Query 028533
Match_columns 208
No_of_seqs 140 out of 1046
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 13:00:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028533.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028533hhsearch_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 2.1E-52 4.4E-57 342.1 10.9 116 90-208 1-116 (143)
2 PRK09216 rplM 50S ribosomal pr 100.0 1.5E-51 3.2E-56 337.1 10.1 115 91-208 1-115 (144)
3 TIGR01066 rplM_bact ribosomal 100.0 1.3E-49 2.9E-54 324.2 10.6 105 104-208 9-113 (140)
4 COG0102 RplM Ribosomal protein 100.0 2.9E-49 6.3E-54 325.1 11.3 114 91-207 1-115 (148)
5 cd00392 Ribosomal_L13 Ribosoma 100.0 9.4E-49 2E-53 309.2 9.5 101 108-208 1-101 (114)
6 PLN00205 ribisomal protein L13 100.0 1.9E-47 4.2E-52 325.2 11.2 105 104-208 13-117 (191)
7 KOG3203 Mitochondrial/chloropl 100.0 1.2E-46 2.6E-51 311.9 6.2 106 103-208 18-123 (165)
8 PF00572 Ribosomal_L13: Riboso 100.0 7.1E-47 1.5E-51 303.5 4.1 101 108-208 1-101 (128)
9 TIGR01077 L13_A_E ribosomal pr 100.0 1.4E-32 3.1E-37 224.6 7.8 86 109-206 1-86 (142)
10 PRK06394 rpl13p 50S ribosomal 100.0 2E-30 4.3E-35 212.9 8.4 86 107-207 3-93 (146)
11 PTZ00068 60S ribosomal protein 100.0 1.9E-30 4.2E-35 222.7 8.3 90 106-207 3-93 (202)
12 KOG3204 60S ribosomal protein 99.4 6.7E-13 1.5E-17 114.1 6.2 85 105-208 4-88 (197)
13 PRK15393 NUDIX hydrolase YfcD; 59.0 8.8 0.00019 31.8 2.7 44 105-157 9-53 (180)
14 PLN02399 phospholipid hydroper 50.6 75 0.0016 28.1 7.2 28 21-48 26-55 (236)
15 PF12396 DUF3659: Protein of u 48.5 5.2 0.00011 29.1 -0.3 27 107-133 12-38 (64)
16 PRK03759 isopentenyl-diphospha 46.8 24 0.00053 29.1 3.4 45 106-158 6-51 (184)
17 COG2947 Uncharacterized conser 38.9 8.4 0.00018 32.8 -0.5 14 72-85 90-103 (156)
18 COG2967 ApaG Uncharacterized p 38.9 17 0.00038 30.0 1.3 14 104-117 47-60 (126)
19 TIGR02150 IPP_isom_1 isopenten 38.4 21 0.00047 28.7 1.8 41 109-157 2-43 (158)
20 PF00436 SSB: Single-strand bi 37.5 35 0.00075 24.8 2.7 29 106-150 47-75 (104)
21 cd04496 SSB_OBF SSB_OBF: A sub 33.3 45 0.00098 23.8 2.7 30 105-150 42-71 (100)
22 PRK05853 hypothetical protein; 31.6 83 0.0018 26.6 4.3 29 106-150 42-70 (161)
23 PRK07274 single-stranded DNA-b 30.0 79 0.0017 25.2 3.8 29 106-150 46-74 (131)
24 COG0629 Ssb Single-stranded DN 29.3 50 0.0011 27.2 2.6 28 107-150 51-78 (167)
25 KOG2255 Peptidyl-tRNA hydrolas 27.5 1.2E+02 0.0027 27.2 4.9 82 57-155 22-132 (224)
26 PRK06752 single-stranded DNA-b 27.1 57 0.0012 25.1 2.4 29 106-150 46-74 (112)
27 PRK09010 single-stranded DNA-b 25.4 75 0.0016 27.2 3.1 29 106-150 53-81 (177)
28 PF03447 NAD_binding_3: Homose 25.3 1.1E+02 0.0024 22.9 3.7 35 107-155 60-94 (117)
29 KOG2415 Electron transfer flav 25.3 30 0.00065 34.6 0.7 64 76-150 187-250 (621)
30 PLN02982 galactinol-raffinose 25.1 1.3E+02 0.0028 32.0 5.1 40 73-115 97-136 (865)
31 cd02885 IPP_Isomerase Isopente 24.9 83 0.0018 25.3 3.1 43 107-157 3-46 (165)
32 PRK06863 single-stranded DNA-b 24.7 79 0.0017 26.8 3.0 29 106-150 51-79 (168)
33 PRK07772 single-stranded DNA-b 23.9 71 0.0015 27.6 2.7 28 107-150 53-80 (186)
34 PRK07275 single-stranded DNA-b 23.9 67 0.0015 27.0 2.5 21 106-130 46-66 (162)
35 PRK05733 single-stranded DNA-b 23.3 1.1E+02 0.0024 26.0 3.7 29 106-150 52-80 (172)
36 PRK08486 single-stranded DNA-b 23.2 70 0.0015 27.4 2.5 20 107-130 49-68 (182)
37 PF04989 CmcI: Cephalosporin h 23.1 84 0.0018 27.6 3.0 33 105-150 110-146 (206)
38 PHA02754 hypothetical protein; 23.1 77 0.0017 23.4 2.3 15 143-157 43-57 (67)
39 TIGR00621 ssb single stranded 23.0 66 0.0014 26.6 2.2 28 107-150 51-78 (164)
40 PF04379 DUF525: Protein of un 22.9 46 0.001 25.4 1.2 14 104-117 31-44 (90)
41 PF05892 Tricho_coat: Trichovi 22.6 9.5 0.00021 33.5 -2.9 40 95-138 133-173 (194)
42 PF05691 Raffinose_syn: Raffin 22.4 1.8E+02 0.0039 30.5 5.6 65 34-114 40-104 (747)
43 PF01926 MMR_HSR1: 50S ribosom 21.3 1.9E+02 0.0042 21.1 4.3 24 106-130 82-105 (116)
44 PRK07459 single-stranded DNA-b 21.3 84 0.0018 24.9 2.4 28 107-150 44-71 (121)
45 PRK08763 single-stranded DNA-b 21.0 79 0.0017 26.7 2.3 28 107-150 52-79 (164)
46 PRK13732 single-stranded DNA-b 20.8 83 0.0018 26.9 2.4 29 106-150 53-81 (175)
47 PRK13975 thymidylate kinase; P 20.6 1.1E+02 0.0024 24.6 3.0 24 107-130 166-189 (196)
48 PRK06751 single-stranded DNA-b 20.3 81 0.0018 26.8 2.3 21 106-130 46-66 (173)
49 TIGR00292 thiazole biosynthesi 20.1 31 0.00067 30.3 -0.3 23 107-130 159-181 (254)
No 1
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=2.1e-52 Score=342.05 Aligned_cols=116 Identities=58% Similarity=0.998 Sum_probs=112.8
Q ss_pred cceeccCCCCCCCcccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeee
Q 028533 90 WNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRR 169 (208)
Q Consensus 90 ~~kT~~~k~~~~~~~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~ 169 (208)
