK09880 162 AHQAGDLQGKRVFVSGVG-PIGCLIVAAVKTL 192 (343)
T ss_pred HHhcCCCCCCEEEEECCC-HHHHHHHHHHHHc
Confidence 433333345788888876 8999999999964
No 43
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.29 E-value=87 Score=25.95 Aligned_cols=28 Identities=18% Similarity=0.577 Sum_probs=22.2
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEE
Q 029588 17 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 60 (191)
Q Consensus 17 ~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVV 60 (191)
.||=|- +.|.+|..|+.+|. .|+.|+|-
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 56889999999998 89988774
No 44
>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=20.07 E-value=86 Score=25.51 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=23.0
Q ss_pred eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEe
Q 029588 17 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61 (191)
Q Consensus 17 ~W~vIDA~gqiLGRLAS~VAk~L~GKhKp~y~P~~d~Gd~VVVVN 61 (191)
.|+=|- +.|++|..++..|. .|+.|+|.-
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 67889999999998 899998754
Done!