Query 032585
Match_columns 137
No_of_seqs 123 out of 215
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:21:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032585hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03652 UPF0081: Uncharacteri 99.8 1.4E-18 3E-23 131.0 7.5 73 63-135 1-87 (135)
2 COG0816 Predicted endonuclease 99.7 4.8E-18 1E-22 130.7 7.2 73 62-134 1-88 (141)
3 PRK00109 Holliday junction res 99.7 2.9E-17 6.3E-22 124.2 8.8 72 62-133 3-88 (138)
4 TIGR00250 RNAse_H_YqgF RNAse H 99.7 2.4E-16 5.2E-21 118.2 8.1 68 66-133 1-82 (130)
5 smart00732 YqgFc Likely ribonu 98.3 7.8E-06 1.7E-10 55.8 8.3 69 63-133 1-83 (99)
6 PRK00039 ruvC Holliday junctio 94.0 0.21 4.5E-06 39.0 6.3 47 63-109 2-60 (164)
7 cd00529 RuvC_resolvase Hollida 93.9 0.22 4.8E-06 37.9 6.3 46 64-109 1-58 (154)
8 PF02075 RuvC: Crossover junct 92.8 0.43 9.3E-06 36.4 6.2 45 65-109 1-57 (149)
9 TIGR00228 ruvC crossover junct 85.5 1.4 3E-05 34.8 4.1 45 65-109 1-56 (156)
10 PF04312 DUF460: Protein of un 83.5 5.3 0.00012 31.3 6.6 68 61-131 30-101 (138)
11 PF14239 RRXRR: RRXRR protein 78.4 5.3 0.00012 32.3 5.1 20 62-81 50-69 (176)
12 COG1548 Predicted transcriptio 73.4 8 0.00017 34.1 5.2 72 63-134 3-88 (330)
13 PF14639 YqgF: Holliday-juncti 72.8 28 0.0006 26.9 7.7 70 62-131 4-88 (150)
14 COG0817 RuvC Holliday junction 70.5 5.6 0.00012 31.9 3.4 44 66-109 1-56 (160)
15 PLN03184 chloroplast Hsp70; Pr 65.1 6 0.00013 37.0 3.0 30 51-80 26-56 (673)
16 PF00012 HSP70: Hsp70 protein; 62.9 6.2 0.00013 34.8 2.5 16 65-80 1-16 (602)
17 TIGR01865 cas_Csn1 CRISPR-asso 60.9 6.1 0.00013 38.0 2.3 18 64-81 2-19 (805)
18 KOG1503 Phosphoribosylpyrophos 56.9 19 0.00042 31.6 4.4 62 64-131 127-191 (354)
19 COG3513 Predicted CRISPR-assoc 55.6 12 0.00026 37.4 3.3 19 62-80 3-21 (1088)
20 COG2183 Tex Transcriptional ac 50.0 55 0.0012 32.2 6.7 69 62-134 329-411 (780)
21 PF01548 DEDD_Tnp_IS110: Trans 48.1 48 0.001 23.8 4.7 48 65-113 1-51 (144)
22 PF14450 FtsA: Cell division p 44.8 55 0.0012 23.5 4.6 16 65-80 1-16 (120)
23 PF05188 MutS_II: MutS domain 42.9 1E+02 0.0022 21.4 5.6 49 64-113 2-53 (137)
24 cd06097 Aspergillopepsin_like 42.1 19 0.0004 28.8 2.0 16 63-78 262-277 (278)
25 PF14796 AP3B1_C: Clathrin-ada 41.5 32 0.0007 26.9 3.2 39 26-73 104-143 (145)
26 COG0623 FabI Enoyl-[acyl-carri 41.3 4.5 9.8E-05 34.7 -1.7 45 62-109 168-212 (259)
27 PF00370 FGGY_N: FGGY family o 41.1 71 0.0015 25.0 5.1 16 65-80 2-17 (245)
28 PRK13410 molecular chaperone D 39.7 23 0.00049 33.3 2.4 18 63-80 2-19 (668)
29 TIGR01315 5C_CHO_kinase FGGY-f 39.7 58 0.0013 29.3 4.9 27 64-90 1-33 (541)
30 COG1940 NagC Transcriptional r 38.1 94 0.002 25.3 5.5 20 62-81 5-24 (314)
31 KOG1794 N-Acetylglucosamine ki 37.6 1.5E+02 0.0034 26.4 7.0 73 63-135 3-97 (336)
32 COG1924 Activator of 2-hydroxy 37.5 43 0.00094 30.4 3.7 50 38-87 110-161 (396)
33 TIGR02350 prok_dnaK chaperone 37.0 26 0.00056 31.7 2.3 16 65-80 2-17 (595)
34 PTZ00400 DnaK-type molecular c 36.8 26 0.00057 32.6 2.3 19 62-80 40-58 (663)
35 PRK13411 molecular chaperone D 34.8 31 0.00066 32.1 2.4 17 64-80 3-19 (653)
36 PRK13320 pantothenate kinase; 34.7 2.6E+02 0.0055 22.9 7.7 17 65-81 4-20 (244)
37 PTZ00009 heat shock 70 kDa pro 34.5 33 0.0007 31.9 2.5 19 62-80 3-21 (653)
38 PF00026 Asp: Eukaryotic aspar 34.2 41 0.00089 26.6 2.8 18 62-79 299-316 (317)
39 TIGR01312 XylB D-xylulose kina 33.9 51 0.0011 28.4 3.5 16 66-81 1-16 (481)
40 PF09298 FAA_hydrolase_N: Fuma 33.9 23 0.00051 25.9 1.2 12 71-82 14-25 (107)
41 PRK01433 hscA chaperone protei 33.6 32 0.00069 31.8 2.3 18 63-80 19-36 (595)
42 cd05474 SAP_like SAPs, pepsin- 33.5 37 0.0008 26.9 2.4 18 62-79 277-294 (295)
43 TIGR00241 CoA_E_activ CoA-subs 33.3 75 0.0016 25.4 4.2 17 65-81 2-18 (248)
44 PRK00290 dnaK molecular chaper 33.2 33 0.00071 31.5 2.3 17 64-80 3-19 (627)
45 cd03070 PDI_b_ERp44 PDIb famil 32.3 81 0.0017 22.7 3.8 35 100-134 8-47 (91)
46 PTZ00186 heat shock 70 kDa pre 32.0 39 0.00084 31.8 2.6 19 63-81 27-45 (657)
47 cd05487 renin_like Renin stimu 31.7 38 0.00083 27.8 2.3 19 62-80 308-326 (326)
48 PRK13930 rod shape-determining 31.6 36 0.00078 27.9 2.1 17 64-80 9-25 (335)
49 COG0159 TrpA Tryptophan syntha 31.6 75 0.0016 27.2 4.1 37 96-133 217-263 (265)
50 PRK05183 hscA chaperone protei 31.6 35 0.00076 31.5 2.3 18 63-80 19-36 (616)
51 PRK13310 N-acetyl-D-glucosamin 31.2 89 0.0019 25.3 4.3 17 65-81 2-18 (303)
52 PF06277 EutA: Ethanolamine ut 30.1 2.1E+02 0.0046 26.6 6.9 69 65-133 5-111 (473)
53 TIGR02867 spore_II_P stage II 29.1 56 0.0012 26.5 2.8 24 110-133 113-136 (196)
54 CHL00094 dnaK heat shock prote 28.8 44 0.00095 30.8 2.4 17 64-80 3-19 (621)
55 PRK05082 N-acetylmannosamine k 28.5 1.5E+02 0.0032 23.9 5.1 18 64-81 2-19 (291)
56 COG2433 Uncharacterized conser 28.3 1.7E+02 0.0037 28.3 6.2 62 63-129 244-311 (652)
57 cd05476 pepsin_A_like_plant Ch 27.6 56 0.0012 26.0 2.5 19 62-80 245-263 (265)
58 cd05472 cnd41_like Chloroplast 27.5 55 0.0012 26.4 2.5 19 62-80 279-297 (299)
59 cd06098 phytepsin Phytepsin, a 27.1 48 0.001 27.2 2.1 17 62-78 300-316 (317)
60 COG4012 Uncharacterized protei 26.6 2.9E+02 0.0063 24.7 6.9 64 63-126 1-71 (342)
61 COG0443 DnaK Molecular chapero 26.4 57 0.0012 30.2 2.7 20 62-81 4-23 (579)
62 PF01385 OrfB_IS605: Probable 26.0 40 0.00087 25.4 1.4 20 61-80 122-141 (227)
63 cd06096 Plasmepsin_5 Plasmepsi 25.6 59 0.0013 26.8 2.4 19 62-80 305-323 (326)
64 PF07454 SpoIIP: Stage II spor 25.3 69 0.0015 27.2 2.8 23 110-132 191-213 (268)
65 COG3703 ChaC Uncharacterized p 24.9 64 0.0014 26.6 2.4 19 62-80 57-75 (190)
66 cd05477 gastricsin Gastricsins 24.9 59 0.0013 26.5 2.2 18 62-79 300-317 (318)
67 PTZ00294 glycerol kinase-like 24.7 1.5E+02 0.0033 26.2 4.9 18 64-81 3-20 (504)
68 PRK09557 fructokinase; Reviewe 24.6 1.5E+02 0.0032 24.1 4.5 17 65-81 2-18 (301)
69 PF06723 MreB_Mbl: MreB/Mbl pr 24.2 63 0.0014 28.0 2.4 17 64-80 2-18 (326)
70 cd05486 Cathespin_E Cathepsin 23.5 59 0.0013 26.5 2.0 16 63-78 300-315 (316)
71 TIGR00904 mreB cell shape dete 23.4 62 0.0014 26.8 2.2 15 66-80 5-19 (333)
72 TIGR01991 HscA Fe-S protein as 23.1 54 0.0012 30.1 1.9 16 65-80 1-16 (599)
73 PRK13311 N-acetyl-D-glucosamin 22.7 1.6E+02 0.0035 23.4 4.4 17 65-81 2-18 (256)
74 PF08608 Wyosine_form: Wyosine 22.4 80 0.0017 21.2 2.2 21 114-134 25-45 (62)
75 cd05475 nucellin_like Nucellin 22.1 57 0.0012 26.2 1.6 19 62-80 253-271 (273)
76 TIGR00744 ROK_glcA_fam ROK fam 22.1 1.7E+02 0.0036 23.7 4.4 16 66-81 1-16 (318)
77 smart00842 FtsA Cell division 22.0 76 0.0016 24.2 2.2 16 65-80 1-16 (187)
78 cd05488 Proteinase_A_fungi Fun 21.7 69 0.0015 26.3 2.1 17 62-78 303-319 (320)
79 CHL00163 ycf65 putative riboso 21.7 1.8E+02 0.0039 21.8 4.1 45 64-108 4-51 (99)
80 TIGR01311 glycerol_kin glycero 21.4 2E+02 0.0044 25.3 5.0 18 64-81 2-19 (493)
81 cd05473 beta_secretase_like Be 21.1 87 0.0019 26.2 2.6 19 62-80 327-345 (364)
82 PRK11678 putative chaperone; P 21.1 67 0.0015 28.8 2.0 16 65-80 2-17 (450)
83 COG4820 EutJ Ethanolamine util 20.9 5.1E+02 0.011 22.4 7.1 62 62-133 28-89 (277)
84 PTZ00013 plasmepsin 4 (PM4); P 20.6 97 0.0021 27.8 2.9 19 62-80 430-448 (450)
85 TIGR01174 ftsA cell division p 20.4 3E+02 0.0065 23.2 5.7 16 65-80 2-17 (371)
86 PRK00047 glpK glycerol kinase; 20.1 2.3E+02 0.0049 25.0 5.1 18 64-81 6-23 (498)
No 1
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=99.76 E-value=1.4e-18 Score=131.02 Aligned_cols=73 Identities=27% Similarity=0.322 Sum_probs=63.2
Q ss_pred ceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585 63 GFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR 128 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r 128 (137)
+|+||||||+||||||||| +.+|+|++||...+ ..+++.|.++++++ |||| +++++++.+++|+++
T Consensus 1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~ 80 (135)
T PF03652_consen 1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEE 80 (135)
T ss_dssp -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHH
T ss_pred CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHH
Confidence 6899999999999999994 77899999999653 35788999999886 9999 899999999999999
Q ss_pred HHHhcCC
Q 032585 129 WFYYCDG 135 (137)
Q Consensus 129 L~~~~~~ 135 (137)
|++.+++
