Query 035150
Match_columns 72
No_of_seqs 21 out of 23
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 09:37:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035150hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09353 DUF1995: Domain of un 98.0 9.1E-06 2E-10 56.7 3.6 42 8-55 98-140 (209)
2 PLN02842 nucleotide kinase 95.3 0.035 7.6E-07 45.4 5.1 48 3-53 351-400 (505)
3 TIGR00057 Sua5/YciO/YrdC/YwlC 65.1 9 0.0002 26.9 3.2 42 13-54 23-71 (201)
4 cd01355 AcnX Putative Aconitas 63.5 10 0.00022 30.4 3.5 38 10-47 280-317 (389)
5 PRK11630 hypothetical protein; 62.7 9.4 0.0002 27.1 2.9 42 13-54 29-77 (206)
6 PF06953 ArsD: Arsenical resis 59.5 5.9 0.00013 27.0 1.4 22 37-60 70-91 (123)
7 COG0009 SUA5 Putative translat 58.2 14 0.00029 27.1 3.2 42 12-53 27-75 (211)
8 TIGR03249 KdgD 5-dehydro-4-deo 55.5 24 0.00053 25.7 4.1 37 9-46 101-137 (296)
9 PF04412 DUF521: Protein of un 52.4 27 0.00059 27.9 4.3 40 8-47 289-328 (400)
10 PF12715 Abhydrolase_7: Abhydr 51.4 5.3 0.00012 32.3 0.2 16 37-52 304-319 (390)
11 PF01300 Sua5_yciO_yrdC: Telom 51.4 14 0.0003 25.1 2.2 45 7-54 12-56 (179)
12 cd00952 CHBPH_aldolase Trans-o 50.6 29 0.00063 25.8 3.9 36 10-46 105-142 (309)
13 cd00950 DHDPS Dihydrodipicolin 48.2 34 0.00075 24.3 3.9 37 10-47 97-134 (284)
14 PF00701 DHDPS: Dihydrodipicol 47.3 44 0.00095 24.0 4.3 38 9-47 98-135 (289)
15 cd00408 DHDPS-like Dihydrodipi 47.0 37 0.00081 24.0 3.9 38 10-47 94-131 (281)
16 cd03027 GRX_DEP Glutaredoxin ( 46.7 17 0.00036 20.7 1.8 32 18-49 30-61 (73)
17 cd05014 SIS_Kpsf KpsF-like pro 44.3 73 0.0016 19.4 5.3 41 3-48 43-83 (128)
18 cd01892 Miro2 Miro2 subfamily. 44.2 81 0.0018 20.3 4.9 44 8-51 77-120 (169)
19 COG1679 Predicted aconitase [G 44.1 43 0.00092 27.7 4.3 40 8-47 289-328 (403)
20 PF05320 Pox_RNA_Pol_19: Poxvi 43.7 22 0.00048 26.3 2.4 15 36-50 125-140 (167)
21 PRK10634 tRNA(ANN) t(6)A37 thr 43.5 34 0.00073 24.0 3.2 41 13-53 22-69 (190)
22 cd00951 KDGDH 5-dehydro-4-deox 42.9 51 0.0011 24.0 4.1 35 11-46 97-132 (289)
23 PF14460 Prok-E2_D: Prokaryoti 42.2 16 0.00034 25.4 1.4 21 3-23 82-102 (175)
24 TIGR00674 dapA dihydrodipicoli 41.4 50 0.0011 23.8 3.9 37 11-47 96-132 (285)
25 PF08237 PE-PPE: PE-PPE domain 40.9 64 0.0014 23.4 4.4 38 7-45 1-53 (225)
26 KOG2619 Fucosyltransferase [Ca 40.0 22 0.00048 28.5 2.0 36 25-65 265-300 (372)
27 KOG1594 Uncharacterized enzyme 39.1 17 0.00037 29.1 1.3 17 36-52 199-215 (305)
28 TIGR02181 GRX_bact Glutaredoxi 38.9 24 0.00053 20.1 1.6 35 15-49 25-59 (79)
29 cd03418 GRX_GRXb_1_3_like Glut 38.8 27 0.00058 19.4 1.7 11 39-49 51-61 (75)
30 cd00954 NAL N-Acetylneuraminic 35.2 81 0.0017 22.9 4.2 36 11-47 99-136 (288)
31 COG0676 Uncharacterized enzyme 34.5 13 0.00028 29.2 -0.0 40 17-56 158-207 (287)
32 PRK04147 N-acetylneuraminate l 34.4 82 0.0018 22.9 4.1 35 11-46 102-137 (293)
33 TIGR00683 nanA N-acetylneurami 33.8 85 0.0018 23.0 4.1 37 11-47 99-136 (290)
34 PRK03592 haloalkane dehalogena 33.7 60 0.0013 22.2 3.1 21 33-53 222-242 (295)
35 cd03135 GATase1_DJ-1 Type 1 gl 32.6 58 0.0013 20.4 2.7 23 12-34 2-24 (163)
36 TIGR00725 conserved hypothetic 32.0 51 0.0011 22.5 2.6 11 38-48 114-124 (159)
37 cd04142 RRP22 RRP22 subfamily. 31.3 1.7E+02 0.0037 19.8 5.2 44 8-51 80-128 (198)
38 PF05406 WGR: WGR domain; Int 30.5 1.3E+02 0.0027 18.1 4.0 30 17-63 51-81 (81)
39 PF00852 Glyco_transf_10: Glyc 30.4 44 0.00094 25.3 2.2 38 23-65 240-279 (349)
40 KOG3439 Protein conjugation fa 30.1 1.4E+02 0.0029 21.1 4.4 38 5-44 70-107 (116)
41 cd03132 GATase1_catalase Type 30.0 1.1E+02 0.0023 19.3 3.7 25 10-34 3-27 (142)
42 PF01380 SIS: SIS domain SIS d 30.0 1.3E+02 0.0028 18.0 4.7 40 3-47 49-88 (131)
43 cd04795 SIS SIS domain. SIS (S 29.6 1.1E+02 0.0024 17.1 5.0 38 4-46 44-81 (87)
44 PRK03170 dihydrodipicolinate s 29.4 1E+02 0.0022 22.2 3.9 36 10-46 98-134 (292)
45 COG1559 Aminodeoxychorismate l 29.2 41 0.00089 26.5 1.9 28 16-43 206-234 (342)
46 PF07693 KAP_NTPase: KAP famil 28.6 84 0.0018 22.1 3.2 27 31-57 163-189 (325)
47 PRK03620 5-dehydro-4-deoxygluc 28.5 1.2E+02 0.0026 22.3 4.2 34 12-46 105-139 (303)
48 KOG1455 Lysophospholipase [Lip 28.0 76 0.0017 25.3 3.2 45 7-52 213-259 (313)
49 cd05710 SIS_1 A subgroup of th 27.8 1.6E+02 0.0035 18.4 5.5 42 3-49 43-84 (120)
50 TIGR00441 gmhA phosphoheptose 27.6 1.8E+02 0.004 19.1 5.0 39 5-48 77-115 (154)
51 PRK11574 oxidative-stress-resi 27.6 88 0.0019 20.8 3.1 25 10-34 4-28 (196)
52 PF00071 Ras: Ras family; Int 27.4 1.5E+02 0.0033 18.1 4.2 37 9-45 72-110 (162)
53 PHA02737 hypothetical protein; 27.3 42 0.00091 21.8 1.4 17 6-22 40-56 (72)
54 PRK05449 aspartate alpha-decar 27.3 63 0.0014 22.8 2.4 23 2-24 76-98 (126)
55 TIGR00223 panD L-aspartate-alp 26.3 69 0.0015 22.6 2.5 23 2-24 76-98 (126)
56 cd01673 dNK Deoxyribonucleosid 26.3 1.2E+02 0.0026 19.8 3.5 30 20-49 154-186 (193)
57 cd06919 Asp_decarbox Aspartate 26.0 70 0.0015 22.1 2.4 23 2-24 75-97 (111)
58 COG0864 NikR Predicted transcr 25.9 63 0.0014 22.5 2.2 43 11-53 59-113 (136)
59 cd04146 RERG_RasL11_like RERG/ 25.6 1.7E+02 0.0038 18.1 4.9 41 10-50 73-117 (165)
60 TIGR01382 PfpI intracellular p 25.3 1.1E+02 0.0023 19.6 3.1 24 11-34 2-25 (166)
61 PF00326 Peptidase_S9: Prolyl 25.2 69 0.0015 21.0 2.2 15 38-52 143-157 (213)
62 TIGR02313 HpaI-NOT-DapA 2,4-di 25.1 1.5E+02 0.0033 21.8 4.2 37 10-47 97-135 (294)
63 TIGR02194 GlrX_NrdH Glutaredox 24.8 61 0.0013 18.4 1.7 21 36-58 45-65 (72)
64 COG0131 HisB Imidazoleglycerol 24.7 54 0.0012 24.7 1.8 23 37-59 111-133 (195)
65 PF02261 Asp_decarbox: Asparta 24.7 51 0.0011 22.9 1.6 23 2-24 76-98 (116)
66 smart00879 Brix Brix domain. T 24.6 49 0.0011 21.4 1.4 15 37-51 100-114 (180)
67 cd03136 GATase1_AraC_ArgR_like 24.5 1.1E+02 0.0024 20.0 3.1 23 12-34 2-24 (185)
68 COG3253 ywfI Predicted heme pe 24.3 2E+02 0.0044 22.0 4.8 40 7-46 175-218 (230)
69 TIGR02196 GlrX_YruB Glutaredox 24.3 83 0.0018 16.5 2.1 21 36-59 47-67 (74)
70 KOG1260 Isocitrate lyase [Ener 24.3 51 0.0011 27.9 1.7 23 37-59 309-331 (492)
71 PF02633 Creatininase: Creatin 24.2 1.3E+02 0.0028 21.1 3.6 23 26-48 87-109 (237)
72 PF13167 GTP-bdg_N: GTP-bindin 23.9 91 0.002 20.4 2.6 17 34-50 52-68 (95)
73 TIGR03746 conj_TIGR03746 integ 23.9 69 0.0015 24.2 2.2 11 46-56 115-126 (202)
74 PF00462 Glutaredoxin: Glutare 23.8 1.1E+02 0.0024 16.6 2.6 14 36-49 46-59 (60)
75 cd00945 Aldolase_Class_I Class 23.7 1.4E+02 0.003 19.0 3.3 40 8-47 79-121 (201)
76 TIGR02427 protocat_pcaD 3-oxoa 23.4 69 0.0015 19.7 1.8 17 36-52 190-206 (251)
77 COG0853 PanD Aspartate 1-decar 23.4 1.7E+02 0.0037 20.7 4.0 41 2-53 75-115 (126)
78 PF00450 Peptidase_S10: Serine 23.1 76 0.0016 22.9 2.2 17 36-52 327-343 (415)
79 PHA02857 monoglyceride lipase; 22.7 1.3E+02 0.0029 20.1 3.3 21 33-53 203-223 (276)
80 cd01870 RhoA_like RhoA-like su 22.7 2E+02 0.0044 17.8 5.1 43 9-51 73-117 (175)
81 TIGR00143 hypF [NiFe] hydrogen 22.7 86 0.0019 26.7 2.8 40 13-53 177-223 (711)
82 KOG0817 Acyl-CoA-binding prote 22.1 76 0.0017 22.3 2.0 18 20-37 24-41 (142)
83 PF08283 Gemini_AL1_M: Geminiv 21.7 39 0.00085 22.7 0.5 26 27-55 76-102 (106)
84 smart00174 RHO Rho (Ras homolo 21.6 2.1E+02 0.0046 17.7 5.0 44 8-51 69-114 (174)
85 COG0329 DapA Dihydrodipicolina 21.4 1.7E+02 0.0037 21.8 3.9 36 11-46 102-137 (299)
86 smart00175 RAB Rab subfamily o 21.2 2E+02 0.0044 17.3 5.3 45 9-53 73-119 (164)
87 cd03139 GATase1_PfpI_2 Type 1 21.2 73 0.0016 20.5 1.7 24 12-35 2-25 (183)
88 PTZ00158 40S ribosomal protein 21.1 46 0.00099 22.9 0.8 28 43-70 80-107 (130)
89 PF02955 GSH-S_ATP: Prokaryoti 21.1 65 0.0014 22.7 1.6 18 32-49 78-95 (173)
90 cd04132 Rho4_like Rho4-like su 20.9 2.4E+02 0.0051 17.9 5.2 42 9-50 73-116 (187)
91 PF12697 Abhydrolase_6: Alpha/ 20.7 1.3E+02 0.0028 18.0 2.6 22 32-53 169-190 (228)
92 TIGR03695 menH_SHCHC 2-succiny 20.3 82 0.0018 19.2 1.7 17 36-52 191-207 (251)
93 cd04130 Wrch_1 Wrch-1 subfamil 20.0 2.4E+02 0.0053 17.8 4.8 43 9-51 72-116 (173)
No 1
>PF09353 DUF1995: Domain of unknown function (DUF1995); InterPro: IPR018962 This family of proteins are functionally uncharacterised.
