Query 030391
Match_columns 178
No_of_seqs 145 out of 1107
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 13:01:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030391.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030391hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00159 rpl13 ribosomal prote 100.0 1E-64 2.2E-69 403.7 14.4 143 24-169 1-143 (143)
2 PRK09216 rplM 50S ribosomal pr 100.0 8.1E-64 1.8E-68 398.9 13.3 143 25-170 1-143 (144)
3 TIGR01066 rplM_bact ribosomal 100.0 5.7E-62 1.2E-66 386.7 13.4 133 37-169 8-140 (140)
4 COG0102 RplM Ribosomal protein 100.0 1.3E-61 2.9E-66 386.7 12.5 143 25-170 1-144 (148)
5 PLN00205 ribisomal protein L13 100.0 5.5E-58 1.2E-62 379.1 13.9 138 38-175 13-150 (191)
6 PF00572 Ribosomal_L13: Riboso 100.0 3.5E-58 7.5E-63 359.9 8.1 127 42-168 1-127 (128)
7 cd00392 Ribosomal_L13 Ribosoma 100.0 4.8E-55 1E-59 336.4 11.2 114 42-155 1-114 (114)
8 KOG3203 Mitochondrial/chloropl 100.0 3.2E-55 6.9E-60 351.6 7.2 141 36-176 17-163 (165)
9 TIGR01077 L13_A_E ribosomal pr 100.0 8.3E-45 1.8E-49 289.0 10.6 117 43-171 1-118 (142)
10 PTZ00068 60S ribosomal protein 100.0 2.4E-43 5.1E-48 294.3 10.2 125 41-177 4-129 (202)
11 PRK06394 rpl13p 50S ribosomal 100.0 1E-42 2.3E-47 278.1 11.5 117 41-172 3-124 (146)
12 KOG3204 60S ribosomal protein 99.9 2.1E-23 4.5E-28 173.2 5.8 121 38-177 3-124 (197)
13 PF12396 DUF3659: Protein of u 52.7 4.2 9E-05 28.6 -0.2 29 38-66 9-37 (64)
14 PRK15393 NUDIX hydrolase YfcD; 34.8 31 0.00068 27.7 2.3 44 39-91 9-53 (180)
15 PF00436 SSB: Single-strand bi 34.3 42 0.0009 23.7 2.6 31 38-84 45-75 (104)
16 PHA02754 hypothetical protein; 32.2 43 0.00092 23.7 2.2 16 77-92 43-58 (67)
17 PRK03759 isopentenyl-diphospha 31.0 64 0.0014 25.9 3.5 45 40-92 6-51 (184)
18 PF04379 DUF525: Protein of un 29.8 32 0.00069 25.4 1.4 13 38-50 31-43 (90)
19 cd04496 SSB_OBF SSB_OBF: A sub 26.8 69 0.0015 22.3 2.7 31 39-85 42-72 (100)
20 KOG3974 Predicted sugar kinase 26.3 35 0.00077 30.7 1.3 34 40-75 132-165 (306)
21 PRK10026 arsenate reductase; P 25.7 87 0.0019 25.0 3.3 46 38-87 91-136 (141)
22 COG0629 Ssb Single-stranded DN 25.2 67 0.0014 25.7 2.6 28 41-84 51-78 (167)
23 PRK05853 hypothetical protein; 24.6 73 0.0016 26.0 2.7 30 40-85 42-71 (161)
24 PRK06752 single-stranded DNA-b 24.5 69 0.0015 23.9 2.4 29 40-84 46-74 (112)
25 KOG1154 Gamma-glutamyl kinase 24.3 74 0.0016 28.4 2.9 42 44-97 21-67 (285)
26 PRK07772 single-stranded DNA-b 23.1 73 0.0016 26.6 2.5 22 51-84 59-80 (186)
27 PRK07274 single-stranded DNA-b 22.9 1.1E+02 0.0024 23.6 3.4 30 39-84 45-74 (131)
28 TIGR00292 thiazole biosynthesi 22.4 28 0.0006 29.8 -0.1 24 40-64 158-181 (254)
29 PRK09010 single-stranded DNA-b 21.9 99 0.0022 25.6 3.1 29 40-84 53-81 (177)
30 COG4091 Predicted homoserine d 21.8 1.2E+02 0.0027 28.6 3.9 44 41-97 102-145 (438)
31 PRK08182 single-stranded DNA-b 21.6 90 0.0019 24.9 2.7 28 41-84 54-81 (148)
32 PRK05461 apaG CO2+/MG2+ efflux 21.3 60 0.0013 25.5 1.6 14 38-51 48-61 (127)
33 PF02534 T4SS-DNA_transf: Type 21.2 1.5E+02 0.0032 27.0 4.3 65 3-92 44-108 (469)
34 COG0569 TrkA K+ transport syst 21.1 89 0.0019 26.2 2.7 25 52-87 8-32 (225)
35 PRK06863 single-stranded DNA-b 20.9 1.2E+02 0.0025 25.0 3.3 29 40-84 51-79 (168)
36 PRK08486 single-stranded DNA-b 20.9 86 0.0019 26.0 2.5 21 40-64 48-68 (182)
37 PF01926 MMR_HSR1: 50S ribosom 20.8 2E+02 0.0043 20.4 4.2 8 43-50 50-57 (116)
38 PRK07275 single-stranded DNA-b 20.6 83 0.0018 25.6 2.3 21 40-64 46-66 (162)
39 PRK08763 single-stranded DNA-b 20.1 86 0.0019 25.6 2.3 29 40-84 51-79 (164)
40 TIGR00621 ssb single stranded 20.1 84 0.0018 25.2 2.2 28 41-84 51-78 (164)
41 PF03447 NAD_binding_3: Homose 20.0 1.6E+02 0.0035 21.4 3.6 37 40-90 59-95 (117)
No 1
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=1e-64 Score=403.68 Aligned_cols=143 Identities=61% Similarity=1.054 Sum_probs=139.4
Q ss_pred hhcccccCCCCCccccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeee
Q 030391 24 WNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRR 103 (178)
Q Consensus 24 ~~~t~~~k~~~~~~~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~ 103 (178)
+|+|+++++++ ++|+|+||||+|++||||||.||++|+|||||+|||++||||+|||||||+|.|||+||++|.|++
T Consensus 1 ~~~t~~~~~~~---~~r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~kv~~TG~K~~~K~y~~ 77 (143)
T CHL00159 1 MNKTFIPSKDY---KNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFYVR 77 (143)
T ss_pred CCccccCCchh---cCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEecceeEEeCchhhheEEEe
Confidence 47899999888 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCCCHHHHhhcChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCCCCCCCCeeecc
Q 030391 104 HSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPI 169 (178)
Q Consensus 104 htgypGglk~~t~~~~~~r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~ 169 (178)
|||||||+++.+++++++++|++||++||+||||||.+|+.+|++|+||+|++|||++|+|+++++
T Consensus 78 htg~pGg~k~~~~~~~~~r~P~~il~~aV~gMLPkn~lgr~~~~rLkvy~G~~hph~aq~p~~~~~ 143 (143)
T CHL00159 78 HSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHPHVAQKPIKINI 143 (143)
T ss_pred cCCCCCCcccccHHHHhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCccccCCeecCC
Confidence 999999999999999999999999999999999999999999999999999999999999998863
No 2
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=8.1e-64 Score=398.88 Aligned_cols=143 Identities=57% Similarity=0.953 Sum_probs=139.4
Q ss_pred hcccccCCCCCccccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeec
Q 030391 25 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRH 104 (178)
Q Consensus 25 ~~t~~~k~~~~~~~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~h 104 (178)
|+|+++++++ ++++|+||||+|++||||||.||++|+|||||+|||++||||+|||||||+|.|||+||++|.|++|
T Consensus 1 m~t~~~~~~~---~~~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~h 77 (144)
T PRK09216 1 MKTFSAKPAE---VERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYRH 77 (144)
T ss_pred CCcccCChhh---cCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCceeEEcCchHhheeeEEe
Confidence 4688898887 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCHHHHhhcChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCCCCCCCCeeeccc
Q 030391 105 SGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPIR 170 (178)
Q Consensus 105 tgypGglk~~t~~~~~~r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~ 170 (178)
||||||+++++++++++++|++||++||+||||||.+|+.+|+||+||+|++|||++|+|+.++++
T Consensus 78 tg~pGglk~~~~~~~~~r~P~~il~~aVrgMLPkn~lgr~~~~rLkvy~G~~hp~~~q~p~~~~~~ 143 (144)
T PRK09216 78 SGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHPHAAQQPEVLEIK 143 (144)
T ss_pred cccCCCCEEecHHHHhhhCHHHHHHHHHHhcCCCCccHHHHHhCcEEeCCCCCCccccCCEecccC
Confidence 999999999999999999999999999999999999999999999999999999999999999875
No 3
>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=5.7e-62 Score=386.69 Aligned_cols=133 Identities=62% Similarity=1.047 Sum_probs=130.4
Q ss_pred cccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCH
Q 030391 37 HSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETF 116 (178)
Q Consensus 37 ~~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~ 116 (178)
+++|+|+||||+|++||||||.||++|+|||||+|||++||||+|||||||+|.|||+||++|.|++|||||||++++++
T Consensus 8 ~~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pgg~k~~~~ 87 (140)
T TIGR01066 8 DKKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTF 87 (140)
T ss_pred hhcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEEEEeCchhhceeeEEEcccCCccccccH
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCCCCCCCCeeecc
Q 030391 117 DQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPI 169 (178)
Q Consensus 117 ~~~~~r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~ 169 (178)
+++++++|++||++||+||||||.+|+++|+||+||+|++|||++|+|+.+++
T Consensus 88 ~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkvy~G~~hp~~~q~p~~~~~ 140 (140)
T TIGR01066 88 EEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPHEAQKPIVLDI 140 (140)
T ss_pred HHhhhcCHHHHHHHHHHhcCCCCccHHHHHhCeEEeCCCCCChhhcCCeecCC
Confidence 99999999999999999999999999999999999999999999999998763
No 4
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-61 Score=386.71 Aligned_cols=143 Identities=55% Similarity=0.896 Sum_probs=137.4
Q ss_pred hcccccCCCCCccccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeec
Q 030391 25 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRH 104 (178)
Q Consensus 25 ~~t~~~k~~~~~~~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~h 104 (178)
|+|+++++++ ++++|+||||+|++||||||.||++|+|||||+||||+||||+|||||||+|+|||+|..+|.||+|
T Consensus 1 ~~t~~~k~~~---~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~h 77 (148)
T COG0102 1 MKTFTAKPSE---VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYRH 77 (148)
T ss_pred CceeccCccc---ccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceeeEEecccccceEEEEe
Confidence 5688899998 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCHHHHhh-cChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCCCCCCCCeeeccc
Q 030391 105 SGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPIR 170 (178)
Q Consensus 105 tgypGglk~~t~~~~~~-r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~ 170 (178)
|+||||+++.+++.+.+ +.|++||++||+||||||++||++|++|+||.|+||||.+|+|+.+.+.
