Query psy255 Match_columns 70 No_of_seqs 140 out of 1012 Neff 9.0 Searched_HMMs 46136 Date Fri Aug 16 19:06:07 2013 Command hhsearch -i /work/01045/syshi/Psyhhblits/psy255.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/255hhsearch_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 99.9 5.2E-22 1.1E-26 109.7 7.1 70 1-70 43-115 (117) 2 PLN02762 pyruvate kinase compl 99.8 4.5E-18 9.7E-23 112.1 7.5 69 1-70 436-505 (509) 3 PTZ00066 pyruvate kinase; Prov 99.7 6.6E-18 1.4E-22 111.4 7.5 70 1-70 438-509 (513) 4 PRK09206 pyruvate kinase; Prov 99.7 1.1E-17 2.4E-22 109.5 7.6 70 1-70 397-467 (470) 5 PRK06247 pyruvate kinase; Prov 99.7 1.3E-17 2.9E-22 109.2 7.7 70 1-70 396-467 (476) 6 PTZ00300 pyruvate kinase; Prov 99.7 1.8E-17 4E-22 108.2 7.5 70 1-70 375-450 (454) 7 PRK06354 pyruvate kinase; Prov 99.7 3.5E-17 7.5E-22 109.6 7.5 70 1-70 404-475 (590) 8 cd00288 Pyruvate_Kinase Pyruva 99.7 5.3E-17 1.1E-21 106.7 7.1 70 1-70 402-477 (480) 9 PLN02623 pyruvate kinase 99.7 8.4E-17 1.8E-21 107.2 7.7 70 1-70 503-576 (581) 10 TIGR01064 pyruv_kin pyruvate k 99.7 1.3E-16 2.8E-21 104.8 7.9 70 1-70 400-473 (473) 11 COG0469 PykF Pyruvate kinase [ 99.7 1E-16 2.2E-21 105.0 6.8 70 1-70 402-474 (477) 12 PLN02461 Probable pyruvate kin 99.5 2.3E-14 4.9E-19 94.8 6.9 60 7-70 441-507 (511) 13 PLN02765 pyruvate kinase 99.5 4E-14 8.7E-19 93.8 6.8 60 7-70 454-521 (526) 14 PRK05826 pyruvate kinase; Prov 99.5 6.2E-14 1.3E-18 92.1 7.2 61 1-61 400-461 (465) 15 KOG2323|consensus 99.3 5.4E-12 1.2E-16 83.1 5.5 70 1-70 422-498 (501) 16 PF08541 ACP_syn_III_C: 3-Oxoa 91.0 0.37 8E-06 24.9 2.9 26 33-58 53-78 (90) 17 PRK06816 3-oxoacyl-(acyl carri 86.2 3.1 6.6E-05 27.1 5.2 29 31-59 337-365 (378) 18 PRK12281 rplX 50S ribosomal pr 85.9 0.66 1.4E-05 23.9 1.7 17 45-61 6-22 (76) 19 COG0332 FabH 3-oxoacyl-[acyl-c 85.4 1.2 2.6E-05 28.9 3.0 28 29-56 281-308 (323) 20 smart00739 KOW KOW (Kyprides, 85.1 1.3 2.8E-05 17.6 2.2 16 46-61 2-17 (28) 21 CHL00141 rpl24 ribosomal prote 82.7 1.1 2.5E-05 23.4 1.8 17 45-61 8-24 (83) 22 TIGR03595 Obg_CgtA_exten Obg f 82.6 2.2 4.8E-05 21.4 2.8 17 37-54 46-62 (69) 23 PLN02326 3-oxoacyl-[acyl-carri 82.2 5.8 0.00013 25.9 5.2 28 30-57 339-366 (379) 24 CHL00203 fabH 3-oxoacyl-acyl-c 82.0 3.2 6.9E-05 26.3 3.9 27 31-57 286-312 (326) 25 PF04977 DivIC: Septum formati 81.3 3 6.5E-05 20.8 3.0 21 35-55 56-77 (80) 26 TIGR02620 cas_VVA1548 putative 80.9 2.6 5.6E-05 22.6 2.7 20 36-55 9-41 (93) 27 PF09269 DUF1967: Domain of un 80.0 2.4 5.2E-05 21.2 2.4 17 37-54 46-62 (69) 28 TIGR01079 rplX_bact ribosomal 79.8 1.6 3.5E-05 23.8 1.8 16 45-60 3-18 (104) 29 PRK00004 rplX 50S ribosomal pr 79.3 1.7 3.7E-05 23.7 1.8 17 45-61 4-20 (105) 30 PLN02854 3-ketoacyl-CoA syntha 78.7 5.4 0.00012 27.6 4.3 28 29-56 452-479 (521) 31 PRK09258 3-oxoacyl-(acyl carri 78.0 9.2 0.0002 24.2 5.1 27 31-57 299-325 (338) 32 PRK05963 3-oxoacyl-(acyl carri 77.2 8.2 0.00018 24.4 4.7 27 31-57 287-313 (326) 33 PLN02192 3-ketoacyl-CoA syntha 77.1 5 0.00011 27.7 3.8 27 30-56 441-467 (511) 34 PRK07204 3-oxoacyl-(acyl carri 75.9 8.5 0.00018 24.3 4.5 27 31-57 290-316 (329) 35 COG0794 GutQ Predicted sugar p 75.3 1.7 3.7E-05 26.5 1.1 17 42-58 80-96 (202) 36 TIGR01080 rplX_A_E ribosomal p 73.2 2.4 5.3E-05 23.5 1.3 20 42-61 38-57 (114) 37 PF02261 Asp_decarbox: Asparta 73.2 3.1 6.7E-05 23.2 1.7 14 43-56 76-89 (116) 38 TIGR00223 panD L-aspartate-alp 73.1 3.4 7.3E-05 23.4 1.9 14 44-57 77-90 (126) 39 cd06919 Asp_decarbox Aspartate 73.0 3.4 7.4E-05 22.9 1.9 15 44-58 76-90 (111) 40 COG0853 PanD Aspartate 1-decar 72.8 3.2 7E-05 23.4 1.8 15 44-58 76-90 (126) 41 COG0198 RplX Ribosomal protein 72.2 3.7 8E-05 22.5 1.9 17 45-61 4-20 (104) 42 PLN02377 3-ketoacyl-CoA syntha 72.0 7.7 0.00017 26.7 3.7 27 30-56 437-463 (502) 43 TIGR00739 yajC preprotein tran 71.5 3 6.4E-05 21.8 1.4 16 44-59 36-51 (84) 44 PRK05449 aspartate alpha-decar 71.1 3.9 8.5E-05 23.1 1.9 15 44-58 77-91 (126) 45 PRK01191 rpl24p 50S ribosomal 71.0 3.4 7.4E-05 23.2 1.6 22 40-61 40-61 (120) 46 PTZ00194 60S ribosomal protein 70.1 3.7 8.1E-05 23.7 1.7 22 40-61 41-62 (143) 47 PRK05585 yajC preprotein trans 67.2 4 8.7E-05 22.3 1.4 17 43-59 50-66 (106) 48 COG1862 YajC Preprotein transl 67.0 4.1 9E-05 22.0 1.4 16 44-59 42-57 (97) 49 PF13730 HTH_36: Helix-turn-he 66.2 9.9 0.00021 17.5 2.5 17 30-46 39-55 (55) 50 PRK10696 tRNA 2-thiocytidine b 64.1 18 0.00038 22.4 4.0 27 31-57 11-38 (258) 51 PRK05886 yajC preprotein trans 63.7 5.1 0.00011 22.1 1.4 16 44-59 37-52 (109) 52 COG0031 CysK Cysteine synthase 63.6 15 0.00032 23.8 3.6 28 30-57 43-71 (300) 53 PF01568 Molydop_binding: Moly 63.5 11 0.00024 19.8 2.7 20 38-58 37-56 (110) 54 TIGR02695 azurin azurin. Azuri 63.1 21 0.00045 20.2 3.7 41 27-68 52-93 (125) 55 PRK06840 hypothetical protein; 61.4 30 0.00065 22.0 4.7 25 33-57 298-322 (339) 56 PF02699 YajC: Preprotein tran 61.2 2.7 5.9E-05 21.8 0.0 17 43-59 34-50 (82) 57 PRK12879 3-oxoacyl-(acyl carri 61.2 18 0.00039 22.7 3.7 25 33-57 287-311 (325) 58 PF00467 KOW: KOW motif; Inte 61.1 4.8 0.0001 16.9 0.8 14 48-61 1-14 (32) 59 PRK06531 yajC preprotein trans 61.1 6 0.00013 21.9 1.4 15 45-59 36-50 (113) 60 PRK00888 ftsB cell division pr 60.8 25 0.00055 19.0 4.2 24 35-58 66-90 (105) 61 cd00830 KAS_III Ketoacyl-acyl 59.4 21 0.00045 22.3 3.7 26 32-57 284-309 (320) 62 PF10727 Rossmann-like: Rossma 59.3 7.8 0.00017 21.7 1.6 32 28-59 76-107 (127) 63 PF14120 YhzD: YhzD-like prote 58.6 22 0.00048 17.6 3.0 31 27-57 24-54 (61) 64 COG4393 Predicted membrane pro 58.3 9.8 0.00021 25.2 2.1 36 33-68 333-375 (405) 65 PRK13656 trans-2-enoyl-CoA red 58.3 20 0.00044 24.1 3.6 35 26-60 17-51 (398) 66 cd00831 CHS_like Chalcone and 57.1 22 0.00047 22.9 3.6 26 32-57 325-350 (361) 67 PLN02932 3-ketoacyl-CoA syntha 56.6 23 0.00049 24.4 3.7 26 31-56 414-439 (478) 68 PF09285 Elong-fact-P_C: Elong 56.1 8.4 0.00018 18.7 1.2 14 44-57 36-49 (56) 69 COG2164 Uncharacterized conser 55.1 33 0.00071 19.0 3.5 43 13-55 79-124 (126) 70 PF09652 Cas_VVA1548: Putative 55.0 22 0.00047 19.1 2.8 10 36-45 9-18 (93) 71 PF00595 PDZ: PDZ domain (Also 54.5 8.8 0.00019 19.1 1.2 19 40-59 38-56 (81) 72 COG4821 Uncharacterized protei 54.3 32 0.00069 21.4 3.7 31 28-58 84-114 (243) 73 PF14544 DUF4443: Domain of un 53.9 18 0.00039 20.0 2.4 18 41-58 70-87 (108) 74 PF14136 DUF4303: Domain of un 53.2 34 0.00073 19.3 3.7 27 30-56 105-134 (155) 75 cd02790 MopB_CT_Formate-Dh_H F 53.0 21 0.00046 18.8 2.7 20 38-58 42-61 (116) 76 TIGR00747 fabH 3-oxoacyl-(acyl 53.0 30 0.00065 21.7 3.7 26 33-58 281-306 (318) 77 TIGR03089 conserved hypothetic 53.0 33 0.00071 20.7 3.7 29 29-58 33-62 (227) 78 cd02789 MopB_CT_FmdC-FwdD The 52.7 22 0.00048 19.0 2.7 20 38-58 38-57 (106) 79 COG2425 Uncharacterized protei 52.4 31 0.00066 23.6 3.8 31 27-58 347-377 (437) 80 cd02787 MopB_CT_ydeP The MopB_ 52.2 22 0.00048 18.8 2.7 20 38-58 38-57 (112) 81 TIGR00686 phnA alkylphosphonat 52.0 25 0.00054 19.5 2.8 17 44-60 49-65 (109) 82 TIGR03635 S17_bact 30S ribosom 51.8 19 0.00041 18.2 2.2 16 45-60 48-63 (71) 83 PF13580 SIS_2: SIS domain; PD 51.5 14 0.0003 20.6 1.9 13 46-58 101-113 (138) 84 PF00884 Sulfatase: Sulfatase; 51.2 31 0.00067 20.9 3.5 30 29-60 220-249 (308) 85 cd02777 MopB_CT_DMSOR-like The 51.0 23 0.0005 19.2 2.6 20 38-58 41-60 (127) 86 cd02794 MopB_CT_DmsA-EC The Mo 50.2 25 0.00053 19.0 2.7 20 38-58 37-56 (121) 87 smart00841 Elong-fact-P_C Elon 50.1 13 0.00027 18.1 1.3 15 43-57 35-49 (56) 88 cd02779 MopB_CT_Arsenite-Ox Th 49.7 28 0.0006 18.6 2.8 20 38-58 40-59 (115) 89 cd02791 MopB_CT_Nitrate-R-NapA 49.6 26 0.00056 18.7 2.7 20 38-58 42-61 (122) 90 cd05794 S1_EF-P_repeat_2 S1_EF 49.6 13 0.00027 18.1 1.3 14 44-57 36-49 (56) 91 cd02786 MopB_CT_3 The MopB_CT_ 49.5 26 0.00056 18.6 2.7 20 38-58 38-57 (116) 92 PRK13690 hypothetical protein; 49.0 41 0.00088 20.3 3.5 30 30-59 7-36 (184) 93 COG0318 CaiC Acyl-CoA syntheta 48.7 41 0.00088 22.8 4.0 28 30-58 45-72 (534) 94 KOG3628|consensus 48.7 34 0.00074 26.5 3.7 29 29-57 807-835 (1363) 95 PRK08329 threonine synthase; V 48.2 31 0.00067 22.4 3.3 23 34-56 317-339 (347) 96 COG2824 PhnA Uncharacterized Z 48.1 25 0.00054 19.5 2.4 17 44-60 51-67 (112) 97 cd02775 MopB_CT Molybdopterin- 47.7 30 0.00064 17.6 2.7 20 38-58 30-49 (101) 98 COG1785 PhoA Alkaline phosphat 47.6 44 0.00094 23.2 3.9 27 29-60 328-354 (482) 99 cd00508 MopB_CT_Fdh-Nap-like T 47.2 31 0.00068 18.2 2.8 20 38-58 42-61 (120) 100 PRK09352 3-oxoacyl-(acyl carri 47.1 42 0.00092 21.0 3.7 24 34-57 282-305 (319) 101 cd02781 MopB_CT_Acetylene-hydr 47.0 29 0.00063 18.8 2.7 20 38-58 40-59 (130) 102 TIGR01440 conserved hypothetic 46.9 34 0.00074 20.4 3.0 26 33-58 3-28 (172) 103 PF02631 RecX: RecX family; I 46.5 31 0.00067 18.7 2.7 20 29-48 7-26 (121) 104 PF08840 BAAT_C: BAAT / Acyl-C 46.5 37 0.0008 20.4 3.2 27 31-58 4-30 (213) 105 PRK10220 hypothetical protein; 46.0 35 0.00076 18.9 2.8 17 44-60 50-66 (111) 106 PF09926 DUF2158: Uncharacteri 45.9 20 0.00044 17.1 1.7 14 46-59 1-14 (53) 107 COG4004 Uncharacterized protei 45.7 44 0.00095 18.0 3.0 38 19-58 4-41 (96) 108 PF02938 GAD: GAD domain; Int 45.5 28 0.0006 18.2 2.3 21 38-58 67-87 (95) 109 PRK00139 murE UDP-N-acetylmura 45.4 44 0.00096 22.4 3.7 23 33-58 410-432 (460) 110 PF00356 LacI: Bacterial regul 45.3 22 0.00048 16.3 1.7 40 7-46 3-44 (46) 111 COG5131 URM1 Ubiquitin-like pr 45.1 27 0.00058 18.8 2.2 18 41-58 76-93 (96) 112 cd02788 MopB_CT_NDH-1_NuoG2-N7 44.9 39 0.00084 17.5 2.9 20 38-58 36-55 (96) 113 PF10557 Cullin_Nedd8: Cullin 44.8 19 0.0004 17.8 1.5 23 28-50 42-64 (68) 114 PF06135 DUF965: Bacterial pro 44.6 32 0.00069 17.9 2.4 32 28-60 16-49 (79) 115 PF00366 Ribosomal_S17: Riboso 44.4 26 0.00055 17.6 2.0 17 43-59 41-57 (69) 116 smart00228 PDZ Domain present 44.2 29 0.00064 16.8 2.3 18 41-59 40-57 (85) 117 PF13180 PDZ_2: PDZ domain; PD 44.2 19 0.00042 17.9 1.6 19 40-59 27-45 (82) 118 PRK12390 1-aminocyclopropane-1 44.1 39 0.00085 21.7 3.2 24 34-57 299-322 (337) 119 PF13538 UvrD_C_2: UvrD-like h 44.0 15 0.00032 18.9 1.1 14 46-59 1-14 (104) 120 cd02783 MopB_CT_2 The MopB_CT_ 43.7 33 0.00071 19.6 2.6 21 37-58 38-58 (156) 121 cd02785 MopB_CT_4 The MopB_CT_ 43.5 38 0.00083 18.3 2.8 20 38-58 39-58 (124) 122 cd03701 IF2_IF5B_II IF2_IF5B_I 43.2 6.9 0.00015 20.7 -0.2 16 39-54 20-35 (95) 123 PF04260 DUF436: Protein of un 43.1 31 0.00067 20.6 2.4 26 33-58 3-28 (172) 124 PRK14481 dihydroxyacetone kina 43.0 63 0.0014 21.3 4.0 31 27-57 229-259 (331) 125 cd02778 MopB_CT_Thiosulfate-R- 42.8 40 0.00086 18.0 2.8 20 38-58 37-56 (123) 126 PF02698 DUF218: DUF218 domain 42.6 53 0.0011 18.3 3.4 29 24-56 77-105 (155) 127 COG0365 Acs Acyl-coenzyme A sy 42.5 42 0.00091 23.4 3.3 29 29-58 46-74 (528) 128 COG0361 InfA Translation initi 42.3 17 0.00036 18.8 1.1 15 43-57 44-58 (75) 129 COG4570 Rus Holliday junction 42.3 49 0.0011 18.9 3.1 29 27-55 82-110 (132) 130 PF12897 Aminotran_MocR: Alani 42.0 50 0.0011 22.5 3.5 51 2-58 187-252 (425) 131 PF13076 DUF3940: Protein of u 41.6 36 0.00077 15.1 2.0 17 35-51 5-21 (38) 132 PF14947 HTH_45: Winged helix- 41.3 32 0.00068 17.3 2.1 26 30-55 33-58 (77) 133 PF10844 DUF2577: Protein of u 41.2 25 0.00054 18.8 1.8 14 43-56 74-87 (100) 134 TIGR02362 dhaK1b probable dihy 40.9 59 0.0013 21.4 3.7 30 27-56 226-255 (326) 135 PRK12363 phosphoglycerol trans 40.8 69 0.0015 23.3 4.2 30 29-60 364-393 (703) 136 PRK10646 ADP-binding protein; 40.4 40 0.00086 19.6 2.6 28 27-58 9-36 (153) 137 cd00989 PDZ_metalloprotease PD 40.4 35 0.00075 16.5 2.1 19 40-59 25-43 (79) 138 COG4668 MtlA Mannitol/fructose 40.2 37 0.00081 19.7 2.4 24 26-49 14-37 (142) 139 TIGR02363 dhaK1 dihydroxyaceto 40.1 61 0.0013 21.4 3.6 31 27-57 230-260 (329) 140 PF02080 TrkA_C: TrkA-C domain 39.8 17 0.00037 17.4 0.9 13 45-57 47-59 (71) 141 PF00931 NB-ARC: NB-ARC domain 39.8 60 0.0013 19.8 3.5 27 30-59 2-28 (287) 142 cd02782 MopB_CT_1 The MopB_CT_ 39.7 44 0.00095 18.1 2.7 20 38-58 40-59 (129) 143 TIGR01274 ACC_deam 1-aminocycl 39.6 52 0.0011 21.2 3.3 21 37-57 301-321 (337) 144 COG0179 MhpD 2-keto-4-pentenoa 39.5 61 0.0013 20.6 3.5 27 33-61 212-238 (266) 145 cd02792 MopB_CT_Formate-Dh-Na- 39.4 46 0.00099 17.7 2.7 20 38-58 42-61 (122) 146 cd05793 S1_IF1A S1_IF1A: Trans 39.4 18 0.0004 18.5 1.0 16 40-55 33-48 (77) 147 TIGR00177 molyb_syn molybdenum 39.0 72 0.0016 17.9 4.3 27 28-59 51-77 (144) 148 PRK05610 rpsQ 30S ribosomal pr 38.8 39 0.00085 17.7 2.2 17 44-60 52-68 (84) 149 PF02829 3H: 3H domain; Inter 38.7 45 0.00098 17.9 2.5 19 28-46 79-97 (98) 150 cd03703 aeIF5B_II aeIF5B_II: T 38.6 18 0.00039 19.9 1.0 18 39-56 20-37 (110) 151 COG2412 Uncharacterized conser 38.2 49 0.0011 18.0 2.6 24 35-59 69-92 (101) 152 PF07563 DUF1541: Protein of u 38.1 34 0.00073 16.5 1.7 19 47-65 1-20 (53) 153 PF11302 DUF3104: Protein of u 38.0 26 0.00056 18.1 1.4 14 45-58 5-18 (75) 154 cd04456 S1_IF1A_like S1_IF1A_l 37.8 20 0.00044 18.4 1.0 18 39-56 32-49 (78) 155 PRK05609 nusG transcription an 37.7 26 0.00055 20.3 1.6 17 45-61 126-142 (181) 156 PF01910 DUF77: Domain of unkn 37.6 65 0.0014 16.9 3.2 19 27-45 13-31 (92) 157 TIGR03884 sel_bind_Methan sele 37.3 55 0.0012 16.9 2.5 19 26-44 24-42 (74) 158 PRK09014 rfaH transcriptional 37.1 28 0.0006 19.9 1.6 17 45-61 109-125 (162) 159 PF11737 DUF3300: Protein of u 37.1 24 0.00053 22.1 1.4 55 2-57 67-127 (237) 160 PRK10760 murein hydrolase B; P 36.9 67 0.0014 21.5 3.5 28 28-56 246-273 (359) 161 cd00827 init_cond_enzymes "ini 36.8 76 0.0017 19.8 3.7 27 31-57 287-313 (324) 162 TIGR01955 RfaH transcriptional 36.8 27 0.00058 19.8 1.5 16 46-61 109-124 (159) 163 PRK09275 aspartate aminotransf 36.6 73 0.0016 22.2 3.8 30 27-56 168-197 (527) 164 PF06969 HemN_C: HemN C-termin 36.5 24 0.00051 16.8 1.1 28 28-55 33-61 (66) 165 PRK09371 gas vesicle synthesis 36.3 29 0.00063 17.5 1.4 28 32-59 8-35 (68) 166 PF01176 eIF-1a: Translation i 36.3 24 0.00053 17.2 1.1 17 40-56 36-52 (65) 167 PF14502 HTH_41: Helix-turn-he 36.2 39 0.00086 15.9 1.8 17 31-47 21-37 (48) 168 PF03831 PhnA: PhnA protein; 36.1 22 0.00048 17.3 0.9 15 45-59 9-23 (56) 169 cd02780 MopB_CT_Tetrathionate_ 36.0 57 0.0012 18.1 2.8 20 38-58 37-56 (143) 170 PF05763 DUF835: Protein of un 35.8 85 0.0019 17.8 3.9 52 2-58 27-84 (136) 171 TIGR03338 phnR_burk phosphonat 35.6 95 0.0021 18.2 4.0 14 33-46 51-64 (212) 172 PF00994 MoCF_biosynth: Probab 35.6 82 0.0018 17.5 3.5 27 28-59 41-67 (144) 173 cd02776 MopB_CT_Nitrate-R-NarG 35.6 60 0.0013 18.3 2.8 20 38-58 38-57 (141) 174 cd02793 MopB_CT_DMSOR-BSOR-TMA 35.5 57 0.0012 17.8 2.7 20 38-58 40-59 (129) 175 PF00741 Gas_vesicle: Gas vesi 35.3 24 0.00053 15.9 0.9 25 34-58 3-27 (39) 176 COG2401 ABC-type ATPase fused 35.1 20 0.00043 25.0 0.9 22 46-69 406-427 (593) 177 TIGR02365 dha_L_ycgS dihydroxy 35.0 49 0.0011 19.7 2.5 27 30-56 100-126 (194) 178 smart00419 HTH_CRP helix_turn_ 35.0 45 0.00098 14.3 2.7 21 30-50 22-42 (48) 179 PF08784 RPA_C: Replication pr 34.8 52 0.0011 17.2 2.4 18 29-46 78-95 (102) 180 PRK14483 DhaKLM operon coactiv 34.8 1.3E+02 0.0028 19.9 4.5 30 27-56 229-258 (329) 181 TIGR00922 nusG transcription t 34.6 32 0.00069 19.8 1.6 16 46-61 120-135 (172) 182 TIGR00824 EIIA-man PTS system, 34.6 81 0.0017 17.1 5.4 39 18-59 30-68 (116) 183 KOG3580|consensus 34.4 29 0.00062 25.2 1.6 26 35-60 46-71 (1027) 184 TIGR03844 cysteate_syn cysteat 34.3 63 0.0014 21.6 3.1 24 35-58 354-378 (398) 185 cd03695 CysN_NodQ_II CysN_NodQ 34.2 24 0.00053 17.8 1.0 16 41-56 22-37 (81) 