Query 035140
Match_columns 72
No_of_seqs 155 out of 1057
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 09:31:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02739 5_3_exonuc_N: 5'-3' e 99.9 1.2E-26 2.5E-31 156.5 2.1 67 2-68 64-156 (169)
2 PRK09482 flap endonuclease-lik 99.9 4.1E-25 8.9E-30 157.8 6.1 65 2-66 62-150 (256)
3 smart00475 53EXOc 5'-3' exonuc 99.9 6.8E-24 1.5E-28 151.0 6.7 66 1-66 61-150 (259)
4 PRK14976 5'-3' exonuclease; Pr 99.9 1.2E-23 2.7E-28 151.1 7.5 67 1-67 67-157 (281)
5 cd00008 53EXOc 5'-3' exonuclea 99.9 1.9E-22 4.1E-27 141.5 7.1 65 1-65 62-150 (240)
6 PHA02567 rnh RnaseH; Provision 99.9 2.4E-22 5.2E-27 146.7 6.4 66 1-66 76-174 (304)
7 TIGR00593 pola DNA polymerase 99.8 8.6E-22 1.9E-26 158.2 5.7 66 1-66 61-150 (887)
8 PRK05755 DNA polymerase I; Pro 99.8 2E-20 4.3E-25 149.4 7.7 65 1-65 63-151 (880)
9 PHA00439 exonuclease 99.8 1.7E-20 3.7E-25 136.1 5.7 62 1-64 75-161 (286)
10 COG0258 Exo 5'-3' exonuclease 99.7 4.3E-18 9.3E-23 122.6 4.4 68 1-68 72-164 (310)
11 PRK03980 flap endonuclease-1; 98.9 8.4E-10 1.8E-14 80.1 1.5 58 2-59 38-137 (292)
12 PTZ00217 flap endonuclease-1; 98.7 9.3E-09 2E-13 77.3 2.0 62 2-64 93-196 (393)
13 TIGR03674 fen_arch flap struct 98.6 2.4E-08 5.1E-13 73.5 1.8 62 2-64 85-188 (338)
14 cd00128 XPG Xeroderma pigmento 98.3 1.8E-07 3.9E-12 67.4 0.1 57 4-60 92-183 (316)
15 TIGR00288 conserved hypothetic 87.6 0.57 1.2E-05 31.8 2.6 28 29-56 71-123 (160)
16 TIGR00264 alpha-NAC-related pr 84.7 2.6 5.7E-05 27.4 4.4 42 24-65 9-55 (116)
17 PF01936 NYN: NYN domain; Int 82.4 0.51 1.1E-05 29.3 0.4 14 43-56 99-113 (146)
18 PLN02320 seryl-tRNA synthetase 81.9 4.5 9.8E-05 32.0 5.6 50 20-69 359-409 (502)
19 cd06167 LabA_like LabA_like pr 79.9 0.85 1.8E-05 28.8 0.8 14 43-56 103-117 (149)
20 TIGR00600 rad2 DNA excision re 78.2 3.3 7.2E-05 35.4 4.0 28 25-52 773-818 (1034)
21 COG2877 KdsA 3-deoxy-D-manno-o 72.4 3.6 7.8E-05 30.3 2.5 31 12-42 59-93 (279)
22 PLN02678 seryl-tRNA synthetase 71.5 13 0.00028 28.9 5.5 49 21-69 304-353 (448)
23 COG0172 SerS Seryl-tRNA synthe 70.9 16 0.00035 28.4 5.9 47 21-67 300-347 (429)
24 cd00772 ProRS_core Prolyl-tRNA 70.5 13 0.00028 26.4 5.0 44 21-64 163-208 (264)
25 COG1569 Predicted nucleic acid 69.8 2.9 6.2E-05 28.2 1.4 23 43-65 106-131 (142)
26 PF12813 XPG_I_2: XPG domain c 68.6 6.3 0.00014 28.0 3.0 26 27-52 7-52 (246)
27 TIGR00414 serS seryl-tRNA synt 67.1 6.1 0.00013 30.1 2.9 68 2-69 261-348 (418)
28 TIGR00305 probable toxin-antit 66.9 2.3 5.1E-05 26.0 0.5 10 43-52 102-111 (114)
29 PRK13909 putative recombinatio 66.8 14 0.0003 30.7 5.0 47 8-55 860-908 (910)
30 TIGR00028 Mtu_PIN_fam Mycobact 61.9 6.9 0.00015 23.9 1.9 21 43-65 119-140 (142)
31 PHA02754 hypothetical protein; 61.5 16 0.00034 21.5 3.3 32 19-50 13-46 (67)
32 PRK13397 3-deoxy-7-phosphohept 61.3 5.7 0.00012 28.7 1.7 31 10-42 50-84 (250)
33 PRK05431 seryl-tRNA synthetase 59.3 8.6 0.00019 29.3 2.4 46 21-66 297-343 (425)
34 PF00587 tRNA-synt_2b: tRNA sy 58.4 40 0.00086 21.8 5.2 45 20-64 125-171 (173)
35 PF00411 Ribosomal_S11: Riboso 56.3 20 0.00043 22.4 3.4 38 8-45 31-68 (110)
36 KOG2520 5'-3' exonuclease [Rep 53.7 17 0.00038 30.5 3.4 32 10-42 453-484 (815)
37 PRK01254 hypothetical protein; 53.6 7 0.00015 32.3 1.2 39 8-50 11-49 (707)
38 PF14451 Ub-Mut7C: Mut7-C ubiq 52.5 10 0.00022 22.8 1.5 36 27-62 33-74 (81)
39 KOG1282 Serine carboxypeptidas 51.6 19 0.00041 28.2 3.2 28 26-56 352-381 (454)
40 CHL00041 rps11 ribosomal prote 49.7 52 0.0011 20.9 4.6 37 9-45 45-81 (116)
41 PF01930 Cas_Cas4: Domain of u 48.7 56 0.0012 20.9 4.7 33 9-42 70-102 (162)
42 PF01927 Mut7-C: Mut7-C RNAse 48.6 24 0.00053 22.9 3.0 31 26-56 9-57 (147)
43 TIGR03632 bact_S11 30S ribosom 48.3 57 0.0012 20.4 4.5 37 9-45 32-68 (108)
44 PLN03033 2-dehydro-3-deoxyphos 48.2 28 0.00062 25.9 3.5 31 12-42 58-92 (290)
45 PRK05198 2-dehydro-3-deoxyphos 47.2 30 0.00065 25.4 3.5 31 12-42 52-86 (264)
46 TIGR01362 KDO8P_synth 3-deoxy- 45.2 35 0.00075 25.0 3.5 31 12-42 44-78 (258)
47 PF08497 Radical_SAM_N: Radica 44.7 10 0.00022 28.4 0.7 24 27-50 3-26 (302)
48 PRK10858 nitrogen regulatory p 44.4 27 0.00058 22.1 2.6 18 25-42 12-29 (112)
49 PRK05309 30S ribosomal protein 43.9 70 0.0015 20.7 4.5 37 9-45 49-85 (128)
50 cd00778 ProRS_core_arch_euk Pr 43.9 66 0.0014 22.6 4.8 44 21-64 163-208 (261)
51 PRK12457 2-dehydro-3-deoxyphos 43.9 36 0.00079 25.2 3.5 31 12-42 58-92 (281)
52 PF04900 Fcf1: Fcf1; InterPro 43.6 14 0.0003 22.3 1.1 28 43-70 67-97 (101)
53 PRK13398 3-deoxy-7-phosphohept 42.5 42 0.00092 24.1 3.7 32 10-42 62-96 (266)
54 COG4572 ChaB Putative cation t 42.2 29 0.00062 21.0 2.3 19 11-30 3-21 (76)
55 COG1490 Dtd D-Tyr-tRNAtyr deac 42.2 93 0.002 21.0 5.0 55 7-62 81-142 (145)
56 cd08071 MPN_DUF2466 Mov34/MPN/ 41.6 73 0.0016 19.8 4.3 23 27-49 85-107 (113)
57 COG1432 Uncharacterized conser 40.6 11 0.00025 25.4 0.5 23 43-65 114-143 (181)
58 PF05991 NYN_YacP: YacP-like N 39.8 22 0.00048 23.6 1.7 30 27-56 81-111 (166)
59 cd02414 jag_KH jag_K homology 39.5 76 0.0016 18.2 4.0 16 27-42 2-17 (77)
60 KOG2519 5'-3' exonuclease [Rep 39.1 32 0.00069 27.1 2.7 26 27-52 135-178 (449)
61 PRK01777 hypothetical protein; 38.1 56 0.0012 20.1 3.3 38 28-65 28-77 (95)
62 cd00770 SerRS_core Seryl-tRNA 37.7 83 0.0018 22.6 4.6 31 20-50 177-207 (297)
63 PF08984 DUF1858: Domain of un 37.2 17 0.00036 20.1 0.7 23 20-42 8-30 (59)
64 COG0100 RpsK Ribosomal protein 36.7 1E+02 0.0022 20.4 4.4 37 9-45 50-86 (129)
65 COG4634 Uncharacterized protei 36.5 40 0.00086 21.9 2.5 22 43-64 49-76 (113)
66 PF03841 SelA: L-seryl-tRNA se 36.2 46 0.001 25.5 3.2 10 43-52 206-215 (367)
67 PRK06369 nac nascent polypepti 36.1 94 0.002 20.1 4.2 36 28-63 9-49 (115)
68 PF02120 Flg_hook: Flagellar h 35.6 49 0.0011 18.8 2.6 36 14-49 45-80 (85)
69 KOG0180 20S proteasome, regula 35.3 53 0.0011 23.2 3.1 30 19-50 159-193 (204)
70 KOG2501 Thioredoxin, nucleored 34.6 47 0.001 22.6 2.7 26 29-55 58-84 (157)
71 PF10130 PIN_2: PIN domain; I 34.3 9.9 0.00022 24.7 -0.6 10 43-52 106-115 (133)
72 KOG4366 Predicted thioesterase 34.1 20 0.00042 25.6 0.8 23 6-28 170-192 (213)
73 TIGR00421 ubiX_pad polyprenyl 34.1 53 0.0012 22.2 2.9 25 14-40 151-175 (181)
74 smart00670 PINc Large family o 33.8 22 0.00047 20.8 0.9 10 43-52 100-109 (111)
75 PF08443 RimK: RimK-like ATP-g 33.5 50 0.0011 21.8 2.7 32 18-52 129-160 (190)
76 PF00586 AIRS: AIR synthase re 33.2 61 0.0013 18.9 2.8 24 18-41 69-92 (96)
77 COG2102 Predicted ATPases of P 31.8 70 0.0015 23.0 3.3 21 22-42 97-117 (223)
78 cd01401 PncB_like Nicotinate p 31.7 80 0.0017 24.1 3.8 35 20-54 282-318 (377)
79 cd00779 ProRS_core_prok Prolyl 31.1 1.6E+02 0.0034 20.6 5.0 46 23-70 159-207 (255)
80 cd00771 ThrRS_core Threonyl-tR 30.9 1.1E+02 0.0024 21.8 4.3 29 21-49 155-183 (298)
81 PRK06764 hypothetical protein; 30.8 28 0.0006 22.0 1.0 22 43-64 61-83 (105)
82 smart00484 XPGI Xeroderma pigm 29.8 37 0.00079 19.9 1.4 9 44-52 29-37 (73)
83 PF08285 DPM3: Dolichol-phosph 29.3 78 0.0017 19.4 2.9 21 19-39 70-90 (91)
84 PF13734 Inhibitor_I69: Spi pr 29.0 30 0.00066 21.5 1.0 13 43-55 53-66 (96)
85 COG2266 GTP:adenosylcobinamide 28.8 76 0.0016 22.0 3.0 16 27-42 53-68 (177)
86 COG5458 Uncharacterized conser 28.6 50 0.0011 22.1 2.0 18 11-28 123-140 (144)
87 PF09572 RE_XamI: XamI restric 28.5 99 0.0021 22.7 3.7 38 5-42 80-142 (251)
88 KOG3185 Translation initiation 28.5 41 0.00089 24.2 1.7 49 15-65 85-141 (245)
89 TIGR03358 VI_chp_5 type VI sec 28.5 54 0.0012 22.3 2.2 18 18-35 101-118 (159)
90 PRK10665 nitrogen regulatory p 28.2 67 0.0014 20.2 2.5 18 25-42 12-29 (112)
91 PRK05659 sulfur carrier protei 28.0 96 0.0021 16.9 2.9 40 29-68 18-66 (66)
92 PF06069 PerC: PerC transcript 27.5 1.1E+02 0.0024 18.9 3.3 29 12-40 49-78 (90)
93 PRK00754 signal recognition pa 27.4 62 0.0013 20.1 2.2 38 4-41 6-52 (95)
94 PF02037 SAP: SAP domain; Int 27.4 69 0.0015 15.9 2.0 15 26-40 6-20 (35)
95 PF02696 UPF0061: Uncharacteri 26.9 91 0.002 24.6 3.5 35 15-51 128-164 (487)
96 TIGR02784 addA_alphas double-s 26.9 1.4E+02 0.0031 25.4 4.8 42 9-50 1087-1136(1141)
97 smart00513 SAP Putative DNA-bi 26.6 76 0.0016 15.6 2.1 15 26-40 6-20 (35)
98 COG4274 Uncharacterized conser 26.6 1.2E+02 0.0025 19.5 3.3 27 26-52 32-68 (104)
99 PF08002 DUF1697: Protein of u 25.7 57 0.0012 21.1 1.9 27 26-52 21-53 (137)
100 KOG4720 Ethanolamine kinase [L 25.6 1.4E+02 0.003 23.2 4.1 40 17-56 225-273 (391)
101 PRK00029 hypothetical protein; 25.5 1.1E+02 0.0024 24.3 3.7 35 16-52 129-165 (487)
102 PF10137 TIR-like: Predicted n 24.6 1.7E+02 0.0036 18.8 3.9 15 28-42 15-29 (125)
103 PF14528 LAGLIDADG_3: LAGLIDAD 24.4 73 0.0016 17.7 2.0 15 26-40 34-48 (77)
104 COG1908 FrhD Coenzyme F420-red 24.1 30 0.00064 23.0 0.3 17 26-42 80-96 (132)
105 TIGR02263 benz_CoA_red_C benzo 24.0 99 0.0021 23.1 3.1 21 27-48 341-361 (380)
106 PF11510 FA_FANCE: Fanconi Ana 23.9 55 0.0012 23.9 1.7 23 15-37 5-27 (263)
107 TIGR01721 AMN-like AMP nucleos 23.7 2.1E+02 0.0046 20.7 4.7 26 25-50 137-162 (266)
108 COG3516 Predicted component of 23.7 73 0.0016 22.0 2.2 17 19-35 107-123 (169)
109 COG0347 GlnK Nitrogen regulato 23.6 75 0.0016 20.5 2.1 17 26-42 13-29 (112)
110 PRK03745 signal recognition pa 23.4 81 0.0018 19.9 2.2 37 5-41 4-49 (100)
111 PRK06437 hypothetical protein; 23.3 1.5E+02 0.0033 16.7 3.8 41 28-68 22-67 (67)
112 COG1880 CdhB CO dehydrogenase/ 23.1 93 0.002 21.6 2.6 31 12-42 34-68 (170)
113 COG1921 SelA Selenocysteine sy 23.0 1.2E+02 0.0027 23.5 3.5 24 29-52 179-225 (395)
114 PF01255 Prenyltransf: Putativ 22.9 1.9E+02 0.004 20.1 4.2 24 26-49 27-50 (223)
115 cd06535 CIDE_N_CAD CIDE_N doma 22.8 1.3E+02 0.0028 18.2 2.9 38 28-67 26-72 (77)
116 PRK13396 3-deoxy-7-phosphohept 22.5 1.4E+02 0.0031 22.6 3.7 33 9-42 135-170 (352)
117 PF05591 DUF770: Protein of un 22.4 83 0.0018 21.2 2.2 18 18-35 100-117 (157)
118 PF12621 DUF3779: Phosphate me 22.3 14 0.0003 22.6 -1.5 20 3-22 2-21 (95)
119 KOG0991 Replication factor C, 22.1 32 0.0007 25.8 0.2 31 26-56 178-213 (333)
120 PRK09243 nicotinate phosphorib 22.1 1.6E+02 0.0034 23.0 3.9 42 11-54 258-300 (464)
121 PF00867 XPG_I: XPG I-region; 22.1 36 0.00079 20.3 0.4 20 44-64 29-49 (94)
122 PF02274 Amidinotransf: Amidin 22.0 1.1E+02 0.0023 21.3 2.8 29 14-42 22-50 (281)
123 COG2089 SpsE Sialic acid synth 21.9 2.2E+02 0.0047 21.9 4.5 49 19-67 253-317 (347)
124 PF11130 TraC_F_IV: F pilus as 21.7 1.9E+02 0.0042 19.5 4.0 42 20-61 141-207 (235)
125 PRK01816 hypothetical protein; 21.4 1.7E+02 0.0037 19.7 3.5 26 15-40 87-112 (143)
126 PF00543 P-II: Nitrogen regula 21.3 68 0.0015 19.3 1.5 17 26-42 10-26 (102)
127 cd07399 MPP_YvnB Bacillus subt 21.2 2.4E+02 0.0051 19.0 4.3 30 17-49 15-44 (214)
128 KOG0787 Dehydrogenase kinase [ 21.2 1.7E+02 0.0038 22.9 4.0 40 18-57 257-307 (414)
129 COG0488 Uup ATPase components 21.1 93 0.002 24.7 2.6 39 23-64 186-225 (530)
130 PTZ00472 serine carboxypeptida 21.0 94 0.002 23.9 2.5 22 27-52 355-376 (462)
131 PRK05321 nicotinate phosphorib 20.8 1.8E+02 0.0039 22.4 4.0 44 10-54 276-321 (400)
132 PF04002 RadC: RadC-like JAB d 20.5 1.4E+02 0.003 18.7 2.9 25 27-52 90-114 (123)
133 PF13905 Thioredoxin_8: Thiore 20.5 1.8E+02 0.0038 16.3 4.0 31 22-52 16-47 (95)
134 PRK13015 3-dehydroquinate dehy 20.5 1.1E+02 0.0023 20.6 2.4 27 19-45 75-101 (146)
135 cd06409 PB1_MUG70 The MUG70 pr 20.4 83 0.0018 19.2 1.7 28 29-56 27-69 (86)
136 COG0821 gcpE 1-hydroxy-2-methy 20.1 1.6E+02 0.0034 22.8 3.5 41 6-49 138-178 (361)
137 PRK05395 3-dehydroquinate dehy 20.1 1.1E+02 0.0024 20.6 2.4 27 19-45 75-101 (146)
138 PF08734 GYD: GYD domain; Int 20.0 2.1E+02 0.0045 17.1 3.5 34 23-56 19-53 (91)
No 1
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.92 E-value=1.2e-26 Score=156.46 Aligned_cols=67 Identities=37% Similarity=0.718 Sum_probs=60.8
Q ss_pred CcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccCC
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILSH 57 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~~ 57 (72)
|||+++||+|||||+++|++|..|++.++++++++|+++++ |+|+|+|||| |||++
T Consensus 64 ~fR~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~ 143 (169)
T PF02739_consen 64 TFRKELYPEYKANRKPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDE 143 (169)
T ss_dssp HHHHHCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS
T ss_pred chHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCC
Confidence 79999999999999999999999999999999999999998 9999999999 99999
Q ss_pred --CEEEEEecCCc
Q 035140 58 --SLCLLRIAPRG 68 (72)
Q Consensus 58 --~v~v~~~~k~~ 68 (72)
+|.++++....