T Consensus 81 L~~~~~~ 87 (135)
T PF03652_consen 81 LKKRFPG 87 (135)
T ss_dssp HHHHH-T
T ss_pred HHHhcCC
Confidence 9998743
No 2
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=99.74 E-value=4.8e-18 Score=130.70 Aligned_cols=73 Identities=27% Similarity=0.350 Sum_probs=65.4
Q ss_pred cceEEEeecCCceEEEEeec--ceeeeeeeeEEccch--hHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHH
Q 032585 62 GGFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRGE--KLELQLLEIAQRE----VILG-------SYEPQLNLLSKKK 126 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~~--~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA 126 (137)
++++||||||+||||||+|+ +.+|+|++||.+.+. .+++.|.+++++| |||| +++++++.+++|+
T Consensus 1 ~~~ilalD~G~KrIGvA~sd~~~~~A~pl~~i~~~~~~~~~~~~l~~li~~~~~~~vVVGlP~~m~g~~~~~~~~~~~f~ 80 (141)
T COG0816 1 GMRILALDVGTKRIGVAVSDILGSLASPLETIKRKNGKPQDFNALLKLVKEYQVDTVVVGLPLNMDGTEGPRAELARKFA 80 (141)
T ss_pred CceEEEEecCCceEEEEEecCCCccccchhhheeccccHhhHHHHHHHHHHhCCCEEEEecCcCCCCCcchhHHHHHHHH
Confidence 47899999999999999996 669999999998654 3788899999886 9999 8999999999999
Q ss_pred HHHHHhcC
Q 032585 127 LRWFYYCD 134 (137)
Q Consensus 127 ~rL~~~~~ 134 (137)
++|++.++
T Consensus 81 ~~L~~r~~ 88 (141)
T COG0816 81 ERLKKRFN 88 (141)
T ss_pred HHHHHhcC
Confidence 99999875
No 3
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=99.72 E-value=2.9e-17 Score=124.22 Aligned_cols=72 Identities=25% Similarity=0.285 Sum_probs=64.5
Q ss_pred cceEEEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHH
Q 032585 62 GGFSLGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKL 127 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~ 127 (137)
.+++||||||+||||||+|| +.+|+|++|+...+ ...++.|.+++.++ |||| ++++++..|++|++
T Consensus 3 ~~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~ 82 (138)
T PRK00109 3 SGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFAN 82 (138)
T ss_pred CCcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHHHH
Confidence 46799999999999999995 89999999998754 34678899999886 9999 99999999999999
Q ss_pred HHHHhc
Q 032585 128 RWFYYC 133 (137)
Q Consensus 128 rL~~~~ 133 (137)
+|++.+
T Consensus 83 ~L~~~~ 88 (138)
T PRK00109 83 RLEGRF 88 (138)
T ss_pred HHHHHh
Confidence 999876
No 4
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=99.67 E-value=2.4e-16 Score=118.23 Aligned_cols=68 Identities=21% Similarity=0.255 Sum_probs=61.3
Q ss_pred EEeecCCceEEEEeec--ceeeeeeeeEEccc-hhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHHHHH
Q 032585 66 LGVDLGLSRTGLALSK--GFCVRPLTVLKLRG-EKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLRWFY 131 (137)
Q Consensus 66 LGlD~GtKRIGVAVSd--giiAsPL~tI~~~~-~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~rL~~ 131 (137)
||||||+||||||+|| +.+|+|++|+...+ ...++.|.++++++ |||| +++++|++|++|+++|++
T Consensus 1 laiD~G~kriGvA~~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L~~ 80 (130)
T TIGR00250 1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG 80 (130)
T ss_pred CeEccCCCeEEEEEECCCCCEEeceEEEEecCCcHHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHHHH
Confidence 6999999999999995 88999999998744 45678899999886 9999 999999999999999998
Q ss_pred hc
Q 032585 132 YC 133 (137)
Q Consensus 132 ~~ 133 (137)
.+
T Consensus 81 ~~ 82 (130)
T TIGR00250 81 RF 82 (130)
T ss_pred Hh
Confidence 76
No 5
>smart00732 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.
Probab=98.27 E-value=7.8e-06 Score=55.77 Aligned_cols=69 Identities=19% Similarity=0.193 Sum_probs=49.5
Q ss_pred ceEEEeecCCceEEEEee--cceeeeeeeeEEc-cchhHHHHHHHHhhcc----EEEC-------CCChhhHHHHHHHHH
Q 032585 63 GFSLGVDLGLSRTGLALS--KGFCVRPLTVLKL-RGEKLELQLLEIAQRE----VILG-------SYEPQLNLLSKKKLR 128 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVS--dgiiAsPL~tI~~-~~~~~~~~L~eli~ee----vVVG-------tEgp~A~kVr~FA~r 128 (137)
+++||||+|..+||+|+. ++-+..++.+... +....++.|.+++.++ |+|| ...+.. . ..|++.
T Consensus 1 ~~ilgiD~Ggt~i~~a~~d~~g~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~i~Ig~pg~v~g~~~~~~-~-~~l~~~ 78 (99)
T smart00732 1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRET-E-EAFAEL 78 (99)
T ss_pred CcEEEEccCCCeEEEEEECCCCCEecCEEEEEecCcchHHHHHHHHHHHhCCCEEEEeCCcCCCCCcCHHH-H-HHHHHH
Confidence 368999999999999998 4677777766553 2234577888888774 8888 223333 2 788888
Q ss_pred HHHhc
Q 032585 129 WFYYC 133 (137)
Q Consensus 129 L~~~~ 133 (137)
|++.+
T Consensus 79 l~~~~ 83 (99)
T smart00732 79 LKERF 83 (99)
T ss_pred HHHhh
Confidence 88765
No 6
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=93.96 E-value=0.21 Score=39.05 Aligned_cols=47 Identities=26% Similarity=0.336 Sum_probs=30.7
Q ss_pred ceEEEeecCCceEEEEeec--c--eeeeeeeeEEccc--------hhHHHHHHHHhhcc
Q 032585 63 GFSLGVDLGLSRTGLALSK--G--FCVRPLTVLKLRG--------EKLELQLLEIAQRE 109 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVSd--g--iiAsPL~tI~~~~--------~~~~~~L~eli~ee 109 (137)
+|+||||-|+.++|+||-+ + +..--.++|.... ....+.|.++++++
T Consensus 2 m~iLGIDPgl~~tG~avi~~~~~~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~ 60 (164)
T PRK00039 2 MRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEY 60 (164)
T ss_pred CEEEEEccccCceeEEEEEecCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999973 2 2223334665321 12346777777765
No 7
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=93.92 E-value=0.22 Score=37.86 Aligned_cols=46 Identities=22% Similarity=0.270 Sum_probs=29.3
Q ss_pred eEEEeecCCceEEEEeec--c--eeeeeeeeEEcc-c-------hhHHHHHHHHhhcc
Q 032585 64 FSLGVDLGLSRTGLALSK--G--FCVRPLTVLKLR-G-------EKLELQLLEIAQRE 109 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd--g--iiAsPL~tI~~~-~-------~~~~~~L~eli~ee 109 (137)
|+||||.|+.++|.||-+ + +..--.++|+.. + ....+.|.+++.++
T Consensus 1 rILGIDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~ 58 (154)
T cd00529 1 RILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQF 58 (154)
T ss_pred CEEEEccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 689999999999999973 2 111234466543 1 12345666776664
No 8
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=92.78 E-value=0.43 Score=36.39 Aligned_cols=45 Identities=29% Similarity=0.381 Sum_probs=25.5
Q ss_pred EEEeecCCceEEEEeec----ceeeeeeeeEEccc-----h---hHHHHHHHHhhcc
Q 032585 65 SLGVDLGLSRTGLALSK----GFCVRPLTVLKLRG-----E---KLELQLLEIAQRE 109 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd----giiAsPL~tI~~~~-----~---~~~~~L~eli~ee 109 (137)
|||||-|+.++|.||-+ .+..--.++|+.+. + ...+.|.++++++
T Consensus 1 ILGIDPgl~~tG~avi~~~~~~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~ 57 (149)
T PF02075_consen 1 ILGIDPGLSNTGYAVIEEDGGKLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEY 57 (149)
T ss_dssp EEEEE--SSEEEEEEEEEETTEEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH
T ss_pred CEEECCCCCCeeEEEEEeeCCEEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhh
Confidence 79999999999999972 22223344565422 1 2245666666664
No 9
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=85.45 E-value=1.4 Score=34.75 Aligned_cols=45 Identities=18% Similarity=0.205 Sum_probs=27.9
Q ss_pred EEEeecCCceEEEEeec----ceeeeeeeeEEccc-------hhHHHHHHHHhhcc
Q 032585 65 SLGVDLGLSRTGLALSK----GFCVRPLTVLKLRG-------EKLELQLLEIAQRE 109 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd----giiAsPL~tI~~~~-------~~~~~~L~eli~ee 109 (137)
+||||-|+.++|.||-+ .+..--.++|.... ....+.|.+++.++
T Consensus 1 ILGIDPGl~~tG~gvi~~~~~~~~~v~~G~I~t~~~~~~~RL~~I~~~l~~~i~~y 56 (156)
T TIGR00228 1 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQF 56 (156)
T ss_pred CEeECcccccccEEEEEecCCeEEEEEeeEEECCCCCHHHHHHHHHHHHHHHHHHh
Confidence 69999999999999952 22223344554322 12345666666664
No 10
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=83.50 E-value=5.3 Score=31.31 Aligned_cols=68 Identities=21% Similarity=0.242 Sum_probs=47.4
Q ss_pred ccceEEEeecCCceEEEEeecceeeeeeeeEEccchhHHHHHHHHhhcc---EEEC-CCChhhHHHHHHHHHHHH
Q 032585 61 RGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE---VILG-SYEPQLNLLSKKKLRWFY 131 (137)
Q Consensus 61 ~~gRiLGlD~GtKRIGVAVSdgiiAsPL~tI~~~~~~~~~~L~eli~ee---vVVG-tEgp~A~kVr~FA~rL~~ 131 (137)
+..-|+|||-|+. +|||+-| +-..+|.+...++ -....+.+|+.++ +||- ...|+-..|++++..+..