186 TIGR01916 F420_cofE F420-0:gam 34.0 49 0.0011 20.9 2.4 14 46-59 28-41 (243) 187 smart00354 HTH_LACI helix_turn 34.0 63 0.0014 15.7 2.5 42 7-48 4-47 (70) 188 KOG4146|consensus 33.9 41 0.00089 18.2 1.8 18 41-58 81-98 (101) 189 smart00652 eIF1a eukaryotic tr 33.7 26 0.00056 18.2 1.0 17 39-55 37-53 (83) 190 COG0039 Mdh Malate/lactate deh 33.6 47 0.001 21.7 2.4 21 44-64 65-85 (313) 191 PF12124 Nsp3_PL2pro: Coronavi 33.3 15 0.00032 17.8 0.1 11 45-55 31-41 (66) 192 smart00855 PGAM Phosphoglycera 33.2 76 0.0016 17.5 3.0 29 30-58 122-150 (155) 193 TIGR00405 L26e_arch ribosomal 33.2 38 0.00082 19.0 1.8 18 44-61 85-102 (145) 194 PF02362 B3: B3 DNA binding do 33.0 52 0.0011 16.8 2.2 19 37-56 66-84 (100) 195 cd03280 ABC_MutS2 MutS2 homolo 32.7 20 0.00043 21.1 0.5 21 46-67 24-44 (200) 196 KOG1535|consensus 32.6 77 0.0017 19.6 3.0 29 33-63 164-192 (217) 197 CHL00142 rps17 ribosomal prote 32.4 57 0.0012 17.1 2.2 17 44-60 49-65 (84) 198 PRK13293 F420-0--gamma-glutamy 32.3 67 0.0014 20.3 2.8 17 43-59 27-43 (245) 199 COG1725 Predicted transcriptio 32.2 63 0.0014 18.2 2.5 24 31-54 14-37 (125) 200 PF11181 YflT: Heat induced st 32.1 85 0.0018 16.6 3.5 26 30-56 9-34 (103) 201 cd03697 EFTU_II EFTU_II: Elong 32.0 43 0.00093 17.0 1.7 15 42-56 23-37 (87) 202 PRK12338 hypothetical protein; 31.9 50 0.0011 21.6 2.3 24 28-51 294-317 (319) 203 COG4043 Preprotein translocase 31.9 37 0.00081 18.7 1.5 13 45-57 33-45 (111) 204 cd00986 PDZ_LON_protease PDZ d 31.9 49 0.0011 16.2 1.9 15 44-59 24-38 (79) 205 TIGR00523 eIF-1A eukaryotic/ar 31.6 29 0.00062 18.7 1.0 16 39-54 51-66 (99) 206 PLN02569 threonine synthase 31.6 73 0.0016 22.0 3.1 23 36-58 414-437 (484) 207 cd03702 IF2_mtIF2_II This fami 31.3 27 0.00058 18.6 0.9 17 38-54 19-35 (95) 208 PRK04012 translation initiatio 31.1 30 0.00065 18.7 1.0 17 39-55 53-69 (100) 209 PF00018 SH3_1: SH3 domain; I 31.0 35 0.00077 15.2 1.2 13 46-58 16-28 (48) 210 TIGR03801 asp_4_decarbox aspar 31.0 98 0.0021 21.6 3.7 31 27-57 162-192 (521) 211 cd04089 eRF3_II eRF3_II: domai 31.0 24 0.00053 17.8 0.7 16 41-56 21-36 (82) 212 cd02784 MopB_CT_PHLH The MopB_ 31.0 79 0.0017 17.9 2.8 20 38-58 45-64 (137) 213 PRK09620 hypothetical protein; 30.9 1.3E+02 0.0029 18.4 4.0 43 3-45 129-175 (229) 214 cd04482 RPA2_OBF_like RPA2_OBF 30.8 47 0.001 17.3 1.8 15 44-58 46-60 (91) 215 PF01996 F420_ligase: F420-0:G 30.7 21 0.00046 22.0 0.5 29 30-58 11-40 (228) 216 TIGR01835 HMG-CoA-S_prok 3-hyd 30.7 99 0.0021 20.3 3.5 24 33-56 279-303 (379) 217 PF14338 Mrr_N: Mrr N-terminal 30.6 85 0.0018 16.2 2.8 23 29-51 53-75 (92) 218 TIGR00150 HI0065_YjeE ATPase, 30.6 77 0.0017 17.9 2.7 27 28-58 4-30 (133) 219 PF00392 GntR: Bacterial regul 30.6 70 0.0015 15.1 3.2 20 33-52 5-24 (64) 220 cd03698 eRF3_II_like eRF3_II_l 30.5 26 0.00057 17.7 0.7 15 42-56 23-37 (83) 221 PLN02654 acetate-CoA ligase 30.3 1.2E+02 0.0026 21.3 4.1 26 32-58 129-154 (666) 222 PF14801 GCD14_N: tRNA methylt 30.3 45 0.00098 16.1 1.5 16 42-57 2-17 (54) 223 cd01674 Homoaconitase_Swivel H 30.2 60 0.0013 18.5 2.2 35 28-64 23-59 (129) 224 COG1935 Uncharacterized conser 30.0 41 0.00089 18.9 1.5 14 46-59 39-52 (122) 225 PF13497 DUF4121: Domain of un 29.9 92 0.002 19.9 3.1 53 6-59 7-61 (262) 226 KOG2107|consensus 29.7 26 0.00057 20.9 0.7 14 45-58 119-132 (179) 227 PRK07591 threonine synthase; V 29.7 83 0.0018 21.1 3.1 22 36-57 366-388 (421) 228 smart00326 SH3 Src homology 3 29.7 56 0.0012 14.2 1.8 13 46-58 21-33 (58) 229 PF07848 PaaX: PaaX-like prote 29.6 67 0.0015 16.1 2.1 22 27-48 34-55 (70) 230 PLN02856 fumarylacetoacetase 29.6 48 0.001 22.6 2.0 16 42-57 387-402 (424) 231 PRK14538 putative bifunctional 29.5 1.1E+02 0.0024 22.7 3.9 24 30-57 308-331 (838) 232 cd00990 PDZ_glycyl_aminopeptid 29.3 64 0.0014 15.6 2.1 17 42-59 27-43 (80) 233 cd04487 RecJ_OBF2_like RecJ_OB 29.3 53 0.0012 16.4 1.8 16 44-59 42-57 (73) 234 PF13412 HTH_24: Winged helix- 29.3 63 0.0014 14.2 2.1 18 30-47 31-48 (48) 235 PF14394 DUF4423: Domain of un 29.2 51 0.0011 19.4 1.9 29 30-58 55-85 (171) 236 PF14080 DUF4261: Domain of un 29.1 85 0.0019 15.7 3.0 27 30-56 26-54 (77) 237 COG0011 Uncharacterized conser 29.1 1E+02 0.0023 16.7 3.6 19 27-45 17-35 (100) 238 cd00758 MoCF_BD MoCF_BD: molyb 29.1 1.1E+02 0.0023 16.8 4.1 27 28-59 43-69 (133) 239 KOG1546|consensus 28.8 1.4E+02 0.003 20.0 3.9 25 29-55 120-144 (362) 240 TIGR01085 murE UDP-N-acetylmur 28.8 1.2E+02 0.0025 20.4 3.7 22 34-58 425-446 (464) 241 PF01978 TrmB: Sugar-specific 28.7 71 0.0015 15.3 2.1 20 29-48 35-54 (68) 242 COG1368 MdoB Phosphoglycerol t 28.6 1.6E+02 0.0034 21.0 4.4 33 27-61 461-493 (650) 243 PRK05863 sulfur carrier protei 28.5 58 0.0012 15.7 1.8 13 46-58 50-62 (65) 244 PF02073 Peptidase_M29: Thermo 28.4 1.4E+02 0.0031 20.0 4.0 30 29-58 3-33 (398) 245 PF08980 DUF1883: Domain of un 28.3 17 0.00037 19.5 -0.2 18 41-58 6-23 (94) 246 smart00098 alkPPc Alkaline pho 28.3 1.2E+02 0.0027 20.6 3.7 12 48-59 296-307 (419) 247 PRK10005 dihydroxyacetone kina 28.2 75 0.0016 19.3 2.5 25 30-54 107-131 (210) 248 TIGR03417 chol_sulfatase choli 28.0 1.7E+02 0.0036 20.0 4.3 30 28-59 261-290 (500) 249 PF09138 Urm1: Urm1 (Ubiquitin 27.8 44 0.00095 18.0 1.3 15 44-58 79-93 (96) 250 PF02769 AIRS_C: AIR synthase 27.8 39 0.00083 18.6 1.2 12 47-58 1-12 (153) 251 PRK14479 dihydroxyacetone kina 27.8 1.4E+02 0.0031 21.1 4.1 31 27-57 228-258 (568) 252 PF06838 Met_gamma_lyase: Meth 27.7 22 0.00048 24.0 0.2 18 43-60 90-107 (403) 253 PRK06732 phosphopantothenate-- 27.5 1.5E+02 0.0033 18.1 4.2 43 3-45 135-181 (229) 254 KOG1176|consensus 27.3 1.3E+02 0.0028 21.2 3.7 29 30-58 52-81 (537) 255 cd06259 YdcF-like YdcF-like. Y 27.3 1.2E+02 0.0026 16.7 4.4 32 24-58 74-105 (150) 256 cd01579 AcnA_Bact_Swivel Bacte 27.2 65 0.0014 18.0 2.0 20 45-64 43-62 (121) 257 PRK06944 sulfur carrier protei 27.1 78 0.0017 14.9 2.1 14 45-58 49-62 (65) 258 cd03693 EF1_alpha_II EF1_alpha 27.1 38 0.00083 17.4 1.0 16 41-56 26-41 (91) 259 PRK05638 threonine synthase; V 27.1 99 0.0021 20.8 3.1 23 36-58 331-354 (442) 260 PRK05659 sulfur carrier protei 27.1 65 0.0014 15.3 1.8 16 43-58 48-63 (66) 261 PRK10886 DnaA initiator-associ 27.0 44 0.00095 20.1 1.4 15 44-58 105-119 (196) 262 TIGR02703 carboxysome_A carbox 27.0 54 0.0012 17.1 1.5 14 46-59 44-57 (81) 263 cd03694 GTPBP_II Domain II of 26.9 38 0.00083 17.3 1.0 16 41-56 22-37 (87) 264 COG1817 Uncharacterized protei 26.9 72 0.0016 21.2 2.4 43 2-44 165-217 (346) 265 cd00174 SH3 Src homology 3 dom 26.8 67 0.0015 13.8 1.8 12 46-57 18-29 (54) 266 TIGR02704 carboxysome_B carbox 26.8 57 0.0012 17.0 1.6 14 46-59 43-56 (80) 267 TIGR02828 putative membrane fu 26.7 43 0.00093 19.4 1.3 12 43-55 176-187 (188) 268 PTZ00237 acetyl-CoA synthetase 26.6 1.4E+02 0.0031 20.9 3.9 28 30-58 99-126 (647) 269 PRK06488 sulfur carrier protei 26.6 83 0.0018 15.0 2.1 14 45-58 49-62 (65) 270 COG2104 ThiS Sulfur transfer p 26.5 69 0.0015 16.0 1.8 17 42-58 49-65 (68) 271 PRK06437 hypothetical protein; 26.5 64 0.0014 15.8 1.7 15 43-57 49-63 (67) 272 PF08727 P3A: Poliovirus 3A pr 26.2 56 0.0012 16.0 1.4 16 34-49 30-45 (57) 273 COG4738 Predicted transcriptio 26.1 65 0.0014 18.1 1.8 16 33-48 58-73 (124) 274 COG5471 Uncharacterized conser 26.1 84 0.0018 17.3 2.2 15 43-57 3-17 (107) 275 PRK13759 arylsulfatase; Provis 26.0 1.7E+02 0.0038 19.8 4.2 29 29-59 277-305 (485) 276 PRK00358 pyrH uridylate kinase 26.0 1E+02 0.0023 18.5 2.9 26 31-58 23-48 (231) 277 COG4100 Cystathionine beta-lya 25.9 53 0.0012 21.9 1.7 18 43-60 101-118 (416) 278 TIGR02114 coaB_strep phosphopa 25.9 1.6E+02 0.0035 17.9 4.1 43 3-45 134-180 (227) 279 PRK15031 5-carboxymethyl-2-hyd 25.9 1.3E+02 0.0029 16.9 3.1 25 27-51 16-40 (126) 280 PTZ00471 60S ribosomal protein 25.7 48 0.001 19.0 1.3 15 45-59 4-18 (134) 281 PF09837 DUF2064: Uncharacteri 25.7 1.3E+02 0.0028 16.6 3.3 29 25-58 41-69 (122) 282 PLN00208 translation initiatio 25.7 41 0.0009 19.5 1.0 16 40-55 65-80 (145) 283 PRK10846 bifunctional folylpol 25.6 1.1E+02 0.0024 20.3 3.2 23 33-58 381-403 (416) 284 PRK15448 ethanolamine cataboli 25.6 60 0.0013 17.4 1.6 14 46-59 49-62 (95) 285 PRK09990 DNA-binding transcrip 25.6 1.4E+02 0.0031 18.0 3.5 15 32-46 47-61 (251) 286 cd01614 EutN_CcmL Ethanolamine 25.5 63 0.0014 16.9 1.6 14 46-59 49-62 (83) 287 PF09691 PulS_OutS: Bacterial 25.5 1.3E+02 0.0028 16.6 3.0 19 28-46 47-65 (109) 288 PRK05473 hypothetical protein; 25.5 63 0.0014 17.1 1.6 32 28-60 19-52 (86) 289 PF03079 ARD: ARD/ARD' family; 25.5 24 0.00053 20.5 0.1 13 46-58 119-131 (157) 290 PTZ00414 10 kDa heat shock pro 25.5 50 0.0011 17.9 1.3 10 45-54 62-71 (100) 291 PRK06260 threonine synthase; V 25.5 1.2E+02 0.0026 20.1 3.3 23 36-58 343-366 (397) 292 PRK07445 O-succinylbenzoic aci 25.5 1.7E+02 0.0036 19.4 3.9 30 29-58 25-54 (452) 293 PF14453 ThiS-like: ThiS-like 25.4 63 0.0014 15.7 1.5 14 43-56 42-55 (57) 294 PRK02268 hypothetical protein; 25.4 53 0.0011 18.9 1.4 11 46-56 36-46 (141) 295 PRK08559 nusG transcription an 25.4 1.4E+02 0.003 17.1 3.2 16 46-61 95-110 (153) 296 COG0309 HypE Hydrogenase matur 25.4 50 0.0011 21.9 1.5 12 46-57 161-172 (339) 297 PF13406 SLT_2: Transglycosyla 25.3 1.1E+02 0.0024 19.4 3.0 27 27-54 183-209 (262) 298 cd06449 ACCD Aminocyclopropane 25.3 1.3E+02 0.0027 19.0 3.3 21 36-56 284-304 (307) 299 cd03696 selB_II selB_II: this 25.2 40 0.00086 16.9 0.8 15 42-56 23-37 (83) 300 COG4079 Uncharacterized protei 25.1 65 0.0014 20.6 1.9 17 42-58 258-274 (293) 301 PRK07768 long-chain-fatty-acid 25.1 1.6E+02 0.0035 19.7 3.9 28 30-58 36-63 (545) 302 cd04259 AAK_AK-DapDC AAK_AK-Da 25.0 2E+02 0.0042 18.5 4.4 35 27-67 12-47 (295) 303 cd01337 MDH_glyoxysomal_mitoch 25.0 84 0.0018 20.3 2.4 19 46-64 66-84 (310) 304 PLN03174 Chalcone-flavanone is 25.0 2E+02 0.0043 18.5 4.1 30 28-57 195-224 (278) 305 TIGR02283 MltB_2 lytic murein 25.0 1.7E+02 0.0038 19.0 3.8 27 27-54 184-210 (300) 306 cd08319 Death_RAIDD Death doma 24.8 75 0.0016 16.5 1.8 33 7-39 17-51 (83) 307 COG2144 Selenophosphate synthe 24.8 52 0.0011 21.6 1.5 21 37-57 151-171 (324) 308 PRK14533 groES co-chaperonin G 24.6 54 0.0012 17.4 1.3 12 44-55 52-63 (91) 309 PRK12297 obgE GTPase CgtA; Rev 24.6 98 0.0021 21.0 2.8 17 37-54 399-415 (424) 310 cd03782 MATH_Meprin_Beta Mepri 24.6 92 0.002 18.5 2.4 20 37-56 146-165 (167) 311 KOG0744|consensus 24.6 33 0.00072 23.1 0.6 20 48-68 175-194 (423) 312 cd05290 LDH_3 A subgroup of L- 24.6 71 0.0015 20.5 2.1 20 46-65 66-85 (307) 313 TIGR02316 propion_prpE propion 24.4 1.8E+02 0.0039 20.1 4.1 27 31-58 91-117 (628) 314 PRK04984 fatty acid metabolism 24.4 1.4E+02 0.0029 18.0 3.2 23 32-54 47-71 (239) 315 PRK00561 ppnK inorganic polyph 24.3 2E+02 0.0042 18.3 4.1 31 28-58 12-43 (259) 316 PF00056 Ldh_1_N: lactate/mala 24.3 54 0.0012 18.4 1.3 19 46-64 67-85 (141) 317 cd06541 ASCH ASC-1 homology or 24.3 79 0.0017 16.8 2.0 16 43-58 28-43 (105) 318 KOG0024|consensus 24.3 52 0.0011 21.9 1.4 24 36-59 73-96 (354) 319 cd00136 PDZ PDZ domain, also c 24.2 69 0.0015 15.0 1.6 16 44-59 29-44 (70) 320 COG1243 ELP3 Histone acetyltra 24.2 1.3E+02 0.0029 21.1 3.3 48 7-58 440-493 (515) 321 TIGR03270 methan_mark_4 putati 24.2 1.8E+02 0.0039 17.8 4.0 27 30-59 74-100 (202) 322 TIGR01293 Kv_beta voltage-depe 24.2 2E+02 0.0042 18.3 4.0 14 34-47 132-145 (317) 323 PF10431 ClpB_D2-small: C-term 24.1 1.1E+02 0.0023 15.2 3.5 25 30-54 57-81 (81) 324 PF07076 DUF1344: Protein of u 24.0 73 0.0016 15.8 1.6 15 44-58 36-50 (61) 325 TIGR01756 LDH_protist lactate 24.0 77 0.0017 20.5 2.1 19 46-64 58-76 (313) 326 TIGR02282 MltB lytic murein tr 23.9 1.6E+02 0.0034 19.1 3.5 26 28-54 180-205 (290) 327 PF05382 Amidase_5: Bacterioph 23.9 88 0.0019 18.1 2.2 10 45-54 75-84 (145) 328 PRK00421 murC UDP-N-acetylmura 23.7 1.3E+02 0.0028 20.2 3.2 22 33-56 420-441 (461) 329 PF01878 EVE: EVE domain; Int 23.7 49 0.0011 18.4 1.1 14 45-58 39-52 (143) 330 PF11899 DUF3419: Protein of u 23.7 52 0.0011 22.0 1.3 13 46-58 33-45 (380) 331 cd04496 SSB_OBF SSB_OBF: A sub 23.6 72 0.0016 16.1 1.7 14 45-58 61-74 (100) 332 PF08845 SymE_toxin: Toxin Sym 23.6 1E+02 0.0022 14.8 2.2 20 36-56 29-48 (57) 333 TIGR00008 infA translation ini 23.6 51 0.0011 16.6 1.0 15 43-57 42-56 (68) 334 PRK14137 recX recombination re 23.6 90 0.0019 18.8 2.2 20 29-48 70-89 (195) 335 cd01392 HTH_LacI Helix-turn-he 23.5 86 0.0019 13.8 1.8 38 8-45 2-41 (52) 336 TIGR01759 MalateDH-SF1 malate 23.5 86 0.0019 20.3 2.3 19 46-64 77-95 (323) 337 PF14542 Acetyltransf_CG: GCN5 23.4 1.2E+02 0.0025 15.3 2.4 17 29-45 40-56 (78) 338 PRK08053 sulfur carrier protei 23.4 1E+02 0.0023 14.8 2.2 14 45-58 50-63 (66) 339 COG3494 Uncharacterized protei 23.3 2.1E+02 0.0045 18.5 3.8 32 28-59 151-182 (279) 340 KOG1712|consensus 23.2 85 0.0018 18.9 2.0 20 40-59 113-132 (183) 341 PLN00135 malate dehydrogenase 23.1 90 0.002 20.2 2.3 19 46-64 56-74 (309) 342 PLN02860 o-succinylbenzoate-Co 23.1 1.9E+02 0.0041 19.6 3.9 27 31-58 40-66 (563) 343 cd00992 PDZ_signaling PDZ doma 23.1 73 0.0016 15.3 1.6 16 45-60 43-58 (82) 344 PRK13938 phosphoheptose isomer 23.0 91 0.002 18.7 2.2 15 44-58 109-123 (196) 345 PF14604 SH3_9: Variant SH3 do 22.9 61 0.0013 14.7 1.2 12 46-57 15-26 (49) 346 TIGR02812 fadR_gamma fatty aci 22.9 1.3E+02 0.0028 18.0 2.9 15 33-47 47-61 (235) 347 TIGR01004 PulS_OutS lipoprotei 22.9 1.6E+02 0.0035 16.8 3.1 19 27-45 62-80 (128) 348 PRK03837 transcriptional regul 22.8 1.8E+02 0.0039 17.4 3.5 17 31-47 52-68 (241) 349 PF12212 PAZ_siRNAbind: Piwi/A 22.8 23 0.0005 16.6 -0.3 19 30-48 9-27 (47) 350 PRK14022 UDP-N-acetylmuramoyla 22.7 1.3E+02 0.0028 20.4 3.1 22 34-58 432-454 (481) 351 PF12017 Tnp_P_element: Transp 22.7 2.1E+02 0.0045 17.9 4.9 36 9-45 173-210 (236) 352 PF11580 DUF3239: Protein of u 22.6 80 0.0017 17.9 1.8 22 18-39 89-110 (128) 353 PRK00141 murD UDP-N-acetylmura 22.6 82 0.0018 21.3 2.1 28 29-58 416-443 (473) 354 PTZ00329 eukaryotic translatio 22.5 53 0.0012 19.3 1.1 16 40-55 65-80 (155) 355 PF03144 GTP_EFTU_D2: Elongati 22.5 27 0.00059 16.9 -0.1 15 42-56 9-23 (74) 356 PF00248 Aldo_ket_red: Aldo/ke 22.4 2E+02 0.0042 17.6 3.9 39 10-48 92-133 (283) 357 PF04014 Antitoxin-MazE: Antid 22.4 94 0.002 13.9 2.8 17 40-57 16-32 (47) 358 PF08240 ADH_N: Alcohol dehydr 22.4 58 0.0013 17.0 1.2 12 46-57 53-64 (109) 359 PF05172 Nup35_RRM: Nup53/35/4 22.4 97 0.0021 16.7 2.0 23 34-56 65-87 (100) 360 smart00345 HTH_GNTR helix_turn 22.3 93 0.002 13.8 2.0 18 30-47 34-51 (60) 361 PF00245 Alk_phosphatase: Alka 22.3 1.5E+02 0.0032 20.1 3.3 26 29-59 285-310 (421) 362 PF13700 DUF4158: Domain of un 22.2 1.4E+02 0.0031 17.0 2.9 24 27-50 132-155 (166) 363 PRK00414 gmhA phosphoheptose i 22.2 97 0.0021 18.3 2.2 15 44-58 107-121 (192) 364 PF13604 AAA_30: AAA domain; P 22.2 17 0.00038 21.5 -1.0 20 47-67 15-34 (196) 365 PRK11468 dihydroxyacetone kina 22.2 2.3E+02 0.005 19.0 4.1 17 27-43 229-245 (356) 366 COG1126 GlnQ ABC-type polar am 22.2 34 0.00073 21.5 0.2 18 46-65 25-42 (240) 367 PRK14136 recX recombination re 22.1 94 0.002 20.4 2.2 20 29-48 192-211 (309) 368 PF03319 EutN_CcmL: Ethanolami 22.1 70 0.0015 16.7 1.4 14 46-59 49-62 (83) 369 TIGR01501 MthylAspMutase methy 22.1 1.7E+02 0.0036 16.6 3.3 28 28-58 64-91 (134) 370 cd00886 MogA_MoaB MogA_MoaB fa 22.1 1.6E+02 0.0036 16.6 3.6 29 28-59 44-72 (152) 371 COG0293 FtsJ 23S rRNA methylas 22.0 1.2E+02 0.0027 18.6 2.6 24 36-59 33-56 (205) 372 PF04800 ETC_C1_NDUFA4: ETC co 22.0 83 0.0018 17.1 1.7 13 33-45 58-70 (101) 373 