Probab=97.95 E-value=9.1e-06 Score=56.68 Aligned_cols=42 Identities=24% Similarity=0.377 Sum_probs=35.7
Q ss_pred CCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCccccee-cc
Q 035150 8 EDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGELDRIR-SG 55 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGELDRiR-sg 55 (72)
+|-+++|+++.++.+++..+.+++.+ ||+|+|||+||.+| .|
T Consensus 98 ~~~~vvv~p~~~~l~~~e~~~~~~~~------rpvvl~Np~l~~~~~~g 140 (209)
T PF09353_consen 98 DDILVVVAPSPQELDDVEKLCEAAGG------RPVVLLNPQLEDVRSVG 140 (209)
T ss_pred CCEEEEEECChhhHHHHHHHHHhcCC------CeEEEEecccccCCccc
Confidence 47788888888998888888877544 99999999999999 55
No 2
>PLN02842 nucleotide kinase
Probab=95.34 E-value=0.035 Score=45.37 Aligned_cols=48 Identities=21% Similarity=0.341 Sum_probs=37.8
Q ss_pred CCCCCCCeEEEEEeccCCh--hHHHHHHHHHHHhhhcccceEEEEcCccccee
Q 035150 3 DRVKPEDELFLVAYPYFNV--NEMLVVEELYKEAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 3 drv~~~D~lfVVAYP~fNv--nEml~v~eLye~a~~~~~rpiIifNGELDRiR 53 (72)
++++++|++|++.=|.--| .|+-.++.+ +....+||+|++||-|+-+-
T Consensus 351 ~~~~~~d~~~i~v~P~~~v~~~~~~~~e~~---~~~~~~rpvillnp~LeD~~ 400 (505)
T PLN02842 351 KEVDEEDDMFILVAPQNAVGNCIIDDLQAM---TTAAGKRPVILVNPRLKDLP 400 (505)
T ss_pred CCCCCCCcEEEEEcCCccccccchHHHHHH---HHHhCCCeEEEECCcccccc
Confidence 5789999999999998743 355566666 33468899999999999763
No 3
>TIGR00057 Sua5/YciO/YrdC/YwlC family protein. partial match to sua5, which is involved in regulation of translation initiation. 3' end of sua5 has matches to sua5, BS3690, and weakly to AF0781 and BB0734.
Probab=65.07 E-value=9 Score=26.87 Aligned_cols=42 Identities=24% Similarity=0.362 Sum_probs=33.6
Q ss_pred EEEeccCChhHHH-------HHHHHHHHhhhcccceEEEEcCcccceec
Q 035150 13 LVAYPYFNVNEML-------VVEELYKEAVFNTARKLIIFNGELDRIRS 54 (72)
Q Consensus 13 VVAYP~fNvnEml-------~v~eLye~a~~~~~rpiIifNGELDRiRs 54 (72)
||+||-..+.=+. .+++||+-.-+..+.|++++-++++.++.
T Consensus 23 ii~~PTdTvYgL~~~~~~~~av~ri~~iK~R~~~Kpl~~l~~~~~~l~~ 71 (201)
T TIGR00057 23 IVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNKPLTVLVSDLSEIEK 71 (201)
T ss_pred EEEEeCCCHHHhhcCCCCHHHHHHHHHHhCCCCCCCeEEEECCHHHHHH
Confidence 7888877666553 78999998877889999999998877554
No 4
>cd01355 AcnX Putative Aconitase X catalytic domain. Putative Aconitase X catalytic domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution.
Probab=63.48 E-value=10 Score=30.43 Aligned_cols=38 Identities=13% Similarity=0.245 Sum_probs=32.7
Q ss_pred eEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 10 ELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 10 ~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
++.+++-|+|...|+..+.+|-++..+..++|++||-+
T Consensus 280 dlv~lGcPH~Sl~E~~~la~ll~g~~~~~~~~~~v~t~ 317 (389)
T cd01355 280 DLVVLGCPHASLEELRKLADLLAGRRVAPSVPLYVTTS 317 (389)
T ss_pred CEEEecCCCCCHHHHHHHHHHhcCCccCCCCCEEEEcc
Confidence 47788999999999999999999866666789999944
No 5
>PRK11630 hypothetical protein; Provisional
Probab=62.65 E-value=9.4 Score=27.09 Aligned_cols=42 Identities=10% Similarity=0.268 Sum_probs=33.1
Q ss_pred EEEeccCChhHH-------HHHHHHHHHhhhcccceEEEEcCcccceec
Q 035150 13 LVAYPYFNVNEM-------LVVEELYKEAVFNTARKLIIFNGELDRIRS 54 (72)
Q Consensus 13 VVAYP~fNvnEm-------l~v~eLye~a~~~~~rpiIifNGELDRiRs 54 (72)
||+||--.+.=+ .+|++||+-.-+..+.|++++-++++.+..
T Consensus 29 vi~~PTdTvYgL~~d~~n~~Av~~l~~lK~R~~~Kpl~ll~~~~~~~~~ 77 (206)
T PRK11630 29 VIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELST 77 (206)
T ss_pred EEEEeCCChHhhhcCCCCHHHHHHHHHHcCCCCCCCeEEEECCHHHHHH
Confidence 788886555433 578999998888899999999999876654
No 6
>PF06953 ArsD: Arsenical resistance operon trans-acting repressor ArsD; InterPro: IPR010712 This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent, 0046685 response to arsenic-containing substance; PDB: 3MWH_A 3KGK_A 3KTB_B.
Probab=59.50 E-value=5.9 Score=27.03 Aligned_cols=22 Identities=18% Similarity=0.442 Sum_probs=15.2
Q ss_pred cccceEEEEcCcccceecccccch
Q 035150 37 NTARKLIIFNGELDRIRSGCILHH 60 (72)
Q Consensus 37 ~~~rpiIifNGELDRiRsgYYP~~ 60 (72)
.-+-||++.|||+ ..+|-||..
T Consensus 70 ~e~LPitlVdGei--v~~G~YPt~ 91 (123)
T PF06953_consen 70 AEALPITLVDGEI--VKTGRYPTN 91 (123)
T ss_dssp GGG-SEEEETTEE--EEESS---H
T ss_pred cccCCEEEECCEE--EEecCCCCH
Confidence 4577999999999 678999974
No 7
>COG0009 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]
Probab=58.17 E-value=14 Score=27.13 Aligned_cols=42 Identities=26% Similarity=0.384 Sum_probs=34.1
Q ss_pred EEEEeccC-------ChhHHHHHHHHHHHhhhcccceEEEEcCccccee
Q 035150 12 FLVAYPYF-------NVNEMLVVEELYKEAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 12 fVVAYP~f-------NvnEml~v~eLye~a~~~~~rpiIifNGELDRiR 53 (72)
.+|+||-- |..--.+|+.||+-..+..+.|+|++-+.++-+.
T Consensus 27 ~vVa~PTeTVYGLg~~~~~~~Av~~i~~~K~Rp~~kpLil~~~~~~~l~ 75 (211)
T COG0009 27 GVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDKPLILHVASLEQLK 75 (211)
T ss_pred CEEEEEccchheeecCCCCHHHHHHHHHHhCCCCCCCEEEEeCCHHHHH
Confidence 37888854 4444568999999999999999999999888765
No 8
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=55.47 E-value=24 Score=25.73 Aligned_cols=37 Identities=19% Similarity=0.206 Sum_probs=24.8
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifN 46 (72)
|.+ ++.=|++..---..+.+-|++....++.|+++.|
T Consensus 101 dav-~~~pP~y~~~s~~~i~~~f~~v~~a~~~pvilYn 137 (296)
T TIGR03249 101 DGY-LLLPPYLINGEQEGLYAHVEAVCESTDLGVIVYQ 137 (296)
T ss_pred CEE-EECCCCCCCCCHHHHHHHHHHHHhccCCCEEEEe
Confidence 444 4555766543335566667776667889999999
No 9
>PF04412 DUF521: Protein of unknown function (DUF521); InterPro: IPR007506 This is a group of hypothetical proteins.
Probab=52.44 E-value=27 Score=27.92 Aligned_cols=40 Identities=18% Similarity=0.262 Sum_probs=34.6
Q ss_pred CCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 8 EDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
.=++..++-|++..+|+..+.+|-++.-+..++|++|+-+
T Consensus 289 ~~D~V~lGcPH~S~~El~~ia~ll~gr~~~~~~~~~i~t~ 328 (400)
T PF04412_consen 289 KVDLVALGCPHLSLEELREIAELLEGRKVHPNVPLWITTS 328 (400)
T ss_pred CCCEEEECCCCCCHHHHHHHHHHHhCCCCCCCceEEEECC
Confidence 3357788999999999999999999877779999999865
No 10
>PF12715 Abhydrolase_7: Abhydrolase family; PDB: 3NUZ_C 3G8Y_A.
Probab=51.42 E-value=5.3 Score=32.31 Aligned_cols=16 Identities=31% Similarity=0.497 Sum_probs=11.3
Q ss_pred cccceEEEEcCcccce
Q 035150 37 NTARKLIIFNGELDRI 52 (72)
Q Consensus 37 ~~~rpiIifNGELDRi 52 (72)
-.-||++++||.+||+
T Consensus 304 iAPRPll~~nG~~Dkl 319 (390)
T PF12715_consen 304 IAPRPLLFENGGKDKL 319 (390)
T ss_dssp TTTS-EEESS-B-HHH
T ss_pred hCCCcchhhcCCcccc
Confidence 5679999999999985
No 11
>PF01300 Sua5_yciO_yrdC: Telomere recombination; InterPro: IPR006070 The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation []. The YrdC protein, which consists solely of this domain, forms an alpha/beta twisted open-sheet structure composed of seven alpha helices and seven beta strands []. YrdC from Escherichia coli preferentially binds to double-stranded RNA and DNA. YrdC is predicted to be an rRNA maturation factor, as deletions in its gene lead to immature ribosomal 30S subunits and, consequently, fewer translating ribosomes []. Therefore, YrdC may function by keeping an rRNA structure needed for proper processing of 16S rRNA, especially at lower temperatures. Sua5 is an example of a multi-domain protein that contains an N-terminal YrdC-like domain and a C-terminal Sua5 domain. Sua5 was identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a translation initiation defect in the cytochrome c gene and is required for normal growth in yeast; however its exact function remains unknown []. HypF is involved in the synthesis of the active site of [NiFe]-hydrogenases [].; PDB: 3L7V_A 1KK9_A 1K7J_A 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A 2EQA_A ....
Probab=51.41 E-value=14 Score=25.14 Aligned_cols=45 Identities=22% Similarity=0.414 Sum_probs=30.3
Q ss_pred CCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCcccceec
Q 035150 7 PEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGELDRIRS 54 (72)
Q Consensus 7 ~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGELDRiRs 54 (72)
|+|+.|-++==-+|. .+++.||+-.-+..++|++++-++++.++.