T Consensus 30 ~~~lIVGiDPG~t-tgiAild-L~G~~l~l~S~R~-~~~~evi~~I~~~G~PviVAtDV~p~P~~V~Kia~~f~A 101 (138)
T PF04312_consen 30 RRYLIVGIDPGTT-TGIAILD-LDGELLDLKSSRN-MSRSEVIEWISEYGKPVIVATDVSPPPETVKKIARSFNA 101 (138)
T ss_pred CCCEEEEECCCce-eEEEEEe-cCCcEEEEEeecC-CCHHHHHHHHHHcCCEEEEEecCCCCcHHHHHHHHHhCC
Confidence 4567999999984 8999973 2235665554433 2345677777776 8888 777777888888877654
No 11
>PF14239 RRXRR: RRXRR protein
Probab=78.41 E-value=5.3 Score=32.30 Aligned_cols=20 Identities=35% Similarity=0.566 Sum_probs=17.6
Q ss_pred cceEEEeecCCceEEEEeec
Q 032585 62 GGFSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSd 81 (137)
-.-.+|||-|.|.||+|+.+
T Consensus 50 qpi~lgiDpGsk~tGiav~~ 69 (176)
T PF14239_consen 50 QPIRLGIDPGSKTTGIAVVS 69 (176)
T ss_pred cCEEEEECCCCCeEEEEEEe
Confidence 45679999999999999984
No 12
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=73.43 E-value=8 Score=34.05 Aligned_cols=72 Identities=21% Similarity=0.205 Sum_probs=44.9
Q ss_pred ceEEEeecCCceEEEEeecceee-eeeeeEEc--cchhHHHHHHHHhhcc--EEEC---------CCChhhHHHHHHHHH
Q 032585 63 GFSLGVDLGLSRTGLALSKGFCV-RPLTVLKL--RGEKLELQLLEIAQRE--VILG---------SYEPQLNLLSKKKLR 128 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVSdgiiA-sPL~tI~~--~~~~~~~~L~eli~ee--vVVG---------tEgp~A~kVr~FA~r 128 (137)
..++|||+|.+-+-+|.+||-.- .-+-.++. ..+.+.+.|++++.++ =+|| --...++-|+.-+++
T Consensus 3 ~kilGiDIGGAntk~a~~DG~~~~~d~~YlPMWk~k~rL~~~Lkei~~k~~~~~vgvvMTaELaD~f~tk~eGVe~Ii~~ 82 (330)
T COG1548 3 MKILGIDIGGANTKIASSDGDNYKIDHIYLPMWKKKDRLEETLKEIVHKDNVDYVGVVMTAELADAFKTKAEGVEDIIDT 82 (330)
T ss_pred ceEEEeeccCccchhhhccCCeeeeeEEEeccccchhHHHHHHHHHhccCCcceeEEEeeHHHHHHhhhHHhHHHHHHHH
Confidence 46899999999999999986553 12222222 2234567888888553 3344 122344556666777
Q ss_pred HHHhcC
Q 032585 129 WFYYCD 134 (137)
Q Consensus 129 L~~~~~ 134 (137)
..++|.
T Consensus 83 v~~Af~ 88 (330)
T COG1548 83 VEKAFN 88 (330)
T ss_pred HHHhcC
Confidence 776664
No 13
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=72.77 E-value=28 Score=26.86 Aligned_cols=70 Identities=16% Similarity=0.149 Sum_probs=33.5
Q ss_pred cceEEEeecCCce-----EEEEee-cceeeeeeeeEE-c----cchhHHHHHHHHhhcc----EEECCCChhhHHHHHHH
Q 032585 62 GGFSLGVDLGLSR-----TGLALS-KGFCVRPLTVLK-L----RGEKLELQLLEIAQRE----VILGSYEPQLNLLSKKK 126 (137)
Q Consensus 62 ~gRiLGlD~GtKR-----IGVAVS-dgiiAsPL~tI~-~----~~~~~~~~L~eli~ee----vVVGtEgp~A~kVr~FA 126 (137)
+-|+|||-||.-+ +++.|- +|-.--=+.... . ...++.+.|.+++.++ |+||-.+..+.+..++.
T Consensus 4 ~~rVla~~~g~g~~~~~~~~v~ld~~G~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~kP~vI~v~g~~~~s~~l~~~v 83 (150)
T PF14639_consen 4 GPRVLALSWGSGDGDDAVFCVVLDENGEVLDHLKLVYNERDRERKEEDMERLKKFIEKHKPDVIAVGGNSRESRKLYDDV 83 (150)
T ss_dssp ---EEEEE-TT--TTS-EEEEEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--SSTHHHHHHHHH
T ss_pred CCEEEEEEcCCCCCCCCEEEEEECCCCcEEEEEEEcCCccchHHHHHHHHHHHHHHHHcCCeEEEEcCCChhHHHHHHHH
Confidence 5689999999766 444444 232221111111 1 1134567778888775 88975566666666655
Q ss_pred HHHHH
Q 032585 127 LRWFY 131 (137)
Q Consensus 127 ~rL~~ 131 (137)
+.+-+
T Consensus 84 ~~~v~ 88 (150)
T PF14639_consen 84 RDIVE 88 (150)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 55433
No 14
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=70.53 E-value=5.6 Score=31.88 Aligned_cols=44 Identities=30% Similarity=0.425 Sum_probs=27.2
Q ss_pred EEeecCCceEEEEee--cceeee--eeeeEEccch--------hHHHHHHHHhhcc
Q 032585 66 LGVDLGLSRTGLALS--KGFCVR--PLTVLKLRGE--------KLELQLLEIAQRE 109 (137)
Q Consensus 66 LGlD~GtKRIGVAVS--dgiiAs--PL~tI~~~~~--------~~~~~L~eli~ee 109 (137)
||||-|+.++|.+|- ++-... ..++|....+ .+.+.|.+|+.++
T Consensus 1 lGIDPGl~~~G~gvI~~~~~~l~~v~~G~I~t~~~~~l~~RL~~l~~~l~~vl~~~ 56 (160)
T COG0817 1 LGIDPGLRRTGYGVIEVEGRQLSYLASGVIRTSSDAPLAERLKQLYDGLSEVLDEY 56 (160)
T ss_pred CCcCCCccccceEEEEccCCeEEEEeeeEEecCCCccHHHHHHHHHHHHHHHHHHh
Confidence 699999999999998 232333 3346654321 1245566666654
No 15
>PLN03184 chloroplast Hsp70; Provisional
Probab=65.12 E-value=6 Score=36.95 Aligned_cols=30 Identities=30% Similarity=0.416 Sum_probs=23.1
Q ss_pred ccccccccccc-cceEEEeecCCceEEEEee
Q 032585 51 ATRRKKDSLWR-GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 51 a~~~~~~~~~~-~gRiLGlD~GtKRIGVAVS 80 (137)
|+||--.|.+. .+.++||||||...-||+.
T Consensus 26 ~~~~~~~~~~~~~~~viGIDlGTt~s~va~~ 56 (673)
T PLN03184 26 ARRRAGGPLRVVAEKVVGIDLGTTNSAVAAM 56 (673)
T ss_pred cccccCCCccccCCCEEEEEeCcCcEEEEEE
Confidence 45555555554 5669999999999999987
No 16
>PF00012 HSP70: Hsp70 protein; InterPro: IPR013126 Heat shock proteins, Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region []. Hsp70 proteins have an average molecular weight of 70 kDa [, , ]. In most species,there are many proteins that belong to the hsp70 family. Some of these are only expressed under stress conditions (strictly inducible), while some are present in cells under normal growth conditions and are not heat-inducible (constitutive or cognate) [, ]. Hsp70 proteins can be found in different cellular compartments(nuclear, cytosolic, mitochondrial, endoplasmic reticulum, for example).; PDB: 2P32_D 3D2F_A 2QXL_A 3D2E_C 3C7N_A 3FE1_C 4ANI_C 2V7Y_A 2KHO_A 3DPQ_B ....
Probab=62.87 E-value=6.2 Score=34.83 Aligned_cols=16 Identities=31% Similarity=0.644 Sum_probs=14.1
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
++|||||+..+.||+.
T Consensus 1 viGID~Gt~~~~va~~ 16 (602)
T PF00012_consen 1 VIGIDLGTTNSKVAVF 16 (602)
T ss_dssp EEEEEE-SSEEEEEEE
T ss_pred CEEEEeccCCEEEEEE
Confidence 6899999999999987
No 17
>TIGR01865 cas_Csn1 CRISPR-associated protein, Csn1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.
Probab=60.94 E-value=6.1 Score=38.02 Aligned_cols=18 Identities=33% Similarity=0.829 Sum_probs=16.5
Q ss_pred eEEEeecCCceEEEEeec
Q 032585 64 FSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd 81 (137)
.+||||+|+.-||-||.+
T Consensus 2 y~LGLDiGt~SvGWAVv~ 19 (805)
T TIGR01865 2 YILGLDIGIASVGWAIVE 19 (805)
T ss_pred ceeEEeecccceeEEEEe
Confidence 589999999999999993
No 18
>KOG1503 consensus Phosphoribosylpyrophosphate synthetase-associated protein [Amino acid transport and metabolism; Nucleotide transport and metabolism]
Probab=56.86 E-value=19 Score=31.58 Aligned_cols=62 Identities=18% Similarity=0.097 Sum_probs=47.7
Q ss_pred eEEEeecCCceEEEEeecceeeeeeeeEEccchhHHHHHHHHhhcc---EEECCCChhhHHHHHHHHHHHH
Q 032585 64 FSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE---VILGSYEPQLNLLSKKKLRWFY 131 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSdgiiAsPL~tI~~~~~~~~~~L~eli~ee---vVVGtEgp~A~kVr~FA~rL~~ 131 (137)
+++-+|+-.|-| .|++.-|+..+.+.. =+++.|.+-+++| ++|-..-..+.++..||++|+-
T Consensus 127 hlitmdlhqkei-----qgff~~pvdnlrasp-fllqyiqe~ipdyrnavivaksp~~akka~syaerlrl 191 (354)
T KOG1503|consen 127 HLITMDLHQKEI-----QGFFSIPVDNLRASP-FLLQYIQEEIPDYRNAVIVAKSPGVAKKAQSYAERLRL 191 (354)
T ss_pred eEEeehhhhHhh-----cceecccccccccCH-HHHHHHHHhCccccceEEEecCcchhhHHHhHHHHHhh
Confidence 455666666655 688889999886533 3567888888887 8888666688999999999974
No 19
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=55.59 E-value=12 Score=37.37 Aligned_cols=19 Identities=32% Similarity=0.733 Sum_probs=17.4
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
-..+||+|+|+..+|-||.
T Consensus 3 ~~yilglDIGi~SVGWAvv 21 (1088)
T COG3513 3 KAYILGLDIGINSVGWAVV 21 (1088)
T ss_pred cceEEEeeccccceeeEEe
Confidence 4579999999999999998
No 20
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=49.97 E-value=55 Score=32.15 Aligned_cols=69 Identities=20% Similarity=0.220 Sum_probs=42.6
Q ss_pred cceEEEeecCCceEEEEee--c--ceeeeeeeeEEccc----hhHHHHHHHHhhcc----EEEC--CCChhhHHHHHHHH
Q 032585 62 GGFSLGVDLGLSRTGLALS--K--GFCVRPLTVLKLRG----EKLELQLLEIAQRE----VILG--SYEPQLNLLSKKKL 127 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS--d--giiAsPL~tI~~~~----~~~~~~L~eli~ee----vVVG--tEgp~A~kVr~FA~ 127 (137)
+..+||||-| -|+|+.++ + |..-.--.+++... +...+.|..++..+ |.+| |-+ ..+.+|+.
T Consensus 329 ~~~~lglDPg-~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIGngTaS---rete~fv~ 404 (780)
T COG2183 329 PKATLGLDPG-FRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIGNGTAS---RETEKFVA 404 (780)
T ss_pred CcceeecCCc-cccccEEEEEcCCCceeceeEEEcCCCccchHHHHHHHHHHHHHhCceEEEEecCCcc---hhHHHHHH
Confidence 4489999999 89987766 3 33333333343321 23456778887775 8888 444 44556666
Q ss_pred HHHHhcC
Q 032585 128 RWFYYCD 134 (137)
Q Consensus 128 rL~~~~~ 134 (137)
.|-+..+
T Consensus 405 ~vl~~~~ 411 (780)
T COG2183 405 DVLKELP 411 (780)
T ss_pred HHHHhcc
Confidence 6666554
No 21
>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition. This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=48.06 E-value=48 Score=23.78 Aligned_cols=48 Identities=10% Similarity=-0.012 Sum_probs=29.7
Q ss_pred EEEeecCCceEEEEeecce-eeeeeeeEEccchhHHHHHHHHhhcc--EEEC
Q 032585 65 SLGVDLGLSRTGLALSKGF-CVRPLTVLKLRGEKLELQLLEIAQRE--VILG 113 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSdgi-iAsPL~tI~~~~~~~~~~L~eli~ee--vVVG 113 (137)
++|||+|....=+++.+.. -......+.. +...+..+.+++.+. ++||
T Consensus 1 ~vGiDv~k~~~~v~v~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~~v~ 51 (144)
T PF01548_consen 1 FVGIDVSKDTHDVCVIDPNGEKLRRFKFEN-DPAGLEKLLDWLASLGPVLVV 51 (144)
T ss_pred eEEEEcccCeEEEEEEcCCCcEEEEEEEec-cccchhHHhhhhccccccccc
Confidence 6899999998888887421 2233344443 223456666666664 6666
No 22
>PF14450 FtsA: Cell division protein FtsA; PDB: 1E4F_T 4A2B_A 4A2A_A 1E4G_T.
