Query 031636
Match_columns 156
No_of_seqs 129 out of 1028
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 03:17:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031636.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031636hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0799 Uncharacterized homolo 100.0 6.2E-42 1.3E-46 255.5 12.2 107 18-131 7-113 (115)
2 TIGR00090 iojap_ybeB iojap-lik 100.0 2.3E-40 4.9E-45 241.1 12.3 98 18-122 2-99 (99)
3 PRK11538 ribosome-associated p 100.0 2.3E-40 4.9E-45 243.9 12.3 99 18-123 7-105 (105)
4 PF02410 Oligomerisation: Olig 100.0 8E-39 1.7E-43 232.7 10.5 98 18-122 2-100 (100)
5 KOG3212 Uncharacterized conser 100.0 1.6E-32 3.6E-37 219.1 9.5 132 18-153 71-205 (208)
6 PF14492 EFG_II: Elongation Fa 70.3 5.1 0.00011 27.2 2.8 64 47-119 6-70 (75)
7 COG3565 Predicted dioxygenase 56.0 11 0.00025 28.8 2.6 29 86-114 28-58 (138)
8 COG4576 CcmL Carbon dioxide co 53.2 17 0.00037 26.1 3.0 32 29-61 37-68 (89)
9 TIGR01485 SPP_plant-cyano sucr 50.8 34 0.00074 27.5 4.8 16 47-62 39-54 (249)
10 smart00506 A1pp Appr-1"-p proc 45.6 48 0.001 23.7 4.5 67 45-116 14-86 (133)
11 PF06778 Chlor_dismutase: Chlo 45.6 1.4E+02 0.0029 24.2 7.5 49 20-68 9-61 (193)
12 PF14839 DOR: DOR family 44.6 14 0.00031 30.6 1.7 13 90-102 4-16 (216)
13 PRK03669 mannosyl-3-phosphogly 41.9 28 0.00061 28.4 3.1 21 46-66 41-61 (271)
14 PF07801 DUF1647: Protein of u 40.4 58 0.0012 25.3 4.4 56 11-67 24-81 (142)
15 PRK10513 sugar phosphate phosp 37.9 34 0.00074 27.5 3.0 21 46-66 37-57 (270)
16 TIGR01487 SPP-like sucrose-pho 37.8 34 0.00075 26.7 2.9 19 46-64 35-53 (215)
17 PF00352 TBP: Transcription fa 37.3 54 0.0012 22.6 3.5 30 44-73 55-85 (86)
18 PRK03467 hypothetical protein; 37.3 53 0.0012 25.5 3.8 48 16-63 5-61 (144)
19 PF01656 CbiA: CobQ/CobB/MinD/ 37.0 1.6E+02 0.0034 21.9 6.4 51 20-72 85-143 (195)
20 PF04456 DUF503: Protein of un 36.9 84 0.0018 22.3 4.5 53 20-72 22-78 (90)
21 PF13277 YmdB: YmdB-like prote 35.1 93 0.002 26.5 5.2 84 48-142 30-135 (253)
22 cd07950 Gallate_Doxase_N The N 34.4 1.1E+02 0.0024 25.8 5.6 80 16-100 35-133 (277)
23 PRK01158 phosphoglycolate phos 34.4 45 0.00098 26.0 3.1 19 46-64 37-55 (230)
24 PF07725 LRR_3: Leucine Rich R 33.9 19 0.00041 19.0 0.6 10 115-124 9-18 (20)
25 PRK13363 protocatechuate 4,5-d 33.4 69 0.0015 28.1 4.3 58 17-74 76-169 (335)
26 PRK10530 pyridoxal phosphate ( 31.8 47 0.001 26.6 2.8 19 46-64 37-55 (272)
27 smart00877 BMC Bacterial micro 31.7 1.3E+02 0.0027 20.4 4.6 49 19-69 11-60 (75)
28 TIGR00099 Cof-subfamily Cof su 31.5 50 0.0011 26.4 2.9 20 46-65 33-52 (256)
29 PRK10976 putative hydrolase; P 31.1 46 0.001 26.8 2.7 20 46-65 36-55 (266)
30 TIGR03018 pepcterm_TyrKin exop 30.2 1.4E+02 0.0029 23.4 5.2 47 20-66 138-193 (207)
31 PRK14126 cell division protein 29.6 72 0.0016 22.3 3.1 27 46-73 17-43 (85)
32 TIGR02461 osmo_MPG_phos mannos 29.5 60 0.0013 26.1 3.1 21 46-66 32-52 (225)
33 TIGR01482 SPP-subfamily Sucros 29.4 58 0.0013 25.2 2.9 19 46-64 32-50 (225)
34 cd05006 SIS_GmhA Phosphoheptos 29.2 2.4E+02 0.0052 21.4 6.3 56 17-72 116-173 (177)
35 COG0561 Cof Predicted hydrolas 28.2 57 0.0012 26.2 2.8 21 46-66 37-57 (264)
36 TIGR02463 MPGP_rel mannosyl-3- 28.0 60 0.0013 25.3 2.8 21 46-66 33-53 (221)
37 PF00936 BMC: BMC domain; Int 28.0 1.6E+02 0.0034 19.9 4.5 53 18-72 11-64 (75)
38 PRK12276 putative heme peroxid 27.7 2E+02 0.0044 24.3 6.0 48 19-68 38-91 (248)
39 cd01614 EutN_CcmL Ethanolamine 27.3 96 0.0021 21.8 3.4 31 28-59 36-66 (83)
40 PRK15448 ethanolamine cataboli 27.1 84 0.0018 22.8 3.2 30 29-59 37-66 (95)
41 PF11042 DUF2750: Protein of u 26.9 76 0.0017 22.6 2.9 45 93-137 22-68 (104)
42 PF08282 Hydrolase_3: haloacid 26.7 67 0.0014 24.5 2.8 18 47-64 33-50 (254)
43 COG4680 Uncharacterized protei 26.6 49 0.0011 24.2 1.9 24 92-115 53-80 (98)
44 cd07366 3MGA_Dioxygenase Subun 26.6 1.1E+02 0.0024 26.7 4.4 101 18-120 75-223 (328)
45 PRK15126 thiamin pyrimidine py 26.5 62 0.0013 26.2 2.7 20 46-65 36-55 (272)
46 PF00486 Trans_reg_C: Transcri 26.4 79 0.0017 20.3 2.7 28 118-147 31-58 (77)
47 cd04887 ACT_MalLac-Enz ACT_Mal 26.3 1.8E+02 0.0038 18.4 5.4 49 17-66 12-61 (74)
48 PRK09267 flavodoxin FldA; Vali 26.0 1.1E+02 0.0023 23.1 3.8 25 31-55 29-57 (169)
49 TIGR03884 sel_bind_Methan sele 25.9 1.7E+02 0.0037 20.4 4.4 40 5-54 24-63 (74)
50 PF04455 Saccharop_dh_N: LOR/S 25.9 2.7E+02 0.0058 20.4 6.5 52 18-69 18-71 (103)
51 TIGR01486 HAD-SF-IIB-MPGP mann 25.6 68 0.0015 25.8 2.8 19 47-65 34-52 (256)
52 TIGR02704 carboxysome_B carbox 25.1 81 0.0018 22.2 2.7 31 28-59 30-60 (80)
53 TIGR03371 cellulose_yhjQ cellu 24.9 2.8E+02 0.006 21.7 6.1 37 31-67 115-159 (246)
54 PRK00192 mannosyl-3-phosphogly 24.6 70 0.0015 26.1 2.7 20 47-66 39-58 (273)
55 PRK10678 moaE molybdopterin gu 24.3 1.8E+02 0.004 22.6 4.8 56 18-73 63-121 (150)
56 COG1348 NifH Nitrogenase subun 24.2 4.7E+02 0.01 22.6 7.9 53 20-73 103-170 (278)
57 PF01037 AsnC_trans_reg: AsnC 24.0 1.4E+02 0.003 18.8 3.6 44 18-65 12-55 (74)
58 COG1066 Sms Predicted ATP-depe 23.4 2.5E+02 0.0054 25.9 6.1 98 17-120 156-253 (456)
59 PF10940 DUF2618: Protein of u 23.3 26 0.00056 21.5 -0.1 17 105-121 13-29 (40)
60 PRK12435 ferrochelatase; Provi 23.0 3.2E+02 0.0069 23.5 6.5 55 15-70 231-307 (311)
61 PRK08367 porA pyruvate ferredo 22.7 1.8E+02 0.0039 25.9 5.1 38 29-67 247-284 (394)
62 TIGR02703 carboxysome_A carbox 22.4 1.1E+02 0.0023 21.6 2.9 31 28-59 31-61 (81)
63 PRK00394 transcription factor; 22.3 1.3E+02 0.0029 23.9 3.8 30 44-73 52-82 (179)
64 cd07364 PCA_45_Dioxygenase_B S 22.3 1.9E+02 0.0041 24.4 4.9 80 16-100 35-133 (277)
65 PF13382 Adenine_deam_C: Adeni 22.2 2.5E+02 0.0055 22.2 5.3 65 46-144 65-129 (171)
66 cd06169 BMC Bacterial Micro-Co 22.0 2.3E+02 0.005 18.2 5.0 46 18-64 10-56 (62)
67 TIGR02471 sucr_syn_bact_C sucr 22.0 91 0.002 24.7 2.8 18 47-64 32-49 (236)
68 PF13291 ACT_4: ACT domain; PD 21.9 2.4E+02 0.0051 18.4 4.5 48 18-66 20-69 (80)
69 PF01121 CoaE: Dephospho-CoA k 21.8 2.5E+02 0.0054 22.0 5.2 44 21-64 94-142 (180)
70 PRK01964 4-oxalocrotonate taut 21.8 1.7E+02 0.0038 18.5 3.7 25 49-73 7-31 (64)
71 KOG3348 BolA (bacterial stress 21.7 3.1E+02 0.0067 19.6 6.1 38 20-57 7-46 (85)
72 KOG1349 Gpi-anchor transamidas 21.7 4.1E+02 0.0089 23.1 6.7 82 48-145 32-121 (309)
73 PRK11382 frlB fructoselysine-6 21.4 1.1E+02 0.0025 26.1 3.5 38 13-64 27-64 (340)
74 COG0646 MetH Methionine syntha 21.4 66 0.0014 28.2 2.0 17 51-67 294-310 (311)
75 cd00652 TBP_TLF TATA box bindi 21.2 1.4E+02 0.0031 23.5 3.7 30 44-73 53-83 (174)
76 PF03319 EutN_CcmL: Ethanolami 21.1 1E+02 0.0022 21.7 2.5 30 29-59 37-66 (83)
77 PRK08105 flavodoxin; Provision 21.1 2.1E+02 0.0045 21.6 4.5 35 20-55 21-59 (149)
78 TIGR00013 taut 4-oxalocrotonat 21.0 1.4E+02 0.003 18.6 3.1 25 49-73 7-31 (63)
79 cd02042 ParA ParA and ParB of 20.9 2.7E+02 0.006 18.7 5.2 24 44-67 61-84 (104)
80 PRK05569 flavodoxin; Provision 20.9 3E+02 0.0064 19.8 5.2 34 20-54 21-58 (141)
81 PRK02289 4-oxalocrotonate taut 20.8 1.4E+02 0.0031 18.9 3.1 24 50-73 8-31 (60)
82 cd00491 4Oxalocrotonate_Tautom 20.8 1.8E+02 0.0039 17.7 3.5 24 50-73 7-30 (58)
83 PF14177 YkyB: YkyB-like prote 20.6 2.1E+02 0.0047 22.2 4.4 67 52-121 18-86 (140)
84 PF01455 HupF_HypC: HupF/HypC 20.5 70 0.0015 21.5 1.6 21 90-111 38-58 (68)
85 COG4033 Uncharacterized protei 20.5 2.6E+02 0.0055 20.6 4.6 39 92-151 58-101 (102)
86 PF02780 Transketolase_C: Tran 20.3 1.5E+02 0.0032 21.2 3.4 24 44-67 9-32 (124)
87 cd03130 GATase1_CobB Type 1 gl 20.2 4.2E+02 0.0091 20.8 6.3 53 18-72 13-70 (198)
88 PRK11104 hemG protoporphyrinog 20.2 3E+02 0.0066 21.3 5.4 26 30-55 28-57 (177)
89 COG1444 Predicted P-loop ATPas 20.1 2.2E+02 0.0047 28.0 5.3 30 46-75 261-290 (758)
90 KOG0174 20S proteasome, regula 20.0 2E+02 0.0043 24.0 4.3 35 41-75 53-87 (224)
No 1
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=100.00 E-value=6.2e-42 Score=255.53 Aligned_cols=107 Identities=38% Similarity=0.680 Sum_probs=99.8
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEEE
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI 97 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~Wvl 97 (156)
++.++++|+|+||+||++|||+++|++|||||||||+|.||++|||++|...+|+. |. .+.++||..+++|+|
T Consensus 7 ~~~i~~alddkKAeDIv~lDv~~~s~~tDyfVIatg~s~rhv~Aiad~i~~~~k~~----g~---~~~~~EG~~~~~Wvl 79 (115)
T COG0799 7 LEVIVEALDDKKAEDIVVLDVSGKSSLTDYFVIATGNSSRHVKAIADNVKEELKEA----GE---VPLRIEGLSEGEWVL 79 (115)
T ss_pred HHHHHHHHHhccCCCeEEEEccCCcccccEEEEEEeCchHHHHHHHHHHHHHHHHc----CC---CcccccCCCcCCEEE
Confidence 45899999999999999999999999999999999999999999999999999776 43 356999999999999
Q ss_pred EecCceEEEecChhhhhhcChhhhcCCCCCCCCc
Q 031636 98 IDSGKVIVHALDENARAYYNLEDLWTSEPSKSAT 131 (156)
Q Consensus 98 lD~GdVvVHIft~E~Re~Y~LE~LW~~a~~~~~~ 131 (156)
+|+||||||||+|+.|+|||||+||++++..+.+
T Consensus 80 iD~GdivVHvf~~e~R~~Y~LEklW~d~~~~~~~ 113 (115)
T COG0799 80 IDLGDIVVHVFTPEEREFYNLEKLWGDAPVVDVD 113 (115)
T ss_pred EecCcEEEEecCHHHHHHccHHHHhccCCccCcc
Confidence 9999999999999999999999999999987654
No 2
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=100.00 E-value=2.3e-40 Score=241.11 Aligned_cols=98 Identities=40% Similarity=0.694 Sum_probs=92.9
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEEE
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI 97 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~Wvl 97 (156)