T Consensus 144 ~~~V~~~~~~~~~ 156 (169)
T PF02739_consen 144 NVNVYLLDPGKKK 156 (169)
T ss_dssp -TSEEEEETTTTC
T ss_pred CceEEEeecCCCC
Confidence 77777764333
No 2
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.91 E-value=4.1e-25 Score=157.79 Aligned_cols=65 Identities=31% Similarity=0.564 Sum_probs=62.1
Q ss_pred CcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccCC
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILSH 57 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~~ 57 (72)
+|||++||+|||||++||++|..|++.|+++++++|+++++ |+|+|+|||+ |||++
T Consensus 62 ~fR~~l~p~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~ 141 (256)
T PRK09482 62 GWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSP 141 (256)
T ss_pred ccHHHHhHHHhcCCCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCC
Confidence 39999999999999999999999999999999999999988 9999999999 99999
Q ss_pred CEEEEEecC
Q 035140 58 SLCLLRIAP 66 (72)
Q Consensus 58 ~v~v~~~~k 66 (72)
+|++|++.+
T Consensus 142 ~v~~~~~~~ 150 (256)
T PRK09482 142 TIQIRDYFQ 150 (256)
T ss_pred CeEEEeccc
Confidence 999998653
No 3
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.90 E-value=6.8e-24 Score=150.99 Aligned_cols=66 Identities=39% Similarity=0.735 Sum_probs=63.3
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
++|||++||+|||||++||++|..|++.+++++++||+++++ ++|+|+|||| ||++
T Consensus 61 ~~~R~~l~p~YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~ 140 (259)
T smart00475 61 KTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVS 140 (259)
T ss_pred CccccchhHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCC
Confidence 489999999999999999999999999999999999999998 8899999999 9999
Q ss_pred CCEEEEEecC
Q 035140 57 HSLCLLRIAP 66 (72)
Q Consensus 57 ~~v~v~~~~k 66 (72)
++|.+|++.+
T Consensus 141 ~~v~~~~~~~ 150 (259)
T smart00475 141 DKVSVLDPTK 150 (259)
T ss_pred CCEEEEeccC
Confidence 9999998865
No 4
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.89 E-value=1.2e-23 Score=151.06 Aligned_cols=67 Identities=31% Similarity=0.495 Sum_probs=63.7
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
.+|||++||+||+||++||++|..|++.++++++++|+|+++ |+|+|+|||| ||++
T Consensus 67 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~ 146 (281)
T PRK14976 67 KTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVN 146 (281)
T ss_pred CcccccccHHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCC
Confidence 489999999999999999999999999999999999999998 8999999999 9999
Q ss_pred CCEEEEEecCC
Q 035140 57 HSLCLLRIAPR 67 (72)
Q Consensus 57 ~~v~v~~~~k~ 67 (72)
++|+++++.++
T Consensus 147 ~~v~~~~~~~~ 157 (281)
T PRK14976 147 ENTDVLLKKKG 157 (281)
T ss_pred CCeEEEEecCC
Confidence 99999987654
No 5
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=99.87 E-value=1.9e-22 Score=141.54 Aligned_cols=65 Identities=34% Similarity=0.622 Sum_probs=62.4
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
++|||++||+||+||+++|++|..|++.+++++++||+++++ ++|+|+|||| ||++
T Consensus 62 ~~~R~~l~p~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~ 141 (240)
T cd00008 62 KTFRHELYPEYKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVS 141 (240)
T ss_pred CcccccccHHHHcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCC
Confidence 489999999999999999999999999999999999999998 7999999999 9999
Q ss_pred CCEEEEEec
Q 035140 57 HSLCLLRIA 65 (72)
Q Consensus 57 ~~v~v~~~~ 65 (72)
++|+++++.
T Consensus 142 ~~v~~~~~~ 150 (240)
T cd00008 142 DNVKVVSPM 150 (240)
T ss_pred CCEEEEeCC
Confidence 999999875
No 6
>PHA02567 rnh RnaseH; Provisional
Probab=99.87 E-value=2.4e-22 Score=146.70 Aligned_cols=66 Identities=18% Similarity=0.184 Sum_probs=60.6
Q ss_pred CCcccccCccccCCCCCCchhHHHhH--------HHHHHHHHHcCCccEE-----------------------EEEecCC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGL--------QYLKASIKAMSIKVIE-----------------------IQVVSPN 49 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql--------~~i~~~l~~lgi~~~~-----------------------v~IvS~D 49 (72)
++|||++||+|||||++||++|..|+ +.+++++++||+++++ |+|+|+|
T Consensus 76 ~tfR~elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~D 155 (304)
T PHA02567 76 GYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSD 155 (304)
T ss_pred CCchhhhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCC
Confidence 37999999999999999999988887 7889999999999998 9999999
Q ss_pred CCc-cccC-CCEEEEEecC
Q 035140 50 KDS-QILS-HSLCLLRIAP 66 (72)
Q Consensus 50 KD~-QLv~-~~v~v~~~~k 66 (72)
||| ||++ ++|.+|++.+
T Consensus 156 KDl~QLv~~~~v~~~~~~~ 174 (304)
T PHA02567 156 GDFTQLHKYPGVKQWSPMQ 174 (304)
T ss_pred CChhhccCCCCeEEeecCC
Confidence 999 9995 8999998764
No 7
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.85 E-value=8.6e-22 Score=158.25 Aligned_cols=66 Identities=32% Similarity=0.634 Sum_probs=63.2
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
+||||++||+|||||++||++|..|++.+++++++||||+++ |+|+|+|||+ ||++
T Consensus 61 ~tfR~~~~~~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~ 140 (887)
T TIGR00593 61 PTFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVS 140 (887)
T ss_pred CcchHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCC
Confidence 489999999999999999999999999999999999999998 8999999999 9999
Q ss_pred CCEEEEEecC
Q 035140 57 HSLCLLRIAP 66 (72)
Q Consensus 57 ~~v~v~~~~k 66 (72)
++|+++++.+
T Consensus 141 ~~v~~~~~~~ 150 (887)
T TIGR00593 141 DNVKVLIPKG 150 (887)
T ss_pred CCEEEEeccC
Confidence 9999998754
No 8
>PRK05755 DNA polymerase I; Provisional
Probab=99.82 E-value=2e-20 Score=149.37 Aligned_cols=65 Identities=34% Similarity=0.735 Sum_probs=62.6
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
+||||++||+|||||+++|++|..|++.++++++++|+++++ ++|+|+|||| ||++
T Consensus 63 ~~~R~~~~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~ 142 (880)
T PRK05755 63 KTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVD 142 (880)
T ss_pred CccccccCHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCC
Confidence 489999999999999999999999999999999999999998 8999999999 9999
Q ss_pred CCEEEEEec
Q 035140 57 HSLCLLRIA 65 (72)
Q Consensus 57 ~~v~v~~~~ 65 (72)
++|++|++.
T Consensus 143 ~~v~~~~~~ 151 (880)
T PRK05755 143 DNVTLLDTM 151 (880)
T ss_pred CCEEEeecc
Confidence 999999875
No 9
>PHA00439 exonuclease
Probab=99.82 E-value=1.7e-20 Score=136.07 Aligned_cols=62 Identities=27% Similarity=0.304 Sum_probs=55.9
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE------------------------EEEecCCCCc-ccc
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE------------------------IQVVSPNKDS-QIL 55 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~------------------------v~IvS~DKD~-QLv 55 (72)
+||||++||+|||||++||++ ..|++.++++++++|+++++ |+|+|+|||| ||+
T Consensus 75 ~tfR~elyp~YKanR~~~p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv 153 (286)
T PHA00439 75 VNWRKEVVPTYKANRKAKRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIP 153 (286)
T ss_pred CChHhhhhhHhcCCCCCCCCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcC
Confidence 489999999999999999999 88999999999999999988 6999999999 999
Q ss_pred CCCEEEEEe
Q 035140 56 SHSLCLLRI 64 (72)
Q Consensus 56 ~~~v~v~~~ 64 (72)
+. +.+|.+
T Consensus 154 ~~-~~~~~~ 161 (286)
T PHA00439 154 NC-DFLWCT 161 (286)
T ss_pred cc-eEEEcc
Confidence 76 444443
No 10
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.72 E-value=4.3e-18 Score=122.62 Aligned_cols=68 Identities=28% Similarity=0.474 Sum_probs=64.7
Q ss_pred CCcccccCccccCCCCC-CchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-ccc
Q 035140 1 MNFRHTLYPSYKNNRPP-TPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QIL 55 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~-~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv 55 (72)
++||+++|++||++|++ ||++|..|++.+.+.+.++|++.++ +.|+|+|||+ ||+
T Consensus 72 ~tfR~~~~~~yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~ 151 (310)
T COG0258 72 PTFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLV 151 (310)
T ss_pred CcchHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhc
Confidence 48999999999999999 9999999999999999999999988 9999999999 999
Q ss_pred CCCEEEEEecCCc
Q 035140 56 SHSLCLLRIAPRG 68 (72)
Q Consensus 56 ~~~v~v~~~~k~~ 68 (72)
++++.++++.++.
T Consensus 152 ~~~~~~~~~~~~~ 164 (310)
T COG0258 152 SPNVLVINGKKGE 164 (310)
T ss_pred CCCcEEEeccCCC
Confidence 9999999987764
No 11
>PRK03980 flap endonuclease-1; Provisional
Probab=98.85 E-value=8.4e-10 Score=80.06 Aligned_cols=58 Identities=16% Similarity=0.125 Sum_probs=53.8
Q ss_pred CcccccCccccCCCCCCchhHHH-----------------------hHHHHHHHHHHcCCccEE----------------
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQ-----------------------GLQYLKASIKAMSIKVIE---------------- 42 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~-----------------------Ql~~i~~~l~~lgi~~~~---------------- 42 (72)
++|++.+++||++|.++|+++.. |++.++++|++||||++.
T Consensus 38 ~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g 117 (292)
T PRK03980 38 ELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKG 117 (292)
T ss_pred hHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCC
Confidence 57999999999999999999877 999999999999999999
Q ss_pred --EEEecCCCCc-cccCCCE
Q 035140 43 --IQVVSPNKDS-QILSHSL 59 (72)
Q Consensus 43 --v~IvS~DKD~-QLv~~~v 59 (72)
..|+|+|+|+ |+.+++|
T Consensus 118 ~vd~V~S~D~D~l~fg~~~v 137 (292)
T PRK03980 118 DAWAVGSQDYDSLLFGAPRL 137 (292)
T ss_pred CeEEEecCCcCeeeecCCEE
Confidence 4789999999 9999875
No 12
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.66 E-value=9.3e-09 Score=77.26 Aligned_cols=62 Identities=16% Similarity=0.216 Sum_probs=54.2
Q ss_pred CcccccCccccCCCCCCchhH-----------------------HHhHHHHHHHHHHcCCccEE----------------
Q 035140 2 NFRHTLYPSYKNNRPPTPDTM-----------------------VQGLQYLKASIKAMSIKVIE---------------- 42 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L-----------------------~~Ql~~i~~~l~~lgi~~~~---------------- 42 (72)
++|++.++.||++|+++|+++ ..|++.++++|+.||||++.
T Consensus 93 ~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~~g 172 (393)
T PTZ00217 93 ELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKG 172 (393)
T ss_pred hhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHHHHHHHHHHCC
Confidence 578999999999999999998 78899999999999999999
Q ss_pred --EEEecCCCCc-cccCCCEEEEEe
Q 035140 43 --IQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 43 --v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
..|+|.|+|+ |+.++. .+++.
T Consensus 173 ~v~~ViS~D~D~l~fg~~~-vi~~l 196 (393)
T PTZ00217 173 KVYAVATEDMDALTFGTPV-LLRNL 196 (393)
T ss_pred CeEEEeCCCcCeeecCCcE-EEEcc
Confidence 5589999999 998774 34433
No 13
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=98.57 E-value=2.4e-08 Score=73.53 Aligned_cols=62 Identities=15% Similarity=0.158 Sum_probs=51.8
Q ss_pred CcccccCccccCCCCCCchhHHH-----------------------hHHHHHHHHHHcCCccEE----------------
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQ-----------------------GLQYLKASIKAMSIKVIE---------------- 42 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~-----------------------Ql~~i~~~l~~lgi~~~~---------------- 42 (72)
+||++.++.||+.|+++++++.. |++.++++|++||||++.
T Consensus 85 ~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g 164 (338)
T TIGR03674 85 ELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKG 164 (338)
T ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCC
Confidence 57788888888888887777654 489999999999999999
Q ss_pred -E-EEecCCCCc-cccCCCEEEEEe
Q 035140 43 -I-QVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 43 -v-~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
| .|+|+|+|+ |+.+++| +.+.
T Consensus 165 ~vd~v~S~D~D~l~fg~~~v-i~~~ 188 (338)
T TIGR03674 165 DVDYVGSQDYDSLLFGAPRL-VRNL 188 (338)
T ss_pred CeeEEecCCcCeeeecCCEE-EEec
Confidence 4 889999999 9999987 4443
No 14
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=98.27 E-value=1.8e-07 Score=67.44 Aligned_cols=57 Identities=12% Similarity=0.102 Sum_probs=49.9
Q ss_pred ccccCccccCCCCCCch----------------hHHHhHHHHHHHHHHcCCccEE------------------EEEecCC
Q 035140 4 RHTLYPSYKNNRPPTPD----------------TMVQGLQYLKASIKAMSIKVIE------------------IQVVSPN 49 (72)
Q Consensus 4 R~~~~p~YKanR~~~Pe----------------~L~~Ql~~i~~~l~~lgi~~~~------------------v~IvS~D 49 (72)
|++..++||++|.++|+ ....|++.++++|++||++++. ..|+|.|
T Consensus 92 R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~~g~v~~i~S~D 171 (316)
T cd00128 92 RRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAKKGLVDAIITED 171 (316)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHhCCCeeEEEecC
Confidence 88999999999998887 2478899999999999999998 5799999
Q ss_pred CCc-cccCCCEE
Q 035140 50 KDS-QILSHSLC 60 (72)
Q Consensus 50 KD~-QLv~~~v~ 60 (72)
+|+ |+-.++|.
T Consensus 172 sD~l~fg~~~vi 183 (316)
T cd00128 172 SDLLLFGAPRVY 183 (316)
T ss_pred CCeeeecCceEE
Confidence 999 98776554
No 15
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=87.58 E-value=0.57 Score=31.84 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=21.9
Q ss_pred HHHHHHHcCCccEE------------------------EEEecCCCCc-cccC
Q 035140 29 LKASIKAMSIKVIE------------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 29 i~~~l~~lgi~~~~------------------------v~IvS~DKD~-QLv~ 56 (72)
+.+.+..+|+..+. ++|+|||.|| -|+.
T Consensus 71 l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~ 123 (160)
T TIGR00288 71 LIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVIN 123 (160)
T ss_pred HHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHH
Confidence 35677778876543 8999999999 9983
No 16
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=84.69 E-value=2.6 Score=27.44 Aligned_cols=42 Identities=12% Similarity=0.236 Sum_probs=34.8
Q ss_pred HhHHHHHHHHHHcCCccEE-----EEEecCCCCccccCCCEEEEEec
Q 035140 24 QGLQYLKASIKAMSIKVIE-----IQVVSPNKDSQILSHSLCLLRIA 65 (72)
Q Consensus 24 ~Ql~~i~~~l~~lgi~~~~-----v~IvS~DKD~QLv~~~v~v~~~~ 65 (72)
.|+..+++.+..||+..-+ |+|-+.|+++=+-+++|.+++..