||+||+++.++ .+|+||||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||.+|.|++
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 57899999888 589999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCCchhhhhccChHHHHHHHHhCcCCCCCCC
Q 028533 170 HSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 170 HtgyPGglk~~t~~~l~~r~P~~IlkrAVrGMLPkn~Lr 208 (208)
|||||||+|+++++++++|+|++||++||+||||||+|+
T Consensus 78 htg~pGg~k~~~~~~~~~r~P~~il~~aV~gMLPkn~lg 116 (143)
T CHL00159 78 HSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLG 116 (143)
T ss_pred cCCCCCCcccccHHHHhhcCHHHHHHHHHHhcCCCChhH
Confidence 999999999999999999999999999999999999874
No 2
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=1.5e-51 Score=337.14 Aligned_cols=115 Identities=56% Similarity=0.909 Sum_probs=111.6
Q ss_pred ceeccCCCCCCCcccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeec
Q 028533 91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRH 170 (208)
Q Consensus 91 ~kT~~~k~~~~~~~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~H 170 (208)
|+||++++++ .+|+||||||+||+||||||.||++|+|||||+|+|++||||+|||||||+|+|||+||++|.|++|
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 4799999888 5899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCchhhhhccChHHHHHHHHhCcCCCCCCC
Q 028533 171 SGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 171 tgyPGglk~~t~~~l~~r~P~~IlkrAVrGMLPkn~Lr 208 (208)
||||||+++++++++++|+|++||++||+||||+|+|+
T Consensus 78 tg~pGglk~~~~~~~~~r~P~~il~~aVrgMLPkn~lg 115 (144)
T PRK09216 78 SGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLG 115 (144)
T ss_pred cccCCCCEEecHHHHhhhCHHHHHHHHHHhcCCCCccH
Confidence 99999999999999999999999999999999999874
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=1.3e-49 Score=324.24 Aligned_cols=105 Identities=60% Similarity=0.995 Sum_probs=103.1
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchh
Q 028533 104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFD 183 (208)
Q Consensus 104 ~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~ 183 (208)
.+|+||||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||++|.|++|||||||++.++++
T Consensus 9 ~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pgg~k~~~~~ 88 (140)
T TIGR01066 9 KKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTFE 88 (140)
T ss_pred hcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEEEEeCchhhceeeEEEcccCCccccccHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccChHHHHHHHHhCcCCCCCCC
Q 028533 184 QLQHRIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 184 ~l~~r~P~~IlkrAVrGMLPkn~Lr 208 (208)
++++|+|++||++||+||||||.|+
T Consensus 89 ~~~~r~P~~ii~~aVrGMLPkn~lg 113 (140)
T TIGR01066 89 EMIARKPERVLEHAVKGMLPKNRLG 113 (140)
T ss_pred HhhhcCHHHHHHHHHHhcCCCCccH
Confidence 9999999999999999999999874
No 4
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-49 Score=325.06 Aligned_cols=114 Identities=55% Similarity=0.879 Sum_probs=109.4
Q ss_pred ceeccCCCCCCCcccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeec
Q 028533 91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRH 170 (208)
Q Consensus 91 ~kT~~~k~~~~~~~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~H 170 (208)
|+|++++..+ .+++|+||||+|++||||||.||++|+|||||+||||+||||+|||||||||+|||+|..+|.||+|
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 5789999888 6999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCchhhhhc-cChHHHHHHHHhCcCCCCCC
Q 028533 171 SGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLPKGRK 207 (208)
Q Consensus 171 tgyPGglk~~t~~~l~~-r~P~~IlkrAVrGMLPkn~L 207 (208)
++||||+++.++++++. |.|++||++||+||||||.|
T Consensus 78 s~~~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk~~l 115 (148)
T COG0102 78 SGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPL 115 (148)
T ss_pred eccCCcccccccccccccCCHHHHHHHHHhccCCCChh
Confidence 99999999999977666 99999999999999999876
No 5
>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=9.4e-49 Score=309.24 Aligned_cols=101 Identities=55% Similarity=0.925 Sum_probs=99.8
Q ss_pred EEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchhhhhc
Q 028533 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQH 187 (208)
Q Consensus 108 W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~~l~~ 187 (208)
|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||.+|.|++|++||||+++++++++++
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 cChHHHHHHHHhCcCCCCCCC
Q 028533 188 RIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 188 r~P~~IlkrAVrGMLPkn~Lr 208 (208)
++|++||++||+||||||+|+
T Consensus 81 ~~P~~il~~aV~gMLPkn~~g 101 (114)
T cd00392 81 RAPERILKRAVRGMLPKNKLG 101 (114)
T ss_pred hCHHHHHHHHHHhcCCCChhH
Confidence 999999999999999999874
