Query 035086
Match_columns 73
No_of_seqs 110 out of 977
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 09:04:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035086.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035086hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0035 Upp Uracil phosphoribo 99.9 7E-25 1.5E-29 158.4 4.7 55 8-62 156-210 (210)
2 PF14681 UPRTase: Uracil phosp 99.9 5.3E-25 1.2E-29 155.1 2.8 56 6-61 152-207 (207)
3 PLN02541 uracil phosphoribosyl 99.9 1.4E-24 3E-29 158.5 5.0 55 7-61 189-243 (244)
4 TIGR01091 upp uracil phosphori 99.9 7.2E-23 1.6E-27 144.3 5.0 55 8-62 153-207 (207)
5 PRK00129 upp uracil phosphorib 99.9 8.8E-23 1.9E-27 143.8 4.8 55 8-62 155-209 (209)
6 KOG4203 Armadillo/beta-Catenin 99.2 5.1E-12 1.1E-16 99.4 2.7 53 10-62 421-473 (473)
7 KOG1017 Predicted uracil phosp 97.1 0.00037 8E-09 52.0 2.9 47 7-62 221-267 (267)
8 PF09960 DUF2194: Uncharacteri 73.0 6.3 0.00014 32.6 4.3 34 12-45 402-435 (585)
9 KOG2255 Peptidyl-tRNA hydrolas 49.7 14 0.0003 27.6 2.1 31 34-64 28-58 (224)
10 smart00785 AARP2CN AARP2CN (NU 47.3 8.6 0.00019 23.9 0.6 10 46-55 63-72 (83)
11 PF08142 AARP2CN: AARP2CN (NUC 46.7 8.7 0.00019 23.9 0.6 8 48-55 67-74 (85)
12 PF15608 PELOTA_1: PELOTA RNA 45.7 8.7 0.00019 25.2 0.5 16 40-55 33-48 (100)
13 PF09550 DUF2376: Conserved hy 44.5 22 0.00047 20.0 1.9 15 15-29 29-43 (43)
14 COG2159 Predicted metal-depend 41.8 28 0.00061 25.8 2.7 24 15-38 178-201 (293)
15 PF02991 Atg8: Autophagy prote 40.5 57 0.0012 21.1 3.7 31 20-50 6-41 (104)
16 PF04909 Amidohydro_2: Amidohy 39.6 17 0.00037 24.5 1.2 23 15-37 150-172 (273)
17 cd01611 GABARAP Ubiquitin doma 36.0 73 0.0016 20.8 3.7 32 20-51 14-50 (112)
18 COG0118 HisH Glutamine amidotr 35.5 35 0.00077 25.0 2.4 26 31-56 28-53 (204)
19 COG0031 CysK Cysteine synthase 35.3 55 0.0012 25.1 3.5 36 16-53 182-224 (300)
20 PF14492 EFG_II: Elongation Fa 34.5 51 0.0011 19.6 2.6 31 18-53 23-53 (75)
21 TIGR02216 phage_TIGR02216 phag 33.6 39 0.00085 20.4 2.0 14 16-29 46-59 (60)
22 KOG1654 Microtubule-associated 33.4 69 0.0015 21.7 3.3 32 19-50 17-53 (116)
23 smart00546 CUE Domain that may 32.7 41 0.00088 17.8 1.8 15 17-31 3-17 (43)
24 PF01148 CTP_transf_1: Cytidyl 30.8 21 0.00046 24.4 0.5 22 39-60 223-244 (259)
25 KOG4388 Hormone-sensitive lipa 30.8 36 0.00079 29.5 2.0 23 22-44 782-804 (880)
26 PRK00125 pyrF orotidine 5'-pho 30.4 68 0.0015 24.0 3.2 29 13-55 194-224 (278)
27 cd03144 GATase1_ScBLP_like Typ 30.2 39 0.00086 22.2 1.7 42 16-58 11-59 (114)
28 cd08472 PBP2_CrgA_like_3 The C 29.0 62 0.0013 19.9 2.4 19 17-35 17-35 (202)
29 cd08436 PBP2_LTTR_like_3 The C 28.1 65 0.0014 19.5 2.4 19 17-35 16-34 (194)
30 cd08412 PBP2_PAO1_like The C-t 27.7 68 0.0015 19.5 2.4 18 17-34 16-33 (198)
31 cd08464 PBP2_DntR_like_2 The C 27.5 67 0.0015 19.7 2.4 19 17-35 16-34 (200)
32 PF02550 AcetylCoA_hydro: Acet 26.6 42 0.0009 23.2 1.4 35 22-57 117-151 (198)
33 cd08461 PBP2_DntR_like_3 The C 26.5 72 0.0016 19.5 2.4 17 17-33 16-32 (198)
34 KOG2523 Predicted RNA-binding 26.3 48 0.001 24.0 1.7 46 26-71 91-136 (181)
35 cd05311 NAD_bind_2_malic_enz N 26.1 22 0.00047 25.3 -0.1 12 42-53 158-169 (226)
36 PF05655 AvrD: Pseudomonas avi 25.7 42 0.0009 25.9 1.4 21 51-71 13-33 (311)
37 cd08441 PBP2_MetR The C-termin 25.1 76 0.0016 19.5 2.3 18 17-34 16-33 (198)
38 cd08451 PBP2_BudR The C-termin 25.0 79 0.0017 19.2 2.4 19 16-34 16-34 (199)
39 cd08470 PBP2_CrgA_like_1 The C 25.0 78 0.0017 19.4 2.3 19 17-35 17-35 (197)
40 cd08450 PBP2_HcaR The C-termin 24.9 78 0.0017 19.3 2.3 19 17-35 16-34 (196)
41 cd08471 PBP2_CrgA_like_2 The C 24.6 82 0.0018 19.3 2.4 19 17-35 17-35 (201)
42 PF01887 SAM_adeno_trans: S-ad 24.2 1.3E+02 0.0029 22.1 3.8 25 20-44 50-74 (258)
43 cd08482 PBP2_TrpI The C-termin 24.1 80 0.0017 19.5 2.3 19 17-35 16-34 (195)
44 TIGR02127 pyrF_sub2 orotidine 24.0 1.1E+02 0.0023 22.7 3.3 26 16-55 197-222 (261)
45 PRK05426 peptidyl-tRNA hydrola 23.7 37 0.0008 24.0 0.7 19 46-64 3-21 (189)
46 cd08430 PBP2_IlvY The C-termin 22.9 72 0.0016 19.4 1.9 19 17-35 16-34 (199)
47 cd08444 PBP2_Cbl The C-termina 22.9 87 0.0019 19.5 2.3 19 16-34 15-33 (198)
48 cd02065 B12-binding_like B12 b 22.9 1.4E+02 0.003 18.0 3.2 37 17-53 67-108 (125)
49 cd08467 PBP2_SyrM The C-termin 22.9 90 0.002 19.5 2.4 19 17-35 16-34 (200)
50 PF04327 DUF464: Protein of un 22.8 77 0.0017 19.9 2.0 16 17-32 87-103 (103)
51 cd08481 PBP2_GcdR_like The C-t 22.7 64 0.0014 19.5 1.6 18 17-34 16-33 (194)
52 PF02845 CUE: CUE domain; Int 22.7 87 0.0019 16.5 2.0 15 17-31 2-16 (42)
53 cd08452 PBP2_AlsR The C-termin 22.7 74 0.0016 19.8 1.9 17 17-33 16-32 (197)
54 cd08434 PBP2_GltC_like The sub 22.6 88 0.0019 18.8 2.2 19 17-35 16-34 (195)
55 cd08427 PBP2_LTTR_like_2 The C 22.6 93 0.002 18.8 2.3 19 17-35 16-34 (195)
56 cd08473 PBP2_CrgA_like_4 The C 22.5 92 0.002 19.0 2.3 20 17-36 19-38 (202)
57 cd08479 PBP2_CrgA_like_9 The C 22.5 74 0.0016 19.5 1.9 17 17-33 17-33 (198)
58 cd08438 PBP2_CidR The C-termin 22.4 92 0.002 18.8 2.3 19 17-35 16-34 (197)
59 cd08437 PBP2_MleR The substrat 22.4 88 0.0019 19.2 2.2 19 17-35 16-34 (198)
60 cd08487 PBP2_BlaA The C-termin 22.3 91 0.002 19.0 2.3 19 17-35 16-34 (189)
61 cd08448 PBP2_LTTR_aromatics_li 21.9 1E+02 0.0022 18.7 2.4 18 17-34 16-33 (197)
62 cd08460 PBP2_DntR_like_1 The C 21.8 99 0.0021 19.2 2.4 19 16-34 15-33 (200)
63 cd08422 PBP2_CrgA_like The C-t 21.8 95 0.0021 18.7 2.3 19 17-35 17-35 (197)
64 cd08478 PBP2_CrgA The C-termin 21.7 96 0.0021 19.1 2.3 18 17-34 19-36 (199)
65 cd08477 PBP2_CrgA_like_8 The C 21.6 1E+02 0.0022 18.7 2.4 19 17-35 17-35 (197)
66 KOG1257 NADP+-dependent malic 21.5 45 0.00096 28.1 0.9 26 27-52 453-478 (582)
67 cd05312 NAD_bind_1_malic_enz N 21.3 54 0.0012 24.8 1.3 15 39-53 181-195 (279)