T Consensus 12 PTdT~ygl~~~~~n~---~av~ri~~iK~R~~~Kpl~ll~~~~~~l~~ 56 (179)
T PF01300_consen 12 PTDTVYGLGCDAFNP---EAVERIYKIKQRPKNKPLILLVSSIEQLEE 56 (179)
T ss_dssp EESSSEEEEEETTSH---HHHHHHHHHHTSSTTS--EEEESSHHHHHH
T ss_pred ECCCEEEEEEecCCH---HHHHHHHHhhcccCCCCEEEEECCHHHHHH
Confidence 344554444322343 478999998888889999999999988765
No 12
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=50.58 E-value=29 Score=25.76 Aligned_cols=36 Identities=8% Similarity=0.255 Sum_probs=24.7
Q ss_pred eEEEEEeccC-ChhHHHHHHHHHHHhhhcc-cceEEEEc
Q 035150 10 ELFLVAYPYF-NVNEMLVVEELYKEAVFNT-ARKLIIFN 46 (72)
Q Consensus 10 ~lfVVAYP~f-NvnEml~v~eLye~a~~~~-~rpiIifN 46 (72)
+..+|.-|++ ..++ ..+.+-|+.-...+ +.|+++.|
T Consensus 105 d~vlv~~P~y~~~~~-~~l~~yf~~va~a~~~lPv~iYn 142 (309)
T cd00952 105 DGTMLGRPMWLPLDV-DTAVQFYRDVAEAVPEMAIAIYA 142 (309)
T ss_pred CEEEECCCcCCCCCH-HHHHHHHHHHHHhCCCCcEEEEc
Confidence 3456666754 4454 56667777766667 69999998
No 13
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=48.23 E-value=34 Score=24.35 Aligned_cols=37 Identities=24% Similarity=0.344 Sum_probs=25.4
Q ss_pred eEEEEEeccCC-hhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 10 ELFLVAYPYFN-VNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 10 ~lfVVAYP~fN-vnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
+..++..|++- .++ ..+.+-|++....++.|+++.|=
T Consensus 97 d~v~~~~P~~~~~~~-~~l~~~~~~ia~~~~~pi~lYn~ 134 (284)
T cd00950 97 DAALVVTPYYNKPSQ-EGLYAHFKAIAEATDLPVILYNV 134 (284)
T ss_pred CEEEEcccccCCCCH-HHHHHHHHHHHhcCCCCEEEEEC
Confidence 44566777664 343 44557777777778999999983
No 14
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=47.34 E-value=44 Score=23.96 Aligned_cols=38 Identities=18% Similarity=0.346 Sum_probs=26.3
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
|.+.+ .=|++..---..+.+-|++....++.||++.|=
T Consensus 98 d~v~v-~~P~~~~~s~~~l~~y~~~ia~~~~~pi~iYn~ 135 (289)
T PF00701_consen 98 DAVLV-IPPYYFKPSQEELIDYFRAIADATDLPIIIYNN 135 (289)
T ss_dssp SEEEE-EESTSSSCCHHHHHHHHHHHHHHSSSEEEEEEB
T ss_pred eEEEE-eccccccchhhHHHHHHHHHHhhcCCCEEEEEC
Confidence 44444 447655433335677888888899999999984
No 15
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=47.03 E-value=37 Score=23.98 Aligned_cols=38 Identities=21% Similarity=0.282 Sum_probs=25.9
Q ss_pred eEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 10 ELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 10 ~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
+..++.-|++..-.-..+.+-|++....++.|+++.|=
T Consensus 94 d~v~v~pP~y~~~~~~~~~~~~~~ia~~~~~pi~iYn~ 131 (281)
T cd00408 94 DGVLVVPPYYNKPSQEGIVAHFKAVADASDLPVILYNI 131 (281)
T ss_pred CEEEECCCcCCCCCHHHHHHHHHHHHhcCCCCEEEEEC
Confidence 34555667766532355666677766779999999985
No 16
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=46.73 E-value=17 Score=20.71 Aligned_cols=32 Identities=19% Similarity=0.169 Sum_probs=18.6
Q ss_pred cCChhHHHHHHHHHHHhhhcccceEEEEcCcc
Q 035150 18 YFNVNEMLVVEELYKEAVFNTARKLIIFNGEL 49 (72)
Q Consensus 18 ~fNvnEml~v~eLye~a~~~~~rpiIifNGEL 49 (72)
..|+.+.-..++-.++.......|.|.+||+.
T Consensus 30 ~~di~~~~~~~~el~~~~g~~~vP~v~i~~~~ 61 (73)
T cd03027 30 EINIDIFPERKAELEERTGSSVVPQIFFNEKL 61 (73)
T ss_pred EEECCCCHHHHHHHHHHhCCCCcCEEEECCEE
Confidence 34554433333333444445778999999963
No 17
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=44.29 E-value=73 Score=19.39 Aligned_cols=41 Identities=15% Similarity=0.185 Sum_probs=27.5
Q ss_pred CCCCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCc
Q 035150 3 DRVKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGE 48 (72)
Q Consensus 3 drv~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGE 48 (72)
..++++|-++++.++.-+.+=...++.+ +..+.|+|.+-++
T Consensus 43 ~~~~~~d~vi~iS~sG~t~~~~~~~~~a-----~~~g~~vi~iT~~ 83 (128)
T cd05014 43 GMVTPGDVVIAISNSGETDELLNLLPHL-----KRRGAPIIAITGN 83 (128)
T ss_pred CcCCCCCEEEEEeCCCCCHHHHHHHHHH-----HHCCCeEEEEeCC
Confidence 4567899999999999776544444444 3346677766554
No 18
>cd01892 Miro2 Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=44.17 E-value=81 Score=20.26 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=31.3
Q ss_pred CCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCcccc
Q 035150 8 EDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGELDR 51 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGELDR 51 (72)
+-.+++..|..-+......+.++++........|+|++---.|-
T Consensus 77 ~~d~~llv~d~~~~~s~~~~~~~~~~~~~~~~~p~iiv~NK~Dl 120 (169)
T cd01892 77 ACDVACLVYDSSDPKSFSYCAEVYKKYFMLGEIPCLFVAAKADL 120 (169)
T ss_pred cCCEEEEEEeCCCHHHHHHHHHHHHHhccCCCCeEEEEEEcccc
Confidence 34566777888888877777788876434457898888766664
No 19
>COG1679 Predicted aconitase [General function prediction only]
Probab=44.14 E-value=43 Score=27.71 Aligned_cols=40 Identities=20% Similarity=0.244 Sum_probs=35.5
Q ss_pred CCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 8 EDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
+-++.-++-|++...|+..+.++.++.-...++|++||-|
T Consensus 289 epdli~iGcPHaS~~E~~~la~~l~~r~~~~~~~~~V~~s 328 (403)
T COG1679 289 EPDLIALGCPHASLEELRRLAELLKGRKRPAGVPLYVTTS 328 (403)
T ss_pred CCCEEEeCCCCCCHHHHHHHHHHHhccCCCCCCCEEEEcC
Confidence 3367888999999999999999999987889999999976
No 20
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=43.73 E-value=22 Score=26.32 Aligned_cols=15 Identities=33% Similarity=0.306 Sum_probs=12.7
Q ss_pred hcccceEEEE-cCccc
Q 035150 36 FNTARKLIIF-NGELD 50 (72)
Q Consensus 36 ~~~~rpiIif-NGELD 50 (72)
..+.+||||. ||||=
T Consensus 125 eEg~CPIVIeKNGElL 140 (167)
T PF05320_consen 125 EEGTCPIVIEKNGELL 140 (167)
T ss_pred hcCCCcEEEeeCCeEc
Confidence 5789999997 99983
No 21
>PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional
Probab=43.52 E-value=34 Score=23.99 Aligned_cols=41 Identities=20% Similarity=0.315 Sum_probs=30.9
Q ss_pred EEEeccCChhHH-------HHHHHHHHHhhhcccceEEEEcCccccee
Q 035150 13 LVAYPYFNVNEM-------LVVEELYKEAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 13 VVAYP~fNvnEm-------l~v~eLye~a~~~~~rpiIifNGELDRiR 53 (72)
||+||--.+.=+ .+|+.||+-.-+..+.|++++-++++.+.
T Consensus 22 vv~~PTdTvYgL~~~~~n~~Av~ri~~iK~R~~~Kpl~ll~~~~~~l~ 69 (190)
T PRK10634 22 VIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLK 69 (190)
T ss_pred EEEEeCCchhhhhcCCCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHH
Confidence 677776544332 57889999877788899999999977665
No 22
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=42.86 E-value=51 Score=24.04 Aligned_cols=35 Identities=17% Similarity=0.216 Sum_probs=24.3
Q ss_pred EEEEEeccCC-hhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 11 LFLVAYPYFN-VNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 11 lfVVAYP~fN-vnEml~v~eLye~a~~~~~rpiIifN 46 (72)
..++.=|++. ++| ..+.+-|++-...++.|+++.|
T Consensus 97 ~v~~~pP~y~~~~~-~~i~~~f~~v~~~~~~pi~lYn 132 (289)
T cd00951 97 GILLLPPYLTEAPQ-EGLYAHVEAVCKSTDLGVIVYN 132 (289)
T ss_pred EEEECCCCCCCCCH-HHHHHHHHHHHhcCCCCEEEEe
Confidence 3445556554 454 5666777776667899999999
No 23
>PF14460 Prok-E2_D: Prokaryotic E2 family D
Probab=42.18 E-value=16 Score=25.40 Aligned_cols=21 Identities=29% Similarity=0.496 Sum_probs=16.3
Q ss_pred CCCCCCCeEEEEEeccCChhH
Q 035150 3 DRVKPEDELFLVAYPYFNVNE 23 (72)
Q Consensus 3 drv~~~D~lfVVAYP~fNvnE 23 (72)
+..+|+.+.-+--||+|||.+
T Consensus 82 ~~~rP~~~T~Ly~aPf~NV~~ 102 (175)
T PF14460_consen 82 GNERPTPDTPLYHAPFFNVYS 102 (175)
T ss_pred CCCCCCCCCeeEeCCccccCC
Confidence 455667777778899999974
No 24
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=41.42 E-value=50 Score=23.81 Aligned_cols=37 Identities=24% Similarity=0.346 Sum_probs=23.9
Q ss_pred EEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 11 LFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 11 lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
..++.-|++-.---..+.+-|++-...++.|+++.|=
T Consensus 96 ~v~v~pP~y~~~~~~~i~~~~~~i~~~~~~pi~lYn~ 132 (285)
T TIGR00674 96 GFLVVTPYYNKPTQEGLYQHFKAIAEEVDLPIILYNV 132 (285)
T ss_pred EEEEcCCcCCCCCHHHHHHHHHHHHhcCCCCEEEEEC
Confidence 3445556554322245566677766778999999984
No 25
>PF08237 PE-PPE: PE-PPE domain; InterPro: IPR013228 The human pathogen Mycobacterium tuberculosis harbours a large number of genes that encode proteins whose N-termini contain the characteristic motifs Pro-Glu (PE) or Pro-Pro-Glu (PPE). A subgroup of the PE proteins contains polymorphic GC-rich sequences (PGRS), while a subgroup of the PPE proteins contains major polymorphic tandem repeats (MPTR). The function of most of these proteins remains unknown []. However, the PE_PGRS proteins from Mycobacterium marinum are secreted by components of the ESX-5 system that belongs to the recently defined type VII secretion systems []. It has also been reported that the PE_PGRS family of proteins contains multiple calcium-binding and glycine-rich sequence motifs GGXGXD/NXUX. This sequence repeat constitutes a calcium-binding parallel beta-roll or parallel beta-helix structure and is found in RTX toxins secreted by many Gram-negative bacteria []. This domain is found C-terminal to the PE (IPR000084 from INTERPRO) and PPE (IPR000030 from INTERPRO) domains. The secondary structure of this domain is predicted to be a mixture of alpha helices and beta strands [].
Probab=40.88 E-value=64 Score=23.37 Aligned_cols=38 Identities=21% Similarity=0.362 Sum_probs=26.1
Q ss_pred CCCeEEEEEecc------------CChhHHHHHHHHHHHhhhc---ccceEEEE
Q 035150 7 PEDELFLVAYPY------------FNVNEMLVVEELYKEAVFN---TARKLIIF 45 (72)
Q Consensus 7 ~~D~lfVVAYP~------------fNvnEml~v~eLye~a~~~---~~rpiIif 45 (72)
|+.+...|.||. ||.+...-++.|-. ++.+ ++.|++||
T Consensus 1 p~~~~~~V~YPa~f~P~~g~~~~t~~~Sv~~G~~~L~~-ai~~~~~~~~~vvV~ 53 (225)
T PF08237_consen 1 PGYNVVAVDYPASFWPVTGIGSPTYDESVAEGVANLDA-AIRAAIAAGGPVVVF 53 (225)
T ss_pred CCcceEEecCCchhcCcCCCCCCccchHHHHHHHHHHH-HHHhhccCCCCEEEE
Confidence 345667778877 67787778888754 3333 77887776
No 26
>KOG2619 consensus Fucosyltransferase [Carbohydrate transport and metabolism; Amino acid transport and metabolism]
Probab=40.02 E-value=22 Score=28.52 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=30.0
Q ss_pred HHHHHHHHHhhhcccceEEEEcCcccceecccccchhheee
Q 035150 25 LVVEELYKEAVFNTARKLIIFNGELDRIRSGCILHHSFIII 65 (72)
Q Consensus 25 l~v~eLye~a~~~~~rpiIifNGELDRiRsgYYP~~~f~~~ 65 (72)
-++|.+| .+...+..|||+=- ..+..+-|+.+||-+
T Consensus 265 YVTEKfw-~al~~gsVPVvlg~----~n~e~fvP~~SfI~v 300 (372)
T KOG2619|consen 265 YVTEKFW-NALDAGSVPVVLGP----PNYENFVPPDSFIHV 300 (372)
T ss_pred cccHHHH-hhhhcCcccEEECC----ccccccCCCcceEeh
Confidence 4899999 88899999999843 667788999999864
No 27
>KOG1594 consensus Uncharacterized enzymes related to aldose 1-epimerase [Carbohydrate transport and metabolism]
Probab=39.12 E-value=17 Score=29.06 Aligned_cols=17 Identities=41% Similarity=0.839 Sum_probs=14.8
Q ss_pred hcccceEEEEcCcccce
Q 035150 36 FNTARKLIIFNGELDRI 52 (72)
Q Consensus 36 ~~~~rpiIifNGELDRi 52 (72)
..-.++.|.||||+||+
T Consensus 199 ~tE~~davTF~~e~Drv 215 (305)
T KOG1594|consen 199 FTEQRDAVTFNSEVDRV 215 (305)
T ss_pred ccccCceEeeccceeeE
Confidence 35579999999999998
No 28
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=38.86 E-value=24 Score=20.09 Aligned_cols=35 Identities=6% Similarity=-0.011 Sum_probs=19.8
Q ss_pred EeccCChhHHHHHHHHHHHhhhcccceEEEEcCcc
Q 035150 15 AYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGEL 49 (72)
Q Consensus 15 AYP~fNvnEml~v~eLye~a~~~~~rpiIifNGEL 49 (72)
.|...|+.+--...+-+++.......|.|.+||+.