PRK00364 groES co-chaperonin G 22.0 67 0.0014 17.0 1.4 11 45-55 58-68 (95) 374 cd00756 MoaE MoaE family. Memb 22.0 90 0.0019 17.4 1.9 16 43-58 72-87 (124) 375 PRK07440 hypothetical protein; 22.0 91 0.002 15.4 1.8 15 44-58 53-67 (70) 376 smart00350 MCM minichromosome 21.8 77 0.0017 21.8 1.9 14 44-57 116-129 (509) 377 COG1167 ARO8 Transcriptional r 21.7 2E+02 0.0043 19.5 3.8 33 27-59 132-165 (459) 378 TIGR01683 thiS thiamine biosyn 21.7 94 0.002 14.8 1.8 14 45-58 48-61 (64) 379 PF00501 AMP-binding: AMP-bind 21.7 2.3E+02 0.0049 18.0 4.4 29 29-58 27-55 (417) 380 COG0503 Apt Adenine/guanine ph 21.6 63 0.0014 19.1 1.3 17 43-59 110-126 (179) 381 PRK01215 competence damage-ind 21.5 2E+02 0.0043 18.1 3.6 26 28-58 47-72 (264) 382 PF13545 HTH_Crp_2: Crp-like h 21.4 1.1E+02 0.0024 14.6 2.1 25 30-54 42-67 (76) 383 PRK03670 competence damage-ind 21.4 1.9E+02 0.0041 18.2 3.4 27 28-58 44-70 (252) 384 COG1526 FdhD Uncharacterized p 21.3 2.3E+02 0.0049 18.2 3.8 31 27-58 178-208 (266) 385 PRK05579 bifunctional phosphop 21.1 2.5E+02 0.0053 18.9 4.1 30 26-57 167-196 (399) 386 PRK02866 cyanate hydratase; Va 21.0 71 0.0015 18.6 1.4 12 47-58 128-139 (147) 387 PF14258 DUF4350: Domain of un 21.0 44 0.00095 16.1 0.5 11 45-55 59-69 (70) 388 TIGR01217 ac_ac_CoA_syn acetoa 21.0 2.3E+02 0.0049 19.9 4.1 27 31-58 122-148 (652) 389 PF13086 AAA_11: AAA domain; P 21.0 67 0.0015 18.5 1.4 13 52-65 19-31 (236) 390 TIGR00274 N-acetylmuramic acid 21.0 1.9E+02 0.0042 18.5 3.5 14 45-58 123-136 (291) 391 PF00742 Homoserine_dh: Homose 21.0 1.2E+02 0.0026 18.0 2.4 19 31-49 38-56 (179) 392 PRK09464 pdhR transcriptional 21.0 1.7E+02 0.0037 17.7 3.2 14 33-46 51-64 (254) 393 TIGR00441 gmhA phosphoheptose 21.0 96 0.0021 17.5 2.0 14 45-58 76-89 (154) 394 PLN00165 hypothetical protein; 21.0 36 0.00078 18.1 0.2 12 36-47 16-27 (88) 395 PRK11414 colanic acid/biofilm 21.0 2E+02 0.0043 17.1 3.5 21 32-52 15-35 (221) 396 PF02560 Cyanate_lyase: Cyanat 21.0 63 0.0014 16.6 1.1 11 47-57 54-64 (73) 397 cd00320 cpn10 Chaperonin 10 Kd 20.9 73 0.0016 16.8 1.4 12 45-56 57-68 (93) 398 PRK13294 F420-0--gamma-glutamy 20.8 1.7E+02 0.0037 20.0 3.3 17 44-60 38-54 (448) 399 cd03783 MATH_Meprin_Alpha Mepr 20.7 1.4E+02 0.003 17.8 2.6 19 37-55 146-164 (167) 400 PF02559 CarD_CdnL_TRCF: CarD- 20.7 63 0.0014 16.8 1.1 9 46-54 2-10 (98) 401 cd05007 SIS_Etherase N-acetylm 20.6 1.8E+02 0.004 18.1 3.3 22 36-58 107-128 (257) 402 PRK11523 DNA-binding transcrip 20.6 2.1E+02 0.0046 17.4 3.6 24 31-54 47-72 (253) 403 KOG0479|consensus 20.6 93 0.002 22.8 2.1 14 45-58 226-239 (818) 404 PLN02736 long-chain acyl-CoA s 20.6 2.3E+02 0.0049 19.8 4.0 28 30-58 85-112 (651) 405 cd05792 S1_eIF1AD_like S1_eIF1 20.5 48 0.001 17.1 0.6 18 39-56 32-49 (78) 406 PLN00415 3-ketoacyl-CoA syntha 20.5 1.9E+02 0.0041 20.1 3.5 26 31-56 400-425 (466) 407 PF00166 Cpn10: Chaperonin 10 20.4 75 0.0016 16.6 1.4 13 45-57 57-69 (93) 408 cd01338 MDH_choloroplast_like 20.4 1.1E+02 0.0024 19.8 2.3 19 46-64 76-94 (322) 409 PRK07696 sulfur carrier protei 20.4 1E+02 0.0022 15.0 1.8 14 45-58 51-64 (67) 410 TIGR02389 RNA_pol_rpoA2 DNA-di 20.4 93 0.002 20.8 2.0 25 41-65 36-61 (367) 411 COG2016 Predicted RNA-binding 20.3 1.1E+02 0.0024 18.1 2.1 17 41-57 102-118 (161) 412 PRK13982 bifunctional SbtC-lik 20.3 2.7E+02 0.0058 19.4 4.2 32 27-59 233-266 (475) 413 PF03283 PAE: Pectinacetyleste 20.3 2E+02 0.0043 19.1 3.5 29 30-60 137-165 (361) 414 cd00885 cinA Competence-damage 20.2 2E+02 0.0043 16.8 3.4 26 28-58 43-68 (170) 415 PRK10524 prpE propionyl-CoA sy 20.2 2.4E+02 0.0052 19.4 4.0 27 31-58 92-118 (629) 416 TIGR01266 fum_ac_acetase fumar 20.2 93 0.002 21.2 2.0 17 40-56 377-393 (415) 417 PF00717 Peptidase_S24: Peptid 20.2 65 0.0014 15.2 1.0 14 45-58 10-23 (70) 418 cd00559 Cyanase_C Cyanase C-te 20.1 86 0.0019 15.9 1.4 11 48-58 51-61 (69) 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=99.87 E-value=5.2e-22 Score=109.72 Aligned_cols=70 Identities=30% Similarity=0.493 Sum_probs=64.1 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCC-CHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLR-DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~-~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~-~g~tn~l~v 70 (70) ||+|++++++|||+|+| |+|+..+... +.++.++.+++.++++|++++||.||+++|.+.+ .|.||+||| T Consensus 43 iavt~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~~a~~~~~~~g~~~~gd~vVv~~g~~~~~~g~tn~~~v 115 (117) T PF02887_consen 43 IAVTPNESVARQLSLYWGVYPVLIEEFDKDTEELIAEALEYAKERGLLKPGDKVVVVAGMPFGTPGGTNTIRV 115 (117) T ss_dssp EEEESSHHHHHHGGGSTTEEEEECSSHSHSHHHHHHHHHHHHHHTTSS-TTSEEEEEEESSTTTTSSEEEEEE T ss_pred EEEcCcHHHHhhhhcccceEEEEeccccccHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCCCCCCEEEEE Confidence 58999999999999999 9998776665 8999999999999999999999999999998877 799999986 No 2 >PLN02762 pyruvate kinase complex alpha subunit Probab=99.75 E-value=4.5e-18 Score=112.10 Aligned_cols=69 Identities=16% Similarity=0.313 Sum_probs=65.1 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) ||+|++++++|+|+|+| |+|++.+...+.|++++.+.+.+++.|++++||.||+++|.+. +|.||+|+| T Consensus 436 ia~t~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~~~~~~~~~g~~~~GD~VVv~~g~~~-~g~tn~i~v 505 (509) T PLN02762 436 FAFTDTTSVRRRLNLQWGLIPFRLDFSDDMESNLNKTFSLLKARGMIKSGDLVIAVSDLTP-SSMLQSIQV 505 (509) T ss_pred EEECCCHHHHHHhhcccCcEEEEeCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCC-CCCceEEEE Confidence 58999999999999999 9999887778899999999999999999999999999999877 899999986 No 3 >PTZ00066 pyruvate kinase; Provisional Probab=99.74 E-value=6.6e-18 Score=111.36 Aligned_cols=70 Identities=21% Similarity=0.397 Sum_probs=65.4 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~-~g~tn~l~v 70 (70) +|+|+++.++|||+|+| |+|++.+...+.|+++..|.+.+++.|++++||.||+++|.+.+ .|.||++|| T Consensus 438 ia~t~~~~~~R~L~L~wGV~p~~~~~~~~~~~~i~~a~~~~~~~g~~~~GD~vVv~~g~~~~~~g~tn~irv 509 (513) T PTZ00066 438 LALSASPSVVKSLSVARGVTTYVVNSFQGTDVVIRNAIALAKERGLVESGDSAIAVHGVKEEVAGSSNLMKV 509 (513) T ss_pred EEECCCHHHHHHhhcccCcEEEEecCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCCCCCCeEEEE Confidence 58999999999999999 99998877778899999999999999999999999999999866 799999986 No 4 >PRK09206 pyruvate kinase; Provisional Probab=99.74 E-value=1.1e-17 Score=109.55 Aligned_cols=70 Identities=24% Similarity=0.334 Sum_probs=64.6 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) ||+|++++++|+|+|+| |+|++.+...+.++++..+.+++++.|++++||.||+++|.+...|.||++|| T Consensus 397 ia~t~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~a~~~~~~~g~~~~Gd~vvv~~g~~~~~g~tn~i~v 467 (470) T PRK09206 397 LALTTNEKTARQLVLSKGVVPQLVKEIASTDDFYRLGKELALQSGLAQKGDVVVMVSGALVPSGTTNTASV 467 (470) T ss_pred EEECCCHHHHHHhhcccCcEEEEeCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCCCCCeEEEE Confidence 58999999999999999 99998776778899999999999999999999999999998644799999986 No 5 >PRK06247 pyruvate kinase; Provisional Probab=99.73 E-value=1.3e-17 Score=109.24 Aligned_cols=70 Identities=26% Similarity=0.359 Sum_probs=65.4 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~-~g~tn~l~v 70 (70) +|+|++++++|+|+|+| |+|++.+...+.++++..+.+++++.|++++||.||+++|.+.+ .|.||++|| T Consensus 396 ~a~t~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~a~~~~~~~g~~~~Gd~vvv~~g~~~~~~g~tn~i~v 467 (476) T PRK06247 396 LALTPNPETARRLALTWGVHCVVVDDARDTDDMVRRADRIALAEGFYKRGDRVVIVAGVPPGTPGSTNMLRI 467 (476) T ss_pred EEECCCHHHHHHhhcccCCeeEecCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCCCCCCeEEEE Confidence 58999999999999999 99998877788899999999999999999999999999999866 799999885 No 6 >PTZ00300 pyruvate kinase; Provisional Probab=99.72 E-value=1.8e-17 Score=108.18 Aligned_cols=70 Identities=23% Similarity=0.346 Sum_probs=63.5 Q ss_pred CeecCChhHHhhhcccc-eeeecCCC-----CCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADW-----LRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~-----~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) +|+|++++++|||+|+| |+|++.+. ..+.++++..+.+++++.|++++||.||+++|.+...|+||++|| T Consensus 375 ia~t~~~~~ar~l~l~~GV~p~~~~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~gd~vvi~~g~~~~~g~tn~i~v 450 (454) T PTZ00300 375 VCVTTRLQTCRQLNITQGVESVFFDAERLGHDEGKEQRVAMGVGFAKSKGYVQSGDLMVVVHADHKVKGYANQTRI 450 (454) T ss_pred EEECCCHHHHHHhhcccCcEEEEeccccccccCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCCCCCCEEEE Confidence 58999999999999999 99987653 456789999999999999999999999999999877799999986 No 7 >PRK06354 pyruvate kinase; Provisional Probab=99.71 E-value=3.5e-17 Score=109.57 Aligned_cols=70 Identities=21% Similarity=0.318 Sum_probs=65.4 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~-~g~tn~l~v 70 (70) +|+|++++++|||+|+| |.|++.+...+.++++..+.+++++.|++++||.||+++|.+.+ .|.||++|| T Consensus 404 ~a~t~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~~~~~~~~~g~~~~gd~vv~~~g~~~~~~g~tn~~~v 475 (590) T PRK06354 404 LAVTPNESVARRLQLVWGVTPLLVLDAPSTDETFDAAINVAQESGLLKQGDLVVITAGTLVGESGSTDLMKV 475 (590) T ss_pred EEECCCHHHHHHhhcccCcEEEEeCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCcCCCceeEEE Confidence 58999999999999999 99998877778899999999999999999999999999999876 799999986 No 8 >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=99.70 E-value=5.3e-17 Score=106.70 Aligned_cols=70 Identities=30% Similarity=0.574 Sum_probs=63.9 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCC-----CCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWL-----RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~-----~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) ||+|++++++|+|+|+| |+|++.+.. .+.++++..+.+++++.|++++||.||+++|.+...|.||++|| T Consensus 402 iavT~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~gd~vv~~~g~~~~~~~tn~i~v 477 (480) T cd00288 402 IAVTRNEQTARQLHLYRGVYPVLFEEPKPGWQEDTDARLKAAVNVAKEKGLLKKGDLVVVVQGWPVGSGSTNTMRI 477 (480) T ss_pred EEEcCCHHHhhheeeccCcEEEEecccccccCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCCCCCCeEEEE Confidence 58999999999999999 999876544 78899999999999999999999999999999866689999986 No 9 >PLN02623 pyruvate kinase Probab=99.70 E-value=8.4e-17 Score=107.23 Aligned_cols=70 Identities=14% Similarity=0.221 Sum_probs=63.9 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeec--ccCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG--WKKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g--~~~~-~g~tn~l~v 70 (70) ||+|+++.++|||+|+| |.|++.++..+.|+++..+++.+++.|++++||.||+++| .+.+ .|.||+++| T Consensus 503 ~avT~~~~~aR~L~L~~GV~P~~~~~~~~~e~~i~~a~~~~~~~g~v~~GD~vviv~g~~~p~~~~g~tn~i~V 576 (581) T PLN02623 503 FAFTNEKRIQQRLALYQGVCPIYMQFSDDAEETFARALSLLLNKGMVKEGEEVALVQSGRQPIWRSESTHHIQV 576 (581) T ss_pred EEECCCHHHHHHhhcccccEEEecCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeccCCCCCCCCCCeEEEE Confidence 68999999999999999 9999888778899999999999999999999999999987 4444 699999985 No 10 >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=99.69 E-value=1.3e-16 Score=104.82 Aligned_cols=70 Identities=29% Similarity=0.415 Sum_probs=63.3 Q ss_pred CeecCChhHHhhhcccc-eeeecCCC-CCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc-cCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADW-LRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW-KKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~-~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~-~~~-~g~tn~l~v 70 (70) ||+|++++++|+|+|+| |+|++.+. ..+.++++..+.+++++.|++++||.||+++|+ +.+ .|.||.+|| T Consensus 400 iAvT~~~~v~R~L~L~wGV~Pil~~~~~~~~~~~i~~a~~~l~~~gl~~~GD~VVvv~g~~~~~~~~~~n~i~v 473 (473) T TIGR01064 400 IAVTPNERVARQLALYWGVFPFLVDEEPSDTEARVNKALELLKEKGILKKGDLVVVIQGGAPIGGVGGTNTIRV 473 (473) T ss_pred EEEcCCHHHHHHhhccCCcEEEEeCCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEecCCCCCCCCCCeEEeC Confidence 58999999999999999 99997765 567889999999999999999999999999994 655 789999986 No 11 >COG0469 PykF Pyruvate kinase [Carbohydrate transport and metabolism] Probab=99.68 E-value=1e-16 Score=105.02 Aligned_cols=70 Identities=21% Similarity=0.328 Sum_probs=65.9 Q ss_pred CeecCChhHHhhhcccc-eeeecCC-CCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC-CCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPAD-WLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG-AGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~-~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~-~g~tn~l~v 70 (70) ||+|++++++|+|+|+| |+|++.+ +..+.++.+..+++.+++.|++++||.||+++|.+.+ .|.||++|| T Consensus 402 ia~t~~~~v~r~l~l~~GV~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~gD~vvit~G~~~~~~G~tn~ikv 474 (477) T COG0469 402 IALTPNERVARRLALVWGVYPLLVEEKPTSTDEMVEEAVEKLLESGLVKKGDLVVITAGVPMGTVGTTNTIKV 474 (477) T ss_pred EEECCCHHHHhhhceeecceeEEecCCCCcHHHHHHHHHHHHHhcCcccCCCEEEEecCcccccCCCceeEEE Confidence 58999999999999999 9999887 5788999999999999999999999999999999876 899999986 No 12 >PLN02461 Probable pyruvate kinase Probab=99.54 E-value=2.3e-14 Score=94.82 Aligned_cols=60 Identities=17% Similarity=0.279 Sum_probs=54.0 Q ss_pred hhHHhhhcccc-eeeecCCC------CCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 7 EEIPKQVLIGK-IEPSPADW------LRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 7 ~~~~r~l~l~~-v~~~~~~~------~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) +.++|||+|+| |+|++.+. ..+.++++..|++++++.|++++||.||+++|. |.||.++| T Consensus 441 ~~~ar~l~L~~GV~P~~~~~~~~~~~~~~~~~~i~~a~~~~~~~g~~~~Gd~vvvv~~~----g~tn~i~v 507 (511) T PLN02461 441 EAPARHSLIYRGLIPVLAEGSAKATDSESTEEILEAAIEHAKKKGLCKPGDSVVALHRI----GGASVIKI 507 (511) T ss_pred HHHhhhhheecceEEEEecccccccccCCHHHHHHHHHHHHHHcCCCCCcCEEEEEecC----CCCcEEEE Confidence 89999999999 99987543 457899999999999999999999999999984 88999875 No 13 >PLN02765 pyruvate kinase Probab=99.52 E-value=4e-14 Score=93.84 Aligned_cols=60 Identities=18% Similarity=0.220 Sum_probs=52.5 Q ss_pred hhHHhhhcccc-eeeecCCCCCC-------HHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 7 EEIPKQVLIGK-IEPSPADWLRD-------VDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 7 ~~~~r~l~l~~-v~~~~~~~~~~-------~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) +.++|||+|+| |+|++.+...+ .+.++..+.+++++.|++++||.||++++. |+||.+|| T Consensus 454 ~~~aR~L~L~~GV~P~~~~~~~~~e~~~~~~~~~~~~a~~~~~~~g~~~~GD~vvv~~~~----g~tn~i~v 521 (526) T PLN02765 454 AFQARQCLIVRGLFPMLADPRHSAESTSATNESVLKVALDHGKAAGVIKSHDRVVVCQKV----GDSSVVKI 521 (526) T ss_pred HHHHHHhhcccCCEEEEeccccccccccccHHHHHHHHHHHHHHcCCCCCCCEEEEEecC----CCCceEEE Confidence 89999999999 99987654333 578899999999999999999999999853 89999885 No 14 >PRK05826 pyruvate kinase; Provisional Probab=99.51 E-value=6.2e-14 Score=92.08 Aligned_cols=61 Identities=21% Similarity=0.362 Sum_probs=56.3 Q ss_pred CeecCChhHHhhhcccc-eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~ 61 (70) +|+|++++++|+|+|+| |.|++.+...+.+..+..+++++++.|++++||.||+++|.+.+ T Consensus 400 ~~~t~~~~~~r~l~l~~GV~p~~~~~~~~~~~~~~~a~~~~~~~g~~~~gd~vvvv~g~~~~ 461 (465) T PRK05826 400 FAVTRDEKTQRRLALYRGVYPVLFDSAADTDDAAEEALRLLLEKGLVESGDLVVVTSGDPMG 461 (465) T ss_pred EEEcCCHHHHHHhhcccCcEEEEeCCCCCHHHHHHHHHHHHHHcCCCCCCCEEEEEeCCCCC Confidence 58999999999999999 99998776678899999999999999999999999999998743 No 15 >KOG2323|consensus Probab=99.30 E-value=5.4e-12 Score=83.13 Aligned_cols=70 Identities=37% Similarity=0.613 Sum_probs=62.7 Q ss_pred CeecCChhHHhhhcccc-eeeec------CCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCCCCCCceEeC Q psy255 1 MSSTRSEEIPKQVLIGK-IEPSP------ADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKGAGFTNTLIV 70 (70) Q Consensus 1 ~a~t~~~~~~r~l~l~~-v~~~~------~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g~tn~l~v 70 (70) +++|..