T Consensus 78 s~~~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~aq~p~~l~~~ 144 (148)
T COG0102 78 SGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHEAQKPEALELK 144 (148)
T ss_pred eccCCcccccccccccccCCHHHHHHHHHhccCCCChhHHHHHhCceEecCCCCccccccchhhhhh
Confidence 99999999999966666 9999999999999999999999999999999999999999999987654
No 5
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=5.5e-58 Score=379.09 Aligned_cols=138 Identities=34% Similarity=0.613 Sum_probs=132.9
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCHH
Q 030391 38 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFD 117 (178)
Q Consensus 38 ~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~~ 117 (178)
-.++||||||+||+||||||.||++|+|||||+|||++||||+|||||||+|.|||+||.+|.|++|||||||+++++++
T Consensus 13 ~~r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVINAekI~lTG~K~~~K~Y~~htgypGglk~~~~~ 92 (191)
T PLN00205 13 EGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFYRWHTGYIGHLKERSLK 92 (191)
T ss_pred CCCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccEEEEeCChhhcceEEEecCCCCCcccccHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCCCCCCCCeeeccccceee
Q 030391 118 QLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPIRDKRIQ 175 (178)
Q Consensus 118 ~~~~r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~~~~~~ 175 (178)
++++++|++||++||+||||+|.+|+.++++|+||+|++|||++|+|+++++-.+..+
T Consensus 93 ~~~~r~P~~Il~kAVrGMLPkn~lr~~~~krLkVY~G~~hp~~~q~p~~~~~p~~~~~ 150 (191)
T PLN00205 93 DQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGDKPLEPFVMPPRQVR 150 (191)
T ss_pred HHhccCHHHHHHHHHHhcCCCCchHHHHHhCCEEECCCCCChhccCCeEecCChHHhh
Confidence 9999999999999999999999999999999999999999999999999987655543
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=3.5e-58 Score=359.94 Aligned_cols=127 Identities=56% Similarity=0.943 Sum_probs=125.9
Q ss_pred EEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCHHHHhh
Q 030391 42 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQH 121 (178)
Q Consensus 42 W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~~~~~~ 121 (178)
|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|.+||++|.+|.|++|||||||+++.+++++++
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 cChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCCCCCCCCeeec
Q 030391 122 RIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELP 168 (178)
Q Consensus 122 r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~ 168 (178)
++|++||++||+||||+|.+|+++|+||+||+|++|||++|+|++++
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 99999999999999999999999999999999999999999999987
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=4.8e-55 Score=336.41 Aligned_cols=114 Identities=56% Similarity=0.955 Sum_probs=113.1
Q ss_pred EEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCHHHHhh
Q 030391 42 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQH 121 (178)
Q Consensus 42 W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~~~~~~ 121 (178)
|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|.+||+||++|.|++||+||||+++.+++++++
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 cChhHHHHHHHHccCCCCcchHHHhcCCeeecCC
Q 030391 122 RIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGP 155 (178)
Q Consensus 122 r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~ 155 (178)
++|++||++||+||||||.+|+++|+||+||+|+
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=3.2e-55 Score=351.65 Aligned_cols=141 Identities=48% Similarity=0.715 Sum_probs=134.8
Q ss_pred ccccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCC
Q 030391 36 RHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEET 115 (178)
Q Consensus 36 ~~~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t 115 (178)
.+++|.|++|||++++||||||+||..|+|||||+|||+.||||+|||+||++|.|||+||++|+|++|||||||++..+
T Consensus 17 ~afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K~~qk~Y~~HsGyPG~lk~~~ 96 (165)
T KOG3203|consen 17 LAFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWEQKIYRSHSGYPGGLKQTT 96 (165)
T ss_pred HHHhhhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhheeccchhhhhhhhhcCCCCCchhhhH
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcChhHHHHHHHHccCCCCcchHHHhcCCeeecCCCCC------CCCCCCeeeccccceeec
Q 030391 116 FDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHP------HEAQQPIELPIRDKRIQK 176 (178)
Q Consensus 116 ~~~~~~r~P~~Il~~aVrgMLPkn~lgr~~l~rLkvy~G~~hp------~~~qkp~~~~~~~~~~~~ 176 (178)
+.+++.++|++|+++||+||||||.+++.+|++|+||+|++|| +++++|..+|..++.++.