T Consensus 25 ~~~~~di~~~~~~~~~~~~~~g~~~vP~i~i~g~~ 59 (79)
T TIGR02181 25 TFTEIRVDGDPALRDEMMQRSGRRTVPQIFIGDVH 59 (79)
T ss_pred CcEEEEecCCHHHHHHHHHHhCCCCcCEEEECCEE
Confidence 34455554332222223333346789999999964
No 29
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=38.79 E-value=27 Score=19.43 Aligned_cols=11 Identities=9% Similarity=-0.025 Sum_probs=9.6
Q ss_pred cceEEEEcCcc
Q 035150 39 ARKLIIFNGEL 49 (72)
Q Consensus 39 ~rpiIifNGEL 49 (72)
..|.|++||+.
T Consensus 51 ~vP~v~i~g~~ 61 (75)
T cd03418 51 TVPQIFIGDVH 61 (75)
T ss_pred ccCEEEECCEE
Confidence 78999999974
No 30
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=35.18 E-value=81 Score=22.86 Aligned_cols=36 Identities=14% Similarity=0.336 Sum_probs=22.8
Q ss_pred EEEEEeccCC-hhHHHHHHHHHHHhhhcc-cceEEEEcC
Q 035150 11 LFLVAYPYFN-VNEMLVVEELYKEAVFNT-ARKLIIFNG 47 (72)
Q Consensus 11 lfVVAYP~fN-vnEml~v~eLye~a~~~~-~rpiIifNG 47 (72)
..++.-|++. +++ ..+.+-|++-...+ +.|+++.|=
T Consensus 99 ~v~~~~P~y~~~~~-~~i~~~~~~v~~a~~~lpi~iYn~ 136 (288)
T cd00954 99 AISAITPFYYKFSF-EEIKDYYREIIAAAASLPMIIYHI 136 (288)
T ss_pred EEEEeCCCCCCCCH-HHHHHHHHHHHHhcCCCCEEEEeC
Confidence 3445556554 343 34556666666667 899999984
No 31
>COG0676 Uncharacterized enzymes related to aldose 1-epimerase [Carbohydrate transport and metabolism]
Probab=34.49 E-value=13 Score=29.23 Aligned_cols=40 Identities=28% Similarity=0.424 Sum_probs=26.3
Q ss_pred ccCChhHHHHH----------HHHHHHhhhcccceEEEEcCcccceeccc
Q 035150 17 PYFNVNEMLVV----------EELYKEAVFNTARKLIIFNGELDRIRSGC 56 (72)
Q Consensus 17 P~fNvnEml~v----------~eLye~a~~~~~rpiIifNGELDRiRsgY 56 (72)
|||+|+-...| .++.++..--+.-+++.|+|+.|||=.+=
T Consensus 158 tYF~VgDi~qv~V~GL~~~~~~~~~~~~~~v~~~g~~~~~~~~DriY~~~ 207 (287)
T COG0676 158 TYFRVGDIEQVEVSGLGGVCIDKVLNAEEEVTQHGIVTFPGETDRIYLNP 207 (287)
T ss_pred ceEEecchhheEeccCCceehhhhhhceeeccCCCceeeCCCccEEEEcC
Confidence 89999865543 22222222244566899999999997664
No 32
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=34.36 E-value=82 Score=22.87 Aligned_cols=35 Identities=14% Similarity=0.379 Sum_probs=23.5
Q ss_pred EEEEEeccC-ChhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 11 LFLVAYPYF-NVNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 11 lfVVAYP~f-NvnEml~v~eLye~a~~~~~rpiIifN 46 (72)
..+|.=|++ .+++ ..+.+-|++-...++.|+++.|
T Consensus 102 ~v~v~~P~y~~~~~-~~l~~~f~~va~a~~lPv~iYn 137 (293)
T PRK04147 102 AISAVTPFYYPFSF-EEICDYYREIIDSADNPMIVYN 137 (293)
T ss_pred EEEEeCCcCCCCCH-HHHHHHHHHHHHhCCCCEEEEe
Confidence 344445654 4454 4556667776667889999999
No 33
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=33.82 E-value=85 Score=23.04 Aligned_cols=37 Identities=11% Similarity=0.296 Sum_probs=22.8
Q ss_pred EEEEEeccCChhHHHHHHHHHHHhhhcc-cceEEEEcC
Q 035150 11 LFLVAYPYFNVNEMLVVEELYKEAVFNT-ARKLIIFNG 47 (72)
Q Consensus 11 lfVVAYP~fNvnEml~v~eLye~a~~~~-~rpiIifNG 47 (72)
..+|.-|++...--..+.+-|++-...+ +.|+++.|=
T Consensus 99 ~v~v~~P~y~~~~~~~i~~yf~~v~~~~~~lpv~lYn~ 136 (290)
T TIGR00683 99 CLSAVTPFYYKFSFPEIKHYYDTIIAETGGLNMIVYSI 136 (290)
T ss_pred EEEEeCCcCCCCCHHHHHHHHHHHHhhCCCCCEEEEeC
Confidence 4455667665542345555566554445 799999984
No 34
>PRK03592 haloalkane dehalogenase; Provisional
Probab=33.66 E-value=60 Score=22.20 Aligned_cols=21 Identities=14% Similarity=0.131 Sum_probs=16.9
Q ss_pred HhhhcccceEEEEcCccccee
Q 035150 33 EAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 33 ~a~~~~~rpiIifNGELDRiR 53 (72)
+....-.+|+.+++|+.|++-
T Consensus 222 ~~l~~i~~P~lii~G~~D~~~ 242 (295)
T PRK03592 222 QWLATSDVPKLLINAEPGAIL 242 (295)
T ss_pred HHhccCCCCeEEEeccCCccc
Confidence 344556899999999999975
No 35
>cd03135 GATase1_DJ-1 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. DJ-1 is involved in multiple physiological processes including cancer, Parkinson's disease and male fertility. It is unclear how DJ-1 functions in these. DJ-1 has been shown to possess chaperone activity. DJ-1 is preferentially expressed in the testis and moderately in other tissues; it is induced together with genes involved in oxidative stress response. The Drosophila homologue (DJ-1A) plays an essential role in oxidative stress response and neuronal maintenance. Inhibition of DJ-1A function through RNAi, results in the cellular accumulation of reactive oxygen species, organismal hypersensitivity to oxidative stress, and dysfunction and degeneration of dopaminergic and photoreceptor neurons. DJ-1 has lacks enzymatic activity and the catalytic triad of typical GATase1 domains, however it does contain the highly
Probab=32.59 E-value=58 Score=20.44 Aligned_cols=23 Identities=13% Similarity=0.190 Sum_probs=20.1
Q ss_pred EEEEeccCChhHHHHHHHHHHHh
Q 035150 12 FLVAYPYFNVNEMLVVEELYKEA 34 (72)
Q Consensus 12 fVVAYP~fNvnEml~v~eLye~a 34 (72)
.++.||.|+..|+....+.++.+
T Consensus 2 ~il~~~gf~~~e~~~~~~~~~~a 24 (163)
T cd03135 2 LVILADGFEEIEAVTPVDVLRRA 24 (163)
T ss_pred EEEecCCcchHHHHHHHHHHHHC
Confidence 57899999999999998888854
No 36
>TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE.
Probab=31.99 E-value=51 Score=22.51 Aligned_cols=11 Identities=9% Similarity=0.437 Sum_probs=10.0
Q ss_pred ccceEEEEcCc
Q 035150 38 TARKLIIFNGE 48 (72)
Q Consensus 38 ~~rpiIifNGE 48 (72)
.++|++++||+
T Consensus 114 ~~kpv~~l~~~ 124 (159)
T TIGR00725 114 LGGPVVVLRGT 124 (159)
T ss_pred cCCCEEEEECC
Confidence 68999999986
No 37
>cd04142 RRP22 RRP22 subfamily. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated.
Probab=31.34 E-value=1.7e+02 Score=19.81 Aligned_cols=44 Identities=14% Similarity=0.303 Sum_probs=30.7
Q ss_pred CCeEEEEEeccCChhHHHHHHHHHHHhhh-----cccceEEEEcCcccc
Q 035150 8 EDELFLVAYPYFNVNEMLVVEELYKEAVF-----NTARKLIIFNGELDR 51 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnEml~v~eLye~a~~-----~~~rpiIifNGELDR 51 (72)
+.+++++.|-..|...+..+.++++.... ..+.|+|++---.|.
T Consensus 80 ~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl 128 (198)
T cd04142 80 NSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQ 128 (198)
T ss_pred cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccc
Confidence 45567777888888888888888775443 356788777555554
No 38
>PF05406 WGR: WGR domain; InterPro: IPR008893 This domain is named after the most conserved central motif of the domain. It is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator P33345 from SWISSPROT and other proteins of unknown function.The domain is found in isolation in proteins such as Q9JN21 from SWISSPROT and is between 70 and 80 residues in length. ; PDB: 2EOC_A 2RA8_A 4DQY_C 2CR9_A.
Probab=30.49 E-value=1.3e+02 Score=18.05 Aligned_cols=30 Identities=27% Similarity=0.474 Sum_probs=20.8
Q ss_pred ccCChhHHH-HHHHHHHHhhhcccceEEEEcCcccceecccccchhhe
Q 035150 17 PYFNVNEML-VVEELYKEAVFNTARKLIIFNGELDRIRSGCILHHSFI 63 (72)
Q Consensus 17 P~fNvnEml-~v~eLye~a~~~~~rpiIifNGELDRiRsgYYP~~~f~ 63 (72)
|+-+..|.. ..++++++ +++.||-|+..|.
T Consensus 51 ~f~s~~eA~~~f~~~~~~-----------------K~~~gy~~~~~f~ 81 (81)
T PF05406_consen 51 PFDSEEEAIKEFEKLFKE-----------------KTGKGYEERDNFA 81 (81)
T ss_dssp EESSHHHHHHHHHHHHHH-----------------HHSSTSCCCGG--
T ss_pred eCCCHHHHHHHHHHHHHH-----------------HHcCCCcccccCC
Confidence 555777766 66777765 6888999988873
No 39
>PF00852 Glyco_transf_10: Glycosyltransferase family 10 (fucosyltransferase); InterPro: IPR001503 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 10 GT10 from CAZY comprises enzymes with two known activities; galactoside 3(4)-L-fucosyltransferase (2.4.1.65 from EC) and galactoside 3-fucosyltransferase (2.4.1.152 from EC). The galactoside 3-fucosyltransferases display similarities with the alpha-2 and alpha-6-fucosyltranferases []. The biosynthesis of the carbohydrate antigen sialyl Lewis X (sLe(x)) is dependent on the activity of an galactoside 3-fucosyltransferase. This enzyme catalyses the transfer of fucose from GDP-beta-fucose to the 3-OH of N-acetylglucosamine present in lactosamine acceptors []. Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Galactoside 3(4)-L-fucosyltransferase (2.4.1.65 from EC) belongs to the Lewis blood group system and is associated with Le(a/b) antigen. ; GO: 0008417 fucosyltransferase activity, 0006486 protein glycosylation, 0016020 membrane; PDB: 2NZX_B 2NZW_C 2NZY_C.