+..+||++||| ++|++ .+|.++.|.+++++++.+++.|+++.||.+|++.+...+.|.+|++++ T Consensus 422 i~vt~~~~~aR~~~l~Rgv~Pvl~~~~~~~~~~~~~e~~i~~g~~~~k~~g~~k~gd~~vvv~~~~~~~~~~~~i~v 498 (501) T KOG2323|consen 422 ISVTRPVLAARQSHLYRGIIPVLYARSPVEDWSEDVESRIKFGLDFGKKKGILKKGDVVVVVNKGKGGASVTNTIRV 498 (501) T ss_pred EEEeccHHHHHHHHhhccceeeeecccchhhhhhhHHHHHHHHHHHHHhcchhhcCCEEEEEecccCCccceeeEEE Confidence 47889999999999999 99987 567789999999999999999999999988888887777899998875 No 16 >PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B .... Probab=91.05 E-value=0.37 Score=24.87 Aligned_cols=26 Identities=15% Similarity=0.171 Sum_probs=21.1 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-.++..+.+.|.+++||+|++++-- T Consensus 53 ~~~~L~~~~~~g~~~~Gd~vl~~~~G 78 (90) T PF08541_consen 53 IPINLADALEEGRIKPGDRVLLVGFG 78 (90) T ss_dssp HHHHHHHHHHTTSSCTTEEEEEEEEE T ss_pred HHHHHHHHHHcCCCCCCCEEEEEEEE Confidence 44567788999999999999988643 No 17 >PRK06816 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed Probab=86.17 E-value=3.1 Score=27.14 Aligned_cols=29 Identities=7% Similarity=-0.009 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) ..+-.++..+.+.|.+++||+|++.++.. T Consensus 337 Asipi~L~~a~~~g~~~~Gd~vl~~~~~s 365 (378) T PRK06816 337 ASIYIMLDELLNSGRLKPGQKILCFVPES 365 (378) T ss_pred hHHHHHHHHHHHcCCCCCCCEEEEEEecc Confidence 44566777888899999999999886643 No 18 >PRK12281 rplX 50S ribosomal protein L24; Reviewed Probab=85.93 E-value=0.66 Score=23.90 Aligned_cols=17 Identities=41% Similarity=0.585 Sum_probs=13.7 Q ss_pred CCCCCCeEEEeecccCC Q psy255 45 FLNQGDPVIVVTGWKKG 61 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~ 61 (70) -++.||+|++++|.-.+ T Consensus 6 ~I~kGD~V~Vi~G~dKG 22 (76) T PRK12281 6 KVKKGDMVKVIAGDDKG 22 (76) T ss_pred cccCCCEEEEeEcCCCC Confidence 47899999999996433 No 19 >COG0332 FabH 3-oxoacyl-[acyl-carrier-protein] Probab=85.44 E-value=1.2 Score=28.91 Aligned_cols=28 Identities=11% Similarity=0.179 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) ....+-.++..+.+.|.+++||.+++.. T Consensus 281 saAsiplaL~~~~~~g~ik~Gd~ill~~ 308 (323) T COG0332 281 SAASIPLALDEALREGRIKPGDLVLLEA 308 (323) T ss_pred ccchHHHHHHHHhhhCCCCCCCEEEEEe Confidence 3455777899999999999999999653 No 20 >smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54. Probab=85.14 E-value=1.3 Score=17.60 Aligned_cols=16 Identities=44% Similarity=0.605 Sum_probs=13.1 Q ss_pred CCCCCeEEEeecccCC Q psy255 46 LNQGDPVIVVTGWKKG 61 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~ 61 (70) +++||.|.++.|...+ T Consensus 2 ~~~G~~V~I~~G~~~g 17 (28) T smart00739 2 FEVGDTVRVIAGPFKG 17 (28) T ss_pred CCCCCEEEEeECCCCC Confidence 5799999999997543 No 21 >CHL00141 rpl24 ribosomal protein L24; Validated Probab=82.74 E-value=1.1 Score=23.38 Aligned_cols=17 Identities=35% Similarity=0.679 Sum_probs=13.8 Q ss_pred CCCCCCeEEEeecccCC Q psy255 45 FLNQGDPVIVVTGWKKG 61 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~ 61 (70) .+++||+|++++|.-.+ T Consensus 8 ~I~~GD~V~Vi~G~dKG 24 (83) T CHL00141 8 HVKIGDTVKIISGSDKG 24 (83) T ss_pred cccCCCEEEEeEcCCCC Confidence 57899999999996433 No 22 >TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence. Probab=82.59 E-value=2.2 Score=21.39 Aligned_cols=17 Identities=24% Similarity=0.212 Sum_probs=12.4 Q ss_pred HHHHHhCCCCCCCCeEEE Q psy255 37 IKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~ 54 (70) .+.|++.| +++||.|.+ T Consensus 46 ~~~L~~~G-~~~GD~V~I 62 (69) T TIGR03595 46 EDALRKAG-AKDGDTVRI 62 (69) T ss_pred HHHHHHcC-CCCCCEEEE Confidence 34566777 589999986 No 23 >PLN02326 3-oxoacyl-[acyl-carrier-protein] synthase III Probab=82.18 E-value=5.8 Score=25.88 Aligned_cols=28 Identities=7% Similarity=0.074 Sum_probs=22.4 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) -..+-.++..+.+.|.+++||+|++.+- T Consensus 339 sAsi~~~L~~~~~~g~~~~Gd~vll~~~ 366 (379) T PLN02326 339 AASIPLALDEAVRSGKVKKGDVIATAGF 366 (379) T ss_pred HHHHHHHHHHHHHcCCCCCCCEEEEEEE Confidence 3456667888889999999999998753 No 24 >CHL00203 fabH 3-oxoacyl-acyl-carrier-protein synthase 3; Provisional Probab=82.04 E-value=3.2 Score=26.30 Aligned_cols=27 Identities=4% Similarity=0.110 Sum_probs=21.8 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ..+-.++..+.+.|.+++||+|++.+. T Consensus 286 asi~~~L~~~~~~g~~~~Gd~vll~~~ 312 (326) T CHL00203 286 ASIPLALDEAIQNNKIQPGQIIVLSGF 312 (326) T ss_pred HHHHHHHHHHHHhCCCCCCCEEEEEEE Confidence 445667778888999999999998874 No 25 >PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle Probab=81.29 E-value=3 Score=20.77 Aligned_cols=21 Identities=19% Similarity=0.186 Sum_probs=16.5 Q ss_pred HHHHHHH-hCCCCCCCCeEEEe Q psy255 35 HGIKYGR-DRKFLNQGDPVIVV 55 (70) Q Consensus 35 ~a~~~~~-~~g~~~~GD~vv~~ 55 (70) ...+.|+ +.|+.++|+.|+.+ T Consensus 56 ~ie~~AR~~lgm~~~~E~v~~~ 77 (80) T PF04977_consen 56 YIEKVAREKLGMVKPGEIVFKI 77 (80) T ss_pred HHHHHHHHHcCCcCCCCEEEeC Confidence 3456677 78999999999764 No 26 >TIGR02620 cas_VVA1548 putative CRISPR-associated protein, VVA1548 family. This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats. Probab=80.94 E-value=2.6 Score=22.63 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=13.1 Q ss_pred HHHHHHhCCC-------------CCCCCeEEEe Q psy255 36 GIKYGRDRKF-------------LNQGDPVIVV 55 (70) Q Consensus 36 a~~~~~~~g~-------------~~~GD~vv~~ 55 (70) |.++++++|+ +.+||+|+-+ T Consensus 9 a~eW~~~qG~~iD~~v~HLd~~~i~~GD~ViGt 41 (93) T TIGR02620 9 AQEWLSQQGIQIDHFVDHLDPIDISQGDKVIGT 41 (93) T ss_pred HHHHHHhcCCccceeecccCHHHhcCCCEEEEe Confidence 4566666666 5678887754 No 27 >PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A. Probab=79.99 E-value=2.4 Score=21.24 Aligned_cols=17 Identities=29% Similarity=0.280 Sum_probs=10.2 Q ss_pred HHHHHhCCCCCCCCeEEE Q psy255 37 IKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~ 54 (70) .+.|++.| +++||.|.+ T Consensus 46 ~~~L~~~G-~~~GD~V~I 62 (69) T PF09269_consen 46 EKALRKAG-AKEGDTVRI 62 (69) T ss_dssp HHHHHTTT---TT-EEEE T ss_pred HHHHHHcC-CCCCCEEEE Confidence 35567777 589999876 No 28 >TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes. Probab=79.81 E-value=1.6 Score=23.76 Aligned_cols=16 Identities=38% Similarity=0.611 Sum_probs=13.2 Q ss_pred CCCCCCeEEEeecccC Q psy255 45 FLNQGDPVIVVTGWKK 60 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~ 60 (70) -++.||+|++++|.-. T Consensus 3 ~ikkGD~V~Vi~G~dK 18 (104) T TIGR01079 3 KIKKGDTVKVISGKDK 18 (104) T ss_pred cccCCCEEEEeEcCCC Confidence 3689999999999743 No 29 >PRK00004 rplX 50S ribosomal protein L24; Reviewed Probab=79.32 E-value=1.7 Score=23.66 Aligned_cols=17 Identities=47% Similarity=0.806 Sum_probs=13.7 Q ss_pred CCCCCCeEEEeecccCC Q psy255 45 FLNQGDPVIVVTGWKKG 61 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~ 61 (70) -+++||.|++++|.--+ T Consensus 4 ~i~kGD~V~Vi~G~dKG 20 (105) T PRK00004 4 KIKKGDTVIVIAGKDKG 20 (105) T ss_pred cccCCCEEEEeEcCCCC Confidence 36899999999997443 No 30 >PLN02854 3-ketoacyl-CoA synthase Probab=78.74 E-value=5.4 Score=27.63 Aligned_cols=28 Identities=14% Similarity=0.243 Sum_probs=23.1 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) .-..+-.++.++.++|.+++||+|++++ T Consensus 452 SSASI~~~L~~~~~kGrik~GD~Vl~ia 479 (521) T PLN02854 452 SSSSLWYELAYTEAKGRVSAGDRVWQIA 479 (521) T ss_pred HhhHHHHHHHHHHHcCCCCCCCEEEEEE Confidence 3455777888889999999999998876 No 31 >PRK09258 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed Probab=77.95 E-value=9.2 Score=24.23 Aligned_cols=27 Identities=19% Similarity=0.321 Sum_probs=20.9 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ..+-.++..+.+.|.+++||++++.+- T Consensus 299 as~~~~L~~~~~~g~~~~Gd~vll~~~ 325 (338) T PRK09258 299 ASLPITLAMAAEEGFLKPGDRVALLGI 325 (338) T ss_pred hHHHHHHHHHHHhCCCCCCCEEEEEEe Confidence 345566777788899999999998763 No 32 >PRK05963 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed Probab=77.25 E-value=8.2 Score=24.36 Aligned_cols=27 Identities=7% Similarity=0.254 Sum_probs=20.9 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ..+-.++..+.+.|.+++||+|++.+- T Consensus 287 as~~~~L~~~~~~~~~~~Gd~vll~~~ 313 (326) T PRK05963 287 ATIPLSLSLANLEQPLREGERLLFAAA 313 (326) T ss_pred HHHHHHHHHHHHhCCCCCCCEEEEEEE Confidence 335556677888899999999998764 No 33 >PLN02192 3-ketoacyl-CoA synthase Probab=77.08 E-value=5 Score=27.72 Aligned_cols=27 Identities=11% Similarity=0.273 Sum_probs=22.4 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) -..+-.+++++.++|.+++||+|++++ T Consensus 441 SaSI~~aL~~~eakgrik~GDrVl~ia 467 (511) T PLN02192 441 SSSLWYELAYSEAKGRIKKGDRTWQIA 467 (511) T ss_pred HhHHHHHHHHHHHcCCCCCCCEEEEEE Confidence 345777888888999999999999775 No 34 >PRK07204 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed Probab=75.89 E-value=8.5 Score=24.33 Aligned_cols=27 Identities=7% Similarity=0.231 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ..+-.++..+.+.|.+++||+|++.+- T Consensus 290 as~~~~L~~~~~~g~~~~Gd~vll~~~ 316 (329) T PRK07204 290 ASIPVALFEAIKQKKVQRGNKILLLGT 316 (329) T ss_pred HHHHHHHHHHHHcCCCCCCCEEEEEEE Confidence 345556777788899999999998764 No 35 >COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane] Probab=75.34 E-value=1.7 Score=26.47 Aligned_cols=17 Identities=35% Similarity=0.608 Sum_probs=15.3 Q ss_pred hCCCCCCCCeEEEeecc Q psy255 42 DRKFLNQGDPVIVVTGW 58 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g~ 58 (70) +.|.+++||.|+.++++ T Consensus 80 dlg~i~~~DvviaiS~S 96 (202) T COG0794 80 DLGMITPGDVVIAISGS 96 (202) T ss_pred CccCCCCCCEEEEEeCC Confidence 36899999999999998 No 36 >TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079. Probab=73.25 E-value=2.4 Score=23.53 Aligned_cols=20 Identities=30% Similarity=0.350 Sum_probs=15.7 Q ss_pred hCCCCCCCCeEEEeecccCC Q psy255 42 DRKFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g~~~~ 61 (70) +.=-++.||.|.+++|..-| T Consensus 38 r~~~IkkGD~V~Vi~Gk~KG 57 (114) T TIGR01080 38 RALPVRKGDKVRIMRGDFKG 57 (114) T ss_pred ccceeecCCEEEEecCCCCC Confidence 33468999999999997544 No 37 >PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A .... Probab=73.19 E-value=3.1 Score=23.23 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=9.6 Q ss_pred CCCCCCCCeEEEee Q psy255 43 RKFLNQGDPVIVVT 56 (70) Q Consensus 43 ~g~~~~GD~vv~~~ 56 (70) .-++++||+||+.+ T Consensus 76 Arl~~~GD~vII~s 89 (116) T PF02261_consen 76 ARLVQVGDRVIIMS 89 (116) T ss_dssp GGCS-TT-EEEEEE T ss_pred HhccCCCCEEEEEE Confidence 34678999999987 No 38 >TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group. Probab=73.07 E-value=3.4 Score=23.40 Aligned_cols=14 Identities=29% Similarity=0.475 Sum_probs=11.5 Q ss_pred CCCCCCCeEEEeec Q psy255 44 KFLNQGDPVIVVTG 57 (70) Q Consensus 44 g~~~~GD~vv~~~g 57 (70) -++++||+||+.+= T Consensus 77 rl~~~GD~VII~sy 90 (126) T TIGR00223 77 RCVSVGDIVIIASY 90 (126) T ss_pred hcCCCCCEEEEEEC Confidence 46789999999874 No 39 >cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment Probab=72.98 E-value=3.4 Score=22.88 Aligned_cols=15 Identities=27% Similarity=0.364 Sum_probs=11.8 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) -++++||+||+.+=. T Consensus 76 r~~~~GD~vII~sy~ 90 (111) T cd06919 76 RLGQPGDRVIIMAYA 90 (111) T ss_pred hcCCCCCEEEEEECc Confidence 357899999998743 No 40 >COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism] Probab=72.83 E-value=3.2 Score=23.42 Aligned_cols=15 Identities=27% Similarity=0.461 Sum_probs=12.2 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) -++++||+||+.+-. T Consensus 76 rl~~~GD~VII~sy~ 90 (126) T COG0853 76 RLVQVGDLVIIMSYA 90 (126) T ss_pred hhCCCCCEEEEEEcc Confidence 467999999998754 No 41 >COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis] Probab=72.16 E-value=3.7 Score=22.47 Aligned_cols=17 Identities=41% Similarity=0.667 Sum_probs=13.7 Q ss_pred CCCCCCeEEEeecccCC Q psy255 45 FLNQGDPVIVVTGWKKG 61 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~ 61 (70) .++.||.|++++|.--+ T Consensus 4 ~IrkGD~V~Vi~GkdKG 20 (104) T COG0198 4 KVKKGDTVKVIAGKDKG 20 (104) T ss_pred ceecCCEEEEEecCCCC Confidence 36799999999997543 No 42 >PLN02377 3-ketoacyl-CoA synthase Probab=71.96 E-value=7.7 Score=26.74 Aligned_cols=27 Identities=11% Similarity=0.234 Sum_probs=22.0 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) -..+-.+++++.++|.+++||+|++++ T Consensus 437 SaSI~~aL~~~~~~grik~Gd~Vllia 463 (502) T PLN02377 437 SSSIWYELAYIEAKGRMRKGNRVWQIA 463 (502) T ss_pred hhHHHHHHHHHHHcCCCCCCCeEEEEE Confidence 355677888889999999999988665 No 43 >TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas. Probab=71.54 E-value=3 Score=21.80 Aligned_cols=16 Identities=31% Similarity=0.549 Sum_probs=13.2 Q ss_pred CCCCCCCeEEEeeccc Q psy255 44 KFLNQGDPVIVVTGWK 59 (70) Q Consensus 44 g~~~~GD~vv~~~g~~ 59 (70) .-+++||.|+..+|.. T Consensus 36 ~~L~~Gd~VvT~gGi~ 51 (84) T TIGR00739 36 ESLKKGDKVLTIGGII 51 (84) T ss_pred HhCCCCCEEEECCCeE Confidence 3468999999999875 No 44 >PRK05449 aspartate alpha-decarboxylase; Provisional Probab=71.12 E-value=3.9 Score=23.14 Aligned_cols=15 Identities=27% Similarity=0.408 Sum_probs=11.8 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) -++++||+||+.+=. T Consensus 77 r~~~~GD~vII~ay~ 91 (126) T PRK05449 77 RLVQVGDLVIIAAYA 91 (126) T ss_pred hcCCCCCEEEEEECc Confidence 357899999998743 No 45 >PRK01191 rpl24p 50S ribosomal protein L24P; Validated Probab=71.03 E-value=3.4 Score=23.19 Aligned_cols=22 Identities=36% Similarity=0.407 Sum_probs=16.4 Q ss_pred HHhCCCCCCCCeEEEeecccCC Q psy255 40 GRDRKFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g~~~~ 61 (70) .+..=-++.||.|.+++|..-| T Consensus 40 ~ir~~~IkkGD~V~VisG~~KG 61 (120) T PRK01191 40 GIRSLPVRKGDTVKVMRGDFKG 61 (120) T ss_pred CCccceEeCCCEEEEeecCCCC Confidence 3334468999999999997543 No 46 >PTZ00194 60S ribosomal protein L26; Provisional Probab=70.12 E-value=3.7 Score=23.72 Aligned_cols=22 Identities=32% Similarity=0.445 Sum_probs=16.6 Q ss_pred HHhCCCCCCCCeEEEeecccCC Q psy255 40 GRDRKFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g~~~~ 61 (70) .+..--++.||.|.|++|..-| T Consensus 41 ~~Rs~~IkkGD~V~Vi~Gk~KG 62 (143) T PTZ00194 41 NVRSMPVRKDDEVMVVRGHHKG 62 (143) T ss_pred CCccceeecCCEEEEecCCCCC Confidence 3334468999999999998544 No 47 >PRK05585 yajC preprotein translocase subunit YajC; Validated Probab=67.16 E-value=4 Score=22.28 Aligned_cols=17 Identities=29% Similarity=0.335 Sum_probs=13.8 Q ss_pred CCCCCCCCeEEEeeccc Q psy255 43 RKFLNQGDPVIVVTGWK 59 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~ 59 (70) ..-+++||+|+.++|.. T Consensus 50 ~~~Lk~Gd~VvT~gGi~ 66 (106) T PRK05585 50 LSSLAKGDEVVTNGGII 66 (106) T ss_pred HHhcCCCCEEEECCCeE Confidence 34578999999999875 No 48 >COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion] Probab=67.03 E-value=4.1 Score=21.98 Aligned_cols=16 Identities=31% Similarity=0.557 Sum_probs=13.1 Q ss_pred CCCCCCCeEEEeeccc Q psy255 44 KFLNQGDPVIVVTGWK 59 (70) Q Consensus 44 g~~~~GD~vv~~~g~~ 59 (70) .-+++||.|+..