No 6
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=1.9e-47 Score=325.16 Aligned_cols=105 Identities=40% Similarity=0.678 Sum_probs=103.0
Q ss_pred ccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchh
Q 028533 104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFD 183 (208)
Q Consensus 104 ~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~ 183 (208)
..++||||||+||+||||||+||++|+|||||+|||++||||+|||||||+|+|||+||.+|.|++|||||||+++++++
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 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccChHHHHHHHHhCcCCCCCCC
Q 028533 184 QLQHRIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 184 ~l~~r~P~~IlkrAVrGMLPkn~Lr 208 (208)
++++++|++||++||+||||+|+||
T Consensus 93 ~~~~r~P~~Il~kAVrGMLPkn~lr 117 (191)
T PLN00205 93 DQMAKDPTEVIRKAVLRMLPRNRLR 117 (191)
T ss_pred HHhccCHHHHHHHHHHhcCCCCchH
Confidence 9999999999999999999999985
No 7
>KOG3203 consensus Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-46 Score=311.90 Aligned_cols=106 Identities=53% Similarity=0.781 Sum_probs=103.7
Q ss_pred cccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCch
Q 028533 103 HSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETF 182 (208)
Q Consensus 103 ~~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~ 182 (208)
.++|.|+||||++|+|||||++||.+|+|||||+|||+.||||+|||+||++|.|||+||++|+|++|+||||+++++++
T Consensus 18 afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K~~qk~Y~~HsGyPG~lk~~~~ 97 (165)
T KOG3203|consen 18 AFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWEQKIYRSHSGYPGGLKQTTA 97 (165)
T ss_pred HHhhhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhheeccchhhhhhhhhcCCCCCchhhhHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccChHHHHHHHHhCcCCCCCCC
Q 028533 183 DQLQHRIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 183 ~~l~~r~P~~IlkrAVrGMLPkn~Lr 208 (208)
++++.|+|++|+++||+||||+|+||
T Consensus 98 ~q~~~rdp~~Iv~~AV~gMLPkN~Lr 123 (165)
T KOG3203|consen 98 DQLADRDPCRIVRLAVYGMLPKNLLR 123 (165)
T ss_pred HHHhhhCHHHHHHHHHHhhCccchHH
Confidence 99999999999999999999999987
No 8
>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=7.1e-47 Score=303.49 Aligned_cols=101 Identities=54% Similarity=0.905 Sum_probs=99.0
Q ss_pred EEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchhhhhc
Q 028533 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQH 187 (208)
Q Consensus 108 W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~~l~~ 187 (208)
|+||||+||+|||||+.||++|+|||||+|||++||||+|||||||+|++||+||.+|.|++|+|||||+++.+++++++
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 cChHHHHHHHHhCcCCCCCCC
Q 028533 188 RIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 188 r~P~~IlkrAVrGMLPkn~Lr 208 (208)
++|++||++||+||||+|++|
T Consensus 81 ~~P~~i~~~aVrgMLP~n~~g 101 (128)
T PF00572_consen 81 KDPSRILKRAVRGMLPKNKLG 101 (128)
T ss_dssp SSHHHHHHHHHHTTSTTSHHH
T ss_pred cCHHHHHHHHHHHHCCCChhh
Confidence 999999999999999998753
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=99.97 E-value=1.4e-32 Score=224.60 Aligned_cols=86 Identities=37% Similarity=0.528 Sum_probs=80.5
Q ss_pred EEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchhhhhcc
Q 028533 109 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHR 188 (208)
Q Consensus 109 ~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~~l~~r 188 (208)
+||||+||+||||||.||++|+ |||+|||||||+|++||+|+.+|.||+|+.++|..+..+++++++|
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 5899999999999999999997 9999999999999999999999999999976666666689999999
Q ss_pred ChHHHHHHHHhCcCCCCC
Q 028533 189 IPERIIEHAVRGMLPKGR 206 (208)
Q Consensus 189 ~P~~IlkrAVrGMLPkn~ 206 (208)
+|++||++||+||||+|.
T Consensus 69 ~P~~il~~aVrGMLPk~~ 86 (142)
T TIGR01077 69 APSRIFRRTVRGMLPHKT 86 (142)
T ss_pred CHHHHHHHHHHHhCCCCC
Confidence 999999999999999983
No 10
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=99.96 E-value=2e-30 Score=212.93 Aligned_cols=86 Identities=35% Similarity=0.495 Sum_probs=74.9
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCC----ch
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEE----TF 182 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~----t~ 182 (208)
+-+||||+||+|||||+.||++|+ +||+||||||++|++||+|+.++.|+ ++|+ +.+.. ++
T Consensus 3 ~~~viDA~~~vlGRLAs~IA~~L~------------~Gd~VVViNa~kv~~tG~K~~~~~~y--~~~~-~~k~~~np~~~ 67 (146)
T PRK06394 3 AMVVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGNRERVIEKY--KQRR-ERGSHYNPYRN 67 (146)
T ss_pred ccEEEECCCCchHHHHHHHHHHHh------------CCCEEEEEechheEecCchhhheeeE--eCCC-CCcccCCCCCh
Confidence 458999999999999999999999 69999999999999999998764444 4454 34444 78
Q ss_pred hhhhccChHHHHHHHHhCcCC-CCCC
Q 028533 183 DQLQHRIPERIIEHAVRGMLP-KGRK 207 (208)