Probab=30.43 E-value=44 Score=25.33 Aligned_cols=38 Identities=13% Similarity=0.197 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHhhhcccceEEEE--cCcccceecccccchhheee
Q 035150 23 EMLVVEELYKEAVFNTARKLIIF--NGELDRIRSGCILHHSFIII 65 (72)
Q Consensus 23 Eml~v~eLye~a~~~~~rpiIif--NGELDRiRsgYYP~~~f~~~ 65 (72)
+=-++|.+| +|...+..||+.= ..+.++ +.|+.|||-+
T Consensus 240 ~dYiTEK~~-~al~~g~VPI~~G~~~~~~~~----~~P~~SfI~~ 279 (349)
T PF00852_consen 240 PDYITEKFW-NALLAGTVPIYWGPPRPNYEE----FAPPNSFIHV 279 (349)
T ss_dssp TT---HHHH-HHHHTTSEEEEES---TTHHH----HS-GGGSEEG
T ss_pred CCCCCHHHH-HHHHCCeEEEEECCEeccccc----CCCCCCccch
Confidence 334789999 8899999999985 456665 4899999853
No 40
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=30.07 E-value=1.4e+02 Score=21.07 Aligned_cols=38 Identities=32% Similarity=0.505 Sum_probs=30.9
Q ss_pred CCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEE
Q 035150 5 VKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLII 44 (72)
Q Consensus 5 v~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIi 44 (72)
++..|++|+-..=+|-|+==..+.+||+. -+++-+|++
T Consensus 70 l~as~slflYVN~sFAPsPDq~v~~Ly~c--f~~d~~Lvl 107 (116)
T KOG3439|consen 70 LQASDSLFLYVNNSFAPSPDQIVGNLYEC--FGTDGKLVL 107 (116)
T ss_pred CcccCeEEEEEcCccCCCchhHHHHHHHh--cCCCCEEEE
Confidence 46789999999999999988899999997 445545553
No 41
>cd03132 GATase1_catalase Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Catalase catalyzes the dismutation of hydrogen peroxide (H2O2) to water and oxygen. This group includes the large catalases: Neurospora crassa Catalase-1 and Catalase-3 and, Escherichia coli HP-II. This GATase1-like domain has an essential role in HP-II catalase activity. However, it lacks enzymatic activity and the catalytic triad typical of GATase1 domains. Catalase-1 and -3 are homotetrameric, HP-II is homohexameric. It has been proposed that this domain may facilitate the folding and oligomerization process. The interface between this GATase1-like domain of HP-II and the core of the subunit forms part of a channel which provides access to the deeply buried catalase active sites of HPII. Catalase-1 is associated with non-growing cells; C
Probab=29.98 E-value=1.1e+02 Score=19.25 Aligned_cols=25 Identities=12% Similarity=0.129 Sum_probs=21.9
Q ss_pred eEEEEEeccCChhHHHHHHHHHHHh
Q 035150 10 ELFLVAYPYFNVNEMLVVEELYKEA 34 (72)
Q Consensus 10 ~lfVVAYP~fNvnEml~v~eLye~a 34 (72)
.+.++.||.|...|.....+.++.+
T Consensus 3 ~v~ill~~g~~~~e~~~~~~~~~~a 27 (142)
T cd03132 3 KVGILVADGVDAAELSALKAALKAA 27 (142)
T ss_pred EEEEEEcCCcCHHHHHHHHHHHHHC
Confidence 4778999999999999999998864
No 42
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=29.98 E-value=1.3e+02 Score=18.00 Aligned_cols=40 Identities=10% Similarity=0.252 Sum_probs=24.8
Q ss_pred CCCCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcC
Q 035150 3 DRVKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNG 47 (72)
Q Consensus 3 drv~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNG 47 (72)
..++++|-++++.++.-+..=...++.+ +..+.|+|.+-+
T Consensus 49 ~~~~~~d~vi~is~sg~~~~~~~~~~~a-----k~~g~~vi~iT~ 88 (131)
T PF01380_consen 49 ENLDPDDLVIIISYSGETRELIELLRFA-----KERGAPVILITS 88 (131)
T ss_dssp GGCSTTEEEEEEESSSTTHHHHHHHHHH-----HHTTSEEEEEES
T ss_pred ccccccceeEeeeccccchhhhhhhHHH-----HhcCCeEEEEeC
Confidence 4577888899999888654333344433 345566666654
No 43
>cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=29.56 E-value=1.1e+02 Score=17.08 Aligned_cols=38 Identities=11% Similarity=0.085 Sum_probs=24.4
Q ss_pred CCCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 4 RVKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 4 rv~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifN 46 (72)
..+++|-++++.++..+..-...++.+ +..+.|+|.+-
T Consensus 44 ~~~~~d~~i~iS~sg~t~~~~~~~~~a-----~~~g~~ii~it 81 (87)
T cd04795 44 LLRKGDVVIALSYSGRTEELLAALEIA-----KELGIPVIAIT 81 (87)
T ss_pred cCCCCCEEEEEECCCCCHHHHHHHHHH-----HHcCCeEEEEe
Confidence 456788899999988876533344444 33456776653
No 44
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=29.44 E-value=1e+02 Score=22.16 Aligned_cols=36 Identities=22% Similarity=0.272 Sum_probs=23.7
Q ss_pred eEEEEEecc-CChhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 10 ELFLVAYPY-FNVNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 10 ~lfVVAYP~-fNvnEml~v~eLye~a~~~~~rpiIifN 46 (72)
+..++.-|+ +..++ ..+.+-|++-...++.|+++.|
T Consensus 98 d~v~~~pP~~~~~~~-~~i~~~~~~ia~~~~~pv~lYn 134 (292)
T PRK03170 98 DGALVVTPYYNKPTQ-EGLYQHFKAIAEATDLPIILYN 134 (292)
T ss_pred CEEEECCCcCCCCCH-HHHHHHHHHHHhcCCCCEEEEE
Confidence 344555675 45444 4455667766667889999998
No 45
>COG1559 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]
Probab=29.18 E-value=41 Score=26.54 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=23.9
Q ss_pred eccCChhHHHHHHHHHHH-hhhcccceEE
Q 035150 16 YPYFNVNEMLVVEELYKE-AVFNTARKLI 43 (72)
Q Consensus 16 YP~fNvnEml~v~eLye~-a~~~~~rpiI 43 (72)
+|+-+++|++-+.++=|. +....+||+|
T Consensus 206 lp~~t~~e~ltlASIVEKEa~~~~Erp~I 234 (342)
T COG1559 206 LPGKTPYELLTLASIVEKEAAVDEERPKI 234 (342)
T ss_pred CCCCCHHHHHHHHHHHHHhhcccccchhh
Confidence 689999999999999994 4456899987
No 46
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=28.65 E-value=84 Score=22.06 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=21.1
Q ss_pred HHHhhhcccceEEEEcCcccceecccc
Q 035150 31 YKEAVFNTARKLIIFNGELDRIRSGCI 57 (72)
Q Consensus 31 ye~a~~~~~rpiIifNGELDRiRsgYY 57 (72)
+++......+|||+|==||||.+..+.
T Consensus 163 ~~~~l~~~~~~iViiIDdLDR~~~~~i 189 (325)
T PF07693_consen 163 IKKKLKESKKRIVIIIDDLDRCSPEEI 189 (325)
T ss_pred HHHhhhcCCceEEEEEcchhcCCcHHH
Confidence 345555689999999999999876643
No 47
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=28.51 E-value=1.2e+02 Score=22.33 Aligned_cols=34 Identities=18% Similarity=0.292 Sum_probs=24.0
Q ss_pred EEEEeccCC-hhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 12 FLVAYPYFN-VNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 12 fVVAYP~fN-vnEml~v~eLye~a~~~~~rpiIifN 46 (72)
.++.=|++. ++| ..+.+-|++....++.|+++.|
T Consensus 105 v~~~pP~y~~~~~-~~i~~~f~~va~~~~lpi~lYn 139 (303)
T PRK03620 105 ILLLPPYLTEAPQ-EGLAAHVEAVCKSTDLGVIVYN 139 (303)
T ss_pred EEECCCCCCCCCH-HHHHHHHHHHHHhCCCCEEEEc
Confidence 344556544 444 5566777777778899999999
No 48
>KOG1455 consensus Lysophospholipase [Lipid transport and metabolism]
Probab=27.95 E-value=76 Score=25.30 Aligned_cols=45 Identities=22% Similarity=0.435 Sum_probs=34.6
Q ss_pred CCCeEEEEEeccCChh-HHH-HHHHHHHHhhhcccceEEEEcCcccce
Q 035150 7 PEDELFLVAYPYFNVN-EML-VVEELYKEAVFNTARKLIIFNGELDRI 52 (72)
Q Consensus 7 ~~D~lfVVAYP~fNvn-Eml-~v~eLye~a~~~~~rpiIifNGELDRi 52 (72)
.+|-+-..++|....- ||+ +...| ++..-.-..|++|.+|+=|++
T Consensus 213 ~~npl~y~g~pRl~T~~ElLr~~~~l-e~~l~~vtvPflilHG~dD~V 259 (313)
T KOG1455|consen 213 RSDPLCYTGKPRLKTAYELLRVTADL-EKNLNEVTVPFLILHGTDDKV 259 (313)
T ss_pred hcCCceecCCccHHHHHHHHHHHHHH-HHhcccccccEEEEecCCCcc
Confidence 4566777788888876 999 45555 444567899999999999986
No 49
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=27.77 E-value=1.6e+02 Score=18.43 Aligned_cols=42 Identities=7% Similarity=0.029 Sum_probs=27.5
Q ss_pred CCCCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCcc
Q 035150 3 DRVKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGEL 49 (72)
Q Consensus 3 drv~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGEL 49 (72)
..++++|-++++.+..-+.+=...++.+ ++.+.|+|.+-++-
T Consensus 43 ~~~~~~dl~I~iS~SG~t~~~~~~~~~a-----~~~g~~vi~iT~~~ 84 (120)
T cd05710 43 KRLTEKSVVILASHSGNTKETVAAAKFA-----KEKGATVIGLTDDE 84 (120)
T ss_pred ccCCCCcEEEEEeCCCCChHHHHHHHHH-----HHcCCeEEEEECCC
Confidence 3577888889999888665544454444 23467887776543
No 50
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=27.64 E-value=1.8e+02 Score=19.08 Aligned_cols=39 Identities=18% Similarity=0.146 Sum_probs=28.2
Q ss_pred CCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCc
Q 035150 5 VKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGE 48 (72)
Q Consensus 5 v~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGE 48 (72)
.+++|-++++.|+..+.+=+..++.+ +..+.|+|.+-+.
T Consensus 77 ~~~~D~~i~iS~sG~t~~~~~~~~~a-----~~~g~~ii~iT~~ 115 (154)
T TIGR00441 77 GQKGDVLLGISTSGNSKNVLKAIEAA-----KDKGMKTITLAGK 115 (154)
T ss_pred CCCCCEEEEEcCCCCCHHHHHHHHHH-----HHCCCEEEEEeCC
Confidence 58899999999999876644444444 4457888888664
No 51
>PRK11574 oxidative-stress-resistance chaperone; Provisional
Probab=27.61 E-value=88 Score=20.81 Aligned_cols=25 Identities=12% Similarity=0.104 Sum_probs=22.0
Q ss_pred eEEEEEeccCChhHHHHHHHHHHHh
Q 035150 10 ELFLVAYPYFNVNEMLVVEELYKEA 34 (72)
Q Consensus 10 ~lfVVAYP~fNvnEml~v~eLye~a 34 (72)
.+.|+.||.|...|+....+.++.+
T Consensus 4 ~~~il~~~g~~~~e~~~p~~~l~~a 28 (196)
T PRK11574 4 SALVCLAPGSEETEAVTTIDLLVRG 28 (196)
T ss_pred eEEEEeCCCcchhhHhHHHHHHHHC
Confidence 4789999999999999888888875
No 52
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=27.38 E-value=1.5e+02 Score=18.06 Aligned_cols=37 Identities=5% Similarity=0.146 Sum_probs=28.1
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhhc--ccceEEEE
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVFN--TARKLIIF 45 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~~--~~rpiIif 45 (72)
-+.+++.|-.-|.+-...+..+++..... .+.|+|++
T Consensus 72 ~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivv 110 (162)
T PF00071_consen 72 SDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVV 110 (162)
T ss_dssp ESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEE
T ss_pred cccccccccccccccccccccccccccccccccccceee
Confidence 35788999988988888888888865543 35788777
No 53
>PHA02737 hypothetical protein; Provisional
Probab=27.33 E-value=42 Score=21.82 Aligned_cols=17 Identities=29% Similarity=0.133 Sum_probs=13.4
Q ss_pred CCCCeEEEEEeccCChh
Q 035150 6 KPEDELFLVAYPYFNVN 22 (72)
Q Consensus 6 ~~~D~lfVVAYP~fNvn 22 (72)
+.+|+--+||||--+..