++.++++|+++||+||+||||++.++++||||||||+|.||++|+|++|.+.+|+. |. .++++||.++++|++
T Consensus 2 ~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VI~Tg~S~rh~~aia~~v~~~~k~~----~~---~~~~~EG~~~~~Wil 74 (99)
T TIGR00090 2 LELIVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVEEELKEA----GL---KPLGVEGLEEGDWVL 74 (99)
T ss_pred HHHHHHHHHHcCCCCEEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHc----CC---CcccccCCCCCCEEE
Confidence 56899999999999999999999999999999999999999999999999999876 44 356899999999999
Q ss_pred EecCceEEEecChhhhhhcChhhhc
Q 031636 98 IDSGKVIVHALDENARAYYNLEDLW 122 (156)
Q Consensus 98 lD~GdVvVHIft~E~Re~Y~LE~LW 122 (156)
+|||+|+||||+||.|+|||||+||
T Consensus 75 lD~g~ivVHif~~e~R~~Y~LE~LW 99 (99)
T TIGR00090 75 VDLGDVVVHIFQPEAREFYDLEKLW 99 (99)
T ss_pred EECCCEEEEeCChHHhhhcCHhhcC
Confidence 9999999999999999999999999
No 3
>PRK11538 ribosome-associated protein; Provisional
Probab=100.00 E-value=2.3e-40 Score=243.87 Aligned_cols=99 Identities=35% Similarity=0.670 Sum_probs=92.9
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEEE
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI 97 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~Wvl 97 (156)
++.++++|+++||+||+|+||++.|+++||||||||+|.||++|||++|.+.+++. |. .+.++||..+++|+|
T Consensus 7 ~~~i~~~l~dkKa~DI~vlDv~~~~~~~Dy~VIatg~S~rh~~aia~~v~~~~k~~----~~---~~~~~eG~~~~~Wil 79 (105)
T PRK11538 7 QDFVIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAA----GL---LPLGVEGENAADWIV 79 (105)
T ss_pred HHHHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHc----CC---CCCcccCCCCCCEEE
Confidence 44799999999999999999999999999999999999999999999999998875 44 356899999999999
Q ss_pred EecCceEEEecChhhhhhcChhhhcC
Q 031636 98 IDSGKVIVHALDENARAYYNLEDLWT 123 (156)
Q Consensus 98 lD~GdVvVHIft~E~Re~Y~LE~LW~ 123 (156)
+|||+||||||+|+.|+|||||+||+
T Consensus 80 lD~g~ivVHif~~e~Re~Y~LE~LW~ 105 (105)
T PRK11538 80 VDLGDVIVHVMQEESRRLYELEKLWS 105 (105)
T ss_pred EeCCCEEEEcCCHHHHhhcCHHhhhC
Confidence 99999999999999999999999996
No 4
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=100.00 E-value=8e-39 Score=232.70 Aligned_cols=98 Identities=41% Similarity=0.770 Sum_probs=87.9
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHH-HHHhHHhcccccCCCccccCCCCCEE
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKA-KQRQREVGAKQMMLPSVQGQDTGKWV 96 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~l-k~~~~e~g~~~~~~~~iEG~~~~~Wv 96 (156)
++.++++|+++||+||++||+++.++++||||||||+|.||++|+|++|.+.+ |+. |. .++++||.++++|+
T Consensus 2 ~~~i~~~l~~~k~~dI~v~dv~~~~~~~dy~II~T~~S~rh~~aia~~v~~~~~k~~----~~---~~~~~eG~~~~~W~ 74 (100)
T PF02410_consen 2 LEEIVEALEDKKAEDIVVLDVREKSSWADYFIIATGRSERHVRAIADEVEKALKKEY----GE---RPLRIEGLDESDWV 74 (100)
T ss_dssp HHHHHHHHHHTT-EEEEEEEGCTTBSS-SEEEEEEESSHHHHHHHHHHHHHHH-HHT----T-------EEESTTTTSEE
T ss_pred HHHHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEcCCHHHHHHHHHHHHHHHHHHc----CC---cccccCCCCCCCEE
Confidence 57899999999999999999999999999999999999999999999999999 443 33 35789999999999
Q ss_pred EEecCceEEEecChhhhhhcChhhhc
Q 031636 97 IIDSGKVIVHALDENARAYYNLEDLW 122 (156)
Q Consensus 97 llD~GdVvVHIft~E~Re~Y~LE~LW 122 (156)
++|||+|+||||+||.|+|||||+||
T Consensus 75 lvD~g~ivVHif~~e~R~~Y~LE~LW 100 (100)
T PF02410_consen 75 LVDYGDIVVHIFTPEAREYYDLESLW 100 (100)
T ss_dssp EEEESSEEEEEEEHHHHHHHCHHHHT
T ss_pred EEcccEEEEEcCCHHHHhHcCHhhcC
Confidence 99999999999999999999999999
No 5
>KOG3212 consensus Uncharacterized conserved protein related to IojAP [Function unknown]
Probab=99.98 E-value=1.6e-32 Score=219.12 Aligned_cols=132 Identities=43% Similarity=0.726 Sum_probs=115.6
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEEE
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVI 97 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~Wvl 97 (156)
++.++++|.+.+|.||+|+-+.+.+.|+||+|||||+|.||+.|+|++|++.+|.... .|. ..+++||.++++|++
T Consensus 71 ve~vv~lLrdenadDVfVi~vpeem~y~dh~VIcSgrs~rhl~aiAe~lv~m~Kik~~-kgd---~hvriegk~s~dW~v 146 (208)
T KOG3212|consen 71 VEEVVKLLRDENADDVFVIPVPEEMFYADHTVICSGRSDRHLRAIAEALVYMAKIKSQ-KGD---KHVRIEGKQSSDWIV 146 (208)
T ss_pred HHHHHHHHHhcccCceEEEeccccceeeeeEEEEecCchHHHHHHHHHHHHHHHHhhc-CCC---cccccccccCCCeEE
Confidence 8899999999999999999999999999999999999999999999999999987621 133 467899999999999
Q ss_pred EecCceEEEecChhhhhhcChhhhcCCCCCC--CCchHHHHHHHHHHhhccCCC-Cccc
Q 031636 98 IDSGKVIVHALDENARAYYNLEDLWTSEPSK--SATVQDLQKAFVKVRRKNNSK-KPVE 153 (156)
Q Consensus 98 lD~GdVvVHIft~E~Re~Y~LE~LW~~a~~~--~~~~~~l~~~~~~~~~~~~~~-~~~~ 153 (156)
+|+|.++||+|+||+|++||||.||+..... .....++++-|+..+-+|||+ +|++
T Consensus 147 ~D~g~~vvH~mseeaRe~YdLEsLWa~~S~ddr~sd~~t~p~~fIl~~p~~~S~v~p~k 205 (208)
T KOG3212|consen 147 IDYGKFVVHAMSEEAREYYDLESLWAAESSDDRTSDQDTLPNVFILVRPKNNSKVKPAK 205 (208)
T ss_pred EEeceEEEEecCHHHhhhccHHHHhcccCcCchhhccccCccceEEecCCCCcccChhh
Confidence 9999999999999999999999999986544 222235899999999999987 4443
No 6
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=70.34 E-value=5.1 Score=27.16 Aligned_cols=64 Identities=14% Similarity=0.224 Sum_probs=48.6
Q ss_pred EEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCcccc-CCCCCEEEEecCceEEEecChhhhhhcChh
Q 031636 47 YMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQG-QDTGKWVIIDSGKVIVHALDENARAYYNLE 119 (156)
Q Consensus 47 y~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG-~~~~~WvllD~GdVvVHIft~E~Re~Y~LE 119 (156)
|.+-....+.....++..++.....+- +...++- ...++|+|-=+|.+.+.|....-|+.|++|
T Consensus 6 ~~~~i~p~~~~d~~kl~~aL~~l~~eD---------P~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~ 70 (75)
T PF14492_consen 6 LSVAIEPKNKEDEPKLSEALQKLSEED---------PSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVE 70 (75)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHH----------TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEB
T ss_pred EEEEEEECCHhHHHHHHHHHHHHHhcC---------CeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCe
Confidence 567778888899899988887665543 1122322 345789999999999999999999999987
No 7
>COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]
Probab=56.03 E-value=11 Score=28.81 Aligned_cols=29 Identities=28% Similarity=0.526 Sum_probs=22.9
Q ss_pred ccccCCCCCEEEEec-C-ceEEEecChhhhh
Q 031636 86 SVQGQDTGKWVIIDS-G-KVIVHALDENARA 114 (156)
Q Consensus 86 ~iEG~~~~~WvllD~-G-dVvVHIft~E~Re 114 (156)
-.+|+..+.|+.+|+ | .++.|+-.+..-+
T Consensus 28 ~~~GRstd~wvdfDfyGHQ~v~Hl~~q~~~~ 58 (138)
T COG3565 28 CKEGRSTDTWVDFDFYGHQVVAHLTPQPDSQ 58 (138)
T ss_pred cccccccceEEEeeecccEEEEEecCCcccc
Confidence 357999999999998 4 8999987665433
No 8
>COG4576 CcmL Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]
Probab=53.22 E-value=17 Score=26.14 Aligned_cols=32 Identities=9% Similarity=0.137 Sum_probs=24.9
Q ss_pred CCCceEEEecCCCCCccCEEEEEecCCHHHHHH
Q 031636 29 KADDVKVIPVGEKCDWTDYMVIATGRSTWHVKN 61 (156)
Q Consensus 29 ka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~a 61 (156)
.....+++|.- =..+.+|++|++|+|.||..+
T Consensus 37 ~~~~eVA~Dsv-GAG~gE~VLvs~GSaAR~~~~ 68 (89)
T COG4576 37 DGQCEVAIDSV-GAGTGEWVLLSRGSSARQAHG 68 (89)
T ss_pred ccceEEEEecc-cCCcCcEEEEecchHHHHhhc
Confidence 44578888843 356889999999999999653
No 9
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=50.78 E-value=34 Score=27.52 Aligned_cols=16 Identities=38% Similarity=0.573 Sum_probs=13.0
Q ss_pred EEEEEecCCHHHHHHH
Q 031636 47 YMVIATGRSTWHVKNI 62 (156)
Q Consensus 47 y~VIaTg~S~rh~~ai 62 (156)
.||+|||++...++.+
T Consensus 39 ~fv~aTGR~~~~~~~~ 54 (249)
T TIGR01485 39 LLVYSTGRSPHSYKEL 54 (249)
T ss_pred eEEEEcCCCHHHHHHH
Confidence 7999999998776654
No 10
>smart00506 A1pp Appr-1"-p processing enzyme. Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji).
Probab=45.61 E-value=48 Score=23.65 Aligned_cols=67 Identities=24% Similarity=0.241 Sum_probs=39.6
Q ss_pred cCEEEEEecCCHHHHHHHHHHHHHHHHHHh--HHhcccccCCCccccCCCCCEEEEecC----ceEEEecChhhhhhc
Q 031636 45 TDYMVIATGRSTWHVKNIAQAIIYKAKQRQ--REVGAKQMMLPSVQGQDTGKWVIIDSG----KVIVHALDENARAYY 116 (156)
Q Consensus 45 ~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~--~e~g~~~~~~~~iEG~~~~~WvllD~G----dVvVHIft~E~Re~Y 116 (156)
+|.+|-++-.+..+...++..|.+..=... .++.. ..+- -...+.|++.+.+ ..|+|+.+|....-+
T Consensus 14 ~d~IV~~~n~~~~~~~g~a~~i~~~~g~~~~~~~~~~----~~~~-~~~~G~~~~~~~~~~~~~~Iih~~~p~~~~~~ 86 (133)
T smart00506 14 ADAIVNAANSDGAHGGGVAGAIARAAGKALEKEAFRK----LAGG-ECPVGTAVVTEGGNLPAKYVIHAVGPRASGHS 86 (133)
T ss_pred CCEEEECCCcccCCCCcHHHHHHHHhChHHHHHHHHH----hcCC-CcCCccEEEecCCCCCCCEEEEeCCCCCCCCC
Confidence 576666666666666667777755542110 00000 0000 1346799999986 589999998876544
No 11
>PF06778 Chlor_dismutase: Chlorite dismutase; InterPro: IPR010644 This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyses the disproportionation of chlorite into chloride and oxygen [, ]. Note that many family members are hypothetical proteins.; PDB: 2VXH_B 3NN4_A 3NN2_A 3NN3_D 3NN1_E 3QPI_A 3Q08_Q 3Q09_B 1T0T_V 1VDH_E ....
Probab=45.55 E-value=1.4e+02 Score=24.22 Aligned_cols=49 Identities=8% Similarity=-0.131 Sum_probs=37.2
Q ss_pred HHHHHH---HhCCCC-ceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHH
Q 031636 20 SVVNPT---FDLKAD-DVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIY 68 (156)
Q Consensus 20 ~iv~~L---~dkka~-DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~ 68 (156)
++..++ .+.+.. -+.+.++.+...-+|+|+...+.+.-+++.+...+..
