Query 039146 Match_columns 84 No_of_seqs 100 out of 1004 Neff 7.1 Searched_HMMs 46136 Date Fri Mar 29 06:45:08 2013 Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039146.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039146hhsearch_cdd -cpu 12 -v 0 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF02887 PK_C: Pyruvate kinase 99.8 3.1E-21 6.6E-26 121.7 6.3 59 25-83 1-59 (117) 2 PTZ00066 pyruvate kinase; Prov 99.8 1.5E-19 3.3E-24 137.5 7.7 83 1-83 372-454 (513) 3 PTZ00300 pyruvate kinase; Prov 99.8 1.8E-19 3.9E-24 135.7 7.2 62 22-83 330-391 (454) 4 PLN02461 Probable pyruvate kin 99.8 7.6E-19 1.7E-23 133.7 7.7 83 1-83 356-451 (511) 5 TIGR01064 pyruv_kin pyruvate k 99.8 1.2E-18 2.7E-23 131.6 7.7 61 23-83 356-416 (473) 6 PLN02765 pyruvate kinase 99.8 1.6E-18 3.5E-23 132.2 7.6 83 1-83 369-464 (526) 7 PRK06247 pyruvate kinase; Prov 99.7 2.7E-18 5.9E-23 129.8 7.3 61 23-83 352-412 (476) 8 PRK09206 pyruvate kinase; Prov 99.7 3.1E-18 6.8E-23 129.4 6.8 61 23-83 353-413 (470) 9 PRK06354 pyruvate kinase; Prov 99.7 3.8E-18 8.3E-23 131.7 6.9 80 1-83 341-420 (590) 10 PLN02762 pyruvate kinase compl 99.7 4.8E-18 1E-22 129.3 6.6 61 23-83 392-452 (509) 11 PRK05826 pyruvate kinase; Prov 99.7 9.6E-18 2.1E-22 126.7 6.9 62 22-83 354-416 (465) 12 cd00288 Pyruvate_Kinase Pyruva 99.7 2E-17 4.4E-22 125.3 8.0 83 1-83 336-418 (480) 13 PLN02623 pyruvate kinase 99.7 4.5E-17 9.7E-22 125.4 6.5 60 23-83 460-519 (581) 14 COG0469 PykF Pyruvate kinase [ 99.6 4.1E-16 8.9E-21 118.0 7.1 63 21-83 356-418 (477) 15 KOG2323 Pyruvate kinase [Carbo 99.6 7.9E-16 1.7E-20 116.6 7.1 82 1-82 356-437 (501) 16 COG1751 Uncharacterized conser 95.2 0.098 2.1E-06 35.3 6.1 50 24-73 11-61 (186) 17 PF00582 Usp: Universal stress 89.0 2.1 4.6E-05 25.2 5.6 43 26-69 88-139 (140) 18 PRK04885 ppnK inorganic polyph 88.7 0.74 1.6E-05 32.9 3.9 34 39-72 146-183 (265) 19 KOG2178 Predicted sugar kinase 86.6 0.88 1.9E-05 34.6 3.3 34 38-71 283-320 (409) 20 PRK15005 universal stress prot 86.4 3.3 7.3E-05 25.5 5.5 41 28-69 95-143 (144) 21 PRK01231 ppnK inorganic polyph 83.8 1.7 3.6E-05 31.5 3.6 34 38-71 172-209 (295) 22 cd05008 SIS_GlmS_GlmD_1 SIS (S 83.7 2.1 4.5E-05 26.1 3.6 34 40-74 46-84 (126) 23 cd01987 USP_OKCHK USP domain i 81.9 6.1 0.00013 23.7 5.2 44 26-69 71-123 (124) 24 COG0061 nadF NAD kinase [Coenz 81.8 1.9 4E-05 30.9 3.2 34 38-71 163-200 (281) 25 PRK02649 ppnK inorganic polyph 81.7 2.6 5.6E-05 30.8 3.9 34 38-71 178-215 (305) 26 PRK04539 ppnK inorganic polyph 81.4 2.7 5.8E-05 30.5 3.9 33 39-71 179-215 (296) 27 PLN02935 Bifunctional NADH kin 81.3 2.4 5.1E-05 33.3 3.8 34 38-71 377-414 (508) 28 PRK13509 transcriptional repre 81.0 4.4 9.5E-05 28.4 4.8 54 23-80 78-131 (251) 29 PRK02645 ppnK inorganic polyph 80.8 2.6 5.6E-05 30.6 3.7 35 38-72 176-214 (305) 30 PRK10411 DNA-binding transcrip 80.7 4.7 0.0001 28.2 4.8 53 23-79 78-130 (240) 31 PF00455 DeoRC: DeoR C termina 80.0 4.3 9.4E-05 26.6 4.3 54 23-80 4-58 (161) 32 cd05710 SIS_1 A subgroup of th 78.7 3.9 8.4E-05 25.2 3.6 34 40-74 47-85 (120) 33 PRK02231 ppnK inorganic polyph 78.5 3.8 8.2E-05 29.5 3.9 33 39-71 154-190 (272) 34 PRK14077 pnk inorganic polypho 78.5 3.8 8.3E-05 29.6 3.9 33 39-71 175-211 (287) 35 cd05017 SIS_PGI_PMI_1 The memb 77.9 4 8.6E-05 25.1 3.4 34 40-74 43-81 (119) 36 PRK15456 universal stress prot 77.8 10 0.00022 23.5 5.3 41 28-69 93-141 (142) 37 PRK03372 ppnK inorganic polyph 77.4 3.8 8.3E-05 29.9 3.7 34 38-71 182-219 (306) 38 PRK14075 pnk inorganic polypho 77.4 4.1 9E-05 28.8 3.8 32 39-70 144-179 (256) 39 PRK01911 ppnK inorganic polyph 77.3 3.7 8E-05 29.7 3.6 34 38-71 173-210 (292) 40 PRK03708 ppnK inorganic polyph 76.6 4.7 0.0001 28.9 4.0 34 38-71 162-199 (277) 41 TIGR03127 RuMP_HxlB 6-phospho 76.4 4.3 9.3E-05 26.5 3.5 33 40-73 72-109 (179) 42 PRK00561 ppnK inorganic polyph 75.9 4.6 0.0001 28.9 3.7 34 38-71 134-171 (259) 43 PRK03501 ppnK inorganic polyph 75.3 5.5 0.00012 28.5 3.9 34 38-71 146-183 (264) 44 PRK04761 ppnK inorganic polyph 75.1 5.2 0.00011 28.4 3.8 34 38-71 131-168 (246) 45 PRK01185 ppnK inorganic polyph 74.6 5 0.00011 28.8 3.6 33 39-71 156-192 (271) 46 cd05014 SIS_Kpsf KpsF-like pro 74.5 6.2 0.00013 24.0 3.7 33 40-73 47-84 (128) 47 cd05005 SIS_PHI Hexulose-6-pho 74.1 5.5 0.00012 26.1 3.5 33 40-73 75-112 (179) 48 PLN02929 NADH kinase 74.0 4.9 0.00011 29.5 3.5 27 39-65 194-220 (301) 49 PRK02155 ppnK NAD(+)/NADH kina 73.4 5.8 0.00013 28.7 3.7 34 38-71 173-210 (291) 50 PF11017 DUF2855: Protein of u 72.7 8.4 0.00018 28.5 4.4 39 38-76 133-175 (314) 51 TIGR00441 gmhA phosphoheptose 72.4 6.7 0.00015 25.3 3.6 33 40-73 79-116 (154) 52 PRK15118 universal stress glob 72.3 20 0.00043 22.1 5.8 42 27-69 90-137 (144) 53 PF01513 NAD_kinase: ATP-NAD k 72.1 4.1 8.8E-05 29.0 2.7 32 39-70 189-224 (285) 54 PRK13936 phosphoheptose isomer 70.7 7.7 0.00017 26.2 3.7 33 40-73 111-148 (197) 55 PLN02727 NAD kinase 70.6 6.5 0.00014 33.2 3.8 33 39-71 861-897 (986) 56 PRK11557 putative DNA-binding 70.1 7.8 0.00017 27.0 3.7 33 40-73 175-212 (278) 57 PRK13938 phosphoheptose isomer 69.6 8 0.00017 26.4 3.6 33 40-73 113-150 (196) 58 cd05013 SIS_RpiR RpiR-like pro 69.2 9 0.0002 23.1 3.5 34 40-74 60-98 (139) 59 PF13580 SIS_2: SIS domain; PD 68.4 7.3 0.00016 24.6 3.0 30 40-70 103-137 (138) 60 cd00293 USP_Like Usp: Universa 68.1 19 0.0004 20.8 4.7 40 29-69 82-130 (130) 61 PRK03378 ppnK inorganic polyph 68.0 9.4 0.0002 27.6 3.8 33 39-71 174-210 (292) 62 PF05991 NYN_YacP: YacP-like N 67.3 8.3 0.00018 25.5 3.2 36 42-77 67-108 (166) 63 TIGR01275 ACC_deam_rel pyridox 67.0 18 0.00038 25.8 5.1 40 32-71 157-204 (311) 64 PRK10434 srlR DNA-bindng trans 67.0 15 0.00033 25.8 4.7 53 23-79 76-129 (256) 65 cd05006 SIS_GmhA Phosphoheptos 66.0 11 0.00023 24.7 3.5 33 40-73 101-138 (177) 66 PRK11543 gutQ D-arabinose 5-ph 63.9 12 0.00026 26.6 3.7 34 40-74 89-127 (321) 67 PRK14076 pnk inorganic polypho 63.7 12 0.00026 29.5 3.9 34 38-71 458-495 (569) 68 PRK13937 phosphoheptose isomer 63.6 13 0.00029 24.7 3.7 33 40-73 106-143 (188) 69 PRK10681 DNA-binding transcrip 63.6 17 0.00037 25.4 4.4 53 23-79 77-130 (252) 70 PRK11175 universal stress prot 63.5 28 0.00062 24.2 5.5 44 27-71 94-146 (305) 71 PRK09802 DNA-binding transcrip 63.3 21 0.00045 25.3 4.8 54 23-80 91-145 (269) 72 cd05015 SIS_PGI_1 Phosphogluco 63.3 14 0.00031 23.9 3.7 38 40-77 73-123 (158) 73 PF01380 SIS: SIS domain SIS d 62.1 16 0.00034 22.0 3.6 32 40-72 53-89 (131) 74 PRK03910 D-cysteine desulfhydr 60.7 23 0.0005 25.6 4.8 33 40-72 183-219 (331) 75 cd06167 LabA_like LabA_like pr 59.1 28 0.00061 21.7 4.5 55 25-79 84-139 (149) 76 PF01976 DUF116: Protein of un 57.9 36 0.00078 22.5 4.9 36 32-70 78-114 (158) 77 cd01989 STK_N The N-terminal d 57.6 42 0.00091 20.5 5.6 44 27-70 90-144 (146) 78 COG1737 RpiR Transcriptional r 56.9 56 0.0012 23.2 6.1 38 34-72 171-213 (281) 79 PRK10906 DNA-binding transcrip 56.9 26 0.00057 24.6 4.4 54 23-80 76-130 (252) 80 PRK09982 universal stress prot 56.2 46 0.001 20.6 5.9 43 27-69 90-137 (142) 81 TIGR00288 conserved hypothetic 55.7 32 0.00069 23.0 4.4 51 25-75 90-141 (160) 82 cd08181 PPD-like 1,3-propanedi 55.7 48 0.001 24.3 5.7 48 23-72 66-133 (357) 83 PRK11302 DNA-binding transcrip 55.6 17 0.00037 25.2 3.3 32 40-72 175-211 (284) 84 COG1349 GlpR Transcriptional r 55.0 42 0.0009 23.6 5.2 52 24-79 77-129 (253) 85 PRK05578 cytidine deaminase; V 54.6 42 0.00091 21.5 4.7 48 26-73 55-110 (131) 86 PRK00414 gmhA phosphoheptose i 54.0 15 0.00033 24.7 2.7 33 40-73 111-148 (192) 87 PRK11337 DNA-binding transcrip 53.3 19 0.00042 25.3 3.3 33 40-73 187-224 (292) 88 PRK02947 hypothetical protein; 53.2 36 0.00077 23.8 4.6 34 39-73 105-143 (246) 89 PRK08674 bifunctional phosphog 53.2 13 0.00029 26.9 2.5 33 41-74 79-116 (337) 90 cd01988 Na_H_Antiporter_C The 52.9 46 0.001 19.6 5.5 42 27-69 81-131 (132) 91 PF04851 ResIII: Type III rest 52.0 56 0.0012 20.3 5.1 39 40-80 26-67 (184) 92 PRK10892 D-arabinose 5-phospha 52.0 25 0.00055 25.1 3.7 34 40-74 94-132 (326) 93 PF02887 PK_C: Pyruvate kinase 51.9 23 0.00051 21.6 3.1 39 31-69 29-67 (117) 94 cd04795 SIS SIS domain. SIS (S 51.8 29 0.00063 19.2 3.4 30 40-70 47-81 (87) 95 cd08180 PDD 1,3-propanediol de 51.3 62 0.0013 23.4 5.7 47 23-71 61-117 (332) 96 PRK00331 glucosamine--fructose 51.2 25 0.00055 27.5 3.9 34 40-74 336-374 (604) 97 PRK15482 transcriptional regul 51.0 25 0.00054 24.7 3.5 34 40-74 182-220 (285) 98 PRK14045 1-aminocyclopropane-1 50.7 56 0.0012 23.6 5.4 43 31-73 170-221 (329) 99 PRK08329 threonine synthase; V 50.5 46 0.00099 24.4 4.9 49 24-73 87-137 (347) 100 TIGR00393 kpsF KpsF/GutQ famil 50.0 30 0.00065 23.7 3.8 33 40-73 47-84 (268) 101 PRK11175 universal stress prot 49.7 56 0.0012 22.7 5.1 42 28-70 249-299 (305) 102 TIGR00274 N-acetylmuramic acid 49.4 29 0.00064 25.0 3.7 34 40-74 126-164 (291) 103 PRK10116 universal stress prot 48.3 61 0.0013 19.7 5.5 41 29-69 91-137 (142) 104 cd00578 L-fuc_L-ara-isomerases 48.1 57 0.0012 24.6 5.2 46 28-73 51-98 (452) 105 COG0794 GutQ Predicted sugar p 47.2 43 0.00094 23.3 4.1 33 42-75 88-125 (202) 106 TIGR02815 agaS_fam putative su 46.8 21 0.00046 26.4 2.8 33 42-74 94-132 (372) 107 PRK11382 frlB fructoselysine-6 46.6 35 0.00075 24.9 3.8 33 41-74 93-130 (340) 108 cd05007 SIS_Etherase N-acetylm 46.2 34 0.00075 24.1 3.6 34 40-74 118-156 (257) 109 PRK03659 glutathione-regulated 44.3 46 0.001 26.3 4.4 49 31-79 455-507 (601) 110 PRK12570 N-acetylmuramic acid- 44.2 82 0.0018 22.8 5.4 34 40-74 127-165 (296) 111 COG3199 Predicted inorganic po 43.9 68 0.0015 24.3 5.0 40 31-71 91-131 (355) 112 TIGR01136 cysKM cysteine synth 43.8 71 0.0015 22.6 5.0 42 31-72 152-199 (299) 113 cd07408 MPP_SA0022_N Staphyloc 43.6 98 0.0021 21.4 5.6 53 23-75 154-213 (257) 114 PRK11761 cysM cysteine synthas 42.8 76 0.0016 22.7 5.0 41 32-72 157-203 (296) 115 PRK08197 threonine synthase; V 42.3 71 0.0015 23.8 4.9 49 23-72 109-159 (394) 116 TIGR00161 conserved hypothetic 41.3 83 0.0018 22.0 4.9 49 25-80 92-140 (238) 117 TIGR02128 G6PI_arch bifunction 41.3 39 0.00084 24.6 3.3 30 42-72 68-102 (308) 118 KOG0026 Anthranilate synthase, 40.9 31 0.00066 23.9 2.6 23 49-71 78-100 (223) 119 cd07412 MPP_YhcR_N Bacillus su 40.7 99 0.0021 21.9 5.3 52 23-75 175-241 (288) 120 TIGR01135 glmS glucosamine--fr 40.5 45 0.00097 26.2 3.8 34 40-74 338-376 (607) 121 PRK12483 threonine dehydratase 40.1 81 0.0018 24.8 5.1 42 31-72 175-222 (521) 122 COG1794 RacX Aspartate racemas 39.7 1.4E+02 0.003 21.3 6.5 52 17-69 53-104 (230) 123 PRK00973 glucose-6-phosphate i 39.3 33 0.00072 26.4 2.8 31 42-72 134-176 (446) 124 PRK06372 translation initiatio 39.1 47 0.001 23.8 3.4 39 40-78 158-200 (253) 125 COG0512 PabA Anthranilate/para 39.1 80 0.0017 21.8 4.4 38 35-72 40-83 (191) 126 cd08187 BDH Butanol dehydrogen 38.7 1.2E+02 0.0026 22.4 5.7 48 23-72 69-137 (382) 127 PTZ00295 glucosamine-fructose- 38.1 55 0.0012 26.0 4.0 33 41-74 370-407 (640) 128 PRK10886 DnaA initiator-associ 37.7 1.3E+02 0.0028 20.4 5.8 52 25-76 24-86 (196) 129 PTZ00394 glucosamine-fructose- 37.6 52 0.0011 26.5 3.8 32 42-74 403-439 (670) 130 COG4800 Predicted transcriptio 37.4 1.1E+02 0.0023 20.6 4.6 41 33-77 120-160 (170) 131 cd08194 Fe-ADH6 Iron-containin 37.2 1.4E+02 0.0031 21.9 5.8 47 23-71 63-130 (375) 132 cd01561 CBS_like CBS_like: Thi 37.1 1.1E+02 0.0024 21.4 5.1 42 31-72 149-196 (291) 133 TIGR01138 cysM cysteine syntha 36.5 1.1E+02 0.0024 21.7 5.1 42 31-72 152-199 (290) 134 PRK14075 pnk inorganic polypho 36.5 70 0.0015 22.6 3.9 30 39-70 40-69 (256) 135 TIGR00162 conserved hypothetic 36.2 45 0.00097 22.6 2.8 50 26-80 33-82 (188) 136 PF02254 TrkA_N: TrkA-N domain 36.1 93 0.002 18.3 4.3 49 31-79 53-105 (116) 137 PLN02929 NADH kinase 35.9 80 0.0017 23.2 4.2 34 40-73 64-97 (301) 138 PLN00011 cysteine synthase 35.7 1.3E+02 0.0027 21.8 5.3 42 31-72 163-210 (323) 139 cd08179 NADPH_BDH NADPH-depend 35.7 1.4E+02 0.003 22.0 5.6 34 23-58 64-97 (375) 140 COG0589 UspA Universal stress 35.4 99 0.0022 18.4 5.1 39 30-69 103-150 (154) 141 PRK15411 rcsA colanic acid cap 34.7 1.4E+02 0.0031 20.0 5.7 40 35-74 42-88 (207) 142 PLN02970 serine racemase 34.5 1.4E+02 0.0029 21.7 5.3 42 31-72 165-211 (328) 143 PLN03013 cysteine synthase 34.4 1.3E+02 0.0028 23.2 5.3 42 32-73 270-317 (429) 144 PRK14096 pgi glucose-6-phospha 34.4 47 0.001 26.3 3.0 42 39-80 167-220 (528) 145 cd08193 HVD 5-hydroxyvalerate 34.2 1.7E+02 0.0036 21.5 5.8 48 23-72 66-134 (376) 146 TIGR02638 lactal_redase lactal 34.0 1.8E+02 0.0039 21.5 5.9 35 23-59 69-103 (379) 147 cd01562 Thr-dehyd Threonine de 33.7 1.2E+02 0.0025 21.3 4.7 42 31-72 155-201 (304) 148 PRK06381 threonine synthase; V 33.7 1.3E+02 0.0028 21.4 5.0 45 28-72 152-208 (319) 149 cd08176 LPO Lactadehyde:propan 33.5 1.6E+02 0.0034 21.7 5.5 47 23-71 68-135 (377) 150 PRK10537 voltage-gated potassi 33.3 1.1E+02 0.0024 23.1 4.8 47 33-79 295-345 (393) 151 PRK05441 murQ N-acetylmuramic 33.1 1.4E+02 0.0031 21.5 5.1 34 40-74 131-169 (299) 152 COG2222 AgaS Predicted phospho 32.7 43 0.00092 24.9 2.4 33 42-74 89-125 (340) 153 PLN02981 glucosamine:fructose- 32.2 70 0.0015 25.8 3.7 33 41-74 411-448 (680) 154 PRK14101 bifunctional glucokin 31.8 64 0.0014 25.6 3.4 32 40-72 515-551 (638) 155 TIGR01137 cysta_beta cystathio 31.6 1.4E+02 0.0031 22.3 5.1 41 31-71 159-205 (454) 156 PRK09860 putative alcohol dehy 31.4 2E+02 0.0043 21.4 5.8 47 23-71 71-138 (383) 157 KOG2541 Palmitoyl protein thio 31.4 1.5E+02 0.0032 21.9 4.9 45 26-70 78-122 (296) 158 PRK10624 L-1,2-propanediol oxi 31.1 2.1E+02 0.0045 21.1 5.9 34 24-59 71-104 (382) 159 PRK10717 cysteine synthase A; 30.8 1.5E+02 0.0032 21.3 5.0 42 31-72 165-212 (330) 160 cd02554 PseudoU_synth_RluF Pse 30.6 59 0.0013 21.5 2.6 22 40-61 42-63 (164) 161 PF11197 DUF2835: Protein of u 29.8 37 0.00079 19.6 1.3 27 38-64 17-44 (68) 162 PRK03562 glutathione-regulated 29.7 1.3E+02 0.0027 24.1 4.7 48 32-79 456-507 (621) 163 PRK06721 threonine synthase; R 29.6 1.8E+02 0.0039 21.3 5.3 50 23-73 57-108 (352) 164 PF06613 KorB_C: KorB C-termin 29.6 7.5 0.00016 22.0 -1.5 24 42-65 8-31 (60) 165 PF01634 HisG: ATP phosphoribo 29.5 39 0.00085 22.5 1.7 25 31-55 96-121 (163) 166 PRK07048 serine/threonine dehy 29.5 1.7E+02 0.0037 20.9 5.1 42 32-73 163-209 (321) 167 PLN02565 cysteine synthase 29.5 1.4E+02 0.003 21.7 4.6 41 32-72 162-208 (322) 168 PRK06848 hypothetical protein; 29.3 1.6E+02 0.0035 19.0 4.8 26 48-73 95-120 (139) 169 TIGR00093 pseudouridine syntha 29.0 60 0.0013 20.2 2.4 21 39-59 6-26 (128) 170 PRK06382 threonine dehydratase 29.0 1.6E+02 0.0035 22.0 5.0 43 30-72 162-209 (406) 171 PRK08638 threonine dehydratase 29.0 1.6E+02 0.0035 21.5 4.9 41 32-72 166-211 (333) 172 cd07411 MPP_SoxB_N Thermus the 28.8 2E+02 0.0044 19.9 6.6 52 23-74 166-218 (264) 173 PRK15454 ethanol dehydrogenase 28.2 2.3E+02 0.0049 21.2 5.7 36 23-60 89-124 (395) 174 PF01513 NAD_kinase: ATP-NAD k 28.2 71 0.0015 22.6 2.9 35 37-71 73-108 (285) 175 PF00072 Response_reg: Respons 28.0 1.2E+02 0.0026 17.1 4.8 42 33-74 36-82 (112) 176 PRK10669 putative cation:proto 28.0 1.4E+02 0.0031 23.2 4.7 48 32-79 473-524 (558) 177 PF12847 Methyltransf_18: Meth 27.9 98 0.0021 17.8 3.1 35 43-77 5-39 (112) 178 PRK09533 bifunctional transald 27.8 57 0.0012 27.7 2.6 36 38-73 505-553 (948) 179 PF04009 DUF356: Protein of un 27.7 1E+02 0.0022 19.4 3.2 33 48-80 65-97 (107) 180 cd06556 ICL_KPHMT Members of t 27.5 2.2E+02 0.0047 20.0 5.2 46 26-74 157-202 (240) 181 cd04819 PA_2 PA_2: Protease-as 27.4 76 0.0016 19.7 2.6 42 32-73 62-109 (127) 182 PRK01911 ppnK inorganic polyph 26.6 1.4E+02 0.003 21.6 4.2 31 40-70 64-95 (292) 183 COG0279 GmhA Phosphoheptose is 26.5 2.2E+02 0.0047 19.5 6.2 59 23-81 22-91 (176) 184 cd04815 PA_M28_2 PA_M28_2: Pro 26.5 1.1E+02 0.0024 19.2 3.3 42 32-73 68-116 (134) 185 cd06446 Trp-synth_B Tryptophan 26.1 1.8E+02 0.0038 21.4 4.7 48 25-72 66-115 (365) 186 PTZ00187 succinyl-CoA syntheta 26.0 1.5E+02 0.0032 21.9 4.3 37 34-70 218-259 (317) 187 PRK03868 glucose-6-phosphate i 26.0 75 0.0016 24.2 2.8 19 41-59 112-130 (410) 188 TIGR01444 fkbM_fam methyltrans 25.6 82 0.0018 19.2 2.5 33 48-80 7-39 (143) 189 PHA02558 uvsW UvsW helicase; P 25.5 2.4E+02 0.0052 21.7 5.5 41 40-80 130-175 (501) 190 PRK04539 ppnK inorganic polyph 25.4 1.5E+02 0.0032 21.6 4.1 31 40-70 68-99 (296) 191 TIGR00631 uvrb excinuclease AB 25.3 1.6E+02 0.0034 23.9 4.6 39 42-80 32-71 (655) 192 TIGR00260 thrC threonine synth 25.3 2.6E+02 0.0056 19.9 6.3 48 25-73 55-104 (328) 193 PRK04885 ppnK inorganic polyph 25.2 1.4E+02 0.003 21.3 3.9 30 40-69 35-67 (265) 194 TIGR00263 trpB tryptophan synt 24.9 2E+02 0.0044 21.4 4.9 38 32-69 204-250 (385) 195 cd01398 RPI_A RPI_A: Ribose 5- 24.8 1.5E+02 0.0033 20.3 3.9 28 49-76 22-55 (213) 196 PRK08639 threonine dehydratase 24.8 2.2E+02 0.0047 21.4 5.1 41 32-72 167-215 (420) 197 PRK06352 threonine synthase; V 24.7 2.5E+02 0.0054 20.6 5.3 49 23-72 57-107 (351) 198 cd00640 Trp-synth-beta_II Tryp 24.6 2.3E+02 0.005 19.1 5.3 42 30-71 140-188 (244) 199 cd02130 PA_ScAPY_like PA_ScAPY 24.6 64 0.0014 19.7 1.9 40 32-71 60-102 (122) 200 COG0324 MiaA tRNA delta(2)-iso 24.6 1E+02 0.0022 22.8 3.1 39 41-81 5-45 (308) 201 COG2890 HemK Methylase of poly 24.4 2.7E+02 0.0058 19.9 5.6 53 21-73 92-144 (280) 202 PRK07334 threonine dehydratase 24.2 2E+02 0.0043 21.4 4.8 42 31-72 161-207 (403) 203 PRK00702 ribose-5-phosphate is 23.7 2.6E+02 0.0056 19.4 5.2 51 25-79 7-62 (220) 204 PRK07591 threonine synthase; V 23.6 2.6E+02 0.0056 21.1 5.3 49 23-72 119-169 (421) 205 PF14824 Sirohm_synth_M: Siroh 23.6 39 0.00084 16.5 0.6 18 44-61 6-23 (30) 206 PRK08618 ornithine cyclodeamin 23.4 84 0.0018 22.7 2.6 32 40-72 192-223 (325) 207 PF09754 PAC2: PAC2 family; I 23.3 1.1E+02 0.0025 20.3 3.1 54 22-80 80-133 (219) 208 KOG1467 Translation initiation 23.2 80 0.0017 25.2 2.5 39 40-78 434-476 (556) 209 PRK00865 glutamate racemase; P 23.1 2.7E+02 0.0059 19.5 5.5 43 27-69 54-97 (261) 210 TIGR00021 rpiA ribose 5-phosph 23.0 1.6E+02 0.0034 20.5 3.7 29 49-77 22-56 (218) 211 TIGR02127 pyrF_sub2 orotidine 22.9 2.9E+02 0.0062 19.7 5.1 45 23-67 167-214 (261) 212 COG2515 Acd 1-aminocyclopropan 22.8 3.2E+02 0.007 20.5 5.5 32 39-70 179-214 (323) 213 cd08551 Fe-ADH iron-containing 22.7 3.1E+02 0.0067 20.0 5.7 47 24-72 64-131 (370) 214 COG2242 CobL Precorrin-6B meth 22.7 2.6E+02 0.0057 19.2 5.2 59 21-79 16-74 (187) 215 TIGR00511 ribulose_e2b2 ribose 22.7 1E+02 0.0023 22.3 2.9 39 40-78 190-232 (301) 216 PF02225 PA: PA domain; Inter 22.7 48 0.0011 19.0 1.0 39 32-70 49-90 (101) 217 COG1184 GCD2 Translation initi 22.4 1.3E+02 0.0029 22.1 3.4 68 10-77 162-235 (301) 218 PF08241 Methyltransf_11: Meth 22.4 1.2E+02 0.0025 16.5 2.6 29 48-77 5-33 (95) 219 PF07085 DRTGG: DRTGG domain; 22.3 88 0.0019 18.5 2.2 10 36-45 57-66 (105) 220 PF00849 PseudoU_synth_2: RNA 22.3 93 0.002 19.5 2.4 20 40-59 50-69 (164) 221 PRK05638 threonine synthase; V 22.1 2.5E+02 0.0054 21.2 5.0 50 23-73 94-145 (442) 222 PRK14077 pnk inorganic polypho 21.9 1.9E+02 0.0042 20.8 4.2 31 40-70 64-95 (287) 223 cd02870 PseudoU_synth_RsuA_lik 21.9 88 0.0019 19.7 2.2 20 40-59 43-62 (146) 224 TIGR01354 cyt_deam_tetra cytid 21.8 2.2E+02 0.0047 17.8 4.6 34 40-73 66-107 (127) 225 cd02550 PseudoU_synth_Rsu_Rlu_ 21.5 93 0.002 19.7 2.3 26 35-60 37-64 (154) 226 cd08183 Fe-ADH2 Iron-containin 21.4 3.4E+02 0.0073 19.9 5.5 35 23-59 58-92 (374) 227 TIGR03528 2_3_DAP_am_ly diamin 21.4 2.5E+02 0.0055 21.1 4.8 41 31-71 210-262 (396) 228 PF06506 PrpR_N: Propionate ca 21.4 2.1E+02 0.0045 18.6 4.0 32 37-72 31-62 (176) 229 cd07410 MPP_CpdB_N Escherichia 21.4 2.5E+02 0.0054 19.5 4.6 51 23-74 167-229 (277) 230 cd02555 PSSA_1 PSSA_1: Pseudou 21.2 1.1E+02 0.0024 20.3 2.7 24 36-59 50-75 (177) 231 PRK06110 hypothetical protein; 21.2 2.8E+02 0.006 19.9 4.9 42 31-72 159-205 (322) 232 COG1844 Uncharacterized protei 21.0 95 0.0021 20.0 2.1 57 23-79 39-97 (125) 233 cd08184 Fe-ADH3 Iron-containin 21.0 3.5E+02 0.0076 19.9 5.8 36 23-60 61-99 (347) 234 PF00107 ADH_zinc_N: Zinc-bind 20.9 98 0.0021 18.4 2.2 29 28-57 2-30 (130) 235 COG1432 Uncharacterized conser 20.9 1.6E+02 0.0034 19.6 3.3 37 26-62 96-132 (181) 236 PRK01231 ppnK inorganic polyph 20.8 2E+02 0.0043 20.8 4.0 31 40-70 62-93 (295) 237 PRK04457 spermidine synthase; 20.7 2.8E+02 0.0062 19.4 4.8 37 41-77 68-104 (262) 238 PF00532 Peripla_BP_1: Peripla 20.7 2.2E+02 0.0048 19.8 4.2 42 31-72 47-88 (279) 239 PRK01077 cobyrinic acid a,c-di 20.7 2.8E+02 0.006 21.1 4.9 40 32-71 106-151 (451) 240 PF14606 Lipase_GDSL_3: GDSL-l 20.6 92 0.002 21.1 2.2 20 54-73 84-103 (178) 241 PRK08298 cytidine deaminase; V 20.6 2.5E+02 0.0054 18.1 4.6 26 48-73 87-112 (136) 242 cd06449 ACCD Aminocyclopropane 20.5 3.2E+02 0.007 19.3 6.5 33 40-72 174-210 (307) 243 PF02056 Glyco_hydro_4: Family 20.4 2.5E+02 0.0055 19.0 4.3 34 42-75 138-172 (183) 244 PRK09224 threonine dehydratase 20.3 3.1E+02 0.0067 21.3 5.2 41 32-72 159-205 (504) No 1 >PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP:ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C .... Probab=99.84 E-value=3.1e-21 Score=121.68 Aligned_cols=59 Identities=42% Similarity=0.642 Sum_probs=55.4 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) +|+++.+++.+|.++++++||++|.||+||+++|||||++|||++|+++.++|+|+|.+ T Consensus 1 Teaia~aa~~~A~~~~ak~Ivv~T~sG~ta~~isk~RP~~pIiavt~~~~~~r~l~l~~ 59 (117) T PF02887_consen 1 TEAIARAAVELAEDLNAKAIVVFTESGRTARLISKYRPKVPIIAVTPNESVARQLSLYW 59 (117) T ss_dssp HHHHHHHHHHHHHHHTESEEEEE-SSSHHHHHHHHT-TSSEEEEEESSHHHHHHGGGST T ss_pred CHHHHHHHHHHHHhcCCCEEEEECCCchHHHHHHhhCCCCeEEEEcCcHHHHhhhhccc Confidence 58999999999999999999999999999999999999999999999999999999976 No 2 >PTZ00066 pyruvate kinase; Provisional Probab=99.80 E-value=1.5e-19 Score=137.51 Aligned_cols=83 Identities=30% Similarity=0.450 Sum_probs=68.5 Q ss_pred CCcccchHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 1 AEKVFNHNLFFKKVINYVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 1 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) ||+.++|..+|.........+.+..++++.+|+.+|.++++++||++|.||+||+++|||||.+||||+|+++.++|+|+ T Consensus 372 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~aa~~~A~~l~a~aIv~~T~SG~TAr~iSk~RP~~pIia~t~~~~~~R~L~ 451 (513) T PTZ00066 372 AETCIDYRVLYHAIHLAVPTPVSVQEAVARSAVETAEDINAKLIIALTETGNTARLISKYRPSCTILALSASPSVVKSLS 451 (513) T ss_pred HhhccchHHhhhhhhccccCCCchhhHHHHHHHHHHHhCCCCEEEEECCCcHHHHHHHhhCCCCCEEEECCCHHHHHHhh Confidence 46666666555443321222224578999999999999999999999999999999999999999999999999999999 Q ss_pred ccc Q 039146 81 WTF 83 (84) Q Consensus 81 l~~ 83 (84) |++ T Consensus 452 L~w 454 (513) T PTZ00066 452 VAR 454 (513) T ss_pred ccc Confidence 986 No 3 >PTZ00300 pyruvate kinase; Provisional Probab=99.79 E-value=1.8e-19 Score=135.66 Aligned_cols=62 Identities=42% Similarity=0.600 Sum_probs=59.4 Q ss_pred CCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 22 MSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 22 ~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) .+..+++|++++.+|.++++++||++|.||+||+++|||||++||||+|+++.++|+|+|.+ T Consensus 330 ~~~~~~ia~sa~~~a~~l~a~aIiv~T~sG~tA~~vs~~RP~~pIia~t~~~~~ar~l~l~~ 391 (454) T PTZ00300 330 MSAEEAVCSSAVNSVYETKAKALVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQ 391 (454) T ss_pred CChHHHHHHHHHHHHHhCCCCEEEEECCCcHHHHHHHhhCCCCCEEEECCCHHHHHHhhccc Confidence 35679999999999999999999999999999999999999999999999999999999986 No 4 >PLN02461 Probable pyruvate kinase Probab=99.77 E-value=7.6e-19 Score=133.70 Aligned_cols=83 Identities=46% Similarity=0.644 Sum_probs=67.8 Q ss_pred CCcccchHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecC-------- Q 039146 1 AEKVFNHNLFFKKVINYVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIP-------- 72 (84) Q Consensus 1 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~-------- 72 (84) +|+.++|..+|.........+.+..+++|.+|+.+|.++++++||++|.||+||+++|||||.