T Consensus 97 ~~q~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p~~~Ni~~~~~q~~~vp~r~~e~~~ 163 (165)
T KOG3203|consen 97 ADQLADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHPEKVNIGSELHQPQGVPKRLDEYTF 163 (165)
T ss_pred HHHHhhhCHHHHHHHHHHhhCccchHHHHHhheeeccCCccCchhhhhHHHhccccCCCchhHHHhh
Confidence 9999999999999999999999999999999999999999999 778888888887776654
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=8.3e-45 Score=289.02 Aligned_cols=117 Identities=34% Similarity=0.485 Sum_probs=110.5
Q ss_pred EEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCHHHHhhc
Q 030391 43 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHR 122 (178)
Q Consensus 43 ~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~~~~~~r 122 (178)
+||||+||+||||||.||++|+ |||+|||||||+|.+||+|+++|.||+|+.++|+....++++++++
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 5899999999999999999996 9999999999999999999999999999965555555589999999
Q ss_pred ChhHHHHHHHHccCCCC-cchHHHhcCCeeecCCCCCCCCCCCeeecccc
Q 030391 123 IPERIIEHAVRGMLPKG-RLGRELFTHLKVYKGPNHPHEAQQPIELPIRD 171 (178)
Q Consensus 123 ~P~~Il~~aVrgMLPkn-~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~~ 171 (178)
+|++||++||+||||+| .+|+.+|+||+||+|+||||++|+|+++|.++
T Consensus 69 ~P~~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~~h~~~~qk~~~~~~a~ 118 (142)
T TIGR01077 69 APSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL 118 (142)
T ss_pred CHHHHHHHHHHHhCCCCChhHHHHHhCcEEecCCCCCccccCccccChhh
Confidence 99999999999999996 89999999999999999999999999999987
No 10
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=2.4e-43 Score=294.32 Aligned_cols=125 Identities=27% Similarity=0.432 Sum_probs=114.2
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCHHHHh
Q 030391 41 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQ 120 (178)
Q Consensus 41 ~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~~~~~ 120 (178)
+|+||||+|++||||||.||+.|+ +||+|||||||+|.|||+++++|.||+|.-..+.......+++|
T Consensus 4 ~w~vIDA~g~vLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iTG~k~~~K~~y~~~lk~~~~~nP~~g~~~ 71 (202)
T PTZ00068 4 KVIVIDCKGHLLGRLASVVAKELL------------LGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNTNPRRGPFH 71 (202)
T ss_pred ceEEEECCCCcHHHHHHHHHHHHh------------CCCEEEEEecceeEeecchhhheeeeEeeeEeeccCCCCcchhc
Confidence 799999999999999999999998 99999999999999999999999999983222222333368999
Q ss_pred hcChhHHHHHHHHccCCC-CcchHHHhcCCeeecCCCCCCCCCCCeeeccccceeecc
Q 030391 121 HRIPERIIEHAVRGMLPK-GRLGRELFTHLKVYKGPNHPHEAQQPIELPIRDKRIQKQ 177 (178)
Q Consensus 121 ~r~P~~Il~~aVrgMLPk-n~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~~~~~~~~ 177 (178)
++.|++||++||+||||+ |.+|+++|+||+||+|+||||++++++++|.++|+.+++
T Consensus 72 ~r~P~~Il~raVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~~vvp~A~r~~rl~ 129 (202)
T PTZ00068 72 HRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSALRVLRLK 129 (202)
T ss_pred ccCHHHHHHHHHhhhCCCCChhHHHHHhCCEEecCCCCchhccCcccccchhhhhccC
Confidence 999999999999999996 899999999999999999999999999999999998876
No 11
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00 E-value=1e-42 Score=278.12 Aligned_cols=117 Identities=34% Similarity=0.473 Sum_probs=106.6
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCC----CH
Q 030391 41 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEE----TF 116 (178)
Q Consensus 41 ~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~----t~ 116 (178)
+-+||||+||+||||||.||++|+ +||+|||||||+|.+||+|+.++ .+|++|+ |++.. ++
T Consensus 3 ~~~viDA~~~vlGRLAs~IA~~L~------------~Gd~VVViNa~kv~~tG~K~~~~--~~y~~~~-~~k~~~np~~~ 67 (146)
T PRK06394 3 AMVVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGNRERVI--EKYKQRR-ERGSHYNPYRN 67 (146)
T ss_pred ccEEEECCCCchHHHHHHHHHHHh------------CCCEEEEEechheEecCchhhhe--eeEeCCC-CCcccCCCCCh
Confidence 468999999999999999999999 69999999999999999998874 4445554 45555 78
Q ss_pred HHHhhcChhHHHHHHHHccCC-CCcchHHHhcCCeeecCCCCCCCCCCCeeeccccc
Q 030391 117 DQLQHRIPERIIEHAVRGMLP-KGRLGRELFTHLKVYKGPNHPHEAQQPIELPIRDK 172 (178)
Q Consensus 117 ~~~~~r~P~~Il~~aVrgMLP-kn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~~~ 172 (178)
+++++++|++||++||+|||| ||.+|+.+|+||+||+|+||||++|+|++++.+++
T Consensus 68 ~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~~rLkvy~G~~h~~~~qkp~~~~~a~~ 124 (146)
T PRK06394 68 GPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEADL 124 (146)