T Consensus 9 e~~~~~~~~~~~~~~~~~~~Y~~~G~radaDl~~w~~~~~~~~lq~~~~~l~~ 61 (193)
T PF06778_consen 9 EFEAFLEEWEEAGDGVLRGVYSVSGLRADADLMFWWHAPDLEDLQEAERRLRR 61 (193)
T ss_dssp HHHHHHHHHHHTTTTEEEEEEEETTTSTT-SEEEEEEESSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCceEEEEEEeecccCCCcEEEEEeCCCHHHHHHHHHHHHh
Confidence 555555 444444 4889999999999999999999999999887766643
No 12
>PF14839 DOR: DOR family
Probab=44.57 E-value=14 Score=30.62 Aligned_cols=13 Identities=15% Similarity=0.688 Sum_probs=11.1
Q ss_pred CCCCCEEEEecCc
Q 031636 90 QDTGKWVIIDSGK 102 (156)
Q Consensus 90 ~~~~~WvllD~Gd 102 (156)
..+++|+|||+.+
T Consensus 4 ~edD~WilVD~~~ 16 (216)
T PF14839_consen 4 EEDDEWILVDFID 16 (216)
T ss_pred cccCCeEEEEecC
Confidence 3578999999988
No 13
>PRK03669 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=41.88 E-value=28 Score=28.45 Aligned_cols=21 Identities=5% Similarity=0.205 Sum_probs=16.2
Q ss_pred CEEEEEecCCHHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i 66 (156)
=.||||||++...++.+++.+
T Consensus 41 i~~viaTGR~~~~i~~~~~~l 61 (271)
T PRK03669 41 VPVILCSSKTAAEMLPLQQTL 61 (271)
T ss_pred CeEEEEcCCCHHHHHHHHHHh
Confidence 368999999998877665544
No 14
>PF07801 DUF1647: Protein of unknown function (DUF1647); InterPro: IPR012444 This entry consists of hypothetical proteins of unknown function.
Probab=40.36 E-value=58 Score=25.29 Aligned_cols=56 Identities=18% Similarity=0.149 Sum_probs=37.3
Q ss_pred HhccCCCHHHHHHHHHhCCCCc--eEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHH
Q 031636 11 LARKRPSMTSVVNPTFDLKADD--VKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAII 67 (156)
Q Consensus 11 ~~~~~~~~~~iv~~L~dkka~D--I~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~ 67 (156)
..+++++= ..++.|++.+..| -..+|++....-..-+|++||.|+-|.......+.
T Consensus 24 ~iGkkF~C-~~l~~Le~l~l~~~~~~~v~l~~~~~n~~~vvfVSa~S~~h~~~~~~~i~ 81 (142)
T PF07801_consen 24 SIGKKFDC-SLLETLEDLKLLDNPGPFVDLSSSSKNSSDVVFVSATSDNHFNESMKSIS 81 (142)
T ss_pred ccCceecc-hHHHHHhhhhhccCCCcceecccccccCCccEEEEEecchHHHHHHHHHH
Confidence 34444442 2344555554322 37778877667778899999999999988777663
No 15
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=37.86 E-value=34 Score=27.53 Aligned_cols=21 Identities=24% Similarity=0.289 Sum_probs=15.9
Q ss_pred CEEEEEecCCHHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i 66 (156)
-.|+||||++...+..+++.+
T Consensus 37 ~~~~iaTGR~~~~~~~~~~~l 57 (270)
T PRK10513 37 VNVVLTTGRPYAGVHRYLKEL 57 (270)
T ss_pred CEEEEecCCChHHHHHHHHHh
Confidence 359999999999876655443
No 16
>TIGR01487 SPP-like sucrose-phosphate phosphatase-like hydrolase, Archaeal. TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases.
Probab=37.76 E-value=34 Score=26.68 Aligned_cols=19 Identities=16% Similarity=0.153 Sum_probs=15.0
Q ss_pred CEEEEEecCCHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~ 64 (156)
-.++||||++...++.+++
T Consensus 35 ~~~~~~TGR~~~~~~~~~~ 53 (215)
T TIGR01487 35 IPVSLVTGNTVPFARALAV 53 (215)
T ss_pred CEEEEEcCCcchhHHHHHH
Confidence 4579999999988776654
No 17
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=37.29 E-value=54 Score=22.56 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=22.6
Q ss_pred ccCEEEEEec-CCHHHHHHHHHHHHHHHHHH
Q 031636 44 WTDYMVIATG-RSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 44 ~~Dy~VIaTg-~S~rh~~aia~~i~~~lk~~ 73 (156)
+..--|++|| +|..+++...+.+...+++.
T Consensus 55 F~sGki~itGaks~~~~~~a~~~i~~~L~~~ 85 (86)
T PF00352_consen 55 FSSGKIVITGAKSEEEAKKAIEKILPILQKL 85 (86)
T ss_dssp ETTSEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred EcCCEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 3445567776 59999999999888887653
No 18
>PRK03467 hypothetical protein; Provisional
Probab=37.25 E-value=53 Score=25.51 Aligned_cols=48 Identities=17% Similarity=0.126 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHhCCCCceEEEecCCC----CCcc-----CEEEEEecCCHHHHHHHH
Q 031636 16 PSMTSVVNPTFDLKADDVKVIPVGEK----CDWT-----DYMVIATGRSTWHVKNIA 63 (156)
Q Consensus 16 ~~~~~iv~~L~dkka~DI~ViDv~~~----~~~~-----Dy~VIaTg~S~rh~~aia 63 (156)
.++..|.++|...+.-.+++.+-.+. |-|+ --|+++|..++||.+.+.
T Consensus 5 ~~~~~I~~fl~~~hvltLa~~~~~~~w~A~cFY~fd~~~~~l~~~S~~~TrH~~~~~ 61 (144)
T PRK03467 5 DTLTAISRWLAKQHVVTLCVGQEGELWCANCFYVFDAQKVAFYLLTEEKTRHGQMMG 61 (144)
T ss_pred hHHHHHHHHHHhCcEEEEEEEcCCCcceEEEEEEEcCCCeEEEEEcCCCCHHHHHHh
Confidence 34567999999999999999987654 3332 246999999999988653
No 19
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=37.03 E-value=1.6e+02 Score=21.94 Aligned_cols=51 Identities=12% Similarity=0.161 Sum_probs=35.2
Q ss_pred HHHHHHHhCCCCceEEEecCCC--------CCccCEEEEEecCCHHHHHHHHHHHHHHHHH
Q 031636 20 SVVNPTFDLKADDVKVIPVGEK--------CDWTDYMVIATGRSTWHVKNIAQAIIYKAKQ 72 (156)
Q Consensus 20 ~iv~~L~dkka~DI~ViDv~~~--------~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~ 72 (156)
.+.+.+.... -|+++||.+.. -..+|++|+.+..+...+..+...+ +.++.
T Consensus 85 ~~l~~l~~~~-yD~iiiD~~~~~~~~~~~~l~~ad~viv~~~~~~~~i~~~~~~~-~~l~~ 143 (195)
T PF01656_consen 85 EILESLIKSD-YDYIIIDTPPGLSDPVRNALAAADYVIVPIEPDPSSIEGAERLI-ELLKR 143 (195)
T ss_dssp HHHHHHHHTT-SSEEEEEECSSSSHHHHHHHHTSSEEEEEEESSHHHHHHHHHHH-HHHHH
T ss_pred HHHHHhhhcc-ccceeecccccccHHHHHHHHhCceeeeecCCcHHHHHHHHHHH-HHHHH
Confidence 3444433333 99999999764 2368999999999998877766543 44444
No 20
>PF04456 DUF503: Protein of unknown function (DUF503); InterPro: IPR007546 This is a family of conserved hypothetical bacterial proteins, including TT1725 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), which has a ferredoxin-like alpha+beta-sandwich fold [].; PDB: 1J27_A.
Probab=36.87 E-value=84 Score=22.25 Aligned_cols=53 Identities=19% Similarity=0.161 Sum_probs=35.8
Q ss_pred HHHHHHHhC-C-CCceEEEecCCCC--CccCEEEEEecCCHHHHHHHHHHHHHHHHH
Q 031636 20 SVVNPTFDL-K-ADDVKVIPVGEKC--DWTDYMVIATGRSTWHVKNIAQAIIYKAKQ 72 (156)
Q Consensus 20 ~iv~~L~dk-k-a~DI~ViDv~~~~--~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~ 72 (156)
.+++.|.++ + --||.|-++.... ..+..-|.+-|+|..|+..+.+.+.+.+..
T Consensus 22 ~vvksl~~klr~rfnvSvaEv~~~D~~q~a~lg~a~vs~~~~~~~~~l~~v~~~ie~ 78 (90)
T PF04456_consen 22 QVVKSLIDKLRNRFNVSVAEVGHQDSWQRAVLGFAVVSNSRAHAEQILDKVERFIEE 78 (90)
T ss_dssp HHHHHHHHHHHHHSS-EEEEEE-TT-SSEEEEEEEEEES-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhCCeEEEEecCCCcccEEEEEEEEEECCHHHHHHHHHHHHHHHHh
Confidence 344444443 2 2489998886654 446777788899999999999999888844
No 21
>PF13277 YmdB: YmdB-like protein; PDB: 2CV9_B 2Z06_C.
Probab=35.09 E-value=93 Score=26.46 Aligned_cols=84 Identities=14% Similarity=0.172 Sum_probs=48.2
Q ss_pred EEEEecCCHHHHHHHHHHHHHHHHHHhHHh---------------------c-ccccCCCccccCCCCCEEEEecCceEE
Q 031636 48 MVIATGRSTWHVKNIAQAIIYKAKQRQREV---------------------G-AKQMMLPSVQGQDTGKWVIIDSGKVIV 105 (156)
Q Consensus 48 ~VIaTg~S~rh~~aia~~i~~~lk~~~~e~---------------------g-~~~~~~~~iEG~~~~~WvllD~GdVvV 105 (156)
||||-|.|..|...|...+.+.|.+.+..+ . ++|. ..-+|....+|.+++.++.-|
T Consensus 30 fVIaNgENaa~G~Git~~~~~~L~~~GvDviT~GNH~wdkkei~~~i~~~~~ilRPa--N~p~~~pG~G~~i~~~~g~kv 107 (253)
T PF13277_consen 30 FVIANGENAAGGFGITPKIAEELFKAGVDVITMGNHIWDKKEIFDFIDKEPRILRPA--NYPPGTPGRGYRIFEKNGKKV 107 (253)
T ss_dssp EEEEE-TTTTTTSS--HHHHHHHHHHT-SEEE--TTTTSSTTHHHHHHH-SSEE--T--TS-TT-SSBSEEEEEETTEEE
T ss_pred EEEECCcccCCCCCCCHHHHHHHHhcCCCEEecCcccccCcHHHHHHhcCCCcEECC--CCCCCCCcCcEEEEEECCEEE
Confidence 566777777776666666666666553311 0 1111 112356677999999999988
Q ss_pred EecChhhhhhcChhhhcCCCCCCCCchHHHHHHHHHH
Q 031636 106 HALDENARAYYNLEDLWTSEPSKSATVQDLQKAFVKV 142 (156)
Q Consensus 106 HIft~E~Re~Y~LE~LW~~a~~~~~~~~~l~~~~~~~ 142 (156)
-|+.=-.|-|+ +..+-|+..+++.+.+.
T Consensus 108 ~ViNl~Gr~fm---------~~~~~PF~~~d~~l~~l 135 (253)
T PF13277_consen 108 AVINLMGRVFM---------PPIDCPFRAADRLLEEL 135 (253)
T ss_dssp EEEEEE--TTS------------S-HHHHHHHHHHH-
T ss_pred EEEECcccccC---------CCCCChHHHHHHHHHhc
Confidence 88887788777 45568888888888876
No 22
>cd07950 Gallate_Doxase_N The N-terminal domain of the Class III extradiol dioxygenase, Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. In this subfamily, the subunits A and B are fused to make a single polypeptide chain. The dimer interface for this subfamily may resemble the tetramer interface of classical LigAB en
Probab=34.40 E-value=1.1e+02 Score=25.83 Aligned_cols=80 Identities=14% Similarity=0.055 Sum_probs=52.7
Q ss_pred CCHHHHHHHHHhCCCCceEEEecCCCCCc-cC---EEEEEecCCHHH---------------HHHHHHHHHHHHHHHhHH
Q 031636 16 PSMTSVVNPTFDLKADDVKVIPVGEKCDW-TD---YMVIATGRSTWH---------------VKNIAQAIIYKAKQRQRE 76 (156)
Q Consensus 16 ~~~~~iv~~L~dkka~DI~ViDv~~~~~~-~D---y~VIaTg~S~rh---------------~~aia~~i~~~lk~~~~e 76 (156)
..++++.+.+.+.+.+=|+|++-.....+ .| .|.|.++.+... -..+|+.|.+.+.+.+..
T Consensus 35 ~a~~~~~~~i~~~~PD~iVvi~~dH~~~f~~d~~p~f~Ig~~~~~~~~d~~~~~~~~~~~~g~~~LA~~i~~~~~~~g~~ 114 (277)
T cd07950 35 DGYEPVKQWLAEQKPDVLFMVYNDHVTSFFFDHYSAFALGVGDSYEVADEGGGPRDLPPIRGHAALAQHIAESLVADEFD 114 (277)
T ss_pred HHHHHHHHHHHHhCCCEEEEEcCcHHHHhccccCCcEEEEecccccccccccCCccCCCCCCCHHHHHHHHHHHHhcCCC
Confidence 34667888888888888888885555544 68 899998888732 356788888877765321
Q ss_pred hcccccCCCccccCCCCCEEEEec
Q 031636 77 VGAKQMMLPSVQGQDTGKWVIIDS 100 (156)
Q Consensus 77 ~g~~~~~~~~iEG~~~~~WvllD~ 100 (156)
.. ....-|.+.+.|+-+-+
T Consensus 115 ~~-----~~~~~~lDHG~~vPL~~ 133 (277)
T cd07950 115 LT-----FFQDKPLDHGCFSPLSL 133 (277)
T ss_pred ee-----eccCCCCCceeeeeHHH
Confidence 11 11112566778875544
No 23
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=34.35 E-value=45 Score=26.00 Aligned_cols=19 Identities=21% Similarity=0.258 Sum_probs=14.2
Q ss_pred CEEEEEecCCHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~ 64 (156)
-.|+||||++...+..++.