68 PF01281 Ribosomal_L9_N: Ribos 21.1 38 0.00082 19.3 0.3 10 48-57 9-18 (48)
69 cd02068 radical_SAM_B12_BD B12 20.9 1E+02 0.0022 19.3 2.3 36 18-53 57-100 (127)
70 cd08475 PBP2_CrgA_like_6 The C 20.9 1E+02 0.0023 18.7 2.3 18 17-34 17-34 (199)
71 PF10945 DUF2629: Protein of u 20.7 67 0.0015 18.3 1.3 16 14-29 23-38 (44)
72 KOG0907 Thioredoxin [Posttrans 20.6 1.4E+02 0.0031 19.0 3.0 21 19-39 42-62 (106)
73 cd08414 PBP2_LTTR_aromatics_li 20.5 1.1E+02 0.0024 18.4 2.4 18 17-34 16-33 (197)
74 cd08462 PBP2_NodD The C-termin 20.3 1.1E+02 0.0024 19.0 2.4 19 17-35 16-34 (200)
75 cd08442 PBP2_YofA_SoxR_like Th 20.3 1.1E+02 0.0024 18.5 2.3 18 17-34 16-33 (193)
76 cd08465 PBP2_ToxR The C-termin 20.3 1.1E+02 0.0023 19.2 2.4 18 17-34 16-33 (200)
77 cd08466 PBP2_LeuO The C-termin 20.2 1.1E+02 0.0025 18.6 2.4 17 17-33 16-32 (200)
78 cd08486 PBP2_CbnR The C-termin 20.1 1.1E+02 0.0023 19.2 2.3 17 17-33 17-33 (198)
79 PF13905 Thioredoxin_8: Thiore 20.1 1.4E+02 0.0031 17.1 2.7 27 15-41 18-47 (95)
80 cd08431 PBP2_HupR The C-termin 20.1 1E+02 0.0022 18.8 2.2 19 17-35 16-34 (195)
81 PF12362 DUF3646: DNA polymera 20.1 98 0.0021 20.4 2.2 19 16-34 97-115 (117)
No 1
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=99.91 E-value=7e-25 Score=158.36 Aligned_cols=55 Identities=44% Similarity=0.740 Sum_probs=51.5
Q ss_pred hcccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCCC
Q 035086 8 LCVSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGTD 62 (73)
Q Consensus 8 l~~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt~ 62 (73)
+.+++++|||+||+++.++||+++||||+||++|||++||+||+||||||+|||+
T Consensus 156 I~~v~~vAapeGi~~v~~~~p~v~I~ta~iD~~Lne~gYIvPGLGDaGDR~fGt~ 210 (210)
T COG0035 156 IKVVSLVAAPEGIKAVEKAHPDVEIYTAAIDEGLNEKGYIVPGLGDAGDRLFGTK 210 (210)
T ss_pred EEEEEEEecHHHHHHHHHhCCCCeEEEEEeccccccCCCCccCCCcccccccCCC
Confidence 4455669999999999999999999999999999999999999999999999985
No 2
>PF14681 UPRTase: Uracil phosphoribosyltransferase; PDB: 1V9S_B 1UPF_A 1UPU_D 1JLR_B 1BD4_A 1BD3_C 1JLS_D 1XTV_C 1XTU_H 3G6W_C ....
Probab=99.90 E-value=5.3e-25 Score=155.07 Aligned_cols=56 Identities=39% Similarity=0.771 Sum_probs=50.1
Q ss_pred hhhcccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCC
Q 035086 6 SALCVSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGT 61 (73)
Q Consensus 6 ~~l~~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt 61 (73)
+.+.+++++||++||+++.++||+++||||+||++||+++||+||+||||||||||
T Consensus 152 ~~I~~v~~ias~~Gl~~l~~~~P~v~I~ta~iD~~L~~~~~i~PGlGD~GdR~fgT 207 (207)
T PF14681_consen 152 ENIIIVSVIASPEGLERLLKAFPDVRIYTAAIDPELNENGYIVPGLGDAGDRYFGT 207 (207)
T ss_dssp GEEEEEEEEEEHHHHHHHHHHSTTSEEEEEEEESEEETTSEEESS-S-HHHHHHT-
T ss_pred ceEEEEEEEecHHHHHHHHHhCCCeEEEEEEEccccCCCCCccCCCCChHhcccCc
Confidence 34567788999999999999999999999999999999999999999999999997
No 3
>PLN02541 uracil phosphoribosyltransferase
Probab=99.90 E-value=1.4e-24 Score=158.48 Aligned_cols=55 Identities=35% Similarity=0.605 Sum_probs=52.6
Q ss_pred hhcccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCC
Q 035086 7 ALCVSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGT 61 (73)
Q Consensus 7 ~l~~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt 61 (73)
.+.++|+||||+||+++.++||+++||||+||++||+++||+|||||||||||||
T Consensus 189 ~I~~v~~ias~~Gl~~i~~~fP~v~I~ta~ID~~Lne~~yIvPGlGDaGDR~fGt 243 (244)
T PLN02541 189 QIRVVCAVAAPPALKKLSEKFPGLHVYAGIIDEEVNEKGYIVPGLGDAGDRSFGT 243 (244)
T ss_pred cEEEEEEEECHHHHHHHHHHCcCCEEEEEEECccccCCCcCcCCCCCccccccCC
Confidence 4667788999999999999999999999999999999999999999999999998
No 4
>TIGR01091 upp uracil phosphoribosyltransferase. that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins.
Probab=99.87 E-value=7.2e-23 Score=144.26 Aligned_cols=55 Identities=40% Similarity=0.675 Sum_probs=51.7
Q ss_pred hcccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCCC
Q 035086 8 LCVSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGTD 62 (73)
Q Consensus 8 l~~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt~ 62 (73)
+.+++++++|+|++++.++||+++|||++||++||+++||+||+||||||||||.
T Consensus 153 I~v~~ll~~~~gl~~l~~~~p~v~i~~~~id~~l~~~~yivPGlGd~Gdr~fgt~ 207 (207)
T TIGR01091 153 IKVLSIVAAPEGIEAVEKAHPDVDIYTAAIDEKLNDNGYIVPGLGDAGDRAFGTK 207 (207)
T ss_pred EEEEEEecCHHHHHHHHHHCCCCEEEEEEECCCccCCccCcCCCCCccccccCCC
Confidence 4556779999999999999999999999999999999999999999999999983
No 5
>PRK00129 upp uracil phosphoribosyltransferase; Reviewed
Probab=99.87 E-value=8.8e-23 Score=143.76 Aligned_cols=55 Identities=38% Similarity=0.645 Sum_probs=51.4
Q ss_pred hcccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCCC
Q 035086 8 LCVSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGTD 62 (73)
Q Consensus 8 l~~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt~ 62 (73)
+.+++++++++|++++.++||+++||||+||++||+++||+||+||||||||||.
T Consensus 155 I~~~~ll~~~~gl~~l~~~~p~v~i~~~~iD~~l~~~~yi~PGlGd~Gdr~fgt~ 209 (209)
T PRK00129 155 IKVLCLVAAPEGIKALEEAHPDVEIYTAAIDEKLNEHGYIVPGLGDAGDRLFGTK 209 (209)
T ss_pred EEEEEEecCHHHHHHHHHHCCCcEEEEEeecCCcCCCCcCCCCCCCccccccCCC
Confidence 4455679999999999999999999999999999999999999999999999983
No 6
>KOG4203 consensus Armadillo/beta-Catenin/plakoglobin [Signal transduction mechanisms; Cytoskeleton]
Probab=99.22 E-value=5.1e-12 Score=99.37 Aligned_cols=53 Identities=58% Similarity=0.955 Sum_probs=49.9
Q ss_pred ccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCCC
Q 035086 10 VSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGTD 62 (73)
Q Consensus 10 ~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt~ 62 (73)
+++++++++|+++++.+||.++++|+++|+.+|+++|++||+|||||||||+.