+||||+|++ T Consensus 356 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~sav~~A~~l~a~aIiv~T~sG~tA~~iSk~RP~~pIia~t~~~~~~~~~~ 435 (511) T PLN02461 356 AEASLDYGALFKEIMRSAPLPMSPLESLASSAVRTANKVKASLIVVLTRGGTTARLVAKYRPAVPILSVVVPEITTDSFD 435 (511) T ss_pred HHhccchhhhhhhhcccccccCChHHHHHHHHHHHHHhCCCCEEEEECCCcHHHHHHHhhCCCCCEEEEecCcccccccc Confidence 466666655554432111113357899999999999999999999999999999999999999999999976 Q ss_pred -----hhhhccccccc Q 039146 73 -----QLKTNQLRWTF 83 (84) Q Consensus 73 -----~~~~r~L~l~~ 83 (84) +.++|+|+|.+ T Consensus 436 w~~~~~~~ar~l~L~~ 451 (511) T PLN02461 436 WSCSDEAPARHSLIYR 451 (511) T ss_pred cccCCHHHhhhhheec Confidence 89999999975 No 5 >TIGR01064 pyruv_kin pyruvate kinase. This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars. Probab=99.76 E-value=1.2e-18 Score=131.62 Aligned_cols=61 Identities=41% Similarity=0.597 Sum_probs=59.2 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) +..++++.+++.+|..+++++||++|.||+||+++|||||.+||||+|+++.++|+|+|+| T Consensus 356 ~~~~~ia~~a~~~a~~~~akaIVv~T~SG~TA~~vSr~rp~~PIiAvT~~~~v~R~L~L~w 416 (473) T TIGR01064 356 TITEAIALSAVEAAEKLDAKAIVVLTESGRTARLLSKYRPNAPIIAVTPNERVARQLALYW 416 (473) T ss_pred ChHHHHHHHHHHHHhhcCCCEEEEEcCChHHHHHHHhhCCCCCEEEEcCCHHHHHHhhccC Confidence 5679999999999999999999999999999999999999999999999999999999986 No 6 >PLN02765 pyruvate kinase Probab=99.76 E-value=1.6e-18 Score=132.21 Aligned_cols=83 Identities=73% Similarity=0.995 Sum_probs=65.6 Q ss_pred CCcccchHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEe-cC------- Q 039146 1 AEKVFNHNLFFKKVINYVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVV-IP------- 72 (84) Q Consensus 1 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t-~~------- 72 (84) +|+.++|...+.......+.+.+..+++|.+++.+|.++++++|||+|.||+||+++|||||.+||||+| ++ T Consensus 369 aE~~~~~~~~~~~~~~~~~~~~~~~~aia~sav~~A~~l~a~aIvv~T~sG~tAr~isk~RP~~pIla~t~~~~~~~~~~ 448 (526) T PLN02765 369 AEKVFNQDLYFKKTVKYVGEPMSHLESIASSAVRAAIKVKASVIIVFTSSGRAARLIAKYRPTMPVLSVVIPRLKTNQLK 448 (526) T ss_pred HHhhcchhhhhhhhhcccccCCCHHHHHHHHHHHHHhhCCCCEEEEECCCcHHHHHHHhhCCCCCEEEEecCcccccccc Confidence 3555555433333211112233457899999999999999999999999999999999999999999999 66 Q ss_pred -----hhhhccccccc Q 039146 73 -----QLKTNQLRWTF 83 (84) Q Consensus 73 -----~~~~r~L~l~~ 83 (84) +.++|+|+|.+ T Consensus 449 ~~~~~~~~aR~L~L~~ 464 (526) T PLN02765 449 WSFTGAFQARQCLIVR 464 (526) T ss_pred cccCcHHHHHHhhccc Confidence 78999999975 No 7 >PRK06247 pyruvate kinase; Provisional Probab=99.75 E-value=2.7e-18 Score=129.85 Aligned_cols=61 Identities=26% Similarity=0.418 Sum_probs=59.1 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) +..++++.+++.+|.++++++||++|.||+||+++|||||.+||||+|+++.++|+|+|.+ T Consensus 352 ~~~~~ia~sa~~~A~~l~a~~Iv~~T~sG~ta~~isk~RP~~pI~a~t~~~~~~r~l~l~~ 412 (476) T PRK06247 352 TKRDAISYAARDIAERLDLAALVAYTSSGDTALRAARERPPLPILALTPNPETARRLALTW 412 (476) T ss_pred CHHHHHHHHHHHHHHhCCCCEEEEEcCCcHHHHHHHhhCCCCCEEEECCCHHHHHHhhccc Confidence 5679999999999999999999999999999999999999999999999999999999986 No 8 >PRK09206 pyruvate kinase; Provisional Probab=99.74 E-value=3.1e-18 Score=129.39 Aligned_cols=61 Identities=28% Similarity=0.385 Sum_probs=59.3 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) +..++++.+++.+|.++++++||++|.||+||+++|||||.+||||+|+++.++|+|+|.+ T Consensus 353 ~~~~~ia~sa~~~A~~l~a~aIv~~T~sG~tA~~is~~RP~~pIia~t~~~~~~r~l~l~~ 413 (470) T PRK09206 353 RITEAVCRGAVETAEKLDAPLIVVATQGGKSARSVRKYFPDATILALTTNEKTARQLVLSK 413 (470) T ss_pred ChHHHHHHHHHHHHhcCCCCEEEEECCCcHHHHHHHhhCCCCCEEEECCCHHHHHHhhccc Confidence 5789999999999999999999999999999999999999999999999999999999986 No 9 >PRK06354 pyruvate kinase; Provisional Probab=99.74 E-value=3.8e-18 Score=131.72 Aligned_cols=80 Identities=26% Similarity=0.420 Sum_probs=66.6 Q ss_pred CCcccchHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 1 AEKVFNHNLFFKKVINYVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 1 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) +|+.++|..++...... ..+..++++.+++.+|.++++++||++|.||+||+++|||||++|||++|+++.++|+|+ T Consensus 341 aE~~~~~~~~~~~~~~~---~~~~~~~ia~aa~~~a~~~~a~~Iv~~T~sG~ta~~vsk~Rp~~pI~a~t~~~~~~r~l~ 417 (590) T PRK06354 341 IEKDLPYRDILSKRPEF---TTTITNAISQAVSHIALQLDAAAIVTLTKSGATARNVSKYRPKTPILAVTPNESVARRLQ 417 (590) T ss_pred HHhccchhhhhhhcccc---CCCHHHHHHHHHHHHHhhcCCCEEEEECCChHHHHHHHhhCCCCCEEEECCCHHHHHHhh Confidence 35555555443322111 235679999999999999999999999999999999999999999999999999999999 Q ss_pred ccc Q 039146 81 WTF 83 (84) Q Consensus 81 l~~ 83 (84) |.+ T Consensus 418 l~~ 420 (590) T PRK06354 418 LVW 420 (590) T ss_pred ccc Confidence 975 No 10 >PLN02762 pyruvate kinase complex alpha subunit Probab=99.73 E-value=4.8e-18 Score=129.32 Aligned_cols=61 Identities=25% Similarity=0.388 Sum_probs=59.0 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) +..++++.+++.+|.++++++||++|.||+||+++|||||.+||||+|+++.++|+|+|.+ T Consensus 392 ~~~~aia~sa~~~A~~l~a~aIv~~T~sG~tA~~iSk~RP~~pIia~t~~~~~~r~l~l~~ 452 (509) T PLN02762 392 RISEEICNSAAKMANNLGVDAIFVYTKHGHMASLLSRNRPDCPIFAFTDTTSVRRRLNLQW 452 (509) T ss_pred chHHHHHHHHHHHHhhcCCCEEEEECCCcHHHHHHHhhCCCCCEEEECCCHHHHHHhhccc Confidence 5679999999999999999999999999999999999999999999999999999999976 No 11 >PRK05826 pyruvate kinase; Provisional Probab=99.72 E-value=9.6e-18 Score=126.66 Aligned_cols=62 Identities=34% Similarity=0.463 Sum_probs=59.5 Q ss_pred CCHHHHHHHHHHHHHHhcC-CcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 22 MSHLESITSSAVRSAIKVK-ASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 22 ~~~~~~ia~~a~~~a~~~~-~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) .+..++++.+++.+|.+++ +++||++|.||+||+++|||||++|||++|+++.++|+|+|.+ T Consensus 354 ~~~~~~ia~aa~~~a~~l~~a~~Ivv~T~sG~ta~~isk~RP~~pI~~~t~~~~~~r~l~l~~ 416 (465) T PRK05826 354 DRIDEAIAMSAMYAANHLKGVKAIVALTESGRTARLISRFRPGAPIFAVTRDEKTQRRLALYR 416 (465) T ss_pred cchHHHHHHHHHHHHHhcCCCCEEEEECCCcHHHHHHHhhCCCCCEEEEcCCHHHHHHhhccc Confidence 3568999999999999999 9999999999999999999999999999999999999999986 No 12 >cd00288 Pyruvate_Kinase Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer. Probab=99.72 E-value=2e-17 Score=125.31 Aligned_cols=83 Identities=37% Similarity=0.607 Sum_probs=67.4 Q ss_pred CCcccchHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 1 AEKVFNHNLFFKKVINYVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 1 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) +|+.++|+.++.......+...+..++++.+|+.+|.++++++||++|.||+||+++|+|||.+|||++|+++.++|+|+ T Consensus 336 aE~~~~~~~~~~~~~~~~~~~~~~~~aia~sAv~~A~~l~akaIVv~T~SG~TA~~lS~~RP~~pIiavT~~~~~~r~l~ 415 (480) T cd00288 336 AEKALSHRVLFNEMRRLTPRPTSTTEAVAMSAVRAAFELGAKAIVVLTTSGRTARLVSKYRPNAPIIAVTRNEQTARQLH 415 (480) T ss_pred HHhccchhhhhhhhhcccccCCChHHHHHHHHHHHHHhcCCCEEEEECCCcHHHHHHHhhCCCCCEEEEcCCHHHhhhee Confidence 35555555444332221111225689999999999999999999999999999999999999999999999999999999 Q ss_pred ccc Q 039146 81 WTF 83 (84) Q Consensus 81 l~~ 83 (84) |.+ T Consensus 416 l~~ 418 (480) T cd00288 416 LYR 418 (480) T ss_pred ecc Confidence 976 No 13 >PLN02623 pyruvate kinase Probab=99.69 E-value=4.5e-17 Score=125.39 Aligned_cols=60 Identities=25% Similarity=0.271 Sum_probs=57.8 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) +..++++.+++.+|..++++ ||++|.||+||+++|||||.+||||+|+++.++|+|+|.+ T Consensus 460 ~~~~~ia~sA~~~A~~l~a~-Ivv~T~sG~tA~~lSr~RP~~pI~avT~~~~~aR~L~L~~ 519 (581) T PLN02623 460 HMSEMFAFHATMMANTLGTS-IIVFTRTGFMAILLSHYRPSGTIFAFTNEKRIQQRLALYQ 519 (581) T ss_pred ChHHHHHHHHHHHHHhcCCc-EEEECCCcHHHHHHHhhCCCCCEEEECCCHHHHHHhhccc Confidence 56789999999999999999 9999999999999999999999999999999999999976 No 14 >COG0469 PykF Pyruvate kinase [Carbohydrate transport and metabolism] Probab=99.64 E-value=4.1e-16 Score=117.97 Aligned_cols=63 Identities=37% Similarity=0.535 Sum_probs=60.2 Q ss_pred CCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccccccc Q 039146 21 PMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLRWTF 83 (84) Q Consensus 21 ~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~l~~ 83 (84) ..+..++|+++++.++..+++++||++|.||.||+++|||||.+|||++|++++++|+|+|.| T Consensus 356 ~~~~~e~ia~aa~~~a~~l~~k~iv~~T~sG~ta~~isk~Rp~~pIia~t~~~~v~r~l~l~~ 418 (477) T COG0469 356 DSSITEAIALAAVDIAEKLDAKAIVTLTESGRTARLLSKYRPEAPIIALTPNERVARRLALVW 418 (477) T ss_pred cccHHHHHHHHHHHHHHhcCCcEEEEEcCCCHHHHHHhcCCCCCcEEEECCCHHHHhhhceee Confidence 346789999999999999999999999999999999999999999999999999999999976 No 15 >KOG2323 consensus Pyruvate kinase [Carbohydrate transport and metabolism] Probab=99.63 E-value=7.9e-16 Score=116.63 Aligned_cols=82 Identities=43% Similarity=0.581 Sum_probs=78.5 Q ss_pred CCcccchHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 1 AEKVFNHNLFFKKVINYVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 1 aE~~~~~~~~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) ||..+||..+|+++.+..+.+++..+++|.+|+.++....+.+|+++|.+|++|+++|+|||.+|||++|.++..+||++ T Consensus 356 aE~~~~~~~~~~~l~~~v~~~~~~ie~~a~~Av~~a~~~~a~aIvv~T~sg~~a~lvskyrP~~PIi~vt~~~~~aR~~~ 435 (501) T KOG2323|consen 356 AEAVIYYDSLFSELGTAVSFPMSTIESLAASAVRAATKCLASAIVVLTKSGYTAILVSKYRPSVPIISVTRPVLAARQSH 435 (501) T ss_pred HHhhHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHHhhcceEEEEEecCcccHHHHhccCCCCCEEEEeccHHHHHHHH Confidence 58889999999999999999999999999999999999999999999999999999999999999999999999999998 Q ss_pred cc Q 039146 81 WT 82 (84) Q Consensus 81 l~ 82 (84) |- T Consensus 436 l~ 437 (501) T KOG2323|consen 436 LY 437 (501) T ss_pred hh Confidence 74 No 16 >COG1751 Uncharacterized conserved protein [Function unknown] Probab=95.21 E-value=0.098 Score=35.33 Aligned_cols=50 Identities=18% Similarity=0.143 Sum_probs=42.6 Q ss_pred HHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCC-CCEEEEecCh Q 039146 24 HLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPT-MPVLSVVIPQ 73 (84) Q Consensus 24 ~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~-~pIia~t~~~ 73 (84) .++..-.-|++-|.+++.+-||+.|.+|+||++++-.=+. .-|++||.-. T Consensus 11 NT~~tle~a~erA~elgik~~vVAS~tG~tA~k~lemveg~lkvVvVthh~ 61 (186) T COG1751 11 NTDETLEIAVERAKELGIKHIVVASSTGYTALKALEMVEGDLKVVVVTHHA 61 (186) T ss_pred chHHHHHHHHHHHHhcCcceEEEEecccHHHHHHHHhcccCceEEEEEeec Confidence 4677777888999999999999999999999999988877 6788887643 No 17 >PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F .... Probab=89.05 E-value=2.1 Score=25.23 Aligned_cols=43 Identities=23% Similarity=0.325 Sum_probs=34.9 Q ss_pred HHHHHHHHHHHHhcCCcEEEEecCC---------chHHHHHHhhCCCCCEEEE Q 039146 26 ESITSSAVRSAIKVKASAIICFTSS---------GRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~T~s---------G~ta~~iS~~Rp~~pIia~ 69 (84) ..++....+.+.+.+++.||+-++. |.++..+.+.-| |||+.+ T Consensus 88 ~~~~~~i~~~~~~~~~dliv~G~~~~~~~~~~~~gs~~~~l~~~~~-~pVlvv 139 (140) T PF00582_consen 88 GDVADAIIEFAEEHNADLIVMGSRGRSGLERLLFGSVAEKLLRHAP-CPVLVV 139 (140) T ss_dssp SSHHHHHHHHHHHTTCSEEEEESSSTTSTTTSSSHHHHHHHHHHTS-SEEEEE T ss_pred eccchhhhhccccccceeEEEeccCCCCccCCCcCCHHHHHHHcCC-CCEEEe Confidence 4566777888999999999998876 688888888665 798876 No 18 >PRK04885 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=88.71 E-value=0.74 Score=32.91 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=29.1 Q ss_pred cCCcEEEEecCCchHHHHHHh----hCCCCCEEEEecC Q 039146 39 VKASAIICFTSSGRAARLIAK----YRPTMPVLSVVIP 72 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~~ 72 (84) ..++.+|+-|.+|.||..+|. .-|.++.+.+|+= T Consensus 146 ~~gDGlIVsTptGSTAYslSaGGPIv~P~~~~~~ltPI 183 (265) T PRK04885 146 FRGDGLCVSTPTGSTAYNKSLGGAVLHPSIEALQLTEI 183 (265) T ss_pred EEcCEEEEECCCChHHHHhhCCCceeCCCCCeEEEEee Confidence 357899999999999999998 7788888888753 No 19 >KOG2178 consensus Predicted sugar kinase [Carbohydrate transport and metabolism] Probab=86.59 E-value=0.88 Score=34.64 Aligned_cols=34 Identities=26% Similarity=0.426 Sum_probs=29.6 Q ss_pred hcCCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) ...++++|+-|.+|.||.-+|. ..|.+|-|.+|+ T Consensus 283 ~vq~DGliVaTPTGSTAYS~sAGGSlvhP~vpAIlvTP 320 (409) T KOG2178|consen 283 KVQGDGLIVATPTGSTAYSASAGGSLVHPSVPAILVTP 320 (409) T ss_pred EEecceEEEecCCchhhhHhhcCCceecCCCCeEEEec Confidence 4568999999999999999875 789999998875 No 20 >PRK15005 universal stress protein F; Provisional Probab=86.36 E-value=3.3 Score=25.48 Aligned_cols=41 Identities=24% Similarity=0.246 Sum_probs=30.7 Q ss_pred HHHHHHHHHHhcCCcEEEEecCC--------chHHHHHHhhCCCCCEEEE Q 039146 28 ITSSAVRSAIKVKASAIICFTSS--------GRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 28 ia~~a~~~a~~~~~~aIv~~T~s--------G~ta~~iS~~Rp~~pIia~ 69 (84) .+...++.+.+.+++.||+-|+. |.++..+-+.= +|||+.+ T Consensus 95 p~~~I~~~a~~~~~DLIV~Gs~~~~~~~~llGS~a~~vl~~a-~cpVlvV 143 (144) T PRK15005 95 PKDRILELAKKIPADMIIIASHRPDITTYLLGSNAAAVVRHA-ECSVLVV 143 (144) T ss_pred HHHHHHHHHHHcCCCEEEEeCCCCCchheeecchHHHHHHhC-CCCEEEe Confidence 45567778889999999998764 56777777654 5888876 No 21 >PRK01231 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=83.80 E-value=1.7 Score=31.53 Aligned_cols=34 Identities=18% Similarity=0.351 Sum_probs=27.8 Q ss_pred hcCCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||..+|. ..|.++.+.+|+ T Consensus 172 ~~~~DGlivsTptGSTAY~lSAGGpIv~p~~~~~~itP 209 (295) T PRK01231 172 SQRSDGLIVSTPTGSTAYALSGGGPIMHPKLDAIVLVP 209 (295) T ss_pred EEEcceEEEeCCCCchhhhhhcCCceecCCCCeEEEEe Confidence 4467999999999999999998 456777777765 No 22 >cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont Probab=83.73 E-value=2.1 Score=26.12 Aligned_cols=34 Identities=18% Similarity=0.233 Sum_probs=25.5 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|++|.||.+... .+|-| .++||++|.++. T Consensus 46 ~~d~~I~iS~sG~t~e~~~~~~~a~~~-g~~vi~iT~~~~ 84 (126) T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEK-GAKTVAITNVVG 84 (126) T ss_pred CCcEEEEEeCCcCCHHHHHHHHHHHHc-CCeEEEEECCCC Confidence 45688999999998764 34445 589999998754 No 23 >cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. Probab=81.90 E-value=6.1 Score=23.66 Aligned_cols=44 Identities=16% Similarity=0.171 Sum_probs=36.0 Q ss_pred HHHHHHHHHHHHhcCCcEEEEecCC---------chHHHHHHhhCCCCCEEEE Q 039146 26 ESITSSAVRSAIKVKASAIICFTSS---------GRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~T~s---------G~ta~~iS~~Rp~~pIia~ 69 (84) ..++...+..+++.+++.||+.++. |.++..+.++-|+|||+.+ T Consensus 71 ~~~~~~I~~~~~~~~~dllviG~~~~~~~~~~~~Gs~~~~v~~~a~~~~v~v~ 123 (124) T cd01987 71 DDVAEAIVEFAREHNVTQIVVGKSRRSRWRELFRGSLVDRLLRRAGNIDVHIV 123 (124) T ss_pred CcHHHHHHHHHHHcCCCEEEeCCCCCchHHHHhcccHHHHHHHhCCCCeEEEe Confidence 3467778888999999999988752 6788999988889999875 No 24 >COG0061 nadF NAD kinase [Coenzyme metabolism] Probab=81.78 E-value=1.9 Score=30.92 Aligned_cols=34 Identities=15% Similarity=0.280 Sum_probs=27.8 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++++++-|.+|.||.-+|.- -|..+.|.+|+ T Consensus 163 ~~r~DGliVsTPTGSTAY~lSAGGPIv~P~l~ai~ltp 200 (281) T COG0061 163 SFRGDGLIVSTPTGSTAYNLSAGGPILHPGLDAIQLTP 200 (281) T ss_pred EEecCEEEEEcCCcHHHHhhhcCCCccCCCCCeEEEee Confidence 34679999999999999999985 56677777765 No 25 >PRK02649 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=81.70 E-value=2.6 Score=30.78 Aligned_cols=34 Identities=26% Similarity=0.447 Sum_probs=27.2 Q ss_pred hcCCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||.-+|. .-|.++.+.+|+ T Consensus 178 ~~~~DGlIVsTPTGSTAYslSAGGPIv~P~~~~~~itP 215 (305) T PRK02649 178 DIAADGVILSTPTGSTAYSLSAGGPVITPDVPVLQLTP 215 (305) T ss_pred EEecCeEEEeCCCcHHHHHhhCCCcccCCCCCeEEEEe Confidence 3468999999999999999998 455666776664 No 26 >PRK04539 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=81.43 E-value=2.7 Score=30.53 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=26.8 Q ss_pred cCCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 39 VKASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) ..++.+|+-|.+|.||..+|. .-|.++.+.+|+ T Consensus 179 ~~~DGlIVsTPTGSTAYslSAGGPIv~P~~~~~~itP 215 (296) T PRK04539 179 QRSDGLIVSTPTGSTAYSLAAGGPIMQAGLHAFTLVP 215 (296) T ss_pred EecCeEEEECCCcHHHHHhhCCCceeCCCCCeEEEEe Confidence 357899999999999999998 456666777764 No 27 >PLN02935 Bifunctional NADH kinase/NAD(+) kinase Probab=81.28 E-value=2.4 Score=33.28 Aligned_cols=34 Identities=26% Similarity=0.333 Sum_probs=28.3 Q ss_pred hcCCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||.-+|. .-|.++.|.+|| T Consensus 377 ~~rgDGLIVSTPTGSTAYsLSAGGPIV~P~l~~ivlTP 414 (508) T PLN02935 377 CVQGDGLILSTTSGSTAYSLAAGGSMVHPQVPGILFTP 414 (508) T ss_pred EEECCcEEEecCccHHHHHHhcCCcccCCCCCeEEEEe Confidence 3457999999999999999998 567778887765 No 28 >PRK13509 transcriptional repressor UlaR; Provisional Probab=81.03 E-value=4.4 Score=28.42 Aligned_cols=54 Identities=17% Similarity=0.084 Sum_probs=41.0 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) +..+.||..|...-.+- +.|+. .+|.|...++++=|..++-.+|.+..++..|. T Consensus 78 ~~K~~IA~~Aa~~I~~g--~~Ifl--d~GsT~~~la~~L~~~~ltVvTnsl~ia~~l~ 131 (251) T PRK13509 78 DEKVRIAKAASQLCNPG--ESVVI--NCGSTAFLLGRELCGKPVQIITNYLPLANYLI 131 (251) T ss_pred HHHHHHHHHHHHhCCCC--CEEEE--CCcHHHHHHHHHhCCCCeEEEeCCHHHHHHHH Confidence 35678888877666443 34444 99999999999988778889999988876653 No 29 >PRK02645 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=80.78 E-value=2.6 Score=30.61 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=28.3 Q ss_pred hcCCcEEEEecCCchHHHHHHh----hCCCCCEEEEecC Q 039146 38 KVKASAIICFTSSGRAARLIAK----YRPTMPVLSVVIP 72 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~~ 72 (84) ...++.+|+-|.+|.||.-+|. ..|.++.+.+||- T Consensus 176 ~~~gDGlIVsTPtGSTAYslSAGGPIv~P~~~~~~vtPi 214 (305) T PRK02645 176 QYQGDGLIVSTPTGSTAYTMAAGGPILHPGIDAIIVTPI 214 (305) T ss_pred EEecCEEEEecCCChhhhhhhcCCcccCCCCCeEEEEec Confidence 3467999999999999999998 4567777777653 No 30 >PRK10411 DNA-binding transcriptional activator FucR; Provisional Probab=80.66 E-value=4.7 Score=28.16 Aligned_cols=53 Identities=13% Similarity=0.132 Sum_probs=41.1 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) +..++||..|..+..+-+ .|+. .+|.|...++++=|..++-++|.+..++..| T Consensus 78 ~~K~~IA~~Aa~lI~~gd--~Ifl--d~GtT~~~l~~~L~~~~ltVvTNs~~ia~~l 130 (240) T PRK10411 78 AHKADIAREALAWIEEGM--VIAL--DASSTCWYLARQLPDINIQVFTNSHPICQEL 130 (240) T ss_pred HHHHHHHHHHHHhCCCCC--EEEE--cCcHHHHHHHHhhCCCCeEEEeCCHHHHHHH Confidence 456788888777665543 4555 8999999999998877888999988877655 No 31 >PF00455 DeoRC: DeoR C terminal sensor domain; InterPro: IPR014036 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after Escherichia coli deoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerization domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ]. Probab=80.03 E-value=4.3 Score=26.56 Aligned_cols=54 Identities=22% Similarity=0.199 Sum_probs=40.0 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCC-CEEEEecChhhhcccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTM-PVLSVVIPQLKTNQLR 80 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~-pIia~t~~~~~~r~L~ 80 (84) +..+.||+.|+++-.+- +.|+. .+|.|...++++=|.. ++-.+|.+..++..|. T Consensus 4 ~~K~~IA~~A~~~I~~~--~~Ifl--d~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l~ 58 (161) T PF00455_consen 4 EEKRAIARKAASLIEDG--DTIFL--DSGTTTLELAKYLPDKKNLTVVTNSLPIANELS 58 (161) T ss_pred HHHHHHHHHHHHhCCCC--CEEEE--ECchHHHHHHHHhhcCCceEEEECCHHHHHHHH Confidence 34678888877666543 33444 8999999999987776 8889999888876653 No 32 >cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Probab=78.73 E-value=3.9 Score=25.22 Aligned_cols=34 Identities=21% Similarity=0.223 Sum_probs=26.0 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|++|.||.+... .+|-+ .+|||++|.++. T Consensus 47 ~~dl~I~iS~SG~t~~~~~~~~~a~~~-g~~vi~iT~~~~ 85 (120) T cd05710 47 EKSVVILASHSGNTKETVAAAKFAKEK-GATVIGLTDDED 85 (120) T ss_pred CCcEEEEEeCCCCChHHHHHHHHHHHc-CCeEEEEECCCC Confidence 34789999999998764 34445 699999998654 No 33 >PRK02231 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=78.50 E-value=3.8 Score=29.45 Aligned_cols=33 Identities=18% Similarity=0.325 Sum_probs=25.8 Q ss_pred cCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 39 VKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ..++.+|+-|.+|.||..+|.- -|.+..+.+|+ T Consensus 154 ~~~DGlIVsTPtGSTAY~lSAGGPIv~P~~~~~~itP 190 (272) T PRK02231 154 QRSDGLIISTPTGSTAYSLSAGGPILTPNLNAIALVP 190 (272) T ss_pred EecCeEEEECCCcHHHHHhhCCCceeCCCCCeEEEEe Confidence 3578999999999999999984 45566666654 No 34 >PRK14077 pnk inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=78.46 E-value=3.8 Score=29.60 Aligned_cols=33 Identities=18% Similarity=0.184 Sum_probs=26.3 Q ss_pred cCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 39 VKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ..++.+|+-|.+|.||.-+|.= -|.++.+.+|| T Consensus 175 ~~~DGlIVSTPTGSTAYslSAGGPIv~P~~~~~~ltP 211 (287) T PRK14077 175 YFGDGVIVATPAGSTAYNMSANGPIIYPLSQVFILTP 211 (287) T ss_pred EEcCEEEEeCCCchhHhHhhcCCcccCCCCCeEEEEe Confidence 4589999999999999999973 45666666654 No 35 >cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain. Probab=77.89 E-value=4 Score=25.06 Aligned_cols=34 Identities=18% Similarity=0.228 Sum_probs=24.8 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|++|.||.|.. ..++-| .++||++|.+.. T Consensus 43 ~~dl~I~iS~SG~t~e~i~~~~~a~~~-g~~iI~IT~~~~ 81 (119) T cd05017 43 RKTLVIAVSYSGNTEETLSAVEQAKER-GAKIVAITSGGK 81 (119) T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHC-CCEEEEEeCCch Confidence 3468888999998764 345555 689999986654 No 36 >PRK15456 universal stress protein UspG; Provisional Probab=77.79 E-value=10 Score=23.48 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=29.8 Q ss_pred HHHHHHHHHHhcCCcEEEEecCC--------chHHHHHHhhCCCCCEEEE Q 039146 28 ITSSAVRSAIKVKASAIICFTSS--------GRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 28 ia~~a~~~a~~~~~~aIv~~T~s--------G~ta~~iS~~Rp~~pIia~ 69 (84) .+....+.+++.+++.||+-|+. |.++..+.+. .+|||+.+ T Consensus 93 ~~~~I~~~a~~~~~DLIVmG~~g~~~~~~llGS~a~~v~~~-a~~pVLvV 141 (142) T PRK15456 93 VRDEVNELAEELGADVVVIGSRNPSISTHLLGSNASSVIRH-ANLPVLVV 141 (142) T ss_pred hHHHHHHHHhhcCCCEEEEcCCCCCccceecCccHHHHHHc-CCCCEEEe Confidence 44456677889999999998863 5566677665 46888875 No 37 >PRK03372 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=77.39 E-value=3.8 Score=29.93 Aligned_cols=34 Identities=21% Similarity=0.263 Sum_probs=27.2 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||.-+|.- -|.++.+.+|+ T Consensus 182 ~~~~DGlIVsTPTGSTAYslSAGGPIv~P~~~~~~itP 219 (306) T PRK03372 182 SFGCDGVLVSTPTGSTAYAFSAGGPVVWPDLEALLVVP 219 (306) T ss_pred EEecCEEEEeCCCchHHHHhhcCCcccCCCCCeEEEEe Confidence 34679999999999999999985 45666777765 No 38 >PRK14075 pnk inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=77.37 E-value=4.1 Score=28.81 Aligned_cols=32 Identities=19% Similarity=0.245 Sum_probs=24.9 Q ss_pred cCCcEEEEecCCchHHHHHHhh----CCCCCEEEEe Q 039146 39 VKASAIICFTSSGRAARLIAKY----RPTMPVLSVV 70 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t 70 (84) ..++.+|+-|.+|.||..+|.- -|.++.+.++ T Consensus 144 ~~~DG~ivsTptGSTaY~lSaGGpiv~p~~~~l~It 179 (256) T PRK14075 144 FFADGVVISTPTGSTAYSLSLGGPIILPNCEVFEIT 179 (256) T ss_pred EecCEEEEeCCCchHHHHhhCCCceeCCCCCeEEee Confidence 4578999999999999999984 3455555554 No 39 >PRK01911 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=77.32 E-value=3.7 Score=29.75 Aligned_cols=34 Identities=15% Similarity=0.133 Sum_probs=26.7 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||.-+|.- -|.+..+.+|| T Consensus 173 ~~~~DGlIVsTPTGSTAYslSAGGPIv~P~~~~~~ltP 210 (292) T PRK01911 173 SYWADGLIVATPTGSTGYSLSCGGPIIVPDAKSFVITP 210 (292) T ss_pred EEeeceeEECCCCcHHHHHhhCCCcccCCCCCEEEEEe Confidence 34689999999999999999985 44566666654 No 40 >PRK03708 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=76.62 E-value=4.7 Score=28.89 Aligned_cols=34 Identities=21% Similarity=0.337 Sum_probs=26.8 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||..+|.- .|..+.+.