+|.. T Consensus 42 ~sL~kGD~VvT~gGi~ 57 (97) T COG1862 42 NSLKKGDEVVTIGGIV 57 (97) T ss_pred HhccCCCEEEEcCCeE Confidence 3468999999998875 No 49 >PF13730 HTH_36: Helix-turn-helix domain Probab=66.25 E-value=9.9 Score=17.50 Aligned_cols=17 Identities=18% Similarity=0.260 Sum_probs=15.0 Q ss_pred HHHHHHHHHHHHhCCCC Q psy255 30 DTRVAHGIKYGRDRKFL 46 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~ 46 (70) ...+..+++.|.+.|++ T Consensus 39 ~~Tv~~~i~~L~~~G~I 55 (55) T PF13730_consen 39 RRTVQRAIKELEEKGLI 55 (55) T ss_pred HHHHHHHHHHHHHCcCC Confidence 67799999999999985 No 50 >PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional Probab=64.13 E-value=18 Score=22.40 Aligned_cols=27 Identities=22% Similarity=0.267 Sum_probs=20.9 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEE-eec Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIV-VTG 57 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~-~~g 57 (70) .+...+.+.+.+.+++++||+|++ +|| T Consensus 11 ~~~~~v~~~i~~~~li~~~~kilVa~SG 38 (258) T PRK10696 11 RLRRQVGQAIADFNMIEEGDRVMVCLSG 38 (258) T ss_pred HHHHHHHHHHHHcCCCCCCCEEEEEecC Confidence 456667777889999999998876 444 No 51 >PRK05886 yajC preprotein translocase subunit YajC; Validated Probab=63.74 E-value=5.1 Score=22.08 Aligned_cols=16 Identities=31% Similarity=0.489 Sum_probs=13.2 Q ss_pred CCCCCCCeEEEeeccc Q psy255 44 KFLNQGDPVIVVTGWK 59 (70) Q Consensus 44 g~~~~GD~vv~~~g~~ 59 (70) .-+++||.|+.++|.. T Consensus 37 ~~Lk~GD~VvT~gGi~ 52 (109) T PRK05886 37 ESLQPGDRVHTTSGLQ 52 (109) T ss_pred HhcCCCCEEEECCCeE Confidence 4468999999998875 No 52 >COG0031 CysK Cysteine synthase [Amino acid transport and metabolism] Probab=63.64 E-value=15 Score=23.81 Aligned_cols=28 Identities=21% Similarity=0.364 Sum_probs=20.6 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEE-Eeec Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVI-VVTG 57 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv-~~~g 57 (70) |..-...++.+.++|++++|+.|| -++| T Consensus 43 DR~A~~mI~~Ae~~G~l~pG~tIVE~TSG 71 (300) T COG0031 43 DRIALYMIEDAEKRGLLKPGGTIVEATSG 71 (300) T ss_pred HHHHHHHHHHHHHcCCCCCCCEEEEcCCC Confidence 344555668899999999999777 3444 No 53 >PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E .... Probab=63.49 E-value=11 Score=19.76 Aligned_cols=20 Identities=20% Similarity=0.106 Sum_probs=14.4 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 37 ~dA~~~Gi-~~Gd~V~v~s~~ 56 (110) T PF01568_consen 37 EDAAKLGI-KDGDWVRVSSPR 56 (110) T ss_dssp HHHHHCT---TTCEEEEEETT T ss_pred HHHHHhcC-cCCCEEEEEecc Confidence 45777885 899999998754 No 54 >TIGR02695 azurin azurin. Azurin is a blue copper-binding protein in the plastocyanin/azurin family (see Pfam model pfam00127). It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The most closely related copper-binding proteins to this family are auracyanins, as in Chloroflexus aurantiacus, which have similar redox activities. Probab=63.06 E-value=21 Score=20.24 Aligned_cols=41 Identities=27% Similarity=0.480 Sum_probs=25.1 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCC-eEEEeecccCCCCCCceE Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGD-PVIVVTGWKKGAGFTNTL 68 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD-~vv~~~g~~~~~g~tn~l 68 (70) .+.+.....++....+.+++.++| +|+.-+.. .+.|.+.++ T Consensus 52 ~d~~~v~~~g~~ag~~~~Yvp~~d~~ViAhTkl-iggGes~sv 93 (125) T TIGR02695 52 ADMQAVATDGMSAGADNNYVKPGDARVIAHTKV-IGGGEKTSV 93 (125) T ss_pred ccHHHHHHHHHhcccccCccCCCCcceEEEccc-cCCCceEEE Confidence 345566667777777899999998 55543332 333444433 No 55 >PRK06840 hypothetical protein; Validated Probab=61.40 E-value=30 Score=22.00 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=18.8 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeec Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) +-.++..+.+.|.+++||++++.+- T Consensus 298 ~~~~L~~~~~~~~~~~Gd~ill~~~ 322 (339) T PRK06840 298 QILSLHLALEQGKLKDGDLVVLVSA 322 (339) T ss_pred HHHHHHHHHHcCCCCCCCEEEEEEE Confidence 4445666778888999999987763 No 56 >PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B. Probab=61.23 E-value=2.7 Score=21.77 Aligned_cols=17 Identities=29% Similarity=0.417 Sum_probs=0.9 Q ss_pred CCCCCCCCeEEEeeccc Q psy255 43 RKFLNQGDPVIVVTGWK 59 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~ 59 (70) ..-+++||.|+..+|.. T Consensus 34 ~~~Lk~Gd~VvT~gGi~ 50 (82) T PF02699_consen 34 LASLKPGDEVVTIGGIY 50 (82) T ss_dssp GG--------------- T ss_pred HHcCCCCCEEEECCcEE Confidence 34578999999999875 No 57 >PRK12879 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed Probab=61.23 E-value=18 Score=22.70 Aligned_cols=25 Identities=8% Similarity=0.231 Sum_probs=19.7 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeec Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) +-.++..+.+.|.+++||++++.+- T Consensus 287 ~~~~L~~~~~~g~~~~Gd~vll~~~ 311 (325) T PRK12879 287 IPLALDLALEQGKIKPGDTLLLYGF 311 (325) T ss_pred HHHHHHHHHHcCCCCCCCEEEEEEE Confidence 4456677778899999999988764 No 58 >PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A .... Probab=61.14 E-value=4.8 Score=16.90 Aligned_cols=14 Identities=50% Similarity=0.650 Sum_probs=11.2 Q ss_pred CCCeEEEeecccCC Q psy255 48 QGDPVIVVTGWKKG 61 (70) Q Consensus 48 ~GD~vv~~~g~~~~ 61 (70) +||.|.+++|...+ T Consensus 1 ~Gd~V~V~~G~~~G 14 (32) T PF00467_consen 1 VGDTVKVISGPFKG 14 (32) T ss_dssp TTSEEEESSSTTTT T ss_pred CCCEEEEeEcCCCC Confidence 58999999997544 No 59 >PRK06531 yajC preprotein translocase subunit YajC; Validated Probab=61.07 E-value=6 Score=21.93 Aligned_cols=15 Identities=27% Similarity=0.574 Sum_probs=12.6 Q ss_pred CCCCCCeEEEeeccc Q psy255 45 FLNQGDPVIVVTGWK 59 (70) Q Consensus 45 ~~~~GD~vv~~~g~~ 59 (70) -+++||.|+-.+|.. T Consensus 36 sLk~GD~VvT~GGi~ 50 (113) T PRK06531 36 AIQKGDEVVTIGGLY 50 (113) T ss_pred hcCCCCEEEECCCcE Confidence 368999999998875 No 60 >PRK00888 ftsB cell division protein FtsB; Reviewed Probab=60.84 E-value=25 Score=19.03 Aligned_cols=24 Identities=8% Similarity=0.046 Sum_probs=17.8 Q ss_pred HHHHHHH-hCCCCCCCCeEEEeecc Q psy255 35 HGIKYGR-DRKFLNQGDPVIVVTGW 58 (70) Q Consensus 35 ~a~~~~~-~~g~~~~GD~vv~~~g~ 58 (70) ...+.++ +.|++++|+.++.+... T Consensus 66 yiEe~AR~~Lg~vk~gEivy~~~~~ 90 (105) T PRK00888 66 AIEERARNELGMVKPGETFYRIVPD 90 (105) T ss_pred HHHHHHHHHcCCCCCCCEEEEeCCC Confidence 3444566 47999999999977654 No 61 >cd00830 KAS_III Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. KASIII initiates this process by specifically using acetyl-CoA over acyl-CoA. Probab=59.42 E-value=21 Score=22.29 Aligned_cols=26 Identities=15% Similarity=0.232 Sum_probs=20.2 Q ss_pred HHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 32 RVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 32 ~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) .+-.++..+.+.|.+++||++++.+- T Consensus 284 s~~~~L~~~~~~~~~~~G~~vll~~~ 309 (320) T cd00830 284 SIPLALDEAIEEGKLKKGDLVLLLGF 309 (320) T ss_pred HHHHHHHHHHHcCCCCCCCEEEEEEE Confidence 34556677788899999999998764 No 62 >PF10727 Rossmann-like: Rossmann-like domain; InterPro: IPR019665 This entry represents an NAD/NADP-binding domain with a core Rossmann-type fold, found in an uncharacterised protein family thought to be putative NADP oxidoreductase coenzyme F420-dependent proteins and/or NAD-dependent glycerol-3-phosphate dehydrogenase-like proteins. This Rossmann-fold domain consists of 3-layers alpha/beta/alpha, where the six beta strands are parallel in the order 321456.; PDB: 3DFU_A 3C24_A. Probab=59.30 E-value=7.8 Score=21.73 Aligned_cols=32 Identities=16% Similarity=0.030 Sum_probs=21.9 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) -+|+.|....+.+...|...+|..|+-++|.. T Consensus 76 vpDdaI~~va~~La~~~~~~~g~iVvHtSGa~ 107 (127) T PF10727_consen 76 VPDDAIAEVAEQLAQYGAWRPGQIVVHTSGAL 107 (127) T ss_dssp S-CCHHHHHHHHHHCC--S-TT-EEEES-SS- T ss_pred echHHHHHHHHHHHHhccCCCCcEEEECCCCC Confidence 35678999999999999999999999999873 No 63 >PF14120 YhzD: YhzD-like protein Probab=58.61 E-value=22 Score=17.61 Aligned_cols=31 Identities=6% Similarity=0.163 Sum_probs=25.8 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) .+.++....+...++++|+.+..-++|--+| T Consensus 24 ~~D~eAK~~G~~~L~Ek~~~~~THR~v~~~G 54 (61) T PF14120_consen 24 ANDEEAKEIGEQKLKEKGYEEKTHRCVSSSG 54 (61) T ss_pred CCHHHHHHHHHHHHHHCChhhcceeeeCCCC Confidence 4667888899999999999999888876555 No 64 >COG4393 Predicted membrane protein [Function unknown] Probab=58.33 E-value=9.8 Score=25.24 Aligned_cols=36 Identities=28% Similarity=0.304 Sum_probs=27.2 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeeccc------CC-CCCCceE Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGWK------KG-AGFTNTL 68 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~~------~~-~g~tn~l 68 (70) .-.|...+=++|++++||.||-++... .| +|++|-+ T Consensus 333 vfDAC~iCGd~GYv~e~dqvICv~C~VrmfipSIGk~GGCNPv 375 (405) T COG4393 333 VFDACDICGDQGYVMEGDQVICVRCDVRMFIPSIGKKGGCNPV 375 (405) T ss_pred eehHHHhccccceEeECCEEEEEEccEEEEcccCCCCCCCCCC Confidence 445777888999999999999887642 24 6777743 No 65 >PRK13656 trans-2-enoyl-CoA reductase; Provisional Probab=58.30 E-value=20 Score=24.14 Aligned_cols=35 Identities=17% Similarity=0.270 Sum_probs=29.0 Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccC Q psy255 26 LRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 26 ~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~ 60 (70) ....+..+.+=+++.|.+|-+..|.+.+++.|... T Consensus 17 p~gc~~~v~~qi~~~~~~~~~~~ggK~aLVTGaSs 51 (398) T PRK13656 17 PVGCEANVKEQIEYVKAQGPIANGPKKVLVIGASS 51 (398) T ss_pred CHHHHHHHHHHHHHHHhcCCcCCCCCEEEEECCCc Confidence 34577888888999999999999999998888643 No 66 >cd00831 CHS_like Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy, after the starter molecule is loaded onto the active site cysteine, a carboxylative condensation reation extends the polyketide chain. Plant-specific PKS are dimeric iterative PKSs, using coenzyme A esters to deliver substrate to the active site, but they differ in the choice of starter molecule and the number of condensation reactions. Probab=57.08 E-value=22 Score=22.90 Aligned_cols=26 Identities=15% Similarity=0.207 Sum_probs=20.5 Q ss_pred HHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 32 RVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 32 ~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) .+-.++..+.+.|.+++||++++++- T Consensus 325 si~~~L~~~~~~g~~~~Gd~vll~~~ 350 (361) T cd00831 325 SVLYVLAYMEAKGRVKRGDRGLLIAF 350 (361) T ss_pred cHHHHHHHHHHhCCCCCCCEEEEEEE Confidence 35566777888899999999988764 No 67 >PLN02932 3-ketoacyl-CoA synthase Probab=56.56 E-value=23 Score=24.38 Aligned_cols=26 Identities=12% Similarity=0.314 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) ..+-.++.++.++|.+++||+|+.++ T Consensus 414 aSI~~~L~~~ea~grik~Gd~vl~ia 439 (478) T PLN02932 414 SSIWYELAYTEAKGRMKKGDRIWQIA 439 (478) T ss_pred hHHHHHHHHHHHcCCCCCCCEEEEEE Confidence 44566778888899999999998775 No 68 >PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H. Probab=56.08 E-value=8.4 Score=18.68 Aligned_cols=14 Identities=36% Similarity=0.572 Sum_probs=8.0 Q ss_pred CCCCCCCeEEEeec Q psy255 44 KFLNQGDPVIVVTG 57 (70) Q Consensus 44 g~~~~GD~vv~~~g 57 (70) -|++.||+|++-.- T Consensus 36 ~FI~~Gd~I~VdT~ 49 (56) T PF09285_consen 36 LFIEEGDKIKVDTR 49 (56) T ss_dssp TT--TT-EEEEETT T ss_pred ceecCCCEEEEECC Confidence 46889999988543 No 69 >COG2164 Uncharacterized conserved protein [Function unknown] Probab=55.11 E-value=33 Score=19.01 Aligned_cols=43 Identities=19% Similarity=0.121 Sum_probs=24.0 Q ss_pred hcccc-eeeecCCCC--CCHHHHHHHHHHHHHhCCCCCCCCeEEEe Q psy255 13 VLIGK-IEPSPADWL--RDVDTRVAHGIKYGRDRKFLNQGDPVIVV 55 (70) Q Consensus 13 l~l~~-v~~~~~~~~--~~~~~~~~~a~~~~~~~g~~~~GD~vv~~ 55 (70) |+|.. -.|+..+.. .+.-+.+-...+-+-...-++.||+|++- T Consensus 79 lClFFGkTpmsddkiqPaSaVNvIGrIv~~lE~lk~v~dGe~v~ve 124 (126) T COG2164 79 LCLFFGKTPMSDDKIQPASAVNVIGRIVKNLELLKSVDDGERVIVE 124 (126) T ss_pred EEEEecCCcCcccccCccchHHHHHHHHhhHHhhhcccCCceEEEe Confidence 44444 455433321 23334455555555556668899999873 No 70 >PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes. Probab=55.02 E-value=22 Score=19.13 Aligned_cols=10 Identities=10% Similarity=0.511 Sum_probs=6.3 Q ss_pred HHHHHHhCCC Q psy255 36 GIKYGRDRKF 45 (70) Q Consensus 36 a~~~~~~~g~ 45 (70) |+++++++|+ T Consensus 9 AieW~~~qg~ 18 (93) T PF09652_consen 9 AIEWAKQQGI 18 (93) T ss_pred HHHHHHHhCC Confidence 4566666665 No 71 >PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A .... Probab=54.46 E-value=8.8 Score=19.07 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=15.3 Q ss_pred HHhCCCCCCCCeEEEeeccc Q psy255 40 GRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g~~ 59 (70) +...| ++.||.++-+-|.. T Consensus 38 a~~~g-l~~GD~Il~INg~~ 56 (81) T PF00595_consen 38 AERAG-LKVGDRILEINGQS 56 (81) T ss_dssp HHHHT-SSTTEEEEEETTEE T ss_pred HHhcc-cchhhhhheeCCEe Confidence 34568 89999999998864 No 72 >COG4821 Uncharacterized protein containing SIS (Sugar ISomerase) phosphosugar binding domain [General function prediction only] Probab=54.29 E-value=32 Score=21.44 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=21.5 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.-++++-..+...++--+++||.+++++-+ T Consensus 84 s~lErieg~~~~~l~~~~i~~~DVliviSnS 114 (243) T COG4821 84 SYLERIEGYAKLFLHRLQIRPNDVLIVISNS 114 (243) T ss_pred chhHhhhhHHHHHHHHhcCCCCCEEEEEeCC Confidence 3445566666665555557999999999876 No 73 >PF14544 DUF4443: Domain of unknown function (DUF4443); PDB: 2P8T_A. Probab=53.92 E-value=18 Score=19.98 Aligned_cols=18 Identities=22% Similarity=0.291 Sum_probs=9.5 Q ss_pred HhCCCCCCCCeEEEeecc Q psy255 41 RDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g~ 58 (70) ++..-+..||.||++.|. T Consensus 70 ~~l~~~~egD~IIIt~ae 87 (108) T PF14544_consen 70 EKLESLSEGDLIIITWAE 87 (108) T ss_dssp HH--S--TT-EEEEEE-S T ss_pred HHhhCccCCCEEEEEccC Confidence 333445899999999886 No 74 >PF14136 DUF4303: Domain of unknown function (DUF4303) Probab=53.23 E-value=34 Score=19.30 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=20.0 Q ss_pred HHHHHHHHHHHHhCCCCCCC---CeEEEee Q psy255 30 DTRVAHGIKYGRDRKFLNQG---DPVIVVT 56 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~G---D~vv~~~ 56 (70) -+.+..|+..+++.|++..| |.++.++ T Consensus 105 ~~~~~~aL~~l~~eg~f~~~~~~~i~~~v~ 134 (155) T PF14136_consen 105 LEAMVEALKQLDQEGFFGNGKREDIFFFVS 134 (155) T ss_pred HHHHHHHHHHHHHhcccCCCCccceEEEEE Confidence 35577888999999999998 5543443 No 75 >cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=53.03 E-value=21 Score=18.80 Aligned_cols=20 Identities=15% Similarity=0.199 Sum_probs=15.4 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 42 ~dA~~lgi-~~Gd~V~v~~~~ 61 (116) T cd02790 42 EDAKRLGI-EDGEKVRVSSRR 61 (116) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 45677886 899999988754 No 76 >TIGR00747 fabH 3-oxoacyl-(acyl-carrier-protein) synthase III. Active site residues include Cys112, His244 and Asn274 of E. coli FabH. Cys-112 is the site of acyl group attachment. Probab=52.99 E-value=30 Score=21.67 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=20.4 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-.++..+.+.|-+++||+|++.