T Consensus 421 ~~~ll~~~~~~~~~~~~f~~v~~v~~~~d~~~~~~~~~~pg~g~~~dryfg~~ 473 (473)
T KOG4203|consen 421 FLNLLAAPQGIHEVAYAFPKVKIVTSQIDKLLNEKRYVVPGLGNFGDRYFGTD 473 (473)
T ss_pred HHHHHhhhhhhhHHHHhcccceeehhhhcccccccceECcccccchhhccCCC
Confidence 44558999999999999999999999999999999999999999999999973
No 7
>KOG1017 consensus Predicted uracil phosphoribosyltransferase [General function prediction only]
Probab=97.15 E-value=0.00037 Score=52.00 Aligned_cols=47 Identities=34% Similarity=0.641 Sum_probs=41.5
Q ss_pred hhcccccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCcccccccCCC
Q 035086 7 ALCVSESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGTD 62 (73)
Q Consensus 7 ~l~~~svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt~ 62 (73)
++.++|++.+|-|.+.+.++||.++|+|+.|.+--.+ .||..||||.
T Consensus 221 ~IiL~sLF~tP~gak~i~~~fP~itiltseihpvaPn---------HFgqkYFGtd 267 (267)
T KOG1017|consen 221 NIILVSLFITPTGAKNITRKFPYITILTSEIHPVAPN---------HFGQKYFGTD 267 (267)
T ss_pred cEEEEEeeecchhhHHHHHhCCeEEEEeecceecCcc---------cccchhcCCC
Confidence 4667889999999999999999999999999997765 4789999974
No 8
>PF09960 DUF2194: Uncharacterized protein conserved in bacteria (DUF2194); InterPro: IPR018695 This family of prokaryotic proteins has no known function; however it may be a membrane protein.
Probab=73.03 E-value=6.3 Score=32.59 Aligned_cols=34 Identities=21% Similarity=0.184 Sum_probs=27.4
Q ss_pred ccccCHHHHHHHHHhCCCcEEEEEeccCCCCCCC
Q 035086 12 ESHQAPQGVHVVCKSFPRLKIVTSEIDIGLNEDF 45 (73)
Q Consensus 12 svias~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~ 45 (73)
|=+-+++|.+.+.+.||+++++.+.-..+-.+..
T Consensus 402 SNils~eG~e~L~~~~P~ik~IaS~Y~~~~~~~~ 435 (585)
T PF09960_consen 402 SNILSEEGREALKKAFPEIKTIASLYFGDDEEGE 435 (585)
T ss_pred ccccCHHHHHHHHHhCCCeEEEEEeeecCCcCCc
Confidence 3457899999999999999999888776655433
No 9
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=49.71 E-value=14 Score=27.58 Aligned_cols=31 Identities=23% Similarity=0.469 Sum_probs=25.5
Q ss_pred EEeccCCCCCCCeeecCCCcccccccCCCCC
Q 035086 34 TSEIDIGLNEDFRVIPGMGEFGDRYFGTDDD 64 (73)
Q Consensus 34 ta~ID~~Ld~~~yIvPGlGD~GDR~fgt~~~ 64 (73)
.+..-+....+-+++-||||.|..|.||..+
T Consensus 28 ~c~l~~~~~~k~wli~GLGNPg~~y~gTRHn 58 (224)
T KOG2255|consen 28 HCDLKPRVSIKPWLIVGLGNPGSKYVGTRHN 58 (224)
T ss_pred eeecccCCCCCceEEEecCCCcccccccchh
Confidence 4456677777789999999999999999754
No 10
>smart00785 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU PUBMED:15112237.
Probab=47.25 E-value=8.6 Score=23.93 Aligned_cols=10 Identities=50% Similarity=1.075 Sum_probs=7.7
Q ss_pred eeecCCCccc
Q 035086 46 RVIPGMGEFG 55 (73)
Q Consensus 46 yIvPGlGD~G 55 (73)
-=+||+|||-
T Consensus 63 VHIpG~GDfq 72 (83)
T smart00785 63 VHIPGLGDFQ 72 (83)
T ss_pred EEeCCcCCeE
Confidence 3479999973
No 11
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=46.73 E-value=8.7 Score=23.92 Aligned_cols=8 Identities=63% Similarity=1.460 Sum_probs=6.8
Q ss_pred ecCCCccc
Q 035086 48 IPGMGEFG 55 (73)
Q Consensus 48 vPGlGD~G 55 (73)
+||+|||-
T Consensus 67 IpG~GDFq 74 (85)
T PF08142_consen 67 IPGVGDFQ 74 (85)
T ss_pred eCCcCCeE
Confidence 79999974
No 12
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=45.71 E-value=8.7 Score=25.24 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=13.6
Q ss_pred CCCCCCeeecCCCccc
Q 035086 40 GLNEDFRVIPGMGEFG 55 (73)
Q Consensus 40 ~Ld~~~yIvPGlGD~G 55 (73)
++++-.+|.||+|.+-
T Consensus 33 gI~diN~IKPGIgEaT 48 (100)
T PF15608_consen 33 GISDINLIKPGIGEAT 48 (100)
T ss_pred CCCCcccccCChhHHH
Confidence 6778889999999864
No 13
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=44.45 E-value=22 Score=20.02 Aligned_cols=15 Identities=13% Similarity=0.361 Sum_probs=13.1
Q ss_pred cCHHHHHHHHHhCCC
Q 035086 15 QAPQGVHVVCKSFPR 29 (73)
Q Consensus 15 as~~Gi~~v~~~fP~ 29 (73)
-+..+++++.++|||
T Consensus 29 l~R~~L~~Lm~~~PD 43 (43)
T PF09550_consen 29 LDRAELDALMRRFPD 43 (43)
T ss_pred CCHHHHHHHHHHCcC
Confidence 367899999999997
No 14
>COG2159 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]
Probab=41.77 E-value=28 Score=25.80 Aligned_cols=24 Identities=33% Similarity=0.551 Sum_probs=20.5
Q ss_pred cCHHHHHHHHHhCCCcEEEEEecc
Q 035086 15 QAPQGVHVVCKSFPRLKIVTSEID 38 (73)
Q Consensus 15 as~~Gi~~v~~~fP~v~Ivta~ID 38 (73)
+.|-=++.++.+||+++|+.+..=
T Consensus 178 ~~p~~~~~va~~fP~l~IVl~H~G 201 (293)
T COG2159 178 SDPLYLDDVARKFPELKIVLGHMG 201 (293)
T ss_pred CCchHHHHHHHHCCCCcEEEEecC
Confidence 556678999999999999998774
No 15
>PF02991 Atg8: Autophagy protein Atg8 ubiquitin like; InterPro: IPR004241 Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N terminus and the C terminus of Atg19. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [] Related proteins that belong to this group include the human ganglioside expression factor and a symbiosis-related fungal protein.; PDB: 3ECI_A 3D32_B 1GNU_A 1KM7_A 1KLV_A 1KOT_A 3DOW_A 1KJT_A 1V49_A 2ZJD_C ....
Probab=40.51 E-value=57 Score=21.14 Aligned_cols=31 Identities=10% Similarity=0.323 Sum_probs=20.5
Q ss_pred HHHHHHhCCC-cEEEEEecc----CCCCCCCeeecC
Q 035086 20 VHVVCKSFPR-LKIVTSEID----IGLNEDFRVIPG 50 (73)
Q Consensus 20 i~~v~~~fP~-v~Ivta~ID----~~Ld~~~yIvPG 50 (73)
.+++.++||+ +.|++=-.. +.||.+.|++|.
T Consensus 6 ~~~ir~kyP~~IPVIvEr~~~s~lp~ldk~KfLvp~ 41 (104)
T PF02991_consen 6 SERIREKYPDKIPVIVERYPKSKLPDLDKKKFLVPK 41 (104)
T ss_dssp HHHHHHHSTTEEEEEEEE-TTSSS---SSSEEEEET
T ss_pred HHHHHHHCCCccEEEEEEccCCChhhcCccEEEEcC
Confidence 4678899999 666654433 366888899996
No 16
>PF04909 Amidohydro_2: Amidohydrolase; InterPro: IPR006992 These proteins are related to the metal-dependent hydrolase superfamily []. The family includes 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase which converts alpha-amino-beta-carboxymuconate-epsilon- semialdehyde (ACMS) to alpha-aminomuconate semialdehyde (AMS). ACMS can be converted non-enzymatically to quinolate, a potent endogenous excitoxin of neuronal cells which is implicated in the pathogenesis of various neurodegenerative disorders. In the presence of AMCSD, ACMS is converted to AMS, a benign catabolite. 2-amino-3-(3-oxoprop-2-enyl)-but-2-enedioate = 2-aminomuconate semialdehyde + CO2. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2QPX_A 4D8L_A 3K4W_I 3IRS_B 4DZI_B 3S4T_G 2GWG_B 3IJ6_A 2DVX_C 2DVT_C ....