T Consensus 9 r~~~~mkkmMk~MGi~~~eidV~~ViIk~~~k~ivf~~p~V~~m~~~ 55 (116)
T TIGR00264 9 KMLKQMQKMMKQMGMEMEDLDVEEVIIVFDDEEWIFENPKVQVMDIL 55 (116)
T ss_pred ccHHHHHHHHHHcCCCccccccEEEEEEeCCceEEEecCeeEEEecC
Confidence 4567789999999987764 99999999997778899998754
No 17
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=82.36 E-value=0.51 Score=29.27 Aligned_cols=14 Identities=29% Similarity=0.399 Sum_probs=9.8
Q ss_pred EEEecCCCCc-cccC
Q 035140 43 IQVVSPNKDS-QILS 56 (72)
Q Consensus 43 v~IvS~DKD~-QLv~ 56 (72)
++|+|||.|| .++.
T Consensus 99 ivLvSgD~Df~~~v~ 113 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVR 113 (146)
T ss_dssp EEEE---GGGHHHHH
T ss_pred EEEEECcHHHHHHHH
Confidence 8999999999 8874
No 18
>PLN02320 seryl-tRNA synthetase
Probab=81.87 E-value=4.5 Score=31.97 Aligned_cols=50 Identities=2% Similarity=0.007 Sum_probs=42.2
Q ss_pred hhHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEEEEecCCce
Q 035140 20 DTMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCLLRIAPRGF 69 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v~~~~k~~~ 69 (72)
+++..-+..+.+++..||+|.-.+.+.|+|=.+ .-..=.+.+|-|..+.+
T Consensus 359 ~e~e~ll~~~e~i~~~LgLpyrvv~l~tgDLg~~a~kkyDiEvW~P~~~~y 409 (502)
T PLN02320 359 SFHEELIQIEEDLFTSLGLHFKTLDMATADLGAPAYRKFDIEAWMPGLGRY 409 (502)
T ss_pred HHHHHHHHHHHHHHHHcCCCeEEEEecCCccchhhhheEEEEEEecCCCcE
Confidence 345666788899999999999999999999988 77777899999986654
No 19
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=79.88 E-value=0.85 Score=28.77 Aligned_cols=14 Identities=29% Similarity=0.408 Sum_probs=12.5
Q ss_pred EEEecCCCCc-cccC
Q 035140 43 IQVVSPNKDS-QILS 56 (72)
Q Consensus 43 v~IvS~DKD~-QLv~ 56 (72)
++|+|||.|| .++.
T Consensus 103 ivLvSgD~Df~~~i~ 117 (149)
T cd06167 103 IVLVSGDSDFVPLVE 117 (149)
T ss_pred EEEEECCccHHHHHH
Confidence 8899999999 8874
No 20
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.17 E-value=3.3 Score=35.39 Aligned_cols=28 Identities=11% Similarity=0.113 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHcCCccEE------------------EEEecCCCCc
Q 035140 25 GLQYLKASIKAMSIKVIE------------------IQVVSPNKDS 52 (72)
Q Consensus 25 Ql~~i~~~l~~lgi~~~~------------------v~IvS~DKD~ 52 (72)
.+..++++|+.||||++. -.|+|.|.|+
T Consensus 773 m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~ 818 (1034)
T TIGR00600 773 MILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDI 818 (1034)
T ss_pred HHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccce
Confidence 366789999999999999 6789999998
No 21
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=72.37 E-value=3.6 Score=30.31 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=27.4
Q ss_pred cCCCCCC----chhHHHhHHHHHHHHHHcCCccEE
Q 035140 12 KNNRPPT----PDTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 12 KanR~~~----Pe~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
||||... -..|.+.++.+.++=+.+|+|++.
T Consensus 59 KANRsSi~s~RGpGLeeglki~~~vK~efgv~ilT 93 (279)
T COG2877 59 KANRSSIHSYRGPGLEEGLKILQEVKEEFGVPILT 93 (279)
T ss_pred cccccccccccCCCHHHHHHHHHHHHHHcCCceee
Confidence 8999876 367888899999999999999998
No 22
>PLN02678 seryl-tRNA synthetase
Probab=71.47 E-value=13 Score=28.88 Aligned_cols=49 Identities=12% Similarity=0.049 Sum_probs=39.3
Q ss_pred hHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEEEEecCCce
Q 035140 21 TMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCLLRIAPRGF 69 (72)
Q Consensus 21 ~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v~~~~k~~~ 69 (72)
.+-.-+..+.+++..||+|.-.+.++|||=.+ .--.=.+.+|.|..+++
T Consensus 304 ~~e~~l~~~~~i~~~L~lpyrvv~~~sgdlg~~a~~~yDiE~W~P~~~~y 353 (448)
T PLN02678 304 MHEEMLKNSEDFYQSLGIPYQVVSIVSGALNDAAAKKYDLEAWFPASKTY 353 (448)
T ss_pred HHHHHHHHHHHHHHHcCCCeEEEeecccccCCchhhceeeEeeccccCCc
Confidence 34555678889999999997779999999888 65555788999987655
No 23
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=70.89 E-value=16 Score=28.41 Aligned_cols=47 Identities=4% Similarity=0.001 Sum_probs=38.4
Q ss_pred hHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEEEEecCC
Q 035140 21 TMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCLLRIAPR 67 (72)
Q Consensus 21 ~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v~~~~k~ 67 (72)
++-.-+....++++.|++|.-.+.++|||=-+ ..-.=.+.+|-|.-+
T Consensus 300 ~~E~m~~~ae~il~~LeLPyRvv~lctGDlgf~a~kkYDlEvWlP~q~ 347 (429)
T COG0172 300 ELEEMLGNAEEVLQELELPYRVVNLCTGDLGFSAAKKYDLEVWLPGQN 347 (429)
T ss_pred HHHHHHHHHHHHHHHhCCCceEeeeccCCcCCcccCceeEEEEecCCC
Confidence 35556777889999999999999999998888 665668999988744
No 24
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=70.55 E-value=13 Score=26.38 Aligned_cols=44 Identities=16% Similarity=0.054 Sum_probs=36.7
Q ss_pred hHHHhHHHHHHHHHHcC-CccEEEEEecCCCCc-cccCCCEEEEEe
Q 035140 21 TMVQGLQYLKASIKAMS-IKVIEIQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 21 ~L~~Ql~~i~~~l~~lg-i~~~~v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
++..-+....++++.+| +|...+...++|+-+ ..-+..+.+|.|
T Consensus 163 e~~~~~~~~~~i~~~l~~lp~~~~~~~~~d~~~g~~~~~d~e~~~p 208 (264)
T cd00772 163 EFLNMLSAYAEIARDLAAIDFIEGEADEGAKFAGASKSREFEALME 208 (264)
T ss_pred HHHHHHHHHHHHHHhcCCccEEEEEcCCCccccCCcCCEEEEEECC
Confidence 45555677789999999 998889999999888 878888888887
No 25
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=69.75 E-value=2.9 Score=28.16 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=17.9
Q ss_pred EEEecCCCCc-cccCCC--EEEEEec
Q 035140 43 IQVVSPNKDS-QILSHS--LCLLRIA 65 (72)
Q Consensus 43 v~IvS~DKD~-QLv~~~--v~v~~~~ 65 (72)
-+|+|||+|+ -|=+++ +.+..|.
T Consensus 106 ~~lvTgD~dLL~lr~~n~~~~Iltp~ 131 (142)
T COG1569 106 DYLVTGDQDLLVLRDENKRVEILTPQ 131 (142)
T ss_pred CEEEEcchhhheecccCCcEEEcCHH
Confidence 4899999999 876665 7777653
No 26
>PF12813 XPG_I_2: XPG domain containing
Probab=68.58 E-value=6.3 Score=28.00 Aligned_cols=26 Identities=12% Similarity=0.290 Sum_probs=21.9
Q ss_pred HHHHHHHHHc---CCccEE-----------------EEEecCCCCc
Q 035140 27 QYLKASIKAM---SIKVIE-----------------IQVVSPNKDS 52 (72)
Q Consensus 27 ~~i~~~l~~l---gi~~~~-----------------v~IvS~DKD~ 52 (72)
+.+.++|..+ |+++.. +.|+|+|.||
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~~VLt~DSDf 52 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPGEADRECAALARKWGCPVLTNDSDF 52 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCCeEEccCCCE
Confidence 5567778887 998887 8999999999
No 27
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=67.15 E-value=6.1 Score=30.05 Aligned_cols=68 Identities=9% Similarity=0.064 Sum_probs=43.5
Q ss_pred CcccccCccccCCCCC---------------Cch----hHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEE
Q 035140 2 NFRHTLYPSYKNNRPP---------------TPD----TMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCL 61 (72)
Q Consensus 2 t~R~~~~p~YKanR~~---------------~Pe----~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v 61 (72)
.||.|.-+.-|..|.- .|+ .+...+....++++.||+|...+.+.|+|.-. ---.-.+.+
T Consensus 261 ~FR~E~g~~G~~t~GL~Rv~qF~k~E~~~f~~~e~s~~~~~~~~~~~~~i~~~Lglp~r~v~~~t~dlg~~a~~~ydiE~ 340 (418)
T TIGR00414 261 CFRSEAGSYGKDTKGLIRVHQFNKVELVKFCKPEESAEELEEMTSDAEQILQELELPYRVVNLCSGDLGFSAAKKYDLEV 340 (418)
T ss_pred cccCCCCccCCCCCccccccceeeeeEEEEcCHHHHHHHHHHHHHHHHHHHHHcCCceEEEecCccccccCHhhhhhHHH
Confidence 5777775544555531 244 35566778889999999998878888888654 322334555
Q ss_pred EEecCCce
Q 035140 62 LRIAPRGF 69 (72)
Q Consensus 62 ~~~~k~~~ 69 (72)
|.|..+++
T Consensus 341 w~p~~~~~ 348 (418)
T TIGR00414 341 WMPGQNTY 348 (418)
T ss_pred hCCCcCce
Confidence 65655443
No 28
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=66.93 E-value=2.3 Score=26.00 Aligned_cols=10 Identities=10% Similarity=0.225 Sum_probs=8.9
Q ss_pred EEEecCCCCc
Q 035140 43 IQVVSPNKDS 52 (72)
Q Consensus 43 v~IvS~DKD~ 52 (72)
-.|||+|||+
T Consensus 102 d~iVT~Dkdl 111 (114)
T TIGR00305 102 NALITGDTDL 111 (114)
T ss_pred CEEEECCHHH
Confidence 4899999997
No 29
>PRK13909 putative recombination protein RecB; Provisional
Probab=66.78 E-value=14 Score=30.66 Aligned_cols=47 Identities=21% Similarity=0.265 Sum_probs=37.6
Q ss_pred CccccCCCCCCchhHHHhHHHHHHHH-HHcCCccEEEEEecCCCCc-ccc
Q 035140 8 YPSYKNNRPPTPDTMVQGLQYLKASI-KAMSIKVIEIQVVSPNKDS-QIL 55 (72)
Q Consensus 8 ~p~YKanR~~~Pe~L~~Ql~~i~~~l-~~lgi~~~~v~IvS~DKD~-QLv 55 (72)
-=+||.+|++ ++.-..|+..=++++ +.||-..++..++..|.+- .+|
T Consensus 860 IiDYKTg~~~-~~~y~~Ql~~Y~~~L~~~~~~~~v~~~Lvy~~~~~~~~v 908 (910)
T PRK13909 860 VIDYKSSKKY-QEEHKAQVSHYKEAIKEILPKKKVEAYIVYLLEDKIEIL 908 (910)
T ss_pred EEEECCCCCC-hHHHHHHHHHHHHHHHHHcCCCeeEEEEEEecCCceeEE
Confidence 3489999965 688899999999999 8899999997777766654 443
No 30
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=61.86 E-value=6.9 Score=23.89 Aligned_cols=21 Identities=5% Similarity=0.029 Sum_probs=16.6
Q ss_pred EEEecCCCCc-cccCCCEEEEEec
Q 035140 43 IQVVSPNKDS-QILSHSLCLLRIA 65 (72)
Q Consensus 43 v~IvS~DKD~-QLv~~~v~v~~~~ 65 (72)
..++|.|+|| +. +.+.+++|-
T Consensus 119 ~~lvT~D~~f~~~--~~~~i~~P~ 140 (142)
T TIGR00028 119 AELVTFDRGFARF--AGIRWRDPL 140 (142)
T ss_pred CEEEecCCCcccc--CCCeeeCCC
Confidence 6788999999 64 467888775
No 31
>PHA02754 hypothetical protein; Provisional
Probab=61.50 E-value=16 Score=21.49 Aligned_cols=32 Identities=16% Similarity=0.172 Sum_probs=24.1
Q ss_pred chhHHHhHHHHHHHHHHcCCccEE--EEEecCCC
Q 035140 19 PDTMVQGLQYLKASIKAMSIKVIE--IQVVSPNK 50 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~lgi~~~~--v~IvS~DK 50 (72)
-.++.+.+..+++.|..-|+-+-. ++-+||||
T Consensus 13 eK~Fke~MRelkD~LSe~GiYi~RIkai~~SGdk 46 (67)
T PHA02754 13 EKDFKEAMRELKDILSEAGIYIDRIKAITTSGDK 46 (67)
T ss_pred HhHHHHHHHHHHHHHhhCceEEEEEEEEEecCCE
Confidence 456788888999999999986555 55566665
No 32
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=61.33 E-value=5.7 Score=28.69 Aligned_cols=31 Identities=23% Similarity=0.537 Sum_probs=24.2
Q ss_pred cccCCCCCCch----hHHHhHHHHHHHHHHcCCccEE
Q 035140 10 SYKNNRPPTPD----TMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 10 ~YKanR~~~Pe----~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
.|| ||...-. .+ ++++.+++..+.+|++++.
T Consensus 50 ~~k-pRts~~sf~G~G~-~gl~~L~~~~~~~Gl~~~T 84 (250)
T PRK13397 50 AYK-PRTSAASFQGLGL-QGIRYLHEVCQEFGLLSVS 84 (250)
T ss_pred ccC-CCCCCcccCCCCH-HHHHHHHHHHHHcCCCEEE
Confidence 466 8876421 23 5899999999999999998
No 33
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=59.27 E-value=8.6 Score=29.32 Aligned_cols=46 Identities=2% Similarity=-0.051 Sum_probs=31.3
Q ss_pred hHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEEEEecC
Q 035140 21 TMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCLLRIAP 66 (72)
Q Consensus 21 ~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v~~~~k 66 (72)
++...+..+.++++.||+|...+.+.|+|.-. .--.-++.+|.|..
T Consensus 297 ~~~~~l~~~~~i~~~Lglpyr~v~~~s~dlg~~a~~~~DiE~w~p~~ 343 (425)
T PRK05431 297 ELEELTANAEEILQKLELPYRVVLLCTGDLGFSAAKTYDLEVWLPSQ 343 (425)
T ss_pred HHHHHHHHHHHHHHHcCCcEEEEEcCCcccCCchHheecHHHhCccc
Confidence 35666788889999999997777888888644 33333444455543
No 34
>PF00587 tRNA-synt_2b: tRNA synthetase class II core domain (G, H, P, S and T) This Prosite entry contains all class II enzymes. seryl tRNA synthetase structure; InterPro: IPR002314 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain includes the glycine, histidine, proline, threonine and serine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3UH0_A 3UGT_C 3UGQ_A 1B76_B 1GGM_B 1ATI_A 1ADY_C 1ADJ_C 2I4O_A 2I4M_B ....
Probab=58.45 E-value=40 Score=21.80 Aligned_cols=45 Identities=7% Similarity=0.003 Sum_probs=30.7
Q ss_pred hhHHHhHHHHHHHHHHcCC-ccEEEEEecCCCCc-cccCCCEEEEEe
Q 035140 20 DTMVQGLQYLKASIKAMSI-KVIEIQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi-~~~~v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
+.+...+..+.++++.||+ +.-.+...++|... .--.-.+..|.|
T Consensus 125 ~~~~~~~~~~~~i~~~lgl~~~~~~~~~~~~~~~~~~~~~d~e~~~~ 171 (173)
T PF00587_consen 125 EEFEELLELYKEILEKLGLEPYRIVLSSSGELGAYAKYEFDIEAWFP 171 (173)
T ss_dssp HHHHHHHHHHHHHHHHTTSGCEEEEEEETCTSCTTSSEEEEEEEEET
T ss_pred HHHHHHHHHHHHHHHHcCCceEEEEEcCCCccCCCHHHcccHHHhCc
Confidence 4567778889999999999 65556666667655 443445555554
No 35
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=56.26 E-value=20 Score=22.45 Aligned_cols=38 Identities=21% Similarity=0.374 Sum_probs=30.4
Q ss_pred CccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 8 YPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 8 ~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
--.||..|+.+|..-......+-+.+..+|+..+.+.|
T Consensus 31 ~~gfK~~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i 68 (110)
T PF00411_consen 31 SLGFKGARKSTPYAAQQAAEKIAKKAKELGIKTVRVKI 68 (110)
T ss_dssp TSSTTTTCGSSHHHHHHHHHHHHHHHHCTTEEEEEEEE
T ss_pred ccccccccccCHHHHHHHHHHHHHHHHHcCCeEEEEEE
Confidence 34799999999988777777777888889998877554
No 36
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=53.65 E-value=17 Score=30.52 Aligned_cols=32 Identities=16% Similarity=0.212 Sum_probs=22.7
Q ss_pred cccCCCCCCchhHHHhHHHHHHHHHHcCCccEE
Q 035140 10 SYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 10 ~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
.|+.-|-... -.-.-+..++++|+.+|||++.