T Consensus 37 ~~~~iaTGR~~~~~~~~~~ 55 (230)
T PRK01158 37 IPVILATGNVLCFARAAAK 55 (230)
T ss_pred CEEEEEcCCchHHHHHHHH
Confidence 4688999999887665443
No 24
>PF07725 LRR_3: Leucine Rich Repeat; InterPro: IPR011713 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by the IPR001611 from INTERPRO model.
Probab=33.86 E-value=19 Score=19.00 Aligned_cols=10 Identities=50% Similarity=1.109 Sum_probs=8.1
Q ss_pred hcChhhhcCC
Q 031636 115 YYNLEDLWTS 124 (156)
Q Consensus 115 ~Y~LE~LW~~ 124 (156)
+.+||.||..
T Consensus 9 ~S~lekLW~G 18 (20)
T PF07725_consen 9 YSKLEKLWEG 18 (20)
T ss_pred CCChHHhcCc
Confidence 5689999975
No 25
>PRK13363 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=33.36 E-value=69 Score=28.05 Aligned_cols=58 Identities=12% Similarity=0.136 Sum_probs=40.2
Q ss_pred CHHHHHHHHHhCCCCceEEEecCCCCCcc----CEEEEEecCCHHH--------------------------------HH
Q 031636 17 SMTSVVNPTFDLKADDVKVIPVGEKCDWT----DYMVIATGRSTWH--------------------------------VK 60 (156)
Q Consensus 17 ~~~~iv~~L~dkka~DI~ViDv~~~~~~~----Dy~VIaTg~S~rh--------------------------------~~ 60 (156)
.++++.+.+.+.+..=|+||--.....+. ++|.|.+|.+-+= -.
T Consensus 76 a~~~~~~~i~~~~PDvlViispdh~~~F~~~~~p~f~I~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~gd~ 155 (335)
T PRK13363 76 AIERMRDAIEAARIDVAVIVGNDQMELFTTDNNPAFAIYYGETIRNNPASREKLPSLPPGVKAAMPGYMPDAETTYPVVP 155 (335)
T ss_pred HHHHHHHHHHHhCCCEEEEEcCCchhhcccccCCceEEeecceeccchhhccccccccccccccccccCCCCCcCCCCCH
Confidence 35667777888877777776555434444 8899988876651 16
Q ss_pred HHHHHHHHHHHHHh
Q 031636 61 NIAQAIIYKAKQRQ 74 (156)
Q Consensus 61 aia~~i~~~lk~~~ 74 (156)
.+|+.|.+.+.+.+
T Consensus 156 eLA~~I~~~l~~~G 169 (335)
T PRK13363 156 ELARHMIRRLVDDG 169 (335)
T ss_pred HHHHHHHHHHHHcC
Confidence 68888888887764
No 26
>PRK10530 pyridoxal phosphate (PLP) phosphatase; Provisional
Probab=31.76 E-value=47 Score=26.55 Aligned_cols=19 Identities=26% Similarity=0.319 Sum_probs=14.1
Q ss_pred CEEEEEecCCHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~ 64 (156)
-.|+||||++...+..+++
T Consensus 37 ~~~~iaTGR~~~~~~~~~~ 55 (272)
T PRK10530 37 YKVIIVTGRHHVAIHPFYQ 55 (272)
T ss_pred CEEEEEcCCChHHHHHHHH
Confidence 3599999999887655444
No 27
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=31.71 E-value=1.3e+02 Score=20.38 Aligned_cols=49 Identities=20% Similarity=0.203 Sum_probs=32.7
Q ss_pred HHHHHHHHh-CCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHH
Q 031636 19 TSVVNPTFD-LKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYK 69 (156)
Q Consensus 19 ~~iv~~L~d-kka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~ 69 (156)
...+.+++. .|+-||.++++...|+ .-++++.+| ..-.+++..+...+.
T Consensus 11 ~~~i~aaD~a~KaA~V~l~~~~~~~~-g~~~~~v~G-dvs~V~~Av~a~~~~ 60 (75)
T smart00877 11 AAAIEAADAALKAANVELVGYESIGG-GKVTVIITG-DVAAVRAAVEAGLEA 60 (75)
T ss_pred HHHHHHHHHHhhhcCcEEEEEEecCC-CEEEEEEEE-cHHHHHHHHHHHHHH
Confidence 344455555 4888999999987776 568999999 444555544444443
No 28
>TIGR00099 Cof-subfamily Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences.
Probab=31.47 E-value=50 Score=26.43 Aligned_cols=20 Identities=45% Similarity=0.471 Sum_probs=15.1
Q ss_pred CEEEEEecCCHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQA 65 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~ 65 (156)
-.|+||||++.+.+..+.+.
T Consensus 33 ~~~~iaTGR~~~~~~~~~~~ 52 (256)
T TIGR00099 33 IKVVLATGRPYKEVKNILKE 52 (256)
T ss_pred CeEEEEeCCCHHHHHHHHHH
Confidence 57899999998876655443
No 29
>PRK10976 putative hydrolase; Provisional
Probab=31.15 E-value=46 Score=26.76 Aligned_cols=20 Identities=35% Similarity=0.343 Sum_probs=15.4
Q ss_pred CEEEEEecCCHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQA 65 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~ 65 (156)
-.|+||||++...++.+.+.
T Consensus 36 ~~~~iaTGR~~~~~~~~~~~ 55 (266)
T PRK10976 36 IHFVFATGRHHVDVGQIRDN 55 (266)
T ss_pred CEEEEEcCCChHHHHHHHHh
Confidence 57999999999876655543
No 30
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=30.23 E-value=1.4e+02 Score=23.41 Aligned_cols=47 Identities=11% Similarity=0.129 Sum_probs=31.5
Q ss_pred HHHHHHHhCCCCceEEEecCCC---------CCccCEEEEEecCCHHHHHHHHHHH
Q 031636 20 SVVNPTFDLKADDVKVIPVGEK---------CDWTDYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 20 ~iv~~L~dkka~DI~ViDv~~~---------~~~~Dy~VIaTg~S~rh~~aia~~i 66 (156)
.+.+.+.++-..|+++||.... ...+|++||++-.+...+..+.+.+
T Consensus 138 ~~l~~l~~~y~~D~IiiD~pp~~~~~~~~~l~~~aD~viiV~~~~~~~~~~~~~~~ 193 (207)
T TIGR03018 138 SLLHELARRYPDRIIIIDTPPLLVFSEARALARLVGQIVLVVEEGRTTQEAVKEAL 193 (207)
T ss_pred HHHHHHHhhCCCCEEEEECCCCcchhHHHHHHHhCCEEEEEEECCCCCHHHHHHHH
Confidence 3444444442239999999753 2367999999888877776666654
No 31
>PRK14126 cell division protein ZapA; Provisional
Probab=29.60 E-value=72 Score=22.33 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=22.6
Q ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
+|-|.| ..|..|++.+|..|.+.+++-
T Consensus 17 ~Y~i~~-~e~ee~l~~vA~~vd~km~ei 43 (85)
T PRK14126 17 QYTIVG-DESTSHIRMVAAIVDDKMREL 43 (85)
T ss_pred EEEecC-CCcHHHHHHHHHHHHHHHHHH
Confidence 577765 668999999999999998875
No 32
>TIGR02461 osmo_MPG_phos mannosyl-3-phosphoglycerate phosphatase. Members of this family are mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70). It acts sequentially after mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) in a two-step pathway of biosynthesis of the compatible solute mannosylglycerate, a typical osmolyte of thermophiles.
Probab=29.54 E-value=60 Score=26.10 Aligned_cols=21 Identities=5% Similarity=0.059 Sum_probs=15.2
Q ss_pred CEEEEEecCCHHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i 66 (156)
-.+|||||++.+.+..+++.+
T Consensus 32 ~~~vi~TgR~~~~~~~~~~~l 52 (225)
T TIGR02461 32 FPIVFVSSKTRAEQEYYREEL 52 (225)
T ss_pred CEEEEEeCCCHHHHHHHHHHc
Confidence 457899999999876554433
No 33
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=29.43 E-value=58 Score=25.20 Aligned_cols=19 Identities=26% Similarity=0.335 Sum_probs=14.5
Q ss_pred CEEEEEecCCHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~ 64 (156)
-.|+||||++...+..++.
T Consensus 32 i~~~~aTGR~~~~~~~~~~ 50 (225)
T TIGR01482 32 IPVVLVTGNSVQFARALAK 50 (225)
T ss_pred CEEEEEcCCchHHHHHHHH
Confidence 3789999999887765443
No 34
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=29.21 E-value=2.4e+02 Score=21.39 Aligned_cols=56 Identities=7% Similarity=0.048 Sum_probs=38.8
Q ss_pred CHHHHHHHHHhCCCCceEEEec--CCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHH
Q 031636 17 SMTSVVNPTFDLKADDVKVIPV--GEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQ 72 (156)
Q Consensus 17 ~~~~iv~~L~dkka~DI~ViDv--~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~ 72 (156)
.+-++++.+.++++.=|.+-+. +....++|+.+.+......|+..+-..+.-.+.+
T Consensus 116 ~~i~~~~~ak~~Ga~vI~IT~~~~s~La~~aD~~l~~~~~~~~~~~~~~~~~~~~~~~ 173 (177)
T cd05006 116 NVLKALEAAKERGMKTIALTGRDGGKLLELADIEIHVPSDDTPRIQEVHLLIGHILCE 173 (177)
T ss_pred HHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEEeCCCChHHHHHHHHHHHHHHHH
Confidence 3445666777776665555555 3357789999999988888887766666555544
No 35
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=28.16 E-value=57 Score=26.24 Aligned_cols=21 Identities=33% Similarity=0.366 Sum_probs=16.8
Q ss_pred CEEEEEecCCHHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i 66 (156)
-+++||||++.+-++.+.+.+
T Consensus 37 ~~v~iaTGR~~~~~~~~~~~l 57 (264)
T COG0561 37 VKVVLATGRPLPDVLSILEEL 57 (264)
T ss_pred CEEEEECCCChHHHHHHHHHc
Confidence 478999999998877766655
No 36
>TIGR02463 MPGP_rel mannosyl-3-phosphoglycerate phosphatase-related protein. This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbor-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (TIGR02460). Members of this family are like to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate.
Probab=27.99 E-value=60 Score=25.30 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=16.8
Q ss_pred CEEEEEecCCHHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i 66 (156)
=.++||||++..-++.+++.+
T Consensus 33 i~~~i~TgR~~~~~~~~~~~l 53 (221)
T TIGR02463 33 IPVILCTSKTAAEVEYLQKAL 53 (221)
T ss_pred CeEEEEcCCCHHHHHHHHHHc
Confidence 358999999999887776654
No 37
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=27.97 E-value=1.6e+02 Score=19.89 Aligned_cols=53 Identities=25% Similarity=0.263 Sum_probs=37.8
Q ss_pred HHHHHHHHHh-CCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHH
Q 031636 18 MTSVVNPTFD-LKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQ 72 (156)
Q Consensus 18 ~~~iv~~L~d-kka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~ 72 (156)
+...+.+++. .|+-||.++++...| -.-++++.+| +...+++..+...+.+.+
T Consensus 11 ~~~~i~aaD~alKaa~V~l~~~~~~~-~g~~~~~i~G-~vs~V~~Av~a~~~~~~~ 64 (75)
T PF00936_consen 11 IAAAIVAADAALKAANVELVEIELIC-GGKVTVIITG-DVSAVKAAVDAAEEAAGK 64 (75)
T ss_dssp HHHHHHHHHHHHHHSSEEEEEEEEES-TTEEEEEEEE-SHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhcCCEEEEEEEecC-CCeEEEEEEE-CHHHHHHHHHHHHHHHhh
Confidence 3344455555 488999999998777 4578899999 677777777766666544
No 38
>PRK12276 putative heme peroxidase; Provisional
Probab=27.67 E-value=2e+02 Score=24.29 Aligned_cols=48 Identities=6% Similarity=0.050 Sum_probs=35.3
Q ss_pred HHHHHHHHhCCCCce------EEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHH
Q 031636 19 TSVVNPTFDLKADDV------KVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIY 68 (156)
Q Consensus 19 ~~iv~~L~dkka~DI------~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~ 68 (156)
+++..+|+...+..+ .+.++.+.. +|+|+...+.+...++++-..+.+
T Consensus 38 ~e~~~~l~~~~~~~~~~~g~~~~Y~v~G~r--ADlm~w~~~~~~~~lq~~~~~~~~ 91 (248)
T PRK12276 38 DEFLAFLEKWEEVEAAKQGSHAIYSIVGQK--ADLMLMILRPTMEELNEIENELNK 91 (248)
T ss_pred HHHHHHHHHHhhcccccccceeEEEeeccc--ceEEEEEeCCCHHHHHHHHHHHHh
Confidence 355555554333333 489998766 799999999999999988777764
No 39
>cd01614 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation,
Probab=27.28 E-value=96 Score=21.85 Aligned_cols=31 Identities=13% Similarity=0.249 Sum_probs=24.8
Q ss_pred CCCCceEEEecCCCCCccCEEEEEecCCHHHH
Q 031636 28 LKADDVKVIPVGEKCDWTDYMVIATGRSTWHV 59 (156)
Q Consensus 28 kka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~ 59 (156)
.++.-++++|.-+ +...|++++++|.+.||.
T Consensus 36 ~~g~~~VA~D~vG-AG~Ge~Vlv~~Gs~Ar~~ 66 (83)
T cd01614 36 PKGEPLVAVDPVG-AGVGEWVLVATGSAARQA 66 (83)
T ss_pred cCCCEEEEEECCC-CCCCCEEEEeCChHHhhh
Confidence 3567788888865 567999999999888874
No 40
>PRK15448 ethanolamine catabolic microcompartment shell protein EutN; Provisional
Probab=27.09 E-value=84 Score=22.75 Aligned_cols=30 Identities=10% Similarity=0.141 Sum_probs=24.8
Q ss_pred CCCceEEEecCCCCCccCEEEEEecCCHHHH
Q 031636 29 KADDVKVIPVGEKCDWTDYMVIATGRSTWHV 59 (156)
Q Consensus 29 ka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~ 59 (156)
.+.-++++|.-+ +...|++++++|+|.|+.