Probab=39.65 E-value=17 Score=24.53 Aligned_cols=23 Identities=22% Similarity=0.590 Sum_probs=18.2
Q ss_pred cCHHHHHHHHHhCCCcEEEEEec
Q 035086 15 QAPQGVHVVCKSFPRLKIVTSEI 37 (73)
Q Consensus 15 as~~Gi~~v~~~fP~v~Ivta~I 37 (73)
+.+.=+..+.++||+++|+.+..
T Consensus 150 ~~~~~~~~~~~~~P~l~ii~~H~ 172 (273)
T PF04909_consen 150 ADPEELEELLERFPDLRIILAHL 172 (273)
T ss_dssp HHHHHHTTHHHHSTTSEEEESGG
T ss_pred HHHHHHHHHHHHhcCCeEEEecC
Confidence 45666788999999999987643
No 17
>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein. GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=36.03 E-value=73 Score=20.81 Aligned_cols=32 Identities=13% Similarity=0.341 Sum_probs=21.7
Q ss_pred HHHHHHhCCC-cEEEEEecc----CCCCCCCeeecCC
Q 035086 20 VHVVCKSFPR-LKIVTSEID----IGLNEDFRVIPGM 51 (73)
Q Consensus 20 i~~v~~~fP~-v~Ivta~ID----~~Ld~~~yIvPGl 51 (73)
.+++.++||+ +.|++=... |.|+.+.|++|+=
T Consensus 14 ~~~ir~kyp~~iPVIvE~~~~~~~p~l~k~KflVp~~ 50 (112)
T cd01611 14 VERIRAKYPDRIPVIVERYPKSDLPDLDKKKYLVPSD 50 (112)
T ss_pred HHHHHHHCCCceEEEEEEcCCCCcccccCceEEecCC
Confidence 4668889999 555543322 4678888999963
No 18
>COG0118 HisH Glutamine amidotransferase [Amino acid transport and metabolism]
Probab=35.45 E-value=35 Score=25.00 Aligned_cols=26 Identities=31% Similarity=0.607 Sum_probs=19.7
Q ss_pred EEEEEeccCCCCCCCeeecCCCcccc
Q 035086 31 KIVTSEIDIGLNEDFRVIPGMGEFGD 56 (73)
Q Consensus 31 ~Ivta~ID~~Ld~~~yIvPGlGD~GD 56 (73)
..+|..-++-...++-|+||.|.|++
T Consensus 28 ~~vs~d~~~i~~AD~liLPGVGaf~~ 53 (204)
T COG0118 28 VVVSRDPEEILKADKLILPGVGAFGA 53 (204)
T ss_pred eEEecCHHHHhhCCEEEecCCCCHHH
Confidence 45555555556788999999999876
No 19
>COG0031 CysK Cysteine synthase [Amino acid transport and metabolism]
Probab=35.26 E-value=55 Score=25.10 Aligned_cols=36 Identities=28% Similarity=0.365 Sum_probs=23.6
Q ss_pred CHHHHHHHH-HhCCCcEEEEEeccCCC------CCCCeeecCCCc
Q 035086 16 APQGVHVVC-KSFPRLKIVTSEIDIGL------NEDFRVIPGMGE 53 (73)
Q Consensus 16 s~~Gi~~v~-~~fP~v~Ivta~ID~~L------d~~~yIvPGlGD 53 (73)
+-.|+.+.. +++|+++++. +||.= .+..+.++|||.
T Consensus 182 TitGvar~Lk~~~p~i~iv~--vdP~~S~~~~~G~g~~~i~GIG~ 224 (300)
T COG0031 182 TITGVARYLKERNPNVRIVA--VDPEGSVLLSGGEGPHKIEGIGA 224 (300)
T ss_pred hHHHHHHHHHhhCCCcEEEE--ECCCCCcccCCCCCCcccCCCCC
Confidence 445666554 5799999875 45532 124588999986
No 20
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=34.48 E-value=51 Score=19.55 Aligned_cols=31 Identities=29% Similarity=0.536 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCc
Q 035086 18 QGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGE 53 (73)
Q Consensus 18 ~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD 53 (73)
++|+++.++-|-+++ ..|++-++ +++-|+|+
T Consensus 23 ~aL~~l~~eDP~l~~---~~d~et~e--~~l~g~Ge 53 (75)
T PF14492_consen 23 EALQKLSEEDPSLRV---ERDEETGE--LILSGMGE 53 (75)
T ss_dssp HHHHHHHHH-TTSEE---EEETTTSE--EEEEESSH
T ss_pred HHHHHHHhcCCeEEE---EEcchhce--EEEEECCH
Confidence 689999999999998 56665443 88899986
No 21
>TIGR02216 phage_TIGR02216 phage conserved hypothetical protein. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA.
Probab=33.56 E-value=39 Score=20.39 Aligned_cols=14 Identities=7% Similarity=0.318 Sum_probs=12.9
Q ss_pred CHHHHHHHHHhCCC
Q 035086 16 APQGVHVVCKSFPR 29 (73)
Q Consensus 16 s~~Gi~~v~~~fP~ 29 (73)
+..+++++..+|||
T Consensus 46 ~Ra~Ld~Lm~~fPD 59 (60)
T TIGR02216 46 DRAALDALLAAWPD 59 (60)
T ss_pred CHHHHHHHHHHCcC
Confidence 67899999999997
No 22
>KOG1654 consensus Microtubule-associated anchor protein involved in autophagy and membrane trafficking [Cytoskeleton]
Probab=33.41 E-value=69 Score=21.74 Aligned_cols=32 Identities=13% Similarity=0.395 Sum_probs=22.9
Q ss_pred HHHHHHHhCCC-cEEEEEecc----CCCCCCCeeecC
Q 035086 19 GVHVVCKSFPR-LKIVTSEID----IGLNEDFRVIPG 50 (73)
Q Consensus 19 Gi~~v~~~fP~-v~Ivta~ID----~~Ld~~~yIvPG 50 (73)
-.+++.++||+ +.+++=--. |.||.+.|+||-
T Consensus 17 E~~~Ir~kyP~riPVIvEk~~~~~lp~lDK~KyLVP~ 53 (116)
T KOG1654|consen 17 EVRRIREKYPDRIPVIVEKAGKSQLPDLDKKKYLVPD 53 (116)
T ss_pred HHHHHHHHCCCCCcEEEEecccccCcccccceeeccc
Confidence 35678999998 666654222 367888999994
No 23
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=32.73 E-value=41 Score=17.79 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.5
Q ss_pred HHHHHHHHHhCCCcE
Q 035086 17 PQGVHVVCKSFPRLK 31 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~ 31 (73)
.+.++.+.+.||++.
T Consensus 3 ~~~v~~L~~mFP~l~ 17 (43)
T smart00546 3 DEALHDLKDMFPNLD 17 (43)
T ss_pred HHHHHHHHHHCCCCC
Confidence 467899999999874
No 24
>PF01148 CTP_transf_1: Cytidylyltransferase family; InterPro: IPR000374 Phosphatidate cytidylyltransferase (2.7.7.41 from EC) [, , ] (also known as CDP- diacylglycerol synthase) (CDS) is the enzyme that catalyzes the synthesis of CDP-diacylglycerol from CTP and phosphatidate (PA): CTP + phosphatidate = diphosphate + CDP-diacylglycerol CDP-diacylglycerol is an important branch point intermediate in both prokaryotic and eukaryotic organisms. CDS is a membrane-bound enzyme.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0016020 membrane
Probab=30.81 E-value=21 Score=24.44 Aligned_cols=22 Identities=32% Similarity=0.594 Sum_probs=17.9
Q ss_pred CCCCCCCeeecCCCcccccccC
Q 035086 39 IGLNEDFRVIPGMGEFGDRYFG 60 (73)
Q Consensus 39 ~~Ld~~~yIvPGlGD~GDR~fg 60 (73)
-+.-|-|.++||=|..-||.-+
T Consensus 223 ~~iKD~g~lipghGg~lDr~d~ 244 (259)
T PF01148_consen 223 AGIKDSGNLIPGHGGILDRFDS 244 (259)
T ss_pred hhcccccccccCcCCcccchHh
Confidence 3556889999999999999743
No 25
>KOG4388 consensus Hormone-sensitive lipase HSL [Lipid transport and metabolism]
Probab=30.77 E-value=36 Score=29.52 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=20.0
Q ss_pred HHHHhCCCcEEEEEeccCCCCCC
Q 035086 22 VVCKSFPRLKIVTSEIDIGLNED 44 (73)
Q Consensus 22 ~v~~~fP~v~Ivta~ID~~Ld~~ 44 (73)
...++.|+++|++.++||-|||-
T Consensus 782 e~l~qLPp~~i~ac~mDP~LDD~ 804 (880)
T KOG4388|consen 782 EMLKQLPPVHIVACAMDPMLDDS 804 (880)
T ss_pred HHHhcCCCceEEEeccCcchhHH
Confidence 45677899999999999999885
No 26
>PRK00125 pyrF orotidine 5'-phosphate decarboxylase; Reviewed
Probab=30.40 E-value=68 Score=24.04 Aligned_cols=29 Identities=31% Similarity=0.474 Sum_probs=20.5
Q ss_pred cccC--HHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCccc
Q 035086 13 SHQA--PQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFG 55 (73)
Q Consensus 13 vias--~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~G 55 (73)
+++| |+=+.++.+.+|+.. .++||+|--|
T Consensus 194 VVgaT~p~e~~~iR~~~~~~~--------------iL~PGigaQG 224 (278)
T PRK00125 194 VVGATFPPELAAVRKILGGMP--------------LLIPGIGAQG 224 (278)
T ss_pred EECCCCHHHHHHHHHhCCCCe--------------EEeCCcCCCC
Confidence 4566 777777877777643 5889998554
No 27
>cd03144 GATase1_ScBLP_like Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Biotin-apoprotein ligase modifies proteins by covalently attaching biotin. ScBLP is known to biotinylate acety-CoA carboxylase and pyruvate carboxylase. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, the Cys residue found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow in a typical GATase1 domain is conserved.