T Consensus 453 k~~~~r~~~e-vt~~m~~e~QElL~~fGIPyI~ 484 (815)
T KOG2520|consen 453 KYIQSRGADE-VTSDMFKELQELLRLFGIPYII 484 (815)
T ss_pred HHHHhccCch-hHHHHHHHHHHHHHHcCCceec
Confidence 3455554443 3344578899999999999998
No 37
>PRK01254 hypothetical protein; Provisional
Probab=53.64 E-value=7 Score=32.27 Aligned_cols=39 Identities=15% Similarity=0.239 Sum_probs=30.8
Q ss_pred CccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEEecCCC
Q 035140 8 YPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQVVSPNK 50 (72)
Q Consensus 8 ~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DK 50 (72)
|+.|.|.+-.+. .-||.-++-++++|+..+.+++||||-
T Consensus 11 ~~~~~~~~~~~~----~fLP~t~~em~~~Gwd~~DiilVtGDA 49 (707)
T PRK01254 11 YPKYWAECFGPA----PFLPMSREEMDQLGWDSCDIIIVTGDA 49 (707)
T ss_pred cCccchhhcCCC----CcCCCCHHHHHHcCCCccCEEEEeCcc
Confidence 566777766542 257889999999999999999999984
No 38
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=52.49 E-value=10 Score=22.83 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=24.6
Q ss_pred HHHHHHHHHcCCccEEEEEecCC---CCc-cccC--CCEEEE
Q 035140 27 QYLKASIKAMSIKVIEIQVVSPN---KDS-QILS--HSLCLL 62 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~D---KD~-QLv~--~~v~v~ 62 (72)
.-+++++++||+|.-+|-++.-| .|+ ..+. +.|.||
T Consensus 33 ~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 33 ATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAVY 74 (81)
T ss_pred CcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEEE
Confidence 45889999999999995443323 455 5554 467777
No 39
>KOG1282 consensus Serine carboxypeptidases (lysosomal cathepsin A) [Posttranslational modification, protein turnover, chaperones; Amino acid transport and metabolism]
Probab=51.58 E-value=19 Score=28.16 Aligned_cols=28 Identities=21% Similarity=0.215 Sum_probs=21.1
Q ss_pred HHHHHHHHHHcCCccEEEEEecCCCCc--cccC
Q 035140 26 LQYLKASIKAMSIKVIEIQVVSPNKDS--QILS 56 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~v~IvS~DKD~--QLv~ 56 (72)
+|.+++++...| +.+.|+|||.|+ ..+.
T Consensus 352 ~p~~~~~~~~~~---~rvliysGD~D~~~p~~g 381 (454)
T KOG1282|consen 352 LPIHKKLIASGG---YRVLIYSGDHDLVVPFLG 381 (454)
T ss_pred HHHHHHHhhcCc---eEEEEEeCCcceeCcchh
Confidence 577777777666 567899999999 4443
No 40
>CHL00041 rps11 ribosomal protein S11
Probab=49.68 E-value=52 Score=20.88 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=27.4
Q ss_pred ccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 9 PSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 9 p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
..||..|+.+|-.-...-+.+-+.+..+|+..+.+.+
T Consensus 45 ~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~i 81 (116)
T CHL00041 45 CGFKGARKGTPFAAQTAAENAIRTVIDQGMKRAEVMI 81 (116)
T ss_pred eeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE
Confidence 3689999999866554455666677778999988554
No 41
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=48.73 E-value=56 Score=20.86 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=27.5
Q ss_pred ccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE
Q 035140 9 PSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 9 p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
=+||+.++..... ..|+..---+|+.+|+++-.
T Consensus 70 ~E~K~~~~~~~~~-~~Ql~~Y~~lL~~~g~~v~~ 102 (162)
T PF01930_consen 70 VEIKSGRKPREEH-RMQLAAYALLLEEFGIPVKR 102 (162)
T ss_pred EEEecCCCCcchh-HHHHHHHHHHHHhcCcccee
Confidence 3789999887777 88888777788899999986
No 42
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=48.57 E-value=24 Score=22.87 Aligned_cols=31 Identities=10% Similarity=0.135 Sum_probs=25.2
Q ss_pred HHHHHHHHHHcCCccEE-----------------EEEecCCCCc-cccC
Q 035140 26 LQYLKASIKAMSIKVIE-----------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~-----------------v~IvS~DKD~-QLv~ 56 (72)
+..+.+.|+.+|+.++. -+|+|.|++| ....
T Consensus 9 L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~RillTrd~~l~~~~~ 57 (147)
T PF01927_consen 9 LGRLARWLRLLGYDTLYSRDIDDDEILELAREEGRILLTRDRDLLKRRR 57 (147)
T ss_pred HHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCeEEEECCHHHHHHhh
Confidence 45677899999998888 6899999999 5543
No 43
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=48.31 E-value=57 Score=20.40 Aligned_cols=37 Identities=16% Similarity=0.288 Sum_probs=28.0
Q ss_pred ccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 9 PSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 9 p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
..||..|+.+|-.-...-+.+-+.+..+|+..+.+.+
T Consensus 32 ~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~ 68 (108)
T TIGR03632 32 VGFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYV 68 (108)
T ss_pred eeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE
Confidence 4689999999877555555666777789999888554
No 44
>PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=48.21 E-value=28 Score=25.90 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=25.7
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCccEE
Q 035140 12 KNNRPPTP----DTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 12 KanR~~~P----e~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
||||...- ..+.+.|.+++++=+.+|+|+++
T Consensus 58 KApRTSp~sFrG~G~eeGL~iL~~vk~~~glpvvT 92 (290)
T PLN03033 58 KANRTSSKSFRGPGMAEGLKILEKVKVAYDLPIVT 92 (290)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCceEE
Confidence 47998653 34678899999999999999998
No 45
>PRK05198 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=47.23 E-value=30 Score=25.42 Aligned_cols=31 Identities=23% Similarity=0.404 Sum_probs=25.0
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCccEE
Q 035140 12 KNNRPPTP----DTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 12 KanR~~~P----e~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
||||...- ..+.+-|.+++++=+.+|+|+++
T Consensus 52 KapRTSp~sFqG~G~eeGL~~L~~vk~~~GlpvvT 86 (264)
T PRK05198 52 KANRSSIHSFRGPGLEEGLKILQEVKETFGVPVLT 86 (264)
T ss_pred CCCCCCCCCCCCCChHHHHHHHHHHHHHHCCceEE
Confidence 36887653 24567899999999999999998
No 46
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide.
Probab=45.20 E-value=35 Score=25.01 Aligned_cols=31 Identities=19% Similarity=0.390 Sum_probs=25.0
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCccEE
Q 035140 12 KNNRPPTP----DTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 12 KanR~~~P----e~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
||||...- ..+.+.|.+++++=+.+|+|+++
T Consensus 44 KapRTsp~sFqG~G~eeGL~iL~~vk~~~glpvvT 78 (258)
T TIGR01362 44 KANRSSIHSFRGPGLEEGLKILQKVKEEFGVPILT 78 (258)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHhCCceEE
Confidence 46997653 24567899999999999999998
No 47
>PF08497 Radical_SAM_N: Radical SAM N-terminal; InterPro: IPR013704 This domain tends to occur to the N terminus of PF04055 from PFAM radical SAM domain in hypothetical bacterial proteins. Proteins in this entry are radical SAM proteins, they catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=44.72 E-value=10 Score=28.43 Aligned_cols=24 Identities=13% Similarity=0.234 Sum_probs=19.4
Q ss_pred HHHHHHHHHcCCccEEEEEecCCC
Q 035140 27 QYLKASIKAMSIKVIEIQVVSPNK 50 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~DK 50 (72)
|.-++-+++.|+..+.+++||||-
T Consensus 3 P~t~~em~~rGWd~lDvilVtGDA 26 (302)
T PF08497_consen 3 PTTREEMKARGWDELDVILVTGDA 26 (302)
T ss_pred CCCHHHHHHcCCccccEEEEeCcc
Confidence 445677888999999999999984
No 48
>PRK10858 nitrogen regulatory protein P-II 1; Provisional
Probab=44.37 E-value=27 Score=22.07 Aligned_cols=18 Identities=11% Similarity=0.265 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHcCCccEE
Q 035140 25 GLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 25 Ql~~i~~~l~~lgi~~~~ 42 (72)
.++.+++.|..+|++.+.
T Consensus 12 kl~~v~~aL~~~G~~g~T 29 (112)
T PRK10858 12 KLDDVREALAEVGITGMT 29 (112)
T ss_pred HHHHHHHHHHHCCCCeEE
Confidence 367789999999999888
No 49
>PRK05309 30S ribosomal protein S11; Validated
Probab=43.90 E-value=70 Score=20.71 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=28.0
Q ss_pred ccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 9 PSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 9 p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
..||..|+.+|..-...-+.+-+.+..+|+..+.+.+
T Consensus 49 ~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~i 85 (128)
T PRK05309 49 LGFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFV 85 (128)
T ss_pred cEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE
Confidence 3689999999876655556666777789999888554
No 50
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=43.90 E-value=66 Score=22.60 Aligned_cols=44 Identities=14% Similarity=0.056 Sum_probs=27.4
Q ss_pred hHHHhHHHHHHHHHHc-CCccEEEEEecCCCCc-cccCCCEEEEEe
Q 035140 21 TMVQGLQYLKASIKAM-SIKVIEIQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 21 ~L~~Ql~~i~~~l~~l-gi~~~~v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
++...+....++++.+ |+|...+...++|+-+ -.-.-.+.++-|
T Consensus 163 ~~~~~~~~~~~i~~~llgl~~~~~~~~~~d~~~~a~~~~~ie~~~p 208 (261)
T cd00778 163 EVLQILDLYKEFYEDLLAIPVVKGRKTEWEKFAGADYTYTIEAMMP 208 (261)
T ss_pred HHHHHHHHHHHHHHHhCCCeEEEecCCccccCCCCccceEEEEEee
Confidence 3555567788888888 9997665556666644 332334455544
No 51
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=43.89 E-value=36 Score=25.21 Aligned_cols=31 Identities=23% Similarity=0.328 Sum_probs=25.1
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCccEE
Q 035140 12 KNNRPPTP----DTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 12 KanR~~~P----e~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
||||...- ..|.+.|.+++++=+.+|+|+++
T Consensus 58 KapRTSp~sFqG~G~eeGL~iL~~vk~~~GlpvvT 92 (281)
T PRK12457 58 KANRSSIHSYRGVGLDEGLRIFEEVKARFGVPVIT 92 (281)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCceEE
Confidence 46887653 24667899999999999999998
No 52
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=43.56 E-value=14 Score=22.35 Aligned_cols=28 Identities=7% Similarity=0.084 Sum_probs=20.6
Q ss_pred EEEecCCCCc--ccc-CCCEEEEEecCCcee
Q 035140 43 IQVVSPNKDS--QIL-SHSLCLLRIAPRGFE 70 (72)
Q Consensus 43 v~IvS~DKD~--QLv-~~~v~v~~~~k~~~~ 70 (72)
.+|+|.|+++ +|- .+.|-+....++...
T Consensus 67 ~~VaT~D~~Lr~~lr~~~GvPvi~l~~~~~~ 97 (101)
T PF04900_consen 67 YIVATQDKELRRRLRKIPGVPVIYLRRNVLI 97 (101)
T ss_pred EEEEecCHHHHHHHhcCCCCCEEEEECCEEE
Confidence 6789999999 666 577877776655443
No 53
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=42.53 E-value=42 Score=24.13 Aligned_cols=32 Identities=22% Similarity=0.299 Sum_probs=23.9
Q ss_pred cccCCCCCC--chh-HHHhHHHHHHHHHHcCCccEE
Q 035140 10 SYKNNRPPT--PDT-MVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 10 ~YKanR~~~--Pe~-L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
.|| +|... .++ ...++..+++.++.+|++++.
T Consensus 62 ~~k-pRTs~~s~~G~g~~gl~~l~~~~~~~Gl~~~t 96 (266)
T PRK13398 62 AFK-PRTSPYSFQGLGEEGLKILKEVGDKYNLPVVT 96 (266)
T ss_pred eec-CCCCCCccCCcHHHHHHHHHHHHHHcCCCEEE
Confidence 355 77652 121 367889999999999999998
No 54
>COG4572 ChaB Putative cation transport regulator [General function prediction only]
Probab=42.17 E-value=29 Score=21.02 Aligned_cols=19 Identities=21% Similarity=0.357 Sum_probs=15.3
Q ss_pred ccCCCCCCchhHHHhHHHHH
Q 035140 11 YKNNRPPTPDTMVQGLQYLK 30 (72)
Q Consensus 11 YKanR~~~Pe~L~~Ql~~i~ 30 (72)
||++ ...|++.+.|||.--
T Consensus 3 yk~~-sdlp~~vr~~lp~ha 21 (76)
T COG4572 3 YKTK-SDLPEEVRHQLPSHA 21 (76)
T ss_pred cccc-ccccHHHHHHhHHHH
Confidence 7777 679999999998543
No 55
>COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis]
Probab=42.16 E-value=93 Score=21.03 Aligned_cols=55 Identities=22% Similarity=0.431 Sum_probs=34.2
Q ss_pred cCccccCCCCC------CchhHHHhHHHHHHHHHHcCCccEEEEEecCCCCccccCC-CEEEE
Q 035140 7 LYPSYKNNRPP------TPDTMVQGLQYLKASIKAMSIKVIEIQVVSPNKDSQILSH-SLCLL 62 (72)
Q Consensus 7 ~~p~YKanR~~------~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~QLv~~-~v~v~ 62 (72)
+|.+-|.+|.| .|+.-.+-.+.+-+.|+..|+++-. =.+-.|-+-+|+|+ .|++|
T Consensus 81 L~adt~kG~RPsFs~aa~p~~A~~lYe~f~~~lr~~~~~V~t-G~FgA~M~V~LvNdGPVTi~ 142 (145)
T COG1490 81 LYADTKKGRRPSFSKAAKPDQAEELYEYFVELLRELGIKVET-GRFGADMQVSLVNDGPVTIL 142 (145)
T ss_pred EeecccCCCCCCccccCChHHHHHHHHHHHHHHHhcCCccee-eeeeceeEEEEecCCCeEEE
Confidence 45555544433 3555556677888899999966544 34444555578875 67776
No 56
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=41.64 E-value=73 Score=19.83 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=20.0
Q ss_pred HHHHHHHHHcCCccEEEEEecCC
Q 035140 27 QYLKASIKAMSIKVIEIQVVSPN 49 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~D 49 (72)
..++++++.|||..+.-+|++++
T Consensus 85 ~~l~~~~~~l~i~llDHiIi~~~ 107 (113)
T cd08071 85 KRLKEAGELLGIRLLDHIIVGDG 107 (113)
T ss_pred HHHHHHHHHCCCEEeeEEEEcCC
Confidence 67889999999999998888754
No 57
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=40.57 E-value=11 Score=25.36 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=16.5
Q ss_pred EEEecCCCCc-cccC----C--CEEEEEec
Q 035140 43 IQVVSPNKDS-QILS----H--SLCLLRIA 65 (72)
Q Consensus 43 v~IvS~DKD~-QLv~----~--~v~v~~~~ 65 (72)
++++|+|.|| -+|. . .|.+....
T Consensus 114 ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~ 143 (181)
T COG1432 114 IVLFSGDGDFIPLVEAARDKGKRVEVAGIE 143 (181)
T ss_pred EEEEcCCccHHHHHHHHHHcCCEEEEEecC
Confidence 8899999999 7763 2 45555443
No 58
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=39.79 E-value=22 Score=23.63 Aligned_cols=30 Identities=10% Similarity=0.368 Sum_probs=23.6
Q ss_pred HHHHHHHHHcCCccEEEEEecCCCCc-cccC
Q 035140 27 QYLKASIKAMSIKVIEIQVVSPNKDS-QILS 56 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~ 56 (72)
.+|.+++..++-+.-.|++||+|+.. +.+.
T Consensus 81 ~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~ 111 (166)
T PF05991_consen 81 DYIERLVRELKNRPRQVTVVTSDREIQRAAR 111 (166)
T ss_pred HHHHHHHHHhccCCCeEEEEeCCHHHHHHHh
Confidence 34778888888755779999999999 6653
No 59
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=39.48 E-value=76 Score=18.22 Aligned_cols=16 Identities=19% Similarity=0.378 Sum_probs=12.3
Q ss_pred HHHHHHHHHcCCccEE
Q 035140 27 QYLKASIKAMSIKVIE 42 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~ 42 (72)
.++.++++.||++.--
T Consensus 2 ~~L~~il~~mg~~~~v 17 (77)
T cd02414 2 EFLEEVLELMGIEADV 17 (77)
T ss_pred hHHHHHHHHcCCCcEE
Confidence 3678999999986543
No 60
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=39.14 E-value=32 Score=27.12 Aligned_cols=26 Identities=23% Similarity=0.359 Sum_probs=21.7
Q ss_pred HHHHHHHHHcCCccEE------------------EEEecCCCCc
Q 035140 27 QYLKASIKAMSIKVIE------------------IQVVSPNKDS 52 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~------------------v~IvS~DKD~ 52 (72)
..++.+|..||||++. --++|.|-|.