Q Consensus 183 ~~l~~r~P~~IlkrAVrGMLP-kn~L 207 (208)
+++++|+|++||++||+|||| ||++
T Consensus 68 ~~~~~r~P~~il~~AV~gMLP~kn~~ 93 (146)
T PRK06394 68 GPKYPRRPDRIFKRTIRGMLPYKKPR 93 (146)
T ss_pred HHhhhcCHHHHHHHHHHhcCCCCChh
Confidence 999999999999999999999 7765
No 11
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=99.96 E-value=1.9e-30 Score=222.73 Aligned_cols=90 Identities=31% Similarity=0.467 Sum_probs=78.7
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchhhh
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQL 185 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~~l 185 (208)
.+|+||||+||+||||||.||+.|+ +||+|||||||+|.|||+|+.+|.||+|.-+.+.......+++
T Consensus 3 ~~w~vIDA~g~vLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iTG~k~~~K~~y~~~lk~~~~~nP~~g~~ 70 (202)
T PTZ00068 3 KKVIVIDCKGHLLGRLASVVAKELL------------LGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNTNPRRGPF 70 (202)
T ss_pred CceEEEECCCCcHHHHHHHHHHHHh------------CCCEEEEEecceeEeecchhhheeeeEeeeEeeccCCCCcchh
Confidence 3799999999999999999999999 9999999999999999999999999999333332222336899
Q ss_pred hccChHHHHHHHHhCcCCC-CCC
Q 028533 186 QHRIPERIIEHAVRGMLPK-GRK 207 (208)
Q Consensus 186 ~~r~P~~IlkrAVrGMLPk-n~L 207 (208)
|+|.|++||++||+||||| |.+
T Consensus 71 ~~r~P~~Il~raVrGMLPkk~~~ 93 (202)
T PTZ00068 71 HHRAPSDIFWRTVRGMLPHKTKR 93 (202)
T ss_pred cccCHHHHHHHHHhhhCCCCChh
Confidence 9999999999999999998 543
No 12
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=99.38 E-value=6.7e-13 Score=114.13 Aligned_cols=85 Identities=33% Similarity=0.574 Sum_probs=73.2
Q ss_pred cceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceeeEEeCccccceeeeeccCCCCCCCCCchhh
Q 028533 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQ 184 (208)
Q Consensus 105 ~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI~vTG~K~~~K~Y~~HtgyPGglk~~t~~~ 184 (208)
..+-.+||+.||++||||+.+|+.|+ .|..|||+.||.|.++|+-+.+|-|-++.-. ..++
T Consensus 4 ~~~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~lrk~~~-------~ng~ 64 (197)
T KOG3204|consen 4 EVKLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLFLRKRLN-------RNGP 64 (197)
T ss_pred eEEEeeccchhhhhhhHHHHHHHHHh------------cCCeEEEEEEeEEEEecceecchHHHhhhhc-------ccCc
Confidence 34678999999999999999999999 9999999999999999998888855544211 1278
Q ss_pred hhccChHHHHHHHHhCcCCCCCCC
Q 028533 185 LQHRIPERIIEHAVRGMLPKGRKQ 208 (208)
Q Consensus 185 l~~r~P~~IlkrAVrGMLPkn~Lr 208 (208)
+|.|-|.+|++++|+||+|++.-|
T Consensus 65 ~hfr~ps~i~~~~vrgm~~~kt~r 88 (197)
T KOG3204|consen 65 FHFRAPSRILQKAVRGMYPHKTKR 88 (197)
T ss_pred chhhhHHHHHHHhhccccccCCCc
Confidence 999999999999999999998643
No 13
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=58.97 E-value=8.8 Score=31.81 Aligned_cols=44 Identities=11% Similarity=0.198 Sum_probs=30.0
Q ss_pred cceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEece-eeEE
Q 028533 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE-KVAV 157 (208)
Q Consensus 105 ~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAe-kI~v 157 (208)
..-|.|+|..|+++|+.....+.. .|. +| .+..|+|+|.+ +|.+
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 346999999999999985555443 222 22 36688889974 4544
No 14
>PLN02399 phospholipid hydroperoxide glutathione peroxidase
Probab=50.57 E-value=75 Score=28.15 Aligned_cols=28 Identities=32% Similarity=0.463 Sum_probs=18.0
Q ss_pred CCCccccccccccccCCCCcc--ccccccc
Q 028533 21 SSSFKTLNTGTTISSSTTPFL--GFSVASA 48 (208)
Q Consensus 21 ~~sf~~~~~~~~~~~~~~~~~--~~~~~~~ 48 (208)
+++|.--.++.++.+++|+|+ ||++..+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 (236)
T PLN02399 26 SMAFLVPSLKSSTGISKSAFLSNGFSLKSP 55 (236)
T ss_pred ccccccceeeeccccccchhhccccccccC
Confidence 455555556677778888887 5555544
No 15
>PF12396 DUF3659: Protein of unknown function (DUF3659) ; InterPro: IPR022124 This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
Probab=48.52 E-value=5.2 Score=29.13 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=23.8
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCC
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKN 133 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKh 133 (208)
.=.|+|.+|+++|||..--++.|.|+-
T Consensus 12 ~G~V~d~~G~~vG~vveGd~k~L~G~~ 38 (64)
T PF12396_consen 12 DGNVVDDDGNVVGRVVEGDPKKLVGKK 38 (64)
T ss_pred CCeEECCCCCEEEEEecCCHHHhcCCc
Confidence 346899999999999999999999873
No 16
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=46.82 E-value=24 Score=29.09 Aligned_cols=45 Identities=11% Similarity=0.066 Sum_probs=31.5
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEece-eeEEe
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE-KVAVS 158 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAe-kI~vT 158 (208)
..|.|+|.+|+.+|+.....+....|.. |+ .-.|+|+|.+ +|.+.