Probab=44.82 E-value=55 Score=23.49 Aligned_cols=16 Identities=31% Similarity=0.547 Sum_probs=14.1
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
+.+||+|+..|-++|.
T Consensus 1 i~~iDiGs~~~~~~i~ 16 (120)
T PF14450_consen 1 IVVIDIGSSKTKVAIA 16 (120)
T ss_dssp EEEEEE-SSSEEEEEE
T ss_pred CEEEEcCCCcEEEEEE
Confidence 5799999999999999
No 23
>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....
Probab=42.90 E-value=1e+02 Score=21.40 Aligned_cols=49 Identities=18% Similarity=0.119 Sum_probs=31.0
Q ss_pred eEEEeec--CCceEEEEeecceee-eeeeeEEccchhHHHHHHHHhhccEEEC
Q 032585 64 FSLGVDL--GLSRTGLALSKGFCV-RPLTVLKLRGEKLELQLLEIAQREVILG 113 (137)
Q Consensus 64 RiLGlD~--GtKRIGVAVSdgiiA-sPL~tI~~~~~~~~~~L~eli~eevVVG 113 (137)
.+++|-. ....+|+|..|-.+. .-++.+.. -.++...|..+.+.|||+.
T Consensus 2 yl~aI~~~~~~~~~gla~~D~sTGe~~~~~~~d-~~~L~~~L~~~~P~EIi~~ 53 (137)
T PF05188_consen 2 YLAAIYEKNDEDSYGLAYIDLSTGEFYVTEFED-YSELKSELARLSPREIIIP 53 (137)
T ss_dssp EEEEEEEETCSSEEEEEEEETTTTEEEEEEEEC-HHHHHHHHHHH-ESEEEEE
T ss_pred EEEEEEEecCCCEEEEEEEECCCCEEEEEEeCC-HHHHHHHHHhcCCeEEEEc
Confidence 3566666 667799999962222 22333321 2456788999999999988
No 24
>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin. The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive aspergillosis owing to its elastolytic activity and Aspergillopepsins from the mold A. saitoi are used in fermentation industry. Aspartic proteinases are a group of proteolytic enzymes in which the scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in a DT(S)G motif at the active site. They have a similar fold composed of two beta-barrel domains. Between the N-terminal and C-terminal domains, each of which contributes one catalytic aspartic residue, there is an extended active-
Probab=42.10 E-value=19 Score=28.83 Aligned_cols=16 Identities=25% Similarity=0.337 Sum_probs=13.3
Q ss_pred ceEEEeecCCceEEEE
Q 032585 63 GFSLGVDLGLSRTGLA 78 (137)
Q Consensus 63 gRiLGlD~GtKRIGVA 78 (137)
+.+..+|++.+|||+|
T Consensus 262 ~~y~vfD~~~~~ig~A 277 (278)
T cd06097 262 AQYVVFDVGGPKLGFA 277 (278)
T ss_pred ceeEEEcCCCceeeec
Confidence 4456699999999998
No 25
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=41.50 E-value=32 Score=26.89 Aligned_cols=39 Identities=31% Similarity=0.537 Sum_probs=29.6
Q ss_pred eeecCCC-CccccccccccccccCccccccccccccccceEEEeecCCc
Q 032585 26 FHLNRTR-NFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLS 73 (137)
Q Consensus 26 ~~~~~~~-~~~~~~~~~~~~~~~~pna~~~~~~~~~~~gRiLGlD~GtK 73 (137)
|++..++ +...++....-++.|.|++.-- -.|||||++.
T Consensus 104 I~i~~k~l~~g~~i~~F~~I~~L~pg~s~t---------~~lgIDF~DS 143 (145)
T PF14796_consen 104 IHIGEKKLPAGMRIHEFPEIESLEPGASVT---------VSLGIDFNDS 143 (145)
T ss_pred eEECCCCCCCCcEeeccCcccccCCCCeEE---------EEEEEecccC
Confidence 6777665 6677777777888889988643 5799999974
No 26
>COG0623 FabI Enoyl-[acyl-carrier-protein]
Probab=41.34 E-value=4.5 Score=34.68 Aligned_cols=45 Identities=20% Similarity=0.266 Sum_probs=34.4
Q ss_pred cceEEEeecCCceEEEEeecceeeeeeeeEEccchhHHHHHHHHhhcc
Q 032585 62 GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE 109 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSdgiiAsPL~tI~~~~~~~~~~L~eli~ee 109 (137)
.-||||-|+|.+ ||=| +.+.|-|+.|+-.+.-..+..+.++.++.
T Consensus 168 svRyLA~dlG~~--gIRV-NaISAGPIrTLAasgI~~f~~~l~~~e~~ 212 (259)
T COG0623 168 SVRYLAADLGKE--GIRV-NAISAGPIRTLAASGIGDFRKMLKENEAN 212 (259)
T ss_pred HHHHHHHHhCcc--CeEE-eeecccchHHHHhhccccHHHHHHHHHhh
Confidence 457888899887 5555 78889999999877766677777776654
No 27
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=41.07 E-value=71 Score=25.01 Aligned_cols=16 Identities=31% Similarity=0.520 Sum_probs=14.3
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
+||||+||.-+=+++-
T Consensus 2 ~lgiDiGTts~K~~l~ 17 (245)
T PF00370_consen 2 YLGIDIGTTSVKAVLF 17 (245)
T ss_dssp EEEEEECSSEEEEEEE
T ss_pred EEEEEEcccceEEEEE
Confidence 7999999998888887
No 28
>PRK13410 molecular chaperone DnaK; Provisional
Probab=39.75 E-value=23 Score=33.27 Aligned_cols=18 Identities=33% Similarity=0.588 Sum_probs=16.4
Q ss_pred ceEEEeecCCceEEEEee
Q 032585 63 GFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVS 80 (137)
+.++||||||...-||+.
T Consensus 2 ~~viGIDlGTt~s~va~~ 19 (668)
T PRK13410 2 GRIVGIDLGTTNSVVAVM 19 (668)
T ss_pred CcEEEEEeCCCcEEEEEE
Confidence 468999999999999997
No 29
>TIGR01315 5C_CHO_kinase FGGY-family pentulose kinase. This model represents a subfamily of the FGGY family of carbohydrate kinases. This subfamily is closely related to a set of ribulose kinases, and many members are designated ribitol kinase. However, the member from Klebsiella pneumoniae, from a ribitol catabolism operon, accepts D-ribulose and to a lesser extent D-arabinitol and ribitol (PubMed:9639934 and JW Lengeler, personal communication); its annotation in GenBank as ribitol kinase is imprecise and may have affected public annotation of related proteins.
Probab=39.69 E-value=58 Score=29.28 Aligned_cols=27 Identities=15% Similarity=0.327 Sum_probs=20.0
Q ss_pred eEEEeecCCceEEEEeec---ceee---eeeee
Q 032585 64 FSLGVDLGLSRTGLALSK---GFCV---RPLTV 90 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd---giiA---sPL~t 90 (137)
+++|||+||..|=+++-| .+++ .|+.+
T Consensus 1 ~~lgID~GTts~Ka~l~d~~G~i~~~~~~~~~~ 33 (541)
T TIGR01315 1 HYIGVDVGTGSARACIIDSTGDILALAAQNIKT 33 (541)
T ss_pred CEEEEEecCcCEEEEEEcCCCCEEEEEEeeeee
Confidence 489999999999888883 4544 44544
No 30
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=38.13 E-value=94 Score=25.25 Aligned_cols=20 Identities=30% Similarity=0.458 Sum_probs=18.1
Q ss_pred cceEEEeecCCceEEEEeec
Q 032585 62 GGFSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSd 81 (137)
...++|||+|...|=+|+.|
T Consensus 5 ~~~~lgidIggt~i~~~l~d 24 (314)
T COG1940 5 AMTVLGIDIGGTKIKVALVD 24 (314)
T ss_pred CcEEEEEEecCCEEEEEEEC
Confidence 56899999999999999994
No 31
>KOG1794 consensus N-Acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=37.63 E-value=1.5e+02 Score=26.42 Aligned_cols=73 Identities=14% Similarity=0.018 Sum_probs=49.8
Q ss_pred ceEEEeecCCceEEEEeec---ce--eeeeeeeEEc-c-chhHHHHHHHHhhcc--------------EEEC-CCChhhH
Q 032585 63 GFSLGVDLGLSRTGLALSK---GF--CVRPLTVLKL-R-GEKLELQLLEIAQRE--------------VILG-SYEPQLN 120 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVSd---gi--iAsPL~tI~~-~-~~~~~~~L~eli~ee--------------vVVG-tEgp~A~ 120 (137)
+.|.|+|=|..++=+-|.+ .+ .+...+|..- . .....+.|.+++.+. +++| +-.++-.
T Consensus 3 ~~y~GvEGgaT~s~~Vivd~~~~~~~~a~~~~Tnh~~ig~~~~~~rie~~i~~A~~k~g~d~~~~lr~lgL~lSg~d~e~ 82 (336)
T KOG1794|consen 3 DFYGGVEGGATCSRLVIVDEDGTILGRAVGGGTNHWLIGSTTCASRIEDMIREAKEKAGWDKKGPLRSLGLGLSGTDQED 82 (336)
T ss_pred ceeEeecCCcceeEEEEECCCCCEeeEeeccccccccCCchHHHHHHHHHHHHHHhhcCCCccCccceeeeecccCCchh
Confidence 5677888888777777773 22 2245555542 1 133456777777661 7888 7778888
Q ss_pred HHHHHHHHHHHhcCC
Q 032585 121 LLSKKKLRWFYYCDG 135 (137)
Q Consensus 121 kVr~FA~rL~~~~~~ 135 (137)
..+++.+.++..+|+
T Consensus 83 ~~~~lv~~~R~~fps 97 (336)
T KOG1794|consen 83 KNRKLVTEFRDKFPS 97 (336)
T ss_pred HHHHHHHHHHHhccc
Confidence 899999999998875
No 32
>COG1924 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]
Probab=37.49 E-value=43 Score=30.43 Aligned_cols=50 Identities=22% Similarity=0.298 Sum_probs=35.1
Q ss_pred ccccccccccCccccccccccccccceEEEeecCCceEEEEee-c-ceeeee
Q 032585 38 IGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALS-K-GFCVRP 87 (137)
Q Consensus 38 ~~~~~~~~~~~pna~~~~~~~~~~~gRiLGlD~GtKRIGVAVS-d-giiAsP 87 (137)
..+..+.+++--=..|+.+.+.+.++.+||||.|+..+=.++= | ..+...
T Consensus 110 ~~~~~~~e~l~~f~~r~~~~~~~~~~~~LGID~GSTtTK~VLm~d~~~I~~~ 161 (396)
T COG1924 110 LSAFTRMEALEEFVERHSKLREYQGMYTLGIDSGSTTTKAVLMEDGKEILYG 161 (396)
T ss_pred hhhhhhHHHHHHHHHHhhhhhhhcCcEEEEEecCCcceeEEEEeCCCeEEEE
Confidence 4445555555444566666677889999999999999988887 4 434433
No 33
>TIGR02350 prok_dnaK chaperone protein DnaK. Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.
Probab=37.02 E-value=26 Score=31.72 Aligned_cols=16 Identities=31% Similarity=0.638 Sum_probs=14.9
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
++||||||..+=+|+-
T Consensus 2 viGIDlGtt~s~va~~ 17 (595)
T TIGR02350 2 IIGIDLGTTNSCVAVM 17 (595)
T ss_pred EEEEEeCcccEEEEEE
Confidence 7999999999999987
No 34
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=36.85 E-value=26 Score=32.65 Aligned_cols=19 Identities=32% Similarity=0.555 Sum_probs=16.8
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
.+.++||||||...-||+.