T Consensus 37 ~g~~~VAvD~vG-AG~Ge~Vlv~~GssAR~~ 66 (95)
T PRK15448 37 DGQCAVAIDNIG-AGTGEWVLLVSGSSARQA 66 (95)
T ss_pred CCCEEEEEECCC-CCCCCEEEEeCChHHhhh
Confidence 466778889876 778999999999988874
No 41
>PF11042 DUF2750: Protein of unknown function (DUF2750); InterPro: IPR021284 This family is conserved in Proteobacteria. The function is not known.
Probab=26.87 E-value=76 Score=22.59 Aligned_cols=45 Identities=20% Similarity=0.356 Sum_probs=38.5
Q ss_pred CCEEEEec--CceEEEecChhhhhhcChhhhcCCCCCCCCchHHHHH
Q 031636 93 GKWVIIDS--GKVIVHALDENARAYYNLEDLWTSEPSKSATVQDLQK 137 (156)
Q Consensus 93 ~~WvllD~--GdVvVHIft~E~Re~Y~LE~LW~~a~~~~~~~~~l~~ 137 (156)
++|++++. ++.++-+.+.+.+.---...-|++.....++.++.-+
T Consensus 22 ~g~~~~~~~~~~~~~p~W~~~~~A~~~~~~ew~~~~~~~I~L~~Fle 68 (104)
T PF11042_consen 22 DGWVLCDSDEGEDVLPFWPSKEFAEACATDEWADYKPKEISLDEFLE 68 (104)
T ss_pred CcEEEeecCCCcEEEEeCCCHHHHHHHHhcccccCeEEEEEHHHHHH
Confidence 45999988 5668999999999988888999999988999888744
No 42
>PF08282 Hydrolase_3: haloacid dehalogenase-like hydrolase; InterPro: IPR013200 The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification []. This HAD domain is found in several distinct enzymes including: Phospholipid-transporting ATPase 1 (3.6.3.1 from EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [] 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (3.1.3.45 from EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [] Mannosyl-3-phosphoglycerate phosphatase (3.1.3.70 from EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [] Phosphoglycolate phopshatase (3.1.3.18 from EC), which catalyses the dephosphorylation of 2-phosphoglycolate [] ; PDB: 2B30_B 3R4C_A 1XVI_B 3IJ5_B 3MMZ_C 3L7Y_A 1XPJ_C 1RLT_B 1RLM_B 2HF2_A ....
Probab=26.71 E-value=67 Score=24.53 Aligned_cols=18 Identities=44% Similarity=0.571 Sum_probs=14.2
Q ss_pred EEEEEecCCHHHHHHHHH
Q 031636 47 YMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 47 y~VIaTg~S~rh~~aia~ 64 (156)
.++||||++.+-+..+..
T Consensus 33 ~~~i~TGR~~~~~~~~~~ 50 (254)
T PF08282_consen 33 KLVIATGRSYSSIKRLLK 50 (254)
T ss_dssp EEEEECSSTHHHHHHHHH
T ss_pred EEEEEccCcccccccccc
Confidence 789999999887655544
No 43
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.64 E-value=49 Score=24.19 Aligned_cols=24 Identities=29% Similarity=0.497 Sum_probs=19.3
Q ss_pred CCCEEEEecC----ceEEEecChhhhhh
Q 031636 92 TGKWVIIDSG----KVIVHALDENARAY 115 (156)
Q Consensus 92 ~~~WvllD~G----dVvVHIft~E~Re~ 115 (156)
.+.|+++|.| .+||||+-+-.|=|
T Consensus 53 ~Dnr~Vfdi~GN~yRLIvhv~y~~~ki~ 80 (98)
T COG4680 53 LDNRVVFDIGGNKYRLIVHVAYEFHKIF 80 (98)
T ss_pred ccceEEEEcCCCEEEEEEEEEeecceEE
Confidence 4689999996 69999987766644
No 44
>cd07366 3MGA_Dioxygenase Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate. 3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to 3-O-Methylgallate by O-demethylase. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=26.58 E-value=1.1e+02 Score=26.68 Aligned_cols=101 Identities=14% Similarity=0.098 Sum_probs=58.7
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccC----EEEEEecCCHH----H--------------------------HHHHH
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTD----YMVIATGRSTW----H--------------------------VKNIA 63 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~D----y~VIaTg~S~r----h--------------------------~~aia 63 (156)
++++.+.+.+.+..=|+||--.....+.+ .|.|.+|.+-. + -..+|
T Consensus 75 ~~~~~~~i~~~~PDvlVIispDH~~~f~~~~~P~f~I~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~eLA 154 (328)
T cd07366 75 LDRLADFIRAARIDVAVIVGDDQKELFDEALLPAFAIYYGDTITNGPRTREQLDRMPPHEAAAGYAPDEARTYPCHPELA 154 (328)
T ss_pred HHHHHHHHHHhCCCEEEEEcCccHhhhccccCCceEEeecceeecChhhccccccccccccccccCCCCCcCCCCCHHHH
Confidence 56777888888877777776655566767 78888766532 2 25678
Q ss_pred HHHHHHHHHHhHHhcccccCCCccc-cCCCCCEEEEecC----ce-EEEecC--------hhhhhhcChhh
Q 031636 64 QAIIYKAKQRQREVGAKQMMLPSVQ-GQDTGKWVIIDSG----KV-IVHALD--------ENARAYYNLED 120 (156)
Q Consensus 64 ~~i~~~lk~~~~e~g~~~~~~~~iE-G~~~~~WvllD~G----dV-vVHIft--------~E~Re~Y~LE~ 120 (156)
+.|.+.+.+.+.....-. ....+ |...+-|+++-+. ++ ||+|+. +..++.|.|=+
T Consensus 155 ~~I~~~l~~~G~dv~~~~--~~~~~~~lDHG~~~~l~~~~p~~~iPVVpisin~~~~p~~ps~~r~y~lG~ 223 (328)
T cd07366 155 RHLIKHTVADGFDVAALD--HLPDTVGIPHAFGFIYRRIMGDLVIPVVPVLINTFYPPNQPSARRCFEFGR 223 (328)
T ss_pred HHHHHHHHHcCCCeeeec--ccCcccCCCcchhhHHHHhcCCCCCcEEEEeecCCCCCCCCCHHHHHHHHH
Confidence 888888776633111100 00111 3455567665553 44 666653 35566666533
No 45
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=26.51 E-value=62 Score=26.21 Aligned_cols=20 Identities=30% Similarity=0.373 Sum_probs=15.2
Q ss_pred CEEEEEecCCHHHHHHHHHH
Q 031636 46 DYMVIATGRSTWHVKNIAQA 65 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~ 65 (156)
-.|+||||++..-++.+.+.
T Consensus 36 ~~~~iaTGR~~~~~~~~~~~ 55 (272)
T PRK15126 36 ITLTFATGRHVLEMQHILGA 55 (272)
T ss_pred CEEEEECCCCHHHHHHHHHH
Confidence 46899999999877665543
No 46
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=26.35 E-value=79 Score=20.27 Aligned_cols=28 Identities=25% Similarity=0.508 Sum_probs=22.9
Q ss_pred hhhhcCCCCCCCCchHHHHHHHHHHhhccC
Q 031636 118 LEDLWTSEPSKSATVQDLQKAFVKVRRKNN 147 (156)
Q Consensus 118 LE~LW~~a~~~~~~~~~l~~~~~~~~~~~~ 147 (156)
+|.+|.+.. +.+...|..+.-+.|++=.
T Consensus 31 ~~~~w~~~~--~~~~~~l~~~I~rLR~kL~ 58 (77)
T PF00486_consen 31 IEALWGDEE--DVSDNSLDVHISRLRKKLE 58 (77)
T ss_dssp HHHHTSSSS--TTCTHHHHHHHHHHHHHHH
T ss_pred CChhhhccc--ccchhhHHHHHHHHHHHHh
Confidence 578999988 7788889999998888643
No 47
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.27 E-value=1.8e+02 Score=18.42 Aligned_cols=49 Identities=20% Similarity=0.226 Sum_probs=35.2
Q ss_pred CHHHHHHHHHhCCCCceEEEecCCC-CCccCEEEEEecCCHHHHHHHHHHH
Q 031636 17 SMTSVVNPTFDLKADDVKVIPVGEK-CDWTDYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 17 ~~~~iv~~L~dkka~DI~ViDv~~~-~~~~Dy~VIaTg~S~rh~~aia~~i 66 (156)
.+..|+.++.+. +-+|.-++.+.. ..++..-+.....+..|+..+.+.+
T Consensus 12 ~L~~i~~~i~~~-~~nI~~v~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L 61 (74)
T cd04887 12 MLGRVTTAIGEA-GGDIGAIDLVEQGRDYTVRDITVDAPSEEHAETIVAAV 61 (74)
T ss_pred hHHHHHHHHHHc-CCcEEEEEEEEecCCEEEEEEEEEcCCHHHHHHHHHHH
Confidence 466888888776 456776666432 3566666778999999998876665
No 48
>PRK09267 flavodoxin FldA; Validated
Probab=26.03 E-value=1.1e+02 Score=23.14 Aligned_cols=25 Identities=12% Similarity=0.214 Sum_probs=17.8
Q ss_pred CceEEEecCCCCC----ccCEEEEEecCC
Q 031636 31 DDVKVIPVGEKCD----WTDYMVIATGRS 55 (156)
Q Consensus 31 ~DI~ViDv~~~~~----~~Dy~VIaTg~S 55 (156)
.++.++|+.+... -.|.+||++..=
T Consensus 29 ~~~~~~~~~~~~~~~l~~~d~vi~g~pt~ 57 (169)
T PRK09267 29 DVADVVDIAKASKEDFEAYDLLILGIPTW 57 (169)
T ss_pred CceEEEEhhhCCHhhHhhCCEEEEEecCc
Confidence 3778889877532 269999997654
No 49
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=25.95 E-value=1.7e+02 Score=20.43 Aligned_cols=40 Identities=3% Similarity=0.042 Sum_probs=29.9
Q ss_pred ccchHHHhccCCCHHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecC
Q 031636 5 TKESETLARKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGR 54 (156)
Q Consensus 5 ~~~~~~~~~~~~~~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~ 54 (156)
+++.+++.. ++.+-...+.|.-|+.+++.-. .. +|+|+|+
T Consensus 24 ~~d~d~Al~------eM~e~A~~lGAnAVVGvr~d~s---~~-eV~ayGT 63 (74)
T TIGR03884 24 SDNVDEIVE------NLREKVKAKGGMGLIAFRITCA---DG-KFLGYGT 63 (74)
T ss_pred cCCHHHHHH------HHHHHHHHcCCCEEEEEEEEcC---CC-EEEEEEE
Confidence 345555554 7888888999999999998644 22 9999986
No 50
>PF04455 Saccharop_dh_N: LOR/SDH bifunctional enzyme conserved region ; InterPro: IPR007545 Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to saccharopine dehydrogenase conserved region (IPR005097 from INTERPRO) in eukaryotes [, ].; PDB: 3C2Q_B 3MGJ_A.
Probab=25.89 E-value=2.7e+02 Score=20.39 Aligned_cols=52 Identities=15% Similarity=0.178 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCC-CceEEEecCCCCCccC-EEEEEecCCHHHHHHHHHHHHHH
Q 031636 18 MTSVVNPTFDLKA-DDVKVIPVGEKCDWTD-YMVIATGRSTWHVKNIAQAIIYK 69 (156)
Q Consensus 18 ~~~iv~~L~dkka-~DI~ViDv~~~~~~~D-y~VIaTg~S~rh~~aia~~i~~~ 69 (156)
+..+.+.+.+..| -.|.=++|.....-.. ..+..+|.+..|+.+|...|...
T Consensus 18 l~~vLD~I~d~GG~F~i~~~~vG~~~~d~S~a~l~V~a~d~~~L~~Il~~L~~l 71 (103)
T PF04455_consen 18 LNRVLDIIMDMGGDFEILEFDVGKSKDDTSYARLQVSAPDEEHLDEILDELHQL 71 (103)
T ss_dssp HHHHHHHHHHTT-EEEEEEEE--SSTTS-EEEEEEEEESSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCEEEEEEEeCCCCCCceeEEEEEecCCHHHHHHHHHHHHHH
Confidence 5667777778877 5888899976543333 45668999999999988877654
No 51
>TIGR01486 HAD-SF-IIB-MPGP mannosyl-3-phosphoglycerate phosphatase family. This small group of proteins is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. Several members of this family from thermophiles (and from Dehalococcoides ethenogenes) are now known to act as mannosyl-3-phosphoglycerate (MPG) phosphatase. In these cases, the enzyme acts after MPG synthase to make the compatible solute mannosylglycerate. We propose that other mesophilic members of this family do not act as mannosyl-3-phosphoglycerate phosphatase. A member of this family is found in Escherichia coli, which appears to lack MPG synthase. Mannosylglycerate is imported in E. coli by phosphoenolpyruvate-dependent transporter (PubMed:14645248), but it appears the phosphorylation is not on the glycerate moiety, that the phosphorylated import is degraded by an alpha-mannosidase from an adjacent gene, and that E. coli would have no pathway to obta
Probab=25.60 E-value=68 Score=25.83 Aligned_cols=19 Identities=11% Similarity=0.193 Sum_probs=14.4
Q ss_pred EEEEEecCCHHHHHHHHHH
Q 031636 47 YMVIATGRSTWHVKNIAQA 65 (156)
Q Consensus 47 y~VIaTg~S~rh~~aia~~ 65 (156)
.++||||++...+..+.+.
T Consensus 34 ~~~~~TgR~~~~~~~~~~~ 52 (256)
T TIGR01486 34 PVIPCTSKTAAEVEYLRKE 52 (256)
T ss_pred eEEEEcCCCHHHHHHHHHH
Confidence 3899999999987665543
No 52
>TIGR02704 carboxysome_B carboxysome peptide B. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to Pfam family pfam03319, participate in other types of shell such as the ethanolamine degradation organelle.