T ss_pred HHhhhcCHHHHHHHHHHhcCCCCChhHHHHHhCcEEecCCCCCcccCCCEEecHHHH
Confidence 999999999999999999999 89999999999999999999999999999999876
No 12
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2.1e-23 Score=173.20 Aligned_cols=121 Identities=30% Similarity=0.538 Sum_probs=107.4
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCccccceeeeeccCCCCCCCCCCHH
Q 030391 38 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFD 117 (178)
Q Consensus 38 ~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~~K~Y~~htgypGglk~~t~~ 117 (178)
...+-.+||+.||++|||||.+|+.|+ .|+.|||+.||.|.+||+.+++|-|-++. =+. -+
T Consensus 3 ~~~~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~lrk~---~~~----ng 63 (197)
T KOG3204|consen 3 LEVKLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLFLRKR---LNR----NG 63 (197)
T ss_pred ceEEEeeccchhhhhhhHHHHHHHHHh------------cCCeEEEEEEeEEEEecceecchHHHhhh---hcc----cC
Confidence 345778999999999999999999998 99999999999999999999999443332 111 16
Q ss_pred HHhhcChhHHHHHHHHccCC-CCcchHHHhcCCeeecCCCCCCCCCCCeeeccccceeecc
Q 030391 118 QLQHRIPERIIEHAVRGMLP-KGRLGRELFTHLKVYKGPNHPHEAQQPIELPIRDKRIQKQ 177 (178)
Q Consensus 118 ~~~~r~P~~Il~~aVrgMLP-kn~lgr~~l~rLkvy~G~~hp~~~qkp~~~~~~~~~~~~~ 177 (178)
++|++-|++|++++|+||+| +++.|+.++++|.+|+|.++|++.|++.++|.+.++..++
T Consensus 64 ~~hfr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r~v~p~a~~v~~lk 124 (197)
T KOG3204|consen 64 PFHFRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKRLVVPVAFQVLRLK 124 (197)
T ss_pred cchhhhHHHHHHHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCCccCCcceeeeccc
Confidence 99999999999999999999 5899999999999999999999999999999999987654
No 13
>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=52.70 E-value=4.2 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.391 Sum_probs=25.5
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcC
Q 030391 38 SDKTWYVVDATDKILGRLASTIAIHIRGK 66 (178)
Q Consensus 38 ~~r~W~vIDA~g~~LGRLAs~VAk~L~GK 66 (178)
+++.=.|+|.+|.++|||..--++.|.|+
T Consensus 9 Vnk~G~V~d~~G~~vG~vveGd~k~L~G~ 37 (64)
T PF12396_consen 9 VNKDGNVVDDDGNVVGRVVEGDPKKLVGK 37 (64)
T ss_pred ECCCCeEECCCCCEEEEEecCCHHHhcCC
Confidence 45566799999999999999999999887
No 14
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=34.82 E-value=31 Score=27.74 Aligned_cols=44 Identities=11% Similarity=0.198 Sum_probs=29.1
Q ss_pred cceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecc-eeee
Q 030391 39 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE-KVAV 91 (178)
Q Consensus 39 ~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINae-kI~~ 91 (178)
..-|.|+|..|+++|+.....+.. .|- ++ .+-.|+|+|.+ +|.+
T Consensus 9 ~e~~~~~d~~~~~~g~~~~~~~~~-~~~----~h----~~~~v~v~~~~g~iLL 53 (180)
T PRK15393 9 TEWVDIVNENNEVIAQASREQMRA-QCL----RH----RATYIVVHDGMGKILV 53 (180)
T ss_pred ceEEEEECCCCCEeeEEEHHHHhh-CCC----ce----EEEEEEEECCCCeEEE
Confidence 346999999999999985555543 222 12 34578888874 4444
No 15
>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=34.29 E-value=42 Score=23.71 Aligned_cols=31 Identities=32% Similarity=0.475 Sum_probs=20.7
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 38 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 38 ~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
..-.|+=+-+ -|.+|..++..|. .||.|.|.
T Consensus 45 ~~~~~~~v~~----~g~~A~~~~~~l~------------kG~~V~V~ 75 (104)
T PF00436_consen 45 EKTDWINVVA----WGKLAENVAEYLK------------KGDRVYVE 75 (104)
T ss_dssp EEEEEEEEEE----EHHHHHHHHHH--------------TT-EEEEE
T ss_pred cceEEEEEEe----eeecccccceEEc------------CCCEEEEE
Confidence 3345666654 5889999999996 89987765
No 16
>PHA02754 hypothetical protein; Provisional
Probab=32.24 E-value=43 Score=23.70 Aligned_cols=16 Identities=19% Similarity=0.557 Sum_probs=13.8
Q ss_pred CCCEEEEEecceeeec
Q 030391 77 MGAYVIVVNAEKVAVS 92 (178)
Q Consensus 77 ~Gd~VVVINaekI~~t 92 (178)
.||++|||-|+-|.+.
T Consensus 43 SGdkIVVi~aD~I~i~ 58 (67)
T PHA02754 43 SGDKIVVITADAIKIE 58 (67)
T ss_pred cCCEEEEEEcceEEEE
Confidence 7999999999988764
No 17
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=30.98 E-value=64 Score=25.88 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=31.0
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecc-eeeec
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE-KVAVS 92 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINae-kI~~t 92 (178)
..|.++|++|..+|+.....+....|. +++.+ .|+|+|.+ +|.+.