T Consensus 40 ~~~viGIDlGTt~s~va~~ 58 (663)
T PTZ00400 40 TGDIVGIDLGTTNSCVAIM 58 (663)
T ss_pred cCcEEEEEECcccEEEEEE
Confidence 3579999999999999987
No 35
>PRK13411 molecular chaperone DnaK; Provisional
Probab=34.78 E-value=31 Score=32.12 Aligned_cols=17 Identities=29% Similarity=0.538 Sum_probs=15.8
Q ss_pred eEEEeecCCceEEEEee
Q 032585 64 FSLGVDLGLSRTGLALS 80 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVS 80 (137)
.++||||||..+=||+-
T Consensus 3 ~viGIDlGTt~s~va~~ 19 (653)
T PRK13411 3 KVIGIDLGTTNSCVAVL 19 (653)
T ss_pred cEEEEEeCcccEEEEEE
Confidence 68999999999999997
No 36
>PRK13320 pantothenate kinase; Reviewed
Probab=34.74 E-value=2.6e+02 Score=22.93 Aligned_cols=17 Identities=35% Similarity=0.493 Sum_probs=15.7
Q ss_pred EEEeecCCceEEEEeec
Q 032585 65 SLGVDLGLSRTGLALSK 81 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd 81 (137)
+|.||.|-.||=.|+.+
T Consensus 4 ~L~iDiGNT~ik~~~~~ 20 (244)
T PRK13320 4 NLVIDIGNTTTKLAVFE 20 (244)
T ss_pred EEEEEeCCCcEEEEEEE
Confidence 79999999999999984
No 37
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=34.51 E-value=33 Score=31.89 Aligned_cols=19 Identities=26% Similarity=0.515 Sum_probs=16.6
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
.+.++|||||+..+=||+.
T Consensus 3 ~~~~iGIDlGTt~s~va~~ 21 (653)
T PTZ00009 3 KGPAIGIDLGTTYSCVGVW 21 (653)
T ss_pred cccEEEEEeCcccEEEEEE
Confidence 4568999999999989887
No 38
>PF00026 Asp: Eukaryotic aspartyl protease The Prosite entry also includes Pfam:PF00077.; InterPro: IPR001461 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A1 (pepsin family, clan AA). The type example is pepsin A from Homo sapiens (Human) . More than 70 aspartic peptidases, from all from eukaryotic organisms, have been identified. These include pepsins, cathepsins, and renins. The enzymes are synthesised with signal peptides, and the proenzymes are secreted or passed into the lysosomal/endosomal system, where acidification leads to autocatalytic activation. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residues in both the P1 and P1' positions []. Crystallography has shown the active site to form a groove across the junction of the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors within the active site []. Specificity is determined by several hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. Cysteine residues are well conserved within the pepsin family, pepsin itself containing three disulphide loops. The first loop is found in all but the fungal enzymes, and is usually around five residues in length, but is longer in barrierpepsin and candidapepsin; the second loop is also small and found only in the animal enzymes; and the third loop is the largest, found in all members of the family, except for the cysteine-free polyporopepsin. The loops are spread unequally throughout the two lobes, suggesting that they formed after the initial gene duplication and fusion event []. This family does not include the retroviral nor retrotransposon aspartic proteases which are much smaller and appear to be homologous to the single domain aspartic proteases.; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1CZI_E 3CMS_A 1CMS_A 4CMS_A 1YG9_A 2NR6_A 3LIZ_A 1FLH_A 3UTL_A 1QRP_E ....
Probab=34.16 E-value=41 Score=26.57 Aligned_cols=18 Identities=22% Similarity=0.307 Sum_probs=15.8
Q ss_pred cceEEEeecCCceEEEEe
Q 032585 62 GGFSLGVDLGLSRTGLAL 79 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAV 79 (137)
+..++.+|+..+|||+|-
T Consensus 299 ~~~y~vfD~~~~~ig~A~ 316 (317)
T PF00026_consen 299 RNYYVVFDYENNRIGFAQ 316 (317)
T ss_dssp TTEEEEEETTTTEEEEEE
T ss_pred hceEEEEeCCCCEEEEec
Confidence 567889999999999994
No 39
>TIGR01312 XylB D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization.
Probab=33.88 E-value=51 Score=28.37 Aligned_cols=16 Identities=44% Similarity=0.603 Sum_probs=14.7
Q ss_pred EEeecCCceEEEEeec
Q 032585 66 LGVDLGLSRTGLALSK 81 (137)
Q Consensus 66 LGlD~GtKRIGVAVSd 81 (137)
+|||+|+..+=+++.|
T Consensus 1 lgIDiGtt~ik~~l~d 16 (481)
T TIGR01312 1 LGIDLGTSGVKALLVD 16 (481)
T ss_pred CceeecCcceEEEEEC
Confidence 6899999999999994
No 40
>PF09298 FAA_hydrolase_N: Fumarylacetoacetase N-terminal; InterPro: IPR015377 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation []. This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders [, ]. The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole []. FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures []. This entry represents the N-terminal domain of fumarylacetoacetase.; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process; PDB: 1QCN_B 1QCO_B 2HZY_A 1QQJ_B 1HYO_A.
Probab=33.88 E-value=23 Score=25.90 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=9.8
Q ss_pred CCceEEEEeecc
Q 032585 71 GLSRTGLALSKG 82 (137)
Q Consensus 71 GtKRIGVAVSdg 82 (137)
++.|+||||+|.
T Consensus 14 ~~pR~gvaIGd~ 25 (107)
T PF09298_consen 14 PSPRVGVAIGDQ 25 (107)
T ss_dssp ESEEEEEEETTE
T ss_pred CCCeeEEEECCE
Confidence 568999999963
No 41
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=33.60 E-value=32 Score=31.82 Aligned_cols=18 Identities=22% Similarity=0.604 Sum_probs=16.4
Q ss_pred ceEEEeecCCceEEEEee
Q 032585 63 GFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVS 80 (137)
.-++||||||.-..||+.
T Consensus 19 ~~viGIDlGTT~S~va~~ 36 (595)
T PRK01433 19 QIAVGIDFGTTNSLIAIA 36 (595)
T ss_pred ceEEEEEcCcccEEEEEE
Confidence 468999999999999997
No 42
>cd05474 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins. SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode preproenzymes, approximately 60 amino acid longer than the mature enzyme, which are processed when transported via the secretory pathway. The mature enzymes contain sequence motifs typical for all aspartyl proteinases, including the two conserved aspartate residues other active site and conserved cysteine residues implicated in the maintenance of the three-dimensional structure. Most Sap proteins contain putative N-glycosylation sites, but it remains to be determined which Sap proteins are glycosylated. This family of aspartate proteases
Probab=33.51 E-value=37 Score=26.93 Aligned_cols=18 Identities=22% Similarity=0.082 Sum_probs=15.5
Q ss_pred cceEEEeecCCceEEEEe
Q 032585 62 GGFSLGVDLGLSRTGLAL 79 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAV 79 (137)
++.++.+|++.+|||+|=
T Consensus 277 ~~~y~vfD~~~~~ig~a~ 294 (295)
T cd05474 277 RSAYVVYDLDNNEISLAQ 294 (295)
T ss_pred hcEEEEEECCCCEEEeec
Confidence 456889999999999983
No 43
>TIGR00241 CoA_E_activ CoA-substrate-specific enzyme activase, putative. This domain may be involved in generating or regenerating the active sites of enzymes related to (R)-2-hydroxyglutaryl-CoA dehydratase and benzoyl-CoA reductase.
Probab=33.30 E-value=75 Score=25.41 Aligned_cols=17 Identities=41% Similarity=0.636 Sum_probs=15.1
Q ss_pred EEEeecCCceEEEEeec
Q 032585 65 SLGVDLGLSRTGLALSK 81 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd 81 (137)
++|||.|+.-+=.++-+
T Consensus 2 ~lGIDiGtts~K~vl~d 18 (248)
T TIGR00241 2 SLGIDSGSTTTKMVLME 18 (248)
T ss_pred EEEEEcChhheEEEEEc
Confidence 68999999999888875
No 44
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=33.22 E-value=33 Score=31.49 Aligned_cols=17 Identities=29% Similarity=0.536 Sum_probs=15.6
Q ss_pred eEEEeecCCceEEEEee
Q 032585 64 FSLGVDLGLSRTGLALS 80 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVS 80 (137)
.++||||||..+-||+-
T Consensus 3 ~viGIDlGTt~s~va~~ 19 (627)
T PRK00290 3 KIIGIDLGTTNSCVAVM 19 (627)
T ss_pred cEEEEEeCcccEEEEEE
Confidence 58999999999999987
No 45
>cd03070 PDI_b_ERp44 PDIb family, ERp44 subfamily, first redox inactive TRX-like domain b; ERp44 is an endoplasmic reticulum (ER)-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. Through the formation of reversible mixed disulfides, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. ERp44 also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol. Similar to PDI, the b domain of ERp44 is likely involved in binding to substrates.
Probab=32.33 E-value=81 Score=22.73 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=26.8
Q ss_pred HHHHHHhhc-cEEEC----CCChhhHHHHHHHHHHHHhcC
Q 032585 100 LQLLEIAQR-EVILG----SYEPQLNLLSKKKLRWFYYCD 134 (137)
Q Consensus 100 ~~L~eli~e-evVVG----tEgp~A~kVr~FA~rL~~~~~ 134 (137)
+.|..+-.+ ..||| .+++.-..-++.|..|+..|.
T Consensus 8 ~eL~~id~~kr~iIgYF~~~~~~eY~~f~kvA~~lr~dC~ 47 (91)
T cd03070 8 DELNNVDRSKRNIIGYFESKDSDEYDNFRKVANILRDDCS 47 (91)
T ss_pred HHHHhhCcCCceEEEEEcCCCChhHHHHHHHHHHHhhcCe
Confidence 444443333 49999 888999999999999998774
No 46
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=31.99 E-value=39 Score=31.79 Aligned_cols=19 Identities=37% Similarity=0.511 Sum_probs=16.8
Q ss_pred ceEEEeecCCceEEEEeec
Q 032585 63 GFSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVSd 81 (137)
+.++||||||...-||+.+
T Consensus 27 ~~viGIDLGTTnS~vA~~~ 45 (657)
T PTZ00186 27 GDVIGVDLGTTYSCVATMD 45 (657)
T ss_pred ceEEEEEeCcCeEEEEEEe
Confidence 4699999999999999973
No 47
>cd05487 renin_like Renin stimulates production of angiotensin and thus affects blood pressure. Renin, also known as angiotensinogenase, is a circulating enzyme that participates in the renin-angiotensin system that mediates extracellular volume, arterial vasoconstriction, and consequently mean arterial blood pressure. The enzyme is secreted by the kidneys from specialized juxtaglomerular cells in response to decreases in glomerular filtration rate (a consequence of low blood volume), diminished filtered sodium chloride and sympathetic nervous system innervation. The enzyme circulates in the blood stream and hydrolyzes angiotensinogen secreted from the liver into the peptide angiotensin I. Angiotensin I is further cleaved in the lungs by endothelial bound angiotensin converting enzyme (ACE) into angiotensin II, the final active peptide. Renin is a member of the aspartic protease family. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate r
Probab=31.73 E-value=38 Score=27.84 Aligned_cols=19 Identities=32% Similarity=0.363 Sum_probs=15.7
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
++.+.-+|++.+|||+|.+
T Consensus 308 r~~y~vfD~~~~~IGfA~a 326 (326)
T cd05487 308 RKFYTEFDRQNNRIGFALA 326 (326)
T ss_pred hccEEEEeCCCCEEeeeeC
Confidence 3567779999999999964
No 48
>PRK13930 rod shape-determining protein MreB; Provisional
Probab=31.63 E-value=36 Score=27.88 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=14.5
Q ss_pred eEEEeecCCceEEEEee
Q 032585 64 FSLGVDLGLSRTGLALS 80 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVS 80 (137)
+.+|||+|+..+-++..