+|+ T Consensus 162 ~~~gDGvIvsTptGSTAY~lSaGGpIv~p~~~~~~vtP 199 (277) T PRK03708 162 EVRADGLIISTPTGSTAYAMSAGGPFVDPRLDAILIAP 199 (277) T ss_pred EEecCEEEEeCCCchHHHHhhCCCcccCCCCCeEEEEe Confidence 34678999999999999999985 45666676664 No 41 >TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. Probab=76.43 E-value=4.3 Score=26.53 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=25.6 Q ss_pred CCcEEEEecCCchHHHHH-----HhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARLI-----AKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~i-----S~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.||.|...+ +|-| .+|||++|.++ T Consensus 72 ~~Dv~I~iS~sG~t~~~i~~~~~ak~~-g~~ii~IT~~~ 109 (179) T TIGR03127 72 KGDLLIAISGSGETESLVTVAKKAKEI-GATVAAITTNP 109 (179) T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHC-CCeEEEEECCC Confidence 447899999999988654 4555 69999999765 No 42 >PRK00561 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=75.93 E-value=4.6 Score=28.88 Aligned_cols=34 Identities=18% Similarity=0.267 Sum_probs=27.7 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||..+|.- -|.++.+.+|+ T Consensus 134 ~~~gDGlIVsTPtGSTAYslSAGGPIv~P~~~~~~itP 171 (259) T PRK00561 134 KYRGSGLLIGPRTGSTALAKSAKGAVIFPRIDVIQIIE 171 (259) T ss_pred EEecCEEEEeCchHHHHHHHhCCCCccCCCCCeEEEEe Confidence 34679999999999999999974 45677777765 No 43 >PRK03501 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=75.27 E-value=5.5 Score=28.52 Aligned_cols=34 Identities=18% Similarity=0.293 Sum_probs=26.7 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||.-+|.- -|.++.+.+|+ T Consensus 146 ~~~~DGlIVsTPtGSTAY~lSAGGPIv~P~~~~~~itP 183 (264) T PRK03501 146 TFRGDGMVVSTPTGSTAYNKSVRGAVVDPLIPCFQVSE 183 (264) T ss_pred EEecCEEEEeCCCchHHHHhhcCCcccCCCCCeEEEEe Confidence 34689999999999999999985 44666666654 No 44 >PRK04761 ppnK inorganic polyphosphate/ATP-NAD kinase; Reviewed Probab=75.10 E-value=5.2 Score=28.42 Aligned_cols=34 Identities=12% Similarity=0.157 Sum_probs=26.3 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) +..++.+|+-|.+|.||..+|.- .|.++.+.+|+ T Consensus 131 ~~~gDGlIVSTPtGSTAY~lSAGGPIv~P~~~~~~itP 168 (246) T PRK04761 131 ELVCDGVLVATPAGSTAYNLSAHGPILPLGSNLLALTP 168 (246) T ss_pred EEecCeEEEeCCcCHHHHHhhCCCcccCCCCCeEEEEe Confidence 44689999999999999999985 44555666554 No 45 >PRK01185 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=74.57 E-value=5 Score=28.79 Aligned_cols=33 Identities=18% Similarity=0.247 Sum_probs=25.8 Q ss_pred cCCcEEEEecCCchHHHHHHhhC----CCCCEEEEec Q 039146 39 VKASAIICFTSSGRAARLIAKYR----PTMPVLSVVI 71 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~R----p~~pIia~t~ 71 (84) ..++.+|+-|.+|.||..+|.-= |.++.+.+|| T Consensus 156 ~~~DGlIVsTPTGSTAYslSAGGPIv~P~~~~~~ltP 192 (271) T PRK01185 156 FKADGVIVATPTGSTSYSSSAGGPILLPNLEGMVISY 192 (271) T ss_pred EEeeEEEEeCCCchHHHHhhCCCceeCCCCCeEEEEe Confidence 45789999999999999999853 4556666654 No 46 >cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway. Probab=74.49 E-value=6.2 Score=24.00 Aligned_cols=33 Identities=18% Similarity=0.326 Sum_probs=25.1 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~~ 73 (84) .-+.+|+++.+|.+.. ..+|-| .+|||++|.+. T Consensus 47 ~~d~vi~iS~sG~t~~~~~~~~~a~~~-g~~vi~iT~~~ 84 (128) T cd05014 47 PGDVVIAISNSGETDELLNLLPHLKRR-GAPIIAITGNP 84 (128) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEeCCC Confidence 3478999999998875 334555 69999999865 No 47 >cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI. Probab=74.11 E-value=5.5 Score=26.09 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=25.3 Q ss_pred CCcEEEEecCCchHHHHH-----HhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARLI-----AKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~i-----S~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.+|++...+ ++-+ .+|||++|.+. T Consensus 75 ~~D~vI~iS~sG~t~~~i~~~~~ak~~-g~~iI~IT~~~ 112 (179) T cd05005 75 PGDLLIAISGSGETSSVVNAAEKAKKA-GAKVVLITSNP 112 (179) T ss_pred CCCEEEEEcCCCCcHHHHHHHHHHHHC-CCeEEEEECCC Confidence 347889999999987754 3444 79999998754 No 48 >PLN02929 NADH kinase Probab=74.04 E-value=4.9 Score=29.45 Aligned_cols=27 Identities=26% Similarity=0.378 Sum_probs=22.7 Q ss_pred cCCcEEEEecCCchHHHHHHhhCCCCC Q 039146 39 VKASAIICFTSSGRAARLIAKYRPTMP 65 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~Rp~~p 65 (84) ..++.+++-|.+|.||..+|.-=|-.| T Consensus 194 ~~~DGliVsTpTGSTAY~lSAGG~i~P 220 (301) T PLN02929 194 VRSSGLRVSTAAGSTAAMLSAGGFPMP 220 (301) T ss_pred eecCcEEEeCCccHHHHHHhcCCCCCC Confidence 467899999999999999999884444 No 49 >PRK02155 ppnK NAD(+)/NADH kinase family protein; Provisional Probab=73.35 E-value=5.8 Score=28.65 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=26.9 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||..+|.- .|.++.+.+|+ T Consensus 173 ~~~gDGlIVsTPtGSTAYslSaGGPIv~p~~~~~~ltP 210 (291) T PRK02155 173 NQRSDGLIVATPTGSTAYALSAGGPILHPQLPGWVLVP 210 (291) T ss_pred EEecCeEEEECCCchhhhhhhcCCcccCCCCCeEEEEe Confidence 34679999999999999999984 45666666654 No 50 >PF11017 DUF2855: Protein of unknown function (DUF2855); InterPro: IPR021276 This family of proteins has no known function. Probab=72.66 E-value=8.4 Score=28.46 Aligned_cols=39 Identities=15% Similarity=0.097 Sum_probs=33.7 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEecChhhh Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVIPQLKT 76 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~~~~~ 76 (84) ..+++-||+.+-|.+||+-++.. ++...+|++|+...+. T Consensus 133 ~~ga~~vvl~SASSKTA~glA~~L~~~~~~~~~vglTS~~N~~ 175 (314) T PF11017_consen 133 FFGAAQVVLSSASSKTAIGLAYCLKKQRGPPKVVGLTSARNVA 175 (314) T ss_pred cCCccEEEEeccchHHHHHHHHHhhccCCCceEEEEecCcchh Confidence 56789999999999999988876 8889999999877654 No 51 >TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi. Probab=72.43 E-value=6.7 Score=25.29 Aligned_cols=33 Identities=18% Similarity=0.336 Sum_probs=25.6 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.||.|... .+|-| .+|||++|.+. T Consensus 79 ~~D~~i~iS~sG~t~~~~~~~~~a~~~-g~~ii~iT~~~ 116 (154) T TIGR00441 79 KGDVLLGISTSGNSKNVLKAIEAAKDK-GMKTITLAGKD 116 (154) T ss_pred CCCEEEEEcCCCCCHHHHHHHHHHHHC-CCEEEEEeCCC Confidence 44789999999988764 45656 79999999754 No 52 >PRK15118 universal stress global response regulator UspA; Provisional Probab=72.33 E-value=20 Score=22.06 Aligned_cols=42 Identities=17% Similarity=0.216 Sum_probs=29.4 Q ss_pred HHHHHHHHHHHhcCCcEEEEecCCch------HHHHHHhhCCCCCEEEE Q 039146 27 SITSSAVRSAIKVKASAIICFTSSGR------AARLIAKYRPTMPVLSV 69 (84) Q Consensus 27 ~ia~~a~~~a~~~~~~aIv~~T~sG~------ta~~iS~~Rp~~pIia~ 69 (84) ..+...++.|++.+++.||+.|+.+. ++..+-+ +.+|||+.+ T Consensus 90 ~p~~~I~~~a~~~~~DLIV~Gs~~~~~~~lgSva~~v~~-~a~~pVLvv 137 (144) T PRK15118 90 DLGQVLVDAIKKYDMDLVVCGHHQDFWSKLMSSARQLIN-TVHVDMLIV 137 (144) T ss_pred CHHHHHHHHHHHhCCCEEEEeCcccHHHHHHHHHHHHHh-hCCCCEEEe Confidence 34556677889999999999888432 3333333 457999988 No 53 >PF01513 NAD_kinase: ATP-NAD kinase; InterPro: IPR002504 Members of this family are ATP-NAD kinases 2.7.1.23 from EC. The enzymes catalyse the phosphorylation of NAD to NADP utilizing ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus.; GO: 0003951 NAD+ kinase activity, 0008152 metabolic process; PDB: 1U0T_B 1U0R_D 1Y3H_A 1Y3I_A 3AFO_B 1YT5_B 2AN1_A 2I2A_A 3V8P_A 2I1W_A .... Probab=72.10 E-value=4.1 Score=29.01 Aligned_cols=32 Identities=19% Similarity=0.364 Sum_probs=24.5 Q ss_pred cCCcEEEEecCCchHHHHHHh----hCCCCCEEEEe Q 039146 39 VKASAIICFTSSGRAARLIAK----YRPTMPVLSVV 70 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t 70 (84) ..++.+++.|.+|.||..+|. ..|..+.+.+| T Consensus 189 ~~~dGlivsTptGSTay~lSaGGpiv~p~~~~~~~t 224 (285) T PF01513_consen 189 YRGDGLIVSTPTGSTAYSLSAGGPIVHPGLDVIILT 224 (285) T ss_dssp EEESEEEEEETGGGGTHHHHTT--EE-TTSSEEEEE T ss_pred EEEeeeEEEecCCceEEEEecCccEeccCcceeEEE Confidence 457889999999999999997 45666665554 No 54 >PRK13936 phosphoheptose isomerase; Provisional Probab=70.66 E-value=7.7 Score=26.16 Aligned_cols=33 Identities=21% Similarity=0.333 Sum_probs=26.0 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~~ 73 (84) +-+.++.+|.||++.- ..++-| .+|||++|... T Consensus 111 ~~Dv~i~iS~sG~t~~~~~~~~~ak~~-g~~iI~IT~~~ 148 (197) T PRK13936 111 PGDVLLAISTSGNSANVIQAIQAAHER-EMHVVALTGRD 148 (197) T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHC-CCeEEEEECCC Confidence 5588999999999874 445666 79999999843 No 55 >PLN02727 NAD kinase Probab=70.60 E-value=6.5 Score=33.20 Aligned_cols=33 Identities=24% Similarity=0.380 Sum_probs=27.8 Q ss_pred cCCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 39 VKASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) ..++.+|+-|.+|.||.-+|. ..|.++.|.+|+ T Consensus 861 yrgDGLIVSTPTGSTAYSLSAGGPIVhP~v~aIvITP 897 (986) T PLN02727 861 VQGDGVIVATPTGSTAYSTAAGGSMVHPNVPCMLFTP 897 (986) T ss_pred eecceEEEECCCchHHhHhhcCCceeCCCCCeEEEEe Confidence 357999999999999999998 567777887775 No 56 >PRK11557 putative DNA-binding transcriptional regulator; Provisional Probab=70.05 E-value=7.8 Score=27.04 Aligned_cols=33 Identities=15% Similarity=0.045 Sum_probs=25.4 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~~ 73 (84) .-+.+|++|.+|.+.. ..+|-+ .++||++|.+. T Consensus 175 ~~Dv~I~iS~sg~~~~~~~~~~~ak~~-ga~iI~IT~~~ 212 (278) T PRK11557 175 PDDLLLAISYSGERRELNLAADEALRV-GAKVLAITGFT 212 (278) T ss_pred CCCEEEEEcCCCCCHHHHHHHHHHHHc-CCCEEEEcCCC Confidence 4578999999998874 444555 79999999864 No 57 >PRK13938 phosphoheptose isomerase; Provisional Probab=69.57 E-value=8 Score=26.37 Aligned_cols=33 Identities=12% Similarity=0.241 Sum_probs=25.9 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.||.|... .+|-| .+|||++|.+. T Consensus 113 ~~DllI~iS~SG~t~~vi~a~~~Ak~~-G~~vI~iT~~~ 150 (196) T PRK13938 113 PGDTLFAISTSGNSMSVLRAAKTAREL-GVTVVAMTGES 150 (196) T ss_pred CCCEEEEEcCCCCCHHHHHHHHHHHHC-CCEEEEEeCCC Confidence 44789999999998765 55556 79999999754 No 58 >cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate. Probab=69.20 E-value=9 Score=23.06 Aligned_cols=34 Identities=24% Similarity=0.289 Sum_probs=25.3 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) .-+.+|++|.+|.+... .++-+ .++|+++|.+.. T Consensus 60 ~~~~~i~iS~~g~~~~~~~~~~~a~~~-g~~iv~iT~~~~ 98 (139) T cd05013 60 PGDVVIAISFSGETKETVEAAEIAKER-GAKVIAITDSAN 98 (139) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHc-CCeEEEEcCCCC Confidence 44788999999997654 24555 689999988764 No 59 >PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D .... Probab=68.42 E-value=7.3 Score=24.64 Aligned_cols=30 Identities=30% Similarity=0.519 Sum_probs=21.2 Q ss_pred CCcEEEEecCCchHHHHH-----HhhCCCCCEEEEe Q 039146 40 KASAIICFTSSGRAARLI-----AKYRPTMPVLSVV 70 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~i-----S~~Rp~~pIia~t 70 (84) .-+.+|++|.||+++..+ +|-| .+++|++| T Consensus 103 ~gDvli~iS~SG~s~~vi~a~~~Ak~~-G~~vIalT 137 (138) T PF13580_consen 103 PGDVLIVISNSGNSPNVIEAAEEAKER-GMKVIALT 137 (138) T ss_dssp TT-EEEEEESSS-SHHHHHHHHHHHHT-T-EEEEEE T ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHC-CCEEEEEe Confidence 458999999999997654 6666 78888876 No 60 >cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity. Probab=68.12 E-value=19 Score=20.81 Aligned_cols=40 Identities=23% Similarity=0.287 Sum_probs=29.7 Q ss_pred HHHHHHHHHhcCCcEEEEecC---------CchHHHHHHhhCCCCCEEEE Q 039146 29 TSSAVRSAIKVKASAIICFTS---------SGRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 29 a~~a~~~a~~~~~~aIv~~T~---------sG~ta~~iS~~Rp~~pIia~ 69 (84) +....+.+++.+++.+|+-+. .|.++..+.+. .++|++.+ T Consensus 82 ~~~i~~~~~~~~~dlvvig~~~~~~~~~~~~~~~~~~ll~~-~~~pvliv 130 (130) T cd00293 82 AEAILEAAEELGADLIVMGSRGRSGLRRLLLGSVAERVLRH-APCPVLVV 130 (130) T ss_pred HHHHHHHHHHcCCCEEEEcCCCCCccceeeeccHHHHHHhC-CCCCEEeC Confidence 667788888889998887653 56677777765 77888753 No 61 >PRK03378 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=67.98 E-value=9.4 Score=27.64 Aligned_cols=33 Identities=18% Similarity=0.341 Sum_probs=25.6 Q ss_pred cCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 39 VKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ..++.+|+-|.+|.||..+|.- -|.++.+.+|| T Consensus 174 ~~~DGlIvsTptGSTAYslSAGGPii~P~~~~~~itP 210 (292) T PRK03378 174 QRSDGLIISTPTGSTAYSLSAGGPILTPSLDAITLVP 210 (292) T ss_pred EEccEEEEeCCCchHHhHhhcCCceeCCCCCeEEEEe Confidence 3578999999999999999874 45666666654 No 62 >PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown. Probab=67.30 E-value=8.3 Score=25.49 Aligned_cols=36 Identities=22% Similarity=0.290 Sum_probs=26.9 Q ss_pred cEEEEecCCchHH-----HHHHhhCC-CCCEEEEecChhhhc Q 039146 42 SAIICFTSSGRAA-----RLIAKYRP-TMPVLSVVIPQLKTN 77 (84) Q Consensus 42 ~aIv~~T~sG~ta-----~~iS~~Rp-~~pIia~t~~~~~~r 77 (84) ..=|+||..|.|| +++...+. ...|+++|+|..+.+ T Consensus 67 gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~ 108 (166) T PF05991_consen 67 GIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQR 108 (166) T ss_pred ceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHH Confidence 3347788888887 56677776 688999998887754 No 63 >TIGR01275 ACC_deam_rel pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family. This model represents a family of pyridoxal phosphate-dependent enzymes closely related to (and often designated as putative examples of) 1-aminocyclopropane-1-carboxylate deaminase. It appears that members of this family include both D-cysteine desulfhydrase (EC 4.4.1.15) and 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7). Probab=67.00 E-value=18 Score=25.80 Aligned_cols=40 Identities=15% Similarity=0.224 Sum_probs=30.2 Q ss_pred HHHHHHhc----CCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 32 AVRSAIKV----KASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 32 a~~~a~~~----~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) +.++.+.+ +.++||+..-+|.|.-=+++ ++|+++||++-+ T Consensus 157 ~~EI~~q~~~~~~~D~vv~~vGtGgt~~Gi~~~lk~~~~~~~vigV~~ 204 (311) T TIGR01275 157 VLEIATQLESEVKFDSIVVAAGSGGTIAGLSLGLSILNEDIRPVGVAV 204 (311) T ss_pred HHHHHHHHhcCCCCCEEEEeCCcHHHHHHHHHHHHHhCCCCcEEEEEe Confidence 45556655 47999999999998865544 489999998853 No 64 >PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional Probab=66.99 E-value=15 Score=25.76 Aligned_cols=53 Identities=17% Similarity=0.122 Sum_probs=39.1 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCC-CEEEEecChhhhccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTM-PVLSVVIPQLKTNQL 79 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~-pIia~t~~~~~~r~L 79 (84) +..+.||..|..+..+- +.|+. .+|.|...++++=|.. ++-.+|.+..++..| T Consensus 76 ~~K~~IA~~Aa~~I~~g--~tIfl--d~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l 129 (256) T PRK10434 76 HKKELIAEAAVSLIHDG--DSIIL--DAGSTVLQMVPLLSRFNNITVMTNSLHIVNAL 129 (256) T ss_pred HHHHHHHHHHHhhCCCC--CEEEE--cCcHHHHHHHHHhccCCCeEEEECCHHHHHHH Confidence 34678888876655333 34444 8999999999988765 588999988777655 No 65 >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=66.03 E-value=11 Score=24.67 Aligned_cols=33 Identities=21% Similarity=0.283 Sum_probs=25.3 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.||.|.- ..+|-| .+|||++|.+. T Consensus 101 ~~Dv~I~iS~SG~t~~~i~~~~~ak~~-Ga~vI~IT~~~ 138 (177) T cd05006 101 PGDVLIGISTSGNSPNVLKALEAAKER-GMKTIALTGRD 138 (177) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCEEEEEeCCC Confidence 4478899999999854 445666 69999999664 No 66 >PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional Probab=63.85 E-value=12 Score=26.59 Aligned_cols=34 Identities=15% Similarity=0.228 Sum_probs=26.4 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|++|.||+|... .+|-+ .+|||++|.+.. T Consensus 89 ~~d~~i~iS~sG~t~~~~~~~~~ak~~-g~~vI~iT~~~~ 127 (321) T PRK11543 89 SRDVMLFISYSGGAKELDLIIPRLEDK-SIALLAMTGKPT 127 (321) T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHc-CCeEEEEECCCC Confidence 44789999999998663 45556 799999998653 No 67 >PRK14076 pnk inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=63.74 E-value=12 Score=29.46 Aligned_cols=34 Identities=29% Similarity=0.358 Sum_probs=26.5 Q ss_pred hcCCcEEEEecCCchHHHHHHhh----CCCCCEEEEec Q 039146 38 KVKASAIICFTSSGRAARLIAKY----RPTMPVLSVVI 71 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~ 71 (84) ...++.+|+-|.+|.||..+|.= -|.++.+.+|| T Consensus 458 ~~~~DGlivsTptGSTaYslSAGGPiv~p~~~~~~~tP 495 (569) T PRK14076 458 EVRADGIIISTPTGSTAYSLSAGGPIVEPTVDGFIIVP 495 (569) T ss_pred EEECCEEEEeCCCchHHHHhhCCCceeCCCCCeEEEEe Confidence 34678999999999999999974 45666666654 No 68 >PRK13937 phosphoheptose isomerase; Provisional Probab=63.59 E-value=13 Score=24.72 Aligned_cols=33 Identities=15% Similarity=0.235 Sum_probs=25.6 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) +-+.++++|.||.|... .+|-| .+|+|++|.+. T Consensus 106 ~~Dl~i~iS~sG~t~~~~~~~~~ak~~-g~~~I~iT~~~ 143 (188) T PRK13937 106 PGDVLIGISTSGNSPNVLAALEKAREL-GMKTIGLTGRD 143 (188) T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHC-CCeEEEEeCCC Confidence 34789999999988654 45666 79999999754 No 69 >PRK10681 DNA-binding transcriptional repressor DeoR; Provisional Probab=63.56 E-value=17 Score=25.42 Aligned_cols=53 Identities=11% Similarity=0.028 Sum_probs=39.0 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCC-CEEEEecChhhhccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTM-PVLSVVIPQLKTNQL 79 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~-pIia~t~~~~~~r~L 79 (84) +..+.||..|..+-.+- +.|+. .+|.|...++++=|+. ++-.+|.+..++..| T Consensus 77 ~~K~~IA~~Aa~lI~~g--~tIfl--D~GtT~~~la~~L~~~~~ltvvTnsl~i~~~l 130 (252) T PRK10681 77 EEKRRAAQLAATLVEPN--QTLFF--DCGTTTPWIIEAIDNELPFTAVCYSLNTFLAL 130 (252) T ss_pred HHHHHHHHHHHhhcCCC--CEEEE--ECCccHHHHHHhcCCCCCeEEEECCHHHHHHH Confidence 34678888876665433 34444 8999999999998864 788898888777655 No 70 >PRK11175 universal stress protein UspE; Provisional Probab=63.47 E-value=28 Score=24.17 Aligned_cols=44 Identities=14% Similarity=0.080 Sum_probs=31.9 Q ss_pred HHHHHHHHHHHhcCCcEEEEecCC---------chHHHHHHhhCCCCCEEEEec Q 039146 27 SITSSAVRSAIKVKASAIICFTSS---------GRAARLIAKYRPTMPVLSVVI 71 (84) Q Consensus 27 ~ia~~a~~~a~~~~~~aIv~~T~s---------G~ta~~iS~~Rp~~pIia~t~ 71 (84) .........+.+.+++.||+-+.. |.++..+-+. .+|||+.+-. T Consensus 94 ~~~~~i~~~a~~~~~DLiV~G~~~~~~~~~~~~gs~~~~l~~~-~~~pvlvv~~ 146 (305) T PRK11175 94 RPFEAIIQEVIAGGHDLVVKMTHQHDKLESVIFTPTDWHLLRK-CPCPVLMVKD 146 (305) T ss_pred CcHHHHHHHHHhcCCCEEEEeCCCCcHHHhhccChhHHHHHhc-CCCCEEEecc Confidence 445567788888999999998763 4566666654 5699999843 No 71 >PRK09802 DNA-binding transcriptional regulator AgaR; Provisional Probab=63.34 E-value=21 Score=25.33 Aligned_cols=54 Identities=20% Similarity=0.133 Sum_probs=39.6 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCC-CEEEEecChhhhcccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTM-PVLSVVIPQLKTNQLR 80 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~-pIia~t~~~~~~r~L~ 80 (84) +..+.||..|..+-.+- +.|+. .+|.|...++++=|.. ++-.+|.+..++..|. T Consensus 91 ~~K~~IA~~Aa~~I~dg--d~Ifl--d~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l~ 145 (269) T PRK09802 91 AMKRSVAKAAVELIQPG--HRVIL--DSGTTTFEIARLMRKHTDVIAMTNGMNVANALL 145 (269) T ss_pred HHHHHHHHHHHhhCCCC--CEEEE--CCchHHHHHHHhcCcCCCeEEEeCCHHHHHHHH Confidence 34678888866665433 44555 8999999999997764 6889999888876653 No 72 >cd05015 SIS_PGI_1 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), autocrine motility factor (AMF), and maturation factor (MF). Evidence suggests that PGI, NLK, AMF, and MF are closely related or identical. NLK is a neurotrophic growth factor that promotes regeneration and survival of neurons. The dimeric form of NLK has isomerase function, whereas its monomeric form carries out neurotrophic activity. AMF is a cytokine that stimulates cell migration and metastasis. MF mediates the differentiation of human myeloid leukemic HL-60 cells to terminal monocytic cells. Probab=63.30 E-value=14 Score=23.92 Aligned_cols=38 Identities=13% Similarity=0.125 Sum_probs=27.7 Q ss_pred CCcEEEEecCCchHHHHHHhhC-------------CCCCEEEEecChhhhc Q 039146 40 KASAIICFTSSGRAARLIAKYR-------------PTMPVLSVVIPQLKTN 77 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~R-------------p~~pIia~t~~~~~~r 77 (84) .-..+|+.|.||.|.-.++.+| ....++++|.+..... T Consensus 73 ~~tlvi~iSkSG~T~Et~~~~~~a~~~l~~~~~~~~~~~~vaiT~~~s~l~ 123 (158) T cd05015 73 ETTLFIVISKSGTTLETLANARLAREWLEEAGGDDLAKHFVAITDNGSGLL 123 (158) T ss_pred ccEEEEEEECCcCCHHHHHHHHHHHHHHHHhccccccceEEEEcCCChHHH Confidence 4567888999999876555443 5778999988766443 No 73 >PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A .... Probab=62.06 E-value=16 Score=21.98 Aligned_cols=32 Identities=31% Similarity=0.423 Sum_probs=22.9 Q ss_pred CCcEEEEecCCchHHHHH-----HhhCCCCCEEEEecC Q 039146 40 KASAIICFTSSGRAARLI-----AKYRPTMPVLSVVIP 72 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~i-----S~~Rp~~pIia~t~~ 72 (84) +-+.+|+++.+|.+...+ +|-+ .+|||++|.+ T Consensus 53 ~~d~vi~is~sg~~~~~~~~~~~ak~~-g~~vi~iT~~ 89 (131) T PF01380_consen 53 PDDLVIIISYSGETRELIELLRFAKER-GAPVILITSN 89 (131) T ss_dssp TTEEEEEEESSSTTHHHHHHHHHHHHT-TSEEEEEESS T ss_pred ccceeEeeeccccchhhhhhhHHHHhc-CCeEEEEeCC Confidence 347788889999887643 4433 6888988854 No 74 >PRK03910 D-cysteine desulfhydrase; Validated Probab=60.73 E-value=23 Score=25.59 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=26.5 Q ss_pred CCcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 40 KASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) ..++||+..-+|.|+. .+-.++|+++||++-+. T Consensus 183 ~~d~vv~~vGtGgt~~Gi~~~~k~~~~~~~vigVe~~ 219 (331) T PRK03910 183 DFDAVVVASGSGGTHAGLAAGLAALGPDIPVIGVTVS 219 (331) T ss_pred CCCEEEEeCCcHHHHHHHHHHHHHhCCCCeEEEEEec Confidence 4789999999999985 44455799999998763 No 75 >cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. Probab=59.08 E-value=28 Score=21.70 Aligned_cols=55 Identities=16% Similarity=0.198 Sum_probs=39.3 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCC-CCEEEEecChhhhccc Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPT-MPVLSVVIPQLKTNQL 79 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~-~pIia~t~~~~~~r~L 79 (84) --.++.-+.+.+.+.+.+.||.+|.+|.-+..+.+.|-. +.|+.++......+.| T Consensus 84 D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L 139 (149) T cd06167 84 DVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSREL 139 (149) T ss_pred cHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHH Confidence 356777788888887889999999999888776665544 6667666654444433 No 76 >PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein. Probab=57.90 E-value=36 Score=22.52 Aligned_cols=36 Identities=31% Similarity=0.485 Sum_probs=26.2 Q ss_pred HHHHHHhcCCcEEEEecCCchHHH-HHHhhCCCCCEEEEe Q 039146 32 AVRSAIKVKASAIICFTSSGRAAR-LIAKYRPTMPVLSVV 70 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~sG~ta~-~iS~~Rp~~pIia~t 70 (84) ..+++++.+.+..|+ .+|..|+ .+-++||+ -|||+. T Consensus 78 l~~lae~~g~~v~i~--~Ggt~ar~~ik~~~p~-~iigVA 114 (158) T PF01976_consen 78 LKKLAEKYGYKVYIA--TGGTLARKIIKEYRPK-AIIGVA 114 (158) T ss_pred HHHHHHHcCCEEEEE--cChHHHHHHHHHhCCC-EEEEEe Confidence 567899999994444 5666666 67788888 677664 No 77 >cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine kinases. The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding. Probab=57.55 E-value=42 Score=20.51 Aligned_cols=44 Identities=16% Similarity=0.078 Sum_probs=30.1 Q ss_pred HHHHHHHHHHHhcCCcEEEEecCC---------c-hHHHHHHhhC-CCCCEEEEe Q 039146 27 SITSSAVRSAIKVKASAIICFTSS---------G-RAARLIAKYR-PTMPVLSVV 70 (84) Q Consensus 27 ~ia~~a~~~a~~~~~~aIv~~T~s---------G-~ta~~iS~~R-p~~pIia~t 70 (84) ..+...++.|++.+++.||+-++. | .++..+.+.= |.|||+.+. T Consensus 90 ~~~~~I~~~a~~~~~dlIV~Gs~g~~~l~~~~~gssva~~Vi~~a~~~c~Vlvv~ 144 (146) T cd01989 90 DVAKAIVEYVADHGITKLVMGASSDNHFSMKFKKSDVASSVLKEAPDFCTVYVVS 144 (146) T ss_pred cHHHHHHHHHHHcCCCEEEEeccCCCceeecccCCchhHHHHhcCCCCceEEEEe Confidence 566777888999999998887641 2 3555444433 348999884 No 78 >COG1737 RpiR Transcriptional regulators [Transcription] Probab=56.94 E-value=56 Score=23.16 Aligned_cols=38 Identities=21% Similarity=0.264 Sum_probs=28.6 Q ss_pred HHHHhcCCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecC Q 039146 34 RSAIKVKASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 34 ~~a~~~~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~ 72 (84) .++..-+-+.+|++|.||++.- ..+|-| .