T Consensus 135 dEak~LL~lmGIp~i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~ 178 (449)
T KOG2519|consen 135 DEAKRLLSLMGIPVLDAPGEAEAQCAALNKAGKVYAVATEDSDA 178 (449)
T ss_pred HHHHHHHHHcCCeeecCCchHHHHHHHHhhcCceeeeeccccch
Confidence 3688999999999998 4578888886
No 61
>PRK01777 hypothetical protein; Validated
Probab=38.05 E-value=56 Score=20.11 Aligned_cols=38 Identities=13% Similarity=0.244 Sum_probs=28.9
Q ss_pred HHHHHHHHcCCccE--E-------EEEecCCCCc-cccC--CCEEEEEec
Q 035140 28 YLKASIKAMSIKVI--E-------IQVVSPNKDS-QILS--HSLCLLRIA 65 (72)
Q Consensus 28 ~i~~~l~~lgi~~~--~-------v~IvS~DKD~-QLv~--~~v~v~~~~ 65 (72)
.+.+++.++||+.- + +-|.+-..++ +.+. +.|.+|.|-
T Consensus 28 Tv~dal~~sgi~~~~pei~~~~~~vgI~Gk~v~~d~~L~dGDRVeIyrPL 77 (95)
T PRK01777 28 TVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPL 77 (95)
T ss_pred cHHHHHHHcCCCccCcccccccceEEEeCeECCCCCcCCCCCEEEEecCC
Confidence 36788899998665 2 6678888888 7775 579999874
No 62
>cd00770 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer.
Probab=37.73 E-value=83 Score=22.60 Aligned_cols=31 Identities=0% Similarity=0.129 Sum_probs=23.5
Q ss_pred hhHHHhHHHHHHHHHHcCCccEEEEEecCCC
Q 035140 20 DTMVQGLQYLKASIKAMSIKVIEIQVVSPNK 50 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DK 50 (72)
+++...+..+.++++.||++...+..-|+|.
T Consensus 177 ~~~~~~l~~~~~i~~~lgl~~~~~~~~~~dl 207 (297)
T cd00770 177 EELEELISNAEEILQELGLPYRVVNICTGDL 207 (297)
T ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEccCccc
Confidence 4466778888999999999977666666664
No 63
>PF08984 DUF1858: Domain of unknown function (DUF1858); InterPro: IPR015077 This protein has no known function. It is found in various hypothetical bacterial proteins. ; PDB: 2K53_A 2K5E_A 2FI0_A.
Probab=37.24 E-value=17 Score=20.12 Aligned_cols=23 Identities=4% Similarity=0.083 Sum_probs=18.6
Q ss_pred hhHHHhHHHHHHHHHHcCCccEE
Q 035140 20 DTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
.++..+.|.+.++|..+|+.++.
T Consensus 8 ~el~~~yP~~~~il~~~gf~~l~ 30 (59)
T PF08984_consen 8 YELLEQYPELIEILVSYGFHCLG 30 (59)
T ss_dssp HHHHHH-GGGHHHHHHTTGGGGG
T ss_pred HHHHHHCHHHHHHHHHcCCcccC
Confidence 47889999999999999987653
No 64
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=36.69 E-value=1e+02 Score=20.39 Aligned_cols=37 Identities=24% Similarity=0.316 Sum_probs=24.4
Q ss_pred ccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 9 PSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 9 p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
-.||+.|+.+|=.--..-+.+.+....+|+..++|.+
T Consensus 50 ~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v~v 86 (129)
T COG0100 50 MGFKGSRKSTPYAAQLAAEDAAKKAKEHGIKSVEVKV 86 (129)
T ss_pred ceEcCCCCCCHHHHHHHHHHHHHHHHHhCccEEEEEE
Confidence 4689999888755433334444555559999998544
No 65
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.50 E-value=40 Score=21.92 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=15.8
Q ss_pred EEEecCCCCc-ccc----CC-CEEEEEe
Q 035140 43 IQVVSPNKDS-QIL----SH-SLCLLRI 64 (72)
Q Consensus 43 v~IvS~DKD~-QLv----~~-~v~v~~~ 64 (72)
-+|+|-|+|| -|. ++ ++-+++.
T Consensus 49 ~iivTkDsDF~~la~~~G~Ppki~wLr~ 76 (113)
T COG4634 49 RIIVTKDSDFADLALTLGSPPKIVWLRC 76 (113)
T ss_pred cEEEEcCccHHHHHHHcCCCCeEEEEEe
Confidence 7899999999 764 23 5655554
No 66
>PF03841 SelA: L-seryl-tRNA selenium transferase; InterPro: IPR018319 In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This family describes SelA. A close homologue of SelA is found in Helicobacter pylori, but all other required elements are missing and the protein is shorter at the N terminus than SelA from other species. The trusted cut-off is set above the score generated for Helicobacter pylori putative SelA.; PDB: 2AEV_A 2AEU_A.
Probab=36.24 E-value=46 Score=25.48 Aligned_cols=10 Identities=20% Similarity=0.046 Sum_probs=9.4
Q ss_pred EEEecCCCCc
Q 035140 43 IQVVSPNKDS 52 (72)
Q Consensus 43 v~IvS~DKD~ 52 (72)
.+++||||.+
T Consensus 206 lV~fSGdKlL 215 (367)
T PF03841_consen 206 LVTFSGDKLL 215 (367)
T ss_dssp EEEEETTSSS
T ss_pred EEEEECCCcC
Confidence 8999999988
No 67
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=36.08 E-value=94 Score=20.09 Aligned_cols=36 Identities=19% Similarity=0.275 Sum_probs=27.1
Q ss_pred HHHHHHHHcCCc-----cEEEEEecCCCCccccCCCEEEEE
Q 035140 28 YLKASIKAMSIK-----VIEIQVVSPNKDSQILSHSLCLLR 63 (72)
Q Consensus 28 ~i~~~l~~lgi~-----~~~v~IvS~DKD~QLv~~~v~v~~ 63 (72)
.+++++..||+. +-+|+|-++|+.+-+-++.|.+..
T Consensus 9 k~rkmmkkmGik~e~i~v~~V~Ir~~~~~~Vi~~P~V~~m~ 49 (115)
T PRK06369 9 KMKQMMKQMGIDVEELDVEEVIIRLKDKEIVFENPQVTVMD 49 (115)
T ss_pred HHHHHHHHcCCcchhcCeEEEEEEeCCEEEEEcCCeEEEEe
Confidence 457789999998 233899999966677778888654
No 68
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=35.64 E-value=49 Score=18.80 Aligned_cols=36 Identities=25% Similarity=0.427 Sum_probs=25.7
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCccEEEEEecCC
Q 035140 14 NRPPTPDTMVQGLQYLKASIKAMSIKVIEIQVVSPN 49 (72)
Q Consensus 14 nR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~D 49 (72)
.++.+-+-|..+++.+++.|...|+.+..+.+-.++
T Consensus 45 ~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~~~ 80 (85)
T PF02120_consen 45 ENPETKELLRQNLPELKERLQAQGLEVVNLSVSQGS 80 (85)
T ss_dssp -SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEESS-
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEECC
Confidence 344455678999999999999999988775554443
No 69
>KOG0180 consensus 20S proteasome, regulatory subunit beta type PSMB3/PUP3 [Posttranslational modification, protein turnover, chaperones]
Probab=35.29 E-value=53 Score=23.23 Aligned_cols=30 Identities=17% Similarity=0.461 Sum_probs=20.3
Q ss_pred chhHHHhHHHHHHHHHHcCCccEE-----EEEecCCC
Q 035140 19 PDTMVQGLQYLKASIKAMSIKVIE-----IQVVSPNK 50 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~lgi~~~~-----v~IvS~DK 50 (72)
||+|.+-+ .+.+|.+.--..++ |+|++.||
T Consensus 159 pd~LFeti--sQa~Lna~DRDalSGwGa~vyiI~kdk 193 (204)
T KOG0180|consen 159 PDELFETI--SQALLNAVDRDALSGWGAVVYIITKDK 193 (204)
T ss_pred HHHHHHHH--HHHHHhHhhhhhhccCCeEEEEEccch
Confidence 78886654 44566666555555 78888887
No 70
>KOG2501 consensus Thioredoxin, nucleoredoxin and related proteins [General function prediction only]
Probab=34.56 E-value=47 Score=22.58 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=17.8
Q ss_pred HHHHHHHcCCccEEEEEecCCCCc-ccc
Q 035140 29 LKASIKAMSIKVIEIQVVSPNKDS-QIL 55 (72)
Q Consensus 29 i~~~l~~lgi~~~~v~IvS~DKD~-QLv 55 (72)
+.+.+..-|- .++|+.||+|+|- ++-
T Consensus 58 fYe~l~~~~~-~fEVvfVS~D~~~~~~~ 84 (157)
T KOG2501|consen 58 FYEELKDNAA-PFEVVFVSSDRDEESLD 84 (157)
T ss_pred HHHHHHhcCC-ceEEEEEecCCCHHHHH
Confidence 3333333333 7889999999999 764
No 71
>PF10130 PIN_2: PIN domain; InterPro: IPR019298 This entry represents a set of bacterial and archaeal proteins that are predicted to be RNases (from similarities to 5'-exonucleases).
Probab=34.35 E-value=9.9 Score=24.73 Aligned_cols=10 Identities=20% Similarity=0.285 Sum_probs=9.2
Q ss_pred EEEecCCCCc
Q 035140 43 IQVVSPNKDS 52 (72)
Q Consensus 43 v~IvS~DKD~ 52 (72)
+-|.|+||||
T Consensus 106 ~~IWT~Dkdl 115 (133)
T PF10130_consen 106 APIWTEDKDL 115 (133)
T ss_pred CCeecCcHHH
Confidence 7799999998
No 72
>KOG4366 consensus Predicted thioesterase [General function prediction only]
Probab=34.07 E-value=20 Score=25.59 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=19.7
Q ss_pred ccCccccCCCCCCchhHHHhHHH
Q 035140 6 TLYPSYKNNRPPTPDTMVQGLQY 28 (72)
Q Consensus 6 ~~~p~YKanR~~~Pe~L~~Ql~~ 28 (72)
+++|.|-.||++.|+++...+..
T Consensus 170 e~c~~~~e~~ae~ped~~~~ls~ 192 (213)
T KOG4366|consen 170 ELCPRTNEKRAEIPEDLLKWLSE 192 (213)
T ss_pred HHhhhhccCcccCChHHHhhccc
Confidence 67899999999999999776654
No 73
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases. In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis. It catalyzes the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of Pfam model pfam02441.
Probab=34.07 E-value=53 Score=22.19 Aligned_cols=25 Identities=16% Similarity=0.387 Sum_probs=19.9
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCcc
Q 035140 14 NRPPTPDTMVQGLQYLKASIKAMSIKV 40 (72)
Q Consensus 14 nR~~~Pe~L~~Ql~~i~~~l~~lgi~~ 40 (72)
+|+..++++...+ +.++++.||++.
T Consensus 151 ~~p~~~~~~~~~i--~~~~l~~lg~~~ 175 (181)
T TIGR00421 151 TRPKSVEDMIDFI--VGRVLDQLGIEN 175 (181)
T ss_pred CCCCCHHHHHHHH--HHHHHHHcCCCc
Confidence 6677788888876 779999999863
No 74
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=33.78 E-value=22 Score=20.76 Aligned_cols=10 Identities=20% Similarity=0.498 Sum_probs=8.8
Q ss_pred EEEecCCCCc
Q 035140 43 IQVVSPNKDS 52 (72)
Q Consensus 43 v~IvS~DKD~ 52 (72)
++|+|.|+++
T Consensus 100 ~~lvT~D~~l 109 (111)
T smart00670 100 VVLVTNDRDL 109 (111)
T ss_pred CEEEeCCccc
Confidence 6799999987
No 75
>PF08443 RimK: RimK-like ATP-grasp domain; InterPro: IPR013651 This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK []. It has an unusual nucleotide-binding fold referred to as palmate, or ATP-grasp fold. This domain is found in a number of enzymes of known structure as well as in urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis.; PDB: 1UC8_B 1UC9_A.
Probab=33.45 E-value=50 Score=21.80 Aligned_cols=32 Identities=13% Similarity=0.344 Sum_probs=21.9
Q ss_pred CchhHHHhHHHHHHHHHHcCCccEEEEEecCCCCc
Q 035140 18 TPDTMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS 52 (72)
Q Consensus 18 ~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~ 52 (72)
.|+++ ...+.++.+++|++...+.|+..|.++
T Consensus 129 l~~e~---~~~a~~~~~~lgl~~~giDi~~~~~~~ 160 (190)
T PF08443_consen 129 LPEEI---KELALKAARALGLDFAGIDILDTNDGP 160 (190)
T ss_dssp --HHH---HHHHHHHHHHTT-SEEEEEEEEETTEE
T ss_pred CCHHH---HHHHHHHHHHhCCCEEEEEEEecCCCe
Confidence 45554 345778899999999998888776655
No 76
>PF00586 AIRS: AIR synthase related protein, N-terminal domain; InterPro: IPR000728 This family includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; GO: 0003824 catalytic activity; PDB: 3VIU_A 2Z1T_A 2Z1U_A 3C9U_B 3C9S_A 3C9R_A 1VQV_A 3C9T_B 3M84_A 3QTY_A ....
Probab=33.22 E-value=61 Score=18.93 Aligned_cols=24 Identities=8% Similarity=0.362 Sum_probs=19.3
Q ss_pred CchhHHHhHHHHHHHHHHcCCccE
Q 035140 18 TPDTMVQGLQYLKASIKAMSIKVI 41 (72)
Q Consensus 18 ~Pe~L~~Ql~~i~~~l~~lgi~~~ 41 (72)
.++.|.+-+.-+.+.++.+|++++
T Consensus 69 ~~~~l~~~~~Gi~~~~~~~g~~iv 92 (96)
T PF00586_consen 69 SPEELKEIVKGIAEACREFGIPIV 92 (96)
T ss_dssp BHHHHHHHHHHHHHHHHHHT-EEE
T ss_pred CHHHHHHHHHHHHHHHHHhCCcEe
Confidence 456788888899999999999875
No 77
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=31.75 E-value=70 Score=22.97 Aligned_cols=21 Identities=10% Similarity=0.067 Sum_probs=18.8
Q ss_pred HHHhHHHHHHHHHHcCCccEE
Q 035140 22 MVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 22 L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
...|..++..+++.+|+.+++
T Consensus 97 s~yqk~rve~lc~~lGl~~~~ 117 (223)
T COG2102 97 SEYQKERVERLCEELGLKVYA 117 (223)
T ss_pred hHHHHHHHHHHHHHhCCEEee
Confidence 467899999999999998888
No 78
>cd01401 PncB_like Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi.
Probab=31.73 E-value=80 Score=24.10 Aligned_cols=35 Identities=14% Similarity=0.009 Sum_probs=28.0
Q ss_pred hhHHHhHHHHHHHHHHcCC-ccEEEEEecCCCCc-cc
Q 035140 20 DTMVQGLQYLKASIKAMSI-KVIEIQVVSPNKDS-QI 54 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi-~~~~v~IvS~DKD~-QL 54 (72)
-++..+-..+++.++.+|+ |...++++|+|=|. -+
T Consensus 282 GD~~~~~~k~r~~~~~~Gi~p~~K~iv~Sd~Lde~~i 318 (377)
T cd01401 282 GDPFEWGEKAIAHYEKLGIDPKTKTLVFSDGLDVEKA 318 (377)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCcEEEEcCCCCHHHH
Confidence 3566677888999999998 77768899999886 44
No 79
>cd00779 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.