T Consensus 9 ~~vgiDlGt~~t~i~~~ 25 (335)
T PRK13930 9 KDIGIDLGTANTLVYVK 25 (335)
T ss_pred cceEEEcCCCcEEEEEC
Confidence 56999999998888775
No 49
>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=31.62 E-value=75 Score=27.20 Aligned_cols=37 Identities=19% Similarity=0.044 Sum_probs=27.1
Q ss_pred hhHHHHHHHHhhccEEEC-------CCC---hhhHHHHHHHHHHHHhc
Q 032585 96 EKLELQLLEIAQREVILG-------SYE---PQLNLLSKKKLRWFYYC 133 (137)
Q Consensus 96 ~~~~~~L~eli~eevVVG-------tEg---p~A~kVr~FA~rL~~~~ 133 (137)
.+.++++.++ .+-+||| +++ ...+.+++|++.|+..+
T Consensus 217 ~e~~~~v~~~-ADGVIVGSAiV~~i~~~~~~~~~~~~~~l~~~l~~~~ 263 (265)
T COG0159 217 PEQAAQVAEA-ADGVIVGSAIVKIIEEGLDEEALEELRALVKELKAAL 263 (265)
T ss_pred HHHHHHHHHh-CCeEEEcHHHHHHHHhccchhhHHHHHHHHHHHHHHh
Confidence 4456667777 6679999 443 47889999999998765
No 50
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=31.58 E-value=35 Score=31.49 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=16.2
Q ss_pred ceEEEeecCCceEEEEee
Q 032585 63 GFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVS 80 (137)
..++||||||...-||+.
T Consensus 19 ~~~iGIDlGTt~s~va~~ 36 (616)
T PRK05183 19 RLAVGIDLGTTNSLVATV 36 (616)
T ss_pred CeEEEEEeccccEEEEEE
Confidence 358999999999999997
No 51
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional
Probab=31.17 E-value=89 Score=25.34 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=15.7
Q ss_pred EEEeecCCceEEEEeec
Q 032585 65 SLGVDLGLSRTGLALSK 81 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd 81 (137)
++|||+|...|-+++.|
T Consensus 2 ~lgidig~t~i~~~l~d 18 (303)
T PRK13310 2 YYGFDIGGTKIELGVFN 18 (303)
T ss_pred eEEEEeCCCcEEEEEEC
Confidence 68999999999999995
No 52
>PF06277 EutA: Ethanolamine utilisation protein EutA; InterPro: IPR009377 Proteins in this entry are EutA ethanolamine utilization proteins, reactivating factors for ethanolamine ammonia lyase, encoded by the ethanolamine utilization eut operon. The holoenzyme of adenosylcobalamin-dependent ethanolamine ammonia-lyase (EutBC, IPR0092462 from INTERPRO, IPR010628 from INTERPRO), which is part of the ethanolamine utilization pathway [, , ], undergoes suicidal inactivation during catalysis as well as inactivation in the absence of substrate. The inactivation involves the irreversible cleavage of the Co-C bond of the coenzyme. The inactivated holoenzyme undergoes rapid and continuous reactivation in the presence of ATP, Mg2+, and free adenosylcobalamin in permeabilised cells (in situ), homogenate, and cell extracts of Escherichia coli. The EutA protein is essential for reactivation. It was demonstrated with purified recombinant EutA that both the suicidally inactivated and O2-inactivated holoethanolamine ammonia lyase underwent rapid reactivation in vitro by EutA in the presence of adenosylcobalamin, ATP, and Mg2+ []. The inactive enzyme-cyanocobalamin complex was also activated in situ and in vitro by EutA under the same conditions. Thus EutA is believed to be the only component of the reactivating factor for ethanolamine ammonia lyase. Reactivation and activation occur through the exchange of modified coenzyme for free intact adenosylcobalamin []. Bacteria that harbor the ethanolamine utilization pathway can use ethanolamine as a source of carbon and nitrogen. For more information on the ethanolamine utilization pathway, please see IPR009194 from INTERPRO, IPR012408 from INTERPRO.
Probab=30.07 E-value=2.1e+02 Score=26.57 Aligned_cols=69 Identities=23% Similarity=0.187 Sum_probs=44.4
Q ss_pred EEEeecCCceEEEEeec---ceee----eeeeeE------Eccc----------hhHHHHHHHHhhcc------------
Q 032585 65 SLGVDLGLSRTGLALSK---GFCV----RPLTVL------KLRG----------EKLELQLLEIAQRE------------ 109 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd---giiA----sPL~tI------~~~~----------~~~~~~L~eli~ee------------ 109 (137)
.+|||+||..+=|=+|. .-.| -|--.| -+++ .-+.+.|++++++|
T Consensus 5 SVGIDIGTSTTQlvfSrl~l~n~a~~~~vPri~I~dkeViYrS~I~fTPl~~~~~ID~~al~~iv~~eY~~Agi~p~~I~ 84 (473)
T PF06277_consen 5 SVGIDIGTSTTQLVFSRLTLENRASGFSVPRIEIVDKEVIYRSPIYFTPLLSQTEIDAEALKEIVEEEYRKAGITPEDID 84 (473)
T ss_pred EEEEeecCCceeEEEEEeEEEeccCCCccceEEEeccEEEecCCccccCCCCCCccCHHHHHHHHHHHHHHcCCCHHHCc
Confidence 68999999999998882 2112 122111 1111 12467888888774
Q ss_pred ---EEECCCChhhHHHHHHHHHHHHhc
Q 032585 110 ---VILGSYEPQLNLLSKKKLRWFYYC 133 (137)
Q Consensus 110 ---vVVGtEgp~A~kVr~FA~rL~~~~ 133 (137)
|++=-|+..-+.++.....|....
T Consensus 85 TGAVIITGETArKeNA~~v~~~Ls~~a 111 (473)
T PF06277_consen 85 TGAVIITGETARKENAREVLHALSGFA 111 (473)
T ss_pred cccEEEecchhhhhhHHHHHHHHHHhc
Confidence 444467777788888888887654
No 53
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=29.06 E-value=56 Score=26.50 Aligned_cols=24 Identities=8% Similarity=0.124 Sum_probs=21.0
Q ss_pred EEECCCChhhHHHHHHHHHHHHhc
Q 032585 110 VILGSYEPQLNLLSKKKLRWFYYC 133 (137)
Q Consensus 110 vVVGtEgp~A~kVr~FA~rL~~~~ 133 (137)
||||.+.|.-++-.+||++|...+
T Consensus 113 fVvG~~np~~~~N~~fA~~l~~~~ 136 (196)
T TIGR02867 113 FVIGKNNPHFEKNLQLANKLHAKL 136 (196)
T ss_pred EEEcCCCCCHHHHHHHHHHHHHHH
Confidence 999988899999999999988754
No 54
>CHL00094 dnaK heat shock protein 70
Probab=28.81 E-value=44 Score=30.76 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=15.8
Q ss_pred eEEEeecCCceEEEEee
Q 032585 64 FSLGVDLGLSRTGLALS 80 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVS 80 (137)
.++||||||..+=||+.
T Consensus 3 ~viGIDlGTt~s~va~~ 19 (621)
T CHL00094 3 KVVGIDLGTTNSVVAVM 19 (621)
T ss_pred ceEEEEeCcccEEEEEE
Confidence 68999999999999997
No 55
>PRK05082 N-acetylmannosamine kinase; Provisional
Probab=28.48 E-value=1.5e+02 Score=23.91 Aligned_cols=18 Identities=28% Similarity=0.442 Sum_probs=16.5
Q ss_pred eEEEeecCCceEEEEeec
Q 032585 64 FSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd 81 (137)
.++|+|+|..++-+++.|
T Consensus 2 ~~lgvdig~~~i~~~l~d 19 (291)
T PRK05082 2 TTLAIDIGGTKIAAALVG 19 (291)
T ss_pred cEEEEEECCCEEEEEEEc
Confidence 489999999999999995
No 56
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=28.30 E-value=1.7e+02 Score=28.32 Aligned_cols=62 Identities=23% Similarity=0.390 Sum_probs=39.9
Q ss_pred ceEEEeecCCceEEEEee--cceeeeeeeeEEccchhHHHHHHHHhhcc---EEEC-CCChhhHHHHHHHHHH
Q 032585 63 GFSLGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLELQLLEIAQRE---VILG-SYEPQLNLLSKKKLRW 129 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVS--dgiiAsPL~tI~~~~~~~~~~L~eli~ee---vVVG-tEgp~A~kVr~FA~rL 129 (137)
--|+|||-|+ .+|||+- || ..|-+...++ -+...+.+++.++ +||- .-+|+-+-|++.|..+
T Consensus 244 ~lIVGIDPGi-TtgiAvldldG---evl~~~S~r~-~~~~eVve~I~~lG~PvvVAtDVtp~P~~V~KiAasf 311 (652)
T COG2433 244 SLIVGIDPGI-TTGIAVLDLDG---EVLDLESRRG-IDRSEVVEFISELGKPVVVATDVTPAPETVKKIAASF 311 (652)
T ss_pred ceEEEeCCCc-eeeEEEEecCC---cEEeeecccc-CCHHHHHHHHHHcCCceEEEccCCCChHHHHHHHHHc
Confidence 5689999998 4899997 34 2333332222 2356788888887 8888 5566655555555443
No 57
>cd05476 pepsin_A_like_plant Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants. This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which
Probab=27.59 E-value=56 Score=25.98 Aligned_cols=19 Identities=37% Similarity=0.431 Sum_probs=16.1
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
++.+..+|++.+|||+|-+
T Consensus 245 ~~~~~vFD~~~~~iGfa~~ 263 (265)
T cd05476 245 QNFLVEYDLENSRLGFAPA 263 (265)
T ss_pred ccEEEEEECCCCEEeeecC
Confidence 4567779999999999965
No 58
>cd05472 cnd41_like Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This fami
Probab=27.51 E-value=55 Score=26.37 Aligned_cols=19 Identities=26% Similarity=0.322 Sum_probs=15.5
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
+..++.+|++.+|||+|-+
T Consensus 279 ~~~~vvfD~~~~~igfa~~ 297 (299)
T cd05472 279 QTFRVVYDVAGGRIGFAPG 297 (299)
T ss_pred cceEEEEECCCCEEeEecC
Confidence 3456789999999999964
No 59
>cd06098 phytepsin Phytepsin, a plant homolog of mammalian lysosomal pepsins. Phytepsin, a plant homolog of mammalian lysosomal pepsins, resides in grains, roots, stems, leaves and flowers. Phytepsin may participate in metabolic turnover and in protein processing events. In addition, it highly expressed in several plant tissues undergoing apoptosis. Phytepsin contains an internal region consisting of about 100 residues not present in animal or microbial pepsins. This region is thus called a plant specific insert. The insert is highly similar to saponins, which are lysosomal sphingolipid-activating proteins in mammalian cells. The saponin-like domain may have a role in the vacuolar targeting of phytepsin. Phytepsin, as its animal counterparts, possesses a topology typical of all aspartic proteases. They are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved fro
Probab=27.11 E-value=48 Score=27.23 Aligned_cols=17 Identities=35% Similarity=0.577 Sum_probs=14.3
Q ss_pred cceEEEeecCCceEEEE
Q 032585 62 GGFSLGVDLGLSRTGLA 78 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVA 78 (137)
+.-+..+|++.+|||+|
T Consensus 300 r~~y~VfD~~~~~iGfA 316 (317)
T cd06098 300 GAYHTVFDYGNLRVGFA 316 (317)
T ss_pred cccEEEEeCCCCEEeec
Confidence 34567799999999998
No 60
>COG4012 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.64 E-value=2.9e+02 Score=24.66 Aligned_cols=64 Identities=14% Similarity=0.140 Sum_probs=43.7
Q ss_pred ceEEEeecCCceEEEEeecceee-eeeeeEEccchhHHHHHHHHhhc--c-EEEC---CCChhhHHHHHHH
Q 032585 63 GFSLGVDLGLSRTGLALSKGFCV-RPLTVLKLRGEKLELQLLEIAQR--E-VILG---SYEPQLNLLSKKK 126 (137)
Q Consensus 63 gRiLGlD~GtKRIGVAVSdgiiA-sPL~tI~~~~~~~~~~L~eli~e--e-vVVG---tEgp~A~kVr~FA 126 (137)
+.+|++|+|.-..-|-.=++-.- ++.-|.+.+..-....|+-+.++ + +++| --||.+..+++-.