Probab=25.13 E-value=81 Score=22.19 Aligned_cols=31 Identities=10% Similarity=0.041 Sum_probs=25.2
Q ss_pred CCCCceEEEecCCCCCccCEEEEEecCCHHHH
Q 031636 28 LKADDVKVIPVGEKCDWTDYMVIATGRSTWHV 59 (156)
Q Consensus 28 kka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~ 59 (156)
..+.-++++|.-+ +...|++++++|++.|+.
T Consensus 30 ~~g~~~VAvD~vG-AG~Ge~Vlv~~GsaAr~~ 60 (80)
T TIGR02704 30 AKGKISVAVDPVG-APEGKWVFTASGSAARFA 60 (80)
T ss_pred CCCCEEEEEECCC-CCCCCEEEEeCCHHHhcc
Confidence 4677788889876 778999999999877764
No 53
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=24.89 E-value=2.8e+02 Score=21.72 Aligned_cols=37 Identities=14% Similarity=0.131 Sum_probs=26.8
Q ss_pred CceEEEecCCC--------CCccCEEEEEecCCHHHHHHHHHHHH
Q 031636 31 DDVKVIPVGEK--------CDWTDYMVIATGRSTWHVKNIAQAII 67 (156)
Q Consensus 31 ~DI~ViDv~~~--------~~~~Dy~VIaTg~S~rh~~aia~~i~ 67 (156)
.|.++||...- -..+|++||.+-.+..-+.++...+.
T Consensus 115 ~D~viiD~pp~~~~~~~~~l~~ad~vii~~~~~~~s~~~~~~~~~ 159 (246)
T TIGR03371 115 RDWVLIDVPRGPSPITRQALAAADLVLVVVNADAACYATLHQQAL 159 (246)
T ss_pred CCEEEEECCCCchHHHHHHHHhCCeEEEEeCCCHHHHHHHHHHHH
Confidence 39999999873 13589999999888766666554443
No 54
>PRK00192 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=24.59 E-value=70 Score=26.14 Aligned_cols=20 Identities=10% Similarity=0.217 Sum_probs=15.6
Q ss_pred EEEEEecCCHHHHHHHHHHH
Q 031636 47 YMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 47 y~VIaTg~S~rh~~aia~~i 66 (156)
-++||||++...+..+++.+
T Consensus 39 ~~~iaTgR~~~~~~~~~~~l 58 (273)
T PRK00192 39 PVIPCTSKTAAEVEVLRKEL 58 (273)
T ss_pred EEEEEcCCCHHHHHHHHHHc
Confidence 57889999999987765543
No 55
>PRK10678 moaE molybdopterin guanine dinucleotide biosynthesis protein MoaE; Provisional
Probab=24.33 E-value=1.8e+02 Score=22.61 Aligned_cols=56 Identities=18% Similarity=-0.011 Sum_probs=36.2
Q ss_pred HHHHHHHHHhC-CCCceEEEecCCCCCcc--CEEEEEecCCHHHHHHHHHHHHHHHHHH
Q 031636 18 MTSVVNPTFDL-KADDVKVIPVGEKCDWT--DYMVIATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 18 ~~~iv~~L~dk-ka~DI~ViDv~~~~~~~--Dy~VIaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
+..|+.-+..+ ...+|.|.---+.-... -.+|.+++...+..-..++.+.+.+|..
T Consensus 63 l~~I~~ea~~~~~~~~v~i~HR~G~l~~Ge~~v~Vav~s~HR~~Af~A~~~~id~lK~~ 121 (150)
T PRK10678 63 LAEIVDEARSRWPLGRVTVIHRVGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTR 121 (150)
T ss_pred HHHHHHHHHHhCCCCcEEEEEeEecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhhc
Confidence 44555555554 45777776654443333 4566667777777777788999999875
No 56
>COG1348 NifH Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism]
Probab=24.23 E-value=4.7e+02 Score=22.58 Aligned_cols=53 Identities=21% Similarity=0.154 Sum_probs=35.2
Q ss_pred HHHHHHHhCCCC----ceEEEecCCC-----------CCccCEEEEEecCCHHHHHHHHHHHHHHHHHH
Q 031636 20 SVVNPTFDLKAD----DVKVIPVGEK-----------CDWTDYMVIATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 20 ~iv~~L~dkka~----DI~ViDv~~~-----------~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
..++.|++.+|- |++++||-+. ..++|.+-|+|..-.--+.| |++|.+-+++.
T Consensus 103 tai~~Le~lgaf~~~~DvviyDVLGDVVCGGFAmPiReg~AdeiyIVtSge~MalYA-ANNI~kgi~k~ 170 (278)
T COG1348 103 TAINLLEELGAFEEDLDVVIYDVLGDVVCGGFAMPIREGYADEIYIVTSGEMMALYA-ANNIAKGIRKY 170 (278)
T ss_pred HHHHHHHHhCCccccCCEEEEeccCceeecceeeehhcccCcEEEEEecCchHHHHH-HHHHHHHHHHH
Confidence 345667777664 9999999663 45888887777666555555 55555555443
No 57
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=24.03 E-value=1.4e+02 Score=18.81 Aligned_cols=44 Identities=7% Similarity=0.089 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHH
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQA 65 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~ 65 (156)
.+.+++.|.+.. -|..+-..++-.||++.+.+.|..++..+...
T Consensus 12 ~~~~~~~l~~~p----~V~~~~~vtG~~d~~~~v~~~d~~~l~~~i~~ 55 (74)
T PF01037_consen 12 YDEFAEALAEIP----EVVECYSVTGEYDLILKVRARDMEELEEFIRE 55 (74)
T ss_dssp HHHHHHHHHTST----TEEEEEEESSSSSEEEEEEESSHHHHHHHHHH
T ss_pred HHHHHHHHHcCC----CEEEEEEEeCCCCEEEEEEECCHHHHHHHHHH
Confidence 455666665532 23333444667899999999999998876554
No 58
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=23.36 E-value=2.5e+02 Score=25.94 Aligned_cols=98 Identities=12% Similarity=0.169 Sum_probs=64.9
Q ss_pred CHHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEE
Q 031636 17 SMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWV 96 (156)
Q Consensus 17 ~~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~Wv 96 (156)
.++.|...+++ +--|++|||-=. +-|++- +=...-|..|++..+.++....|+++...-+- -....||.-.+-=+
T Consensus 156 ~~e~I~~~l~~-~~p~lvVIDSIQ-T~~s~~-~~SapGsVsQVRe~t~~L~~~AK~~~i~~fiV--GHVTKeG~IAGPrv 230 (456)
T COG1066 156 NLEDIIAELEQ-EKPDLVVIDSIQ-TLYSEE-ITSAPGSVSQVREVAAELMRLAKTKNIAIFIV--GHVTKEGAIAGPRV 230 (456)
T ss_pred CHHHHHHHHHh-cCCCEEEEeccc-eeeccc-ccCCCCcHHHHHHHHHHHHHHHHHcCCeEEEE--EEEcccccccCchh
Confidence 47778888877 446888998532 222221 22345688899999999999999875311000 01134676666668
Q ss_pred EEecCceEEEecChhhhhhcChhh
Q 031636 97 IIDSGKVIVHALDENARAYYNLED 120 (156)
Q Consensus 97 llD~GdVvVHIft~E~Re~Y~LE~ 120 (156)
|=.+-|.|++ |.-+....|++=+
T Consensus 231 LEHmVDtVly-FEGd~~~~~RiLR 253 (456)
T COG1066 231 LEHMVDTVLY-FEGDRHSRYRILR 253 (456)
T ss_pred eeeeeeEEEE-EeccCCCceeeee
Confidence 8788888887 7777777787755
No 59
>PF10940 DUF2618: Protein of unknown function (DUF2618); InterPro: IPR021237 This bacterial family of proteins has no known function. The sequences within the family are highly conserved.
Probab=23.34 E-value=26 Score=21.52 Aligned_cols=17 Identities=12% Similarity=0.294 Sum_probs=13.7
Q ss_pred EEecChhhhhhcChhhh
Q 031636 105 VHALDENARAYYNLEDL 121 (156)
Q Consensus 105 VHIft~E~Re~Y~LE~L 121 (156)
-|||.|..|.+|+.--+
T Consensus 13 rHiMmpshR~~Fd~~~f 29 (40)
T PF10940_consen 13 RHIMMPSHRSCFDFSFF 29 (40)
T ss_pred hhhhchhhhcccchhhh
Confidence 38999999999987543
No 60
>PRK12435 ferrochelatase; Provisional
Probab=23.01 E-value=3.2e+02 Score=23.47 Aligned_cols=55 Identities=13% Similarity=0.205 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHhC-CCCceEEEecCCC--------------------CCccCEEEEEe-cCCHHHHHHHHHHHHHHH
Q 031636 15 RPSMTSVVNPTFDL-KADDVKVIPVGEK--------------------CDWTDYMVIAT-GRSTWHVKNIAQAIIYKA 70 (156)
Q Consensus 15 ~~~~~~iv~~L~dk-ka~DI~ViDv~~~--------------------~~~~Dy~VIaT-g~S~rh~~aia~~i~~~l 70 (156)
.|++.+..+-|.++ ..++|+|+-++=. ... .|+.+.+ ..|..++++|++.|.+.+
T Consensus 231 ~P~t~d~l~~l~~~~G~k~v~vvpigFvsDhlETl~Eldie~~e~a~~~G~-~~~r~~~lN~~p~fi~~La~lv~~~~ 307 (311)
T PRK12435 231 GPDVQDLTRDLYEEHGYKSFIYTPVGFVAEHLEVLYDNDYECKVVTDEIGA-KYYRPEMPNADPLFIDALADVVLKKL 307 (311)
T ss_pred CCCHHHHHHHHHHhcCCceEEEECCchhhhhHHHHHHHHHHHHHHHHHcCC-cEEeccCCCCCHHHHHHHHHHHHHHH
Confidence 36777777667655 6678888764321 333 4777756 788889998888887654
No 61
>PRK08367 porA pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed
Probab=22.74 E-value=1.8e+02 Score=25.90 Aligned_cols=38 Identities=8% Similarity=0.072 Sum_probs=26.2
Q ss_pred CCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHHHHH
Q 031636 29 KADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQAII 67 (156)
Q Consensus 29 ka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~~i~ 67 (156)
-+.....++--. +.-+|++|||.|.+.+.++...+.++
T Consensus 247 ~grky~~~e~yg-~eDAe~viV~~GS~~~~~keav~~LR 284 (394)
T PRK08367 247 FGRKYQKIEEYR-TEDAEIIFVTMGSLAGTLKEFVDKLR 284 (394)
T ss_pred hCCccceeEEeC-CCCCCEEEEEeCccHHHHHHHHHHHH
Confidence 344444444321 33589999999999999888777664
No 62
>TIGR02703 carboxysome_A carboxysome peptide A. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to Pfam family pfam03319, participate in other types of shell such as the ethanolamine degradation organelle.
Probab=22.41 E-value=1.1e+02 Score=21.59 Aligned_cols=31 Identities=6% Similarity=0.082 Sum_probs=25.0
Q ss_pred CCCCceEEEecCCCCCccCEEEEEecCCHHHH
Q 031636 28 LKADDVKVIPVGEKCDWTDYMVIATGRSTWHV 59 (156)
Q Consensus 28 kka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~ 59 (156)
..+.-++++|.-+ +...|++++++|++.|+.
T Consensus 31 ~~g~~~VAvD~vG-AG~Ge~Vlv~~Gs~AR~~ 61 (81)
T TIGR02703 31 PGGARQVAVDAIG-CKPGDWVLCVGSSAAREA 61 (81)
T ss_pred CCCCEEEEEECCC-CCCCCEEEEeCCHHHhhh
Confidence 3566678889765 778999999999988874
No 63
>PRK00394 transcription factor; Reviewed
Probab=22.32 E-value=1.3e+02 Score=23.85 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=23.7
Q ss_pred ccCEEEEEec-CCHHHHHHHHHHHHHHHHHH
Q 031636 44 WTDYMVIATG-RSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 44 ~~Dy~VIaTg-~S~rh~~aia~~i~~~lk~~ 73 (156)
|..-=|+||| +|..+++..++.+.+.+++.
T Consensus 52 f~sGKiv~tGa~S~~~a~~a~~~~~~~l~~~ 82 (179)
T PRK00394 52 FRSGKVVCTGAKSVEDLHEAVKIIIKKLKEL 82 (179)
T ss_pred EcCCcEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 3455577887 99999999999898888765
No 64
>cd07364 PCA_45_Dioxygenase_B Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate. Protocatechuate 4,5-dioxygenase (LigAB) catalyzes the oxidization and subsequent ring-opening of protocatechuate (or 3,4-dihydroxybenzoic acid, PCA), an intermediate in the breakdown of lignin and other compounds. Protocatechuate 4,5-dioxygenase is an aromatic ring opening dioxygenase belonging to the class III extradiol enzyme family, a group of enyzmes that cleaves aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon using a non-heme Fe(II). LigAB is composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. The B subunit (LigB) is the catalytic subunit of LigAB.