Probab=30.18 E-value=39 Score=22.23 Aligned_cols=42 Identities=17% Similarity=0.180 Sum_probs=24.4
Q ss_pred CHHHHHHHHHhCCC---cEEEEEeccCC----CCCCCeeecCCCcccccc
Q 035086 16 APQGVHVVCKSFPR---LKIVTSEIDIG----LNEDFRVIPGMGEFGDRY 58 (73)
Q Consensus 16 s~~Gi~~v~~~fP~---v~Ivta~ID~~----Ld~~~yIvPGlGD~GDR~ 58 (73)
++.-++++.+.+.. ++.+++..-.. .+-+..|+|| |.|++-.
T Consensus 11 ~~~~~~~~~~~L~~~~~v~~~~~~~I~~~~~~~~ad~lVlPG-Ga~~~~~ 59 (114)
T cd03144 11 SPGSLKHLAELLRLYLAVSTVTADELAVGPWESKTALLVVPG-GADLPYC 59 (114)
T ss_pred CHHHHHHHHHHHhhccceeeecHHHHhcCchhhCCCEEEECC-CChHHHH
Confidence 45556666665543 44444433221 2346799999 9987643
No 28
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=28.95 E-value=62 Score=19.86 Aligned_cols=19 Identities=5% Similarity=0.158 Sum_probs=15.6
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++-+.++.++||+++|-..
T Consensus 17 ~~~l~~~~~~~P~i~v~~~ 35 (202)
T cd08472 17 IPALPDFLARYPDIELDLG 35 (202)
T ss_pred HHHHHHHHHHCCCcEEEEE
Confidence 6778999999999877654
No 29
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=28.13 E-value=65 Score=19.46 Aligned_cols=19 Identities=16% Similarity=0.256 Sum_probs=15.2
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.-+.++.++||++++-..
T Consensus 16 ~~~l~~~~~~~P~v~i~i~ 34 (194)
T cd08436 16 PELLARFHRRHPGVDIRLR 34 (194)
T ss_pred HHHHHHHHHHCCCcEEEEe
Confidence 6778999999999766543
No 30
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=27.67 E-value=68 Score=19.51 Aligned_cols=18 Identities=11% Similarity=0.346 Sum_probs=14.4
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
++=+.++.++||++++-.
T Consensus 16 ~~~l~~~~~~~P~i~l~i 33 (198)
T cd08412 16 PGLLRRFREAYPGVEVRV 33 (198)
T ss_pred HHHHHHHHHHCCCcEEEE
Confidence 677899999999976544
No 31
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=27.51 E-value=67 Score=19.65 Aligned_cols=19 Identities=16% Similarity=0.284 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.-+.++.++||++++-.-
T Consensus 16 ~~~l~~~~~~~P~v~l~i~ 34 (200)
T cd08464 16 PPLLAALRAEAPGVRLVFR 34 (200)
T ss_pred HHHHHHHHHHCCCcEEEEe
Confidence 5668999999999766443
No 32
>PF02550 AcetylCoA_hydro: Acetyl-CoA hydrolase/transferase N-terminal domain; InterPro: IPR003702 This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase 3.1.2.1 from EC from yeast catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) 2.8.3 from EC produces succinyl-CoA, and acetate-CoA transferase 2.8.3.8 from EC utilises acyl-CoA and acetate to form acetyl-CoA.; GO: 0003824 catalytic activity, 0006084 acetyl-CoA metabolic process; PDB: 2NVV_C 2G39_A 3D3U_A 3S8D_B 3QLI_B 3QLK_B 3GK7_B 3QDQ_A 3EH7_A 2OAS_A ....
Probab=26.60 E-value=42 Score=23.19 Aligned_cols=35 Identities=9% Similarity=0.083 Sum_probs=20.3
Q ss_pred HHHHhCCCcEEEEEeccCCCCCCCeeecCCCccccc
Q 035086 22 VVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDR 57 (73)
Q Consensus 22 ~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR 57 (73)
.+.+.+..+.+...++ ..+|++||+.+|++.--.|
T Consensus 117 ~~~~~~~~~Dvaii~v-Sp~De~Gy~slG~s~~~~~ 151 (198)
T PF02550_consen 117 LFRRGFIPIDVAIIQV-SPMDEHGYFSLGTSVDYTK 151 (198)
T ss_dssp HHHTTSSH-SEEEEEE-CEE-TTSEEECTTBHBTHH
T ss_pred HHHcCCCCCCEEEEEe-cCcCCCCCEeecHHHHhHH
Confidence 3444444344444444 5779999999999854444
No 33
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=26.46 E-value=72 Score=19.54 Aligned_cols=17 Identities=12% Similarity=0.342 Sum_probs=13.8
Q ss_pred HHHHHHHHHhCCCcEEE
Q 035086 17 PQGVHVVCKSFPRLKIV 33 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Iv 33 (73)
+.-+..+.++||+++|-
T Consensus 16 ~~~l~~f~~~~P~v~i~ 32 (198)
T cd08461 16 PPLLAALRQEAPGVRVA 32 (198)
T ss_pred HHHHHHHHHHCCCcEEE
Confidence 67789999999997553
No 34
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=26.35 E-value=48 Score=24.03 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=38.4
Q ss_pred hCCCcEEEEEeccCCCCCCCeeecCCCcccccccCCCCCCcceeec
Q 035086 26 SFPRLKIVTSEIDIGLNEDFRVIPGMGEFGDRYFGTDDDDQQVVIR 71 (73)
Q Consensus 26 ~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~GDR~fgt~~~~~~~~~~ 71 (73)
.||.+++--+||-.-|+.-.-+.||+=..|+.+.-..+.++.+.++
T Consensus 91 ~~~~~qvD~GAIkfvlsGAnIMcPGlts~g~~l~~~~ekd~~V~i~ 136 (181)
T KOG2523|consen 91 IFPHVQVDRGAIKFVLSGANIMCPGLTSPGAKLPPGVEKDTIVAIM 136 (181)
T ss_pred ccceEEecCcceeeeecCCceEcccCCCCcccCCCCccCCCEEEEE
Confidence 3667888888999999999999999999999998777677777654
No 35
>cd05311 NAD_bind_2_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydroph
Probab=26.08 E-value=22 Score=25.33 Aligned_cols=12 Identities=17% Similarity=0.235 Sum_probs=9.5
Q ss_pred CCCCeeecCCCc
Q 035086 42 NEDFRVIPGMGE 53 (73)
Q Consensus 42 d~~~yIvPGlGD 53 (73)
-++.||.||||-
T Consensus 158 ~nn~~~fPg~~~ 169 (226)
T cd05311 158 VNNVLGFPGIFR 169 (226)
T ss_pred cceeeecchhhH
Confidence 356799999984
No 36
>PF05655 AvrD: Pseudomonas avirulence D protein (AvrD); InterPro: IPR008799 This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae [].
Probab=25.65 E-value=42 Score=25.93 Aligned_cols=21 Identities=29% Similarity=0.525 Sum_probs=18.1
Q ss_pred CCcccccccCCCCCCcceeec
Q 035086 51 MGEFGDRYFGTDDDDQQVVIR 71 (73)
Q Consensus 51 lGD~GDR~fgt~~~~~~~~~~ 71 (73)
||+.-.||||..-..+.|.++
T Consensus 13 LG~~~~RyFG~Gyk~~~y~i~ 33 (311)
T PF05655_consen 13 LGPSEQRYFGSGYKRVKYSIS 33 (311)
T ss_pred cCCcccCCccCCccceeeEEE
Confidence 789999999998888888764
No 37
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=25.13 E-value=76 Score=19.52 Aligned_cols=18 Identities=6% Similarity=0.117 Sum_probs=14.6
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
++-+.++.++||+++|-.