+.. T Consensus 281 ~~~~L~~~~~~~~~~~Gd~vll~~~G 306 (318) T TIGR00747 281 IPLALDELLRTGRIKPGDLLLLVAFG 306 (318) T ss_pred HHHHHHHHHHcCCCCCCCEEEEEEEe Confidence 44566778889999999999987653 No 77 >TIGR03089 conserved hypothetical protein TIGR03089. This protein family is found, so far, only in the Actinobacteria (Streptomyces, Mycobacterium, Corynebacterium, Nocardia, Propionibacterium, etc.) and never more than one to a genome. Members show twilight-level sequence similarity to family of AMP-binding enzymes described by Pfam model pfam00501. Probab=52.97 E-value=33 Score=20.72 Aligned_cols=29 Identities=17% Similarity=0.064 Sum_probs=20.7 Q ss_pred HHHHHHHHHHHHHh-CCCCCCCCeEEEeecc Q psy255 29 VDTRVAHGIKYGRD-RKFLNQGDPVIVVTGW 58 (70) Q Consensus 29 ~~~~~~~a~~~~~~-~g~~~~GD~vv~~~g~ 58 (70) ..+.+...-+.+++ .|+ ++||+|.+.... T Consensus 33 l~~~~~~~a~~L~~~~Gv-~~GdrV~i~~~n 62 (227) T TIGR03089 33 LANWVAKTANLLQDELDA-EPGSRVALDLPA 62 (227) T ss_pred HHHHHHHHHHHHHHHhCC-CCCCEEEEECCC Confidence 34556666667777 685 899999988754 No 78 >cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=52.71 E-value=22 Score=18.95 Aligned_cols=20 Identities=20% Similarity=0.119 Sum_probs=15.2 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.++. T Consensus 38 ~dA~~lgi-~~Gd~V~v~~~~ 57 (106) T cd02789 38 EDYKLLGK-PEGDKVKVTSEF 57 (106) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 44677886 799999888765 No 79 >COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only] Probab=52.43 E-value=31 Score=23.60 Aligned_cols=31 Identities=16% Similarity=0.365 Sum_probs=26.8 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .|...-+..|++.+++.++.+ .|.|++|-|. T Consensus 347 TD~~~~l~~al~~~k~~~~~~-adiv~ITDg~ 377 (437) T COG2425 347 TDITKALRSALEDLKSRELFK-ADIVVITDGE 377 (437) T ss_pred CChHHHHHHHHHHhhcccccC-CCEEEEeccH Confidence 456677889999999999988 9999999885 No 80 >cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=52.21 E-value=22 Score=18.84 Aligned_cols=20 Identities=15% Similarity=0.121 Sum_probs=15.7 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 38 ~dA~~lgI-~dGd~V~v~s~~ 57 (112) T cd02787 38 DDIARLGL-KAGDRVDLESAF 57 (112) T ss_pred HHHHHhCC-CCCCEEEEEecC Confidence 44677785 799999998865 No 81 >TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997). Probab=52.03 E-value=25 Score=19.46 Aligned_cols=17 Identities=35% Similarity=0.632 Sum_probs=13.8 Q ss_pred CCCCCCCeEEEeecccC Q psy255 44 KFLNQGDPVIVVTGWKK 60 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~ 60 (70) ..++.||.|+++-.... T Consensus 49 ~~L~dGDsV~liKDLkV 65 (109) T TIGR00686 49 NLLANGDSVILIKDLKV 65 (109) T ss_pred CCccCCCEEEEEeeccc Confidence 37899999999987643 No 82 >TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17. Probab=51.82 E-value=19 Score=18.21 Aligned_cols=16 Identities=19% Similarity=0.109 Sum_probs=13.5 Q ss_pred CCCCCCeEEEeecccC Q psy255 45 FLNQGDPVIVVTGWKK 60 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~ 60 (70) .++.||.|.+..+-|. T Consensus 48 ~~k~GD~V~I~ecrPl 63 (71) T TIGR03635 48 ECKVGDVVRIIETRPL 63 (71) T ss_pred CCCCCCEEEEEEcCCc Confidence 4899999999988764 No 83 >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=51.50 E-value=14 Score=20.59 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=9.3 Q ss_pred CCCCCeEEEeecc Q psy255 46 LNQGDPVIVVTGW 58 (70) Q Consensus 46 ~~~GD~vv~~~g~ 58 (70) +++||.+++++.+ T Consensus 101 ~~~gDvli~iS~S 113 (138) T PF13580_consen 101 IRPGDVLIVISNS 113 (138) T ss_dssp --TT-EEEEEESS T ss_pred CCCCCEEEEECCC Confidence 6899999999986 No 84 >PF00884 Sulfatase: Sulfatase; InterPro: IPR000917 Sulphatases 3.1.6. from EC are enzymes that hydrolyze various sulphate esters. The sequence of different types of sulphatases are available and have shown to be structurally related [, , ]; these include: arylsulphatase A 3.1.6.8 from EC (ASA), a lysosomal enzyme which hydrolyses cerebroside sulphate; arylsulphatase B 3.1.6.12 from EC (ASB), which hydrolyses the sulphate ester group from N-acetylgalactosamine 4-sulphate residues of dermatan sulphate; arylsulphatase C (ASD) and E (ASE); steryl-sulphatase 3.1.6.2 from EC (STS), a membrane bound microsomal enzyme which hydrolyses 3-beta-hydroxy steroid sulphates; iduronate 2-sulphatase precursor 3.1.6.13 from EC (IDS), a lysosomal enzyme that hydrolyses the 2-sulphate groups from non-reducing-terminal iduronic acid residues in dermatan sulphate and heparan sulphate; N-acetylgalactosamine-6-sulphatase 3.1.6.4 from EC, which hydrolyses the 6-sulphate groups of the N-acetyl-d-galactosamine 6-sulphate units of chondroitin sulphate and the D-galactose 6-sulphate units of keratan sulphate; glucosamine-6-sulphatase 3.1.6.14 from EC (G6S), which hydrolyses the N-acetyl-D-glucosamine 6-sulphate units of heparan sulphate and keratan sulphate; N-sulphoglucosamine sulphohydrolase 3.10.1.1 from EC (sulphamidase), the lysosomal enzyme that catalyses the hydrolysis of N-sulpho-d-glucosamine into glucosamine and sulphate; sea urchin embryo arylsulphatase 3.1.6.1 from EC; green algae arylsulphatase 3.1.6.1 from EC, which plays an important role in the mineralisation of sulphates; and arylsulphatase 3.1.6.1 from EC from Escherichia coli (aslA), Klebsiella aerogenes (gene atsA) and Pseudomonas aeruginosa (gene atsA). ; GO: 0008484 sulfuric ester hydrolase activity, 0008152 metabolic process; PDB: 1P49_A 1FSU_A 2QZU_A 2W5Q_A 2W5T_A 2W5S_A 2W5R_A 3LXQ_A 1HDH_B 1E33_P .... Probab=51.21 E-value=31 Score=20.88 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=22.8 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecccC Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~ 60 (70) .|..+...++.++++|. ..+.+|++.|.+. T Consensus 220 ~D~~l~~~~~~l~~~~~--~d~TiiiitsDHG 249 (308) T PF00884_consen 220 VDDQLGRFIEYLKEQGL--YDNTIIIITSDHG 249 (308) T ss_dssp HHHHHHHHHHHHHHTTC--GGGEEEEEEESSS T ss_pred HHHHhhhhhhhhhhcCC--cccceeEEecCcC Confidence 45678888999999997 4557777777653 No 85 >cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom Probab=50.97 E-value=23 Score=19.25 Aligned_cols=20 Identities=25% Similarity=0.222 Sum_probs=15.1 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.++. T Consensus 41 ~dA~~lgi-~~Gd~V~v~s~~ 60 (127) T cd02777 41 LDAAARGI-KDGDIVRVFNDR 60 (127) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 45677886 789999887754 No 86 >cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=50.22 E-value=25 Score=18.95 Aligned_cols=20 Identities=25% Similarity=0.337 Sum_probs=15.1 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.++. T Consensus 37 ~~A~~~gi-~~Gd~V~v~s~~ 56 (121) T cd02794 37 LDAAARGI-KDGDRVLVFNDR 56 (121) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 44677785 789999988765 No 87 >smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970. Probab=50.05 E-value=13 Score=18.07 Aligned_cols=15 Identities=40% Similarity=0.578 Sum_probs=11.0 Q ss_pred CCCCCCCCeEEEeec Q psy255 43 RKFLNQGDPVIVVTG 57 (70) Q Consensus 43 ~g~~~~GD~vv~~~g 57 (70) -.|++.||+|++-.- T Consensus 35 P~FI~~Gd~I~V~T~ 49 (56) T smart00841 35 PLFINEGDKIKVDTR 49 (56) T ss_pred CCcccCCCEEEEECC Confidence 357899999877543 No 88 >cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. Probab=49.66 E-value=28 Score=18.63 Aligned_cols=20 Identities=20% Similarity=0.348 Sum_probs=15.2 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-|++.|+ ++||.|.+.+.. T Consensus 40 ~dA~~lgi-~~Gd~V~v~s~~ 59 (115) T cd02779 40 EDAKREGL-KNGDLVEVYNDY 59 (115) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 45677785 799999987754 No 89 >cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs Probab=49.61 E-value=26 Score=18.68 Aligned_cols=20 Identities=20% Similarity=0.194 Sum_probs=15.4 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ +.||.|.+..+. T Consensus 42 ~dA~~lgi-~~Gd~V~v~~~~ 61 (122) T cd02791 42 EDAARLGL-KEGDLVRVTSRR 61 (122) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 45777886 799999887654 No 90 >cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P Probab=49.60 E-value=13 Score=18.07 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=10.5 Q ss_pred CCCCCCCeEEEeec Q psy255 44 KFLNQGDPVIVVTG 57 (70) Q Consensus 44 g~~~~GD~vv~~~g 57 (70) -|++.||+|++-.- T Consensus 36 ~FI~~Gd~I~V~T~ 49 (56) T cd05794 36 LFIKEGEKIKVDTR 49 (56) T ss_pred CeecCCCEEEEECC Confidence 46789999887544 No 91 >cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=49.48 E-value=26 Score=18.58 Aligned_cols=20 Identities=25% Similarity=0.328 Sum_probs=14.6 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 38 ~dA~~lgi-~~Gd~V~v~s~~ 57 (116) T cd02786 38 ADAAARGI-ADGDLVVVFNDR 57 (116) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 45677785 789999887644 No 92 >PRK13690 hypothetical protein; Provisional Probab=48.98 E-value=41 Score=20.32 Aligned_cols=30 Identities=7% Similarity=0.017 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) .+....+++.+.+...+++||.+|+=..+. T Consensus 7 ~~~~~~~~~El~~~a~l~~g~i~VvGcSTS 36 (184) T PRK13690 7 KKQTRQILEELLEQANLKPGQIFVLGCSTS 36 (184) T ss_pred HHHHHHHHHHHHHhhCCCCCCEEEEecchH Confidence 445677788888888899999999855443 No 93 >COG0318 CaiC Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism] Probab=48.69 E-value=41 Score=22.85 Aligned_cols=28 Identities=18% Similarity=0.111 Sum_probs=21.3 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +++.......+.+.| +++||+|.+.... T Consensus 45 ~~~~~~~A~~L~~~~-v~~gdrVail~~N 72 (534) T COG0318 45 DRRANRLAAALQALG-VKPGDRVAILLPN 72 (534) T ss_pred HHHHHHHHHHHHHcC-CCCCCEEEEECCC Confidence 455555556788888 9999999988765 No 94 >KOG3628|consensus Probab=48.67 E-value=34 Score=26.47 Aligned_cols=29 Identities=31% Similarity=0.460 Sum_probs=24.9 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) -+.+.+...+++.+++.++.||.|+++-- T Consensus 807 f~krva~i~~~l~~k~~lk~Gd~V~Lmy~ 835 (1363) T KOG3628|consen 807 FHKRVARIAEYLQDKGHLKAGDHVVLMYP 835 (1363) T ss_pred HHHHHHHHHHHHHhcccCCCCCeEEEEcC Confidence 46778888899999999999999998753 No 95 >PRK08329 threonine synthase; Validated Probab=48.20 E-value=31 Score=22.36 Aligned_cols=23 Identities=9% Similarity=0.056 Sum_probs=15.8 Q ss_pred HHHHHHHHhCCCCCCCCeEEEee Q psy255 34 AHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 34 ~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) -.++..+.++|.+++|++||++. T Consensus 317 ~Aa~~~l~~~g~i~~~~~Vv~~~ 339 (347) T PRK08329 317 LAAYWKLLEEGLIEGGSKVLLPL 339 (347) T ss_pred HHHHHHHHHhCCCCCCCeEEEEe Confidence 33455677888888888877544 No 96 >COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism] Probab=48.07 E-value=25 Score=19.47 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=13.8 Q ss_pred CCCCCCCeEEEeecccC Q psy255 44 KFLNQGDPVIVVTGWKK 60 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~ 60 (70) ..++.||.|+++-..+. T Consensus 51 n~L~dGDsV~lIKDLkV 67 (112) T COG2824 51 NLLADGDSVTLIKDLKV 67 (112) T ss_pred cEeccCCeEEEEEeeee Confidence 47899999999886643 No 97 >cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is Probab=47.71 E-value=30 Score=17.61 Aligned_cols=20 Identities=20% Similarity=0.132 Sum_probs=14.5 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.+++.|+ +.||+|.+.... T Consensus 30 ~da~~lgl-~~Gd~v~v~~~~ 49 (101) T cd02775 30 EDAAALGI-KDGDLVRVESRR 49 (101) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 45667786 689999877654 No 98 >COG1785 PhoA Alkaline phosphatase [Inorganic ion transport and metabolism] Probab=47.60 E-value=44 Score=23.21 Aligned_cols=27 Identities=19% Similarity=0.451 Sum_probs=17.3 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecccC Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~ 60 (70) .|+.++.|++++++. |+.+||+.+.+. T Consensus 328 fd~Avq~al~fA~k~-----~~TLVIvTADH~ 354 (482) T COG1785 328 FDEAVQAALDFAEKD-----GNTLVIVTADHE 354 (482) T ss_pred HHHHHHHHHHHHhcC-----CCeEEEEecccc Confidence 355566677777665 786666666553 No 99 >cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=47.24 E-value=31 Score=18.18 Aligned_cols=20 Identities=20% Similarity=0.147 Sum_probs=15.6 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.++. T Consensus 42 ~dA~~lgi-~~Gd~V~v~~~~ 61 (120) T cd00508 42 EDAARLGI-KDGDLVRVSSRR 61 (120) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 35777886 799999988754 No 100 >PRK09352 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed Probab=47.10 E-value=42 Score=20.98 Aligned_cols=24 Identities=13% Similarity=0.099 Sum_probs=17.9 Q ss_pred HHHHHHHHhCCCCCCCCeEEEeec Q psy255 34 AHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 34 ~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) -..+..+.+.|-+++||++++.+- T Consensus 282 ~~~L~~~~~~g~~~~Gd~vll~s~ 305 (319) T PRK09352 282 PLALDEAVRDGRIKRGDLVLLEGF 305 (319) T ss_pred HHHHHHHHHcCCCCCCCEEEEEEE Confidence 344556667888999999987764 No 101 >cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=47.01 E-value=29 Score=18.79 Aligned_cols=20 Identities=25% Similarity=0.114 Sum_probs=15.1 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+.+.|+ ++||.|.+.++. T Consensus 40 ~dA~~~gi-~~Gd~V~v~s~~ 59 (130) T cd02781 40 ETAAKLGI-ADGDWVWVETPR 59 (130) T ss_pred HHHHHcCC-CCCCEEEEECCC Confidence 45677886 799999887754 No 102 >TIGR01440 conserved hypothetical protein TIGR01440. Members of this family are uncharacterized proteins of about 180 amino acids from the Bacillus/Clostridium group of Gram-positive bacteria, found in no more than one copy per genome. Probab=46.92 E-value=34 Score=20.42 Aligned_cols=26 Identities=15% Similarity=0.184 Sum_probs=19.9 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ...+++.+.+...+++||.+|+=..+ T Consensus 3 ~~~~~~El~~~a~l~~g~i~VvGcST 28 (172) T TIGR01440 3 LTTVLEELKDASNLKKGDLFVIGCST 28 (172) T ss_pred HHHHHHHHHHhhCCCCCCEEEEecch Confidence 35567778888889999999975544 No 103 >PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A. Probab=46.52 E-value=31 Score=18.69 Aligned_cols=20 Identities=5% Similarity=0.212 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHhCCCCCC Q psy255 29 VDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~ 48 (70) +++.++.+++.+++.|++.+ T Consensus 7 ~~e~I~~vi~~l~~~gyidD 26 (121) T PF02631_consen 7 SEEAIEEVIDRLKELGYIDD 26 (121) T ss_dssp -HHHHHHHHHHHHHTTSS-H T ss_pred CHHHHHHHHHHHHHcCCCCH Confidence 56889999999999999843 No 104 >PF08840 BAAT_C: BAAT / Acyl-CoA thioester hydrolase C terminal; InterPro: IPR014940 Acyl-CoA thioesterases are a group of enzymes that catalyse the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH), providing the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. Bile acid-CoA:amino acid N-acetyltransferase (BAAT) is involved in bile acid metabolism and may also act as an acyl-CoA thioesterase that regulates intracellular levels of free fatty acids []. This entry represents a catalytic domain is found at the C terminus of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases. ; PDB: 3K2I_B 3HLK_B. Probab=46.47 E-value=37 Score=20.35 Aligned_cols=27 Identities=7% Similarity=0.064 Sum_probs=19.9 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.++.|+++++++..+. +++|.++..+ T Consensus 4 Eyfe~Ai~~L~~~p~v~-~~~Igi~G~S 30 (213) T PF08840_consen 4 EYFEEAIDWLKSHPEVD-PDKIGIIGIS 30 (213) T ss_dssp HHHHHHHHHHHCSTTB---SSEEEEEET T ss_pred HHHHHHHHHHHhCCCCC-CCCEEEEEEC Confidence 45889999999999875 6777776544 No 105 >PRK10220 hypothetical protein; Provisional Probab=45.99 E-value=35 Score=18.92 Aligned_cols=17 Identities=35% Similarity=0.577 Sum_probs=13.8 Q ss_pred CCCCCCCeEEEeecccC Q psy255 44 KFLNQGDPVIVVTGWKK 60 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~ 60 (70) ..