T Consensus 40 ~~td~kv~VaYP~~Edp 56 (72)
T PHA02737 40 KATDQKSIVAYFEGEDP 56 (72)
T ss_pred eccCceEEEEccCCCCc
Confidence 46789999999985544
No 54
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=27.32 E-value=63 Score=22.75 Aligned_cols=23 Identities=26% Similarity=0.354 Sum_probs=20.0
Q ss_pred CCCCCCCCeEEEEEeccCChhHH
Q 035150 2 ADRVKPEDELFLVAYPYFNVNEM 24 (72)
Q Consensus 2 adrv~~~D~lfVVAYP~fNvnEm 24 (72)
|..++++|.+.+.+|=.++..|+
T Consensus 76 Ar~~~~GD~vII~ay~~~~~~e~ 98 (126)
T PRK05449 76 ARLVQVGDLVIIAAYAQMDEEEA 98 (126)
T ss_pred HhcCCCCCEEEEEECccCCHHHH
Confidence 45789999999999999998864
No 55
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=26.35 E-value=69 Score=22.61 Aligned_cols=23 Identities=22% Similarity=0.224 Sum_probs=19.9
Q ss_pred CCCCCCCCeEEEEEeccCChhHH
Q 035150 2 ADRVKPEDELFLVAYPYFNVNEM 24 (72)
Q Consensus 2 adrv~~~D~lfVVAYP~fNvnEm 24 (72)
|..++++|.+.+.+|=.++..|.
T Consensus 76 Arl~~~GD~VII~sy~~~~~~e~ 98 (126)
T TIGR00223 76 ARCVSVGDIVIIASYVTMPDEEA 98 (126)
T ss_pred HhcCCCCCEEEEEECCcCCHHHH
Confidence 46789999999999999988764
No 56
>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
Probab=26.25 E-value=1.2e+02 Score=19.81 Aligned_cols=30 Identities=10% Similarity=0.208 Sum_probs=23.2
Q ss_pred ChhHHHHHHHHHHHhhhc---ccceEEEEcCcc
Q 035150 20 NVNEMLVVEELYKEAVFN---TARKLIIFNGEL 49 (72)
Q Consensus 20 NvnEml~v~eLye~a~~~---~~rpiIifNGEL 49 (72)
+..-+..+++-|+..... ...|+++.||+-
T Consensus 154 ~~~~~~~l~~~y~~~~~~~~~~~~~~~vid~~~ 186 (193)
T cd01673 154 PLDYLEDLHEAYEKWFLPQMYEKAPVLIIDANE 186 (193)
T ss_pred CHHHHHHHHHHHHHHHhhccCCCCCEEEEECCc
Confidence 345566899999988875 568999999975
No 57
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=26.01 E-value=70 Score=22.11 Aligned_cols=23 Identities=26% Similarity=0.485 Sum_probs=19.6
Q ss_pred CCCCCCCCeEEEEEeccCChhHH
Q 035150 2 ADRVKPEDELFLVAYPYFNVNEM 24 (72)
Q Consensus 2 adrv~~~D~lfVVAYP~fNvnEm 24 (72)
|.+++++|.+.+.+|=.++..|.
T Consensus 75 Ar~~~~GD~vII~sy~~~~~~e~ 97 (111)
T cd06919 75 ARLGQPGDRVIIMAYALMDEEEA 97 (111)
T ss_pred HhcCCCCCEEEEEECccCCHHHH
Confidence 45789999999999999987754
No 58
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=25.87 E-value=63 Score=22.45 Aligned_cols=43 Identities=19% Similarity=0.433 Sum_probs=31.1
Q ss_pred EEEEEeccCC---hhHHHHHHHHHHHhhh-------cc--cceEEEEcCccccee
Q 035150 11 LFLVAYPYFN---VNEMLVVEELYKEAVF-------NT--ARKLIIFNGELDRIR 53 (72)
Q Consensus 11 lfVVAYP~fN---vnEml~v~eLye~a~~-------~~--~rpiIifNGELDRiR 53 (72)
...|+|++++ ...+..++.-|.+.+. .+ ---+++..|+.+|+|
T Consensus 59 ~i~vvy~h~~~~~~~~l~~iqhey~~~iiss~h~hl~~~~ClE~~vv~G~~~~i~ 113 (136)
T COG0864 59 VITVVYDHEKRDVEEKLADIQHEYTDIIISSLHVHLDGDNCLEVIVVKGDSERIR 113 (136)
T ss_pred EEEEEEccccchHHHHHHHHhhhccceEEEEeeEEcCCCceEEEEEEecCchhHH
Confidence 5679999999 4566677777877665 22 123788889998886
No 59
>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily. RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu
Probab=25.59 E-value=1.7e+02 Score=18.08 Aligned_cols=41 Identities=12% Similarity=0.192 Sum_probs=26.5
Q ss_pred eEEEEEeccCChhHHHHHHHHHHHhhh----cccceEEEEcCccc
Q 035150 10 ELFLVAYPYFNVNEMLVVEELYKEAVF----NTARKLIIFNGELD 50 (72)
Q Consensus 10 ~lfVVAYP~fNvnEml~v~eLye~a~~----~~~rpiIifNGELD 50 (72)
..+++.|..-|.+-...++.+++.... ....|+|++---.|
T Consensus 73 d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilv~nK~D 117 (165)
T cd04146 73 DGFVLVYSITDRSSFDEISQLKQLIREIKKRDREIPVILVGNKAD 117 (165)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCc
Confidence 467888888888766666666654333 34788877644444
No 60
>TIGR01382 PfpI intracellular protease, PfpI family. The member of this family from Pyrococcus horikoshii has been solved to 2 Angstrom resolution. It is an ATP-independent intracellular protease that crystallizes as a hexameric ring. Cys-101 is proposed as the active site residue in a catalytic triad with the adjacent His-102 and a Glu residue from an adjacent monomer. A member of this family from Bacillus subtilis, GSP18, has been shown to be expressed in response to several forms of stress. A role in the degradation of small peptides has been suggested. A closely related family consists of the thiamine biosynthesis protein ThiJ and its homologs.
Probab=25.28 E-value=1.1e+02 Score=19.56 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=20.2
Q ss_pred EEEEEeccCChhHHHHHHHHHHHh
Q 035150 11 LFLVAYPYFNVNEMLVVEELYKEA 34 (72)
Q Consensus 11 lfVVAYP~fNvnEml~v~eLye~a 34 (72)
+.++.+|.|+..|+....+.++++
T Consensus 2 v~il~~~g~~~~e~~~~~~~l~~a 25 (166)
T TIGR01382 2 LLVLTTDEFEDSELLYPLDRLREA 25 (166)
T ss_pred EEEEecCCchHHHHHHHHHHHHHC
Confidence 467899999999999888887754
No 61
>PF00326 Peptidase_S9: Prolyl oligopeptidase family This family belongs to family S9 of the peptidase classification.; InterPro: IPR001375 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain covers the active site serine of the serine peptidases belonging to MEROPS peptidase family S9 (prolyl oligopeptidase family, clan SC). The protein fold of the peptidase domain for members of this family resembles that of serine carboxypeptidase D, the type example of clan SC. Examples of protein families containing this domain are: Prolyl endopeptidase (3.4.21.26 from EC) (PE) (also called post-proline cleaving enzyme). PE is an enzyme that cleaves peptide bonds on the C-terminal side of prolyl residues. The sequence of PE has been obtained from a mammalian species (pig) and from bacteria (Flavobacterium meningosepticum and Aeromonas hydrophila); there is a high degree of sequence conservation between these sequences. Escherichia coli protease II (3.4.21.83 from EC) (oligopeptidase B) (gene prtB) which cleaves peptide bonds on the C-terminal side of lysyl and argininyl residues. Dipeptidyl peptidase IV (3.4.14.5 from EC) (DPP IV). DPP IV is an enzyme that removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline. Saccharomyces cerevisiae (Baker's yeast) vacuolar dipeptidyl aminopeptidases A and B (DPAP A and DPAP B), encoded by the STE13 and DAP2 genes respectively. DPAP A is responsible for the proteolytic maturation of the alpha-factor precursor. Acylamino-acid-releasing enzyme (3.4.19.1 from EC) (acyl-peptide hydrolase). This enzyme catalyses the hydrolysis of the amino-terminal peptide bond of an N-acetylated protein to generate a N-acetylated amino acid and a protein with a free amino-terminus. These proteins belong to MEROPS peptidase families S9A, S9B and S9C.; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis; PDB: 2AJ8_D 1ORV_D 2AJB_C 2BUC_D 1ORW_D 2AJC_D 2AJD_C 2BUA_A 2HU8_B 3O4J_B ....
Probab=25.21 E-value=69 Score=21.02 Aligned_cols=15 Identities=27% Similarity=0.377 Sum_probs=13.4
Q ss_pred ccceEEEEcCcccce
Q 035150 38 TARKLIIFNGELDRI 52 (72)
Q Consensus 38 ~~rpiIifNGELDRi 52 (72)
...|+++++|+-|.+
T Consensus 143 ~~~P~li~hG~~D~~ 157 (213)
T PF00326_consen 143 IKPPVLIIHGENDPR 157 (213)
T ss_dssp GGSEEEEEEETTBSS
T ss_pred CCCCEEEEccCCCCc
Confidence 689999999999974
No 62
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=25.10 E-value=1.5e+02 Score=21.78 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=24.8
Q ss_pred eEEEEEec-cCChhHHHHHHHHHHHhhhcc-cceEEEEcC
Q 035150 10 ELFLVAYP-YFNVNEMLVVEELYKEAVFNT-ARKLIIFNG 47 (72)
Q Consensus 10 ~lfVVAYP-~fNvnEml~v~eLye~a~~~~-~rpiIifNG 47 (72)
+..++.-| ||.+++ ..+.+-|+.-+..+ +.|+++.|=
T Consensus 97 d~v~v~pP~y~~~~~-~~l~~~f~~ia~a~~~lpv~iYn~ 135 (294)
T TIGR02313 97 DAAMVIVPYYNKPNQ-EALYDHFAEVADAVPDFPIIIYNI 135 (294)
T ss_pred CEEEEcCccCCCCCH-HHHHHHHHHHHHhccCCCEEEEeC
Confidence 34555567 555555 55666667666677 899999983
No 63
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=24.81 E-value=61 Score=18.43 Aligned_cols=21 Identities=19% Similarity=0.074 Sum_probs=14.7
Q ss_pred hcccceEEEEcCcccceeccccc
Q 035150 36 FNTARKLIIFNGELDRIRSGCIL 58 (72)
Q Consensus 36 ~~~~rpiIifNGELDRiRsgYYP 58 (72)
.....|.|++||+ ..-+||=|
T Consensus 45 g~~~vP~v~~~g~--~~~~G~~~ 65 (72)
T TIGR02194 45 GFRQVPVIVADGD--LSWSGFRP 65 (72)
T ss_pred CCcccCEEEECCC--cEEeccCH
Confidence 4468999999985 35556554
No 64
>COG0131 HisB Imidazoleglycerol-phosphate dehydratase [Amino acid transport and metabolism]
Probab=24.72 E-value=54 Score=24.72 Aligned_cols=23 Identities=26% Similarity=0.431 Sum_probs=20.2
Q ss_pred cccceEEEEcCcccceecccccc
Q 035150 37 NTARKLIIFNGELDRIRSGCILH 59 (72)
Q Consensus 37 ~~~rpiIifNGELDRiRsgYYP~ 59 (72)
=++||-.++|+|+.|-+-|=|+.
T Consensus 111 lSGRp~lv~~~~f~~~~vG~~~t 133 (195)
T COG0131 111 LSGRPYLVFNAEFTREKVGDFDT 133 (195)
T ss_pred cCCCeeEEEecccCccccCCcch
Confidence 58999999999999999886663
No 65
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=24.69 E-value=51 Score=22.91 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=18.5
Q ss_pred CCCCCCCCeEEEEEeccCChhHH
Q 035150 2 ADRVKPEDELFLVAYPYFNVNEM 24 (72)
Q Consensus 2 adrv~~~D~lfVVAYP~fNvnEm 24 (72)
|.+++++|.+.+++|=.++..|.
T Consensus 76 Arl~~~GD~vII~sy~~~~~~e~ 98 (116)
T PF02261_consen 76 ARLVQVGDRVIIMSYAQVDEEEA 98 (116)
T ss_dssp GGCS-TT-EEEEEEEEEEEHHHH
T ss_pred HhccCCCCEEEEEEcccCCHHHH
Confidence 56789999999999999998875
No 66
>smart00879 Brix Brix domain. The Brix domain is found in a number of eukaryotic proteins including SSF proteins from yeast and humans, Arabidopsis thaliana Peter Pan-like protein and several hypothetical proteins.