T Consensus 6 E~~~~vd~~~~~~g~~~r~~~~~~~~~----~h~av----~v~i~~~~g~vLL~ 51 (184)
T PRK03759 6 ELVVLLDEQGVPTGTAEKAAAHTADTP----LHLAF----SCYLFDADGRLLVT 51 (184)
T ss_pred eeEEEECCCCCCcccccHHHHHhcCCC----eeeEE----EEEEEcCCCeEEEE
Confidence 579999999999999887777644443 33332 47777754 45553
No 18
>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=29.83 E-value=32 Score=25.40 Aligned_cols=13 Identities=23% Similarity=0.647 Sum_probs=10.7
Q ss_pred ccceEEEEeCCCC
Q 030391 38 SDKTWYVVDATDK 50 (178)
Q Consensus 38 ~~r~W~vIDA~g~ 50 (178)
..|.|.|.|++|+
T Consensus 31 ~sR~W~I~d~~g~ 43 (90)
T PF04379_consen 31 LSRHWIITDADGH 43 (90)
T ss_dssp EEEEEEEEETTS-
T ss_pred EccEEEEEeCCCC
Confidence 5699999999985
No 19
>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=26.79 E-value=69 Score=22.25 Aligned_cols=31 Identities=32% Similarity=0.516 Sum_probs=23.3
Q ss_pred cceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEe
Q 030391 39 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVN 85 (178)
Q Consensus 39 ~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVIN 85 (178)
.-.|+=+-+ -|.+|..+++.|. .||.|+|.=
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 456766654 4569999999987 899988753
No 20
>KOG3974 consensus Predicted sugar kinase [Carbohydrate transport and metabolism]
Probab=26.33 E-value=35 Score=30.73 Aligned_cols=34 Identities=26% Similarity=0.213 Sum_probs=28.2
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCC
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSV 75 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~ 75 (178)
...+||||+|--| ++...++.+.|-++.+.|||+
T Consensus 132 dvP~VIDaDGL~L--v~q~~e~l~~~~~~viLTPNv 165 (306)
T KOG3974|consen 132 DVPLVIDADGLWL--VEQLPERLIGGYPKVILTPNV 165 (306)
T ss_pred CCcEEEcCCceEe--hhhchhhhhccCceeeeCCcH
Confidence 4789999999754 455566699999999999997
No 21
>PRK10026 arsenate reductase; Provisional
Probab=25.70 E-value=87 Score=24.95 Aligned_cols=46 Identities=15% Similarity=0.020 Sum_probs=32.8
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecc
Q 030391 38 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE 87 (178)
Q Consensus 38 ~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINae 87 (178)
.=+..+|+|.+|.++||=.+.|-.+| ++. |.-.=..+.|..+ +|+.
T Consensus 91 LIKRPIi~~~~~a~i~Rp~e~v~~~l-~~~-~~~~~~~~~~~~~--~~~~ 136 (141)
T PRK10026 91 LINRPIVVTPLGTRLCRPSEVVLEIL-PDA-QKGAFTKEDGEKV--VDEA 136 (141)
T ss_pred ceeCcEEEcCCCeEEECCHHHHHHHh-ccc-ccccccccCCeEe--ecCC
Confidence 44678999999999999777777776 665 4444445667655 6664
No 22
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=25.24 E-value=67 Score=25.71 Aligned_cols=28 Identities=36% Similarity=0.529 Sum_probs=22.5
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 41 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 41 ~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
.|+=|= +.|++|..++.+|. .|+-|+|.
T Consensus 51 ~~~~vv----~wgk~Ae~~~~yl~------------KG~~V~Ve 78 (167)
T COG0629 51 DWIRVV----IWGKLAENAAEYLK------------KGSLVYVE 78 (167)
T ss_pred ceEEEE----EehHHHHHHHHHhc------------CCCEEEEE
Confidence 676553 57889999999997 79888774
No 23
>PRK05853 hypothetical protein; Validated
Probab=24.55 E-value=73 Score=26.02 Aligned_cols=30 Identities=33% Similarity=0.492 Sum_probs=22.9
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEe
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVN 85 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVIN 85 (178)
-.|+-|- +.|++|..++++|. .|+.|+|.-
T Consensus 42 T~wi~V~----~wg~lAe~v~~~L~------------KG~~V~V~G 71 (161)
T PRK05853 42 SLFITVN----CWGRLVTGVGAALG------------KGAPVIVVG 71 (161)
T ss_pred ccEEEEE----EEhHHHHHHHHHcC------------CCCEEEEEE
Confidence 3565554 57889999999996 798888753
No 24
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=24.54 E-value=69 Score=23.91 Aligned_cols=29 Identities=10% Similarity=0.083 Sum_probs=22.2
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
-.|+=+- +.|++|..++.+|. .||.|.|.
T Consensus 46 t~~~~v~----~wg~~Ae~~~~~l~------------KG~~V~V~ 74 (112)
T PRK06752 46 VDFINCV----VWRKSAENVTEYCT------------KGSLVGIT 74 (112)
T ss_pred EEEEEEE----EehHHHHHHHHhcC------------CCCEEEEE
Confidence 4677664 56789999999986 78887764
No 25
>KOG1154 consensus Gamma-glutamyl kinase [Amino acid transport and metabolism]
Probab=24.34 E-value=74 Score=28.41 Aligned_cols=42 Identities=31% Similarity=0.389 Sum_probs=29.9
Q ss_pred EEeCC--CCCchhhHHHH---HHHHhcCCCCccCCCCCCCCEEEEEecceeeecCcccc
Q 030391 44 VVDAT--DKILGRLASTI---AIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRT 97 (178)
Q Consensus 44 vIDA~--g~~LGRLAs~V---Ak~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~ 97 (178)
|.|.+ |--|||||+.| +++= ..|..|++|-+.-|.|-=.+.+
T Consensus 21 it~e~~~~laLgrla~IVEqV~~L~------------~~G~evilVSSGaVA~G~qrLr 67 (285)
T KOG1154|consen 21 ITREDTCGLALGRLASIVEQVSELQ------------RMGREVILVSSGAVAFGRQRLR 67 (285)
T ss_pred EECCCCccchHHHHHHHHHHHHHHH------------hcCceEEEEecchhhhhHHHhh
Confidence 44444 45899999987 3333 4899999999999988433444
No 26
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=23.15 E-value=73 Score=26.63 Aligned_cols=22 Identities=32% Similarity=0.371 Sum_probs=19.1
Q ss_pred CchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 51 ILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 51 ~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
+.|++|..+|+.|. .||.|+|.