T Consensus 16 ~~~l~~~~~~~P~i~i~i 33 (198)
T cd08441 16 MPVLDQFRERWPDVELDL 33 (198)
T ss_pred HHHHHHHHHhCCCeEEEE
Confidence 678999999999976543
No 38
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=25.00 E-value=79 Score=19.24 Aligned_cols=19 Identities=11% Similarity=0.371 Sum_probs=14.9
Q ss_pred CHHHHHHHHHhCCCcEEEE
Q 035086 16 APQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 16 s~~Gi~~v~~~fP~v~Ivt 34 (73)
-|+-++++.++||+++|-.
T Consensus 16 l~~~l~~~~~~~P~i~l~i 34 (199)
T cd08451 16 VPGLIRRFREAYPDVELTL 34 (199)
T ss_pred cHHHHHHHHHHCCCcEEEE
Confidence 4788999999999865533
No 39
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=24.98 E-value=78 Score=19.37 Aligned_cols=19 Identities=16% Similarity=0.322 Sum_probs=15.4
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++=+.++.++||++++-..
T Consensus 17 ~~~l~~f~~~~P~v~l~i~ 35 (197)
T cd08470 17 APLVNDFMQRYPKLEVDIE 35 (197)
T ss_pred HHHHHHHHHHCCCeEEEEE
Confidence 6778999999999876543
No 40
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=24.89 E-value=78 Score=19.27 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.=++++.++||+++|-.-
T Consensus 16 ~~~l~~~~~~~P~i~l~i~ 34 (196)
T cd08450 16 PEVLPILREEHPDLDVELS 34 (196)
T ss_pred HHHHHHHHhhCCCcEEEEE
Confidence 5678899999999866543
No 41
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=24.62 E-value=82 Score=19.26 Aligned_cols=19 Identities=5% Similarity=0.104 Sum_probs=14.6
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.=+.++.++||+++|-..
T Consensus 17 ~~~l~~~~~~~P~v~i~i~ 35 (201)
T cd08471 17 LPIITDFLDAYPEVSVRLL 35 (201)
T ss_pred HHHHHHHHHHCCCcEEEEE
Confidence 4668899999999876543
No 42
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=24.20 E-value=1.3e+02 Score=22.15 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=17.6
Q ss_pred HHHHHHhCCCcEEEEEeccCCCCCC
Q 035086 20 VHVVCKSFPRLKIVTSEIDIGLNED 44 (73)
Q Consensus 20 i~~v~~~fP~v~Ivta~ID~~Ld~~ 44 (73)
|......||+=+|+.+-|||++..+
T Consensus 50 L~~a~~~fP~gtvhl~vVDPgVGt~ 74 (258)
T PF01887_consen 50 LAQAYPYFPKGTVHLAVVDPGVGTE 74 (258)
T ss_dssp HHHHHGGS-TTEEEEEE--TTTTSS
T ss_pred HHHHHhhCCCCCEEEEEECCCCCCC
Confidence 4566778999999999999988653
No 43
>cd08482 PBP2_TrpI The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold. TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cy
Probab=24.06 E-value=80 Score=19.50 Aligned_cols=19 Identities=11% Similarity=0.181 Sum_probs=15.1
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++-+.++.++||++++-..
T Consensus 16 ~~~i~~f~~~~P~v~i~~~ 34 (195)
T cd08482 16 IPRLPAFQAALPDIDLQLS 34 (195)
T ss_pred HhhHHHHHHHCCCceEEEE
Confidence 4568999999999887654
No 44
>TIGR02127 pyrF_sub2 orotidine 5'-phosphate decarboxylase, subfamily 2. This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. See TIGR01740 for a related but distinct subfamily of the same enzyme.
Probab=23.98 E-value=1.1e+02 Score=22.65 Aligned_cols=26 Identities=23% Similarity=0.497 Sum_probs=17.7
Q ss_pred CHHHHHHHHHhCCCcEEEEEeccCCCCCCCeeecCCCccc
Q 035086 16 APQGVHVVCKSFPRLKIVTSEIDIGLNEDFRVIPGMGEFG 55 (73)
Q Consensus 16 s~~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~yIvPGlGD~G 55 (73)
+|+=++++.+.+|+.. .+.||+|--|
T Consensus 197 ~p~e~~~iR~~~~~~~--------------il~PGigaqG 222 (261)
T TIGR02127 197 SPGDLLRLRIEMPTAP--------------FLVPGFGAQG 222 (261)
T ss_pred CHHHHHHHHHhCCCCe--------------EEeCCcCCCC
Confidence 6676777777666554 4889998443
No 45
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=23.74 E-value=37 Score=24.05 Aligned_cols=19 Identities=32% Similarity=0.646 Sum_probs=16.2
Q ss_pred eeecCCCcccccccCCCCC
Q 035086 46 RVIPGMGEFGDRYFGTDDD 64 (73)
Q Consensus 46 yIvPGlGD~GDR~fgt~~~ 64 (73)
+++=|||+.|.+|-.|+.+
T Consensus 3 ~LivGLGNPG~~Y~~TRHN 21 (189)
T PRK05426 3 KLIVGLGNPGPEYANTRHN 21 (189)
T ss_pred EEEEEeCCCchhhCcCchH
Confidence 5778999999999998754
No 46
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=22.94 E-value=72 Score=19.42 Aligned_cols=19 Identities=16% Similarity=0.240 Sum_probs=14.5
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.=+.++.++||+++|-.-
T Consensus 16 ~~~l~~~~~~~P~v~l~~~ 34 (199)
T cd08430 16 PPILERFRAQHPQVEIKLH 34 (199)
T ss_pred cHHHHHHHHHCCCceEEEE
Confidence 5568999999998765443
No 47
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=22.94 E-value=87 Score=19.52 Aligned_cols=19 Identities=26% Similarity=0.457 Sum_probs=15.1
Q ss_pred CHHHHHHHHHhCCCcEEEE
Q 035086 16 APQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 16 s~~Gi~~v~~~fP~v~Ivt 34 (73)
-++=+.++.++||+++|-.
T Consensus 15 l~~~l~~~~~~~P~v~l~i 33 (198)
T cd08444 15 LPWVVQAFKEQFPNVHLVL 33 (198)
T ss_pred hhHHHHHHHHHCCCeEEEE
Confidence 4788999999999876544
No 48
>cd02065 B12-binding_like B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.
Probab=22.94 E-value=1.4e+02 Score=18.04 Aligned_cols=37 Identities=19% Similarity=0.156 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCC-CcEEEEEeccCCCCCC----CeeecCCCc
Q 035086 17 PQGVHVVCKSFP-RLKIVTSEIDIGLNED----FRVIPGMGE 53 (73)
Q Consensus 17 ~~Gi~~v~~~fP-~v~Ivta~ID~~Ld~~----~yIvPGlGD 53 (73)
-+-+.++.++.| +++++.+.-..-.+.+ -+++.|-|.
T Consensus 67 ~~~~~~~~~~~p~~~~ivvGG~~~t~~~~~~~~d~~~~Ge~e 108 (125)
T cd02065 67 MKLVIEALKELGIDIPVVVGGAHPTADPEEPKVDAVVIGEGE 108 (125)
T ss_pred HHHHHHHHHhcCCCCeEEEeCCcCCccccccccceeeeCCeE
Confidence 345667888899 9999999877766553 355555444
No 49
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=22.87 E-value=90 Score=19.48 Aligned_cols=19 Identities=16% Similarity=0.190 Sum_probs=15.0
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.-+.++.++||+++|-.-
T Consensus 16 ~~~l~~~~~~~P~i~l~~~ 34 (200)
T cd08467 16 PRLAPRLRERAPGLDLRLC 34 (200)
T ss_pred HHHHHHHHhhCCCCEEEEe
Confidence 5677999999999876544
No 50
>PF04327 DUF464: Protein of unknown function (DUF464); InterPro: IPR007422 This entry is represented by Bacteriophage Cp-1, Orf13. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2IDL_A 2G0J_D 2G0I_B 2P92_B 1S12_C.
Probab=22.84 E-value=77 Score=19.90 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=12.9
Q ss_pred HHHHHHHHHhCCC-cEE
Q 035086 17 PQGVHVVCKSFPR-LKI 32 (73)
Q Consensus 17 ~~Gi~~v~~~fP~-v~I 32 (73)
.-|++.+.++||+ ++|
T Consensus 87 ~~gL~~i~~~Yp~~Iki 103 (103)
T PF04327_consen 87 LLGLKSIEEQYPDYIKI 103 (103)
T ss_dssp HHHHHHHHHHTTTTEEE
T ss_pred HHHHHHHHHHhhhhccC
Confidence 4599999999998 554
No 51
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=22.74 E-value=64 Score=19.55 Aligned_cols=18 Identities=6% Similarity=0.034 Sum_probs=13.5
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
++=+.++.++||+++|-.