Probab=24.61 E-value=49 Score=21.42 Aligned_cols=15 Identities=33% Similarity=0.558 Sum_probs=12.3
Q ss_pred cccceEEEEcCcccc
Q 035150 37 NTARKLIIFNGELDR 51 (72)
Q Consensus 37 ~~~rpiIifNGELDR 51 (72)
...+|+++|||.-+.
T Consensus 100 ~~~~P~li~~~~~~~ 114 (180)
T smart00879 100 TGSRPLLIFNNFFTE 114 (180)
T ss_pred CCCccEEEECCCCCc
Confidence 456999999998765
No 67
>cd03136 GATase1_AraC_ArgR_like AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to the Pseudomonas aeruginosa ArgR regulator. ArgR functions in the control of expression of certain genes of arginine biosynthesis and catabolism. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in some sequences in the sharp turn betwee
Probab=24.47 E-value=1.1e+02 Score=20.02 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=19.8
Q ss_pred EEEEeccCChhHHHHHHHHHHHh
Q 035150 12 FLVAYPYFNVNEMLVVEELYKEA 34 (72)
Q Consensus 12 fVVAYP~fNvnEml~v~eLye~a 34 (72)
-++.||.|+..|.....|++..+
T Consensus 2 ~il~~~g~~~~~~~~~~dv~~~a 24 (185)
T cd03136 2 GFLLLPGFSLLALASAIEPLRAA 24 (185)
T ss_pred EEEEeCCCchHHHHHHHHHHHHH
Confidence 37899999999999998888754
No 68
>COG3253 ywfI Predicted heme peroxidase involved in anaerobic stress response [General function prediction only]
Probab=24.29 E-value=2e+02 Score=22.02 Aligned_cols=40 Identities=18% Similarity=0.149 Sum_probs=33.0
Q ss_pred CCCeEEEEEeccCChhHHH-HHHHHHHHhhh---cccceEEEEc
Q 035150 7 PEDELFLVAYPYFNVNEML-VVEELYKEAVF---NTARKLIIFN 46 (72)
Q Consensus 7 ~~D~lfVVAYP~fNvnEml-~v~eLye~a~~---~~~rpiIifN 46 (72)
=+|.=|||+|=.-.+.++. .|+||....+. +-..|++++|
T Consensus 175 i~DyEwvV~~e~ddi~~~v~lv~elR~~EAr~~~~~e~pff~G~ 218 (230)
T COG3253 175 IGDYEWVVTYEADDILAWVDLVEELRFTEARKWIGEETPFFVGR 218 (230)
T ss_pred ccceEEEEEEecCcHHHHHHHHHHHHHHHHHHHHhccCCeeeec
Confidence 3688999999999999998 89999887666 5667877764
No 69
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=24.29 E-value=83 Score=16.51 Aligned_cols=21 Identities=14% Similarity=0.066 Sum_probs=15.1
Q ss_pred hcccceEEEEcCcccceecccccc
Q 035150 36 FNTARKLIIFNGELDRIRSGCILH 59 (72)
Q Consensus 36 ~~~~rpiIifNGELDRiRsgYYP~ 59 (72)
..++.|.++++|+ +-+||-|.
T Consensus 47 ~~~~vP~~~~~~~---~~~g~~~~ 67 (74)
T TIGR02196 47 GQRGVPVIVIGHK---IIVGFDPE 67 (74)
T ss_pred CCCcccEEEECCE---EEeeCCHH
Confidence 4578999999975 36666553
No 70
>KOG1260 consensus Isocitrate lyase [Energy production and conversion]
Probab=24.27 E-value=51 Score=27.94 Aligned_cols=23 Identities=26% Similarity=0.314 Sum_probs=19.9
Q ss_pred cccceEEEEcCcccceecccccc
Q 035150 37 NTARKLIIFNGELDRIRSGCILH 59 (72)
Q Consensus 37 ~~~rpiIifNGELDRiRsgYYP~ 59 (72)
.-....|.|-=||-|++.|+||.
T Consensus 309 ei~~~~i~fdw~lpr~keG~y~~ 331 (492)
T KOG1260|consen 309 EIGVSEIFFDWELPRTKEGRYRF 331 (492)
T ss_pred hhhhhhhhcccccccccCceecC
Confidence 44478899999999999999985
No 71
>PF02633 Creatininase: Creatinine amidohydrolase; InterPro: IPR003785 This family includes the enzymes creatininase and 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase, also known as formamide hydrolase. Creatinase or creatinine amidohydrolase (3.5.2.10 from EC) catalyses the hydrolysis of creatinine to creatine, which can then be metabolised to urea and sarcosine by creatinase (3.5.3.3 from EC). Creatininase is a member of the urease-related amidohydrolase superfamily []. Formamide hydrolase catalyzes the hydrolysis of the formamide of 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphate (FAPy) to form 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (APy) (3.5.1.102 from EC). ; PDB: 3A6K_F 3A6F_A 3A6D_B 1J2U_B 3A6J_C 1J2T_A 3A6G_C 3A6H_F 1Q3K_E 3A6L_C ....
Probab=24.24 E-value=1.3e+02 Score=21.14 Aligned_cols=23 Identities=17% Similarity=0.495 Sum_probs=16.5
Q ss_pred HHHHHHHHhhhcccceEEEEcCc
Q 035150 26 VVEELYKEAVFNTARKLIIFNGE 48 (72)
Q Consensus 26 ~v~eLye~a~~~~~rpiIifNGE 48 (72)
.++++-+.....+=|+||++||-
T Consensus 87 ~l~di~~sl~~~Gf~~ivivngH 109 (237)
T PF02633_consen 87 LLRDILRSLARHGFRRIVIVNGH 109 (237)
T ss_dssp HHHHHHHHHHHHT--EEEEEESS
T ss_pred HHHHHHHHHHHcCCCEEEEEECC
Confidence 56677677777888999999984
No 72
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=23.94 E-value=91 Score=20.36 Aligned_cols=17 Identities=24% Similarity=0.493 Sum_probs=13.1
Q ss_pred hhhcccceEEEEcCccc
Q 035150 34 AVFNTARKLIIFNGELD 50 (72)
Q Consensus 34 a~~~~~rpiIifNGELD 50 (72)
.+...+.-+|+||++|.
T Consensus 52 ~~~~~~~d~vvfd~~Ls 68 (95)
T PF13167_consen 52 LIEELDADLVVFDNELS 68 (95)
T ss_pred HHhhcCCCEEEECCCCC
Confidence 34457889999999985
No 73
>TIGR03746 conj_TIGR03746 integrating conjugative element protein, PFL_4703 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown.
Probab=23.88 E-value=69 Score=24.16 Aligned_cols=11 Identities=55% Similarity=0.848 Sum_probs=9.3
Q ss_pred cCcc-cceeccc
Q 035150 46 NGEL-DRIRSGC 56 (72)
Q Consensus 46 NGEL-DRiRsgY 56 (72)
|||| ||+|+=|
T Consensus 115 ~geLr~R~R~vy 126 (202)
T TIGR03746 115 NGELRQRVRGVY 126 (202)
T ss_pred cchHhhheeeeE
Confidence 6999 9999855
No 74
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=23.76 E-value=1.1e+02 Score=16.56 Aligned_cols=14 Identities=7% Similarity=0.142 Sum_probs=12.0
Q ss_pred hcccceEEEEcCcc
Q 035150 36 FNTARKLIIFNGEL 49 (72)
Q Consensus 36 ~~~~rpiIifNGEL 49 (72)
.....|.|.++|+.
T Consensus 46 g~~~~P~v~i~g~~ 59 (60)
T PF00462_consen 46 GVRTVPQVFIDGKF 59 (60)
T ss_dssp SSSSSSEEEETTEE
T ss_pred CCCccCEEEECCEE
Confidence 67899999999974
No 75
>cd00945 Aldolase_Class_I Class I aldolases. The class I aldolases use an active-site lysine which stablilzes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.
Probab=23.68 E-value=1.4e+02 Score=18.97 Aligned_cols=40 Identities=18% Similarity=-0.095 Sum_probs=21.1
Q ss_pred CCeEEEEEeccCChhH-HHHHHHHHHHhhhc--ccceEEEEcC
Q 035150 8 EDELFLVAYPYFNVNE-MLVVEELYKEAVFN--TARKLIIFNG 47 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnE-ml~v~eLye~a~~~--~~rpiIifNG 47 (72)
-|.+.++..+|+.++. ...+.+.|++.... ++.|+++.|-
T Consensus 79 ad~i~v~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~pv~iy~~ 121 (201)
T cd00945 79 ADEIDVVINIGSLKEGDWEEVLEEIAAVVEAADGGLPLKVILE 121 (201)
T ss_pred CCEEEEeccHHHHhCCCHHHHHHHHHHHHHHhcCCceEEEEEE
Confidence 3555555555544430 23344444444443 5889888773
No 76
>TIGR02427 protocat_pcaD 3-oxoadipate enol-lactonase. Members of this family are 3-oxoadipate enol-lactonase. Note that the substrate is known as 3-oxoadipate enol-lactone, 2-oxo-2,3-dihydrofuran-5-acetate, 4,5-Dihydro-5-oxofuran-2-acetate, and 5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the catalyzes the fourth step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate, and vanillate all can be converted in one step to protocatechuate. This enzyme also acts in catechol degradation. In genomes that catabolize both catechol and protocatechuate, two forms of this enzyme may be found. All members of the seed alignment for this model were chosen from within protocatechuate degradation operons of at least three genes of the pathway, from genomes with the complete pathway through beta-ketoadipate.
Probab=23.44 E-value=69 Score=19.72 Aligned_cols=17 Identities=18% Similarity=0.089 Sum_probs=14.4
Q ss_pred hcccceEEEEcCcccce
Q 035150 36 FNTARKLIIFNGELDRI 52 (72)
Q Consensus 36 ~~~~rpiIifNGELDRi 52 (72)
.....|+.+++|+-|++
T Consensus 190 ~~~~~Pvlii~g~~D~~ 206 (251)
T TIGR02427 190 GAIAVPTLCIAGDQDGS 206 (251)
T ss_pred hhcCCCeEEEEeccCCc
Confidence 45678999999999886
No 77
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=23.42 E-value=1.7e+02 Score=20.75 Aligned_cols=41 Identities=15% Similarity=0.268 Sum_probs=30.3
Q ss_pred CCCCCCCCeEEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEcCccccee
Q 035150 2 ADRVKPEDELFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 2 adrv~~~D~lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifNGELDRiR 53 (72)
|..++++|.+-+++|-.++-.|. +...-+++++|+.=+=..
T Consensus 75 Arl~~~GD~VII~sy~~~~e~e~-----------~~~~Pkvv~~d~~N~i~~ 115 (126)
T COG0853 75 ARLVQVGDLVIIMSYAQMSEEEA-----------KTHKPKVVVVDEKNEIVD 115 (126)
T ss_pred HhhCCCCCEEEEEEcccCCHHHH-----------hccCCeEEEECCCCchhh
Confidence 45689999999999999987653 556667777777544333
No 78
>PF00450 Peptidase_S10: Serine carboxypeptidase; InterPro: IPR001563 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S10 (clan SC). The type example is carboxypeptidase Y from Saccharomyces cerevisiae (Baker's yeast) []. All known carboxypeptidases are either metallo carboxypeptidases or serine carboxypeptidases (3.4.16.5 from EC and 3.4.16.6 from EC). The catalytic activity of the serine carboxypeptidases, like that of the trypsin family serine proteases, is provided by a charge relay system involving an aspartic acid residue hydrogen-bonded to a histidine, which is itself hydrogen-bonded to a serine []. The sequences surrounding the active site serine and histidine residues are highly conserved in all the serine carboxypeptidases.; GO: 0004185 serine-type carboxypeptidase activity, 0006508 proteolysis; PDB: 1AC5_A 1WHS_B 3SC2_B 1WHT_A 1BCR_A 1BCS_A 1GXS_A 1IVY_A 1WPX_A 1YSC_A ....