+|||++|.. T Consensus 171 ~~~~~~~~Dv~i~iS~sG~t~e~i~~a~~ak~~-ga~vIaiT~~ 213 (281) T COG1737 171 QLALLTPGDVVIAISFSGYTREIVEAAELAKER-GAKVIAITDS 213 (281) T ss_pred HHHhCCCCCEEEEEeCCCCcHHHHHHHHHHHHC-CCcEEEEcCC Confidence 4444445679999999999865 456667 5999999877 No 79 >PRK10906 DNA-binding transcriptional repressor GlpR; Provisional Probab=56.91 E-value=26 Score=24.56 Aligned_cols=54 Identities=13% Similarity=0.038 Sum_probs=39.2 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCC-CCEEEEecChhhhcccc Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPT-MPVLSVVIPQLKTNQLR 80 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~-~pIia~t~~~~~~r~L~ 80 (84) +..+.||..|+....+- +.|+. .+|.|...++++=|. .++-.+|.+..++..|. T Consensus 76 ~~K~~IA~~Aa~~I~~g--~tIfl--D~GtT~~~la~~L~~~~~ltVvTNsl~ia~~l~ 130 (252) T PRK10906 76 EEKERIARKVASQIPNG--ATLFI--DIGTTPEAVAHALLNHSNLRIVTNNLNVANTLM 130 (252) T ss_pred HHHHHHHHHHHhhCCCC--CEEEE--cCcHHHHHHHHHhcCCCCcEEEECcHHHHHHHh Confidence 44678888876665433 44554 899999999998776 47888988888776653 No 80 >PRK09982 universal stress protein UspD; Provisional Probab=56.17 E-value=46 Score=20.62 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=28.7 Q ss_pred HHHHHHHHHHHhcCCcEEEEecCCchHHHHHH-----hhCCCCCEEEE Q 039146 27 SITSSAVRSAIKVKASAIICFTSSGRAARLIA-----KYRPTMPVLSV 69 (84) Q Consensus 27 ~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS-----~~Rp~~pIia~ 69 (84) ..+...++.|++.+++.||+-+..+...+.++ --+.+|||+.+ T Consensus 90 ~p~~~I~~~A~~~~aDLIVmG~~~~~~~~~~~va~~V~~~s~~pVLvv 137 (142) T PRK09982 90 EMPETLLEIMQKEQCDLLVCGHHHSFINRLMPAYRGMINKMSADLLIV 137 (142) T ss_pred CHHHHHHHHHHHcCCCEEEEeCChhHHHHHHHHHHHHHhcCCCCEEEe Confidence 45566677899999999999875333233332 12568898887 No 81 >TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized. Probab=55.70 E-value=32 Score=23.03 Aligned_cols=51 Identities=10% Similarity=-0.010 Sum_probs=38.7 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCC-CCEEEEecChhh Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPT-MPVLSVVIPQLK 75 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~-~pIia~t~~~~~ 75 (84) --.++.-+++++..-+.+.++.+|.+|.-.+++.+.|-. ..|+++...... T Consensus 90 Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~t 141 (160) T TIGR00288 90 DVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGF 141 (160) T ss_pred cHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCC Confidence 346777788888777889999999999999999776654 777777644433 No 82 >cd08181 PPD-like 1,3-propanediol dehydrogenase-like (PPD). 1,3-propanediol dehydrogenase-like (PPD). This family is a member of the iron-containing alcohol dehydrogenase superfamily, and exhibits a dehydroquinate synthase-like fold. Protein sequence similarity search and other biochemical evidences suggest that they are close to the iron-containing 1,3-propanediol dehydrogenase (EC 1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the oxidation of propane-1,3-diol to 3-hydroxypropanal with the simultaneous reduction of NADP+ to NADPH. The protein structure of Thermotoga maritima TM0920 gene contains one NADP+ and one iron ion. Probab=55.68 E-value=48 Score=24.30 Aligned_cols=48 Identities=25% Similarity=0.241 Sum_probs=36.4 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHh--------------------hCCCCCEEEEecC Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAK--------------------YRPTMPVLSVVIP 72 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~--------------------~Rp~~pIia~t~~ 72 (84) ++.......+++.+.+.+++.||. -.|.++.-++| +++..|+|++-+. T Consensus 66 ~p~~~~v~~~~~~~~~~~~D~IIa--vGGGSviD~aK~ia~~~~~~~~~~~~~~~~~~~~~~P~i~VPTt 133 (357) T cd08181 66 NPSLETIMEAVEIAKKFNADFVIG--IGGGSPLDAAKAIAVLIKNPDLKVELYFRSKYLKALPVVAIPTT 133 (357) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEE--eCCchHHHHHHHHHHHHhCCCcHHHHhcccccCCCCCEEEEeCC Confidence 455555666778888899998887 58888888887 4778999988443 No 83 >PRK11302 DNA-binding transcriptional regulator HexR; Provisional Probab=55.58 E-value=17 Score=25.24 Aligned_cols=32 Identities=16% Similarity=0.401 Sum_probs=24.9 Q ss_pred CCcEEEEecCCchHHHHH-----HhhCCCCCEEEEecC Q 039146 40 KASAIICFTSSGRAARLI-----AKYRPTMPVLSVVIP 72 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~i-----S~~Rp~~pIia~t~~ 72 (84) +-+.+|++|.+|++...+ +|-+ .++||++|.. T Consensus 175 ~~D~vI~iS~sG~t~~~~~~~~~ak~~-g~~vI~IT~~ 211 (284) T PRK11302 175 DGDVVVLISHTGRTKSLVELAQLAREN-GATVIAITSA 211 (284) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHc-CCeEEEECCC Confidence 457899999999887644 5555 7999999963 No 84 >COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism] Probab=55.04 E-value=42 Score=23.58 Aligned_cols=52 Identities=13% Similarity=0.121 Sum_probs=39.6 Q ss_pred HHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCC-EEEEecChhhhccc Q 039146 24 HLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMP-VLSVVIPQLKTNQL 79 (84) Q Consensus 24 ~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~p-Iia~t~~~~~~r~L 79 (84) ....||..|+.+.. +-+.|+. .+|.|...++++=|+-+ +-++|.+-.++..| T Consensus 77 eK~~IA~~Aa~lI~--~g~~ifl--d~GTT~~~la~~L~~~~~ltviTNsl~ia~~l 129 (253) T COG1349 77 EKRAIAKAAATLIE--DGDTIFL--DAGTTTLALARALPDDNNLTVITNSLNIAAAL 129 (253) T ss_pred HHHHHHHHHHhhCC--CCCEEEE--CCCcHHHHHHHHhCcCCCeEEEeCCHHHHHHH Confidence 35678888777765 3355555 89999999999999777 88998887766544 No 85 >PRK05578 cytidine deaminase; Validated Probab=54.61 E-value=42 Score=21.47 Aligned_cols=48 Identities=23% Similarity=0.293 Sum_probs=31.3 Q ss_pred HHHHHHHHHHHHhcCCcEEEEe-------cCCchHHHHHHhhC-CCCCEEEEecCh Q 039146 26 ESITSSAVRSAIKVKASAIICF-------TSSGRAARLIAKYR-PTMPVLSVVIPQ 73 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~-------T~sG~ta~~iS~~R-p~~pIia~t~~~ 73 (84) |..|...+.....-+.++|++. |..|..-+.|+.|. |+.+|+....+. T Consensus 55 E~~Ai~~av~~G~~~i~~i~vv~~~~~~~sPCG~CRQ~l~e~~~~~~~v~l~~~~~ 110 (131) T PRK05578 55 ERTAIFKAISEGGGRLVAIACVGETGEPLSPCGRCRQVLAEFGGPDLLVTLVAKDG 110 (131) T ss_pred HHHHHHHHHHcCCCceEEEEEEecCCCccCccHHHHHHHHHhCCCCcEEEEEcCCC Confidence 4444443333444466788874 56677789999996 788888775554 No 86 >PRK00414 gmhA phosphoheptose isomerase; Reviewed Probab=53.99 E-value=15 Score=24.67 Aligned_cols=33 Identities=15% Similarity=0.369 Sum_probs=25.3 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.||.|.-. .+|-| .+|||++|.+. T Consensus 111 ~~Dv~I~iS~SG~t~~~i~~~~~ak~~-g~~iI~iT~~~ 148 (192) T PRK00414 111 EGDVLLGISTSGNSGNIIKAIEAARAK-GMKVITLTGKD 148 (192) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEeCCC Confidence 34788889999987654 45666 89999999764 No 87 >PRK11337 DNA-binding transcriptional repressor RpiR; Provisional Probab=53.28 E-value=19 Score=25.26 Aligned_cols=33 Identities=15% Similarity=0.360 Sum_probs=25.0 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.+|.+... .++-+ .++||++|.+. T Consensus 187 ~~Dl~I~iS~sG~t~~~~~~~~~ak~~-g~~ii~IT~~~ 224 (292) T PRK11337 187 EGDVVLVVSHSGRTSDVIEAVELAKKN-GAKIICITNSY 224 (292) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEeCCC Confidence 45788999999988754 34455 69999998765 No 88 >PRK02947 hypothetical protein; Provisional Probab=53.24 E-value=36 Score=23.79 Aligned_cols=34 Identities=26% Similarity=0.256 Sum_probs=26.5 Q ss_pred cCCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 39 VKASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) -.-+.+|++|.||++.-. .++-| .+|||++|... T Consensus 105 ~~~Dv~i~iS~sG~t~~~i~~~~~a~~~-g~~vI~iT~~~ 143 (246) T PRK02947 105 RPGDVLIVVSNSGRNPVPIEMALEAKER-GAKVIAVTSLA 143 (246) T ss_pred CCCCEEEEEeCCCCCHHHHHHHHHHHHC-CCEEEEEcCCc Confidence 355899999999998753 44555 79999999876 No 89 >PRK08674 bifunctional phosphoglucose/phosphomannose isomerase; Validated Probab=53.22 E-value=13 Score=26.93 Aligned_cols=33 Identities=15% Similarity=0.186 Sum_probs=23.8 Q ss_pred CcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 41 ASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) -+.+|++|.||.|... .++-| .++||++|.+.. T Consensus 79 ~dlvI~iS~SG~T~e~~~a~~~a~~~-ga~vIaIT~~~~ 116 (337) T PRK08674 79 KTLVIAVSYSGNTEETLSAVEQALKR-GAKIIAITSGGK 116 (337) T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHC-CCeEEEECCCch Confidence 3678889999987654 34445 589999986543 No 90 >cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio Probab=52.93 E-value=46 Score=19.61 Aligned_cols=42 Identities=24% Similarity=0.204 Sum_probs=28.9 Q ss_pred HHHHHHHHHHHhcCCcEEEEecCC---------chHHHHHHhhCCCCCEEEE Q 039146 27 SITSSAVRSAIKVKASAIICFTSS---------GRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 27 ~ia~~a~~~a~~~~~~aIv~~T~s---------G~ta~~iS~~Rp~~pIia~ 69 (84) .+....++.+++.+++.||+-+.. |.++..+-+ +.+|||+.+ T Consensus 81 ~~~~~I~~~a~~~~~dlIV~G~~~~~~~~~~~lGs~~~~v~~-~~~~pvlvv 131 (132) T cd01988 81 DIASGILRTAKERQADLIIMGWHGSTSLRDRLFGGVIDQVLE-SAPCDVAVV 131 (132) T ss_pred CHHHHHHHHHHhcCCCEEEEecCCCCCccceecCchHHHHHh-cCCCCEEEe Confidence 455667788889999988887653 344555553 456888765 No 91 >PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3.1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B .... Probab=52.02 E-value=56 Score=20.32 Aligned_cols=39 Identities=21% Similarity=0.095 Sum_probs=28.9 Q ss_pred CCcEEEEecCCchHHHHHH---hhCCCCCEEEEecChhhhcccc Q 039146 40 KASAIICFTSSGRAARLIA---KYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS---~~Rp~~pIia~t~~~~~~r~L~ 80 (84) +--.+...|-+|.|--.+. +... +++.++++..+..|+. T Consensus 26 ~~~ll~~~tGsGKT~~~~~~~~~l~~--~~l~~~p~~~l~~Q~~ 67 (184) T PF04851_consen 26 RRVLLNAPTGSGKTIIALALILELAR--KVLIVAPNISLLEQWY 67 (184) T ss_dssp SEEEEEESTTSSHHHHHHHHHHHHHC--EEEEEESSHHHHHHHH T ss_pred CCEEEEECCCCCcChhhhhhhhcccc--ceeEecCHHHHHHHHH Confidence 4456788899999977553 3332 8888999988888764 No 92 >PRK10892 D-arabinose 5-phosphate isomerase; Provisional Probab=51.97 E-value=25 Score=25.08 Aligned_cols=34 Identities=15% Similarity=0.342 Sum_probs=26.3 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) .-+.+|++|.||.|... .++-+ .+|||++|.++. T Consensus 94 ~~d~~I~iS~sG~t~~~~~~~~~ak~~-g~~vi~iT~~~~ 132 (326) T PRK10892 94 PQDVVIAISNSGESSEILALIPVLKRL-HVPLICITGRPE 132 (326) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCcEEEEECCCC Confidence 44789999999998764 45555 699999998753 No 93 >PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP:ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C .... Probab=51.92 E-value=23 Score=21.60 Aligned_cols=39 Identities=26% Similarity=0.221 Sum_probs=30.3 Q ss_pred HHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEE Q 039146 31 SAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 31 ~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~ 69 (84) .+..++..-+.--|+++|.+-.++|+++-++--.|++.- T Consensus 29 ta~~isk~RP~~pIiavt~~~~~~r~l~l~~GV~p~~~~ 67 (117) T PF02887_consen 29 TARLISKYRPKVPIIAVTPNESVARQLSLYWGVYPVLIE 67 (117) T ss_dssp HHHHHHHT-TSSEEEEEESSHHHHHHGGGSTTEEEEECS T ss_pred HHHHHHhhCCCCeEEEEcCcHHHHhhhhcccceEEEEec Confidence 455666666666799999999999999999987776543 No 94 >cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Probab=51.78 E-value=29 Score=19.23 Aligned_cols=30 Identities=37% Similarity=0.624 Sum_probs=22.4 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEe Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVV 70 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t 70 (84) +-+.++++|.+|++... .+|.+ .++++++| T Consensus 47 ~~d~~i~iS~sg~t~~~~~~~~~a~~~-g~~ii~it 81 (87) T cd04795 47 KGDVVIALSYSGRTEELLAALEIAKEL-GIPVIAIT 81 (87) T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHc-CCeEEEEe Confidence 55789999999987753 34555 58899887 No 95 >cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat Probab=51.32 E-value=62 Score=23.37 Aligned_cols=47 Identities=13% Similarity=0.166 Sum_probs=33.4 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHh----------hCCCCCEEEEec Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAK----------YRPTMPVLSVVI 71 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~----------~Rp~~pIia~t~ 71 (84) ++.......++..+.+.++++||. -.|.++.-++| ++|..|+|++-+ T Consensus 61 ~p~~~~v~~~~~~~~~~~~d~Iia--iGGGs~~D~aKa~a~~~~~~~~~~~~p~i~VPT 117 (332) T cd08180 61 DPPIEVVAKGIKKFLDFKPDIVIA--LGGGSAIDAAKAIIYFAKKLGKKKKPLFIAIPT 117 (332) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEE--ECCchHHHHHHHHHHHHhCCCCCCCCCEEEeCC Confidence 344455556677788889998886 57777777776 566789998843 No 96 >PRK00331 glucosamine--fructose-6-phosphate aminotransferase; Reviewed Probab=51.25 E-value=25 Score=27.53 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=26.0 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|++|.||.|.-. .+|-+ .+|+|++|.+.. T Consensus 336 ~~dlvI~iS~SG~T~e~i~a~~~ak~~-ga~~IaIT~~~~ 374 (604) T PRK00331 336 PKTLVIAISQSGETADTLAALRLAKEL-GAKTLAICNVPG 374 (604) T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHHHC-CCCEEEEECCCC Confidence 34688999999998764 45556 699999998643 No 97 >PRK15482 transcriptional regulator MurR; Provisional Probab=50.99 E-value=25 Score=24.70 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=25.8 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|++|.+|++... .++-+ .++||++|.+.. T Consensus 182 ~~Dv~i~iS~sg~t~~~~~~~~~a~~~-g~~iI~IT~~~~ 220 (285) T PRK15482 182 KGDVQIAISYSGSKKEIVLCAEAARKQ-GATVIAITSLAD 220 (285) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCEEEEEeCCCC Confidence 34789999999998764 34555 699999997653 No 98 >PRK14045 1-aminocyclopropane-1-carboxylate deaminase; Provisional Probab=50.72 E-value=56 Score=23.63 Aligned_cols=43 Identities=14% Similarity=0.153 Sum_probs=32.1 Q ss_pred HHHHHHHhc-----CCcEEEEecCCchHHHHHHhh----CCCCCEEEEecCh Q 039146 31 SAVRSAIKV-----KASAIICFTSSGRAARLIAKY----RPTMPVLSVVIPQ 73 (84) Q Consensus 31 ~a~~~a~~~-----~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~~ 73 (84) .+.++.+.+ +.++||+.+-+|.|.-=++++ .|++.|+++-+.. T Consensus 170 ~~~EI~~q~~~~~~~~d~vv~~vGtGGt~aGi~~~lk~~~~~~kVigv~~~~ 221 (329) T PRK14045 170 AVGEIATQVKKLGVRFDSIVVAVGSGGTLAGLSLGLAILNAEWRVVGIAVGS 221 (329) T ss_pred HHHHHHHHHHhcCCCCCEEEEeCCcHHHHHHHHHHHHHhCCCCeEEEEEecC Confidence 334565554 478999999999998755553 5999999997754 No 99 >PRK08329 threonine synthase; Validated Probab=50.54 E-value=46 Score=24.37 Aligned_cols=49 Identities=20% Similarity=0.114 Sum_probs=34.5 Q ss_pred HHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecCh Q 039146 24 HLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIPQ 73 (84) Q Consensus 24 ~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~~ 73 (84) ..+--+...+..+.+.+.+.||+.| +|++++.+|.+ +-..+.+.+++.. T Consensus 87 fKdRga~~~i~~a~~~g~~~vv~aS-sGN~g~alA~~aa~~G~~~~v~vp~~ 137 (347) T PRK08329 87 FKDRGTYVTVAKLKEEGINEVVIDS-SGNAALSLALYSLSEGIKVHVFVSYN 137 (347) T ss_pred CHHHHHHHHHHHHHHcCCCEEEEEC-CCcHHHHHHHHHHHcCCcEEEEECCC Confidence 4556666667677778888888865 99999877765 3356777776653 No 100 >TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli. Probab=49.96 E-value=30 Score=23.74 Aligned_cols=33 Identities=12% Similarity=0.174 Sum_probs=25.6 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~ 73 (84) +-+.+|++|.||.|... .+|-+ .++||++|... T Consensus 47 ~~d~~i~iS~sG~t~~~~~~~~~a~~~-g~~ii~iT~~~ 84 (268) T TIGR00393 47 PNDVVLMISYSGESLELLNLIPHLKRL-SHKIIAFTGSP 84 (268) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHc-CCcEEEEECCC Confidence 44789999999998764 45556 69999999764 No 101 >PRK11175 universal stress protein UspE; Provisional Probab=49.73 E-value=56 Score=22.67 Aligned_cols=42 Identities=17% Similarity=0.075 Sum_probs=31.5 Q ss_pred HHHHHHHHHHhcCCcEEEEecC---------CchHHHHHHhhCCCCCEEEEe Q 039146 28 ITSSAVRSAIKVKASAIICFTS---------SGRAARLIAKYRPTMPVLSVV 70 (84) Q Consensus 28 ia~~a~~~a~~~~~~aIv~~T~---------sG~ta~~iS~~Rp~~pIia~t 70 (84) .+....+.+++.+++.||+-|. -|.++..+.+. .+|||+.+= T Consensus 249 ~~~~I~~~a~~~~~DLIVmG~~~~~~~~~~llGS~a~~v~~~-~~~pVLvv~ 299 (305) T PRK11175 249 PEEVIPDLAEHLDAELVILGTVGRTGLSAAFLGNTAEHVIDH-LNCDLLAIK 299 (305) T ss_pred HHHHHHHHHHHhCCCEEEECCCccCCCcceeecchHHHHHhc-CCCCEEEEc Confidence 4445667788999999998773 26788888864 459999883 No 102 >TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity. Probab=49.42 E-value=29 Score=25.04 Aligned_cols=34 Identities=18% Similarity=0.246 Sum_probs=26.6 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) .-+.+|++|.||+|.-. .+|-+ .+++|++|.++. T Consensus 126 ~~DvvI~IS~SG~T~~vi~al~~Ak~~-Ga~tIaIT~~~~ 164 (291) T TIGR00274 126 KNDVVVGIAASGRTPYVIAGLQYARSL-GALTISIACNPK 164 (291) T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHC-CCeEEEEECCCC Confidence 45889999999999864 45555 689999987654 No 103 >PRK10116 universal stress protein UspC; Provisional Probab=48.32 E-value=61 Score=19.65 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=26.3 Q ss_pred HHHHHHHHHhcCCcEEEEecCCc-hHHHHHH-----hhCCCCCEEEE Q 039146 29 TSSAVRSAIKVKASAIICFTSSG-RAARLIA-----KYRPTMPVLSV 69 (84) Q Consensus 29 a~~a~~~a~~~~~~aIv~~T~sG-~ta~~iS-----~~Rp~~pIia~ 69 (84) .......+++.+++.||+-|+.- ...+.+| =.+.+|||+.+ T Consensus 91 ~~~I~~~a~~~~~DLiV~g~~~~~~~~~~~s~a~~v~~~~~~pVLvv 137 (142) T PRK10116 91 SEHILEVCRKHHFDLVICGNHNHSFFSRASCSAKRVIASSEVDVLLV 137 (142) T ss_pred HHHHHHHHHHhCCCEEEEcCCcchHHHHHHHHHHHHHhcCCCCEEEE Confidence 45566788889999888876532 1222222 14568899887 No 104 >cd00578 L-fuc_L-ara-isomerases L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute. Probab=48.14 E-value=57 Score=24.64 Aligned_cols=46 Identities=13% Similarity=0.099 Sum_probs=35.3 Q ss_pred HHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecCh Q 039146 28 ITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIPQ 73 (84) Q Consensus 28 ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~~ 73 (84) =+..++......++++||+...++.++..+... ..+.||+-+...+ T Consensus 51 ~~~~~~~~~~~~~~d~ii~~~~tf~~~~~~~~~~~~~~~Pvll~a~~~ 98 (452) T cd00578 51 EARKAAEEFNEANCDGLIVWMHTFGPAKMWIAGLSELRKPVLLLATQF 98 (452) T ss_pred HHHHHHHHHhhcCCcEEEEcccccccHHHHHHHHHhcCCCEEEEeCCC Confidence 344555666666899999999999999877775 6789999887554 No 105 >COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane] Probab=47.23 E-value=43 Score=23.26 Aligned_cols=33 Identities=21% Similarity=0.358 Sum_probs=25.2 Q ss_pred cEEEEecCCchHHHHH-----HhhCCCCCEEEEecChhh Q 039146 42 SAIICFTSSGRAARLI-----AKYRPTMPVLSVVIPQLK 75 (84) Q Consensus 42 ~aIv~~T~sG~ta~~i-----S~~Rp~~pIia~t~~~~~ 75 (84) +.++.+|.||.|.-.+ +| |-..+||++|.++.. T Consensus 88 DvviaiS~SGeT~el~~~~~~aK-~~g~~liaiT~~~~S 125 (202) T COG0794 88 DVVIAISGSGETKELLNLAPKAK-RLGAKLIAITSNPDS 125 (202) T ss_pred CEEEEEeCCCcHHHHHHHHHHHH-HcCCcEEEEeCCCCC Confidence 6778889999997643 33 347999999988764 No 106 >TIGR02815 agaS_fam putative sugar isomerase, AgaS family. Some members of this protein family are found in regions associated with N-acetyl-galactosamine and galactosamine untilization and are suggested to be isomerases. Probab=46.84 E-value=21 Score=26.41 Aligned_cols=33 Identities=15% Similarity=0.183 Sum_probs=23.8 Q ss_pred cEEEEecCCchHHHHHH-----hhCC-CCCEEEEecChh Q 039146 42 SAIICFTSSGRAARLIA-----KYRP-TMPVLSVVIPQL 74 (84) Q Consensus 42 ~aIv~~T~sG~ta~~iS-----~~Rp-~~pIia~t~~~~ 74 (84) ..+|++|+||.|.-.+. |-+. .++++++|.+.. T Consensus 94 ~lvi~iSqSGeT~etv~a~~~ak~~~~g~~~i~it~~~~ 132 (372) T TIGR02815 94 TLLVSFARSGNSPESVAAVELADQLLPECYHLVLTCNEE 132 (372) T ss_pred eEEEEEeCCcCcHHHHHHHHHHHHhCCCCcEEEEEcCCC Confidence 46888999999876553 3332 689999988644 No 107 >PRK11382 frlB fructoselysine-6-P-deglycase; Provisional Probab=46.56 E-value=35 Score=24.87 Aligned_cols=33 Identities=9% Similarity=0.099 Sum_probs=25.2 Q ss_pred CcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 41 ASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) -+.+|++|.||.|.-. .+|-+ .+++|++|.+.. T Consensus 93 ~~lvI~iS~SGeT~e~i~al~~ak~~-Ga~~I~IT~~~~ 130 (340) T PRK11382 93 RCAVIGVSDYGKTEEVIKALELGRAC-GALTAAFTKRAD 130 (340) T ss_pred CCEEEEEcCCCCCHHHHHHHHHHHHc-CCeEEEEECCCC Confidence 3578889999988654 45666 589999998754 No 108 >cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate. Probab=46.21 E-value=34 Score=24.08 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=26.0 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|.+|.||+|... .+|-+ .+|++++|.++. T Consensus 118 ~~DvvI~IS~SG~T~~vi~al~~Ak~~-Ga~~I~It~~~~ 156 (257) T cd05007 118 ERDVVIGIAASGRTPYVLGALRYARAR-GALTIGIACNPG 156 (257) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEECCCC Confidence 45788999999988763 45655 689999987653 No 109 >PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional Probab=44.32 E-value=46 Score=26.29 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=36.5 Q ss_pred HHHHHHHhcCCcEEEEecCCchHHHH----HHhhCCCCCEEEEecChhhhccc Q 039146 31 SAVRSAIKVKASAIICFTSSGRAARL----IAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 31 ~a~~~a~~~~~~aIv~~T~sG~ta~~----iS~~Rp~~pIia~t~~~~~~r~L 79 (84) ...+.+.--+++++|+.+.+-..... +-+..|+.+|++-++|+.-...| T Consensus 455 ~~L~~agi~~A~~vv~~~~d~~~n~~i~~~~r~~~p~~~IiaRa~~~~~~~~L 507 (601) T PRK03659 455 ELLRAAGAEKAEAIVITCNEPEDTMKIVELCQQHFPHLHILARARGRVEAHEL 507 (601) T ss_pred HHHHhcCCccCCEEEEEeCCHHHHHHHHHHHHHHCCCCeEEEEeCCHHHHHHH Confidence 34445555588999998888766643 45568999999999998877655 No 110 >PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed Probab=44.24 E-value=82 Score=22.77 Aligned_cols=34 Identities=15% Similarity=0.141 Sum_probs=24.7 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~~~ 74 (84) .-+.+|.+|.||.|.. ..++-+ .+++|++|.++. T Consensus 127 ~~DvvI~IS~SG~T~~vi~al~~Ak~~-Ga~~IaIT~~~~ 165 (296) T PRK12570 127 ADDVVVGIAASGRTPYVIGALEYAKQI-GATTIALSCNPD 165 (296) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEECCCC Confidence 4488899999999943 445555 688999986643 No 111 >COG3199 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only] Probab=43.94 E-value=68 Score=24.25 Aligned_cols=40 Identities=25% Similarity=0.335 Sum_probs=28.8 Q ss_pred HHHHHHHhcCCcEEEEecCCchHHHHHHhh-CCCCCEEEEec Q 039146 31 SAVRSAIKVKASAIICFTSSGRAARLIAKY-RPTMPVLSVVI 71 (84) Q Consensus 31 ~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~-Rp~~pIia~t~ 71 (84) .+++.-.+.+++.|+.. -.-.|||-++.- ++++||+++.. T Consensus 91 ~~~r~~~~~gVdlIvfa-GGDGTarDVa~av~~~vPvLGipa 131 (355) T COG3199 91 NAVRRMVERGVDLIVFA-GGDGTARDVAEAVGADVPVLGIPA 131 (355) T ss_pred HHHHHHHhcCceEEEEe-CCCccHHHHHhhccCCCceEeecc Confidence 34445556678855554 555689988888 99999999854 No 112 >TIGR01136 cysKM cysteine synthases. This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff. Probab=43.76 E-value=71 Score=22.63 Aligned_cols=42 Identities=7% Similarity=0.134 Sum_probs=32.2 Q ss_pred HHHHHHHhcC--CcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 31 SAVRSAIKVK--ASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~~--~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) .+.++.+.++ .+.||+..-+|.++. .+..++|...|+++.+. T Consensus 152 ~~~Ei~~ql~~~~d~iv~~vG~Gg~~~G~~~~~~~~~~~~~vi~Ve~~ 199 (299) T TIGR01136 152 TGPEIWRDTDGRIDHFVAGVGTGGTITGVGRYLKEQNPNIKIVAVEPA 199 (299) T ss_pred HHHHHHHhcCCCCCEEEEcCchhHHHHHHHHHHHHhCCCCEEEEEecC Confidence 4557777774 899999999998874 45556799999999764 No 113 >cd07408 MPP_SA0022_N Staphylococcus aureus SA0022 and related proteins, N-terminal metallophosphatase domain. SA0022 is an uncharacterized Staphylococcus aureus UshA-like protein with two putative domains, an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. SA0022 also contains a putative C-terminal cell wall anchor domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet Probab=43.59 E-value=98 Score=21.39 Aligned_cols=53 Identities=11% Similarity=0.052 Sum_probs=35.4 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHH-------HHHHhhCCCCCEEEEecChhh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAA-------RLIAKYRPTMPVLSVVIPQLK 75 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta-------~~iS~~Rp~~pIia~t~~~~~ 75 (84) +..+++....+....+-+++.||+++..|.-. +.+++.-|.+.+|.-.