T Consensus 6 E~~~~vd~~~~~~g~~~r~~~~~~~~~~----h~----av~v~i~~~~g~vLL~ 51 (184)
T PRK03759 6 ELVVLLDEQGVPTGTAEKAAAHTADTPL----HL----AFSCYLFDADGRLLVT 51 (184)
T ss_pred eeEEEECCCCCCcccccHHHHHhcCCCe----ee----EEEEEEEcCCCeEEEE
Confidence 4799999999999998888775444542 22 2357778754 56553
No 17
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=38.93 E-value=8.4 Score=32.79 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=11.7
Q ss_pred cCcchhhhhhhccc
Q 028533 72 PDNQRWMFEQSEVN 85 (208)
Q Consensus 72 ~~~~r~m~~~~e~~ 85 (208)
||+|||+|++++++
T Consensus 90 ~e~pRW~~Vdv~~v 103 (156)
T COG2947 90 PEDPRWYCVDVRFV 103 (156)
T ss_pred cCCCCeeEEeeHHH
Confidence 47999999998754
No 18
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=38.90 E-value=17 Score=30.00 Aligned_cols=14 Identities=14% Similarity=0.669 Sum_probs=12.4
Q ss_pred ccceEEEEeCCCCC
Q 028533 104 SDKTWYVVDATDKI 117 (208)
Q Consensus 104 ~~r~W~VIDA~gqi 117 (208)
..|-|+|=||.|++
T Consensus 47 lsR~W~ITd~~g~v 60 (126)
T COG2967 47 LSRYWLITDGNGRV 60 (126)
T ss_pred eeeEEEEecCCCcE
Confidence 57999999999986
No 19
>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=38.41 E-value=21 Score=28.69 Aligned_cols=41 Identities=17% Similarity=0.163 Sum_probs=29.8
Q ss_pred EEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEece-eeEE
Q 028533 109 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE-KVAV 157 (208)
Q Consensus 109 ~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAe-kI~v 157 (208)
.|+|.+|+.+|+.....+....|... .+-.|+|+|.+ +|.+
T Consensus 2 ~~~d~~~~~~g~~~r~~~~~~~g~~h--------~~v~v~v~~~~g~vLl 43 (158)
T TIGR02150 2 ILVDENDNPIGTASKAEVHLQETPLH--------RAFSVFLFNEEGQLLL 43 (158)
T ss_pred EEECCCCCEeeeeeHHHhhhcCCCeE--------EEEEEEEEcCCCeEEE
Confidence 58999999999988877765444422 25568889875 6665
No 20
>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=37.53 E-value=35 Score=24.79 Aligned_cols=29 Identities=34% Similarity=0.500 Sum_probs=20.3
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
..|+=|-+ -|.+|..++.+|. .||.|.|.
T Consensus 47 ~~~~~v~~----~g~~A~~~~~~l~------------kG~~V~V~ 75 (104)
T PF00436_consen 47 TDWINVVA----WGKLAENVAEYLK------------KGDRVYVE 75 (104)
T ss_dssp EEEEEEEE----EHHHHHHHHHH--------------TT-EEEEE
T ss_pred eEEEEEEe----eeecccccceEEc------------CCCEEEEE
Confidence 45766655 4889999999997 89988775
No 21
>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=33.30 E-value=45 Score=23.84 Aligned_cols=30 Identities=33% Similarity=0.528 Sum_probs=23.3
Q ss_pred cceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 105 ~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
...|+=|-+ -|.+|..++++|+ .||.|+|.
T Consensus 42 ~~~~~~v~~----~g~~a~~~~~~~~------------kG~~V~v~ 71 (100)
T cd04496 42 ETDWIRVVA----FGKLAENAAKYLK------------KGDLVYVE 71 (100)
T ss_pred ccEEEEEEE----EhHHHHHHHHHhC------------CCCEEEEE
Confidence 346777755 4559999999997 89999886
No 22
>PRK05853 hypothetical protein; Validated
Probab=31.60 E-value=83 Score=26.56 Aligned_cols=29 Identities=34% Similarity=0.504 Sum_probs=22.8
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
-.|+-|- +-|++|..++++|. .|+.|+|.
T Consensus 42 T~wi~V~----~wg~lAe~v~~~L~------------KG~~V~V~ 70 (161)
T PRK05853 42 SLFITVN----CWGRLVTGVGAALG------------KGAPVIVV 70 (161)
T ss_pred ccEEEEE----EEhHHHHHHHHHcC------------CCCEEEEE
Confidence 3576554 56789999999997 79888886
No 23
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=30.03 E-value=79 Score=25.21 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=22.6
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
..||-|-+ -|++|..++++|. .|+.|.|-
T Consensus 46 t~w~~v~~----fg~~Ae~v~~~l~------------KG~~V~V~ 74 (131)
T PRK07274 46 ADFINVVL----WGKLAETLASYAS------------KGSLISID 74 (131)
T ss_pred EEEEEEEE----ehHHHHHHHHHcC------------CCCEEEEE
Confidence 46887754 5789999999987 68877764
No 24
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=29.27 E-value=50 Score=27.21 Aligned_cols=28 Identities=36% Similarity=0.544 Sum_probs=22.8
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
.||=| -+-|++|..++++|+ .|+.|+|.
T Consensus 51 ~~~~v----v~wgk~Ae~~~~yl~------------KG~~V~Ve 78 (167)
T COG0629 51 DWIRV----VIWGKLAENAAEYLK------------KGSLVYVE 78 (167)
T ss_pred ceEEE----EEehHHHHHHHHHhc------------CCCEEEEE
Confidence 56655 357889999999997 79988886
No 25
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=27.50 E-value=1.2e+02 Score=27.21 Aligned_cols=82 Identities=20% Similarity=0.253 Sum_probs=50.5
Q ss_pred ccceEEEeccccccccCcchhhhhhhcccCCcc---------------------cceeccCCCCCCCcc-cceEEEE---
Q 028533 57 KRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDI---------------------WNNTWYPKAADHRHS-DKTWYVV--- 111 (208)
Q Consensus 57 ~~~~~v~c~~~~~~v~~~~r~m~~~~e~~g~~~---------------------~~kT~~~k~~~~~~~-~r~W~VI--- 111 (208)
...|+|+|.-+. .+++-|||-+.+---|+.+ -+.|+-+|+.+-+.. ...-+++
T Consensus 22 ~qr~~~~c~l~~--~~~~k~wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp 99 (224)
T KOG2255|consen 22 KQRFSVHCDLKP--RVSIKPWLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRP 99 (224)
T ss_pred ccchheeeeccc--CCCCCceEEEecCCCcccccccchhhHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCc
Confidence 566888998754 3355589998886656443 345555544332111 1223333
Q ss_pred ----eCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceee
Q 028533 112 ----DATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKV 155 (208)
Q Consensus 112 ----DA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI 155 (208)
++.|.-+|++|+.-++.++ +||||--|--
T Consensus 100 ~qymN~SgesV~kva~~y~i~~~---------------~ivvIhDEl~ 132 (224)
T KOG2255|consen 100 QQYMNFSGESVGKVAALYKIPLR---------------HIVVIHDELE 132 (224)
T ss_pred HhhhccccchhhhhHHhhcchhe---------------eEEEEecccc
Confidence 3678888898888887775 6777765543
No 26
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=27.11 E-value=57 Score=25.13 Aligned_cols=29 Identities=10% Similarity=0.083 Sum_probs=22.3
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
-.|+-|- +-|++|..++++|. .||.|.|.