Probab=31.13 E-value=1.6e+02 Score=20.62 Aligned_cols=46 Identities=15% Similarity=0.122 Sum_probs=27.2
Q ss_pred HHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccC--CCEEEEEecCCcee
Q 035140 23 VQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILS--HSLCLLRIAPRGFE 70 (72)
Q Consensus 23 ~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~--~~v~v~~~~k~~~~ 70 (72)
...+....++++.||||...+...+ .|| ...+ =++-+|.|..+..|
T Consensus 159 ~~i~~~~~~il~~Lgl~~~~~~~~~--~~~gg~~s~~~~~e~~~~~~~~~e 207 (255)
T cd00779 159 EKMYQAYSRIFKRLGLPFVKVEADS--GAIGGSLSHEFHVLSPLKITKGIE 207 (255)
T ss_pred HHHHHHHHHHHHHcCCcEEEEEecC--CCCCCcccEEEEEEEecCCCCeEE
Confidence 3555667899999999875544323 344 4444 25556656554444
No 80
>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=30.91 E-value=1.1e+02 Score=21.85 Aligned_cols=29 Identities=7% Similarity=0.094 Sum_probs=24.5
Q ss_pred hHHHhHHHHHHHHHHcCCccEEEEEecCC
Q 035140 21 TMVQGLQYLKASIKAMSIKVIEIQVVSPN 49 (72)
Q Consensus 21 ~L~~Ql~~i~~~l~~lgi~~~~v~IvS~D 49 (72)
++...+..+.++++.+|++.+.+.+.+.|
T Consensus 155 e~~e~l~~~~~~l~~lgl~~~~i~l~~~~ 183 (298)
T cd00771 155 EIKGVLDLIKEVYSDFGFFDYKVELSTRP 183 (298)
T ss_pred HHHHHHHHHHHHHHHcCCCcEEEEEEcCh
Confidence 45567888999999999998888888886
No 81
>PRK06764 hypothetical protein; Provisional
Probab=30.85 E-value=28 Score=21.99 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=15.5
Q ss_pred EEEecCCCCc-cccCCCEEEEEe
Q 035140 43 IQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 43 v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
+.|+||||.. ||-.-.++.-.|
T Consensus 61 idilsgdkeaiqlnkyti~f~kp 83 (105)
T PRK06764 61 IDVLSGDKEAIQLNKYTIRFSKP 83 (105)
T ss_pred eeeecCChhheEeeeeEEEecCC
Confidence 8899999999 984434443333
No 82
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=29.82 E-value=37 Score=19.90 Aligned_cols=9 Identities=11% Similarity=0.442 Sum_probs=7.9
Q ss_pred EEecCCCCc
Q 035140 44 QVVSPNKDS 52 (72)
Q Consensus 44 ~IvS~DKD~ 52 (72)
.|+|.|-|+
T Consensus 29 av~s~D~D~ 37 (73)
T smart00484 29 AIITEDSDL 37 (73)
T ss_pred EEEcCccce
Confidence 589999998
No 83
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=29.26 E-value=78 Score=19.44 Aligned_cols=21 Identities=10% Similarity=0.270 Sum_probs=18.4
Q ss_pred chhHHHhHHHHHHHHHHcCCc
Q 035140 19 PDTMVQGLQYLKASIKAMSIK 39 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~lgi~ 39 (72)
-++|..|+...|+-+++-|+.
T Consensus 70 ~~eL~~eI~eAK~dLr~kGv~ 90 (91)
T PF08285_consen 70 AKELQKEIKEAKADLRKKGVD 90 (91)
T ss_pred HHHHHHHHHHHHHHHHHcCCC
Confidence 357999999999999999985
No 84
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=28.96 E-value=30 Score=21.50 Aligned_cols=13 Identities=31% Similarity=0.396 Sum_probs=11.4
Q ss_pred EEEecCCCCc-ccc
Q 035140 43 IQVVSPNKDS-QIL 55 (72)
Q Consensus 43 v~IvS~DKD~-QLv 55 (72)
-+|||||+-+ .++
T Consensus 53 FVIVSgDdr~~~IL 66 (96)
T PF13734_consen 53 FVIVSGDDRMGPIL 66 (96)
T ss_dssp EEEEESBTTS-SEE
T ss_pred EEEEECCCCcccee
Confidence 7899999999 875
No 85
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]
Probab=28.76 E-value=76 Score=22.05 Aligned_cols=16 Identities=31% Similarity=0.461 Sum_probs=9.9
Q ss_pred HHHHHHHHHcCCccEE
Q 035140 27 QYLKASIKAMSIKVIE 42 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~ 42 (72)
|..++.+.+-|+++++
T Consensus 53 p~t~~~~~~~gv~vi~ 68 (177)
T COG2266 53 PKTKEYLESVGVKVIE 68 (177)
T ss_pred HhHHHHHHhcCceEEE
Confidence 4455666666666666
No 86
>COG5458 Uncharacterized conserved protein [Function unknown]
Probab=28.56 E-value=50 Score=22.07 Aligned_cols=18 Identities=17% Similarity=0.135 Sum_probs=14.8
Q ss_pred ccCCCCCCchhHHHhHHH
Q 035140 11 YKNNRPPTPDTMVQGLQY 28 (72)
Q Consensus 11 YKanR~~~Pe~L~~Ql~~ 28 (72)
=||.+..||.+|+.++..
T Consensus 123 g~ag~~~mP~dLrreLae 140 (144)
T COG5458 123 GKAGGADMPADLRRELAE 140 (144)
T ss_pred CCCccccCCHHHHHHHHH
Confidence 378889999999888754
No 87
>PF09572 RE_XamI: XamI restriction endonuclease; InterPro: IPR019072 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the XamI restriction endonuclease which recognises GTCGAC but cleavage site unknown. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=28.53 E-value=99 Score=22.67 Aligned_cols=38 Identities=13% Similarity=0.206 Sum_probs=30.1
Q ss_pred cccCccccCCCCCCchhHH-------------------------HhHHHHHHHHHHcCCccEE
Q 035140 5 HTLYPSYKNNRPPTPDTMV-------------------------QGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 5 ~~~~p~YKanR~~~Pe~L~-------------------------~Ql~~i~~~l~~lgi~~~~ 42 (72)
.++||=...+|.|+++++. .|+..|++.|++.|..-..
T Consensus 80 p~~FpWl~~~~~Pt~~Ei~~aA~ivadrL~~avA~piiRnaqErRQe~~i~~~L~~~GYt~~~ 142 (251)
T PF09572_consen 80 PDRFPWLGRGRAPTEEEIERAATIVADRLCGAVADPIIRNAQERRQEAAIAEWLEARGYTKVP 142 (251)
T ss_pred cccccccCCCCCCCHHHHHHHHHHHHHHHHhhhcchHHHhHHHHHHHHHHHHHHHhcCceEcc
Confidence 3578888999999987743 4788999999999986554
No 88
>KOG3185 consensus Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis]
Probab=28.52 E-value=41 Score=24.25 Aligned_cols=49 Identities=22% Similarity=0.462 Sum_probs=35.1
Q ss_pred CCCCchhHHHhHHHHHHHHHHcCCccEE---EEEecCCCC--c-cccCC--CEEEEEec
Q 035140 15 RPPTPDTMVQGLQYLKASIKAMSIKVIE---IQVVSPNKD--S-QILSH--SLCLLRIA 65 (72)
Q Consensus 15 R~~~Pe~L~~Ql~~i~~~l~~lgi~~~~---v~IvS~DKD--~-QLv~~--~v~v~~~~ 65 (72)
|...|++.. +..+.|-|.+||=.... |-++.+|-| - +++.+ .|.||+-.
T Consensus 85 RnSLPd~V~--i~RveErlsALGNviaCNDyvAlvH~dldketEeii~dVL~VeVfRqt 141 (245)
T KOG3185|consen 85 RNSLPDEVV--IQRVEERLSALGNVIACNDYVALVHPDLDKETEEIIADVLKVEVFRQT 141 (245)
T ss_pred HhcCCccee--eehhhhHHhhhcCEEEecceeEEecCccchhHHHHHHHHhheeeeeec
Confidence 556677764 45688999999965555 888888655 4 88876 67887644
No 89
>TIGR03358 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=28.48 E-value=54 Score=22.28 Aligned_cols=18 Identities=28% Similarity=0.493 Sum_probs=15.7
Q ss_pred CchhHHHhHHHHHHHHHH
Q 035140 18 TPDTMVQGLQYLKASIKA 35 (72)
Q Consensus 18 ~Pe~L~~Ql~~i~~~l~~ 35 (72)
-|+.+..|+|.+++++++
T Consensus 101 ~Pd~Ia~qVp~L~~Llel 118 (159)
T TIGR03358 101 SPDAVAKQVPELKKLLEA 118 (159)
T ss_pred CHHHHHHHhHHHHHHHHH
Confidence 489999999999988875
No 90
>PRK10665 nitrogen regulatory protein P-II 2; Provisional
Probab=28.22 E-value=67 Score=20.24 Aligned_cols=18 Identities=11% Similarity=0.357 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHcCCccEE
Q 035140 25 GLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 25 Ql~~i~~~l~~lgi~~~~ 42 (72)
.+..+++.|..+|++.+.
T Consensus 12 kl~~v~~AL~~~G~~g~T 29 (112)
T PRK10665 12 KLEDVREALSSIGIQGLT 29 (112)
T ss_pred HHHHHHHHHHHCCCCcEE
Confidence 357788999999999888
No 91
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=27.98 E-value=96 Score=16.92 Aligned_cols=40 Identities=13% Similarity=0.173 Sum_probs=24.2
Q ss_pred HHHHHHHcCCccEEEEE------ecCCCCc-cccC--CCEEEEEecCCc
Q 035140 29 LKASIKAMSIKVIEIQV------VSPNKDS-QILS--HSLCLLRIAPRG 68 (72)
Q Consensus 29 i~~~l~~lgi~~~~v~I------vS~DKD~-QLv~--~~v~v~~~~k~~ 68 (72)
+.+++..+|++.-.+.+ ++...-. ..+. +.|.++.+.-||
T Consensus 18 l~~lL~~l~~~~~~vav~vNg~iv~r~~~~~~~l~~gD~vei~~~vgGG 66 (66)
T PRK05659 18 VAALLAREGLAGRRVAVEVNGEIVPRSQHASTALREGDVVEIVHALGGG 66 (66)
T ss_pred HHHHHHhcCCCCCeEEEEECCeEeCHHHcCcccCCCCCEEEEEEEecCC
Confidence 67888999997666322 2222222 4444 578888776544
No 92
>PF06069 PerC: PerC transcriptional activator; InterPro: IPR024684 This family includes PerC, which is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria []. It also includes a number of uncharacterised proteins, such as Orf40 from bacteriophage SfV.
Probab=27.46 E-value=1.1e+02 Score=18.92 Aligned_cols=29 Identities=31% Similarity=0.424 Sum_probs=19.5
Q ss_pred cCCCCCCc-hhHHHhHHHHHHHHHHcCCcc
Q 035140 12 KNNRPPTP-DTMVQGLQYLKASIKAMSIKV 40 (72)
Q Consensus 12 KanR~~~P-e~L~~Ql~~i~~~l~~lgi~~ 40 (72)
|++|++.| ++|..-=..+.+....|||..
T Consensus 49 kakR~p~~~~~f~~l~~Aa~~T~~~MGi~~ 78 (90)
T PF06069_consen 49 KAKRPPEPPDNFGDLRKAADRTQKRMGIDQ 78 (90)
T ss_pred hcccCCCChhHHHHHHHHHHHHHHHcCCCC
Confidence 67777665 455555556777788899953
No 93
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=27.45 E-value=62 Score=20.08 Aligned_cols=38 Identities=11% Similarity=0.288 Sum_probs=26.6
Q ss_pred ccccCccccCCCCC------CchhH---HHhHHHHHHHHHHcCCccE
Q 035140 4 RHTLYPSYKNNRPP------TPDTM---VQGLQYLKASIKAMSIKVI 41 (72)
Q Consensus 4 R~~~~p~YKanR~~------~Pe~L---~~Ql~~i~~~l~~lgi~~~ 41 (72)
|.-+||.|=..+.. .|-++ .+.+..|.+++..||+++.
T Consensus 6 r~vIyP~Y~d~~~tr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~ 52 (95)
T PRK00754 6 RIVIWPAYIDSTRSRSEGRIISRKLAVKEPRLEEIIEAAEKLGLNPE 52 (95)
T ss_pred cEEEeeccccCCCChhhcCccCHHHhccCCCHHHHHHHHHHcCCCeE
Confidence 45689999655332 45555 3457788899999999974
No 94
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=27.42 E-value=69 Score=15.95 Aligned_cols=15 Identities=20% Similarity=0.310 Sum_probs=11.3
Q ss_pred HHHHHHHHHHcCCcc
Q 035140 26 LQYLKASIKAMSIKV 40 (72)
Q Consensus 26 l~~i~~~l~~lgi~~ 40 (72)
.+.+++.|...|++.
T Consensus 6 v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 6 VAELKEELKERGLST 20 (35)
T ss_dssp HHHHHHHHHHTTS-S
T ss_pred HHHHHHHHHHCCCCC
Confidence 356889999999875
No 95
>PF02696 UPF0061: Uncharacterized ACR, YdiU/UPF0061 family; InterPro: IPR003846 The proteins in this entry are functionally uncharacterised.
Probab=26.93 E-value=91 Score=24.63 Aligned_cols=35 Identities=14% Similarity=0.184 Sum_probs=24.3
Q ss_pred CCCCchhHHHhHHHHHHHHHHcCCccEE--EEEecCCCC
Q 035140 15 RPPTPDTMVQGLQYLKASIKAMSIKVIE--IQVVSPNKD 51 (72)
Q Consensus 15 R~~~Pe~L~~Ql~~i~~~l~~lgi~~~~--v~IvS~DKD 51 (72)
|...-..+++-| +-|++.+||||... .+|.|++.-
T Consensus 128 rAvLrssIREyL--~SEAm~aLGIPTTRaLalv~t~~~~ 164 (487)
T PF02696_consen 128 RAVLRSSIREYL--CSEAMHALGIPTTRALALVTTGEEP 164 (487)
T ss_pred cchHHHHHHHHH--HHHHHHhCCCCccceeEEEEcCCee
Confidence 333445555554 67899999999999 677776543
No 96
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=26.87 E-value=1.4e+02 Score=25.45 Aligned_cols=42 Identities=21% Similarity=0.333 Sum_probs=29.0
Q ss_pred ccccCCCCCC------chhHHHhHHHHHHHHHHcC--CccEEEEEecCCC
Q 035140 9 PSYKNNRPPT------PDTMVQGLQYLKASIKAMS--IKVIEIQVVSPNK 50 (72)
Q Consensus 9 p~YKanR~~~------Pe~L~~Ql~~i~~~l~~lg--i~~~~v~IvS~DK 50 (72)
=+||.+|++. ++....|+..-..++..++ .++-...+++.+-
T Consensus 1087 iDYKT~~~~~~~~~~~~~~y~~QL~~Y~~~~~~~~p~~~v~~~L~~~~~~ 1136 (1141)
T TIGR02784 1087 VDYKTNRPVPATPEEVPPAYLRQLALYRALLEPLYPGKTVEAALLWTEAP 1136 (1141)
T ss_pred EEcCCCCCCCCChhhhhhHHHHHHHHHHHHHHHHcCCCeEEEEEEECCCC
Confidence 4799999742 2347899999999999874 3444455666544
No 97
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=26.63 E-value=76 Score=15.59 Aligned_cols=15 Identities=20% Similarity=0.304 Sum_probs=12.2
Q ss_pred HHHHHHHHHHcCCcc
Q 035140 26 LQYLKASIKAMSIKV 40 (72)
Q Consensus 26 l~~i~~~l~~lgi~~ 40 (72)
.+.+++.|..+|++.
T Consensus 6 ~~~Lk~~l~~~gl~~ 20 (35)
T smart00513 6 VSELKDELKKRGLST 20 (35)
T ss_pred HHHHHHHHHHcCCCC
Confidence 356889999999985
No 98
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=26.60 E-value=1.2e+02 Score=19.50 Aligned_cols=27 Identities=26% Similarity=0.370 Sum_probs=21.9
Q ss_pred HHHHHHHHHHcCCccEE----------EEEecCCCCc
Q 035140 26 LQYLKASIKAMSIKVIE----------IQVVSPNKDS 52 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~----------v~IvS~DKD~ 52 (72)
....++.++.+|+.+.+ |.|+-.|.|.
T Consensus 32 ~~av~~~les~G~k~~~~y~T~GeYD~V~i~EapDda 68 (104)
T COG4274 32 AAAVRALLESMGGKVKEQYWTLGEYDVVAIVEAPDDA 68 (104)
T ss_pred HHHHHHHHHHcCcEEEEEEEeeccccEEEEEecCCHH
Confidence 35688999999999988 7777777775
No 99
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=25.67 E-value=57 Score=21.07 Aligned_cols=27 Identities=11% Similarity=0.332 Sum_probs=17.9
Q ss_pred HHHHHHHHHHcCCccEE------EEEecCCCCc
Q 035140 26 LQYLKASIKAMSIKVIE------IQVVSPNKDS 52 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~------v~IvS~DKD~ 52 (72)
+..++++++.+|+.-+. =+|+++|.|-
T Consensus 21 MaeLr~~l~~~Gf~~V~Tyi~SGNvvf~~~~~~ 53 (137)
T PF08002_consen 21 MAELREALEDLGFTNVRTYIQSGNVVFESDRDP 53 (137)
T ss_dssp HHHHHHHHHHCT-EEEEEETTTTEEEEEESS-H
T ss_pred HHHHHHHHHHcCCCCceEEEeeCCEEEecCCCh
Confidence 46688999999998888 3444455553
No 100
>KOG4720 consensus Ethanolamine kinase [Lipid transport and metabolism]
Probab=25.65 E-value=1.4e+02 Score=23.19 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=30.8
Q ss_pred CCchhHHHhHHHHHHHHHHcCCccEE--------EEEecCCCCc-cccC
Q 035140 17 PTPDTMVQGLQYLKASIKAMSIKVIE--------IQVVSPNKDS-QILS 56 (72)
Q Consensus 17 ~~Pe~L~~Ql~~i~~~l~~lgi~~~~--------v~IvS~DKD~-QLv~ 56 (72)
+.|++|.+-+..+++.+..|+=|++- -+|+..-|.- ++|+
T Consensus 225 ~~~~~L~~Ei~~l~E~l~~L~sPVVFcHNDLL~~Niiy~~~~~~v~fID 273 (391)
T KOG4720|consen 225 PSPEDLGEEISKLKEMLSMLKSPVVFCHNDLLCGNIIYDSEKGSVEFID 273 (391)
T ss_pred CCHHHHHHHHHHHHHHHHhhCCCeEEeecchhhcceeeccccCcEEEEe
Confidence 45789999999999999999999876 4455555554 5554
No 101
>PRK00029 hypothetical protein; Validated
Probab=25.47 E-value=1.1e+02 Score=24.26 Aligned_cols=35 Identities=11% Similarity=0.059 Sum_probs=23.4
Q ss_pred CCCchhHHHhHHHHHHHHHHcCCccEE--EEEecCCCCc
Q 035140 16 PPTPDTMVQGLQYLKASIKAMSIKVIE--IQVVSPNKDS 52 (72)
Q Consensus 16 ~~~Pe~L~~Ql~~i~~~l~~lgi~~~~--v~IvS~DKD~ 52 (72)
...-..+++-| +-|++.+||||... .+|.|+++=+
T Consensus 129 AvLrssiREyL--~SEAMhaLGIPTTRaLalv~tge~V~ 165 (487)
T PRK00029 129 AVLRSSIREYL--ASEAMHALGIPTTRALSLVETGEPVY 165 (487)
T ss_pred hhhhhHHHHHH--HHHHHHhcCCCccceEEEEecCCcee
Confidence 33334455544 66899999999999 6677765434
No 102
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=24.64 E-value=1.7e+02 Score=18.84 Aligned_cols=15 Identities=7% Similarity=0.173 Sum_probs=9.7
Q ss_pred HHHHHHHHcCCccEE
Q 035140 28 YLKASIKAMSIKVIE 42 (72)
Q Consensus 28 ~i~~~l~~lgi~~~~ 42 (72)
.++++|+.+|+.++.