+..||.|+++-.... T Consensus 50 ~~L~dGDsV~viKDLkV 66 (111) T PRK10220 50 NLLADGDSVTIVKDLKV 66 (111) T ss_pred CCccCCCEEEEEeeccc Confidence 37899999999987643 No 106 >PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function. Probab=45.91 E-value=20 Score=17.09 Aligned_cols=14 Identities=29% Similarity=0.370 Sum_probs=11.8 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) ++.||.|-+-+|.| T Consensus 1 f~~GDvV~LKSGGp 14 (53) T PF09926_consen 1 FKIGDVVQLKSGGP 14 (53) T ss_pred CCCCCEEEEccCCC Confidence 47899999999876 No 107 >COG4004 Uncharacterized protein conserved in archaea [Function unknown] Probab=45.68 E-value=44 Score=17.99 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=20.5 Q ss_pred eeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 19 EPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 19 ~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +|+.-....++|. +...++.+- -++-.+||++|-..+. T Consensus 4 yp~krGf~~~~dr-i~~~l~e~g-~~v~~eGD~ivas~pg 41 (96) T COG4004 4 YPVKRGFKPDPDR-IMRGLSELG-WTVSEEGDRIVASSPG 41 (96) T ss_pred cccccCCCCCHHH-HHHHHHHhC-eeEeecccEEEEecCC Confidence 3444444445544 444443333 4566799987766553 No 108 >PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D. Probab=45.52 E-value=28 Score=18.24 Aligned_cols=21 Identities=29% Similarity=0.232 Sum_probs=13.9 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.+.+.--+++||.+.+++|. T Consensus 67 ~~l~~~~~a~~GD~ll~~Ag~ 87 (95) T PF02938_consen 67 KALIERLGAKPGDLLLFVAGK 87 (95) T ss_dssp HHHHHHTT--TTEEEEEEEES T ss_pred HHHHHHhCCCCCCEEEEECCC Confidence 344444457999999999986 No 109 >PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional Probab=45.43 E-value=44 Score=22.39 Aligned_cols=23 Identities=30% Similarity=0.478 Sum_probs=13.2 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .+.|++.+++ .+++||.|+ ++|. T Consensus 410 ~~~Ai~~~~~--~~~~gDvVL-v~G~ 432 (460) T PRK00139 410 RAEAIRYAIA--QAKPGDVVL-IAGK 432 (460) T ss_pred HHHHHHHHHH--hcCCCCEEE-EEEc Confidence 3445555554 467899554 5554 No 110 >PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A .... Probab=45.33 E-value=22 Score=16.30 Aligned_cols=40 Identities=8% Similarity=0.077 Sum_probs=24.3 Q ss_pred hhHHhhhcccc--eeeecCCCCCCHHHHHHHHHHHHHhCCCC Q psy255 7 EEIPKQVLIGK--IEPSPADWLRDVDTRVAHGIKYGRDRKFL 46 (70) Q Consensus 7 ~~~~r~l~l~~--v~~~~~~~~~~~~~~~~~a~~~~~~~g~~ 46 (70) .++|+.+.++. |.-...+...=.++..+...+.+.+.|+. T Consensus 3 ~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~ 44 (46) T PF00356_consen 3 KDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYR 44 (46) T ss_dssp HHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB- T ss_pred HHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCC Confidence 35677777777 44444333333456677777777887763 No 111 >COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones] Probab=45.09 E-value=27 Score=18.75 Aligned_cols=18 Identities=22% Similarity=0.516 Sum_probs=13.0 Q ss_pred HhCCCCCCCCeEEEeecc Q psy255 41 RDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g~ 58 (70) ++.-.++.||.|++++-. T Consensus 76 ke~y~ledgDiIvfistl 93 (96) T COG5131 76 KERYPLEDGDIIVFISTL 93 (96) T ss_pred cccccCCCCCEEEEEecc Confidence 445677888888887654 No 112 >cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups Probab=44.95 E-value=39 Score=17.53 Aligned_cols=20 Identities=20% Similarity=0.079 Sum_probs=15.0 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.++. T Consensus 36 ~dA~~lGi-~~Gd~V~v~s~~ 55 (96) T cd02788 36 ADAARLGL-ADGDLVEFSLGD 55 (96) T ss_pred HHHHHcCC-CCCCEEEEEECC Confidence 35677786 789999887754 No 113 >PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C .... Probab=44.78 E-value=19 Score=17.75 Aligned_cols=23 Identities=4% Similarity=0.221 Sum_probs=17.7 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCC Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGD 50 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD 50 (70) -+...+..+++.|.++++++-++ T Consensus 42 ~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68) T PF10557_consen 42 PSVSDIKKRIESLIEKEYIERDE 64 (68) T ss_dssp --HHHHHHHHHHHHHTTSEEEES T ss_pred CCHHHHHHHHHHHHHhhhhhcCC Confidence 34677999999999999987543 No 114 >PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown. Probab=44.65 E-value=32 Score=17.94 Aligned_cols=32 Identities=6% Similarity=0.181 Sum_probs=23.2 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEE--EeecccC Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVI--VVTGWKK 60 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv--~~~g~~~ 60 (70) +..+.+..+-+.++++|. .|=+.+| +++|.|. T Consensus 16 ~~~~iL~~Vy~AL~EKGY-nPinQivGYllSGDPa 49 (79) T PF06135_consen 16 EIREILKQVYAALEEKGY-NPINQIVGYLLSGDPA 49 (79) T ss_pred hHHHHHHHHHHHHHHcCC-ChHHHHHhheecCCCc Confidence 456778888899999998 5555555 5677664 No 115 >PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q .... Probab=44.42 E-value=26 Score=17.56 Aligned_cols=17 Identities=18% Similarity=0.167 Sum_probs=13.2 Q ss_pred CCCCCCCCeEEEeeccc Q psy255 43 RKFLNQGDPVIVVTGWK 59 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~ 59 (70) ...++.||.|.+..+.| T Consensus 41 ~~~~~vGD~V~I~e~rP 57 (69) T PF00366_consen 41 NNICKVGDKVRIRECRP 57 (69) T ss_dssp TSSSTTTSEEEEEEEEE T ss_pred ccCCCCCCEEEEEeeec Confidence 45667899999987765 No 116 >smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities. Probab=44.18 E-value=29 Score=16.77 Aligned_cols=18 Identities=28% Similarity=0.411 Sum_probs=14.2 Q ss_pred HhCCCCCCCCeEEEeeccc Q psy255 41 RDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g~~ 59 (70) ...| +++||.++-+.|.. T Consensus 40 ~~~g-l~~GD~I~~In~~~ 57 (85) T smart00228 40 AKAG-LKVGDVILEVNGTS 57 (85) T ss_pred HHcC-CCCCCEEEEECCEE Confidence 3456 89999999888864 No 117 >PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C .... Probab=44.18 E-value=19 Score=17.92 Aligned_cols=19 Identities=21% Similarity=0.422 Sum_probs=14.0 Q ss_pred HHhCCCCCCCCeEEEeeccc Q psy255 40 GRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g~~ 59 (70) +.+.| +++||.++-+-|.+ T Consensus 27 A~~aG-l~~GD~I~~ing~~ 45 (82) T PF13180_consen 27 AAKAG-LQPGDIILAINGKP 45 (82) T ss_dssp HHHTT-S-TTEEEEEETTEE T ss_pred HHHCC-CCCCcEEEEECCEE Confidence 34567 68999999988875 No 118 >PRK12390 1-aminocyclopropane-1-carboxylate deaminase; Provisional Probab=44.12 E-value=39 Score=21.70 Aligned_cols=24 Identities=17% Similarity=0.145 Sum_probs=17.8 Q ss_pred HHHHHHHHhCCCCCCCCeEEEeec Q psy255 34 AHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 34 ~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) -.++..+.++|.+.+|++||+++- T Consensus 299 ~aa~~~~~~~g~~~~~~~vv~~ht 322 (337) T PRK12390 299 MHGMIDLVRKGEFPEGSKVLYAHL 322 (337) T ss_pred HHHHHHHHhcCCCCCCCeEEEEeC Confidence 345566777788889999998774 No 119 >PF13538 UvrD_C_2: UvrD-like helicase C-terminal domain; PDB: 1W36_G 3K70_G 3DMN_A 3UPU_B 3GPL_A 3E1S_A 3GP8_A. Probab=43.98 E-value=15 Score=18.95 Aligned_cols=14 Identities=21% Similarity=0.418 Sum_probs=8.4 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +++||+++++.... T Consensus 1 ~~~gD~vv~~~n~~ 14 (104) T PF13538_consen 1 FRPGDKVVITRNDS 14 (104) T ss_dssp --TT-EEEE-CTBT T ss_pred CcCcCEEEEEeeCC Confidence 46899999998764 No 120 >cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=43.69 E-value=33 Score=19.61 Aligned_cols=21 Identities=24% Similarity=0.129 Sum_probs=16.2 Q ss_pred HHHHHhCCCCCCCCeEEEeecc Q psy255 37 IKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~~~g~ 58 (70) -+.|++.|+ +.||.|.+.+.. T Consensus 38 p~dA~~~GI-~dGd~V~v~s~~ 58 (156) T cd02783 38 PKTAKELGI-KDGDWVWVESVN 58 (156) T ss_pred HHHHHHcCC-CCCCEEEEEcCC Confidence 356778886 799999988743 No 121 >cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=43.48 E-value=38 Score=18.27 Aligned_cols=20 Identities=25% Similarity=0.189 Sum_probs=15.3 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.++. T Consensus 39 ~dA~~~gi-~~Gd~V~v~s~~ 58 (124) T cd02785 39 IDAAARGI-AHGDLVEVYNDR 58 (124) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 45677886 789999888764 No 122 >cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma. Probab=43.20 E-value=6.9 Score=20.71 Aligned_cols=16 Identities=19% Similarity=0.260 Sum_probs=13.2 Q ss_pred HHHhCCCCCCCCeEEE Q psy255 39 YGRDRKFLNQGDPVIV 54 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~ 54 (70) .+.++|.++.||.+|. T Consensus 20 viV~~GtL~~Gd~iv~ 35 (95) T cd03701 20 VIVQNGTLKKGDVIVA 35 (95) T ss_pred EEEEcCeEecCCEEEE Confidence 4567899999999886 No 123 >PF04260 DUF436: Protein of unknown function (DUF436) ; InterPro: IPR006340 Members of this family are uncharacterised proteins of about 180 amino acids from the Bacillus/Clostridium group of Gram-positive bacteria, found in no more than one copy per genome. ; PDB: 1V8D_C. Probab=43.06 E-value=31 Score=20.61 Aligned_cols=26 Identities=12% Similarity=0.099 Sum_probs=15.6 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ...+++.+.+..-+++||.+|+=.+. T Consensus 3 ~~~~~~El~~~a~l~~g~i~VvGcST 28 (172) T PF04260_consen 3 LRQALEELLEQANLKPGQIFVVGCST 28 (172) T ss_dssp HHHHHHHHHHHS---TT-EEEEEE-H T ss_pred HHHHHHHHHHhcCCCCCCEEEEeeeH Confidence 45667777888888999999885544 No 124 >PRK14481 dihydroxyacetone kinase subunit DhaK; Provisional Probab=43.00 E-value=63 Score=21.29 Aligned_cols=31 Identities=19% Similarity=0.183 Sum_probs=23.1 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ...+++++..++.+.+.--+++||.++++-. T Consensus 229 ~~a~~l~~~m~~~ll~~~~~~~gd~v~lLvN 259 (331) T PRK14481 229 KPADEIAEELLEKILEDLKLVAGDEVLVLVN 259 (331) T ss_pred CCHHHHHHHHHHHHHhhcCCCCCCeEEEEEe Confidence 4567788888888777656789988887543 No 125 >cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=42.77 E-value=40 Score=17.99 Aligned_cols=20 Identities=20% Similarity=0.205 Sum_probs=15.0 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 37 ~dA~~~gi-~~Gd~V~v~s~~ 56 (123) T cd02778 37 ETAARLGI-KDGDRVEVSSAR 56 (123) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 45677886 799999887754 No 126 >PF02698 DUF218: DUF218 domain; InterPro: IPR003848 This domain of unknown function is found in several uncharacterised proteins.; PDB: 3CA8_A. Probab=42.57 E-value=53 Score=18.25 Aligned_cols=29 Identities=14% Similarity=0.207 Sum_probs=17.3 Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 24 DWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 24 ~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) +...++.+.+.++.+.++++|+ ..+++++ T Consensus 77 ~~s~~T~ena~~~~~~~~~~~~----~~iilVT 105 (155) T PF02698_consen 77 PKSTNTYENARFSKRLLKERGW----QSIILVT 105 (155) T ss_dssp ----SHHHHHHHHHHHHHT-SS----S-EEEE- T ss_pred CCCCCHHHHHHHHHHHHHhhcC----CeEEEEC Confidence 3456788888888899999998 4555444 No 127 >COG0365 Acs Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism] Probab=42.50 E-value=42 Score=23.41 Aligned_cols=29 Identities=21% Similarity=0.100 Sum_probs=20.1 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ..+........|++.+-+ +||+|.+.--. T Consensus 46 L~~~v~r~A~~L~~~~gv-kGDrV~iymp~ 74 (528) T COG0365 46 LRREVARLANALKDLGGV-KGDRVAIYMPN 74 (528) T ss_pred HHHHHHHHHHHHHHhCCC-CCCEEEEEcCC Confidence 334455566778887766 99999986543 No 128 >COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis] Probab=42.34 E-value=17 Score=18.76 Aligned_cols=15 Identities=33% Similarity=0.341 Sum_probs=11.2 Q ss_pred CCCCCCCCeEEEeec Q psy255 43 RKFLNQGDPVIVVTG 57 (70) Q Consensus 43 ~g~~~~GD~vv~~~g 57 (70) +=++.+||.|++--. T Consensus 44 ~i~I~~GD~V~Ve~~ 58 (75) T COG0361 44 RIRILPGDVVLVELS 58 (75) T ss_pred eEEeCCCCEEEEEec Confidence 457889999987543 No 129 >COG4570 Rus Holliday junction resolvase [DNA replication, recombination, and repair] Probab=42.26 E-value=49 Score=18.95 Aligned_cols=29 Identities=7% Similarity=0.097 Sum_probs=25.6 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEe Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVV 55 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~ 55 (70) .|.|+++....+.+-+.|+.++...|+=+ T Consensus 82 pDlDNl~K~l~Daltk~g~~~DD~Qive~ 110 (132) T COG4570 82 PDLDNLLKALLDALTKAGVWKDDAQIVEI 110 (132) T ss_pred ccHHHHHHHHHHHHhhcceecccceeEEE Confidence 57899999999999999999999888854 No 130 >PF12897 Aminotran_MocR: Alanine-glyoxylate amino-transferase; InterPro: IPR024551 This entry represents a family of putative aminotransferases.; PDB: 3D6K_C 3EZ1_A 3PPL_B. Probab=42.02 E-value=50 Score=22.52 Aligned_cols=51 Identities=14% Similarity=0.022 Sum_probs=24.0 Q ss_pred eecCChhHHhhhc----------ccc-----eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 2 SSTRSEEIPKQVL----------IGK-----IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 2 a~t~~~~~~r~l~----------l~~-----v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ++|.+.++.|+|+ ++| |+.++.+. ....+...++.+++.| ..|+|.+.+.. T Consensus 187 G~tySde~vrrlA~m~~AA~DFRI~WDNAY~vHhL~~~~---~~~~~~nil~~~~~AG---npdrv~~F~ST 252 (425) T PF12897_consen 187 GITYSDEVVRRLAAMKTAAPDFRIFWDNAYAVHHLYDEE---PRDALLNILDACAKAG---NPDRVYVFAST 252 (425) T ss_dssp -----HHHHHHHHHS--SSTT-EEEEE-TTTT-BSSSSS---S------HHHHHHHTT----TTSEEEEEES T ss_pred CccCCHHHHHHHhcCCcCCcCeEEEeecCceEeeccccc---cchhhhHHHHHHHHcC---CCCeEEEEecc Confidence 4678888888885 467 44433221 1122235666777777 56777766654 No 131 >PF13076 DUF3940: Protein of unknown function (DUF3940) Probab=41.57 E-value=36 Score=15.14 Aligned_cols=17 Identities=12% Similarity=-0.042 Sum_probs=13.6 Q ss_pred HHHHHHHhCCCCCCCCe Q psy255 35 HGIKYGRDRKFLNQGDP 51 (70) Q Consensus 35 ~a~~~~~~~g~~~~GD~ 51 (70) .-++.+.+.|+.+.+|+ T Consensus 5 ~lI~~Li~~Giyk~~dr 21 (38) T PF13076_consen 5 FLIEKLIQSGIYKKEDR 21 (38) T ss_pred HHHHHHHHcCCcCccch Confidence 34678899999999885 No 132 >PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A. Probab=41.34 E-value=32 Score=17.29 Aligned_cols=26 Identities=8% Similarity=0.087 Sum_probs=20.1 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEe Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVV 55 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~ 55 (70) ...+...++.+.+.|+++.++....+ T Consensus 33 ~~~~~~yL~~L~~~gLI~~~~~~Y~l 58 (77) T PF14947_consen 33 YSTLKKYLKELEEKGLIKKKDGKYRL 58 (77) T ss_dssp HHHHHHHHHHHHHTTSEEEETTEEEE T ss_pred HHHHHHHHHHHHHCcCeeCCCCEEEE Confidence 46788889999999999876555443 No 133 >PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function Probab=41.23 E-value=25 Score=18.76 Aligned_cols=14 Identities=29% Similarity=0.446 Sum_probs=11.4 Q ss_pred CCCCCCCCeEEEee Q psy255 43 RKFLNQGDPVIVVT 56 (70) Q Consensus 43 ~g~~~~GD~vv~~~ 56 (70) ..-++.||.|+++. T Consensus 74 ~~~Lk~GD~V~ll~ 87 (100) T PF10844_consen 74 TDGLKVGDKVLLLR 87 (100) T ss_pred ecCCcCCCEEEEEE Confidence 34579999999987 No 134 >TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex. Probab=40.86 E-value=59 Score=21.39 Aligned_cols=30 Identities=7% Similarity=-0.075 Sum_probs=22.3 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) .+.+++++..++.+.+.--+++||.|+++- T Consensus 226 ~~a~elv~~l~~~ll~~~~~~~gd~v~vlv 255 (326) T TIGR02362 226 VSSEHLAVELVNKLKLKFRWQADDHYAVLV 255 (326) T ss_pred CCHHHHHHHHHHHHHhhcCCCCCCEEEEEe Confidence 456778888888877765667999888654 No 135 >PRK12363 phosphoglycerol transferase I; Provisional Probab=40.78 E-value=69 Score=23.33 Aligned_cols=30 Identities=13% Similarity=0.225 Sum_probs=24.4 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecccC Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~ 60 (70) .