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 3677664 56789999999986 68888775
No 27
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=25.42 E-value=75 Score=27.18 Aligned_cols=29 Identities=28% Similarity=0.497 Sum_probs=22.4
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
-.||-| .+-|++|..++++|+ .|+.|.|.
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 466789999999997 67777664
No 28
>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=25.32 E-value=1.1e+02 Score=22.93 Aligned_cols=35 Identities=20% Similarity=0.191 Sum_probs=23.8
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEeceee
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKV 155 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAekI 155 (208)
.=+||||.+. .-++..+...|. .|-+||..|-.=+
T Consensus 60 ~dvvVE~t~~--~~~~~~~~~~L~------------~G~~VVt~nk~al 94 (117)
T PF03447_consen 60 IDVVVECTSS--EAVAEYYEKALE------------RGKHVVTANKGAL 94 (117)
T ss_dssp -SEEEE-SSC--HHHHHHHHHHHH------------TTCEEEES-HHHH
T ss_pred CCEEEECCCc--hHHHHHHHHHHH------------CCCeEEEECHHHh
Confidence 3499999665 456677788887 7999998886533
No 29
>KOG2415 consensus Electron transfer flavoprotein ubiquinone oxidoreductase [Energy production and conversion]
Probab=25.25 E-value=30 Score=34.63 Aligned_cols=64 Identities=23% Similarity=0.398 Sum_probs=52.5
Q ss_pred hhhhhhhcccCCcccceeccCCCCCCCcccceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 76 RWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 76 r~m~~~~e~~g~~~~~kT~~~k~~~~~~~~r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
|||.+.+|.+|-.|+ |--+ -.-+++|++|.+.|-.-.-+-.-=-|+-|-+|.+.++.-..|.|.
T Consensus 187 ~wLg~kAEe~GvEiy-----Pg~a------aSevly~edgsVkGiaT~D~GI~k~G~pKd~FerGme~hak~Tif 250 (621)
T KOG2415|consen 187 RWLGEKAEELGVEIY-----PGFA------ASEVLYDEDGSVKGIATNDVGISKDGAPKDTFERGMEFHAKVTIF 250 (621)
T ss_pred HHHHHHHHhhCceec-----cccc------hhheeEcCCCcEeeEeeccccccCCCCccccccccceecceeEEE
Confidence 999999999999984 3222 133899999999997777777777899999999999998888775
No 30
>PLN02982 galactinol-raffinose galactosyltransferase/ghydrolase, hydrolyzing O-glycosyl compounds
Probab=25.12 E-value=1.3e+02 Score=32.00 Aligned_cols=40 Identities=8% Similarity=0.375 Sum_probs=25.7
Q ss_pred CcchhhhhhhcccCCcccceeccCCCCCCCcccceEEEEeCCC
Q 028533 73 DNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATD 115 (208)
Q Consensus 73 ~~~r~m~~~~e~~g~~~~~kT~~~k~~~~~~~~r~W~VIDA~g 115 (208)
++-||||--- =.--||+.|+-+.+.-+..+-+|+++|..+
T Consensus 97 ~~~rFms~FR---fK~WWmt~~vG~~G~Dip~ETQ~llle~~~ 136 (865)
T PLN02982 97 EGRDFLSIFR---FKTWWSTMWIGSSGSDLQMETQWVLLKVPE 136 (865)
T ss_pred cCceEEeeee---hhhhccchhhcCCCCCCChhheEEEEEcCC
Confidence 6677776432 222467777766444344567999999886
No 31
>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=24.86 E-value=83 Score=25.27 Aligned_cols=43 Identities=16% Similarity=0.127 Sum_probs=27.0
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEEece-eeEE
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAE-KVAV 157 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVINAe-kI~v 157 (208)
.|-|+|..|++.|+..-..+....+. |+ ..-.|+|+|.+ +|.+
T Consensus 3 ~~~~~d~~~~~~g~~~r~~~~~~~~~----~~----~~v~v~i~~~~~~iLl 46 (165)
T cd02885 3 LVILVDEDDNPIGTAEKLEAHLKGTL----LH----RAFSVFLFNSKGRLLL 46 (165)
T ss_pred EEEEECCCCCCccccCHHHHhhcCCc----ce----eEEEEEEEcCCCcEEE
Confidence 68899999999997555555443322 11 13347778875 4444
No 32
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=24.67 E-value=79 Score=26.83 Aligned_cols=29 Identities=24% Similarity=0.312 Sum_probs=21.9
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
-.||-|. +.|++|..++++|. .|+.|+|.
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 3698885 56788999999987 56666654
No 33
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=23.94 E-value=71 Score=27.59 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=22.1
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
.|+=|- +-|++|..+|++|. .||.|+|.