T Consensus 16 ~~~l~~f~~~~P~i~i~i 33 (194)
T cd08481 16 IPRLPDFLARHPDITVNL 33 (194)
T ss_pred HhhhhHHHHHCCCceEEE
Confidence 345788999999976543
No 52
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=22.74 E-value=87 Score=16.45 Aligned_cols=15 Identities=27% Similarity=0.419 Sum_probs=11.5
Q ss_pred HHHHHHHHHhCCCcE
Q 035086 17 PQGVHVVCKSFPRLK 31 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~ 31 (73)
.+-++.+.+.||++.
T Consensus 2 ~~~v~~L~~mFP~~~ 16 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLD 16 (42)
T ss_dssp HHHHHHHHHHSSSS-
T ss_pred HHHHHHHHHHCCCCC
Confidence 456889999999864
No 53
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=22.72 E-value=74 Score=19.77 Aligned_cols=17 Identities=35% Similarity=0.503 Sum_probs=13.5
Q ss_pred HHHHHHHHHhCCCcEEE
Q 035086 17 PQGVHVVCKSFPRLKIV 33 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Iv 33 (73)
++=++++.++||+++|-
T Consensus 16 ~~~l~~~~~~~P~v~i~ 32 (197)
T cd08452 16 PPIVREYRKKFPSVKVE 32 (197)
T ss_pred HHHHHHHHHHCCCcEEE
Confidence 56688999999987654
No 54
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=22.65 E-value=88 Score=18.80 Aligned_cols=19 Identities=16% Similarity=0.382 Sum_probs=14.6
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.-+.++.++||++++-.-
T Consensus 16 ~~~l~~~~~~~P~i~i~i~ 34 (195)
T cd08434 16 PDLIRAFRKEYPNVTFELH 34 (195)
T ss_pred HHHHHHHHHhCCCeEEEEe
Confidence 5678999999999765433
No 55
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=22.59 E-value=93 Score=18.83 Aligned_cols=19 Identities=16% Similarity=0.398 Sum_probs=15.2
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++-+.++.++||+++|-..
T Consensus 16 ~~~l~~~~~~~P~i~l~~~ 34 (195)
T cd08427 16 PRALARLRRRHPDLEVHIV 34 (195)
T ss_pred HHHHHHHHHHCCCceEEEE
Confidence 6788999999999766443
No 56
>cd08473 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=22.52 E-value=92 Score=18.98 Aligned_cols=20 Identities=5% Similarity=0.222 Sum_probs=15.4
Q ss_pred HHHHHHHHHhCCCcEEEEEe
Q 035086 17 PQGVHVVCKSFPRLKIVTSE 36 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta~ 36 (73)
+.-+.++.++||++++-...
T Consensus 19 ~~~l~~~~~~~P~i~i~~~~ 38 (202)
T cd08473 19 APLLPRFMAAYPQVRLQLEA 38 (202)
T ss_pred HHHHHHHHHHCCCeEEEEEE
Confidence 56688999999998775543
No 57
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=22.50 E-value=74 Score=19.49 Aligned_cols=17 Identities=18% Similarity=0.448 Sum_probs=13.4
Q ss_pred HHHHHHHHHhCCCcEEE
Q 035086 17 PQGVHVVCKSFPRLKIV 33 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Iv 33 (73)
+.=+.++.++||++++-
T Consensus 17 ~~~l~~f~~~~P~i~i~ 33 (198)
T cd08479 17 APALSDFAKRYPELEVQ 33 (198)
T ss_pred HHHHHHHHHHCCCeEEE
Confidence 56688899999997554
No 58
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=22.44 E-value=92 Score=18.82 Aligned_cols=19 Identities=5% Similarity=0.205 Sum_probs=15.3
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++-++++.++||+++|-..
T Consensus 16 ~~~l~~~~~~~p~v~i~i~ 34 (197)
T cd08438 16 APLLAAFRQRYPNIELELV 34 (197)
T ss_pred HHHHHHHHHHCcCeEEEEE
Confidence 6788999999999876543
No 59
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=22.43 E-value=88 Score=19.21 Aligned_cols=19 Identities=21% Similarity=0.085 Sum_probs=15.0
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++=+.++.++||+++|-..
T Consensus 16 ~~~l~~~~~~~P~v~i~~~ 34 (198)
T cd08437 16 PKLAKDLIKTGLMIQIDTY 34 (198)
T ss_pred HHHHHHHHHhCCceEEEEE
Confidence 6778999999999766543
No 60
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=22.32 E-value=91 Score=18.99 Aligned_cols=19 Identities=5% Similarity=0.011 Sum_probs=14.6
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
+.-+.++.++||++++-.-
T Consensus 16 ~~~l~~f~~~~P~i~l~i~ 34 (189)
T cd08487 16 LPRLAEFRQLHPFIELRLR 34 (189)
T ss_pred hHHHHHHHHHCCCceEEee
Confidence 4558999999999876543
No 61
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=21.91 E-value=1e+02 Score=18.66 Aligned_cols=18 Identities=11% Similarity=0.416 Sum_probs=14.0
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
+.=+.++.++||+++|-.
T Consensus 16 ~~~l~~~~~~~P~i~i~i 33 (197)
T cd08448 16 PRILRAFRAEYPGIEVAL 33 (197)
T ss_pred HHHHHHHHHHCCCCeEEE
Confidence 566889999999976643
No 62
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=21.85 E-value=99 Score=19.17 Aligned_cols=19 Identities=16% Similarity=0.277 Sum_probs=14.4
Q ss_pred CHHHHHHHHHhCCCcEEEE
Q 035086 16 APQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 16 s~~Gi~~v~~~fP~v~Ivt 34 (73)
-++=+.++.++||+++|-.
T Consensus 15 l~~~l~~~~~~~P~v~v~l 33 (200)
T cd08460 15 GPALLAAVAAEAPGVRLRF 33 (200)
T ss_pred HHHHHHHHHHHCCCCEEEE
Confidence 3567889999999976533
No 63
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=21.77 E-value=95 Score=18.68 Aligned_cols=19 Identities=5% Similarity=0.148 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++=+.++.++||++++-..
T Consensus 17 ~~~l~~~~~~~P~v~i~i~ 35 (197)
T cd08422 17 APLLAEFLARYPDVRLELV 35 (197)
T ss_pred HHHHHHHHHhCCceEEEEe
Confidence 5668999999999766443
No 64
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=21.75 E-value=96 Score=19.05 Aligned_cols=18 Identities=6% Similarity=0.209 Sum_probs=14.5
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
+.=+.++.++||++++-.
T Consensus 19 ~~~l~~f~~~~P~v~i~~ 36 (199)
T cd08478 19 APLIAKFRERYPDIELEL 36 (199)
T ss_pred HHHHHHHHHHCCCeEEEE
Confidence 567889999999987654
No 65
>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=21.65 E-value=1e+02 Score=18.74 Aligned_cols=19 Identities=5% Similarity=0.197 Sum_probs=14.6
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++=+.++.++||++++-..