T Consensus 15 ~v~~~L~~~~~ep~i 29 (125)
T PF10137_consen 15 AVERFLEKLGLEPII 29 (125)
T ss_pred HHHHHHHhCCCceEE
Confidence 456677777776665
No 103
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=24.43 E-value=73 Score=17.73 Aligned_cols=15 Identities=20% Similarity=0.319 Sum_probs=9.6
Q ss_pred HHHHHHHHHHcCCcc
Q 035140 26 LQYLKASIKAMSIKV 40 (72)
Q Consensus 26 l~~i~~~l~~lgi~~ 40 (72)
+..++.+|..+||..
T Consensus 34 l~~v~~lL~~lGi~~ 48 (77)
T PF14528_consen 34 LEDVQKLLLRLGIKA 48 (77)
T ss_dssp HHHHHHHHHHTT--E
T ss_pred HHHHHHHHHHCCCee
Confidence 445667888999976
No 104
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=24.10 E-value=30 Score=23.03 Aligned_cols=17 Identities=24% Similarity=0.391 Sum_probs=13.5
Q ss_pred HHHHHHHHHHcCCccEE
Q 035140 26 LQYLKASIKAMSIKVIE 42 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~ 42 (72)
++.++++|+.+||-.=.
T Consensus 80 ~~~lke~l~elgie~eR 96 (132)
T COG1908 80 MELLKELLKELGIEPER 96 (132)
T ss_pred HHHHHHHHHHhCCCcce
Confidence 67899999999985444
No 105
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=23.97 E-value=99 Score=23.07 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=16.3
Q ss_pred HHHHHHHHHcCCccEEEEEecC
Q 035140 27 QYLKASIKAMSIKVIEIQVVSP 48 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~ 48 (72)
+.+++.++..|||++.+. +|.
T Consensus 341 ~~lk~~l~e~GIP~L~id-~~~ 361 (380)
T TIGR02263 341 PMLAARCKEHGIPQIAFK-YAE 361 (380)
T ss_pred HHHHHHHHHCCCCEEEEE-ecC
Confidence 567888899999999873 443
No 106
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins. The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex []. This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any beta-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus. ; PDB: 2ILR_A.
Probab=23.85 E-value=55 Score=23.91 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=16.1
Q ss_pred CCCCchhHHHhHHHHHHHHHHcC
Q 035140 15 RPPTPDTMVQGLQYLKASIKAMS 37 (72)
Q Consensus 15 R~~~Pe~L~~Ql~~i~~~l~~lg 37 (72)
..+.|++...|++.++++++..+
T Consensus 5 ~~~lp~~~~~~~~~lk~ll~~~~ 27 (263)
T PF11510_consen 5 SVELPKHIQDQVPRLKELLETES 27 (263)
T ss_dssp -----HHHHHHHHHHHHHHHHHH
T ss_pred hhhCcHHHHHHHHHHHHHHHHhh
Confidence 45789999999999999998653
No 107
>TIGR01721 AMN-like AMP nucleosidase, putative. The sequences in the clade represented by this model are most closely related to the AMP nucleosidase found in TIGR01717. These sequences are found only in Chlamydia and Porphyromonas and differ sufficiently from the characterized AMP nucleosidase to put some doubt on assignment of this name.
Probab=23.72 E-value=2.1e+02 Score=20.73 Aligned_cols=26 Identities=4% Similarity=-0.132 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHcCCccEEEEEecCCC
Q 035140 25 GLQYLKASIKAMSIKVIEIQVVSPNK 50 (72)
Q Consensus 25 Ql~~i~~~l~~lgi~~~~v~IvS~DK 50 (72)
-+..+.+.++.+|++...-.++|+|-
T Consensus 137 l~~~l~~a~~~~g~~~~~G~v~TtD~ 162 (266)
T TIGR01721 137 VQKAITSALENKGKDYHIGITHTTNI 162 (266)
T ss_pred HHHHHHHHHHHcCCCeEEEEEEcCCC
Confidence 44668888999999998888999985
No 108
>COG3516 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.67 E-value=73 Score=22.04 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=15.5
Q ss_pred chhHHHhHHHHHHHHHH
Q 035140 19 PDTMVQGLQYLKASIKA 35 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~ 35 (72)
|+.+..|+|.++++|++
T Consensus 107 P~~Va~qVp~L~kLLea 123 (169)
T COG3516 107 PDAVARQVPELKKLLEA 123 (169)
T ss_pred HHHHHHhhHHHHHHHHH
Confidence 88999999999999885
No 109
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=23.55 E-value=75 Score=20.50 Aligned_cols=17 Identities=12% Similarity=0.259 Sum_probs=14.8
Q ss_pred HHHHHHHHHHcCCccEE
Q 035140 26 LQYLKASIKAMSIKVIE 42 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~ 42 (72)
++.+++.|+..|++.+.
T Consensus 13 l~~vkeaL~~~G~~gmT 29 (112)
T COG0347 13 LDDVKEALEKAGVPGMT 29 (112)
T ss_pred hHHHHHHHHHcCCCceE
Confidence 47789999999998887
No 110
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=23.39 E-value=81 Score=19.86 Aligned_cols=37 Identities=24% Similarity=0.446 Sum_probs=25.3
Q ss_pred cccCccccCCCCC------CchhHH---HhHHHHHHHHHHcCCccE
Q 035140 5 HTLYPSYKNNRPP------TPDTMV---QGLQYLKASIKAMSIKVI 41 (72)
Q Consensus 5 ~~~~p~YKanR~~------~Pe~L~---~Ql~~i~~~l~~lgi~~~ 41 (72)
--+||.|=..+.. .|.++. +-+..|.+++.+||++++
T Consensus 4 ~vIyP~Y~D~~~sr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~ 49 (100)
T PRK03745 4 FVVWPSELDSRLSRKYGRIVPKNLAVERPTLEEIVDAAEALGFKVI 49 (100)
T ss_pred EEEeeccccCcCChhhcCccCHHHcccCCCHHHHHHHHHHcCCCcE
Confidence 3478888555443 455543 446778889999999984
No 111
>PRK06437 hypothetical protein; Provisional
Probab=23.30 E-value=1.5e+02 Score=16.66 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=24.1
Q ss_pred HHHHHHHHcCCccEEEEEecCCCC--c-cccC--CCEEEEEecCCc
Q 035140 28 YLKASIKAMSIKVIEIQVVSPNKD--S-QILS--HSLCLLRIAPRG 68 (72)
Q Consensus 28 ~i~~~l~~lgi~~~~v~IvS~DKD--~-QLv~--~~v~v~~~~k~~ 68 (72)
.+.++++.||++.-.+.+.=+.+- . ..++ +.|.++.+..||
T Consensus 22 tv~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Veiv~~V~GG 67 (67)
T PRK06437 22 TVNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLILEVFSGG 67 (67)
T ss_pred cHHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEEEecccCC
Confidence 377889999997555322211111 2 3343 578888777654
No 112
>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]
Probab=23.11 E-value=93 Score=21.56 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=22.1
Q ss_pred cCCCCCC---chhH-HHhHHHHHHHHHHcCCccEE
Q 035140 12 KNNRPPT---PDTM-VQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 12 KanR~~~---Pe~L-~~Ql~~i~~~l~~lgi~~~~ 42 (72)
||+|+-| |..+ -+.++.+.++.+.++||++.
T Consensus 34 kAkrPLlivGp~~~dee~~E~~vKi~ekfnipiva 68 (170)
T COG1880 34 KAKRPLLIVGPLALDEELLELAVKIIEKFNIPIVA 68 (170)
T ss_pred hcCCceEEecccccCHHHHHHHHHHHHhcCCceEe
Confidence 6777754 3333 34467888899999999877
No 113
>COG1921 SelA Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]
Probab=23.03 E-value=1.2e+02 Score=23.47 Aligned_cols=24 Identities=21% Similarity=0.104 Sum_probs=19.9
Q ss_pred HHHHHHHcCCccEE-----------------------EEEecCCCCc
Q 035140 29 LKASIKAMSIKVIE-----------------------IQVVSPNKDS 52 (72)
Q Consensus 29 i~~~l~~lgi~~~~-----------------------v~IvS~DKD~ 52 (72)
+.++....|+|++. .+++||||=|
T Consensus 179 l~~ia~~~~lpvivD~aSg~~v~~e~~l~~~la~GaDLV~~SgdKll 225 (395)
T COG1921 179 LVEIAHEKGLPVIVDLASGALVDKEPDLREALALGADLVSFSGDKLL 225 (395)
T ss_pred HHHHHHHcCCCEEEecCCccccccccchhHHHhcCCCEEEEecchhc
Confidence 66778899999987 7889999865
No 114
>PF01255 Prenyltransf: Putative undecaprenyl diphosphate synthase; InterPro: IPR001441 Synonym(s): Di-trans-poly-cis-undecaprenyl-diphosphate synthase, Undecaprenyl pyrophosphate synthetase, Undecaprenyl pyrophosphate synthase, UPP synthetase Di-trans-poly-cis-decaprenylcistransferase (2.5.1.31 from EC) (UPP synthetase) generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) []. This bacterial enzyme is also found in archaebacteria and in a number of uncharacterised proteins including some from yeasts. This entry also matches related enzymes that transfer alkyl groups, such as dehydrodolichyl diphosphate synthase.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 2D2R_B 2DTN_B 1F75_B 1X07_A 2E9D_A 1JP3_A 3QAS_A 1X09_A 1V7U_B 2E9A_A ....
Probab=22.91 E-value=1.9e+02 Score=20.07 Aligned_cols=24 Identities=17% Similarity=0.199 Sum_probs=17.9
Q ss_pred HHHHHHHHHHcCCccEEEEEecCC
Q 035140 26 LQYLKASIKAMSIKVIEIQVVSPN 49 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~v~IvS~D 49 (72)
+..+-+.+..+||+.++++.+|.|
T Consensus 27 l~~i~~~~~~~gI~~lTvYaFS~e 50 (223)
T PF01255_consen 27 LKEIVEWCLELGIKYLTVYAFSTE 50 (223)
T ss_dssp HHHHHHHHHHCT-SEEEEEEEETT
T ss_pred HHHHHHHHHHcCCCEEEEEEecch
Confidence 445556667799999999999975
No 115
>cd06535 CIDE_N_CAD CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and the release of active DFF40/CAD nuclease.
Probab=22.78 E-value=1.3e+02 Score=18.22 Aligned_cols=38 Identities=13% Similarity=0.235 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCccE--E------EEEecCCCCc-cccCCCEEEEEecCC
Q 035140 28 YLKASIKAMSIKVI--E------IQVVSPNKDS-QILSHSLCLLRIAPR 67 (72)
Q Consensus 28 ~i~~~l~~lgi~~~--~------v~IvS~DKD~-QLv~~~v~v~~~~k~ 67 (72)
.+.+.++.|+++.- . =..|| -|+ |.+.+|+.+.-..++
T Consensus 26 L~~K~~~~l~l~~~~~~l~L~eDGTeVt--EeyF~tLp~nT~lmvL~~g 72 (77)
T cd06535 26 LLRKGCRLLQLPCAGSRLCLYEDGTEVT--EEYFPTLPDNTELVLLTPG 72 (77)
T ss_pred HHHHHHHHhCCCCCCcEEEEecCCcEeh--HHHHhcCCCCcEEEEEcCC
Confidence 35567788888732 2 22345 499 999998777655543
No 116
>PRK13396 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=22.48 E-value=1.4e+02 Score=22.61 Aligned_cols=33 Identities=24% Similarity=0.321 Sum_probs=24.3
Q ss_pred ccccCCCCCCc--hhH-HHhHHHHHHHHHHcCCccEE
Q 035140 9 PSYKNNRPPTP--DTM-VQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 9 p~YKanR~~~P--e~L-~~Ql~~i~~~l~~lgi~~~~ 42 (72)
..|| +|...- .++ ..++++++++.+.+|+++++
T Consensus 135 g~~k-pRtsp~sf~G~g~~gl~~L~~~~~e~Gl~~~t 170 (352)
T PRK13396 135 GAYK-PRTSPYAFQGHGESALELLAAAREATGLGIIT 170 (352)
T ss_pred eeec-CCCCCcccCCchHHHHHHHHHHHHHcCCcEEE
Confidence 3456 775431 111 67899999999999999998
No 117
>PF05591 DUF770: Protein of unknown function (DUF770); InterPro: IPR008312 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, these proteins are encoded in type VI secretion loci (including the SCI genomic island in Salmonella enterica and the imp locus in Rhizobium leguminosarum) implicated in pathogenicity and protein secretion [, , [].
Probab=22.44 E-value=83 Score=21.20 Aligned_cols=18 Identities=17% Similarity=0.388 Sum_probs=15.5
Q ss_pred CchhHHHhHHHHHHHHHH
Q 035140 18 TPDTMVQGLQYLKASIKA 35 (72)
Q Consensus 18 ~Pe~L~~Ql~~i~~~l~~ 35 (72)
-|+.+..|+|.++++++.
T Consensus 100 ~Pd~v~~qVp~L~~Llel 117 (157)
T PF05591_consen 100 HPDAVAEQVPELRKLLEL 117 (157)
T ss_pred CHHHHHHhhHHHHHHHHH
Confidence 389999999999988874
No 118
>PF12621 DUF3779: Phosphate metabolism protein ; InterPro: IPR022257 This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with PF02714 from PFAM. There are two completely conserved residues (W and D) that may be functionally important. This family is likely to be involved in phosphate metabolism however there is little accompanying literature to confirm this.
Probab=22.33 E-value=14 Score=22.64 Aligned_cols=20 Identities=35% Similarity=0.647 Sum_probs=16.5
Q ss_pred cccccCccccCCCCCCchhH
Q 035140 3 FRHTLYPSYKNNRPPTPDTM 22 (72)
Q Consensus 3 ~R~~~~p~YKanR~~~Pe~L 22 (72)
|+-++|.+|++.|+.+|+..
T Consensus 2 f~P~i~~~~~~~~~~lp~~~ 21 (95)
T PF12621_consen 2 FHPEIYASYKALRSLLPEDY 21 (95)
T ss_pred CCchhhcCHHHHHhhCCCcc
Confidence 56788999999999888664
No 119
>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]
Probab=22.14 E-value=32 Score=25.79 Aligned_cols=31 Identities=23% Similarity=0.264 Sum_probs=25.3
Q ss_pred HHHHHHHHHHcCCccEE----EEEecCCCCc-cccC
Q 035140 26 LQYLKASIKAMSIKVIE----IQVVSPNKDS-QILS 56 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~----v~IvS~DKD~-QLv~ 56 (72)
+..+.++.++=+++... .+|.|+|-|| |-++
T Consensus 178 L~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQalN 213 (333)
T KOG0991|consen 178 LKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQALN 213 (333)
T ss_pred HHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHHH
Confidence 56677777888887766 8999999999 9875
No 120
>PRK09243 nicotinate phosphoribosyltransferase; Validated
Probab=22.09 E-value=1.6e+02 Score=23.01 Aligned_cols=42 Identities=12% Similarity=0.078 Sum_probs=31.4
Q ss_pred ccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cc
Q 035140 11 YKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QI 54 (72)
Q Consensus 11 YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QL 54 (72)
+++=|.. --++......+++.|+..|++.+. +|+|+|=|. .+
T Consensus 258 ~~gVRlD-SGDl~~l~~~vr~~ld~~G~~~~k-Ii~S~gLde~~i 300 (464)
T PRK09243 258 LGGVRID-SGDLAYLSKKVRKMLDEAGFTDTK-IVASNDLDEYTI 300 (464)
T ss_pred CceeeCC-CCCHHHHHHHHHHHHHHCCCCCcE-EEEeCCCCHHHH
Confidence 3444544 246777788899999999999866 799999886 54
No 121
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=22.08 E-value=36 Score=20.27 Aligned_cols=20 Identities=10% Similarity=0.262 Sum_probs=10.5
Q ss_pred EEecCCCCc-cccCCCEEEEEe
Q 035140 44 QVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 44 ~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
.|+|.|.|+ =. .-...+.+.