T Consensus 59 ~Wg~~Ae~va~~L~------------KGd~V~V~ 80 (186)
T PRK07772 59 IWRQAAENVAESLT------------KGMRVIVT 80 (186)
T ss_pred EecHHHHHHHHhcC------------CCCEEEEE
Confidence 57889999999986 89998885
No 27
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=22.93 E-value=1.1e+02 Score=23.59 Aligned_cols=30 Identities=23% Similarity=0.313 Sum_probs=23.3
Q ss_pred cceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 39 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 39 ~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
.-.|+-|=+ .|++|..++.+|. .|+.|.|-
T Consensus 45 ~t~w~~v~~----fg~~Ae~v~~~l~------------KG~~V~V~ 74 (131)
T PRK07274 45 EADFINVVL----WGKLAETLASYAS------------KGSLISID 74 (131)
T ss_pred EEEEEEEEE----ehHHHHHHHHHcC------------CCCEEEEE
Confidence 357887754 5889999999986 78887764
No 28
>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=22.39 E-value=28 Score=29.77 Aligned_cols=24 Identities=29% Similarity=0.300 Sum_probs=20.4
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHh
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIR 64 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~ 64 (178)
+--+||||+|+- +++++.+++.+-
T Consensus 158 ~Ak~VVdATG~~-a~v~~~l~~~~~ 181 (254)
T TIGR00292 158 RSRVVVDATGHD-AEIVAVCAKKIV 181 (254)
T ss_pred EcCEEEEeecCC-chHHHHHHHHcC
Confidence 456899999987 799999999874
No 29
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=21.91 E-value=99 Score=25.59 Aligned_cols=29 Identities=28% Similarity=0.497 Sum_probs=22.6
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
-.|+=| .+.|++|..++++|+ .|+.|.|.
T Consensus 53 t~w~~V----~~fgk~Ae~~~~~L~------------KGs~V~Ve 81 (177)
T PRK09010 53 TEWHRV----VLFGKLAEVAGEYLR------------KGSQVYIE 81 (177)
T ss_pred eEEEEE----EEehhHHHHHHHhcC------------CCCEEEEE
Confidence 468777 467789999999997 78777764
No 30
>COG4091 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=21.85 E-value=1.2e+02 Score=28.56 Aligned_cols=44 Identities=20% Similarity=0.175 Sum_probs=31.8
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceeeecCcccc
Q 030391 41 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRT 97 (178)
Q Consensus 41 ~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~~tG~k~~ 97 (178)
--.||||+|.+. +++.++--.+ +.|.+||.+|.|-=+.-|.-..
T Consensus 102 IdvIIdATG~p~--vGA~~~l~Ai-----------~h~KHlVMmNVEaDvtIGp~Lk 145 (438)
T COG4091 102 IDVIIDATGVPE--VGAKIALEAI-----------LHGKHLVMMNVEADVTIGPILK 145 (438)
T ss_pred ceEEEEcCCCcc--hhhHhHHHHH-----------hcCCeEEEEEeeeceeecHHHH
Confidence 358999999985 4556655443 5788999999997666676443
No 31
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=21.63 E-value=90 Score=24.86 Aligned_cols=28 Identities=29% Similarity=0.303 Sum_probs=21.2
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 41 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 41 ~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
.|+=|- ..|++|..++++|. .||.|.|.
T Consensus 54 ~w~~V~----~wg~~Ae~v~~~l~------------KG~~V~V~ 81 (148)
T PRK08182 54 FWAPVE----LWHRDAEHWARLYQ------------KGMRVLVE 81 (148)
T ss_pred EEEEEE----EEhHHHHHHHHhcC------------CCCEEEEE
Confidence 476453 56789999999986 78877764
No 32
>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed
Probab=21.28 E-value=60 Score=25.49 Aligned_cols=14 Identities=21% Similarity=0.752 Sum_probs=11.6
Q ss_pred ccceEEEEeCCCCC
Q 030391 38 SDKTWYVVDATDKI 51 (178)
Q Consensus 38 ~~r~W~vIDA~g~~ 51 (178)
..|.|.|.|++|++
T Consensus 48 ~~R~W~I~d~~g~~ 61 (127)
T PRK05461 48 LSRHWLITDANGRV 61 (127)
T ss_pred EeeeEEEEECCCCE
Confidence 55999999998763
No 33
>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues. These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane
Probab=21.24 E-value=1.5e+02 Score=26.96 Aligned_cols=65 Identities=17% Similarity=0.031 Sum_probs=44.4
Q ss_pred eeeeeecCCCCCCccchhhhhhhcccccCCCCCccccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEE
Q 030391 3 FVGVLLTPRHPPLTCRFLWDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVI 82 (178)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~t~~~k~~~~~~~~r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VV 82 (178)
|.|+++.+-.++-+++... ..+.+. -....+|.|-+|. |+...+..+. ..|..|+
T Consensus 44 ~~h~lvig~tgSGKt~~~v---iP~ll~-------~~~s~iV~D~KgE----l~~~t~~~r~-----------~~G~~V~ 98 (469)
T PF02534_consen 44 FTHVLVIGPTGSGKTTSFV---IPNLLN-------YPGSMIVTDPKGE----LYEKTAGYRK-----------KRGYKVY 98 (469)
T ss_pred ceEEEEEeCCCCCccceee---HhHHHh-------ccCCEEEEECCCc----HHHHHHHHHH-----------HCCCEEE