T Consensus 1 mkila~DvG~GTqDi~~~d~~~EnSl~mVmPspt~~~A~R~R~~~~~g~~l~l~G~~MGGGp~travrrhl 71 (342)
T COG4012 1 MKILAIDVGVGTQDIVAYDGDPENSLRMVMPSPTSTLAQRLRFMLREGPYLALIGVPMGGGPTTRAVRRHL 71 (342)
T ss_pred CceEEEEecCCceeEEEecCCcccceeEeecCchHHHHHHHHHHhccCCcEEEEeeecCCChhhHHHHHHH
Confidence 36899999987777665554333 56656665555567788888866 3 7778 6777777776543
No 61
>COG0443 DnaK Molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=26.37 E-value=57 Score=30.19 Aligned_cols=20 Identities=25% Similarity=0.518 Sum_probs=17.7
Q ss_pred cceEEEeecCCceEEEEeec
Q 032585 62 GGFSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSd 81 (137)
.+.++||||||...=||+.+
T Consensus 4 ~~~~iGIDlGTTNS~vA~~~ 23 (579)
T COG0443 4 AKKAIGIDLGTTNSVVAVMR 23 (579)
T ss_pred CceEEEEEcCCCcEEEEEEe
Confidence 35789999999999999994
No 62
>PF01385 OrfB_IS605: Probable transposase; InterPro: IPR001959 This entry represents a conserved region of a probable transposase family, which is found in a number of uncharacterised bacterial proteins. A novel insertion sequence (IS)-like element of the Bacillus PS3 (Thermophilic bacterium PS-3) that promotes expression of the alanine carrier protein-encoding gene belongs to this entry, including IS891 [], IS1136 [], and IS1341 []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.99 E-value=40 Score=25.40 Aligned_cols=20 Identities=30% Similarity=0.366 Sum_probs=17.2
Q ss_pred ccceEEEeecCCceEEEEee
Q 032585 61 RGGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 61 ~~gRiLGlD~GtKRIGVAVS 80 (137)
..+.++|||+|.+..-++.+
T Consensus 122 ~~~~~vgVDlGi~~~a~~~~ 141 (227)
T PF01385_consen 122 DTEKVVGVDLGIKNLATVSS 141 (227)
T ss_pred ccceeeeeccccceeecccc
Confidence 47899999999998887666
No 63
>cd06096 Plasmepsin_5 Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite. The family contains a group of aspartic proteinases homologous to plasmepsin 5. Plasmepsins are a class of at least 10 enzymes produced by the plasmodium parasite. Through their haemoglobin-degrading activity, they are an important cause of symptoms in malaria sufferers. This family of enzymes is a potential target for anti-malarial drugs. Plasmepsins are aspartic acid proteases, which means their active site contains two aspartic acid residues. These two aspartic acid residue act respectively as proton donor and proton acceptor, catalyzing the hydrolysis of peptide bond in proteins. Aspartic proteinases are composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal l
Probab=25.59 E-value=59 Score=26.81 Aligned_cols=19 Identities=26% Similarity=0.239 Sum_probs=15.9
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
++.++-+|++.+|||+|.+
T Consensus 305 r~~y~vFD~~~~riGfa~~ 323 (326)
T cd06096 305 KNKQIIFDLDNNRIGFVES 323 (326)
T ss_pred cCcEEEEECcCCEEeeEcC
Confidence 4566779999999999976
No 64
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=25.31 E-value=69 Score=27.17 Aligned_cols=23 Identities=9% Similarity=0.017 Sum_probs=21.1
Q ss_pred EEECCCChhhHHHHHHHHHHHHh
Q 032585 110 VILGSYEPQLNLLSKKKLRWFYY 132 (137)
Q Consensus 110 vVVGtEgp~A~kVr~FA~rL~~~ 132 (137)
||||.+.|.-++-.+||.+|...
T Consensus 191 fVvG~~np~~~~N~~fA~~l~~~ 213 (268)
T PF07454_consen 191 FVVGRDNPNWEKNLAFAKQLHAK 213 (268)
T ss_pred EEEcCCCCCHHHHHHHHHHHHHH
Confidence 99999999999999999999874
No 65
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=24.92 E-value=64 Score=26.64 Aligned_cols=19 Identities=42% Similarity=0.590 Sum_probs=17.3
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
-|.+||+|.|..-+|||-=
T Consensus 57 PGlvl~L~~GGsc~GvafR 75 (190)
T COG3703 57 PGLVLGLDRGGSCEGVAYR 75 (190)
T ss_pred CceEEEeeCCCcEEEEEEE
Confidence 6999999999999999964
No 66
>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa. Gastricsin is also called pepsinogen C. Gastricsins are produced in gastric mucosa of mammals. It is synthesized by the chief cells in the stomach as an inactive zymogen. It is self-converted to a mature enzyme under acidic conditions. Human gastricsin is distributed throughout all parts of the stomach. Gastricsin is synthesized as an inactive progastricsin that has an approximately 40 residue prosequence. It is self-converting to a mature enzyme being triggered by a drop in pH from neutrality to acidic conditions. Like other aspartic proteases, gastricsin are characterized by two catalytic aspartic residues at the active site, and display optimal activity at acidic pH. Mature enzyme has a pseudo-2-fold symmetry that passes through the active site between the catalytic aspartate residues. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic aspartate residue, with an exten
Probab=24.91 E-value=59 Score=26.50 Aligned_cols=18 Identities=28% Similarity=0.355 Sum_probs=15.5
Q ss_pred cceEEEeecCCceEEEEe
Q 032585 62 GGFSLGVDLGLSRTGLAL 79 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAV 79 (137)
++.+..+|++..|||+|-
T Consensus 300 ~~~y~vfD~~~~~ig~a~ 317 (318)
T cd05477 300 RQYYSVYDLGNNQVGFAT 317 (318)
T ss_pred hheEEEEeCCCCEEeeee
Confidence 566788999999999984
No 67
>PTZ00294 glycerol kinase-like protein; Provisional
Probab=24.66 E-value=1.5e+02 Score=26.25 Aligned_cols=18 Identities=17% Similarity=0.285 Sum_probs=15.6
Q ss_pred eEEEeecCCceEEEEeec
Q 032585 64 FSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd 81 (137)
-+||||+||.-|=+++-|
T Consensus 3 ~~lgiDiGTts~Ka~l~d 20 (504)
T PTZ00294 3 YIGSIDQGTTSTRFIIFD 20 (504)
T ss_pred EEEEEecCCCceEEEEEC
Confidence 489999999999888883
No 68
>PRK09557 fructokinase; Reviewed
Probab=24.60 E-value=1.5e+02 Score=24.13 Aligned_cols=17 Identities=24% Similarity=0.475 Sum_probs=15.6
Q ss_pred EEEeecCCceEEEEeec
Q 032585 65 SLGVDLGLSRTGLALSK 81 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd 81 (137)
++|+|+|...|-+++.|
T Consensus 2 ~lgidig~t~~~~~l~d 18 (301)
T PRK09557 2 RIGIDLGGTKIEVIALD 18 (301)
T ss_pred EEEEEECCCcEEEEEEC
Confidence 68999999999999984
No 69
>PF06723 MreB_Mbl: MreB/Mbl protein; InterPro: IPR004753 Bacterial cell shape varies greatly between species, and characteristic morphologies are used for identification purposes. In addition to individual cell shape, the way in which groups of cells are arranged is also typical of some bacterial species, especially Gram-positive coccoids. For many years, it was believed that micro-organisms with other than spheroidal cell shapes maintained morphology by means of their external cell walls. Recently, however, studies of the Gram-positive rod Bacillus subtilis have revealed two related genes that are essential for the integrity of cell morphogenesis []. Termed mreB and mbl, the gene products localise close to the cell surface, forming filamentous helical structures. Many homologues have been found in diverse bacterial groups, suggesting a common ancestor []. The crystal structure of MreB from Thermotoga maritima has been resolved using X-ray crystallography []. It consists of 19 beta-strands and 15 alpha- helices, and shows remarkable structural similarity to eukaryotic actin. MreB crystals also contain proto-filaments, with individual proteins assembling into polymers like F-actin, in the same orientation. It is hypothesised therefore, that MreB was the forerunner of actin in early eukaryotes [].; GO: 0000902 cell morphogenesis; PDB: 1JCF_A 1JCE_A 2WUS_A 1JCG_A.
Probab=24.24 E-value=63 Score=27.95 Aligned_cols=17 Identities=35% Similarity=0.593 Sum_probs=13.5
Q ss_pred eEEEeecCCceEEEEee
Q 032585 64 FSLGVDLGLSRTGLALS 80 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVS 80 (137)
+-+|||+||.+|=|.+.
T Consensus 2 ~~igIDLGT~~t~i~~~ 18 (326)
T PF06723_consen 2 KDIGIDLGTSNTRIYVK 18 (326)
T ss_dssp SEEEEEE-SSEEEEEET
T ss_pred CceEEecCcccEEEEEC
Confidence 35899999999988876
No 70
>cd05486 Cathespin_E Cathepsin E, non-lysosomal aspartic protease. Cathepsin E is an intracellular, non-lysosomal aspartic protease expressed in a variety of cells and tissues. The protease has proposed physiological roles in antigen presentation by the MHC class II system, in the biogenesis of the vasoconstrictor peptide endothelin, and in neurodegeneration associated with brain ischemia and aging. Cathepsin E is the only A1 aspartic protease that exists as a homodimer with a disulfide bridge linking the two monomers. Like many other aspartic proteases, it is synthesized as a zymogen which is catalytically inactive towards its natural substrates at neutral pH and which auto-activates in an acidic environment. The overall structure follows the general fold of aspartic proteases of the A1 family, it is composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalyt
Probab=23.52 E-value=59 Score=26.52 Aligned_cols=16 Identities=31% Similarity=0.409 Sum_probs=13.6
Q ss_pred ceEEEeecCCceEEEE
Q 032585 63 GFSLGVDLGLSRTGLA 78 (137)
Q Consensus 63 gRiLGlD~GtKRIGVA 78 (137)
.-+..+|++.+|||+|
T Consensus 300 ~~y~vfD~~~~~IGfA 315 (316)
T cd05486 300 QYYSVFDRGNNRVGFA 315 (316)
T ss_pred ceEEEEeCCCCEeecc
Confidence 4556699999999998
No 71
>TIGR00904 mreB cell shape determining protein, MreB/Mrl family. A close homolog is found in the Archaeon Methanobacterium thermoautotrophicum, and a more distant homolog in Archaeoglobus fulgidus. The family is related to cell division protein FtsA and heat shock protein DnaK.
Probab=23.41 E-value=62 Score=26.80 Aligned_cols=15 Identities=33% Similarity=0.612 Sum_probs=13.7
Q ss_pred EEeecCCceEEEEee
Q 032585 66 LGVDLGLSRTGLALS 80 (137)
Q Consensus 66 LGlD~GtKRIGVAVS 80 (137)
+|||+||..+=|++.
T Consensus 5 ~giDlGt~~s~i~~~ 19 (333)
T TIGR00904 5 IGIDLGTANTLVYVK 19 (333)
T ss_pred eEEecCcceEEEEEC
Confidence 899999999998875
No 72
>TIGR01991 HscA Fe-S protein assembly chaperone HscA. The Heat Shock Cognate proteins HscA and HscB act together as chaperones. HscA resembles DnaK but belongs in a separate clade. The apparent function is to aid assembly of iron-sulfur cluster proteins. Homologs from Buchnera and Wolbachia are clearly in the same clade but are highly derived and score lower than some examples of DnaK.