++... T Consensus 154 d~~~~~~~~~v~~l~~~~~D~iIvl~H~G~~~~~~~~~~~~la~~~~giDvIigGH~H~~ 213 (257) T cd07408 154 DPIEEAKKVIVAALKAKGADVIVALGHLGVDRTSSPWTSTELAANVTGIDLIIDGHSHTT 213 (257) T ss_pred cHHHHHHHHHHHHHHhCCCCEEEEEeCcCcCCCCCCccHHHHHHhCCCceEEEeCCCccc Confidence 45555544424555566899999999988643 677777778877766555443 No 114 >PRK11761 cysM cysteine synthase B; Provisional Probab=42.77 E-value=76 Score=22.66 Aligned_cols=41 Identities=5% Similarity=0.122 Sum_probs=31.1 Q ss_pred HHHHHHhc--CCcEEEEecCCchHH----HHHHhhCCCCCEEEEecC Q 039146 32 AVRSAIKV--KASAIICFTSSGRAA----RLIAKYRPTMPVLSVVIP 72 (84) Q Consensus 32 a~~~a~~~--~~~aIv~~T~sG~ta----~~iS~~Rp~~pIia~t~~ 72 (84) +.++.+.+ ..++||+..-+|.+. +.+..++|...|+++-+. T Consensus 157 ~~Ei~eq~~~~~d~iv~~vG~Gg~~~Gi~~~lk~~~~~~kvigVep~ 203 (296) T PRK11761 157 GPEIWRQTEGRITHFVSSMGTTGTIMGVSRYLKEQNPAVQIVGLQPE 203 (296) T ss_pred HHHHHHhcCCCCCEEEecCCcHHHHHHHHHHHHHhCCCCEEEEEecC Confidence 44566666 379999999999655 566667899999999764 No 115 >PRK08197 threonine synthase; Validated Probab=42.34 E-value=71 Score=23.77 Aligned_cols=49 Identities=18% Similarity=0.123 Sum_probs=33.9 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecC Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIP 72 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~ 72 (84) +..+-.+...+..+.+.+.+.||+.| +|++++.+|.+ +-..+.+.+++. T Consensus 109 SfKdRga~~~i~~a~~~g~~~vv~aS-sGN~g~alA~~aa~~G~~~~v~vp~ 159 (394) T PRK08197 109 SFKARGLAVGVSRAKELGVKHLAMPT-NGNAGAAWAAYAARAGIRATIFMPA 159 (394) T ss_pred CcHHhHHHHHHHHHHHcCCCEEEEeC-CcHHHHHHHHHHHHcCCcEEEEEcC Confidence 34555666667777788888888764 99999877665 335666666654 No 116 >TIGR00161 conserved hypothetical protein TIGR00161. This ortholog set includes MJ0106 from Methanococcus jannaschii and AF1251 from Archaeoglobus fulgidus, but not MJ1210 or AF0525. Probab=41.31 E-value=83 Score=21.95 Aligned_cols=49 Identities=18% Similarity=0.315 Sum_probs=37.8 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) ...++...++.+.+.+++.||+++-- -+. .+| -+++++..++...+.|. T Consensus 92 ~~~~a~~il~~~~~~gv~~Ii~Lgg~--~~~----~~~-~~v~~~at~~~~~~~l~ 140 (238) T TIGR00161 92 VYDMTNAIVEWMVRNNSRELISFNGM--VVR----EKS-QPVFGAANSQELIERLK 140 (238) T ss_pred HHHHHHHHHHHHHHcCCCeEEEEeCc--cCC----CCC-CcEEEEECCHHHHHHHH Confidence 56888899999999999999986543 222 244 78999999888877765 No 117 >TIGR02128 G6PI_arch bifunctional phosphoglucose/phosphomannose isomerase. This bifunctional isomerase is a member of the larger PGI superfamily and only distantly related to other glucose-6-phosphate isomerases. The family is limited to the archaea. Probab=41.26 E-value=39 Score=24.57 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=19.4 Q ss_pred cEEEEecCCchHHHHHH-----hhCCCCCEEEEecC Q 039146 42 SAIICFTSSGRAARLIA-----KYRPTMPVLSVVIP 72 (84) Q Consensus 42 ~aIv~~T~sG~ta~~iS-----~~Rp~~pIia~t~~ 72 (84) +.+|++|.||.|.-.++ +-| .++|+++|.+ T Consensus 68 dlvI~iS~SG~t~e~~~a~~~A~~~-g~~ii~iT~~ 102 (308) T TIGR02128 68 TLLIAVSYSGNTEETLSAVEEAKKK-GAKVIAITSG 102 (308) T ss_pred eEEEEEcCCCCCHHHHHHHHHHHHc-CCEEEEECCC Confidence 46777778887765443 334 5677777754 No 118 >KOG0026 consensus Anthranilate synthase, beta chain [Amino acid transport and metabolism] Probab=40.87 E-value=31 Score=23.87 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=20.7 Q ss_pred CCchHHHHHHhhCCCCCEEEEec Q 039146 49 SSGRAARLIAKYRPTMPVLSVVI 71 (84) Q Consensus 49 ~sG~ta~~iS~~Rp~~pIia~t~ 71 (84) .||-+-..+++|-|++|++++|- T Consensus 78 DsGIs~~~i~~f~~~iP~fGvCM 100 (223) T KOG0026|consen 78 DSGISLQTVLELGPLVPLFGVCM 100 (223) T ss_pred cccchHHHHHHhCCCCceeeeeh Confidence 67888889999999999999973 No 119 >cd07412 MPP_YhcR_N Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain. YhcR is a Bacillus subtilis sugar-nonspecific endonuclease. It cleaves endonucleolytically to yield nucleotide 3'-monophosphate products, similar to Staphylococcus aureus micrococcal nuclease. YhcR appears to be located in the cell wall, and is thought to be a substrate for a Bacillus subtilis sortase. YhcR is the major calcium-activated nuclease of B. subtilis. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated wi Probab=40.71 E-value=99 Score=21.91 Aligned_cols=52 Identities=15% Similarity=0.250 Sum_probs=33.8 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchH---------------HHHHHhhCCCCCEEEEecChhh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRA---------------ARLIAKYRPTMPVLSVVIPQLK 75 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~t---------------a~~iS~~Rp~~pIia~t~~~~~ 75 (84) +..+++-. .+.....-+++.||+++..|.. ..++.+.-|.+.+|...++... T Consensus 175 d~~e~~~~-~v~~lr~~~~D~IIvL~H~G~~~~~~~~~~~~~~~~~~~l~~~~~~~iD~IlgGHsH~~ 241 (288) T cd07412 175 DEVEAINA-VAPELKAGGVDAIVVLAHEGGSTKGGDDTCSAASGPIADIVNRLDPDVDVVFAGHTHQA 241 (288) T ss_pred CHHHHHHH-HHHHHHHCCCCEEEEEeCCCCCCCCCCccccccChhHHHHHhhcCCCCCEEEeCccCcc Confidence 44444333 3333344579999999999976 3455555688888877666554 No 120 >TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing). The member from Methanococcus jannaschii contains an intein. Probab=40.53 E-value=45 Score=26.17 Aligned_cols=34 Identities=24% Similarity=0.232 Sum_probs=26.0 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) .-+.+|++|.||.|.-. .+|-+ .+++|++|.++. T Consensus 338 ~~dlvI~iS~SG~T~e~v~a~~~ak~~-ga~~IaIT~~~~ 376 (607) T TIGR01135 338 KDTLVIAISQSGETADTLAALRLAKEL-GAKTLGICNVPG 376 (607) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHc-CCcEEEEECCCC Confidence 34688999999998764 45556 589999998753 No 121 >PRK12483 threonine dehydratase; Reviewed Probab=40.07 E-value=81 Score=24.81 Aligned_cols=42 Identities=24% Similarity=0.184 Sum_probs=32.7 Q ss_pred HHHHHHHhcC--CcEEEEecCCchHHHHHHh----hCCCCCEEEEecC Q 039146 31 SAVRSAIKVK--ASAIICFTSSGRAARLIAK----YRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~~--~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~~ 72 (84) -+.++.+.++ .++||++.-+|.+.--+++ .+|.+.||+|-+. T Consensus 175 ig~EI~eQ~~~~~D~VvvpvGgGGliaGia~~~K~~~p~vkVIGVep~ 222 (521) T PRK12483 175 VAMEILRQHPGPLDAIFVPVGGGGLIAGIAAYVKYVRPEIKVIGVEPD 222 (521) T ss_pred HHHHHHHHhCCCCCEEEEecCccHHHHHHHHHHHHhCCCCEEEEEEeC Confidence 3566777764 7999999999998766654 4899999999653 No 122 >COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane] Probab=39.66 E-value=1.4e+02 Score=21.29 Aligned_cols=52 Identities=17% Similarity=0.090 Sum_probs=32.8 Q ss_pred hcCCCCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEE Q 039146 17 YVGEPMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 17 ~~~~~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~ 69 (84) ....+.+..+.+..++..+. ..+++.|+..|++-+--.-==+-.-+.|+|-. T Consensus 53 ~~~~w~~~~~~L~~~a~~Le-~~GAd~i~l~~NT~H~~~d~iq~~~~iPllhI 104 (230) T COG1794 53 RAGEWDEAGEILIDAAKKLE-RAGADFIVLPTNTMHKVADDIQKAVGIPLLHI 104 (230) T ss_pred ccCccccHHHHHHHHHHHHH-hcCCCEEEEeCCcHHHHHHHHHHhcCCCeehH Confidence 33456667777877777765 78999999988754332222233446666643 No 123 >PRK00973 glucose-6-phosphate isomerase; Provisional Probab=39.28 E-value=33 Score=26.42 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=22.8 Q ss_pred cEEEEecCCchHHHHHHhhC------------CCCCEEEEecC Q 039146 42 SAIICFTSSGRAARLIAKYR------------PTMPVLSVVIP 72 (84) Q Consensus 42 ~aIv~~T~sG~ta~~iS~~R------------p~~pIia~t~~ 72 (84) -.++|.|.||.|.--++.|| ....++++|.+ T Consensus 134 Tl~iviSKSGtT~ET~~~f~~~~~~l~~~g~~~~~~~vaiTd~ 176 (446) T PRK00973 134 TLFNVISKSGNTAETLANYLIIRGILEKLGLDPKKHLVFTTDP 176 (446) T ss_pred EEEEEEeCCCCCHHHHHHHHHHHHHHHhcCccccceEEEEcCC Confidence 47889999999987666554 44568888774 No 124 >PRK06372 translation initiation factor IF-2B subunit delta; Provisional Probab=39.12 E-value=47 Score=23.76 Aligned_cols=39 Identities=10% Similarity=0.140 Sum_probs=29.3 Q ss_pred CCcEEE----EecCCchHHHHHHhhCCCCCEEEEecChhhhcc Q 039146 40 KASAII----CFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQ 78 (84) Q Consensus 40 ~~~aIv----~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~ 78 (84) ++++|. ++.+.|.....++..+-++|+|++|.+.+..+. T Consensus 158 GAd~V~~nG~v~nkvGT~~~Al~A~~~~vPv~V~~~s~Kf~~~ 200 (253) T PRK06372 158 GSDSVLYDGGLIHKNGTFPLALCARYLKKPFYSLTISMKIERN 200 (253) T ss_pred CccEEecCCCEeehhhHHHHHHHHHHcCCCEEEEeeccccCCC Confidence 566654 567888888877766779999999988777643 No 125 >COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism] Probab=39.10 E-value=80 Score=21.81 Aligned_cols=38 Identities=24% Similarity=0.410 Sum_probs=28.6 Q ss_pred HHHhcCCcEEEEe------cCCchHHHHHHhhCCCCCEEEEecC Q 039146 35 SAIKVKASAIICF------TSSGRAARLIAKYRPTMPVLSVVIP 72 (84) Q Consensus 35 ~a~~~~~~aIv~~------T~sG~ta~~iS~~Rp~~pIia~t~~ 72 (84) ....++.++||+- ...|.+...+-++..+.||+++|=- T Consensus 40 ~~~~~~pd~iviSPGPG~P~d~G~~~~~i~~~~~~~PiLGVCLG 83 (191) T COG0512 40 LIEALKPDAIVISPGPGTPKDAGISLELIRRFAGRIPILGVCLG 83 (191) T ss_pred HHhhcCCCEEEEcCCCCChHHcchHHHHHHHhcCCCCEEEECcc Confidence 4556677877652 2677788899999888999999843 No 126 >cd08187 BDH Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction was 50-fold lower than that in the forward direction. The NADH-BDH had higher activity with longer chained aldehydes and was inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Since members of this superfamily use different divalent ions, preferentially iron or zinc, it has been suggested to be renamed to family III metal-dependent polyol dehydrogenases. Probab=38.70 E-value=1.2e+02 Score=22.37 Aligned_cols=48 Identities=17% Similarity=0.126 Sum_probs=34.1 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh---------------------CCCCCEEEEecC Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY---------------------RPTMPVLSVVIP 72 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~---------------------Rp~~pIia~t~~ 72 (84) ++.......++..+...++++||. -.|.++.-++|. +|..|+|++-+. T Consensus 69 ~p~~~~v~~~~~~~~~~~~D~IIa--iGGGS~iD~aK~ia~~~~~~~~~~~~~~~~~~~~~~~P~iaIPTT 137 (382) T cd08187 69 NPRLETVREGIELCKEEKVDFILA--VGGGSVIDSAKAIAAGAPYDGDVWDFFTGKAKIEKALPVGTVLTL 137 (382) T ss_pred CCCHHHHHHHHHHHHHcCCCEEEE--eCChHHHHHHHHHHhHhhCCCCHHHHhcccCCCCCCCCEEEEeCC Confidence 444556666777888889998887 467766655553 577899998543 No 127 >PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional Probab=38.08 E-value=55 Score=26.03 Aligned_cols=33 Identities=24% Similarity=0.341 Sum_probs=25.5 Q ss_pred CcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 41 ASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) -+.+|++|.||.|+-. .+|-+ .+|+|++|.+.. T Consensus 370 ~~lvI~ISqSGeT~d~i~al~~ak~~-Ga~~IaITn~~~ 407 (640) T PTZ00295 370 DAGVIFISQSGETLDVVRALNLADEL-NLPKISVVNTVG 407 (640) T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHHC-CCCEEEEECCCC Confidence 4688999999998775 44545 589999998764 No 128 >PRK10886 DnaA initiator-associating protein DiaA; Provisional Probab=37.71 E-value=1.3e+02 Score=20.42 Aligned_cols=52 Identities=17% Similarity=0.407 Sum_probs=34.9 Q ss_pred HHHHHHHHHHHHHhc-CCcEEEEecCCc--hHHHHHHh-----h---CCCCCEEEEecChhhh Q 039146 25 LESITSSAVRSAIKV-KASAIICFTSSG--RAARLIAK-----Y---RPTMPVLSVVIPQLKT 76 (84) Q Consensus 25 ~~~ia~~a~~~a~~~-~~~aIv~~T~sG--~ta~~iS~-----~---Rp~~pIia~t~~~~~~ 76 (84) .+.+..++-.++..+ +.+-|.++-..| .+|+.++. | ||..|.++++.|.... T Consensus 24 ~~~i~~a~~~l~~~l~~~~rI~~~G~GgSa~~A~~~a~~l~~~~~~~r~gl~a~~l~~d~~~~ 86 (196) T PRK10886 24 PDAISRAAMTLVQSLLNGNKILCCGNGTSAANAQHFAASMINRFETERPSLPAIALNTDNVVL 86 (196) T ss_pred HHHHHHHHHHHHHHHHcCCEEEEEECcHHHHHHHHHHHHHhccccccCCCcceEEecCcHHHH Confidence 466777777776664 666677775443 35666663 2 9999999997666554 No 129 >PTZ00394 glucosamine-fructose-6-phosphate aminotransferase; Provisional Probab=37.60 E-value=52 Score=26.55 Aligned_cols=32 Identities=13% Similarity=0.064 Sum_probs=25.4 Q ss_pred cEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 42 SAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 42 ~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +.+|++|.||.|+-. .+|-+ .+++|++|.+.. T Consensus 403 dlvI~ISqSGeT~dtl~Al~~Ak~~-Ga~tIaITn~~~ 439 (670) T PTZ00394 403 DVCFFVSQSGETADTLMALQLCKEA-GAMCVGITNVVG 439 (670) T ss_pred CEEEEEECCcCcHHHHHHHHHHHHC-CCcEEEEECCCC Confidence 688899999998865 44656 589999998754 No 130 >COG4800 Predicted transcriptional regulator with an HTH domain [Transcription] Probab=37.41 E-value=1.1e+02 Score=20.56 Aligned_cols=41 Identities=22% Similarity=0.317 Sum_probs=31.6 Q ss_pred HHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhc Q 039146 33 VRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTN 77 (84) Q Consensus 33 ~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r 77 (84) +--|+.-++++|||..-=..|+-.+- ++||+.+-|...+.. T Consensus 120 aVrAErdGakaiVCAPIvS~t~EKiv----nvPV~tIiPk~s~i~ 160 (170) T COG4800 120 AVRAERDGAKAIVCAPIVSSTAEKIV----NVPVITIIPKKSVIE 160 (170) T ss_pred HHHhhhcccceEEecccccHHHHHHc----CCceEEEeccHHHHH Confidence 34577889999999887777877776 899998887655443 No 131 >cd08194 Fe-ADH6 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. Probab=37.23 E-value=1.4e+02 Score=21.94 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=32.4 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHh---------------------hCCCCCEEEEec Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAK---------------------YRPTMPVLSVVI 71 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~---------------------~Rp~~pIia~t~ 71 (84) ++.......++..+...+++.||. -.|.++.-++| +++..|+|++-+ T Consensus 63 ~p~~~~v~~~~~~~~~~~~D~IIa--iGGGS~~D~AKaia~~~~~~~~~~~~~~~~~~~~~~~P~i~IPT 130 (375) T cd08194 63 EPTDESVEEGVKLAKEGGCDVIIA--LGGGSPIDTAKAIAVLATNGGSIRDYKGPRIVDKPGLPLIAIPT 130 (375) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEE--eCCchHHHHHHHHHHHHhCCCCHHHHhCcccccCCCCCEEEECC Confidence 344455556677788889998887 46766665555 467789998843 No 132 >cd01561 CBS_like CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine. Probab=37.13 E-value=1.1e+02 Score=21.43 Aligned_cols=42 Identities=12% Similarity=0.158 Sum_probs=32.3 Q ss_pred HHHHHHHhcC--CcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 31 SAVRSAIKVK--ASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~~--~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) -+.++.+.++ .++||+..-+|.+.. .+..+.|...|+++-+. T Consensus 149 ~~~Ei~~ql~~~~d~vv~~~G~Gg~~~Gi~~~~~~~~~~~~vi~Ve~~ 196 (291) T cd01561 149 TAPEIWEQLDGKVDAFVAGVGTGGTITGVARYLKEKNPNVRIVGVDPV 196 (291) T ss_pred HHHHHHHHcCCCCCEEEEeCChHHHHHHHHHHHHHhCCCCEEEEEecC Confidence 3567777775 799999999998764 45556789999999765 No 133 >TIGR01138 cysM cysteine synthase B. Alternate name: O-acetylserine (thiol)-lyase Probab=36.50 E-value=1.1e+02 Score=21.68 Aligned_cols=42 Identities=2% Similarity=0.067 Sum_probs=31.3 Q ss_pred HHHHHHHhcC--CcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 31 SAVRSAIKVK--ASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~~--~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) -+.++.+.++ .++||+..-+|.+.. .+..+.|.+.||++-+. T Consensus 152 ~~~Ei~~q~~~~~d~iv~~vG~Gg~~~Gv~~~lk~~~~~~kvi~Vep~ 199 (290) T TIGR01138 152 TGPEIWQQTGGRITHFVSSMGTTGTIMGVSRFLKEQNPPVQIVGLQPE 199 (290) T ss_pred HHHHHHHHcCCCCCEEEECCCchHHHHHHHHHHHHhCCCCEEEEEeCC Confidence 4556666664 789999999998765 44556899999999663 No 134 >PRK14075 pnk inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=36.47 E-value=70 Score=22.57 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=25.4 Q ss_pred cCCcEEEEecCCchHHHHHHhhCCCCCEEEEe Q 039146 39 VKASAIICFTSSGRAARLIAKYRPTMPVLSVV 70 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t 70 (84) .+++.||++--+|..-+...++ .+||+++- T Consensus 40 ~~~d~vi~iGGDGT~L~a~~~~--~~Pilgin 69 (256) T PRK14075 40 VTADLIIVVGGDGTVLKAAKKV--GTPLVGFK 69 (256) T ss_pred CCCCEEEEECCcHHHHHHHHHc--CCCEEEEe Confidence 3678999999999988877777 99999984 No 135 >TIGR00162 conserved hypothetical protein TIGR00162. This ortholog set includes MJ1210 from Methanococcus jannaschii and AF0525 from Archaeoglobus fulgidus, but not MJ0106 or AF1251. Probab=36.20 E-value=45 Score=22.57 Aligned_cols=50 Identities=16% Similarity=0.127 Sum_probs=35.3 Q ss_pred HHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 26 ESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) ..++.+.+..+.+++++.||++ .|..+ -.-.-||. |+++..+++..+.|. T Consensus 33 ~e~a~~vld~a~~~gv~~iitL--gG~~~-~~~~trp~--V~~~at~~el~~~l~ 82 (188) T TIGR00162 33 YELVNAIIDVAKKYGARMIYTL--GGYGV-GKLVEEPY--VYGAATSPELVEELK 82 (188) T ss_pred HHHHHHHHHHHHHcCCCEEEEe--cCCcC-CCCCCCCc--eEEEeCCHHHHHHHH Confidence 3499999999999999988875 34322 11223544 889988888776654 No 136 >PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A .... Probab=36.14 E-value=93 Score=18.26 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=34.2 Q ss_pred HHHHHHHhcCCcEEEEecCCchHH----HHHHhhCCCCCEEEEecChhhhccc Q 039146 31 SAVRSAIKVKASAIICFTSSGRAA----RLIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 31 ~a~~~a~~~~~~aIv~~T~sG~ta----~~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) ...+-+.--+++++|+.|.+-... ..+-..-|..+|++...++.-...| T Consensus 53 ~~l~~a~i~~a~~vv~~~~~d~~n~~~~~~~r~~~~~~~ii~~~~~~~~~~~l 105 (116) T PF02254_consen 53 EVLERAGIEKADAVVILTDDDEENLLIALLARELNPDIRIIARVNDPENAELL 105 (116) T ss_dssp HHHHHTTGGCESEEEEESSSHHHHHHHHHHHHHHTTTSEEEEEESSHHHHHHH T ss_pred hHHhhcCccccCEEEEccCCHHHHHHHHHHHHHHCCCCeEEEEECCHHHHHHH Confidence 344455555889999998665443 3444468899999999988776544 No 137 >PLN02929 NADH kinase Probab=35.91 E-value=80 Score=23.18 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=28.2 Q ss_pred CCcEEEEecCCchHHHHHHhhCCCCCEEEEecCh Q 039146 40 KASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~ 73 (84) +++.||++--+|..-+....+...+||+++-.++ T Consensus 64 ~~Dlvi~lGGDGT~L~aa~~~~~~iPvlGIN~Gp 97 (301) T PLN02929 64 DVDLVVAVGGDGTLLQASHFLDDSIPVLGVNSDP 97 (301) T ss_pred CCCEEEEECCcHHHHHHHHHcCCCCcEEEEECCC Confidence 6799999999999888777776679999997653 No 138 >PLN00011 cysteine synthase Probab=35.75 E-value=1.3e+02 Score=21.77 Aligned_cols=42 Identities=12% Similarity=0.081 Sum_probs=31.5 Q ss_pred HHHHHHHhc--CCcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 31 SAVRSAIKV--KASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~--~~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) .+.++.+.+ +.++||+..-+|.|.. .+-.++|...||++-+. T Consensus 163 ~~~EI~~q~~~~~D~iv~~vGtGGt~aGi~~~lk~~~~~~kvigVe~~ 210 (323) T PLN00011 163 TGPEIWRDSAGKVDILVAGVGTGGTATGVGKFLKEKNKDIKVCVVEPV 210 (323) T ss_pred HHHHHHHhcCCCCCEEEEeCCchHHHHHHHHHHHhhCCCCEEEEEecC Confidence 455666554 5899999999997764 45556899999999764 No 139 >cd08179 NADPH_BDH NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria. NADPH-dependent butanol dehydrogenase (BDH) is involved in the butanol and ethanol formation pathway of some bacteria. The fermentation process is characterized by an acid producing growth phase, followed by a solvent producing phase. The latter phase is associated with the induction of solventogenic enzymes such as butanol dehydrogenase. The activity of the enzymes require NADPH as cofactor, as well as divalent ions zinc or iron. This family is a member of the iron-containing alcohol dehydrogenase superfamily. Protein structure has a dehydroquinate synthase-like fold. Probab=35.71 E-value=1.4e+02 Score=22.00 Aligned_cols=34 Identities=12% Similarity=0.049 Sum_probs=23.0 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHH Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIA 58 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS 58 (84) ++.......++..+...++++||.+ .|.++.-++ T Consensus 64 ~p~~~~v~~~~~~~~~~~~D~IIav--GGGSviD~A 97 (375) T cd08179 64 DPSVETVLKGAEAMREFEPDWIIAL--GGGSPIDAA 97 (375) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEEe--CCccHHHHH Confidence 4555666667788888899988874 555444333 No 140 >COG0589 UspA Universal stress protein UspA and related nucleotide-binding proteins [Signal transduction mechanisms] Probab=35.40 E-value=99 Score=18.39 Aligned_cols=39 Identities=23% Similarity=0.238 Sum_probs=27.0 Q ss_pred HHHHHHHHhcCCcEEEEecC---------CchHHHHHHhhCCCCCEEEE Q 039146 30 SSAVRSAIKVKASAIICFTS---------SGRAARLIAKYRPTMPVLSV 69 (84) Q Consensus 30 ~~a~~~a~~~~~~aIv~~T~---------sG~ta~~iS~~Rp~~pIia~ 69 (84) ......+.+.+++.||+-+. -|.++..+.+.- +||++.+ T Consensus 103 ~~i~~~a~~~~adliV~G~~g~~~l~~~llGsvs~~v~~~~-~~pVlvv 150 (154) T COG0589 103 EEILELAEEEDADLIVVGSRGRSGLSRLLLGSVAEKVLRHA-PCPVLVV 150 (154) T ss_pred HHHHHHHHHhCCCEEEECCCCCccccceeeehhHHHHHhcC-CCCEEEE Confidence 34455566668898888774 567777777655 6777766 No 141 >PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional Probab=34.68 E-value=1.4e+02 Score=19.96 Aligned_cols=40 Identities=10% Similarity=0.126 Sum_probs=27.0 Q ss_pred HHHhcCCcEEEEe------cCC-chHHHHHHhhCCCCCEEEEecChh Q 039146 35 SAIKVKASAIICF------TSS-GRAARLIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 35 ~a~~~~~~aIv~~------T~s-G~ta~~iS~~Rp~~pIia~t~~~~ 74 (84) ......++.+++. -.+ ....+.+.+..|.++|+.++.... T Consensus 42 ~~~~~~pDlvLlDl~~~l~~~~g~~~i~~i~~~~p~~~iivlt~~~~ 88 (207) T PRK15411 42 ACDSLRPSVVFINEDCFIHDASNSQRIKQIINQHPNTLFIVFMAIAN 88 (207) T ss_pred HHhccCCCEEEEeCcccCCCCChHHHHHHHHHHCCCCeEEEEECCCc Confidence 3455567888777 123 345557777889999999987654 No 142 >PLN02970 serine racemase Probab=34.47 E-value=1.4e+02 Score=21.66 Aligned_cols=42 Identities=21% Similarity=0.197 Sum_probs=32.6 Q ss_pred HHHHHHHhc-CCcEEEEecCCchHHHHHHhh----CCCCCEEEEecC Q 039146 31 SAVRSAIKV-KASAIICFTSSGRAARLIAKY----RPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~-~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~ 72 (84) -+.++.+.+ ..++||+..-+|.+..-++++ .|...||++-+. T Consensus 165 ~g~Ei~~ql~~~D~vv~~vG~GG~~~Gi~~~lk~~~~~~kvi~Vep~ 211 (328) T PLN02970 165 IALEFLEQVPELDVIIVPISGGGLISGIALAAKAIKPSIKIIAAEPK 211 (328) T ss_pred HHHHHHHhccCCCEEEEeeCchHHHHHHHHHHHhcCCCCEEEEEEEC Confidence 345555555 479999999999988777766 899999999663 No 143 >PLN03013 cysteine synthase Probab=34.36 E-value=1.3e+02 Score=23.20 Aligned_cols=42 Identities=14% Similarity=0.149 Sum_probs=30.9 Q ss_pred HHHHHHhc--CCcEEEEecCCchHHH----HHHhhCCCCCEEEEecCh Q 039146 32 AVRSAIKV--KASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 32 a~~~a~~~--~~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~~ 73 (84) +.++.+.+ +.++||+..-+|.+.. .+-...|++.|+++-+.. T Consensus 270 g~EI~eq~~~~~D~vV~~vGtGGtisGiar~lKe~~P~vkVigVep~g 317 (429) T PLN03013 270 GPEIWDDTKGKVDIFVAGIGTGGTITGVGRFIKEKNPKTQVIGVEPTE 317 (429) T ss_pred HHHHHHhcCCCCCEEEEeCCccHHHHHHHHHHHhhCCCCEEEEEEeCC Confidence 45566655 4899999999996654 555557999999996643 No 144 >PRK14096 pgi glucose-6-phosphate isomerase; Provisional Probab=34.35 E-value=47 Score=26.32 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=28.9 Q ss_pred cCCcEEEEecCCchHHHHHHhhC------------CCCCEEEEecChhhhcccc Q 039146 39 VKASAIICFTSSGRAARLIAKYR------------PTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~~R------------p~~pIia~t~~~~~~r~L~ 80 (84) +.--.+||.|.||.|.-.++.++ ....++|+|.+....++++ T Consensus 167 ~~~TLviViSKSGtT~ET~~n~~~~~~~l~~~G~~~~~h~VAVT~~~s~L~~~A 220 (528) T PRK14096 167 LATTLVVVISKSGGTPETRNGMLEAKAAYEAAGLDFASHAVAITMKGSKLDQLA 220 (528) T ss_pred CCcEEEEEEeCCCCCHHHHHHHHHHHHHHHhhcccccceEEEEECCCcHHhhhc Confidence 44457888999999876555443 2357889988666566655 No 145 >cd08193 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene. Probab=34.19 E-value=1.7e+02 Score=21.53 Aligned_cols=48 Identities=25% Similarity=0.344 Sum_probs=32.8 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh---------------------CCCCCEEEEecC Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY---------------------RPTMPVLSVVIP 72 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~---------------------Rp~~pIia~t~~ 72 (84) ++.......+++.+.+.++++||. -.|.++.-++|+ ++..|+|++-+. T Consensus 66 ~p~~~~v~~~~~~~~~~~~D~IIa--iGGGs~iD~aK~ia~~~~~~~~~~~~~~~~~~~~~~~p~i~IPTT 134 (376) T cd08193 66 DPPEAVVEAAVEAARAAGADGVIG--FGGGSSMDVAKLVAVLAGSDQPLADMYGVDLVAGPRLPLILVPTT 134 (376) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEE--eCCchHHHHHHHHHHHHHCCCCHHHHhCCCccCCCCCCEEEeCCC Confidence 344555556677777889998887 467766655554 467899988443 No 146 >TIGR02638 lactal_redase lactaldehyde reductase. This clade of genes encoding iron-containing alcohol dehydrogenase (pfam00465) proteins is generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in lactaldehyde which is reduced by this enzyme to 1,2 propanediol. This protein is alternatively known by the name 1,2 propanediol oxidoreductase. This enzyme is active under anaerobic conditions in E. coli while being inactivated by reactive oxygen species under aerobic conditions. Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase. Probab=34.00 E-value=1.8e+02 Score=21.49 Aligned_cols=35 Identities=17% Similarity=0.110 Sum_probs=24.8 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAK 59 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~ 59 (84) ++.......+++.+...++++||. -.|.++.-++| T Consensus 69 ~p~~~~v~~~~~~~~~~~~D~Iia--iGGGSviD~aK 103 (379) T TIGR02638 69 NPTITVVKAGVAAFKASGADYLIA--IGGGSPIDTAK 103 (379) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEE--eCChHHHHHHH Confidence 444555666778888889998887 47766666664 No 147 >cd01562 Thr-dehyd Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly converted into NH4+. The direct deamination is catalyzed by threonine dehydratase, in which pyridoxal phosphate (PLP) is the prosthetic group. Threonine dehydratase is widely distributed in all three major phylogenetic divisions. Probab=33.75 E-value=1.2e+02 Score=21.33 Aligned_cols=42 Identities=19% Similarity=0.145 Sum_probs=31.8 Q ss_pred HHHHHHHhc-CCcEEEEecCCchHHHHHHhh----CCCCCEEEEecC Q 039146 31 SAVRSAIKV-KASAIICFTSSGRAARLIAKY----RPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~-~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~ 72 (84) .+.++...+ +.++||+..-+|.|..-++++ .|...|+++.+. T Consensus 155 ~~~Ei~~q~~~~d~vv~~vGtGgt~~Gi~~~lk~~~~~~kvigv~~~ 201 (304) T cd01562 155 IGLEILEQVPDLDAVFVPVGGGGLIAGIATAVKALSPNTKVIGVEPE 201 (304) T ss_pred HHHHHHHhcCCCCEEEEecCHHHHHHHHHHHHHHhCCCCEEEEEEEC Confidence 355666666 479999999999988765554 788899998773 No 148 >PRK06381 threonine synthase; Validated Probab=33.65 E-value=1.3e+02 Score=21.45 Aligned_cols=45 Identities=11% Similarity=-0.000 Sum_probs=33.0 Q ss_pred HHHHHHHHHHhcC--CcEEEEecCCchHHHHHHhh----------CCCCCEEEEecC Q 039146 28 ITSSAVRSAIKVK--ASAIICFTSSGRAARLIAKY----------RPTMPVLSVVIP 72 (84) Q Consensus 28 ia~~a~~~a~~~~--~~aIv~~T~sG~ta~~iS~~----------Rp~~pIia~t~~ 72 (84) ....+.++.+.++ .++||+..-+|.+.--++++ .|...|+++.+. T Consensus 152 ~~t~a~Ei~~ql~~~~D~vv~~vGtGgt~~Gl~~~~~~~~~~g~~~~~~~vigVe~~ 208 (319) T PRK06381 152 YSAIAYEIYEALGDVPDAVAVPVGNGTTLAGIYHGFRRLYDRGKTSRMPRMIGVSTS 208 (319) T ss_pred HHHHHHHHHHHhCCCCCEEEEcCCccHHHHHHHHHHHHHHhCCCcCCCCEEEEEeeC Confidence 3444556666664 69999999999998866664 577889988653 No 149 >cd08176 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to Probab=33.47 E-value=1.6e+02 Score=21.72 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=31.6 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh---------------------CCCCCEEEEec Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY---------------------RPTMPVLSVVI 71 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~---------------------Rp~~pIia~t~ 71 (84) ++.......++..+...++++||. -.|.++.-++|. ++..|+|++-+ T Consensus 68 ~p~~~~v~~~~~~~~~~~~D~IIa--vGGGS~iD~aK~ia~~~~~~~~~~~~~~~~~~~~~~~P~i~IPT 135 (377) T cd08176 68 NPTITNVKDGLAVFKKEGCDFIIS--IGGGSPHDCAKAIGIVATNGGDIRDYEGVAKSKKPAVPIVAINT 135 (377) T ss_pred CCCHHHHHHHHHHHHhcCCCEEEE--eCCcHHHHHHHHHHHHHhCCCCHHHHhCcCccCCCCCCEEEeCC Confidence 344444555677788889998887 466666555542 46789998844 No 150 >PRK10537 voltage-gated potassium channel; Provisional Probab=33.31 E-value=1.1e+02 Score=23.08 Aligned_cols=47 Identities=11% Similarity=0.162 Sum_probs=32.6 Q ss_pred HHHHHhcCCcEEEEecCCchH----HHHHHhhCCCCCEEEEecChhhhccc Q 039146 33 VRSAIKVKASAIICFTSSGRA----ARLIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 33 ~~~a~~~~~~aIv~~T~sG~t----a~~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) .+-|.--+++++++.|.+-.. +....+..|++.|++.+.+++-..+| T Consensus 295 L~~AgI~~A~aVI~~t~dD~~Nl~ivL~ar~l~p~~kIIa~v~~~~~~~~L 345 (393) T PRK10537 295 LKKAGAARARAILALRDNDADNAFVVLAAKEMSSDVKTVAAVNDSKNLEKI 345 (393) T ss_pred HHhcCcccCCEEEEcCCChHHHHHHHHHHHHhCCCCcEEEEECCHHHHHHH Confidence 344444478999998876543 33445677999999999988766544 No 151 >PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed Probab=33.09 E-value=1.4e+02 Score=21.54 Aligned_cols=34 Identities=15% Similarity=0.218 Sum_probs=25.2 Q ss_pred CCcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 40 KASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) +-+.+|.+|.||+|... .+|-+ .+++|++|.++. T Consensus 131 ~~DvvI~IS~SG~T~~vi~al~~Ak~~-Ga~tI~IT~~~~ 169 (299) T PRK05441 131 AKDVVVGIAASGRTPYVIGALEYARER-GALTIGISCNPG 169 (299) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEECCCC Confidence 45788999999998764 45555 689999987643 No 152 >COG2222 AgaS Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane] Probab=32.68 E-value=43 Score=24.92 Aligned_cols=33 Identities=18% Similarity=0.237 Sum_probs=24.7 Q ss_pred cEEEEecCCchHHHHHHhh----CCCCCEEEEecChh Q 039146 42 SAIICFTSSGRAARLIAKY----RPTMPVLSVVIPQL 74 (84) Q Consensus 42 ~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~~~ 74 (84) .++|++++||.|+-.++.. .+.+.+|++|..+. T Consensus 89 ~lvi~~S~SG~TpE~vaa~~~a~~~ga~~i~lT~~~d 125 (340) T COG2222 89 SLVIAFSQSGNTPESVAAAELAKEGGALTIALTNEED 125 (340) T ss_pred eEEEEEeCCCCCHHHHHHHHHhccCCCeEEEEecCCC Confidence 4788999999988766544 45588999886554 No 153 >PLN02981 glucosamine:fructose-6-phosphate aminotransferase Probab=32.17 E-value=70 Score=25.84 Aligned_cols=33 Identities=15% Similarity=0.104 Sum_probs=25.0 Q ss_pred CcEEEEecCCchHHHH-----HHhhCCCCCEEEEecChh Q 039146 41 ASAIICFTSSGRAARL-----IAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~-----iS~~Rp~~pIia~t~~~~ 74 (84) -+.+|++|.||.|.-. .+|-+ .+++|++|.+.. T Consensus 411 ~~lvI~ISqSGeT~eti~Al~~Ak~~-Ga~~IaITn~~~ 448 (680) T PLN02981 411 EDTAVFVSQSGETADTLRALEYAKEN-GALCVGITNTVG 448 (680) T ss_pred CCeEEEEeCCcCCHHHHHHHHHHHHC-CCcEEEEECCCC Confidence 3578889999998765 45555 589999987653 No 154 >PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional Probab=31.78 E-value=64 Score=25.58 Aligned_cols=32 Identities=25% Similarity=0.362 Sum_probs=24.6 Q ss_pred CCcEEEEecCCchHHH-----HHHhhCCCCCEEEEecC Q 039146 40 KASAIICFTSSGRAAR-----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~-----~iS~~Rp~~pIia~t~~ 72 (84) .-+.+|++|.+|++.. ..+|-| .++||++|.+ T Consensus 515 ~~DvvI~iS~sG~t~e~i~~~~~Ak~~-Ga~vIaIT~~ 551 (638) T PRK14101 515 KGDVIVAVSKSGRAPELLRVLDVAMQA-GAKVIAITSS 551 (638) T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHC-CCeEEEEcCC Confidence 4478999999999854 445555 7999999974 No 155 >TIGR01137 cysta_beta cystathionine beta-synthase. Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. The function of any bacterial member included in this family is proposed but not proven. Probab=31.59 E-value=1.4e+02 Score=22.26 Aligned_cols=41 Identities=12% Similarity=0.118 Sum_probs=31.5 Q ss_pred HHHHHHHhc--CCcEEEEecCCchHHHHHHh----hCCCCCEEEEec Q 039146 31 SAVRSAIKV--KASAIICFTSSGRAARLIAK----YRPTMPVLSVVI 71 (84) Q Consensus 31 ~a~~~a~~~--~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~ 71 (84) .+.++.+.+ +.++||+..-+|.|..-+++ .+|.+.|+++-+ T Consensus 159 ~~~Ei~~q~~~~~d~vv~~vG~Gg~~~G~~~~~~~~~~~~~vi~ve~ 205 (454) T TIGR01137 159 TGPEILEQCEGKLDMFVAGAGTGGTITGIARYLKESNPKCRIVGADP 205 (454) T ss_pred hHHHHHHHhCCCCCEEEEecCchHHHHHHHHHHHhhCCCCEEEEEec Confidence 355666666 47999999999988764444 679999999966 No 156 >PRK09860 putative alcohol dehydrogenase; Provisional Probab=31.42 E-value=2e+02 Score=21.35 Aligned_cols=47 Identities=13% Similarity=0.283 Sum_probs=31.7 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh---------------------CCCCCEEEEec Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY---------------------RPTMPVLSVVI 71 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~---------------------Rp~~pIia~t~ 71 (84) ++.......+++.+...+++.||.+ .|.++.-.+|. ++..|+|++-+ T Consensus 71 np~~~~v~~~~~~~~~~~~D~Iiai--GGGS~iD~AK~ia~~~~~~~~~~~~~~~~~~~~~~~p~iaIPT 138 (383) T PRK09860 71 NPTTENVAAGLKLLKENNCDSVISL--GGGSPHDCAKGIALVAANGGDIRDYEGVDRSAKPQLPMIAINT 138 (383) T ss_pred CcCHHHHHHHHHHHHHcCCCEEEEe--CCchHHHHHHHHHHHHHCCCCHHHHhCcCccCCCCCCEEEEeC Confidence 4455555677888889999988874 66555444432 46789998843 No 157 >KOG2541 consensus Palmitoyl protein thioesterase [Lipid transport and metabolism; Posttranslational modification, protein turnover, chaperones] Probab=31.39 E-value=1.5e+02 Score=21.92 Aligned_cols=45 Identities=13% Similarity=0.246 Sum_probs=33.4 Q ss_pred HHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEe Q 039146 26 ESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVV 70 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t 70 (84) +.++.....+.+..+-=-||.++..|--+|.+..+.|.-||.-+. T Consensus 78 ~~~ce~v~~m~~lsqGynivg~SQGglv~Raliq~cd~ppV~n~I 122 (296) T KOG2541|consen 78 DVACEKVKQMPELSQGYNIVGYSQGGLVARALIQFCDNPPVKNFI 122 (296) T ss_pred HHHHHHHhcchhccCceEEEEEccccHHHHHHHHhCCCCCcceeE Confidence 344444445555554455899999999999999999998887654 No 158 >PRK10624 L-1,2-propanediol oxidoreductase; Provisional Probab=31.12 E-value=2.1e+02 Score=21.13 Aligned_cols=34 Identities=15% Similarity=0.092 Sum_probs=24.0 Q ss_pred HHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHh Q 039146 24 HLESITSSAVRSAIKVKASAIICFTSSGRAARLIAK 59 (84) Q Consensus 24 ~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~ 59 (84) +.......+++.+...++++||. -.|.++.-++| T Consensus 71 p~~~~v~~~~~~~~~~~~D~IIa--iGGGS~iD~aK 104 (382) T PRK10624 71 PTIEVVKEGVEVFKASGADYLIA--IGGGSPQDTCK 104 (382) T ss_pred cCHHHHHHHHHHHHhcCCCEEEE--eCChHHHHHHH Confidence 33445556677888889998887 57777776665 No 159 >PRK10717 cysteine synthase A; Provisional Probab=30.84 E-value=1.5e+02 Score=21.33 Aligned_cols=42 Identities=7% Similarity=0.153 Sum_probs=31.6 Q ss_pred HHHHHHHhcC--CcEEEEecCCchHHHH----HHhhCCCCCEEEEecC Q 039146 31 SAVRSAIKVK--ASAIICFTSSGRAARL----IAKYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~~--~~aIv~~T~sG~ta~~----iS~~Rp~~pIia~t~~ 72 (84) .+.++.+.++ .++||+..-+|.+..- +..++|++.|+++-+. T Consensus 165 ~a~Ei~~ql~~~~d~iv~~vG~GG~~~Gi~~~~k~~~~~~~vi~Vep~ 212 (330) T PRK10717 165 TGPEIWEQTDGKVDGFVCAVGTGGTLAGVSRYLKETNPKVKIVLADPT 212 (330) T ss_pred HHHHHHHhcCCCCCEEEEecCchHHHHHHHHHHHHhCCCCEEEEEcCC Confidence 3666777774 7999999999987664 4445799999998653 No 160 >cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site. Probab=30.60 E-value=59 Score=21.48 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=18.8 Q ss_pred CCcEEEEecCCchHHHHHHhhC Q 039146 40 KASAIICFTSSGRAARLIAKYR 61 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~R 61 (84) +...++++|++|..++.+..-+ T Consensus 42 ~tsGlll~t~dg~~~~~L~~p~ 63 (164) T cd02554 42 DSEGLILLTNDGDLVNKILHAD 63 (164) T ss_pred CCeeEEEEEcCHHHHHHHhhhh Confidence 6789999999999999997533 No 161 >PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV). Probab=29.85 E-value=37 Score=19.57 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=20.6 Q ss_pred hcCCcEEEEecCCchHHHH-HHhhCCCC Q 039146 38 KVKASAIICFTSSGRAARL-IAKYRPTM 64 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~-iS~~Rp~~ 64 (84) .-.++-|++.+.+|++-+. ..++||-. T Consensus 17 ~G~a~~V~v~s~~Gr~v~~Pa~~lRpFv 44 (68) T PF11197_consen 17 QGAASKVVVRSDDGRRVQFPARHLRPFV 44 (68) T ss_pred cccccEEEEEecCCcEEEEeHHHCccee Confidence 3457889999999999884 55678844 No 162 >PRK03562 glutathione-regulated potassium-efflux system protein KefC; Provisional Probab=29.69 E-value=1.3e+02 Score=24.06 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=34.9 Q ss_pred HHHHHHhcCCcEEEEecCCchHHH----HHHhhCCCCCEEEEecChhhhccc Q 039146 32 AVRSAIKVKASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) ..+.+.--+++++|+.|.+-.... .+-+..|+.+|++-+.|..-...| T Consensus 456 ~L~~agi~~A~~vvv~~~d~~~n~~i~~~ar~~~p~~~iiaRa~d~~~~~~L 507 (621) T PRK03562 456 LLESAGAAKAEVLINAIDDPQTSLQLVELVKEHFPHLQIIARARDVDHYIRL 507 (621) T ss_pred HHHhcCCCcCCEEEEEeCCHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHH Confidence 344455557899999888766554 334668999999999998776544 No 163 >PRK06721 threonine synthase; Reviewed Probab=29.59 E-value=1.8e+02 Score=21.31 Aligned_cols=50 Identities=30% Similarity=0.313 Sum_probs=34.6 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecCh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIPQ 73 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~~ 73 (84) +..+-.+...+.-+.+.+.+.||+. .||.+++.+|.+ +...+.+.+.+.. T Consensus 57 S~KdR~a~~~i~~a~~~g~~~vV~a-SsGN~G~alA~~aa~~G~~~~vvvp~~ 108 (352) T PRK06721 57 SFKDRGMVMAVAKAKEEGSEAIICA-STGNTSASAAAYAARLGMKCIIVIPEG 108 (352) T ss_pred chHHHHHHHHHHHHHHCCCCEEEEE-CCcHHHHHHHHHHHHCCCcEEEEECCC Confidence 3456666666777777777878876 589998766544 4467778777653 No 164 >PF06613 KorB_C: KorB C-terminal beta-barrel domain; InterPro: IPR010575 This domain is found in several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This family is found in conjunction with IPR003115 from INTERPRO.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1IGQ_B 1IGU_A. Probab=29.58 E-value=7.5 Score=22.04 Aligned_cols=24 Identities=38% Similarity=0.594 Sum_probs=18.1 Q ss_pred cEEEEecCCchHHHHHHhhCCCCC Q 039146 42 SAIICFTSSGRAARLIAKYRPTMP 65 (84) Q Consensus 42 ~aIv~~T~sG~ta~~iS~~Rp~~p 65 (84) |+||-....|+.||.+-.-||..- T Consensus 8 Kaiv~V~~d~R~arllLnrRps~~ 31 (60) T PF06613_consen 8 KAIVQVEHDGRPARLLLNRRPSSE 31 (60) T ss_dssp SEEEEEEETTEEEEE-TTB--SST T ss_pred ccEEEEEECCchhhhhhccCCCcC Confidence 788888999999999999998754 No 165 >PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions [].ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A .... Probab=29.52 E-value=39 Score=22.52 Aligned_cols=25 Identities=28% Similarity=0.341 Sum_probs=20.9 Q ss_pred HHHHHHHhcC-CcEEEEecCCchHHH Q 039146 31 SAVRSAIKVK-ASAIICFTSSGRAAR 55 (84) Q Consensus 31 ~a~~~a~~~~-~~aIv~~T~sG~ta~ 55 (84) ++++++=.++ |++|+=++.||.|-+ T Consensus 96 GsvE~ap~~glAD~IvDiv~TG~TLr 121 (163) T PF01634_consen 96 GSVELAPPLGLADAIVDIVETGTTLR 121 (163) T ss_dssp S-TTHHHHTTSSSEEEEEESSSHHHH T ss_pred CCccccCCCCCCCEEEEeccCcHHHH Confidence 5677887887 999999999999976 No 166 >PRK07048 serine/threonine dehydratase; Validated Probab=29.52 E-value=1.7e+02 Score=20.93 Aligned_cols=42 Identities=19% Similarity=0.039 Sum_probs=31.5 Q ss_pred HHHHHHhc-CCcEEEEecCCchHHHHHHhh----CCCCCEEEEecCh Q 039146 32 AVRSAIKV-KASAIICFTSSGRAARLIAKY----RPTMPVLSVVIPQ 73 (84) Q Consensus 32 a~~~a~~~-~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~~ 73 (84) +.++.+.+ ..++||+..-+|.+..-++++ .|...|+++-+.. T Consensus 163 ~~EI~~q~~~~D~vv~~vGtGG~~~Gi~~~~k~~~~~~~vigvep~~ 209 (321) T PRK07048 163 AKELFEEVGPLDALFVCLGGGGLLSGCALAARALSPGCKVYGVEPEA 209 (321) T ss_pred HHHHHhhcCCCCEEEEecChhHHHHHHHHHHHHhCCCCEEEEEeeCC Confidence 34555555 579999999999997655555 7999999997643 No 167 >PLN02565 cysteine synthase Probab=29.49 E-value=1.4e+02 Score=21.70 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=31.0 Q ss_pred HHHHHHhc--CCcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 32 AVRSAIKV--KASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 32 a~~~a~~~--~~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) +.++.+.+ +.++||+..-+|.+.. .+..++|.+.||++-+. T Consensus 162 a~Ei~~q~~~~~d~vv~~vG~GG~l~Gi~~~lk~~~p~~kvi~Vep~ 208 (322) T PLN02565 162 GPEIWKGTGGKVDAFVSGIGTGGTITGAGKYLKEQNPDIKLYGVEPV 208 (322) T ss_pred HHHHHHhcCCCCCEEEEcCCchHHHHHHHHHHHHhCCCCEEEEEecC Confidence 45566665 4899999999998765 45555799999999764 No 168 >PRK06848 hypothetical protein; Validated Probab=29.34 E-value=1.6e+02 Score=18.96 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=19.8 Q ss_pred cCCchHHHHHHhhCCCCCEEEEecCh Q 039146 48 TSSGRAARLIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 48 T~sG~ta~~iS~~Rp~~pIia~t~~~ 73 (84) +..|.--+.|+.|.|..+|+....+. T Consensus 95 ~PCG~CRQvl~E~~~~~~v~v~~~~~ 120 (139) T PRK06848 95 SPCGACRELISDYGKNTNVIVPYNDE 120 (139) T ss_pred CCChhhHHHHHHhCCCCEEEEECCCC Confidence 46777788999998888888765443 No 169 >TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. Probab=29.05 E-value=60 Score=20.17 Aligned_cols=21 Identities=10% Similarity=0.297 Sum_probs=18.3 Q ss_pred cCCcEEEEecCCchHHHHHHh Q 039146 39 VKASAIICFTSSGRAARLIAK 59 (84) Q Consensus 39 ~~~~aIv~~T~sG~ta~~iS~ 59 (84) .+...++++|++|..++.++. T Consensus 6 ~~TSGlll~akd~~~~~~L~~ 26 (128) T TIGR00093 6 RDSEGLLLLTNDGELVHRLTH 26 (128) T ss_pred CCCEEEEEEEeCHHHHHHHhC Confidence 356789999999999999986 No 170 >PRK06382 threonine dehydratase; Provisional Probab=29.01 E-value=1.6e+02 Score=21.97 Aligned_cols=43 Identities=14% Similarity=0.167 Sum_probs=32.5 Q ss_pred HHHHHHHHhc-CCcEEEEecCCchHHHHHHh----hCCCCCEEEEecC Q 039146 30 SSAVRSAIKV-KASAIICFTSSGRAARLIAK----YRPTMPVLSVVIP 72 (84) Q Consensus 30 ~~a~~~a~~~-~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~~ 72 (84) .-+.++.+.+ +.++||+..-+|.+..-+++ ..|.+.||++-+. T Consensus 162 t~~~Ei~eq~~~~d~vvvpvG~GG~~~Gv~~~~k~~~p~~~vigVe~~ 209 (406) T PRK06382 162 TIGLEIMEDLPDLDQIIVPVGGGGLISGIALAAKHINPNVKIIGIESE 209 (406) T ss_pred HHHHHHHHhcCCCCEEEEeeChHHHHHHHHHHHHHhCCCCEEEEEEEC Confidence 3455666666 47999999999988765555 4899999999764 No 171 >PRK08638 threonine dehydratase; Validated Probab=28.95 E-value=1.6e+02 Score=21.46 Aligned_cols=41 Identities=17% Similarity=0.191 Sum_probs=31.1 Q ss_pred HHHHHHhc-CCcEEEEecCCchHHHHHHhh----CCCCCEEEEecC Q 039146 32 AVRSAIKV-KASAIICFTSSGRAARLIAKY----RPTMPVLSVVIP 72 (84) Q Consensus 32 a~~~a~~~-~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~ 72 (84) +.++.+++ +.++||+..-+|.+..-++++ .|...||++=+. T Consensus 166 a~Ei~~q~~~~d~vv~~vG~Gg~~~Gv~~~lk~~~~~~~vigVep~ 211 (333) T PRK08638 166 GLEILEDLWDVDTVIVPIGGGGLIAGIAVALKSINPTIHIIGVQSE 211 (333) T ss_pred HHHHHhhcCCCCEEEEEeChhHHHHHHHHHHHHhCCCCEEEEEEEC Confidence 44444444 579999999999988877765 899999998553 No 172 >cd07411 MPP_SoxB_N Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain. SoxB (sulfur oxidation protein B) is a periplasmic thiosulfohydrolase and an essential component of the sulfur oxidation pathway in archaea and bacteria. SoxB has a dinuclear manganese cluster and is thought to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate. SoxB is expressed from the sox (sulfur oxidation) gene cluster, which encodes 15 other sox genes, and has two domains, an N-terminal metallophosphatase domain and a C-terminal 5'-nucleotidase domain. SoxB binds the SoxYZ complex and is thought to function as a sulfate-thiohydrolase. SoxB is closely related to the UshA, YchR, and CpdB proteins, all of which have the same two-domain architecture. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzy Probab=28.81 E-value=2e+02 Score=19.90 Aligned_cols=52 Identities=12% Similarity=0.113 Sum_probs=35.6 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchH-HHHHHhhCCCCCEEEEecChh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRA-ARLIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~t-a~~iS~~Rp~~pIia~t~~~~ 74 (84) +..+++...+.++..+-+++.||+++..|.. .+.+++.-|.+.+|...++.. T Consensus 166 ~~~~~~~~~~~~~~~~~~~D~iI~l~H~g~~~~~~la~~~~~iDlilgGH~H~ 218 (264) T cd07411 166 IREEELQEVVVKLRREEGVDVVVLLSHNGLPVDVELAERVPGIDVILSGHTHE 218 (264) T ss_pred CHHHHHHHHHHHHHHhCCCCEEEEEecCCchhhHHHHhcCCCCcEEEeCcccc Confidence 3445554444555556689999999999874 456676668888876666553 No 173 >PRK15454 ethanol dehydrogenase EutG; Provisional Probab=28.21 E-value=2.3e+02 Score=21.23 Aligned_cols=36 Identities=17% Similarity=0.045 Sum_probs=26.3 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY 60 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~ 60 (84) ++.......+++.+.+.+++.||. -.|.++.-.+|. T Consensus 89 ~P~~~~v~~~~~~~r~~~~D~Iia--vGGGS~iD~AKa 124 (395) T PRK15454 89 EPCITDVCAAVAQLRESGCDGVIA--FGGGSVLDAAKA 124 (395) T ss_pred CcCHHHHHHHHHHHHhcCcCEEEE--eCChHHHHHHHH Confidence 455566677888888999998887 477776665544 No 174 >PF01513 NAD_kinase: ATP-NAD kinase; InterPro: IPR002504 Members of this family are ATP-NAD kinases 2.7.1.23 from EC. The enzymes catalyse the phosphorylation of NAD to NADP utilizing ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus.; GO: 0003951 NAD+ kinase activity, 0008152 metabolic process; PDB: 1U0T_B 1U0R_D 1Y3H_A 1Y3I_A 3AFO_B 1YT5_B 2AN1_A 2I2A_A 3V8P_A 2I1W_A .... Probab=28.21 E-value=71 Score=22.65 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=23.9 Q ss_pred HhcCCcEEEEecCCchHHHHHHhhCC-CCCEEEEec Q 039146 37 IKVKASAIICFTSSGRAARLIAKYRP-TMPVLSVVI 71 (84) Q Consensus 37 ~~~~~~aIv~~T~sG~ta~~iS~~Rp-~~pIia~t~ 71 (84) ...+++.||++--+|..-+....+.+ ..||+++-. T Consensus 73 ~~~~~D~ii~lGGDGT~L~~~~~~~~~~~Pilgin~ 108 (285) T PF01513_consen 73 LEEGVDLIIVLGGDGTFLRAARLFGDYDIPILGINT 108 (285) T ss_dssp HCCCSSEEEEEESHHHHHHHHHHCTTST-EEEEEES T ss_pred cccCCCEEEEECCCHHHHHHHHHhccCCCcEEeecC Confidence 35688999998776655555555554 899999853 No 175 >PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 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 [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A .... Probab=28.01 E-value=1.2e+02 Score=17.08 Aligned_cols=42 Identities=17% Similarity=0.129 Sum_probs=27.6 Q ss_pred HHHHHhcCCcEEEEec-----CCchHHHHHHhhCCCCCEEEEecChh Q 039146 33 VRSAIKVKASAIICFT-----SSGRAARLIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 33 ~~~a~~~~~~aIv~~T-----~sG~ta~~iS~~Rp~~pIia~t~~~~ 74 (84) .......+.+.|++-- ......+.+.+..|..||++++.... T Consensus 36 ~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t~~~~ 82 (112) T PF00072_consen 36 LELLKKHPPDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVTDEDD 82 (112) T ss_dssp HHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEESSTS T ss_pred HHHhcccCceEEEEEeeeccccccccccccccccccccEEEecCCCC Confidence 3444566678777653 12234567777779999999996654 No 176 >PRK10669 putative cation:proton antiport protein; Provisional Probab=27.97 E-value=1.4e+02 Score=23.16 Aligned_cols=48 Identities=13% Similarity=0.065 Sum_probs=32.3 Q ss_pred HHHHHHhcCCcEEEEecCCchHH----HHHHhhCCCCCEEEEecChhhhccc Q 039146 32 AVRSAIKVKASAIICFTSSGRAA----RLIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~sG~ta----~~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) +.+-+.--+++++++.|.+.... ..+-+.+|+.+|++-+.+++-.+.| T Consensus 473 ~L~~a~i~~a~~viv~~~~~~~~~~iv~~~~~~~~~~~iiar~~~~~~~~~l 524 (558) T PRK10669 473 IMQLAHLDCARWLLLTIPNGYEAGEIVASAREKRPDIEIIARAHYDDEVAYI 524 (558) T ss_pred HHHhcCccccCEEEEEcCChHHHHHHHHHHHHHCCCCeEEEEECCHHHHHHH Confidence 34445555788888776654443 3445668999999999888766543 No 177 >PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A .... Probab=27.86 E-value=98 Score=17.78 Aligned_cols=35 Identities=20% Similarity=0.161 Sum_probs=26.7 Q ss_pred EEEEecCCchHHHHHHhhCCCCCEEEEecChhhhc Q 039146 43 AIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTN 77 (84) Q Consensus 43 aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r 77 (84) .+-+-.-+|..+..+++.+|...|+++=.++.... T Consensus 5 vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~ 39 (112) T PF12847_consen 5 VLDLGCGTGRLSIALARLFPGARVVGVDISPEMLE 39 (112) T ss_dssp EEEETTTTSHHHHHHHHHHTTSEEEEEESSHHHHH T ss_pred EEEEcCcCCHHHHHHHhcCCCCEEEEEeCCHHHHH Confidence 34455678899999999888999999877776553 No 178 >PRK09533 bifunctional transaldolase/phosoglucose isomerase; Validated Probab=27.81 E-value=57 Score=27.74 Aligned_cols=36 Identities=14% Similarity=0.067 Sum_probs=25.7 Q ss_pred hcCCcEEEEecCCchHHHHHHhhC-------------CCCCEEEEecCh Q 039146 38 KVKASAIICFTSSGRAARLIAKYR-------------PTMPVLSVVIPQ 73 (84) Q Consensus 38 ~~~~~aIv~~T~sG~ta~~iS~~R-------------p~~pIia~t~~~ 73 (84) ++.--.+|+.|.||.|.--++.+| +...++++|.