T Consensus 29 ~V~t~DsD~l~f-G~~~vi~~~ 49 (94)
T PF00867_consen 29 AVITEDSDLLLF-GAPKVIRKL 49 (94)
T ss_dssp EEE-SSSHHHHT-T-SEEEESS
T ss_pred EEEecCCCEEee-CCCEEEEec
Confidence 477989988 44 434344433
No 122
>PF02274 Amidinotransf: Amidinotransferase; InterPro: IPR003198 This family contains glycine and inosamine amidinotransferases, enzymes which are involved in creatine and streptomycin biosynthesis respectively. This family also includes arginine deiminases, which catalyse the reversible reaction: arginine + H2O = citrulline + NH3 The Streptococcus anti-tumour glycoprotein is also found in this family [].; GO: 0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines, 0005737 cytoplasm; PDB: 2CI7_A 2CI1_A 2CI4_A 2CI3_A 2CI5_A 2C6Z_A 2CI6_A 3I4A_B 3I2E_B 2JAI_A ....
Probab=21.98 E-value=1.1e+02 Score=21.26 Aligned_cols=29 Identities=24% Similarity=0.515 Sum_probs=22.0
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCccEE
Q 035140 14 NRPPTPDTMVQGLQYLKASIKAMSIKVIE 42 (72)
Q Consensus 14 nR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~ 42 (72)
+.+..++....|...+.++|+..|+.++.
T Consensus 22 ~~~~~~~~a~~e~~~l~~~L~~~Gv~V~~ 50 (281)
T PF02274_consen 22 SDPPDPEKAREEHDALVEALRSNGVEVIE 50 (281)
T ss_dssp SS---HHHHHHHHHHHHHHHHTTT-EEEE
T ss_pred cCcchHHHHHHHHHHHHHHHHhCCcEEEE
Confidence 55667888999999999999999988765
No 123
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=21.89 E-value=2.2e+02 Score=21.90 Aligned_cols=49 Identities=24% Similarity=0.264 Sum_probs=36.6
Q ss_pred chhHHHhHHHHHHHHHHcCCccEE--------------EEEecCCCCc-cccC-CCEEEEEecCC
Q 035140 19 PDTMVQGLQYLKASIKAMSIKVIE--------------IQVVSPNKDS-QILS-HSLCLLRIAPR 67 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~lgi~~~~--------------v~IvS~DKD~-QLv~-~~v~v~~~~k~ 67 (72)
|++|+.-...++++-.+||=..-. .+.++.|=-- ..++ +|+++.+|.++
T Consensus 253 P~efk~mv~~ir~~~~alG~~~k~~~~~E~~~~~~~~Rsl~~~kdikkGe~ls~~Nl~~~RP~~g 317 (347)
T COG2089 253 PDEFKEMVDAIRQVEKALGDGEKEILPSEEETRNFARRSLVATKDIKKGEILSEDNLKVLRPGNG 317 (347)
T ss_pred HHHHHHHHHHHHHHHHHhCCCccccChhHHHHHHHHhhheeeecccccCccccccceEEeCCCCC
Confidence 889999999999999999864444 4445444333 5666 79999999876
No 124
>PF11130 TraC_F_IV: F pilus assembly Type-IV secretion system for plasmid transfer
Probab=21.66 E-value=1.9e+02 Score=19.46 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=31.0
Q ss_pred hhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc--cccCCCEEE
Q 035140 20 DTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS--QILSHSLCL 61 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~--QLv~~~v~v 61 (72)
+++......+...|.++|+..-. ..-+..++++ |++.....+
T Consensus 141 ~~l~~~~~~~~~~L~~~gi~~~~~~~~~l~~~l~~~~Np~~~~~~~~~~yd~~~~l~~Qi~~~~~~~ 207 (235)
T PF11130_consen 141 EELNELRERLESSLRSAGIPPRRLDPEDLISWLRRIFNPNPDANWPAPEYDPDEPLREQILDSDTEI 207 (235)
T ss_pred HHHHHHHHHHHHHHHHCCCccEEcCHHHHHHHHHHHcCCCccccCCccCCCCCCCHHHhcCCCCCeE
Confidence 45677777888899999998766 1127788999 998765444
No 125
>PRK01816 hypothetical protein; Provisional
Probab=21.38 E-value=1.7e+02 Score=19.69 Aligned_cols=26 Identities=8% Similarity=0.244 Sum_probs=22.4
Q ss_pred CCCCchhHHHhHHHHHHHHHHcCCcc
Q 035140 15 RPPTPDTMVQGLQYLKASIKAMSIKV 40 (72)
Q Consensus 15 R~~~Pe~L~~Ql~~i~~~l~~lgi~~ 40 (72)
+.+.|..|...+..|++-+.+.|+.+
T Consensus 87 ~tpLPpsL~~Wy~el~~Kl~~~g~~~ 112 (143)
T PRK01816 87 VTPLPPALLNWFYEVREKLQEAGQAL 112 (143)
T ss_pred CCCCChHHHHHHHHHHHHHHHcCCcc
Confidence 46789999999999999999999754
No 126
>PF00543 P-II: Nitrogen regulatory protein P-II members of this family.; InterPro: IPR002187 In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity []. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein []. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome. Other proteins highly similar to glnB are: Bacillus subtilis protein nrgB []. Escherichia coli hypothetical protein ybaI []. ; GO: 0030234 enzyme regulator activity, 0006808 regulation of nitrogen utilization; PDB: 1V3S_B 1V3R_C 2XZW_A 2XUL_A 2V5H_J 2XG8_C 2JJ4_F 1QY7_C 4AFF_A 2XBP_A ....
Probab=21.26 E-value=68 Score=19.27 Aligned_cols=17 Identities=6% Similarity=0.210 Sum_probs=14.4
Q ss_pred HHHHHHHHHHcCCccEE
Q 035140 26 LQYLKASIKAMSIKVIE 42 (72)
Q Consensus 26 l~~i~~~l~~lgi~~~~ 42 (72)
++.+.+.|..+|++.+.
T Consensus 10 ~~~v~~aL~~~G~~g~T 26 (102)
T PF00543_consen 10 LEEVIEALREAGVPGMT 26 (102)
T ss_dssp HHHHHHHHHHTTGSCEE
T ss_pred HHHHHHHHHHCCCCeEE
Confidence 56788899999998887
No 127
>cd07399 MPP_YvnB Bacillus subtilis YvnB and related proteins, metallophosphatase domain. YvnB (BSU35040) is an uncharacterized Bacillus subtilis protein with a metallophosphatase domain. This family includes bacterial and eukaryotic proteins similar to YvnB. YvnB belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for
Probab=21.21 E-value=2.4e+02 Score=18.97 Aligned_cols=30 Identities=10% Similarity=0.210 Sum_probs=22.0
Q ss_pred CCchhHHHhHHHHHHHHHHcCCccEEEEEecCC
Q 035140 17 PTPDTMVQGLQYLKASIKAMSIKVIEIQVVSPN 49 (72)
Q Consensus 17 ~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~D 49 (72)
..|+.+..++..+.+.....++.. +|++||
T Consensus 15 ~~~~~~~~~~~~i~~~~~~~~~d~---iv~~GD 44 (214)
T cd07399 15 SYPEVFDAQTDWIVDNAEALNIAF---VLHLGD 44 (214)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCE---EEECCC
Confidence 567888888888888888777554 456665
No 128
>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]
Probab=21.19 E-value=1.7e+02 Score=22.90 Aligned_cols=40 Identities=18% Similarity=0.307 Sum_probs=27.9
Q ss_pred CchhHH-HhHHHHHHHHHH---------cCCccEEEEEecCCCCc-cccCC
Q 035140 18 TPDTMV-QGLQYLKASIKA---------MSIKVIEIQVVSPNKDS-QILSH 57 (72)
Q Consensus 18 ~Pe~L~-~Ql~~i~~~l~~---------lgi~~~~v~IvS~DKD~-QLv~~ 57 (72)
.|.-|. --++.+|..++| .++|.+.|.|+.||-|+ =.++|
T Consensus 257 vPshL~ymlfElfKNamrATve~h~~~~~~~ppI~V~V~~gdeDl~ikISD 307 (414)
T KOG0787|consen 257 VPSHLYYMLFELFKNAMRATVEHHGDDGDELPPIKVTVAKGDEDLLIKISD 307 (414)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHhccCCCCCCCeEEEEecCCcceEEEEec
Confidence 355553 235566666665 45788999999999999 66665
No 129
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=21.11 E-value=93 Score=24.69 Aligned_cols=39 Identities=15% Similarity=0.218 Sum_probs=26.5
Q ss_pred HHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEEEEe
Q 035140 23 VQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 23 ~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
...+.++.+.|. +.+. .++|||-|++| .=|..+|.-++.
T Consensus 186 ~~~i~WLe~~L~--~~~g-tviiVSHDR~FLd~V~t~I~~ld~ 225 (530)
T COG0488 186 LESIEWLEDYLK--RYPG-TVIVVSHDRYFLDNVATHILELDR 225 (530)
T ss_pred HHHHHHHHHHHH--hCCC-cEEEEeCCHHHHHHHhhheEEecC
Confidence 345667777665 3334 68899999999 767666555543
No 130
>PTZ00472 serine carboxypeptidase (CBP1); Provisional
Probab=20.97 E-value=94 Score=23.90 Aligned_cols=22 Identities=5% Similarity=0.152 Sum_probs=13.9
Q ss_pred HHHHHHHHHcCCccEEEEEecCCCCc
Q 035140 27 QYLKASIKAMSIKVIEIQVVSPNKDS 52 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~DKD~ 52 (72)
+.+.++|+. | +.|.|++||.|+
T Consensus 355 ~~l~~LL~~-g---ikVLiYnGd~D~ 376 (462)
T PTZ00472 355 YTVPGLLED-G---VRVMIYAGDMDF 376 (462)
T ss_pred HHHHHHHhc-C---ceEEEEECCcCe
Confidence 344445542 4 347799999996
No 131
>PRK05321 nicotinate phosphoribosyltransferase; Provisional
Probab=20.75 E-value=1.8e+02 Score=22.38 Aligned_cols=44 Identities=14% Similarity=0.052 Sum_probs=30.9
Q ss_pred cccCCCCCCchhHHHhHHHHHHHHHHcCCcc-EEEEEecCCCCc-cc
Q 035140 10 SYKNNRPPTPDTMVQGLQYLKASIKAMSIKV-IEIQVVSPNKDS-QI 54 (72)
Q Consensus 10 ~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~-~~v~IvS~DKD~-QL 54 (72)
.|++=|-..+ ++..+-..+.+.++.+|+.. -..+|+|+|=|. .+
T Consensus 276 ~~~GvRlDSG-D~~~~~~k~~~~~~~~G~dp~~k~Iv~S~~Lde~~i 321 (400)
T PRK05321 276 LFDGLRHDSG-DPIEWGEKAIAHYEKLGIDPRTKTLVFSDGLDFDKA 321 (400)
T ss_pred cCCEEeeCCC-CHHHHHHHHHHHHHHcCCCCCCeEEEEeCCCCHHHH
Confidence 3455555444 56666777778899999954 447899999886 54
No 132
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=20.54 E-value=1.4e+02 Score=18.74 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=18.8
Q ss_pred HHHHHHHHHcCCccEEEEEecCCCCc
Q 035140 27 QYLKASIKAMSIKVIEIQVVSPNKDS 52 (72)
Q Consensus 27 ~~i~~~l~~lgi~~~~v~IvS~DKD~ 52 (72)
..++++++.+||+.+..+|++ +.++
T Consensus 90 ~~L~~~~~~l~I~llDHiIv~-~~~~ 114 (123)
T PF04002_consen 90 RRLKKAARLLGIELLDHIIVG-DGGY 114 (123)
T ss_dssp HHHHHHHHHHT-EEEEEEEEE-SSEE
T ss_pred HHHHHHHHHcCCeeeeEEEEe-CCcE
Confidence 467889999999999988886 4343
No 133
>PF13905 Thioredoxin_8: Thioredoxin-like; PDB: 1FG4_A 1I5G_A 1OC8_B 1O6J_A 1OC9_B 1O81_A 3FKF_A 1O85_A 1O7U_A 1O8W_A ....
Probab=20.53 E-value=1.8e+02 Score=16.31 Aligned_cols=31 Identities=26% Similarity=0.220 Sum_probs=23.3
Q ss_pred HHHhHHHHHHHHHHcC-CccEEEEEecCCCCc
Q 035140 22 MVQGLQYLKASIKAMS-IKVIEIQVVSPNKDS 52 (72)
Q Consensus 22 L~~Ql~~i~~~l~~lg-i~~~~v~IvS~DKD~ 52 (72)
=...+|.++++.+.++ =.-++++-||.|+|.
T Consensus 16 c~~~~~~l~~l~~~~~~~~~v~~v~Vs~d~~~ 47 (95)
T PF13905_consen 16 CKKELPKLKELYKKYKKKDDVEFVFVSLDEDE 47 (95)
T ss_dssp HHHHHHHHHHHHHHHTTTTTEEEEEEE-SSSH
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEEEEEeCCCH
Confidence 3556788888888888 667778888889885
No 134
>PRK13015 3-dehydroquinate dehydratase; Reviewed
Probab=20.53 E-value=1.1e+02 Score=20.64 Aligned_cols=27 Identities=19% Similarity=0.459 Sum_probs=18.7
Q ss_pred chhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 19 PDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
|-.+..-=-.+++.+.++++|++||-|
T Consensus 75 pga~THtSiAl~DAl~~~~~P~VEVHi 101 (146)
T PRK13015 75 PGAYTHTSVAIRDALAALELPVIEVHI 101 (146)
T ss_pred chHHhhhHHHHHHHHHcCCCCEEEEEc
Confidence 344432233578999999999999554
No 135
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=20.42 E-value=83 Score=19.21 Aligned_cols=28 Identities=7% Similarity=0.063 Sum_probs=19.4
Q ss_pred HHHHHHHcCCccE-------E-------EEEecCCCCc-cccC
Q 035140 29 LKASIKAMSIKVI-------E-------IQVVSPNKDS-QILS 56 (72)
Q Consensus 29 i~~~l~~lgi~~~-------~-------v~IvS~DKD~-QLv~ 56 (72)
..++...+|+... . .+.+|+|-|+ -+|+
T Consensus 27 ~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D~DL~e~v~ 69 (86)
T cd06409 27 RTLISQRLGDDDFETHLYALSYVDDEGDIVLITSDSDLVAAVL 69 (86)
T ss_pred HHHHHHHhCCccccCCcccEEEEcCCCCEEEEeccchHHHHHH
Confidence 3455566777653 1 8889999999 7763
No 136
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=20.14 E-value=1.6e+02 Score=22.75 Aligned_cols=41 Identities=20% Similarity=0.388 Sum_probs=28.0
Q ss_pred ccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEEEEEecCC
Q 035140 6 TLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQVVSPN 49 (72)
Q Consensus 6 ~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~v~IvS~D 49 (72)
++..-|. .++||.|.+.=-+--++++.+|++-+.+-+=++|
T Consensus 138 ~~~~ky~---~pt~ealveSAl~~a~~~e~l~f~~i~iS~K~Sd 178 (361)
T COG0821 138 RLLEKYG---GPTPEALVESALEHAELLEELGFDDIKVSVKASD 178 (361)
T ss_pred HHHHHhc---CCCHHHHHHHHHHHHHHHHHCCCCcEEEEEEcCC
Confidence 4445565 5699999765444456999999998775554444
No 137
>PRK05395 3-dehydroquinate dehydratase; Provisional
Probab=20.06 E-value=1.1e+02 Score=20.58 Aligned_cols=27 Identities=30% Similarity=0.482 Sum_probs=19.0
Q ss_pred chhHHHhHHHHHHHHHHcCCccEEEEE
Q 035140 19 PDTMVQGLQYLKASIKAMSIKVIEIQV 45 (72)
Q Consensus 19 Pe~L~~Ql~~i~~~l~~lgi~~~~v~I 45 (72)
|-.+..-=-.+++.+.++++|++||-|
T Consensus 75 pga~THtSiAl~DAl~~~~~P~VEVHi 101 (146)
T PRK05395 75 PGAYTHTSVALRDALAAVSIPVIEVHL 101 (146)
T ss_pred chHHHHHHHHHHHHHHcCCCCEEEEec
Confidence 444433334678999999999999554
No 138
>PF08734 GYD: GYD domain; InterPro: IPR014845 These proteins of unknown function are usually less than 100 amino acids in length. They may belong to the dimeric alpha/beta barrel superfamily.
Probab=20.01 E-value=2.1e+02 Score=17.12 Aligned_cols=34 Identities=18% Similarity=0.089 Sum_probs=26.7
Q ss_pred HHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccC
Q 035140 23 VQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILS 56 (72)
Q Consensus 23 ~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~ 56 (72)
..-...++++++.+|..+......-|+-|+ -+++
T Consensus 19 ~~R~~a~~~~~e~~Gg~l~~~y~t~G~yD~v~i~e 53 (91)
T PF08734_consen 19 PDRAEAVRALIEALGGKLKSFYWTLGEYDFVVIVE 53 (91)
T ss_pred HHHHHHHHHHHHHcCCEEEEEEEecCCCCEEEEEE
Confidence 334567889999999999998888888887 6553
Done!