T Consensus 53 ~fi~V~----~Wg~~Ae~va~~L~------------KGd~V~V~ 80 (186)
T PRK07772 53 LFLRCS----IWRQAAENVAESLT------------KGMRVIVT 80 (186)
T ss_pred eEEEEE----EecHHHHHHHHhcC------------CCCEEEEE
Confidence 465453 56889999999987 79998886
No 34
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=23.88 E-value=67 Score=26.98 Aligned_cols=21 Identities=14% Similarity=0.120 Sum_probs=16.3
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHh
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIR 130 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~ 130 (208)
-.|+-| .+-|++|..+|++|.
T Consensus 46 tdfi~v----v~wgk~Ae~~~~~l~ 66 (162)
T PRK07275 46 ADFINC----VIWRQQAENLANWAK 66 (162)
T ss_pred eeEEEE----EEEcHHHHHHHHHcC
Confidence 367655 367899999999986
No 35
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=23.31 E-value=1.1e+02 Score=26.01 Aligned_cols=29 Identities=24% Similarity=0.490 Sum_probs=22.9
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
-.||-|. +.|++|..++++|. .|+.|.|-
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 4798886 46789999999987 67777764
No 36
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=23.24 E-value=70 Score=27.39 Aligned_cols=20 Identities=15% Similarity=0.277 Sum_probs=15.9
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHh
Q 028533 107 TWYVVDATDKILGRLASTIAIHIR 130 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~ 130 (208)
.||=|- +-|++|..++++|.
T Consensus 49 ~fi~v~----~fg~~AE~~~~~l~ 68 (182)
T PRK08486 49 CFIDIR----LFGRTAEIANQYLS 68 (182)
T ss_pred eEEEEE----EEhHHHHHHHHHcC
Confidence 676554 56889999999987
No 37
>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=23.14 E-value=84 Score=27.64 Aligned_cols=33 Identities=24% Similarity=0.406 Sum_probs=19.8
Q ss_pred cceEEEEe-CC---CCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 105 DKTWYVVD-AT---DKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 105 ~r~W~VID-A~---gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
.+.|+||| +. .++++-|.. -+.++ -.|||.||=
T Consensus 110 ~~~vlVilDs~H~~~hvl~eL~~-y~plv------------~~G~Y~IVe 146 (206)
T PF04989_consen 110 PHPVLVILDSSHTHEHVLAELEA-YAPLV------------SPGSYLIVE 146 (206)
T ss_dssp -SSEEEEESS----SSHHHHHHH-HHHT--------------TT-EEEET
T ss_pred CCceEEEECCCccHHHHHHHHHH-hCccC------------CCCCEEEEE
Confidence 45788776 54 677777765 44444 489999984
No 38
>PHA02754 hypothetical protein; Provisional
Probab=23.05 E-value=77 Score=23.44 Aligned_cols=15 Identities=20% Similarity=0.589 Sum_probs=12.9
Q ss_pred CCCEEEEEeceeeEE
Q 028533 143 MGAYVIVVNAEKVAV 157 (208)
Q Consensus 143 ~GD~VVVINAekI~v 157 (208)
.||.+|||-|+-|++
T Consensus 43 SGdkIVVi~aD~I~i 57 (67)
T PHA02754 43 SGDKIVVITADAIKI 57 (67)
T ss_pred cCCEEEEEEcceEEE
Confidence 499999999888776
No 39
>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=22.97 E-value=66 Score=26.64 Aligned_cols=28 Identities=36% Similarity=0.555 Sum_probs=22.3
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
.|+-|- +.|++|..++++|. .|+.|+|.
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 577765 56789999999997 78888775
No 40
>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=22.92 E-value=46 Score=25.41 Aligned_cols=14 Identities=21% Similarity=0.674 Sum_probs=11.2
Q ss_pred ccceEEEEeCCCCC
Q 028533 104 SDKTWYVVDATDKI 117 (208)
Q Consensus 104 ~~r~W~VIDA~gqi 117 (208)
..|.|.|.|++|++
T Consensus 31 ~sR~W~I~d~~g~~ 44 (90)
T PF04379_consen 31 LSRHWIITDADGHV 44 (90)
T ss_dssp EEEEEEEEETTS-E
T ss_pred EccEEEEEeCCCCE
Confidence 57999999999854
No 41
>PF05892 Tricho_coat: Trichovirus coat protein; InterPro: IPR008879 This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichoviruses and Vitiviruses.; GO: 0019028 viral capsid
Probab=22.60 E-value=9.5 Score=33.48 Aligned_cols=40 Identities=23% Similarity=0.236 Sum_probs=30.2
Q ss_pred cCCCCCCCcccceEEEEe-CCCCCchhhHHHHHHHHhcCCCCccC
Q 028533 95 YPKAADHRHSDKTWYVVD-ATDKILGRLASTIAIHIRGKNLATYT 138 (208)
Q Consensus 95 ~~k~~~~~~~~r~W~VID-A~gqiLGRLAS~IAk~L~GKhKp~yt 138 (208)
+|+... +-.|+.+| ++|-.+-+|-..=++.++.-|.--|.
T Consensus 133 mp~~g~----k~PqV~FDFn~GL~l~~L~~~e~~vIq~ln~RLfr 173 (194)
T PF05892_consen 133 MPKLGG----KEPQVMFDFNSGLDLSRLTKEEAKVIQNLNQRLFR 173 (194)
T ss_pred hHhhcC----CCCeEeeecccCcchhhcCHHHHHHHHHHHHHHHH
Confidence 455444 67899999 99999999988888877766554443
No 42
>PF05691 Raffinose_syn: Raffinose synthase or seed imbibition protein Sip1; InterPro: IPR008811 This family consists of several raffinose synthase proteins, also known as seed imbibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(1-->2)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase (2.4.1.82 from EC) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway [].