Probab=23.06 E-value=54 Score=30.13 Aligned_cols=16 Identities=31% Similarity=0.555 Sum_probs=14.4
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
++||||||...=||+-
T Consensus 1 ~iGIDlGTtns~va~~ 16 (599)
T TIGR01991 1 AVGIDLGTTNSLVASV 16 (599)
T ss_pred CEEEEEccccEEEEEE
Confidence 4899999999999986
No 73
>PRK13311 N-acetyl-D-glucosamine kinase; Provisional
Probab=22.74 E-value=1.6e+02 Score=23.42 Aligned_cols=17 Identities=24% Similarity=0.419 Sum_probs=15.7
Q ss_pred EEEeecCCceEEEEeec
Q 032585 65 SLGVDLGLSRTGLALSK 81 (137)
Q Consensus 65 iLGlD~GtKRIGVAVSd 81 (137)
++|+|+|...|-+++.|
T Consensus 2 ~lgidiggt~i~~~l~d 18 (256)
T PRK13311 2 YYGFDMGGTKIELGVFD 18 (256)
T ss_pred EEEEEECCCcEEEEEEC
Confidence 68999999999999995
No 74
>PF08608 Wyosine_form: Wyosine base formation; InterPro: IPR013917 The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW []. ; PDB: 2YX0_A 2Z2U_A.
Probab=22.45 E-value=80 Score=21.25 Aligned_cols=21 Identities=5% Similarity=-0.233 Sum_probs=15.5
Q ss_pred CCChhhHHHHHHHHHHHHhcC
Q 032585 114 SYEPQLNLLSKKKLRWFYYCD 134 (137)
Q Consensus 114 tEgp~A~kVr~FA~rL~~~~~ 134 (137)
..-|..+.|.+|++.|.+.++
T Consensus 25 ~nmp~h~eV~~F~~~l~~~~~ 45 (62)
T PF08608_consen 25 GNMPWHEEVLDFAEELAELLG 45 (62)
T ss_dssp GGS--HHHHHHHHHHHHTTST
T ss_pred CCCCcHHHHHHHHHHHHhhcC
Confidence 455778899999999998764
No 75
>cd05475 nucellin_like Nucellins, plant aspartic proteases specifically expressed in nucellar cells during degradation. Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. This degradation is a characteristic of programmed cell death. Nucellins are plant aspartic proteases specifically expressed in nucellar cells during degradation. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region, and two other regions nearly identical to two regions of plant aspartic proteases. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. Although the three-dimensional structures of the two lobes are very similar, the amino acid sequences are more d
Probab=22.13 E-value=57 Score=26.18 Aligned_cols=19 Identities=21% Similarity=0.148 Sum_probs=16.0
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
++.++.+|++.+|||+|-.
T Consensus 253 ~~~~~vfD~~~~riGfa~~ 271 (273)
T cd05475 253 QGLMVIYDNEKQQIGWVRS 271 (273)
T ss_pred EeeEEEEECcCCEeCcccC
Confidence 4567889999999999864
No 76
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase). This alignment models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution.
Probab=22.09 E-value=1.7e+02 Score=23.74 Aligned_cols=16 Identities=31% Similarity=0.582 Sum_probs=14.6
Q ss_pred EEeecCCceEEEEeec
Q 032585 66 LGVDLGLSRTGLALSK 81 (137)
Q Consensus 66 LGlD~GtKRIGVAVSd 81 (137)
+|+|+|...|-+++.|
T Consensus 1 lgidig~t~~~~~l~d 16 (318)
T TIGR00744 1 IGVDIGGTTIKLGVVD 16 (318)
T ss_pred CEEEeCCCEEEEEEEC
Confidence 6899999999999995
No 77
>smart00842 FtsA Cell division protein FtsA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains PUBMED:9352931.
Probab=22.04 E-value=76 Score=24.22 Aligned_cols=16 Identities=25% Similarity=0.520 Sum_probs=14.4
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
+.|||+|+..|=+.++
T Consensus 1 ~~~lDIGs~~ik~vv~ 16 (187)
T smart00842 1 IVGLDIGTSKIKALVA 16 (187)
T ss_pred CEEEEeccceEEEEEE
Confidence 4799999999998888
No 78
>cd05488 Proteinase_A_fungi Fungal Proteinase A , aspartic proteinase superfamily. Fungal Proteinase A, a proteolytic enzyme distributed among a variety of organisms, is a member of the aspartic proteinase superfamily. In Saccharomyces cerevisiae, targeted to the vacuole as a zymogen, activation of proteinases A at acidic pH can occur by two different pathways: a one-step process to release mature proteinase A, involving the intervention of proteinase B, or a step-wise pathway via the auto-activation product known as pseudo-proteinase A. Once active, S. cerevisiae proteinase A is essential to the activities of other yeast vacuolar hydrolases, including proteinase B and carboxypeptidase Y. The mature enzyme is bilobal, with each lobe providing one of the two catalytically essential aspartic acid residues in the active site. The crystal structure of free proteinase A shows that flap loop is atypically pointing directly into the S(1) pocket of the enzyme. Proteinase A preferentially hydro
Probab=21.75 E-value=69 Score=26.26 Aligned_cols=17 Identities=35% Similarity=0.397 Sum_probs=14.3
Q ss_pred cceEEEeecCCceEEEE
Q 032585 62 GGFSLGVDLGLSRTGLA 78 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVA 78 (137)
++-+..+|++.+|||+|
T Consensus 303 ~~~y~vfD~~~~~iG~a 319 (320)
T cd05488 303 RKYYSVYDLGNNAVGLA 319 (320)
T ss_pred hheEEEEeCCCCEEeec
Confidence 34567799999999998
No 79
>CHL00163 ycf65 putative ribosomal protein 3; Validated
Probab=21.72 E-value=1.8e+02 Score=21.79 Aligned_cols=45 Identities=22% Similarity=0.132 Sum_probs=27.6
Q ss_pred eEEEeecCCceEEEEeec--ceeeeeeeeEEc-cchhHHHHHHHHhhc
Q 032585 64 FSLGVDLGLSRTGLALSK--GFCVRPLTVLKL-RGEKLELQLLEIAQR 108 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd--giiAsPL~tI~~-~~~~~~~~L~eli~e 108 (137)
++|=|=..++-|||||-. +--.+||+..-. ...+.++.|+..++.
T Consensus 4 f~lKvlWl~~~iaiAvDq~v~~~t~PlT~yfFWPr~DAWe~LK~~Les 51 (99)
T CHL00163 4 FTLKVLWLENNIGIAVDQIVGNGTSPLTSYFFWPRTDAWELLKLELES 51 (99)
T ss_pred EEEEEEEecCceEEEEeeeeCCCCccCcceeecCCccHHHHHHHHHhc
Confidence 344555668899999962 222588887643 222356777666654
No 80
>TIGR01311 glycerol_kin glycerol kinase. This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases.
Probab=21.39 E-value=2e+02 Score=25.32 Aligned_cols=18 Identities=17% Similarity=0.346 Sum_probs=15.6
Q ss_pred eEEEeecCCceEEEEeec
Q 032585 64 FSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd 81 (137)
.++|||+|+..|=+++-|
T Consensus 2 ~~lgiDiGtt~iKa~l~d 19 (493)
T TIGR01311 2 YILAIDQGTTSSRAIVFD 19 (493)
T ss_pred eEEEEecCCCceEEEEEC
Confidence 479999999999888883
No 81
>cd05473 beta_secretase_like Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two
Probab=21.10 E-value=87 Score=26.23 Aligned_cols=19 Identities=37% Similarity=0.515 Sum_probs=16.5
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
++.+..+|++.+|||+|-+
T Consensus 327 r~~yvvfD~~~~rIGfa~~ 345 (364)
T cd05473 327 EGFYVVFDRANKRVGFAVS 345 (364)
T ss_pred cceEEEEECCCCEEeeEec
Confidence 4567779999999999998
No 82
>PRK11678 putative chaperone; Provisional
Probab=21.10 E-value=67 Score=28.76 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=14.7
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
++||||||.-.=||+.
T Consensus 2 ~iGID~GTtNs~va~~ 17 (450)
T PRK11678 2 FIGFDYGTANCSVAVM 17 (450)
T ss_pred eEEEecCccceeeEEe
Confidence 5899999999999998
No 83
>COG4820 EutJ Ethanolamine utilization protein, possible chaperonin [Amino acid transport and metabolism]
Probab=20.88 E-value=5.1e+02 Score=22.45 Aligned_cols=62 Identities=11% Similarity=0.136 Sum_probs=39.6
Q ss_pred cceEEEeecCCceEEEEeecceeeeeeeeEEccchhHHHHHHHHhhccEEECCCChhhHHHHHHHHHHHHhc
Q 032585 62 GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREVILGSYEPQLNLLSKKKLRWFYYC 133 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVSdgiiAsPL~tI~~~~~~~~~~L~eli~eevVVGtEgp~A~kVr~FA~rL~~~~ 133 (137)
-..++|+|+||.-|=.-|-|+ -.+|+...- ..++.+++-|||- --+..+.||+.-++|++.+
T Consensus 28 sk~~vGVDLGT~~iV~~vlD~-d~~Pvag~~--------~~advVRDGiVvd-f~eaveiVrrlkd~lEk~l 89 (277)
T COG4820 28 SKLWVGVDLGTCDIVSMVLDR-DGQPVAGCL--------DWADVVRDGIVVD-FFEAVEIVRRLKDTLEKQL 89 (277)
T ss_pred CceEEEeecccceEEEEEEcC-CCCeEEEEe--------hhhhhhccceEEe-hhhHHHHHHHHHHHHHHhh
Confidence 467899999999987666542 246766542 2345566667775 1223566777777777654
No 84
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=20.62 E-value=97 Score=27.83 Aligned_cols=19 Identities=16% Similarity=0.235 Sum_probs=15.8
Q ss_pred cceEEEeecCCceEEEEee
Q 032585 62 GGFSLGVDLGLSRTGLALS 80 (137)
Q Consensus 62 ~gRiLGlD~GtKRIGVAVS 80 (137)
+..+.-+|++.+|||+|.+
T Consensus 430 r~~Y~VFD~~n~rIGfA~a 448 (450)
T PTZ00013 430 RKYFTVFDYDKESVGFAIA 448 (450)
T ss_pred ccEEEEEECCCCEEEEEEe
Confidence 4556679999999999975
No 85
>TIGR01174 ftsA cell division protein FtsA. This bacterial cell division protein interacts with FtsZ, the bacterial homolog of tubulin. It is an ATP-binding protein and shows structural similarities to actin and heat shock cognate protein 70.
Probab=20.43 E-value=3e+02 Score=23.19 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=14.7
Q ss_pred EEEeecCCceEEEEee
Q 032585 65 SLGVDLGLSRTGLALS 80 (137)
Q Consensus 65 iLGlD~GtKRIGVAVS 80 (137)
++|||+|+..|=+++.
T Consensus 2 ~~~lDIGs~~ik~vv~ 17 (371)
T TIGR01174 2 IVGLDIGTSKICAIVA 17 (371)
T ss_pred EEEEEeccceEEEEEE
Confidence 6899999999999887
No 86
>PRK00047 glpK glycerol kinase; Provisional
Probab=20.07 E-value=2.3e+02 Score=25.03 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=15.6
Q ss_pred eEEEeecCCceEEEEeec
Q 032585 64 FSLGVDLGLSRTGLALSK 81 (137)
Q Consensus 64 RiLGlD~GtKRIGVAVSd 81 (137)
.+||||+|+..+=+++-|
T Consensus 6 ~~lgiD~GTts~Ka~l~d 23 (498)
T PRK00047 6 YILALDQGTTSSRAIIFD 23 (498)
T ss_pred EEEEEecCCCceEEEEEC
Confidence 589999999999888873
Done!