+. T Consensus 505 ~~e~TLvIViSKSGtT~ET~sa~~~~~~~l~~~~g~~~~~~~VaVTdpg 553 (948) T PRK09533 505 DLARTLFIVSSKSGGTLEPNIFKDYFFARVKEVLGAKAGRHFVAVTDPG 553 (948) T ss_pred CcccEEEEEEeCCCCCHHHHHHHHHHHHHhhhhcccccCCeEEEEeCCC Confidence 444456888899999987776655 356688888643 No 179 >PF04009 DUF356: Protein of unknown function (DUF356); InterPro: IPR007154 Members of this family are around 120 amino acids in length and are found in some archaebacteria. The function of this family is unknown. However it contains a conserved motif IHPPAH that may be involved in its function. Probab=27.68 E-value=1e+02 Score=19.42 Aligned_cols=33 Identities=12% Similarity=0.153 Sum_probs=27.4 Q ss_pred cCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 48 TSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 48 T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) ...|..-.++-+..|.+.|+.+++...+.+.|. T Consensus 65 ~~~~~aI~~lrkIHPPAHIiVis~~~~~y~eL~ 97 (107) T PF04009_consen 65 EDATKAIDRLRKIHPPAHIIVISPRHDVYEELL 97 (107) T ss_pred CCchhHHHHHhhcCCCceEEEECCCchHHHHHH Confidence 456667779999999999999999988877664 No 180 >cd06556 ICL_KPHMT Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), 2-methylisocitrate lyase (MICL), and ketopantoate hydroxymethyltransferase (KPHMT). Probab=27.46 E-value=2.2e+02 Score=20.04 Aligned_cols=46 Identities=13% Similarity=0.057 Sum_probs=34.6 Q ss_pred HHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChh Q 039146 26 ESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~ 74 (84) ++|.+ ...-.+.++++|++...+...++.+++- +..|+++...... T Consensus 157 ~ai~R--a~ay~~AGAd~i~~e~~~~e~~~~i~~~-~~~P~~~~gag~~ 202 (240) T cd06556 157 QLIAD--ALAYAPAGADLIVMECVPVELAKQITEA-LAIPLAGIGAGSG 202 (240) T ss_pred HHHHH--HHHHHHcCCCEEEEcCCCHHHHHHHHHh-CCCCEEEEecCcC Confidence 44444 3455677999999988888999999985 7899998765543 No 181 >cd04819 PA_2 PA_2: Protease-associated (PA) domain subgroup 2. A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuola Probab=27.40 E-value=76 Score=19.74 Aligned_cols=42 Identities=14% Similarity=0.065 Sum_probs=26.7 Q ss_pred HHHHHHhcCCcEEEEecCCch-HHHHHH-h----hCCCCCEEEEecCh Q 039146 32 AVRSAIKVKASAIICFTSSGR-AARLIA-K----YRPTMPVLSVVIPQ 73 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~sG~-ta~~iS-~----~Rp~~pIia~t~~~ 73 (84) -+..|.+.+++++|+++.... ...... . ..|..|++.++..+ T Consensus 62 k~~~A~~~GA~avi~~~~~~g~~~~~~~~~~~~~~~~~IP~v~Is~ed 109 (127) T cd04819 62 KYAKAVAAGAAAFVVVNTVPGVLPATGDEGTEDGPPSPIPAASVSGED 109 (127) T ss_pred HHHHHHHCCCEEEEEEeCCCCcCcccccccccCCCCCCCCEEEEeHHH Confidence 466788999999999864433 221111 1 24678988886544 No 182 >PRK01911 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=26.58 E-value=1.4e+02 Score=21.63 Aligned_cols=31 Identities=19% Similarity=0.327 Sum_probs=24.8 Q ss_pred CCcEEEEecCCchHHHHHHhhCC-CCCEEEEe Q 039146 40 KASAIICFTSSGRAARLIAKYRP-TMPVLSVV 70 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~Rp-~~pIia~t 70 (84) +++.||++--+|..-+....+.+ +.||+++- T Consensus 64 ~~dlvi~lGGDGT~L~aa~~~~~~~~PilGIN 95 (292) T PRK01911 64 SADMVISIGGDGTFLRTATYVGNSNIPILGIN 95 (292) T ss_pred CCCEEEEECCcHHHHHHHHHhcCCCCCEEEEe Confidence 47899999999988776666654 68999883 No 183 >COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism] Probab=26.54 E-value=2.2e+02 Score=19.51 Aligned_cols=59 Identities=19% Similarity=0.310 Sum_probs=37.6 Q ss_pred CHHHHHHHHHHHHHHhc-CCcEEEEecCCchHH-------HH---HHhhCCCCCEEEEecChhhhccccc Q 039146 23 SHLESITSSAVRSAIKV-KASAIICFTSSGRAA-------RL---IAKYRPTMPVLSVVIPQLKTNQLRW 81 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~-~~~aIv~~T~sG~ta-------~~---iS~~Rp~~pIia~t~~~~~~r~L~l 81 (84) ...+.|-.++..+++.+ +-+.|+++-+.|.-+ -+ +-+-||.-|-|+++.|......++- T Consensus 22 ~l~~~I~~aa~~i~~~l~~G~Kvl~cGNGgSaadAqHfaael~gRf~~eR~~lpaIaLt~dsS~lTai~N 91 (176) T COG0279 22 ALIEAIERAAQLLVQSLLNGNKVLACGNGGSAADAQHFAAELTGRFEKERPSLPAIALSTDSSVLTAIAN 91 (176) T ss_pred HhHHHHHHHHHHHHHHHHcCCEEEEECCCcchhhHHHHHHHHhhHHHhcCCCCCeeEeecccHHHhhhhc Confidence 34566666666666555 234466666766543 23 3345899999999988877665544 No 184 >cd04815 PA_M28_2 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies; relatively little is known a Probab=26.49 E-value=1.1e+02 Score=19.23 Aligned_cols=42 Identities=14% Similarity=0.172 Sum_probs=26.8 Q ss_pred HHHHHHhcCCcEEEEecCC------chHHHHHH-hhCCCCCEEEEecCh Q 039146 32 AVRSAIKVKASAIICFTSS------GRAARLIA-KYRPTMPVLSVVIPQ 73 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~s------G~ta~~iS-~~Rp~~pIia~t~~~ 73 (84) ....+.+-+|.++|+.+.+ +.+..+-. -..+..|+++++..+ T Consensus 68 ~~~~A~~~GA~avIv~s~~~~~~~~~~~G~~~~~~~~~~IP~v~is~ed 116 (134) T cd04815 68 GAVEAAKKGAVAVLIRSIGTDSHRSPHTGMMSYDDGVPKIPAAAISVED 116 (134) T ss_pred HHHHHHhCCCEEEEEEecCcccCCCCcCCccccCCCCCCCCEEEechhc Confidence 3678889999999997632 21222211 224679999987554 No 185 >cd06446 Trp-synth_B Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to glyceraldehyde 3-phosphate and indole at the active site of the alpha subunit. In the beta reaction, indole undergoes a PLP-dependent reaction with L-serine to form L-tryptophan at the active site of the beta subunit. Members of this CD, Trp-synth_B, are found in all three major phylogenetic divisions. Probab=26.07 E-value=1.8e+02 Score=21.44 Aligned_cols=48 Identities=10% Similarity=-0.072 Sum_probs=30.0 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecC Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIP 72 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~ 72 (84) .+-.+...+..+.+.+.+.+|+.+.+|.+++.+|.+ +-..+.+.+.+. T Consensus 66 K~R~a~~~~~~a~~~g~~~vv~~~ssGN~g~alA~~a~~~G~~~~ivvp~ 115 (365) T cd06446 66 KINNALGQALLAKRMGKKRVIAETGAGQHGVATATACALFGLECEIYMGA 115 (365) T ss_pred hHHHHHHHHHHHHHcCCCeEEEecCchHHHHHHHHHHHHhCCCeEEEEcC Confidence 444455556666777788888777788888754432 234556666554 No 186 >PTZ00187 succinyl-CoA synthetase alpha subunit; Provisional Probab=26.04 E-value=1.5e+02 Score=21.95 Aligned_cols=37 Identities=24% Similarity=0.226 Sum_probs=27.0 Q ss_pred HHHHhcCCcEEEEecCCc-----hHHHHHHhhCCCCCEEEEe Q 039146 34 RSAIKVKASAIICFTSSG-----RAARLIAKYRPTMPVLSVV 70 (84) Q Consensus 34 ~~a~~~~~~aIv~~T~sG-----~ta~~iS~~Rp~~pIia~t 70 (84) .+.++-+.++|+++-+.| .-++.+...+.+.||+++- T Consensus 218 ~~~~Dp~T~~Ivl~~E~gG~~e~~aa~fi~~~~~~KPVVa~~ 259 (317) T PTZ00187 218 LFLNDPETEGIILIGEIGGTAEEEAAEWIKNNPIKKPVVSFI 259 (317) T ss_pred HHhhCCCccEEEEEEecCCchhHHHHHHHHhhcCCCcEEEEE Confidence 355677889999999998 3345666554578999884 No 187 >PRK03868 glucose-6-phosphate isomerase; Provisional Probab=26.01 E-value=75 Score=24.17 Aligned_cols=19 Identities=21% Similarity=0.319 Sum_probs=13.6 Q ss_pred CcEEEEecCCchHHHHHHh Q 039146 41 ASAIICFTSSGRAARLIAK 59 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~iS~ 59 (84) --.+|+.|.||.|.-.++. T Consensus 112 ~TlviviSKSGtT~ETl~~ 130 (410) T PRK03868 112 NTLFIVISKSGTTIETISI 130 (410) T ss_pred cEEEEEEeCCCCCHHHHHH Confidence 3467888999988765544 No 188 >TIGR01444 fkbM_fam methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548. Probab=25.62 E-value=82 Score=19.19 Aligned_cols=33 Identities=12% Similarity=0.021 Sum_probs=25.1 Q ss_pred cCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 48 TSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 48 T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) +..|..+..+++.-|+..|+++=+++.....|. T Consensus 7 a~~G~~~~~~~~~~~~~~v~~~E~~~~~~~~l~ 39 (143) T TIGR01444 7 ANIGDTSLYFARKGAEGRVIAFEPLPDAYEILE 39 (143) T ss_pred CCccHHHHHHHHhCCCCEEEEEecCHHHHHHHH Confidence 467888888888888888888888877665443 No 189 >PHA02558 uvsW UvsW helicase; Provisional Probab=25.46 E-value=2.4e+02 Score=21.67 Aligned_cols=41 Identities=17% Similarity=0.087 Sum_probs=28.5 Q ss_pred CCcEEEEecCCchHHHH--HHh---hCCCCCEEEEecChhhhcccc Q 039146 40 KASAIICFTSSGRAARL--IAK---YRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~--iS~---~Rp~~pIia~t~~~~~~r~L~ 80 (84) +--.+...|-+|.|... +++ -+...+++.++|....+.|+. T Consensus 130 ~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~ 175 (501) T PHA02558 130 NRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMI 175 (501) T ss_pred CceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHH Confidence 33467888999999743 222 134558999999988887763 No 190 >PRK04539 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=25.39 E-value=1.5e+02 Score=21.55 Aligned_cols=31 Identities=10% Similarity=0.318 Sum_probs=25.1 Q ss_pred CCcEEEEecCCchHHHHHHhhCC-CCCEEEEe Q 039146 40 KASAIICFTSSGRAARLIAKYRP-TMPVLSVV 70 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~Rp-~~pIia~t 70 (84) +++.+|++--+|..-+....+.+ .+||+++- T Consensus 68 ~~D~vi~lGGDGT~L~aa~~~~~~~~PilGIN 99 (296) T PRK04539 68 YCDLVAVLGGDGTFLSVAREIAPRAVPIIGIN 99 (296) T ss_pred CCCEEEEECCcHHHHHHHHHhcccCCCEEEEe Confidence 57899999999988877776654 68999984 No 191 >TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) Probab=25.30 E-value=1.6e+02 Score=23.88 Aligned_cols=39 Identities=18% Similarity=0.230 Sum_probs=28.4 Q ss_pred cEEEEecCCchHHHHHHhhC-CCCCEEEEecChhhhcccc Q 039146 42 SAIICFTSSGRAARLIAKYR-PTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 42 ~aIv~~T~sG~ta~~iS~~R-p~~pIia~t~~~~~~r~L~ 80 (84) ..+.-.|.||.|-.+-.-++ .+.|++.+++|...+.+|. T Consensus 32 ~~l~Gvtgs~kt~~~a~~~~~~~~p~Lvi~~n~~~A~ql~ 71 (655) T TIGR00631 32 QTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLY 71 (655) T ss_pred EEEECCCCcHHHHHHHHHHHHhCCCEEEEECCHHHHHHHH Confidence 34566678887776544444 3679999999999998874 No 192 >TIGR00260 thrC threonine synthase. Involved in threonine biosynthesis it catalyses the reaction O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE + ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor. the enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes. the pyridoxal-phosphate binding site is a Lys (K) residues present at residue 70 of the model. Probab=25.27 E-value=2.6e+02 Score=19.94 Aligned_cols=48 Identities=17% Similarity=0.315 Sum_probs=31.6 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecCh Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIPQ 73 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~~ 73 (84) .+-.+...+..+...+...||+. .||.+++-+|.+ +...+.+.+.+.. T Consensus 55 KdR~a~~~l~~a~~~g~~~vv~a-SsGN~g~a~A~~a~~~g~~~~v~~p~~ 104 (328) T TIGR00260 55 KDRGMAVALTKALELGNDTVLCA-STGNTGAAAAAYAGKAGVKVVILYPAG 104 (328) T ss_pred HhhhHHHHHHHHHHcCCCEEEEe-CCcHHHHHHHHHhccCCCcEEEEECCC Confidence 34445555555556666667764 599999876643 3468888887765 No 193 >PRK04885 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=25.18 E-value=1.4e+02 Score=21.31 Aligned_cols=30 Identities=13% Similarity=0.306 Sum_probs=24.7 Q ss_pred CCcEEEEecCCchHHHHHHhhC---CCCCEEEE Q 039146 40 KASAIICFTSSGRAARLIAKYR---PTMPVLSV 69 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~R---p~~pIia~ 69 (84) +++.+|++--+|..-+..-.+. +++||+++ T Consensus 35 ~~Dlvi~iGGDGT~L~a~~~~~~~~~~iPilGI 67 (265) T PRK04885 35 NPDIVISVGGDGTLLSAFHRYENQLDKVRFVGV 67 (265) T ss_pred CCCEEEEECCcHHHHHHHHHhcccCCCCeEEEE Confidence 5789999999998877776666 48999987 No 194 >TIGR00263 trpB tryptophan synthase, beta subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. the beta chain contains the functional domain for or the synthesis of tryptophan from indole and serine. The enzyme requires pyridoxal-phosphate as a cofactor. The pyridoxal-P attachment site is contained within the conserved region [LIVM]-x-H-x-G-[STA]-H-K-x-N] [K is the pyridoxal-P attachment site] which is present between residues 90-100 of the model. Probab=24.93 E-value=2e+02 Score=21.39 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=0.0 Q ss_pred HHHHHHhc------CCcEEEEecCCchHHHHHHh-h--CCCCCEEEE Q 039146 32 AVRSAIKV------KASAIICFTSSGRAARLIAK-Y--RPTMPVLSV 69 (84) Q Consensus 32 a~~~a~~~------~~~aIv~~T~sG~ta~~iS~-~--Rp~~pIia~ 69 (84) +.++.+.+ ..++||+..-+|.+..-+++ + .|...||++ T Consensus 204 g~Ei~~Ql~~~~~~~pD~vv~~vG~Gg~~~Gv~~~~~~~~~~~iigV 250 (385) T TIGR00263 204 GEEAKEQILEQEGRLPDAVIACVGGGSNAIGIFYAFIDDPSVQLIGV 250 (385) T ss_pred HHHHHHHHHhhhCCCCCEEEEEeCchHHHHHHHHHHhhCCCCeEEEE No 195 >cd01398 RPI_A RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the conversion of phosphosugars into glycolysis intermediates, which are precursors for the synthesis of amino acids, vitamins, nucleotides, and cell wall components. In plants, RPI is part of the Calvin cycle as ribulose 5-phosphate is the carbon dioxide receptor in the first dark reaction of photosynthesis. There are two unrelated types of RPIs (A and B), which catalyze the same reaction, at least one type of RPI is present in an organism. RPI_A is more widely distributed than RPI_B in bacteria, eukaryotes, and archaea. Probab=24.83 E-value=1.5e+02 Score=20.27 Aligned_cols=28 Identities=7% Similarity=0.045 Sum_probs=14.5 Q ss_pred CCchHHHHHHhhCCCC------CEEEEecChhhh Q 039146 49 SSGRAARLIAKYRPTM------PVLSVVIPQLKT 76 (84) Q Consensus 49 ~sG~ta~~iS~~Rp~~------pIia~t~~~~~~ 76 (84) .+|.|+..++++=+.. ++-++|++..++ T Consensus 22 dsGST~~~l~~~L~~~~~~~~~~itvVTnS~~~a 55 (213) T cd01398 22 GTGSTVAYFIEALGERVREEGLNIVGVPTSFQTE 55 (213) T ss_pred CchHHHHHHHHHHHHhhhccCCCEEEEeCcHHHH Confidence 6666665555543321 455565555544 No 196 >PRK08639 threonine dehydratase; Validated Probab=24.81 E-value=2.2e+02 Score=21.43 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=29.9 Q ss_pred HHHHHHhcC----CcEEEEecCCchHHHH----HHhhCCCCCEEEEecC Q 039146 32 AVRSAIKVK----ASAIICFTSSGRAARL----IAKYRPTMPVLSVVIP 72 (84) Q Consensus 32 a~~~a~~~~----~~aIv~~T~sG~ta~~----iS~~Rp~~pIia~t~~ 72 (84) +.++.+.++ .++||+..-+|.+.-- +-..+|++.||++-+. T Consensus 167 g~EI~eq~~~~~~~D~vv~~vG~GG~~aGva~~~k~~~p~~~vigVep~ 215 (420) T PRK08639 167 AVEILEQLEKEGSPDYVFVPVGGGGLISGVTTYLKERSPKTKIIGVEPA 215 (420) T ss_pred HHHHHHhccccCCCCEEEEecChhHHHHHHHHHHHHhCCCCEEEEEEEC Confidence 455566653 7999999999976554 4445899999999654 No 197 >PRK06352 threonine synthase; Validated Probab=24.67 E-value=2.5e+02 Score=20.57 Aligned_cols=49 Identities=29% Similarity=0.324 Sum_probs=32.2 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecC Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIP 72 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~ 72 (84) +..+-.+...+..+.+.+.+.||+. .+|.+++.+|.+ +-..+.+.+.++ T Consensus 57 S~KdR~a~~~i~~a~~~g~~~vV~a-SsGN~G~AlA~~aa~~G~~~~ivvp~ 107 (351) T PRK06352 57 SFKDRGMVMAVAKAKEEGAEAVICA-STGNTSAAAAAYATRAGLKAYIVIPE 107 (351) T ss_pred ChHHHHHHHHHHHHHHCCCCEEEEE-CCcHHHHHHHHHHHHcCCcEEEEEeC Confidence 3456666666666777778877775 688988755433 335677777655 No 198 >cd00640 Trp-synth-beta_II Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehy Probab=24.61 E-value=2.3e+02 Score=19.13 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=30.0 Q ss_pred HHHHHHHHhcC---CcEEEEecCCchHHHHH----HhhCCCCCEEEEec Q 039146 30 SSAVRSAIKVK---ASAIICFTSSGRAARLI----AKYRPTMPVLSVVI 71 (84) Q Consensus 30 ~~a~~~a~~~~---~~aIv~~T~sG~ta~~i----S~~Rp~~pIia~t~ 71 (84) .-+.++.+.++ .+.|++..-+|.++.-+ ....|...|+++-+ T Consensus 140 ~~~~Ei~~q~~~~~~d~ivvp~GtGg~~~G~~~~~~~~~~~~~ii~v~~ 188 (244) T cd00640 140 TIGLEILEQLGGQKPDAVVVPVGGGGNIAGIARALKELLPNVKVIGVEP 188 (244) T ss_pred HHHHHHHHHcCCCCCCEEEEecCccHHHHHHHHHHHHhCCCCEEEEEee Confidence 34556666664 68999999999887744 44568888888744 No 199 >cd02130 PA_ScAPY_like PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY). This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stab Probab=24.59 E-value=64 Score=19.74 Aligned_cols=40 Identities=15% Similarity=0.160 Sum_probs=24.1 Q ss_pred HHHHHHhcCCcEEEEecCCch--HHHHHHhh-CCCCCEEEEec Q 039146 32 AVRSAIKVKASAIICFTSSGR--AARLIAKY-RPTMPVLSVVI 71 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~sG~--ta~~iS~~-Rp~~pIia~t~ 71 (84) -+..|.+.+++++|++...+. ........ .+..|++.++. T Consensus 60 K~~~A~~aGA~~vIv~n~~~~~~~~~~~~~~~~~~Ip~v~Is~ 102 (122) T cd02130 60 KSALAGAAGAAAAIIYNNVPAGGLSGTLGEPSGPYVPTVGISQ 102 (122) T ss_pred HHHHHHHCCCcEEEEEECCCCcccccccCCCCCCEeeEEEecH Confidence 467788999999999976632 11122221 44566666654 No 200 >COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis] Probab=24.58 E-value=1e+02 Score=22.80 Aligned_cols=39 Identities=23% Similarity=0.088 Sum_probs=27.0 Q ss_pred CcEEEEecCCchHHHH--HHhhCCCCCEEEEecChhhhccccc Q 039146 41 ASAIICFTSSGRAARL--IAKYRPTMPVLSVVIPQLKTNQLRW 81 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~--iS~~Rp~~pIia~t~~~~~~r~L~l 81 (84) +-.|+-+|-+|.|+.. +++.- +.+||.+ .+-.+++.|.. T Consensus 5 ~i~I~GPTAsGKT~lai~LAk~~-~~eIIs~-DSmQvYr~mdI 45 (308) T COG0324 5 LIVIAGPTASGKTALAIALAKRL-GGEIISL-DSMQVYRGLDI 45 (308) T ss_pred EEEEECCCCcCHHHHHHHHHHHc-CCcEEec-chhhhcCCCcc Confidence 3456678999999884 45443 6788877 67777776653 No 201 >COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis] Probab=24.45 E-value=2.7e+02 Score=19.86 Aligned_cols=53 Identities=25% Similarity=0.260 Sum_probs=36.1 Q ss_pred CCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecCh Q 039146 21 PMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 21 ~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~ 73 (84) |..-++.+...+...........+=+.|-||-.|..+++.+|.+-|+|+=-++ T Consensus 92 Pr~dTe~Lve~~l~~~~~~~~~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~ 144 (280) T COG2890 92 PRPDTELLVEAALALLLQLDKRILDLGTGSGAIAIALAKEGPDAEVIAVDISP 144 (280) T ss_pred cCCchHHHHHHHHHhhhhcCCcEEEecCChHHHHHHHHhhCcCCeEEEEECCH Confidence 44556666666552222222234446799999999999999999999885444 No 202 >PRK07334 threonine dehydratase; Provisional Probab=24.23 E-value=2e+02 Score=21.44 Aligned_cols=42 Identities=12% Similarity=0.200 Sum_probs=31.6 Q ss_pred HHHHHHHhc-CCcEEEEecCCchHHHHHHh----hCCCCCEEEEecC Q 039146 31 SAVRSAIKV-KASAIICFTSSGRAARLIAK----YRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~-~~~aIv~~T~sG~ta~~iS~----~Rp~~pIia~t~~ 72 (84) .+.++.+.+ +.++||+..-+|.+.--+++ ++|...|+++-+. T Consensus 161 ~~~Ei~~q~~~~d~vv~~vG~GG~~~Gi~~~lk~~~~~~~vi~ve~~ 207 (403) T PRK07334 161 VALEMLEDAPDLDTLVVPIGGGGLISGMATAAKALKPDIEIIGVQTE 207 (403) T ss_pred HHHHHHhcCCCCCEEEEecCHHHHHHHHHHHHHHhCCCCEEEEEEEC Confidence 455566666 46899999999987765555 4899999999764 No 203 >PRK00702 ribose-5-phosphate isomerase A; Provisional Probab=23.70 E-value=2.6e+02 Score=19.41 Aligned_cols=51 Identities=12% Similarity=0.044 Sum_probs=29.1 Q ss_pred HHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCC-----CEEEEecChhhhccc Q 039146 25 LESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTM-----PVLSVVIPQLKTNQL 79 (84) Q Consensus 25 ~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~-----pIia~t~~~~~~r~L 79 (84) .+.+|..|+..- +..-+| +=.+|.|+..++++=+.. .+.++|.+..++..+ T Consensus 7 K~~IA~~Aa~lI---~dg~~I-gLgsGST~~~l~~~L~~~~~~~~~itvVt~S~~~a~~l 62 (220) T PRK00702 7 KKAAAEAAAEYV---EDGMIV-GLGTGSTAAYFIDALGERVKEGLIIGGVPTSEASTELA 62 (220) T ss_pred HHHHHHHHHHhC---CCCCEE-EECCcHHHHHHHHHHHhhhccCCCEEEECCcHHHHHHH Confidence 456666655433 222233 337888887776654432 477777777665443 No 204 >PRK07591 threonine synthase; Validated Probab=23.63 E-value=2.6e+02 Score=21.11 Aligned_cols=49 Identities=20% Similarity=0.283 Sum_probs=34.4 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecC Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIP 72 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~ 72 (84) +-.+-.+...+..+.+.+.+.|++. .+|++++.+|.+ +-..+.+.+++. T Consensus 119 SfKdRga~~~v~~A~~~g~~~vv~a-SsGN~g~alA~~aa~~Gl~~~I~vP~ 169 (421) T PRK07591 119 SFKDRVVSVALTAARELGFTTVACA-STGNLANSVAAHAARAGLDSCVFIPA 169 (421) T ss_pred ChHHHHHHHHHHHHHHcCCCEEEEe-CCCHHHHHHHHHHHHcCCCEEEEEcC Confidence 3455555566777888888888764 889999877665 335677777765 No 205 >PF14824 Sirohm_synth_M: Sirohaem biosynthesis protein central; PDB: 1KYQ_B. Probab=23.59 E-value=39 Score=16.48 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=12.8 Q ss_pred EEEecCCchHHHHHHhhC Q 039146 44 IICFTSSGRAARLIAKYR 61 (84) Q Consensus 44 Iv~~T~sG~ta~~iS~~R 61 (84) =|.+|..|..+++-++.| T Consensus 6 qI~ISTnG~sP~la~~iR 23 (30) T PF14824_consen 6 QIAISTNGKSPRLARLIR 23 (30) T ss_dssp EEEEEESSS-HHHHHHHH T ss_pred EEEEECCCCChHHHHHHH Confidence 366788899998877665 No 206 >PRK08618 ornithine cyclodeaminase; Validated Probab=23.41 E-value=84 Score=22.71 Aligned_cols=32 Identities=16% Similarity=0.093 Sum_probs=26.7 Q ss_pred CCcEEEEecCCchHHHHHHhhCCCCCEEEEecC Q 039146 40 KASAIICFTSSGRAARLIAKYRPTMPVLSVVIP 72 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~ 72 (84) +++.|++.|.++.--.. ...||.+.|+++..+ T Consensus 192 ~aDiVi~aT~s~~p~i~-~~l~~G~hV~~iGs~ 223 (325) T PRK08618 192 EADIIVTVTNAKTPVFS-EKLKKGVHINAVGSF 223 (325) T ss_pred cCCEEEEccCCCCcchH-HhcCCCcEEEecCCC Confidence 67899999999876566 889999999988554 No 207 >PF09754 PAC2: PAC2 family; InterPro: IPR019151 This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass and contains one 20S core particle structure and two 19S regulatory caps. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits [, , , ].; PDB: 3MNF_A 2P90_B 3E35_A 3GAA_D 2WAM_C. Probab=23.26 E-value=1.1e+02 Score=20.30 Aligned_cols=54 Identities=13% Similarity=0.118 Sum_probs=38.8 Q ss_pred CCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhcccc Q 039146 22 MSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQLR 80 (84) Q Consensus 22 ~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L~ 80 (84) ......++...+..+.+.+++-||+++-.+..-+. -|| +++++..++.....+. T Consensus 80 ~~~~~~f~~~l~~~~~~~g~~~vi~l~g~~~~~~~---~~~--~~~~~~~~~~~~~~~~ 133 (219) T PF09754_consen 80 PGRWYEFAEELLDWIKSFGVKEVIVLGGLPAMEPH---ERP--PVYRVATSEELLDKLE 133 (219) T ss_dssp SCGHHHHHHHHHHHHHHTTECEEEEEEEEEESS-T---TS---EEEEEESSGGGHCHSH T ss_pred chHHHHHHHHHHHHHHHcCCCEEEEEeCCcCCCCc---ccc--ceEEEEcCHHHhhhhc Confidence 34577888999999999999999988754443333 455 7888888877665443 No 208 >KOG1467 consensus Translation initiation factor 2B, delta subunit (eIF-2Bdelta/GCD2) [Translation, ribosomal structure and biogenesis] Probab=23.24 E-value=80 Score=25.18 Aligned_cols=39 Identities=21% Similarity=0.234 Sum_probs=30.1 Q ss_pred CCcEEE----EecCCchHHHHHHhhCCCCCEEEEecChhhhcc Q 039146 40 KASAII----CFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQ 78 (84) Q Consensus 40 ~~~aIv----~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~ 78 (84) |+.+|+ ++++-|.....+...+-++|||++|...+-..+ T Consensus 434 GahailsNG~vysR~GTa~valvAna~nVPVlVCCE~yKF~eR 476 (556) T KOG1467|consen 434 GAHAILSNGAVYSRVGTACVALVANAFNVPVLVCCEAYKFHER 476 (556) T ss_pred chhhhhcCcchhhhcchHHHHHHhcccCCCEEEEechhhhhhh Confidence 555554 578999999988888889999999977665443 No 209 >PRK00865 glutamate racemase; Provisional Probab=23.12 E-value=2.7e+02 Score=19.45 Aligned_cols=43 Identities=16% Similarity=0.150 Sum_probs=26.7 Q ss_pred HHHHHHHHHHHhcCCcEEEEecCCchH-HHHHHhhCCCCCEEEE Q 039146 27 SITSSAVRSAIKVKASAIICFTSSGRA-ARLIAKYRPTMPVLSV 69 (84) Q Consensus 27 ~ia~~a~~~a~~~~~~aIv~~T~sG~t-a~~iS~~Rp~~pIia~ 69 (84) ......+.--.+.++++||+.-.+-.. +..--|-+-+.|||++ T Consensus 54 ~~~~~~~~~L~~~g~d~iVIaCNTa~~~~l~~lr~~~~iPvigi 97 (261) T PRK00865 54 ERTLEIVEFLLEYGVKMLVIACNTASAVALPDLRERYDIPVVGI 97 (261) T ss_pred HHHHHHHHHHHhCCCCEEEEeCchHHHHHHHHHHHhCCCCEEee Confidence 334445555556789999988776553 3333333447999994 No 210 >TIGR00021 rpiA ribose 5-phosphate isomerase. This model describes ribose 5-phosphate isomerase, an enzyme of the non-oxidative branch of the pentose phosphate pathway. Probab=22.98 E-value=1.6e+02 Score=20.51 Aligned_cols=29 Identities=7% Similarity=0.111 Sum_probs=14.9 Q ss_pred CCchHHHHHHhhCCCC------CEEEEecChhhhc Q 039146 49 SSGRAARLIAKYRPTM------PVLSVVIPQLKTN 77 (84) Q Consensus 49 ~sG~ta~~iS~~Rp~~------pIia~t~~~~~~r 77 (84) .+|.|...+.++=+.. .+.++|++..++. T Consensus 22 dsGST~~~~~~~L~~~~~~~~l~itvVt~S~~~a~ 56 (218) T TIGR00021 22 GTGSTVAYFIEALGERVKQEGLDIVGVPTSKQTAE 56 (218) T ss_pred CCcHHHHHHHHHHHHhhhccCCCEEEEeCCHHHHH Confidence 6666665555443321 3555666555443 No 211 >TIGR02127 pyrF_sub2 orotidine 5'-phosphate decarboxylase, subfamily 2. This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. See TIGR01740 for a related but distinct subfamily of the same enzyme. Probab=22.87 E-value=2.9e+02 Score=19.69 Aligned_cols=45 Identities=16% Similarity=0.076 Sum_probs=28.9 Q ss_pred CHHHHHHHHHHHHHHh---cCCcEEEEecCCchHHHHHHhhCCCCCEE Q 039146 23 SHLESITSSAVRSAIK---VKASAIICFTSSGRAARLIAKYRPTMPVL 67 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~---~~~~aIv~~T~sG~ta~~iS~~Rp~~pIi 67 (84) +..