Probab=22.30 E-value=1.9e+02 Score=24.44 Aligned_cols=80 Identities=11% Similarity=-0.019 Sum_probs=50.3
Q ss_pred CCHHHHHHHHHhCCCCceEEEecCCCCCccC----EEEEEecCCHH---------------HHHHHHHHHHHHHHHHhHH
Q 031636 16 PSMTSVVNPTFDLKADDVKVIPVGEKCDWTD----YMVIATGRSTW---------------HVKNIAQAIIYKAKQRQRE 76 (156)
Q Consensus 16 ~~~~~iv~~L~dkka~DI~ViDv~~~~~~~D----y~VIaTg~S~r---------------h~~aia~~i~~~lk~~~~e 76 (156)
.-++++.+.+.+.+..=|+||--.....+++ .|.|.++.+.+ =-..+|+.|.+.+.+.+
T Consensus 35 ~a~~~~~~~~~~~~pD~vVvi~~dH~~~f~~~~~P~f~i~~~~~~~~~~~~~g~~~~~~~~g~~~LA~~i~~~~~~~g-- 112 (277)
T cd07364 35 KGYQPARDWIKKNKPDVAIIVYNDHASAFDLDIIPTFAIGTAEEFQPADEGYGPRPVPDVQGHPDLAWHIAQSLILDD-- 112 (277)
T ss_pred HHHHHHHHHHHHhCCCEEEEEcCchHHhhcccCCCceEEeeccccccCccccCCCCCCCCCCCHHHHHHHHHHHHHcC--
Confidence 3466788888888777777764444566777 89999988433 13567888888877663
Q ss_pred hcccccCCCccccCCCCCEEEEec
Q 031636 77 VGAKQMMLPSVQGQDTGKWVIIDS 100 (156)
Q Consensus 77 ~g~~~~~~~~iEG~~~~~WvllD~ 100 (156)
+... ....-|.+.+.|+-+-+
T Consensus 113 --~~~~-~~~~~~lDHG~~vPL~~ 133 (277)
T cd07364 113 --FDMT-IVNEMDVDHGLTVPLSI 133 (277)
T ss_pred --CCEE-ecCCCCCCcchhhhHHH
Confidence 3210 11112566777876644
No 65
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=22.21 E-value=2.5e+02 Score=22.20 Aligned_cols=65 Identities=15% Similarity=0.260 Sum_probs=41.8
Q ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEEEEecCceEEEecChhhhhhcChhhhcCCC
Q 031636 46 DYMVIATGRSTWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGKVIVHALDENARAYYNLEDLWTSE 125 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~WvllD~GdVvVHIft~E~Re~Y~LE~LW~~a 125 (156)
.+=||+-|+|..-|...++.|.+ -.++|++++-|.++-.+=.| +=.|=+
T Consensus 65 shniiviG~~~~dm~~A~n~l~~----------------------~gGG~vvv~~g~v~a~lpLp-------i~GlmS-- 113 (171)
T PF13382_consen 65 SHNIIVIGTNDEDMALAANRLIE----------------------MGGGIVVVDDGEVLAELPLP-------IAGLMS-- 113 (171)
T ss_dssp T--EEEEESSHHHHHHHHHHHHH----------------------TTSEEEEEETTEEEEEEE-T-------BTTTBB--
T ss_pred CCCEEEEECCHHHHHHHHHHHHH----------------------hCCCEEEEECCEEEEEEecc-------ccceec--
Confidence 46788889999999888877732 14689999999988887655 223333
Q ss_pred CCCCCchHHHHHHHHHHhh
Q 031636 126 PSKSATVQDLQKAFVKVRR 144 (156)
Q Consensus 126 ~~~~~~~~~l~~~~~~~~~ 144 (156)
+.|.+++.+.+...++
T Consensus 114 ---~~~~eev~~~~~~l~~ 129 (171)
T PF13382_consen 114 ---DLPAEEVARQLEELEE 129 (171)
T ss_dssp ---SS-HHHHHHHHHHHHH
T ss_pred ---CCCHHHHHHHHHHHHH
Confidence 4566666555555443
No 66
>cd06169 BMC Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypo
Probab=21.95 E-value=2.3e+02 Score=18.21 Aligned_cols=46 Identities=17% Similarity=0.177 Sum_probs=30.9
Q ss_pred HHHHHHHHHh-CCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHH
Q 031636 18 MTSVVNPTFD-LKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 18 ~~~iv~~L~d-kka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~ 64 (156)
......+++. .|+-||.++++...++-.-++++.+|.. .-+++..+
T Consensus 10 ~~~~i~aaD~a~KaA~V~l~~~~~~~~~g~~~~~i~G~~-s~V~~A~~ 56 (62)
T cd06169 10 LAAAIVAADAAVKAADVELVGIERAGGGGLVTLIIRGDV-SAVKAAVE 56 (62)
T ss_pred HHHHHHHHHHHhhhcCeEEEEEEecCCCcEEEEEEEECH-HHHHHHHH
Confidence 3345555555 4888999999988775566788888865 44444333
No 67
>TIGR02471 sucr_syn_bact_C sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial. Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by TIGR02472.
Probab=21.95 E-value=91 Score=24.70 Aligned_cols=18 Identities=39% Similarity=0.217 Sum_probs=14.6
Q ss_pred EEEEEecCCHHHHHHHHH
Q 031636 47 YMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 47 y~VIaTg~S~rh~~aia~ 64 (156)
.|+||||++...++.+..
T Consensus 32 ~~viaTGR~~~~v~~~~~ 49 (236)
T TIGR02471 32 GFGIATGRSVESAKSRYA 49 (236)
T ss_pred eEEEEeCCCHHHHHHHHH
Confidence 599999999988766554
No 68
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=21.95 E-value=2.4e+02 Score=18.36 Aligned_cols=48 Identities=6% Similarity=0.101 Sum_probs=37.3
Q ss_pred HHHHHHHHHhCCCCceEEEecCCC--CCccCEEEEEecCCHHHHHHHHHHH
Q 031636 18 MTSVVNPTFDLKADDVKVIPVGEK--CDWTDYMVIATGRSTWHVKNIAQAI 66 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~~~--~~~~Dy~VIaTg~S~rh~~aia~~i 66 (156)
+..|..++.+. +-+|.-+++... ...+-..+-+...+..|+..+...|
T Consensus 20 L~dI~~~i~~~-~~nI~~i~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L 69 (80)
T PF13291_consen 20 LADITSVISEN-GVNIRSINARTNKDDGTARITLTVEVKDLEHLNQIIRKL 69 (80)
T ss_dssp HHHHHHHHHCS-SSEEEEEEEEE--ETTEEEEEEEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHC-CCCeEEEEeEEeccCCEEEEEEEEEECCHHHHHHHHHHH
Confidence 56888888888 668888888664 4677777788889999998877766
No 69
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=21.83 E-value=2.5e+02 Score=22.03 Aligned_cols=44 Identities=11% Similarity=0.123 Sum_probs=30.0
Q ss_pred HHHHHHhCCCCceEEEecCCC-----CCccCEEEEEecCCHHHHHHHHH
Q 031636 21 VVNPTFDLKADDVKVIPVGEK-----CDWTDYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 21 iv~~L~dkka~DI~ViDv~~~-----~~~~Dy~VIaTg~S~rh~~aia~ 64 (156)
+.+.+...+...++++|++=. ..++|++|..++.-..+++.+.+
T Consensus 94 ~~~~~~~~~~~~~~v~e~pLL~E~~~~~~~D~vi~V~a~~e~ri~Rl~~ 142 (180)
T PF01121_consen 94 IEKFIKRNKSEKVVVVEIPLLFESGLEKLCDEVIVVYAPEEIRIKRLME 142 (180)
T ss_dssp HHHHHHHCHSTSEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHH
T ss_pred HHHHHHhccCCCEEEEEcchhhhhhHhhhhceEEEEECCHHHHHHHHHh
Confidence 344445555558999999742 56799999999998888888765
No 70
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=21.76 E-value=1.7e+02 Score=18.48 Aligned_cols=25 Identities=16% Similarity=0.266 Sum_probs=21.1
Q ss_pred EEEecCCHHHHHHHHHHHHHHHHHH
Q 031636 49 VIATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 49 VIaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
-+..|+|.-|-++++..|.+.+.+.
T Consensus 7 ~l~~grt~eqk~~l~~~it~~l~~~ 31 (64)
T PRK01964 7 QLLEGRPEEKIKNLIREVTEAISAT 31 (64)
T ss_pred EEeCCCCHHHHHHHHHHHHHHHHHH
Confidence 3456999999999999999888765
No 71
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=21.72 E-value=3.1e+02 Score=19.62 Aligned_cols=38 Identities=16% Similarity=0.249 Sum_probs=25.8
Q ss_pred HHHHHHHh-CCCCceEEEecCCCC-CccCEEEEEecCCHH
Q 031636 20 SVVNPTFD-LKADDVKVIPVGEKC-DWTDYMVIATGRSTW 57 (156)
Q Consensus 20 ~iv~~L~d-kka~DI~ViDv~~~~-~~~Dy~VIaTg~S~r 57 (156)
.+-+.|.+ .+.+-|.|.|++.-| +.++..|+.-+...+
T Consensus 7 ~l~~~L~~~l~p~~v~V~D~SgGCG~~F~v~IvS~~FeGK 46 (85)
T KOG3348|consen 7 RLEELLTEALEPEHVEVQDVSGGCGSMFDVVIVSAAFEGK 46 (85)
T ss_pred HHHHHHHhhcCceEEEEEEcCCCccceEEEEEEccccCCh
Confidence 34444443 377899999998765 567877777665544
No 72
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=21.67 E-value=4.1e+02 Score=23.14 Aligned_cols=82 Identities=16% Similarity=0.293 Sum_probs=56.8
Q ss_pred EEEEecC---CHHHHHHHHHHHHHHHHHHhHHhcccccCCCccccCCCCCEEEEecCceEEEecChhhhhhcChh----h
Q 031636 48 MVIATGR---STWHVKNIAQAIIYKAKQRQREVGAKQMMLPSVQGQDTGKWVIIDSGKVIVHALDENARAYYNLE----D 120 (156)
Q Consensus 48 ~VIaTg~---S~rh~~aia~~i~~~lk~~~~e~g~~~~~~~~iEG~~~~~WvllD~GdVvVHIft~E~Re~Y~LE----~ 120 (156)
+.+||.+ +-||+..+-- +...+|.. |..+++=+|+=+.|+..+.=.|.-=.-|+=| .
T Consensus 32 VLv~tSRfwfNYRH~aNvl~-~YrsvKrl---------------GipDsqIilmladd~acn~RN~~pg~Vy~n~~~~~n 95 (309)
T KOG1349|consen 32 VLVCTSRFWFNYRHVANVLS-VYRSVKRL---------------GIPDSQIILMLADDMACNSRNPRPGTVYNNENHALN 95 (309)
T ss_pred EEEecchhhhhHHHHHHHHH-HHHHHHHc---------------CCCcccEEEEeccccccccCCCCCcceecccccccc
Confidence 4456654 6688866432 33344433 4457788999889998888777777777777 6
Q ss_pred hcCCCCCCCCchHHH-HHHHHHHhhc
Q 031636 121 LWTSEPSKSATVQDL-QKAFVKVRRK 145 (156)
Q Consensus 121 LW~~a~~~~~~~~~l-~~~~~~~~~~ 145 (156)
|+++.+.++.-.-+. +|.|.++=-+
T Consensus 96 lygd~vevdyrgyevtvEnflr~LTg 121 (309)
T KOG1349|consen 96 LYGDDVEVDYRGYEVTVENFLRVLTG 121 (309)
T ss_pred ccCCcceeecccchhHHHHHHHHHcC
Confidence 788888776655555 8888888766
No 73
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=21.44 E-value=1.1e+02 Score=26.12 Aligned_cols=38 Identities=13% Similarity=0.239 Sum_probs=25.2
Q ss_pred ccCCCHHHHHHHHHhCCCCceEEEecCCCCCccCEEEEEecCCHHHHHHHHH
Q 031636 13 RKRPSMTSVVNPTFDLKADDVKVIPVGEKCDWTDYMVIATGRSTWHVKNIAQ 64 (156)
Q Consensus 13 ~~~~~~~~iv~~L~dkka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~~aia~ 64 (156)
+..+.+..+++.+..++++.| +++++|.|.--......
T Consensus 27 ~~~~~l~~~~~~l~~~~~~~I--------------~~~g~GsS~~aa~~~~~ 64 (340)
T PRK11382 27 HDVPLVHAIVEEMVKRDIDRI--------------YFVACGSPLNAAQTAKH 64 (340)
T ss_pred hhhHHHHHHHHHHHhCCCCEE--------------EEEEechHHHHHHHHHH
Confidence 344667778888877766666 67778877755544443
No 74
>COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
Probab=21.42 E-value=66 Score=28.20 Aligned_cols=17 Identities=29% Similarity=0.524 Sum_probs=15.0
Q ss_pred EecCCHHHHHHHHHHHH
Q 031636 51 ATGRSTWHVKNIAQAII 67 (156)
Q Consensus 51 aTg~S~rh~~aia~~i~ 67 (156)
|.|+++.|++++++.|.
T Consensus 294 CCGTTPeHIraia~~v~ 310 (311)
T COG0646 294 CCGTTPEHIRAIAEAVK 310 (311)
T ss_pred ccCCCHHHHHHHHHHhc
Confidence 78999999999998773
No 75
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=21.21 E-value=1.4e+02 Score=23.48 Aligned_cols=30 Identities=17% Similarity=0.128 Sum_probs=24.2
Q ss_pred ccCEEEEEec-CCHHHHHHHHHHHHHHHHHH
Q 031636 44 WTDYMVIATG-RSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 44 ~~Dy~VIaTg-~S~rh~~aia~~i~~~lk~~ 73 (156)
|..-=|+||| +|..+++..++.+.+.+++.
T Consensus 53 f~sGKivitGaks~~~~~~a~~~~~~~L~~~ 83 (174)
T cd00652 53 FSSGKMVITGAKSEEDAKLAARKYARILQKL 83 (174)
T ss_pred ECCCEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 4455578887 79999999999998888775
No 76
>PF03319 EutN_CcmL: Ethanolamine utilisation protein EutN/carboxysome; InterPro: IPR004992 The ethanolamine utilization protein EutN is involved in the cobalamin-dependent degradation of ethanolamine []. The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB: 2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the centre. This suggests that EutN forms a pore, with an opening of 26 Amstrong in diameter on one face and 14 Amstrong on the other face []. This entry represents a family of related bacterial proteins with roles in ethanolamine and carbon dioxide metabolism.; PDB: 2QW7_F 2RCF_E 2HD3_F 2Z9H_D.