Probab=22.43 E-value=1.8e+02 Score=30.48 Aligned_cols=65 Identities=15% Similarity=0.219 Sum_probs=43.6
Q ss_pred ccCCCCcccccccccCCCCCcccccceEEEeccccccccCcchhhhhhhcccCCcccceeccCCCCCCCcccceEEEEeC
Q 028533 34 SSSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDA 113 (208)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~c~~~~~~v~~~~r~m~~~~e~~g~~~~~kT~~~k~~~~~~~~r~W~VIDA 113 (208)
......|+|+....+ ++-.|-+-.. + ++.||||--- =..-||+.++-+...-+..+-+|+|++.
T Consensus 40 ~~~~g~f~g~~~~~~---------~sr~v~~lG~--l--~~~rfm~~fR---fK~WWm~p~~G~~g~dip~eTQ~ll~e~ 103 (747)
T PF05691_consen 40 GAVDGAFLGFTADEP---------SSRHVFSLGK--L--RGRRFMSLFR---FKLWWMTPRMGTSGRDIPMETQFLLLES 103 (747)
T ss_pred cCCCceEEcccCCCC---------CcceeEeccc--c--cCceeeehhh---hhhhccccccCCCcccCChhhheeeeec
Confidence 445678999876532 2233434332 3 7889998765 2356799888877755566779999998
Q ss_pred C
Q 028533 114 T 114 (208)
Q Consensus 114 ~ 114 (208)
.
T Consensus 104 ~ 104 (747)
T PF05691_consen 104 P 104 (747)
T ss_pred C
Confidence 7
No 43
>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=21.35 E-value=1.9e+02 Score=21.09 Aligned_cols=24 Identities=25% Similarity=0.321 Sum_probs=15.6
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHh
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIR 130 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~ 130 (208)
--+||||++. .+-.-...+.+.|.
T Consensus 82 ~ii~vv~~~~-~~~~~~~~~~~~l~ 105 (116)
T PF01926_consen 82 LIIYVVDASN-PITEDDKNILRELK 105 (116)
T ss_dssp EEEEEEETTS-HSHHHHHHHHHHHH
T ss_pred EEEEEEECCC-CCCHHHHHHHHHHh
Confidence 4789999877 33344456666664
No 44
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=21.30 E-value=84 Score=24.90 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=21.1
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
.||=|= .-|++|..++++|. .|+.|.|.
T Consensus 44 ~w~~v~----~wg~~Ae~~~~~l~------------KG~~V~V~ 71 (121)
T PRK07459 44 DWFNLE----IWGKTAQVAADYVK------------KGSLIGIT 71 (121)
T ss_pred eEEEEE----EehHHHHHHHHHcC------------CCCEEEEE
Confidence 687553 46789999999986 67776664
No 45
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.95 E-value=79 Score=26.69 Aligned_cols=28 Identities=21% Similarity=0.449 Sum_probs=21.3
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
.||=|- +.|++|..++++|. .|+.|+|-
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 687774 56889999999987 57666664
No 46
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=20.76 E-value=83 Score=26.88 Aligned_cols=29 Identities=31% Similarity=0.498 Sum_probs=22.4
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHhcCCCCccCCCCCCCCEEEEE
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~ytP~~D~GD~VVVI 150 (208)
-.||-|- +.|++|..++++|. .||.|+|.
T Consensus 53 t~w~~Vv----~wgk~Ae~v~~~L~------------KG~~V~Ve 81 (175)
T PRK13732 53 TEWHRVV----LFGKLAEVAGEYLR------------KGAQVYIE 81 (175)
T ss_pred eeEEEEE----EecHHHHHHHHhcC------------CCCEEEEE
Confidence 3687775 45779999999987 68777765
No 47
>PRK13975 thymidylate kinase; Provisional
Probab=20.60 E-value=1.1e+02 Score=24.55 Aligned_cols=24 Identities=25% Similarity=0.414 Sum_probs=21.8
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHh
Q 028533 107 TWYVVDATDKILGRLASTIAIHIR 130 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~ 130 (208)
.|++||++++.+-.++..|.+.|.
T Consensus 166 ~~~~Id~~~~~~eev~~~I~~~i~ 189 (196)
T PRK13975 166 GFIVIDTTNKSIEEVFNEILNKIK 189 (196)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHH
Confidence 599999999999999999998886
No 48
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=20.30 E-value=81 Score=26.83 Aligned_cols=21 Identities=14% Similarity=0.159 Sum_probs=16.5
Q ss_pred ceEEEEeCCCCCchhhHHHHHHHHh
Q 028533 106 KTWYVVDATDKILGRLASTIAIHIR 130 (208)
Q Consensus 106 r~W~VIDA~gqiLGRLAS~IAk~L~ 130 (208)
..||-|= +-|++|..++++|.
T Consensus 46 tdwi~~v----~wgk~Ae~~~~~l~ 66 (173)
T PRK06751 46 ADFINCV----IWRKQAENVANYLK 66 (173)
T ss_pred EEEEEEE----EeCcHHHHHHHHcC
Confidence 3687774 56778999999986
No 49
>TIGR00292 thiazole biosynthesis enzyme. This enzyme is involved in the biosynthesis of the thiamine precursor thiazole, and is repressed by thiamine.This family includes c-thi1, a Citrus gene induced during natural and ethylene induced fruit maturation and is highly homologous to plant and yeast thi genes involved in thiamine biosynthesis.
Probab=20.12 E-value=31 Score=30.31 Aligned_cols=23 Identities=30% Similarity=0.274 Sum_probs=19.8
Q ss_pred eEEEEeCCCCCchhhHHHHHHHHh
Q 028533 107 TWYVVDATDKILGRLASTIAIHIR 130 (208)
Q Consensus 107 ~W~VIDA~gqiLGRLAS~IAk~L~ 130 (208)
--+||||+|+- ++++..+++++.
T Consensus 159 Ak~VVdATG~~-a~v~~~l~~~~~ 181 (254)
T TIGR00292 159 SRVVVDATGHD-AEIVAVCAKKIV 181 (254)
T ss_pred cCEEEEeecCC-chHHHHHHHHcC
Confidence 45899999987 799999999975
Done!