Probab=23.11 E-value=76 Score=22.88 Aligned_cols=17 Identities=35% Similarity=0.839 Sum_probs=11.5
Q ss_pred hcccceEEEEcCcccce
Q 035150 36 FNTARKLIIFNGELDRI 52 (72)
Q Consensus 36 ~~~~rpiIifNGELDRi 52 (72)
.+.+.+++|.||++|=+
T Consensus 327 L~~~irVLiy~Gd~D~i 343 (415)
T PF00450_consen 327 LDNGIRVLIYNGDLDLI 343 (415)
T ss_dssp HHTT-EEEEEEETT-SS
T ss_pred hhccceeEEeccCCCEE
Confidence 34449999999999953
No 79
>PHA02857 monoglyceride lipase; Provisional
Probab=22.75 E-value=1.3e+02 Score=20.12 Aligned_cols=21 Identities=14% Similarity=0.333 Sum_probs=16.7
Q ss_pred HhhhcccceEEEEcCccccee
Q 035150 33 EAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 33 ~a~~~~~rpiIifNGELDRiR 53 (72)
+.+..-..|+.+..|+-|.+-
T Consensus 203 ~~l~~i~~Pvliv~G~~D~i~ 223 (276)
T PHA02857 203 KIIPKIKTPILILQGTNNEIS 223 (276)
T ss_pred HhcccCCCCEEEEecCCCCcC
Confidence 344567899999999999863
No 80
>cd01870 RhoA_like RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl
Probab=22.71 E-value=2e+02 Score=17.83 Aligned_cols=43 Identities=12% Similarity=0.208 Sum_probs=27.3
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhh--cccceEEEEcCcccc
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVF--NTARKLIIFNGELDR 51 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~--~~~rpiIifNGELDR 51 (72)
...+++.|...+..-...+.+.|...+. ..+.|+|++--..|.
T Consensus 73 ~d~~i~v~~~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl 117 (175)
T cd01870 73 TDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDL 117 (175)
T ss_pred CCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhc
Confidence 3466677888777666666665554444 257888877545553
No 81
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=22.69 E-value=86 Score=26.73 Aligned_cols=40 Identities=15% Similarity=0.144 Sum_probs=26.5
Q ss_pred EEEeccCCh-------hHHHHHHHHHHHhhhcccceEEEEcCccccee
Q 035150 13 LVAYPYFNV-------NEMLVVEELYKEAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 13 VVAYP~fNv-------nEml~v~eLye~a~~~~~rpiIifNGELDRiR 53 (72)
+||||.... .--.+|+.||+-.-+ +.+|+++.-++++.++
T Consensus 177 IVaipt~ggy~L~cda~n~~AV~rLr~~K~R-p~KPlavmv~d~~~~~ 223 (711)
T TIGR00143 177 IIAIKGIGGFHLACDARNDEVVERLRLRKNR-PLKPFAVMSPDLESAE 223 (711)
T ss_pred EEEEEcCCcceeecCCCCHHHHHHHHHHhCC-CCCCEEEEECCHHHHH
Confidence 677776654 233577788876666 4578877777776654
No 82
>KOG0817 consensus Acyl-CoA-binding protein [Lipid transport and metabolism]
Probab=22.11 E-value=76 Score=22.30 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=15.2
Q ss_pred ChhHHHHHHHHHHHhhhc
Q 035150 20 NVNEMLVVEELYKEAVFN 37 (72)
Q Consensus 20 NvnEml~v~eLye~a~~~ 37 (72)
.-.|+|.+..|||+|..+
T Consensus 24 ~~ee~L~lYglyKQAt~G 41 (142)
T KOG0817|consen 24 SNEELLKLYGLYKQATVG 41 (142)
T ss_pred CHHHHHHHHHHHHhhccC
Confidence 346999999999998874
No 83
>PF08283 Gemini_AL1_M: Geminivirus rep protein central domain; InterPro: IPR022692 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. This is the central region of the geminivirus rep proteins []. It is found C-terminal to PF00799 from PFAM and is thought to be responsible for oligomerisation.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters
Probab=21.68 E-value=39 Score=22.71 Aligned_cols=26 Identities=31% Similarity=0.578 Sum_probs=17.1
Q ss_pred HHHHHHHhhhcccceE-EEEcCcccceecc
Q 035150 27 VEELYKEAVFNTARKL-IIFNGELDRIRSG 55 (72)
Q Consensus 27 v~eLye~a~~~~~rpi-IifNGELDRiRsg 55 (72)
-+.++..+...+.||+ |+.-|+ .|+|
T Consensus 76 ~~nv~~~aa~rp~rp~SivieG~---sRTG 102 (106)
T PF08283_consen 76 DENVYSVAAARPLRPISIVIEGD---SRTG 102 (106)
T ss_pred HhccCcccccCCCCCCceeEecC---CccC
Confidence 3667766655777876 777776 4554
No 84
>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
Probab=21.58 E-value=2.1e+02 Score=17.69 Aligned_cols=44 Identities=18% Similarity=0.296 Sum_probs=28.5
Q ss_pred CCeEEEEEeccCChhHHHHHHHHHHHhhh--cccceEEEEcCcccc
Q 035150 8 EDELFLVAYPYFNVNEMLVVEELYKEAVF--NTARKLIIFNGELDR 51 (72)
Q Consensus 8 ~D~lfVVAYP~fNvnEml~v~eLye~a~~--~~~rpiIifNGELDR 51 (72)
.-.++++.|-.-|.+....+.+.|...+. .+..|+|++=--.|.
T Consensus 69 ~~d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl 114 (174)
T smart00174 69 DTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVGTKLDL 114 (174)
T ss_pred CCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEecChhh
Confidence 34677888888888766666655554443 457888876555553
No 85
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=21.43 E-value=1.7e+02 Score=21.83 Aligned_cols=36 Identities=22% Similarity=0.287 Sum_probs=25.8
Q ss_pred EEEEEeccCChhHHHHHHHHHHHhhhcccceEEEEc
Q 035150 11 LFLVAYPYFNVNEMLVVEELYKEAVFNTARKLIIFN 46 (72)
Q Consensus 11 lfVVAYP~fNvnEml~v~eLye~a~~~~~rpiIifN 46 (72)
..++.=||+|.---..+.+=|+.....++-|+|+.|
T Consensus 102 ~il~v~PyY~k~~~~gl~~hf~~ia~a~~lPvilYN 137 (299)
T COG0329 102 GILVVPPYYNKPSQEGLYAHFKAIAEAVDLPVILYN 137 (299)
T ss_pred EEEEeCCCCcCCChHHHHHHHHHHHHhcCCCEEEEe
Confidence 345556777766555556666676678899999999
No 86
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=21.23 E-value=2e+02 Score=17.32 Aligned_cols=45 Identities=13% Similarity=0.073 Sum_probs=29.8
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhh--cccceEEEEcCccccee
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVF--NTARKLIIFNGELDRIR 53 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~--~~~rpiIifNGELDRiR 53 (72)
..++++.|..-++.....+..++.+... .++.|++++---.|...
T Consensus 73 ~d~~ilv~d~~~~~s~~~~~~~l~~~~~~~~~~~pivvv~nK~D~~~ 119 (164)
T smart00175 73 AVGALLVYDITNRESFENLKNWLKELREYADPNVVIMLVGNKSDLED 119 (164)
T ss_pred CCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhccc
Confidence 4467777888888777666654444332 36789988876777543
No 87
>cd03139 GATase1_PfpI_2 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=21.21 E-value=73 Score=20.54 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=20.1
Q ss_pred EEEEeccCChhHHHHHHHHHHHhh
Q 035150 12 FLVAYPYFNVNEMLVVEELYKEAV 35 (72)
Q Consensus 12 fVVAYP~fNvnEml~v~eLye~a~ 35 (72)
-++.||.|+..|+....+.++.+-
T Consensus 2 ~ill~~gf~~~~~~~~~d~~~~a~ 25 (183)
T cd03139 2 GILLFPGVEVLDVIGPYEVFGRAP 25 (183)
T ss_pred EEEEeCCCCEehheeHHHHHHHhh
Confidence 367899999999999999888653
No 88
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=21.12 E-value=46 Score=22.95 Aligned_cols=28 Identities=18% Similarity=0.285 Sum_probs=22.4
Q ss_pred EEEcCcccceecccccchhheeeeeeee
Q 035150 43 IIFNGELDRIRSGCILHHSFIIIVLSVN 70 (72)
Q Consensus 43 IifNGELDRiRsgYYP~~~f~~~~~~~~ 70 (72)
-+=.-||.++++||-|.--+-++++|.+
T Consensus 80 Y~~~~~ip~v~~~~lp~~glGi~IlSTS 107 (130)
T PTZ00158 80 DVTLGEFEKWANNILPSRQFGHVVLTTS 107 (130)
T ss_pred ECCcchhhHHhcCCCccccceEEEEECC
Confidence 3344688889999999999999888864
No 89
>PF02955 GSH-S_ATP: Prokaryotic glutathione synthetase, ATP-grasp domain; InterPro: IPR004218 Prokaryotic glutathione synthetase 6.3.2.3 from EC (glutathione synthase) catalyses the conversion of gamma-L-glutamyl-L-cysteine and glycine to orthophosphate and glutathione in the presence of ATP. This is the second step in glutathione biosynthesis. The enzyme is inhibited by 7,8-dihydrofolate, methotrexate and trimethoprim. This is the ATP-binding domain of the enzyme.; GO: 0004363 glutathione synthase activity, 0005524 ATP binding, 0006750 glutathione biosynthetic process; PDB: 1GLV_A 1GSA_A 1GSH_A 2GLT_A.
Probab=21.11 E-value=65 Score=22.71 Aligned_cols=18 Identities=28% Similarity=0.564 Sum_probs=13.3
Q ss_pred HHhhhcccceEEEEcCcc
Q 035150 32 KEAVFNTARKLIIFNGEL 49 (72)
Q Consensus 32 e~a~~~~~rpiIifNGEL 49 (72)
-.++.++++-|++|||+.
T Consensus 78 lp~i~~GDkRii~~nG~~ 95 (173)
T PF02955_consen 78 LPEIKEGDKRIILFNGEP 95 (173)
T ss_dssp -GGGGG-EEEEEEETTEE
T ss_pred cccccCCCEEEEEECCEE
Confidence 345668899999999985
No 90
>cd04132 Rho4_like Rho4-like subfamily. Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=20.93 E-value=2.4e+02 Score=17.93 Aligned_cols=42 Identities=17% Similarity=0.224 Sum_probs=27.3
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhh--cccceEEEEcCccc
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVF--NTARKLIIFNGELD 50 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~--~~~rpiIifNGELD 50 (72)
...+++.|..-|..-...+.+.|...+. ....|+|++---.|
T Consensus 73 ad~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~D 116 (187)
T cd04132 73 VDVLLICYAVDNPTSLDNVEDKWFPEVNHFCPGTPIMLVGLKTD 116 (187)
T ss_pred CCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChh
Confidence 4567788888887767666665544443 35678887654444
No 91
>PF12697 Abhydrolase_6: Alpha/beta hydrolase family; PDB: 3LLC_A 3A2N_E 3A2M_A 3A2L_A 3AFI_F 3C5V_A 3C5W_P 3E0X_A 2ZJF_A 3QYJ_A ....
Probab=20.72 E-value=1.3e+02 Score=18.03 Aligned_cols=22 Identities=27% Similarity=0.345 Sum_probs=17.8
Q ss_pred HHhhhcccceEEEEcCccccee
Q 035150 32 KEAVFNTARKLIIFNGELDRIR 53 (72)
Q Consensus 32 e~a~~~~~rpiIifNGELDRiR 53 (72)
.+.......|+.++.|+-|.+-
T Consensus 169 ~~~~~~~~~pvl~i~g~~D~~~ 190 (228)
T PF12697_consen 169 SEALPRIKVPVLVIHGEDDPIV 190 (228)
T ss_dssp HHHHHGSSSEEEEEEETTSSSS
T ss_pred cccccccCCCeEEeecCCCCCC
Confidence 3455677999999999999864
No 92
>TIGR03695 menH_SHCHC 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase.
Probab=20.32 E-value=82 Score=19.22 Aligned_cols=17 Identities=18% Similarity=0.171 Sum_probs=14.2
Q ss_pred hcccceEEEEcCcccce
Q 035150 36 FNTARKLIIFNGELDRI 52 (72)
Q Consensus 36 ~~~~rpiIifNGELDRi 52 (72)
.....|+.+++|+.|..
T Consensus 191 ~~~~~P~l~i~g~~D~~ 207 (251)
T TIGR03695 191 QALTIPVLYLCGEKDEK 207 (251)
T ss_pred hCCCCceEEEeeCcchH
Confidence 45678999999999964
No 93
>cd04130 Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus,
Probab=20.04 E-value=2.4e+02 Score=17.76 Aligned_cols=43 Identities=16% Similarity=0.340 Sum_probs=26.4
Q ss_pred CeEEEEEeccCChhHHHHHHHHHHHhhh--cccceEEEEcCcccc
Q 035150 9 DELFLVAYPYFNVNEMLVVEELYKEAVF--NTARKLIIFNGELDR 51 (72)
Q Consensus 9 D~lfVVAYP~fNvnEml~v~eLye~a~~--~~~rpiIifNGELDR 51 (72)
-..+|+.|..-|..-...+.+.|-..+. ..+.|+|++-=-.|.
T Consensus 72 a~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~Dl 116 (173)
T cd04130 72 TDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADL 116 (173)
T ss_pred CcEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhh
Confidence 3577888888887766665443333333 256887766545554
Done!