+.++.-+....+. .+...+||..+++.-++.+-+.-|+.+|+ T Consensus 167 ~~~~~V~~~a~~~~~~~~~~g~~GvV~gAT~p~e~~~iR~~~~~~~il 214 (261) T TIGR02127 167 TVYEEVAELAGELNESPGDCSSVGAVVGATSPGDLLRLRIEMPTAPFL 214 (261) T ss_pred CHHHHHHHHHHHhccccCcCCceEEEECCCCHHHHHHHHHhCCCCeEE Confidence 3445555544433322 14789999988888888776666887765 No 212 >COG2515 Acd 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism] Probab=22.81 E-value=3.2e+02 Score=20.47 Aligned_cols=32 Identities=22% Similarity=0.395 Sum_probs=23.2 Q ss_pred cCCcEEEEecCCch-HHHHHHhhC---CCCCEEEEe Q 039146 39 VKASAIICFTSSGR-AARLIAKYR---PTMPVLSVV 70 (84) Q Consensus 39 ~~~~aIv~~T~sG~-ta~~iS~~R---p~~pIia~t 70 (84) ...+.|||.+-||. .|-++..+- |..+||++. T Consensus 179 ~~fD~vVva~gs~gT~AGl~~g~~~~~~~~~ViG~~ 214 (323) T COG2515 179 LKFDSVVVAPGSGGTHAGLLVGLAQLGPDVEVIGID 214 (323) T ss_pred cCCCEEEEeCCCcchHHHHHHHhhhccCCCceEEEe Confidence 56677877776654 566777776 899999764 No 213 >cd08551 Fe-ADH iron-containing alcohol dehydrogenases (Fe-ADH)-like. Large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H. Probab=22.72 E-value=3.1e+02 Score=19.97 Aligned_cols=47 Identities=19% Similarity=0.261 Sum_probs=29.4 Q ss_pred HHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh---------------------CCCCCEEEEecC Q 039146 24 HLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY---------------------RPTMPVLSVVIP 72 (84) Q Consensus 24 ~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~---------------------Rp~~pIia~t~~ 72 (84) ....-...++..+...++++||.+ .|.++.-++|+ .+..|+|++-+. T Consensus 64 p~~~~v~~~~~~~~~~~~d~Iiai--GGGs~~D~AK~va~~~~~~~~~~~~~~~~~~~~~~~p~i~VPTt 131 (370) T cd08551 64 PTLSNVDAAVAAYREEGCDGVIAV--GGGSVLDTAKAIALLATNPGDIWDYEGGKPVIKPALPLIAIPTT 131 (370) T ss_pred CCHHHHHHHHHHHHhcCCCEEEEe--CCchHHHHHHHHHHHHhCCCcHHHHhCcccccCCCCCEEEecCC Confidence 344445556667777889988874 56544443333 357899988544 No 214 >COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism] Probab=22.70 E-value=2.6e+02 Score=19.17 Aligned_cols=59 Identities=12% Similarity=0.004 Sum_probs=41.9 Q ss_pred CCCHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhccc Q 039146 21 PMSHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 21 ~~~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) |++..|--|.....+.-.-+-...=+-.-||..+-..++..|++-+||+=.|++..+.. T Consensus 16 p~TK~EIRal~ls~L~~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~~~~a~~~~ 74 (187) T COG2242 16 PMTKEEIRALTLSKLRPRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELI 74 (187) T ss_pred CCcHHHHHHHHHHhhCCCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEecCHHHHHHH Confidence 34445555555555554555454445678999999999999999999998888776543 No 215 >TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase. Probab=22.68 E-value=1e+02 Score=22.29 Aligned_cols=39 Identities=15% Similarity=0.132 Sum_probs=25.9 Q ss_pred CCcEEE----EecCCchHHHHHHhhCCCCCEEEEecChhhhcc Q 039146 40 KASAII----CFTSSGRAARLIAKYRPTMPVLSVVIPQLKTNQ 78 (84) Q Consensus 40 ~~~aIv----~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~ 78 (84) ++++|. ++.+.|.....++...-++|++++++..+..+. T Consensus 190 Gad~v~~nG~v~nkiGT~~lA~~Ak~~~vPv~V~a~~~K~~~~ 232 (301) T TIGR00511 190 GADAITANGALINKIGTSQLALAAREARVPFMVAAETYKFHPK 232 (301) T ss_pred CccEEecCCCEEEHHhHHHHHHHHHHhCCCEEEEcccceecCC Confidence 555554 445667766655544449999999987776643 No 216 >PF02225 PA: PA domain; InterPro: IPR003137 The PA (Protease associated) domain is found as an insert domain in diverse proteases, which include the MEROPS peptidase families A22B, M28, and S8A []. The PA domain is also found in a plant vacuolar sorting receptor O22925 from SWISSPROT and members of the RZF family, e.g. O43567 from SWISSPROT.; PDB: 3EIF_A 1XF1_B 3BXM_A 2C6P_A 1Z8L_C 3SJF_A 3BHX_A 2C6G_A 3D7F_A 2XEG_A .... Probab=22.65 E-value=48 Score=19.01 Aligned_cols=39 Identities=23% Similarity=0.300 Sum_probs=20.9 Q ss_pred HHHHHHhcCCcEEEEec---CCchHHHHHHhhCCCCCEEEEe Q 039146 32 AVRSAIKVKASAIICFT---SSGRAARLIAKYRPTMPVLSVV 70 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T---~sG~ta~~iS~~Rp~~pIia~t 70 (84) -+..|++.+++++|++. ..+......-......|++.++ T Consensus 49 k~~~a~~~GA~gvIi~~~~~~~~~~~~~~~~~~~~iP~v~I~ 90 (101) T PF02225_consen 49 KVRNAQKAGAKGVIIYNPPPNNGSMIDSEDPDPIDIPVVFIS 90 (101) T ss_dssp HHHHHHHTTESEEEEE-TSCSCTTTTCEBTTTSTBSEEEEE- T ss_pred HHHHHHHcCCEEEEEEeCCccccCcccccCCCCcEEEEEEeC Confidence 34667788999999987 2222222222333446665553 No 217 >COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis] Probab=22.43 E-value=1.3e+02 Score=22.13 Aligned_cols=68 Identities=16% Similarity=0.063 Sum_probs=45.1 Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHhc--CCcEEE----EecCCchHHHHHHhhCCCCCEEEEecChhhhc Q 039146 10 FFKKVINYVGEPMSHLESITSSAVRSAIKV--KASAII----CFTSSGRAARLIAKYRPTMPVLSVVIPQLKTN 77 (84) Q Consensus 10 ~~~~~~~~~~~~~~~~~~ia~~a~~~a~~~--~~~aIv----~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r 77 (84) +.+.+.+......-+.|+.....+.-.... |+++|. ++.+.|.....++..+-++|+++++..-+-.. T Consensus 162 ~ak~L~~~gI~~~~I~Dsa~~~~~~~vd~VivGad~I~~nG~lvnkiGT~~lA~~A~e~~~Pf~v~aesyKf~p 235 (301) T COG1184 162 MAKELRQSGIPVTVIVDSAVGAFMSRVDKVLVGADAILANGALVNKIGTSPLALAARELRVPFYVVAESYKFVP 235 (301) T ss_pred HHHHHHHcCCceEEEechHHHHHHHhCCEEEECccceecCCcEEeccchHHHHHHHHHhCCCEEEEeeeecccc Confidence 444555544333334566666666555444 666664 34688999999999999999999987766554 No 218 >PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B .... Probab=22.37 E-value=1.2e+02 Score=16.51 Aligned_cols=29 Identities=24% Similarity=0.218 Sum_probs=19.9 Q ss_pred cCCchHHHHHHhhCCCCCEEEEecChhhhc Q 039146 48 TSSGRAARLIAKYRPTMPVLSVVIPQLKTN 77 (84) Q Consensus 48 T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r 77 (84) .-+|..+..+++. +..-++++-.++...+ T Consensus 5 ~G~G~~~~~l~~~-~~~~v~~~D~~~~~~~ 33 (95) T PF08241_consen 5 CGTGRFAAALAKR-GGASVTGIDISEEMLE 33 (95) T ss_dssp -TTSHHHHHHHHT-TTCEEEEEES-HHHHH T ss_pred CcCCHHHHHHHhc-cCCEEEEEeCCHHHHH Confidence 3578888888887 7778888877766443 No 219 >PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A. Probab=22.34 E-value=88 Score=18.52 Aligned_cols=10 Identities=40% Similarity=0.514 Sum_probs=4.4 Q ss_pred HHhcCCcEEE Q 039146 36 AIKVKASAII 45 (84) Q Consensus 36 a~~~~~~aIv 45 (84) |...++++|| T Consensus 57 a~~~~i~~iI 66 (105) T PF07085_consen 57 AIEAGIACII 66 (105) T ss_dssp HCCTTECEEE T ss_pred HHHhCCCEEE Confidence 3344455444 No 220 >PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A .... Probab=22.31 E-value=93 Score=19.51 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=17.5 Q ss_pred CCcEEEEecCCchHHHHHHh Q 039146 40 KASAIICFTSSGRAARLIAK 59 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~ 59 (84) +..++++++.++..+..+++ T Consensus 50 ~TsGlll~a~~~~~~~~l~~ 69 (164) T PF00849_consen 50 DTSGLLLFAKDKEAAAKLSK 69 (164) T ss_dssp T-EEEEEEESSHHHHHHHHH T ss_pred cccCCeeccCCccccccccc Confidence 46889999999999999988 No 221 >PRK05638 threonine synthase; Validated Probab=22.06 E-value=2.5e+02 Score=21.24 Aligned_cols=50 Identities=28% Similarity=0.355 Sum_probs=35.1 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhh--CCCCCEEEEecCh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAKY--RPTMPVLSVVIPQ 73 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~--Rp~~pIia~t~~~ 73 (84) +..+-.+...+.-+...+.+.||+ ..||++++.+|.+ +-..+.+.+++.. T Consensus 94 SfKdR~a~~~i~~a~~~g~~~vv~-aSsGN~g~alA~~aa~~G~~~~i~vp~~ 145 (442) T PRK05638 94 SFRDRLATVAVSYGLPYAANGFIV-ASDGNAAASVAAYSARAGKEAFVVVPRK 145 (442) T ss_pred ChHHHHHHHHHHHHHHcCCCEEEE-eCCChHHHHHHHHHHHcCCCEEEEEeCC Confidence 345666666666677778887777 5789999977765 3357777777753 No 222 >PRK14077 pnk inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=21.87 E-value=1.9e+02 Score=20.84 Aligned_cols=31 Identities=19% Similarity=0.174 Sum_probs=24.1 Q ss_pred CCcEEEEecCCchHHHHHHhhCC-CCCEEEEe Q 039146 40 KASAIICFTSSGRAARLIAKYRP-TMPVLSVV 70 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~Rp-~~pIia~t 70 (84) +++.+|++--+|..-+..-.+.+ ++||+++- T Consensus 64 ~~Dlvi~iGGDGT~L~aa~~~~~~~~PilGIN 95 (287) T PRK14077 64 ISDFLISLGGDGTLISLCRKAAEYDKFVLGIH 95 (287) T ss_pred CCCEEEEECCCHHHHHHHHHhcCCCCcEEEEe Confidence 57899999899887766666554 78999883 No 223 >cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins. Probab=21.86 E-value=88 Score=19.72 Aligned_cols=20 Identities=15% Similarity=0.370 Sum_probs=18.0 Q ss_pred CCcEEEEecCCchHHHHHHh Q 039146 40 KASAIICFTSSGRAARLIAK 59 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~ 59 (84) +..++++++.+|..++.++. T Consensus 43 ~TsGlll~ak~~~~~~~l~~ 62 (146) T cd02870 43 DTEGLLLLTNDGELANRLTH 62 (146) T ss_pred CCeeEEEEeCCHHHHHHhhC Confidence 57889999999999999986 No 224 >TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine. Probab=21.81 E-value=2.2e+02 Score=17.83 Aligned_cols=34 Identities=21% Similarity=0.343 Sum_probs=25.0 Q ss_pred CCcEEEEe-------cCCchHHHHHHhhC-CCCCEEEEecCh Q 039146 40 KASAIICF-------TSSGRAARLIAKYR-PTMPVLSVVIPQ 73 (84) Q Consensus 40 ~~~aIv~~-------T~sG~ta~~iS~~R-p~~pIia~t~~~ 73 (84) +.+.|++. +..|..-+.+..+- ++.+|+...++. T Consensus 66 ~i~~i~vv~~~~~~~sPCG~Crq~l~e~~~~~~~v~~~~~~~ 107 (127) T TIGR01354 66 KFVAIAVADSADDPVSPCGACRQVLAEFAGPDTPIYMTNNDG 107 (127) T ss_pred CeEEEEEEeCCCCCcCccHHHHHHHHHhCCCCcEEEEECCCC Confidence 55667664 67788888999997 667887765554 No 225 >cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Probab=21.52 E-value=93 Score=19.74 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=20.9 Q ss_pred HHHhc--CCcEEEEecCCchHHHHHHhh Q 039146 35 SAIKV--KASAIICFTSSGRAARLIAKY 60 (84) Q Consensus 35 ~a~~~--~~~aIv~~T~sG~ta~~iS~~ 60 (84) ....+ +..++++++.+|..++.+++- T Consensus 37 ~vhRLD~~TSGlll~ak~~~~~~~l~~~ 64 (154) T cd02550 37 AAGRLDKDTSGLLLLTNDGRLQRRLTEP 64 (154) T ss_pred EeccCCCCCeeEEEEEcCHHHHHHHhhh Confidence 34445 568999999999999999874 No 226 >cd08183 Fe-ADH2 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria. Probab=21.44 E-value=3.4e+02 Score=19.94 Aligned_cols=35 Identities=17% Similarity=0.150 Sum_probs=22.6 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAARLIAK 59 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~ 59 (84) ++.......++..+...+++.||. -.|.++.-++| T Consensus 58 ~p~~~~v~~~~~~~~~~~~D~IIa--iGGGS~~D~aK 92 (374) T cd08183 58 EPSVELVDAAVAEARNAGCDVVIA--IGGGSVIDAGK 92 (374) T ss_pred CcCHHHHHHHHHHHHhcCCCEEEE--ecCchHHHHHH Confidence 334445556677788889998887 46665554444 No 227 >TIGR03528 2_3_DAP_am_ly diaminopropionate ammonia-lyase. Members of this protein family are the homodimeric, pyridoxal phosphate enzyme diaminopropionate ammonia-lyase, which adds water to remove two amino groups, leaving pyruvate. Probab=21.43 E-value=2.5e+02 Score=21.09 Aligned_cols=41 Identities=17% Similarity=0.199 Sum_probs=25.2 Q ss_pred HHHHHHHhcC------CcEEEEecCCchHHHHHHh-----hCCCCC-EEEEec Q 039146 31 SAVRSAIKVK------ASAIICFTSSGRAARLIAK-----YRPTMP-VLSVVI 71 (84) Q Consensus 31 ~a~~~a~~~~------~~aIv~~T~sG~ta~~iS~-----~Rp~~p-Iia~t~ 71 (84) .+.++.+.++ .++||+..-+|.++--++. ++|..| ||++=+ T Consensus 210 ig~EI~eQl~~~~~~~pD~vvvpvG~Ggl~~gi~~~~~~~~~~~~p~vi~Vep 262 (396) T TIGR03528 210 LALEALEQLKEQGVEKPTHVFLQAGVGSFAGAVQGYFASAYGEERPITVIVEP 262 (396) T ss_pred HHHHHHHHHhhcCCCCCCEEEEcCCcchHHHHHHHHHHHhcCCCCCEEEEEcc Confidence 3445555543 6889998888875544433 366765 666644 No 228 >PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 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 found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A. Probab=21.38 E-value=2.1e+02 Score=18.65 Aligned_cols=32 Identities=31% Similarity=0.441 Sum_probs=19.6 Q ss_pred HhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecC Q 039146 37 IKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIP 72 (84) Q Consensus 37 ~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~ 72 (84) ...+++.||+ -|.||..+.+.= +.||+-+..+ T Consensus 31 ~~~g~dViIs---RG~ta~~lr~~~-~iPVV~I~~s 62 (176) T PF06506_consen 31 ESEGADVIIS---RGGTAELLRKHV-SIPVVEIPIS 62 (176) T ss_dssp TTTT-SEEEE---EHHHHHHHHCC--SS-EEEE--- T ss_pred HhcCCeEEEE---CCHHHHHHHHhC-CCCEEEECCC Confidence 3457786554 577999999877 8999977543 No 229 >cd07410 MPP_CpdB_N Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain. CpdB is a bacterial periplasmic protein with an N-terminal metallophosphatase domain and a C-terminal 3'-nucleotidase domain. This alignment model represents the N-terminal metallophosphatase domain, which has 2',3'-cyclic phosphodiesterase activity, hydrolyzing the 2',3'-cyclic phosphates of adenosine, guanosine, cytosine and uridine to yield nucleoside and phosphate. CpdB also hydrolyzes the chromogenic substrates p-nitrophenyl phosphate (PNPP), bis(PNPP) and p-nitrophenyl phosphorylcholine (NPPC). CpdB is thought to play a scavenging role during RNA hydrolysis by converting the non-transportable nucleotides produced by RNaseI to nucleosides which can easily enter a cell for use as a carbon source. This family also includes YfkN, a Bacillus subtilis nucleotide phosphoesterase with two copies of each of the metallophosphatase and 3'-nucleotidase domains. The N-terminal metallophos Probab=21.35 E-value=2.5e+02 Score=19.49 Aligned_cols=51 Identities=12% Similarity=0.090 Sum_probs=32.9 Q ss_pred CHHHHHHHHHHHHHHhcCCcEEEEecCCchHH------------HHHHhhCCCCCEEEEecChh Q 039146 23 SHLESITSSAVRSAIKVKASAIICFTSSGRAA------------RLIAKYRPTMPVLSVVIPQL 74 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~~~~aIv~~T~sG~ta------------~~iS~~Rp~~pIia~t~~~~ 74 (84) +..+++ ...+.....-+++.||+++..|.-. +.+++.=|.+.+|...++.. T Consensus 167 d~~~~~-~~~v~~lr~~~~D~IIvl~H~g~~~~~~~~~~~~~~~~~la~~~~~vD~IlgGHsH~ 229 (277) T cd07410 167 DPVETA-KKYVPKLRAEGADVVVVLAHGGFERDLEESLTGENAAYELAEEVPGIDAILTGHQHR 229 (277) T ss_pred CHHHHH-HHHHHHHHHcCCCEEEEEecCCcCCCcccccCCccHHHHHHhcCCCCcEEEeCCCcc Confidence 444543 3334444445799999999988653 46666658888886655544 No 230 >cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA. Probab=21.25 E-value=1.1e+02 Score=20.28 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=20.2 Q ss_pred HHhc--CCcEEEEecCCchHHHHHHh Q 039146 36 AIKV--KASAIICFTSSGRAARLIAK 59 (84) Q Consensus 36 a~~~--~~~aIv~~T~sG~ta~~iS~ 59 (84) ...+ +...++++|.+|..++.++. T Consensus 50 VgRLD~dTsGLLl~t~d~~~~~~L~~ 75 (177) T cd02555 50 IGPLDKDASGLLVFSQDGRVLRKLIG 75 (177) T ss_pred ecCCCCCCeeEEEEECCHHHHHHHhC Confidence 3444 67899999999999999986 No 231 >PRK06110 hypothetical protein; Provisional Probab=21.21 E-value=2.8e+02 Score=19.93 Aligned_cols=42 Identities=12% Similarity=-0.004 Sum_probs=31.5 Q ss_pred HHHHHHHhc-CCcEEEEecCCchHHHHHH----hhCCCCCEEEEecC Q 039146 31 SAVRSAIKV-KASAIICFTSSGRAARLIA----KYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~-~~~aIv~~T~sG~ta~~iS----~~Rp~~pIia~t~~ 72 (84) -+.++.+++ +.++||+..-+|.+..-++ .++|+..|+++-+. T Consensus 159 ~~~Ei~~q~~~~D~vv~pvG~Gg~~~Gv~~~~k~~~~~~~vi~Vep~ 205 (322) T PRK06110 159 YALELFRAVPDLDVVYVPIGMGSGICGAIAARDALGLKTRIVGVVSA 205 (322) T ss_pred HHHHHHhhCCCCCEEEEecCHHHHHHHHHHHHHHhCCCCEEEEEeeC Confidence 345566666 4689999999998877665 46899999999764 No 232 >COG1844 Uncharacterized protein conserved in archaea [Function unknown] Probab=21.00 E-value=95 Score=19.99 Aligned_cols=57 Identities=19% Similarity=0.198 Sum_probs=35.8 Q ss_pred CHHHHHHHHHHHHH-HhcCCcEEEEe-cCCchHHHHHHhhCCCCCEEEEecChhhhccc Q 039146 23 SHLESITSSAVRSA-IKVKASAIICF-TSSGRAARLIAKYRPTMPVLSVVIPQLKTNQL 79 (84) Q Consensus 23 ~~~~~ia~~a~~~a-~~~~~~aIv~~-T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r~L 79 (84) +..|-+..+.+--. ..+++.+++=+ -..+..-.++.+..|.+.||++++-..+.+.| T Consensus 39 ~~aD~~~~~ilGe~R~k~~~aa~a~v~~~a~~aI~rIr~IHPPAHiIVIs~r~dvy~el 97 (125) T COG1844 39 ELADEILSSILGEVRKKCKVAAVAEVEEPASKAIGRIRKIHPPAHIIVISPRHDVYKEL 97 (125) T ss_pred hhHHHHHHHHHHHHhcccchhheeeecCccHHHHHHHHhcCCCceEEEeCCCchHHHHH Confidence 34555555544333 22344433322 35566677899999999999999887776554 No 233 >cd08184 Fe-ADH3 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the iron-containing alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron or zinc ions. Members of this family are mainly found in bacteria. Probab=21.00 E-value=3.5e+02 Score=19.92 Aligned_cols=36 Identities=14% Similarity=0.050 Sum_probs=22.6 Q ss_pred CHHHHHHHHHHHHHHhc---CCcEEEEecCCchHHHHHHhh Q 039146 23 SHLESITSSAVRSAIKV---KASAIICFTSSGRAARLIAKY 60 (84) Q Consensus 23 ~~~~~ia~~a~~~a~~~---~~~aIv~~T~sG~ta~~iS~~ 60 (84) +++......+++.+... +++.||. -.|.++.-.+|. T Consensus 61 nPt~~~v~~~~~~~~~~~~~~~D~IIa--iGGGS~iD~AKa 99 (347) T cd08184 61 EPKTDQIDALTAQVKSFDGKLPCAIVG--IGGGSTLDVAKA 99 (347) T ss_pred CcCHHHHHHHHHHHHhhCCCCCCEEEE--eCCcHHHHHHHH Confidence 45555555666677766 8998887 467655544443 No 234 >PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD:alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A .... Probab=20.88 E-value=98 Score=18.37 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=17.4 Q ss_pred HHHHHHHHHHhcCCcEEEEecCCchHHHHH Q 039146 28 ITSSAVRSAIKVKASAIICFTSSGRAARLI 57 (84) Q Consensus 28 ia~~a~~~a~~~~~~aIv~~T~sG~ta~~i 57 (84) +...++++|...+++ ||+.+.+..-...+ T Consensus 2 vG~~a~q~ak~~G~~-vi~~~~~~~k~~~~ 30 (130) T PF00107_consen 2 VGLMAIQLAKAMGAK-VIATDRSEEKLELA 30 (130) T ss_dssp HHHHHHHHHHHTTSE-EEEEESSHHHHHHH T ss_pred hHHHHHHHHHHcCCE-EEEEECCHHHHHHH Confidence 567788888888855 44444444333333 No 235 >COG1432 Uncharacterized conserved protein [Function unknown] Probab=20.87 E-value=1.6e+02 Score=19.62 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=29.3 Q ss_pred HHHHHHHHHHHHhcCCcEEEEecCCchHHHHHHhhCC Q 039146 26 ESITSSAVRSAIKVKASAIICFTSSGRAARLIAKYRP 62 (84) Q Consensus 26 ~~ia~~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp 62 (84) --+|..+..++.+-+++.|+.+|.+|.-...+...|- T Consensus 96 v~la~D~~~l~~~~~~D~ivl~SgD~DF~p~v~~~~~ 132 (181) T COG1432 96 VELAVDAMELADKKNVDTIVLFSGDGDFIPLVEAARD 132 (181) T ss_pred hhhHHHHHHhhcccCCCEEEEEcCCccHHHHHHHHHH Confidence 3566778888888889999999999998887766543 No 236 >PRK01231 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=20.76 E-value=2e+02 Score=20.80 Aligned_cols=31 Identities=19% Similarity=0.293 Sum_probs=24.7 Q ss_pred CCcEEEEecCCchHHHHHHhh-CCCCCEEEEe Q 039146 40 KASAIICFTSSGRAARLIAKY-RPTMPVLSVV 70 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~-Rp~~pIia~t 70 (84) +++.||++--+|..-+....+ .+++||+++- T Consensus 62 ~~d~vi~~GGDGt~l~~~~~~~~~~~Pvlgin 93 (295) T PRK01231 62 VCDLVIVVGGDGSLLGAARALARHNVPVLGIN 93 (295) T ss_pred CCCEEEEEeCcHHHHHHHHHhcCCCCCEEEEe Confidence 578999999999877776666 4689999884 No 237 >PRK04457 spermidine synthase; Provisional Probab=20.72 E-value=2.8e+02 Score=19.39 Aligned_cols=37 Identities=19% Similarity=0.158 Sum_probs=30.1 Q ss_pred CcEEEEecCCchHHHHHHhhCCCCCEEEEecChhhhc Q 039146 41 ASAIICFTSSGRAARLIAKYRPTMPVLSVVIPQLKTN 77 (84) Q Consensus 41 ~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~~~~~r 77 (84) .+.+.+-+-+|..++.+++..|...|.++=.|+.+.+ T Consensus 68 ~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEidp~vi~ 104 (262) T PRK04457 68 QHILQIGLGGGSLAKFIYTYLPDTRQTAVEINPQVIA 104 (262) T ss_pred CEEEEECCCHhHHHHHHHHhCCCCeEEEEECCHHHHH Confidence 3556666778899999999999999999988777764 No 238 >PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A .... Probab=20.71 E-value=2.2e+02 Score=19.79 Aligned_cols=42 Identities=14% Similarity=0.166 Sum_probs=28.6 Q ss_pred HHHHHHHhcCCcEEEEecCCchHHHHHHhhCCCCCEEEEecC Q 039146 31 SAVRSAIKVKASAIICFTSSGRAARLIAKYRPTMPVLSVVIP 72 (84) Q Consensus 31 ~a~~~a~~~~~~aIv~~T~sG~ta~~iS~~Rp~~pIia~t~~ 72 (84) ...+.-...++++||+.+..........-.+.+.|++.+-+. T Consensus 47 ~~i~~l~~~~vDGiI~~s~~~~~~~l~~~~~~~iPvV~~~~~ 88 (279) T PF00532_consen 47 EYIELLLQRRVDGIILASSENDDEELRRLIKSGIPVVLIDRY 88 (279) T ss_dssp HHHHHHHHTTSSEEEEESSSCTCHHHHHHHHTTSEEEEESS- T ss_pred HHHHHHHhcCCCEEEEecccCChHHHHHHHHcCCCEEEEEec Confidence 556666777899999988777744433333448999888655 No 239 >PRK01077 cobyrinic acid a,c-diamide synthase; Validated Probab=20.65 E-value=2.8e+02 Score=21.12 Aligned_cols=40 Identities=23% Similarity=0.369 Sum_probs=23.1 Q ss_pred HHHHHHhcCCcEEEEecCCc---hHHH---HHHhhCCCCCEEEEec Q 039146 32 AVRSAIKVKASAIICFTSSG---RAAR---LIAKYRPTMPVLSVVI 71 (84) Q Consensus 32 a~~~a~~~~~~aIv~~T~sG---~ta~---~iS~~Rp~~pIia~t~ 71 (84) ..++|..+++..|+|...++ ..+. .+..+++..+|.++.- T Consensus 106 ~adiA~~l~~pviLV~~~~~~~~~~a~l~~~~~~~~~~i~i~GvI~ 151 (451) T PRK01077 106 TADIAKLLGAPVVLVVDASGMAQSAAALVLGFATFDPDVRIAGVIL 151 (451) T ss_pred HHHHHHHhCCCEEEEECCchHHHHHHHHHHHHHHhCCCCCEEEEEE Confidence 45788888888888865443 1222 2234555666555543 No 240 >PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B. Probab=20.59 E-value=92 Score=21.11 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=12.3 Q ss_pred HHHHHhhCCCCCEEEEecCh Q 039146 54 ARLIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 54 a~~iS~~Rp~~pIia~t~~~ 73 (84) ...+..-+|.+||+.+++.. T Consensus 84 v~~iR~~hP~tPIllv~~~~ 103 (178) T PF14606_consen 84 VKTIREAHPDTPILLVSPIP 103 (178) T ss_dssp HHHHHTT-SSS-EEEEE--- T ss_pred HHHHHHhCCCCCEEEEecCC Confidence 44677889999999998544 No 241 >PRK08298 cytidine deaminase; Validated Probab=20.59 E-value=2.5e+02 Score=18.08 Aligned_cols=26 Identities=8% Similarity=0.110 Sum_probs=19.5 Q ss_pred cCCchHHHHHHhhCCCCCEEEEecCh Q 039146 48 TSSGRAARLIAKYRPTMPVLSVVIPQ 73 (84) Q Consensus 48 T~sG~ta~~iS~~Rp~~pIia~t~~~ 73 (84) +..|.--+.|+-|.|+.+|+....+. T Consensus 87 sPCG~CRQvl~Ef~~~~~v~~~~~~g 112 (136) T PRK08298 87 SPCGVCQERLFYWGPDVMCAVTNADD 112 (136) T ss_pred CCChhHHHHHHHhCCCCEEEEECCCC Confidence 34456678999999999988876554 No 242 >cd06449 ACCD Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia. Probab=20.53 E-value=3.2e+02 Score=19.33 Aligned_cols=33 Identities=12% Similarity=0.124 Sum_probs=26.5 Q ss_pred CCcEEEEecCCchHHHHHHhh----CCCCCEEEEecC Q 039146 40 KASAIICFTSSGRAARLIAKY----RPTMPVLSVVIP 72 (84) Q Consensus 40 ~~~aIv~~T~sG~ta~~iS~~----Rp~~pIia~t~~ 72 (84) ..+.||+..-+|.|+.-+++. +|...|++|-+. T Consensus 174 ~~d~vv~~~GtGgt~~G~~~~~~~~~~~~~ii~V~~~ 210 (307) T cd06449 174 KFDSIVVCSVTGSTHAGLSVGLAALGRQRRVIGIDAS 210 (307) T ss_pred CCCEEEEeCCchHHHHHHHHHHHhcCCCCeEEEEEec Confidence 478999999999998766554 688899999653 No 243 >PF02056 Glyco_hydro_4: Family 4 glycosyl hydrolase; InterPro: IPR001088 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 4 GH4 from CAZY comprises enzymes with several known activities; 6-phospho-beta-glucosidase (3.2.1.86 from EC); 6-phospho-alpha-glucosidase (3.2.1.122 from EC); alpha-galactosidase (3.2.1.22 from EC). 6-phospho-alpha-glucosidase requires both NAD(H) and divalent metal (Mn2+, Fe2+, Co2+, or Ni2+) for activity [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1U8X_X 1S6Y_A 3FEF_B 1VJT_A 1UP4_A 1UP6_C 1UP7_E 1OBB_A. Probab=20.45 E-value=2.5e+02 Score=19.00 Aligned_cols=34 Identities=18% Similarity=0.371 Sum_probs=25.3 Q ss_pred cEEEEec-CCchHHHHHHhhCCCCCEEEEecChhh Q 039146 42 SAIICFT-SSGRAARLIAKYRPTMPVLSVVIPQLK 75 (84) Q Consensus 42 ~aIv~~T-~sG~ta~~iS~~Rp~~pIia~t~~~~~ 75 (84) ..++=+| ..|-..+.+.|+.|+.+++++|+.+.. T Consensus 138 Aw~iNytNP~~~vt~a~~r~~~~~k~vGlCh~~~~ 172 (183) T PF02056_consen 138 AWLINYTNPMGIVTEALSRYTPKIKVVGLCHGPQG 172 (183) T ss_dssp SEEEE-SSSHHHHHHHHHHHSTTSEEEEE-SHHHH T ss_pred cEEEeccChHHHHHHHHHHhCCCCCEEEECCCHHH Confidence 4466666 567788899999999999999986643 No 244 >PRK09224 threonine dehydratase; Reviewed Probab=20.30 E-value=3.1e+02 Score=21.33 Aligned_cols=41 Identities=20% Similarity=0.233 Sum_probs=30.8 Q ss_pred HHHHHHhcC--CcEEEEecCCchHHH----HHHhhCCCCCEEEEecC Q 039146 32 AVRSAIKVK--ASAIICFTSSGRAAR----LIAKYRPTMPVLSVVIP 72 (84) Q Consensus 32 a~~~a~~~~--~~aIv~~T~sG~ta~----~iS~~Rp~~pIia~t~~ 72 (84) +.++.+.++ .++|++..-+|.+.- .+...+|+..||++-+. T Consensus 159 ~~EI~~q~~~~~D~vvvpvGgGGliaGia~~lk~~~p~~kVigVe~~ 205 (504) T PRK09224 159 AMEILQQHPHPLDAVFVPVGGGGLIAGVAAYIKQLRPEIKVIGVEPE 205 (504) T ss_pred HHHHHHhccCCCCEEEEecChhHHHHHHHHHHHHhCCCCEEEEEEEC Confidence 456666663 689999998886655 45567899999999753 Done!