Probab=21.11 E-value=1e+02 Score=21.72 Aligned_cols=30 Identities=7% Similarity=0.264 Sum_probs=21.3
Q ss_pred CCCceEEEecCCCCCccCEEEEEecCCHHHH
Q 031636 29 KADDVKVIPVGEKCDWTDYMVIATGRSTWHV 59 (156)
Q Consensus 29 ka~DI~ViDv~~~~~~~Dy~VIaTg~S~rh~ 59 (156)
.+.-++++|.-+ ....|++++++|++.||.
T Consensus 37 ~g~~~VA~D~vG-AG~Ge~Vlv~~Gs~Ar~~ 66 (83)
T PF03319_consen 37 TGEPIVAVDTVG-AGVGEWVLVTSGSSARQA 66 (83)
T ss_dssp EEEEEEEEESS----TT-EEEEEETHHHHHH
T ss_pred CCCEEEEEeCCC-CCCCCEEEEECCHHHHHh
Confidence 356778888765 678899999999988874
No 77
>PRK08105 flavodoxin; Provisional
Probab=21.10 E-value=2.1e+02 Score=21.61 Aligned_cols=35 Identities=14% Similarity=0.307 Sum_probs=24.5
Q ss_pred HHHHHHHhCCCCceEEEecCCCCCc----cCEEEEEecCC
Q 031636 20 SVVNPTFDLKADDVKVIPVGEKCDW----TDYMVIATGRS 55 (156)
Q Consensus 20 ~iv~~L~dkka~DI~ViDv~~~~~~----~Dy~VIaTg~S 55 (156)
.|++.|.+ .+.++.++++.....+ ++++||+|.+-
T Consensus 21 ~l~~~l~~-~g~~~~~~~~~~~~~~~~~~~~~vi~~~sT~ 59 (149)
T PRK08105 21 EAEAILTA-QGHEVTLFEDPELSDWQPYQDELVLVVTSTT 59 (149)
T ss_pred HHHHHHHh-CCCceEEechhhCCchhcccCCeEEEEECCC
Confidence 66666764 4677888888765543 47888888764
No 78
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=21.01 E-value=1.4e+02 Score=18.64 Aligned_cols=25 Identities=8% Similarity=0.279 Sum_probs=21.0
Q ss_pred EEEecCCHHHHHHHHHHHHHHHHHH
Q 031636 49 VIATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 49 VIaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
+...|+|.-|-++++..|.+.+.+.
T Consensus 7 i~~~grt~eqK~~l~~~it~~l~~~ 31 (63)
T TIGR00013 7 ILKEGRTDEQKRQLIEGVTEAMAET 31 (63)
T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3346899999999999999988775
No 79
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=20.87 E-value=2.7e+02 Score=18.68 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=15.9
Q ss_pred ccCEEEEEecCCHHHHHHHHHHHH
Q 031636 44 WTDYMVIATGRSTWHVKNIAQAII 67 (156)
Q Consensus 44 ~~Dy~VIaTg~S~rh~~aia~~i~ 67 (156)
.+|++|+.+..+..-++++...+.
T Consensus 61 ~ad~viv~~~~~~~s~~~~~~~~~ 84 (104)
T cd02042 61 AADLVLIPVQPSPLDLDGLEKLLE 84 (104)
T ss_pred HCCEEEEeccCCHHHHHHHHHHHH
Confidence 467777777777776666655443
No 80
>PRK05569 flavodoxin; Provisional
Probab=20.86 E-value=3e+02 Score=19.82 Aligned_cols=34 Identities=9% Similarity=0.115 Sum_probs=24.2
Q ss_pred HHHHHHHhCCCCceEEEecCCCC----CccCEEEEEecC
Q 031636 20 SVVNPTFDLKADDVKVIPVGEKC----DWTDYMVIATGR 54 (156)
Q Consensus 20 ~iv~~L~dkka~DI~ViDv~~~~----~~~Dy~VIaTg~ 54 (156)
.|++.+.+. +.++.++++.+.. .-+|.+|++|..
T Consensus 21 ~i~~~~~~~-g~~v~~~~~~~~~~~~~~~~d~iilgsPt 58 (141)
T PRK05569 21 TIADGAKEA-GAEVTIKHVADAKVEDVLEADAVAFGSPS 58 (141)
T ss_pred HHHHHHHhC-CCeEEEEECCcCCHHHHhhCCEEEEECCC
Confidence 566666554 4578999997743 246999999975
No 81
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=20.84 E-value=1.4e+02 Score=18.87 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=20.9
Q ss_pred EEecCCHHHHHHHHHHHHHHHHHH
Q 031636 50 IATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 50 IaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
+..|+|..|-++|++.|.+.+.+.
T Consensus 8 ~~~Grs~EqK~~L~~~it~a~~~~ 31 (60)
T PRK02289 8 LFEGRSQEQKNALAREVTEVVSRI 31 (60)
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHH
Confidence 345899999999999999998875
No 82
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=20.80 E-value=1.8e+02 Score=17.66 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=20.1
Q ss_pred EEecCCHHHHHHHHHHHHHHHHHH
Q 031636 50 IATGRSTWHVKNIAQAIIYKAKQR 73 (156)
Q Consensus 50 IaTg~S~rh~~aia~~i~~~lk~~ 73 (156)
+..|+|..|-+++++.|.+.+.+.
T Consensus 7 ~~~grt~eqk~~l~~~i~~~l~~~ 30 (58)
T cd00491 7 ILEGRTDEQKRELIERVTEAVSEI 30 (58)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHHH
Confidence 345889999999999999888765
No 83
>PF14177 YkyB: YkyB-like protein
Probab=20.58 E-value=2.1e+02 Score=22.24 Aligned_cols=67 Identities=13% Similarity=0.209 Sum_probs=40.0
Q ss_pred ecCCHHHHHHHHHHHHHHHHHHhH--HhcccccCCCccccCCCCCEEEEecCceEEEecChhhhhhcChhhh
Q 031636 52 TGRSTWHVKNIAQAIIYKAKQRQR--EVGAKQMMLPSVQGQDTGKWVIIDSGKVIVHALDENARAYYNLEDL 121 (156)
Q Consensus 52 Tg~S~rh~~aia~~i~~~lk~~~~--e~g~~~~~~~~iEG~~~~~WvllD~GdVvVHIft~E~Re~Y~LE~L 121 (156)
|+.+.+++..|=..+...+-+.+. ..|.....-|+- + ....=+||.|||..-| ++++.-+|=.|+-|
T Consensus 18 Ta~~p~~LY~LKk~aL~Kll~E~kA~kiGlHfs~npk~-s-~Q~s~vLv~~gdY~FH-iP~~k~Df~~LphL 86 (140)
T PF14177_consen 18 TALNPKYLYQLKKKALQKLLEEGKAKKIGLHFSNNPKY-S-QQQSDVLVKCGDYYFH-IPPTKEDFKKLPHL 86 (140)
T ss_pred ccCChHHHHHHHHHHHHHHHHcCcceEEEEeecCCCcc-h-hhheeeEEEeCcEeec-cCCCcchhhhCCcc
Confidence 566778888876666555544332 123321000111 2 2235599999999999 57777787777666
No 84
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=20.54 E-value=70 Score=21.54 Aligned_cols=21 Identities=24% Similarity=0.667 Sum_probs=13.3
Q ss_pred CCCCCEEEEecCceEEEecChh
Q 031636 90 QDTGKWVIIDSGKVIVHALDEN 111 (156)
Q Consensus 90 ~~~~~WvllD~GdVvVHIft~E 111 (156)
..-|+|+|+..| ..+..++++
T Consensus 38 v~~Gd~VLVHaG-~Ai~~idee 58 (68)
T PF01455_consen 38 VKVGDYVLVHAG-FAIEKIDEE 58 (68)
T ss_dssp B-TT-EEEEETT-EEEEEE-HH
T ss_pred CCCCCEEEEecC-hhheeCCHH
Confidence 457899999999 555555554
No 85
>COG4033 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.53 E-value=2.6e+02 Score=20.63 Aligned_cols=39 Identities=21% Similarity=0.404 Sum_probs=27.2
Q ss_pred CCCEEEEec-----CceEEEecChhhhhhcChhhhcCCCCCCCCchHHHHHHHHHHhhccCCCCc
Q 031636 92 TGKWVIIDS-----GKVIVHALDENARAYYNLEDLWTSEPSKSATVQDLQKAFVKVRRKNNSKKP 151 (156)
Q Consensus 92 ~~~WvllD~-----GdVvVHIft~E~Re~Y~LE~LW~~a~~~~~~~~~l~~~~~~~~~~~~~~~~ 151 (156)
+++|+++-| |..|+-|= ...+++.+...+-.+.+|.|++
T Consensus 58 ~~~~iifpytKPCyGtfVl~i~---------------------~e~eeiek~lek~~~~k~~k~~ 101 (102)
T COG4033 58 SGEAIIFPYTKPCYGTFVLKIK---------------------VEAEEIEKLLEKYKKDKNVKKI 101 (102)
T ss_pred cCCEEEEEeccccceeEEEEec---------------------CCHHHHHHHHHhhcCCCCcccC
Confidence 468999987 88888753 3335666667777777776665
No 86
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=20.32 E-value=1.5e+02 Score=21.24 Aligned_cols=24 Identities=21% Similarity=0.155 Sum_probs=19.5
Q ss_pred ccCEEEEEecCCHHHHHHHHHHHH
Q 031636 44 WTDYMVIATGRSTWHVKNIAQAII 67 (156)
Q Consensus 44 ~~Dy~VIaTg~S~rh~~aia~~i~ 67 (156)
=.|..|||+|....++...++.+.
T Consensus 9 g~di~iia~G~~~~~al~A~~~L~ 32 (124)
T PF02780_consen 9 GADITIIAYGSMVEEALEAAEELE 32 (124)
T ss_dssp SSSEEEEEETTHHHHHHHHHHHHH
T ss_pred CCCEEEEeehHHHHHHHHHHHHHH
Confidence 358999999999888877777664
No 87
>cd03130 GATase1_CobB Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. CobB plays a role in cobalamin biosythesis catalyzing the conversion of cobyrinic acid to cobyrinic acid a,c-diamide. CobB belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobB.
Probab=20.23 E-value=4.2e+02 Score=20.78 Aligned_cols=53 Identities=8% Similarity=0.045 Sum_probs=34.7
Q ss_pred HHHHHHHHHhCCCCceEEEecC---CCCCccCEEEEEecCCHHHHHHHHH--HHHHHHHH
Q 031636 18 MTSVVNPTFDLKADDVKVIPVG---EKCDWTDYMVIATGRSTWHVKNIAQ--AIIYKAKQ 72 (156)
Q Consensus 18 ~~~iv~~L~dkka~DI~ViDv~---~~~~~~Dy~VIaTg~S~rh~~aia~--~i~~~lk~ 72 (156)
..+-.++|+ +-+-++.+++.. .... +|-+||--|.+..++..|.+ .+.+.+++
T Consensus 13 y~e~~~~l~-~~G~~v~~~s~~~~~~l~~-~D~lilPGG~~~~~~~~L~~~~~~~~~i~~ 70 (198)
T cd03130 13 YPENLELLE-AAGAELVPFSPLKDEELPD-ADGLYLGGGYPELFAEELSANQSMRESIRA 70 (198)
T ss_pred cHHHHHHHH-HCCCEEEEECCCCCCCCCC-CCEEEECCCchHHHHHHHHhhHHHHHHHHH
Confidence 445667777 444578887773 3344 79999999988877766644 24455554
No 88
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=20.17 E-value=3e+02 Score=21.26 Aligned_cols=26 Identities=19% Similarity=0.160 Sum_probs=19.1
Q ss_pred CCceEEEecCCCC--Cc--cCEEEEEecCC
Q 031636 30 ADDVKVIPVGEKC--DW--TDYMVIATGRS 55 (156)
Q Consensus 30 a~DI~ViDv~~~~--~~--~Dy~VIaTg~S 55 (156)
+.++.++++.+.. .+ +|.+||+++.-
T Consensus 28 g~~v~~~~~~~~~~~~l~~yD~vIlGspi~ 57 (177)
T PRK11104 28 GIQCDVVNLHRIEEPDLSDYDRVVIGASIR 57 (177)
T ss_pred CCeEEEEEhhhcCccCHHHCCEEEEECccc
Confidence 5678888887653 22 69999999763
No 89
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=20.07 E-value=2.2e+02 Score=28.02 Aligned_cols=30 Identities=10% Similarity=-0.048 Sum_probs=25.6
Q ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHHhH
Q 031636 46 DYMVIATGRSTWHVKNIAQAIIYKAKQRQR 75 (156)
Q Consensus 46 Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~ 75 (156)
-+=||.||.+..-++.+...+.+.+...|.
T Consensus 261 ~~~iiVTAP~~~nv~~Lf~fa~~~l~~lg~ 290 (758)
T COG1444 261 SVRIIVTAPTPANVQTLFEFAGKGLEFLGY 290 (758)
T ss_pred CceEEEeCCCHHHHHHHHHHHHHhHHHhCC
Confidence 468999999999999999998888877643
No 90
>KOG0174 consensus 20S proteasome, regulatory subunit beta type PSMB6/PSMB9/PRE3 [Posttranslational modification, protein turnover, chaperones]
Probab=20.00 E-value=2e+02 Score=23.96 Aligned_cols=35 Identities=17% Similarity=0.110 Sum_probs=30.8
Q ss_pred CCCccCEEEEEecCCHHHHHHHHHHHHHHHHHHhH
Q 031636 41 KCDWTDYMVIATGRSTWHVKNIAQAIIYKAKQRQR 75 (156)
Q Consensus 41 ~~~~~Dy~VIaTg~S~rh~~aia~~i~~~lk~~~~ 75 (156)
+++++|-+..|-.-|.--.+++|+.+...|.-...
T Consensus 53 lT~itD~i~cCRSGSAADtQaiaD~~~Y~L~~~~~ 87 (224)
T KOG0174|consen 53 LTPITDNIYCCRSGSAADTQAIADIVRYHLELYTI 87 (224)
T ss_pred ceeccccEEEecCCchhhHHHHHHHHHHHHHHhhh
Confidence 58899999999999999999999999988876543
Done!