Confidence 4677777767787877664 222221 1237999999964 5667777775 5788999
Q ss_pred EEecceeeec
Q 030391 83 VVNAEKVAVS 92 (178)
Q Consensus 83 VINaekI~~t 92 (178)
|+|-.+..-+
T Consensus 99 vldp~~~~~s 108 (469)
T PF02534_consen 99 VLDPFDPEGS 108 (469)
T ss_pred Eeeccccccc
Confidence 9998776554
No 34
>COG0569 TrkA K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]
Probab=21.15 E-value=89 Score=26.16 Aligned_cols=25 Identities=20% Similarity=0.542 Sum_probs=19.8
Q ss_pred chhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecc
Q 030391 52 LGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE 87 (178)
Q Consensus 52 LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINae 87 (178)
+||+...+|+.|. ..|..|++|-.+
T Consensus 8 ~G~vG~~va~~L~-----------~~g~~Vv~Id~d 32 (225)
T COG0569 8 AGRVGRSVARELS-----------EEGHNVVLIDRD 32 (225)
T ss_pred CcHHHHHHHHHHH-----------hCCCceEEEEcC
Confidence 6899999999997 678777777543
No 35
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=20.93 E-value=1.2e+02 Score=24.96 Aligned_cols=29 Identities=24% Similarity=0.312 Sum_probs=22.7
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
-.|+=|. +.|++|..++++|. .|+.|.|.
T Consensus 51 t~w~~Vv----~fgk~AE~v~~~Lk------------KGs~V~Ve 79 (168)
T PRK06863 51 TEWHRIV----FYRRQAEVAGEYLR------------KGSQVYVE 79 (168)
T ss_pred ceEEEEE----EEhHHHHHHHHHCC------------CCCEEEEE
Confidence 4688885 56889999999986 78777764
No 36
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=20.91 E-value=86 Score=26.02 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=16.0
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHh
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIR 64 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~ 64 (178)
-.|+=|- +.|++|..++.+|.
T Consensus 48 t~fi~v~----~fg~~AE~~~~~l~ 68 (182)
T PRK08486 48 VCFIDIR----LFGRTAEIANQYLS 68 (182)
T ss_pred ceEEEEE----EEhHHHHHHHHHcC
Confidence 3576553 57899999999986
No 37
>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....
Probab=20.84 E-value=2e+02 Score=20.41 Aligned_cols=8 Identities=25% Similarity=0.330 Sum_probs=3.8
Q ss_pred EEEeCCCC
Q 030391 43 YVVDATDK 50 (178)
Q Consensus 43 ~vIDA~g~ 50 (178)
.++|--|-
T Consensus 50 ~~vDtpG~ 57 (116)
T PF01926_consen 50 ILVDTPGI 57 (116)
T ss_dssp EEEESSSC
T ss_pred EEEeCCCC
Confidence 45554443
No 38
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=20.59 E-value=83 Score=25.58 Aligned_cols=21 Identities=14% Similarity=0.120 Sum_probs=16.4
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHh
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIR 64 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~ 64 (178)
-.|+-+ .+.|++|..+|++|.
T Consensus 46 tdfi~v----v~wgk~Ae~~~~~l~ 66 (162)
T PRK07275 46 ADFINC----VIWRQQAENLANWAK 66 (162)
T ss_pred eeEEEE----EEEcHHHHHHHHHcC
Confidence 467655 367899999999986
No 39
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.11 E-value=86 Score=25.61 Aligned_cols=29 Identities=21% Similarity=0.434 Sum_probs=21.8
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
-.||=|- +.|++|..++.+|. .|+.|.|-
T Consensus 51 t~w~~Vv----~fgk~Ae~v~~~L~------------KGs~V~Ve 79 (164)
T PRK08763 51 TEWHRVK----FFGKLGEIAGEYLR------------KGSQCYIE 79 (164)
T ss_pred ceEEEEE----EehHHHHHHHHhcC------------CCCEEEEE
Confidence 3577664 56889999999986 67777663
No 40
>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=20.05 E-value=84 Score=25.24 Aligned_cols=28 Identities=36% Similarity=0.555 Sum_probs=22.3
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 030391 41 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84 (178)
Q Consensus 41 ~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVI 84 (178)
.|+=|- +.|++|..+++.|. .|+.|+|.
T Consensus 51 ~~~~v~----~wg~~Ae~~~~~l~------------KG~~V~V~ 78 (164)
T TIGR00621 51 EWHDIV----IFGRLAEVAAQYLK------------KGSLVYVE 78 (164)
T ss_pred eEEEEE----EehHHHHHHHHhCC------------CCCEEEEE
Confidence 577665 57789999999996 88888874
No 41
>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=20.04 E-value=1.6e+02 Score=21.37 Aligned_cols=37 Identities=22% Similarity=0.206 Sum_probs=25.0
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEecceee
Q 030391 40 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVA 90 (178)
Q Consensus 40 r~W~vIDA~g~~LGRLAs~VAk~L~GKhKp~ytP~~d~Gd~VVVINaekI~ 90 (178)
+--+||||.+. .-+++.+...|. .|-+||..|-.=+.
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 456677778886 88899988865443
Done!