T Consensus 17 ~~~l~~~~~~~P~i~l~i~ 35 (197)
T cd08477 17 TPALAEYLARYPDVRVDLV 35 (197)
T ss_pred HHHHHHHHHHCCCcEEEEE
Confidence 4668889999999766543
No 66
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=21.52 E-value=45 Score=28.08 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=17.2
Q ss_pred CCCcEEEEEeccCCCCCCCeeecCCC
Q 035086 27 FPRLKIVTSEIDIGLNEDFRVIPGMG 52 (73)
Q Consensus 27 fP~v~Ivta~ID~~Ld~~~yIvPGlG 52 (73)
||.|+.=--..-++=.++.||.||+|
T Consensus 453 F~pV~~~gK~~~pgQ~NN~yiFPGi~ 478 (582)
T KOG1257|consen 453 FPPVEYNGKVYVPGQGNNAYIFPGIG 478 (582)
T ss_pred CCCceeCCcEecccCCceeEecchHH
Confidence 66665533333455667789999987
No 67
>cd05312 NAD_bind_1_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH
Probab=21.32 E-value=54 Score=24.83 Aligned_cols=15 Identities=27% Similarity=0.587 Sum_probs=11.0
Q ss_pred CCCCCCCeeecCCCc
Q 035086 39 IGLNEDFRVIPGMGE 53 (73)
Q Consensus 39 ~~Ld~~~yIvPGlGD 53 (73)
+.=-++.|+.||||-
T Consensus 181 p~Q~NN~~iFPGigl 195 (279)
T cd05312 181 PGQGNNAYIFPGIGL 195 (279)
T ss_pred CCCcceeeeccchhh
Confidence 333467799999984
No 68
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=21.07 E-value=38 Score=19.26 Aligned_cols=10 Identities=50% Similarity=1.115 Sum_probs=8.0
Q ss_pred ecCCCccccc
Q 035086 48 IPGMGEFGDR 57 (73)
Q Consensus 48 vPGlGD~GDR 57 (73)
+||+|..||-
T Consensus 9 v~~lG~~Gdi 18 (48)
T PF01281_consen 9 VPGLGKKGDI 18 (48)
T ss_dssp CTTSBSTTEE
T ss_pred ccccCCCCCE
Confidence 6899988873
No 69
>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Probab=20.87 E-value=1e+02 Score=19.32 Aligned_cols=36 Identities=17% Similarity=0.214 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCcEEEEEeccCCCCCCC--------eeecCCCc
Q 035086 18 QGVHVVCKSFPRLKIVTSEIDIGLNEDF--------RVIPGMGE 53 (73)
Q Consensus 18 ~Gi~~v~~~fP~v~Ivta~ID~~Ld~~~--------yIvPGlGD 53 (73)
+=++.+.+++|+.+|+.+......+.+. +++.|=|+
T Consensus 57 ~~~~~ik~~~p~~~iv~GG~~~t~~p~~~~~~~~~D~vv~GEgE 100 (127)
T cd02068 57 ELAKIAKEVLPNVIVVVGGPHATFFPEEILEEPGVDFVVIGEGE 100 (127)
T ss_pred HHHHHHHHHCCCCEEEECCcchhhCHHHHhcCCCCCEEEECCcH
Confidence 3456777889999999888766543222 56666554
No 70
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.86 E-value=1e+02 Score=18.67 Aligned_cols=18 Identities=11% Similarity=0.209 Sum_probs=14.4
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
+.=+.++.++||+++|-.
T Consensus 17 ~~~l~~~~~~~P~v~i~i 34 (199)
T cd08475 17 APLLLELARRHPELELEL 34 (199)
T ss_pred HHHHHHHHHHCCCeEEEE
Confidence 556899999999987654
No 71
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=20.65 E-value=67 Score=18.32 Aligned_cols=16 Identities=6% Similarity=0.169 Sum_probs=13.9
Q ss_pred ccCHHHHHHHHHhCCC
Q 035086 14 HQAPQGVHVVCKSFPR 29 (73)
Q Consensus 14 ias~~Gi~~v~~~fP~ 29 (73)
|+..+.++.+.++||=
T Consensus 23 Isr~e~l~~~~~RWPL 38 (44)
T PF10945_consen 23 ISREERLNQALQRWPL 38 (44)
T ss_pred HHHHHHHHHHHHHChh
Confidence 5788999999999993
No 72
>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=20.63 E-value=1.4e+02 Score=18.98 Aligned_cols=21 Identities=10% Similarity=0.374 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCcEEEEEeccC
Q 035086 19 GVHVVCKSFPRLKIVTSEIDI 39 (73)
Q Consensus 19 Gi~~v~~~fP~v~Ivta~ID~ 39 (73)
=++.++++||++..+.--+|+
T Consensus 42 ~~~~La~~y~~v~Flkvdvde 62 (106)
T KOG0907|consen 42 KFEKLAEKYPDVVFLKVDVDE 62 (106)
T ss_pred HHHHHHHHCCCCEEEEEeccc
Confidence 478999999999999999997
No 73
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=20.53 E-value=1.1e+02 Score=18.44 Aligned_cols=18 Identities=11% Similarity=0.324 Sum_probs=14.5
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
++-+.++.++||+++|-.
T Consensus 16 ~~~l~~~~~~~p~i~i~i 33 (197)
T cd08414 16 PRLLRRFRARYPDVELEL 33 (197)
T ss_pred HHHHHHHHHHCCCcEEEE
Confidence 677899999999976644
No 74
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=20.32 E-value=1.1e+02 Score=18.98 Aligned_cols=19 Identities=16% Similarity=0.298 Sum_probs=14.7
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++-+.++.++||+++|-..
T Consensus 16 ~~~i~~~~~~~P~i~l~i~ 34 (200)
T cd08462 16 PPVIERVAREAPGVRFELL 34 (200)
T ss_pred HHHHHHHHHHCCCCEEEEe
Confidence 6778899999998765443
No 75
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=20.28 E-value=1.1e+02 Score=18.50 Aligned_cols=18 Identities=11% Similarity=0.359 Sum_probs=14.5
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
+.-+.++.++||++++-.
T Consensus 16 ~~~l~~~~~~~P~i~l~i 33 (193)
T cd08442 16 PPLLAAYHARYPKVDLSL 33 (193)
T ss_pred HHHHHHHHHHCCCceEEE
Confidence 677899999999976543
No 76
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=20.28 E-value=1.1e+02 Score=19.18 Aligned_cols=18 Identities=11% Similarity=0.254 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCCcEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivt 34 (73)
++=+.++.++||++++-.
T Consensus 16 ~~~l~~f~~~~P~i~l~i 33 (200)
T cd08465 16 PALMRQLRAEAPGIDLAV 33 (200)
T ss_pred hHHHHHHHHHCCCcEEEE
Confidence 678899999999987643
No 77
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=20.18 E-value=1.1e+02 Score=18.65 Aligned_cols=17 Identities=12% Similarity=0.225 Sum_probs=13.1
Q ss_pred HHHHHHHHHhCCCcEEE
Q 035086 17 PQGVHVVCKSFPRLKIV 33 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Iv 33 (73)
++=+.++.++||++++-
T Consensus 16 ~~~l~~f~~~~P~v~l~ 32 (200)
T cd08466 16 PRLLARLKQLAPNISLR 32 (200)
T ss_pred HHHHHHHHHHCCCCEEE
Confidence 46678899999997553
No 78
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=20.08 E-value=1.1e+02 Score=19.23 Aligned_cols=17 Identities=18% Similarity=0.221 Sum_probs=13.7
Q ss_pred HHHHHHHHHhCCCcEEE
Q 035086 17 PQGVHVVCKSFPRLKIV 33 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Iv 33 (73)
++=+.++.++||+++|-
T Consensus 17 ~~~l~~f~~~~P~v~i~ 33 (198)
T cd08486 17 PLLLRAFLTSTPTATVS 33 (198)
T ss_pred HHHHHHHHHhCCCeEEE
Confidence 56788999999997653
No 79
>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=20.08 E-value=1.4e+02 Score=17.10 Aligned_cols=27 Identities=11% Similarity=0.171 Sum_probs=20.9
Q ss_pred cCHHHHHHHHHhCC---CcEEEEEeccCCC
Q 035086 15 QAPQGVHVVCKSFP---RLKIVTSEIDIGL 41 (73)
Q Consensus 15 as~~Gi~~v~~~fP---~v~Ivta~ID~~L 41 (73)
+.-+.++.+.++++ +++++.-.+|+..
T Consensus 18 ~~~~~l~~l~~~~~~~~~v~~v~Vs~d~~~ 47 (95)
T PF13905_consen 18 KELPKLKELYKKYKKKDDVEFVFVSLDEDE 47 (95)
T ss_dssp HHHHHHHHHHHHHTTTTTEEEEEEE-SSSH
T ss_pred HHHHHHHHHHHHhCCCCCEEEEEEEeCCCH
Confidence 45567888888999 7999999999753
No 80
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=20.07 E-value=1e+02 Score=18.84 Aligned_cols=19 Identities=11% Similarity=-0.143 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q 035086 17 PQGVHVVCKSFPRLKIVTS 35 (73)
Q Consensus 17 ~~Gi~~v~~~fP~v~Ivta 35 (73)
++=+.++.++||+++|-..
T Consensus 16 ~~~l~~~~~~~P~v~i~i~ 34 (195)
T cd08431 16 YPLIAEFYQLNKATRIRLS 34 (195)
T ss_pred HHHHHHHHHHCCCCceEEE
Confidence 5778999999999765443
No 81
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=20.05 E-value=98 Score=20.44 Aligned_cols=19 Identities=37% Similarity=0.429 Sum_probs=14.6
Q ss_pred CHHHHHHHHHhCCCcEEEE
Q 035086 16 APQGVHVVCKSFPRLKIVT 34 (73)
Q Consensus 16 s~~Gi~~v~~~fP~v~Ivt 34 (73)
+..=++.+.++||+.+|+-
T Consensus 97 ~~P~V~avL~~FPgA~I~~ 115 (117)
T PF12362_consen 97 AHPLVKAVLAAFPGAEIVD 115 (117)
T ss_pred hCcHHHHHHHHCCCCEEEe
Confidence 3445788999999998863
Done!