|..+...++.+++.|+.+ +.+|++.|.+. T Consensus 364 sD~aIG~FId~LKksglyd--NTIIV~~GDH~ 393 (703) T PRK12363 364 SDRLIGQLVDRIRNSRYGK--NTIIVIASDHL 393 (703) T ss_pred HHHHHHHHHHHHHhcCCcC--CeEEEEEcCCC Confidence 5677888999999999854 78888888764 No 136 >PRK10646 ADP-binding protein; Provisional Probab=40.44 E-value=40 Score=19.60 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=16.8 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .+.+++.+.+...++ .+++||. |.+.|. T Consensus 9 ~s~~~t~~l~~~la~---~l~~g~v-i~L~Gd 36 (153) T PRK10646 9 PDEQATLDLGARVAK---ACDGATV-IYLYGD 36 (153) T ss_pred CCHHHHHHHHHHHHH---hCCCCcE-EEEECC Confidence 355666666665554 4577874 556664 No 137 >cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins. Probab=40.44 E-value=35 Score=16.49 Aligned_cols=19 Identities=26% Similarity=0.534 Sum_probs=14.6 Q ss_pred HHhCCCCCCCCeEEEeeccc Q psy255 40 GRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g~~ 59 (70) +.+.| +++||.++-+-|.+ T Consensus 25 a~~~g-l~~GD~I~~ing~~ 43 (79) T cd00989 25 AAKAG-LKAGDRILAINGQK 43 (79) T ss_pred HHHcC-CCCCCEEEEECCEE Confidence 34456 59999999998875 No 138 >COG4668 MtlA Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism] Probab=40.25 E-value=37 Score=19.65 Aligned_cols=24 Identities=4% Similarity=0.101 Sum_probs=20.6 Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCC Q psy255 26 LRDVDTRVAHGIKYGRDRKFLNQG 49 (70) Q Consensus 26 ~~~~~~~~~~a~~~~~~~g~~~~G 49 (70) ..+-++.++.+-+.+++.|++.++ T Consensus 14 ~~nK~eAi~~~g~~Lv~~G~V~~~ 37 (142) T COG4668 14 AANKEEAIEFAGEALVEGGYVEPG 37 (142) T ss_pred ccCHHHHHHHHHHHHHHCCCCCHH Confidence 457789999999999999998774 No 139 >TIGR02363 dhaK1 dihydroxyacetone kinase, DhaK subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the DhaK subunit of the latter type of dihydroxyacetone kinase, but it specifically excludes the DhaK paralog DhaK2 (TIGR02362) found in the same operon as DhaK and DhaK in the Firmicutes. Probab=40.06 E-value=61 Score=21.36 Aligned_cols=31 Identities=26% Similarity=0.219 Sum_probs=22.4 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) .+.+++++..++.+.+.--+++||.|+++-. T Consensus 230 ~~a~~l~~~l~~~l~~~~~~~~gd~v~vlvN 260 (329) T TIGR02363 230 KSSDEIADELLDKLLDDLGLQSGDRVIVLVN 260 (329) T ss_pred CCHHHHHHHHHHHHHhhcCCCCCCeEEEEEe Confidence 4567788888888777655689988886543 No 140 >PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 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 C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A .... Probab=39.79 E-value=17 Score=17.36 Aligned_cols=13 Identities=46% Similarity=0.639 Sum_probs=9.4 Q ss_pred CCCCCCeEEEeec Q psy255 45 FLNQGDPVIVVTG 57 (70) Q Consensus 45 ~~~~GD~vv~~~g 57 (70) .+++||.++++.. T Consensus 47 ~l~~gD~l~v~g~ 59 (71) T PF02080_consen 47 VLQAGDILIVVGD 59 (71) T ss_dssp BE-TTEEEEEEEE T ss_pred EECCCCEEEEEEC Confidence 4689999988764 No 141 >PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []. This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A. Probab=39.76 E-value=60 Score=19.78 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=18.5 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) |..++...+.+.+.. ++-.+|.+.|.+ T Consensus 2 e~~~~~l~~~L~~~~---~~~~~v~I~G~~ 28 (287) T PF00931_consen 2 EKEIEKLKDWLLDNS---NEVRVVAIVGMG 28 (287) T ss_dssp HHHHHHHHHHHHTTT---TSSEEEEEEEST T ss_pred HHHHHHHHHHhhCCC---CCeEEEEEEcCC Confidence 445666667777655 777788888863 No 142 >cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=39.74 E-value=44 Score=18.10 Aligned_cols=20 Identities=20% Similarity=0.170 Sum_probs=15.1 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 40 ~dA~~~gi-~~Gd~V~v~s~~ 59 (129) T cd02782 40 DDAAALGL-ADGDKVRVTSAA 59 (129) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 45677886 799999887654 No 143 >TIGR01274 ACC_deam 1-aminocyclopropane-1-carboxylate deaminase. This pyridoxal phosphate-dependent enzyme degrades 1-aminocyclopropane-1-carboxylate, which in plants is a precursor of the ripening hormone ethylene, to ammonia and alpha-ketoglutarate. This model includes all members of this family for which function has been demonstrated experimentally, but excludes a closely related family often annotated as putative members of this family. Probab=39.57 E-value=52 Score=21.17 Aligned_cols=21 Identities=14% Similarity=0.040 Sum_probs=14.1 Q ss_pred HHHHHhCCCCCCCCeEEEeec Q psy255 37 IKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~~~g 57 (70) +..+.++|-+.+|+.||+++- T Consensus 301 ~~~~~~~g~~~~~~~vv~~ht 321 (337) T TIGR01274 301 MIEMIRRGEFKEGSNVLYAHL 321 (337) T ss_pred HHHHHhcCCCCCCCEEEEEeC Confidence 344455566678899998764 No 144 >COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism] Probab=39.51 E-value=61 Score=20.57 Aligned_cols=27 Identities=30% Similarity=0.370 Sum_probs=19.9 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecccCC Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~~~~ 61 (70) +.+.+.++.+.=-+++||.| .+|.|.+ T Consensus 212 i~~lI~~lS~~~tL~pGDvI--~TGTP~G 238 (266) T COG0179 212 IPELIAYLSRFMTLEPGDVI--LTGTPSG 238 (266) T ss_pred HHHHHHHHhCCcccCCCCEE--EeCCCCC Confidence 56667777777888999964 5677754 No 145 >cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=39.43 E-value=46 Score=17.69 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=14.7 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ +.||.|.+.+.. T Consensus 42 ~dA~~lgi-~~Gd~V~v~s~~ 61 (122) T cd02792 42 ELAAERGI-KNGDMVWVSSPR 61 (122) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 35677886 799999877643 No 146 >cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea. Probab=39.36 E-value=18 Score=18.48 Aligned_cols=16 Identities=44% Similarity=0.729 Sum_probs=12.6 Q ss_pred HHhCCCCCCCCeEEEe Q psy255 40 GRDRKFLNQGDPVIVV 55 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~ 55 (70) .+.+=++++||.|++- T Consensus 33 ~rk~iwI~~GD~V~Ve 48 (77) T cd05793 33 MRKRVWINEGDIVLVA 48 (77) T ss_pred hcccEEEcCCCEEEEE Confidence 4456789999999984 No 147 >TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis. Probab=39.04 E-value=72 Score=17.87 Aligned_cols=27 Identities=19% Similarity=0.232 Sum_probs=16.4 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) |..+.+.++++.+.+ .-|.||.+.|.. T Consensus 51 Dd~~~i~~~l~~~~~-----~~DliIttGG~g 77 (144) T TIGR00177 51 DDPEEIREILRKAVD-----EADVVLTTGGTG 77 (144) T ss_pred CCHHHHHHHHHHHHh-----CCCEEEECCCCC Confidence 444556666665543 467777776654 No 148 >PRK05610 rpsQ 30S ribosomal protein S17; Reviewed Probab=38.82 E-value=39 Score=17.66 Aligned_cols=17 Identities=18% Similarity=0.087 Sum_probs=14.0 Q ss_pred CCCCCCCeEEEeecccC Q psy255 44 KFLNQGDPVIVVTGWKK 60 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~ 60 (70) ..++.||.|.+..+-|. T Consensus 52 n~~k~GD~V~I~e~rPl 68 (84) T PRK05610 52 NEAKIGDVVRIMETRPL 68 (84) T ss_pred CCCCCCCEEEEEEcccC Confidence 35899999999988764 No 149 >PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A. Probab=38.66 E-value=45 Score=17.94 Aligned_cols=19 Identities=11% Similarity=0.073 Sum_probs=14.8 Q ss_pred CHHHHHHHHHHHHHhCCCC Q psy255 28 DVDTRVAHGIKYGRDRKFL 46 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~ 46 (70) ..++.++.+.+.|++.|++ T Consensus 79 ~~~e~l~~I~~~L~~~G~L 97 (98) T PF02829_consen 79 PDEEDLDKIEEALKKKGFL 97 (98) T ss_dssp SSHHHHHHHHHHHHHTT-B T ss_pred CCHHHHHHHHHHHHHCCCc Confidence 3467788899999999985 No 150 >cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma. Probab=38.65 E-value=18 Score=19.95 Aligned_cols=18 Identities=22% Similarity=0.218 Sum_probs=14.1 Q ss_pred HHHhCCCCCCCCeEEEee Q psy255 39 YGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~~~ 56 (70) .+...|.++.||.|++-. T Consensus 20 vIl~~GtL~~GD~Iv~g~ 37 (110) T cd03703 20 VILYDGTLREGDTIVVCG 37 (110) T ss_pred EEEECCeEecCCEEEEcc Confidence 345689999999998743 No 151 >COG2412 Uncharacterized conserved protein [Function unknown] Probab=38.18 E-value=49 Score=18.04 Aligned_cols=24 Identities=17% Similarity=0.405 Sum_probs=18.5 Q ss_pred HHHHHHHhCCCCCCCCeEEEeeccc Q psy255 35 HGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 35 ~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) .+++.+.+.|++.+ |.|.-+.|.| T Consensus 69 ~av~~aI~~Gli~~-d~Vl~i~Gvp 92 (101) T COG2412 69 KAVEIAIDAGLIDK-DSVLEIGGVP 92 (101) T ss_pred hhhHHHHhcCccCc-ccEEEEcCee Confidence 45677889999855 7788888876 No 152 >PF07563 DUF1541: Protein of unknown function (DUF1541); InterPro: IPR011438 This domain is found in several hypothetical bacterial proteins as a tandem repeat.; PDB: 2KY9_A 4FIB_B. Probab=38.08 E-value=34 Score=16.47 Aligned_cols=19 Identities=26% Similarity=0.377 Sum_probs=10.5 Q ss_pred CCCCeEEEeecccCC-CCCC Q psy255 47 NQGDPVIVVTGWKKG-AGFT 65 (70) Q Consensus 47 ~~GD~vv~~~g~~~~-~g~t 65 (70) ++||.|++.+.-..+ .|.+ T Consensus 1 ~~G~ev~l~AdHM~GM~gA~ 20 (53) T PF07563_consen 1 KVGSEVTLTADHMPGMKGAT 20 (53) T ss_dssp -TT-EEEESS-SSTTGTT-E T ss_pred CCCcEEEEecccCCccCCCE Confidence 478888888876554 5544 No 153 >PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria. Probab=38.02 E-value=26 Score=18.10 Aligned_cols=14 Identities=36% Similarity=0.401 Sum_probs=11.0 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+|+||.|++-... T Consensus 5 ~Vk~Gd~ViV~~~~ 18 (75) T PF11302_consen 5 SVKPGDTVIVQDEQ 18 (75) T ss_pred ccCCCCEEEEecCc Confidence 36899999987655 No 154 >cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea. Probab=37.78 E-value=20 Score=18.40 Aligned_cols=18 Identities=28% Similarity=0.362 Sum_probs=13.5 Q ss_pred HHHhCCCCCCCCeEEEee Q psy255 39 YGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~~~ 56 (70) ..+..=+++.||.|++-- T Consensus 32 K~Rk~iwI~~GD~VlV~~ 49 (78) T cd04456 32 KLRKNIWIKRGDFLIVDP 49 (78) T ss_pred hhccCEEEcCCCEEEEEe Confidence 344557899999999853 No 155 >PRK05609 nusG transcription antitermination protein NusG; Validated Probab=37.71 E-value=26 Score=20.32 Aligned_cols=17 Identities=24% Similarity=0.184 Sum_probs=13.8 Q ss_pred CCCCCCeEEEeecccCC Q psy255 45 FLNQGDPVIVVTGWKKG 61 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~ 61 (70) .+++||+|-+++|...+ T Consensus 126 ~~~~Gd~VrI~~GPf~G 142 (181) T PRK05609 126 DFEVGEMVRVIDGPFAD 142 (181) T ss_pred CCCCCCEEEEeccCCCC Confidence 36799999999997544 No 156 >PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B. Probab=37.61 E-value=65 Score=16.94 Aligned_cols=19 Identities=21% Similarity=0.282 Sum_probs=13.1 Q ss_pred CCHHHHHHHHHHHHHhCCC Q psy255 27 RDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~ 45 (70) .+....+..+++.+++.|+ T Consensus 13 ~s~~~~V~~~i~~i~~sgl 31 (92) T PF01910_consen 13 ESVSAYVAEAIEVIKESGL 31 (92) T ss_dssp SHHHHHHHHHHHHHHTSSS T ss_pred CCHHHHHHHHHHHHHHcCC Confidence 3556667777777777775 No 157 >TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus. Probab=37.27 E-value=55 Score=16.86 Aligned_cols=19 Identities=16% Similarity=0.055 Sum_probs=16.0 Q ss_pred CCCHHHHHHHHHHHHHhCC Q psy255 26 LRDVDTRVAHGIKYGRDRK 44 (70) Q Consensus 26 ~~~~~~~~~~a~~~~~~~g 44 (70) .+++|+.+++..+.+++.| T Consensus 24 ~~d~d~Al~eM~e~A~~lG 42 (74) T TIGR03884 24 SDNVDEIVENLREKVKAKG 42 (74) T ss_pred cCCHHHHHHHHHHHHHHcC Confidence 3488999999999998887 No 158 >PRK09014 rfaH transcriptional activator RfaH; Provisional Probab=37.09 E-value=28 Score=19.92 Aligned_cols=17 Identities=35% Similarity=0.485 Sum_probs=13.9 Q ss_pred CCCCCCeEEEeecccCC Q psy255 45 FLNQGDPVIVVTGWKKG 61 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~ 61 (70) .+++||+|-++.|...+ T Consensus 109 ~~~~G~~V~I~~Gp~~g 125 (162) T PRK09014 109 TPKPGDKVIITEGAFEG 125 (162) T ss_pred CCCCCCEEEEecCCCCC Confidence 46799999999997544 No 159 >PF11737 DUF3300: Protein of unknown function (DUF3300); InterPro: IPR021728 This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein. Probab=37.07 E-value=24 Score=22.12 Aligned_cols=55 Identities=9% Similarity=-0.034 Sum_probs=35.8 Q ss_pred eecCChhHHhhhc--ccce----eeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 2 SSTRSEEIPKQVL--IGKI----EPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 2 a~t~~~~~~r~l~--l~~v----~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) |++.-+.++.+|+ |-|. ..+.. ...+.-+.|+.--..+.+.|-++..+..-++.- T Consensus 67 aL~~fP~VL~~Ms~~l~WTq~LGdAfl~-q~~dVm~aIQ~LR~~A~~~G~L~s~~qq~V~~~ 127 (237) T PF11737_consen 67 ALVAFPDVLQMMSDDLDWTQQLGDAFLA-QPQDVMDAIQRLRQRAQAAGNLKSTPQQKVTVE 127 (237) T ss_pred HHHhhHHHHHHHccChHHHHHHHHHHHh-CHHHHHHHHHHHHHHHHHcCCcCCCCceEEEEe Confidence 4556677888885 7782 22222 223444556666677889999999998776553 No 160 >PRK10760 murein hydrolase B; Provisional Probab=36.87 E-value=67 Score=21.45 Aligned_cols=28 Identities=21% Similarity=0.273 Sum_probs=22.1 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) +..+.+..+-++++++|| ++|..|.+-. T Consensus 246 ~~~DaiaS~AnyL~~~GW-~~G~pV~~P~ 273 (359) T PRK10760 246 DPVDAIGSVANYFKAHGW-VKGDQVAVPA 273 (359) T ss_pred CcHHHHHHHHHHHHHcCC-CCCCceEecC Confidence 345788888899999999 6887866554 No 161 >cd00827 init_cond_enzymes "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the utlization of CoA substrate primers, as well as the nature of their active site residues. Probab=36.84 E-value=76 Score=19.77 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=20.7 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ..+-.++..+.+.|.+++||++++.+- T Consensus 287 a~~~~~L~~~~~~~~~~~Gd~vl~~~~ 313 (324) T cd00827 287 ASILLGLASLLESGKLKAGDRVLLFSY 313 (324) T ss_pred HHHHHHHHHHHhcCCCCCCCEEEEEEe Confidence 345556777788898999999998764 No 162 >TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes. Probab=36.82 E-value=27 Score=19.76 Aligned_cols=16 Identities=31% Similarity=0.387 Sum_probs=13.3 Q ss_pred CCCCCeEEEeecccCC Q psy255 46 LNQGDPVIVVTGWKKG 61 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~ 61 (70) +++||+|-++.|...+ T Consensus 109 ~~~G~~V~V~~GPf~g 124 (159) T TIGR01955 109 PYKGDKVRITDGAFAG 124 (159) T ss_pred CCCCCEEEEeccCCCC Confidence 6799999999997543 No 163 >PRK09275 aspartate aminotransferase; Provisional Probab=36.60 E-value=73 Score=22.21 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=23.2 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) ....+.+..+...++...++++||.|++.. T Consensus 168 ~Ga~~al~~~~~aL~~~~ll~pGD~Vlv~~ 197 (527) T PRK09275 168 EGGTAAMCYIFDSLKENGLLKAGDKIALMT 197 (527) T ss_pred CCHHHHHHHHHHHHhhhhcCCCCCEEEEeC Confidence 345566777777777778999999999876 No 164 >PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A. Probab=36.49 E-value=24 Score=16.85 Aligned_cols=28 Identities=11% Similarity=0.228 Sum_probs=17.1 Q ss_pred CHHHHHHHHHHHHHhCCCCC-CCCeEEEe Q psy255 28 DVDTRVAHGIKYGRDRKFLN-QGDPVIVV 55 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~-~GD~vv~~ 55 (70) +..+.....++.+.+.|++. .++.+.++ T Consensus 33 ~~~~~~~~~l~~l~~~Gll~~~~~~l~lT 61 (66) T PF06969_consen 33 DFAEEFQKELEELQEDGLLEIDGGRLRLT 61 (66) T ss_dssp -THHH-HHHHHHHHHTTSEEE-SSEEEE- T ss_pred CHHHHHHHHHHHHHHCCCEEEeCCEEEEC Confidence 34555677788899999984 44555544 No 165 >PRK09371 gas vesicle synthesis protein GvpA; Provisional Probab=36.33 E-value=29 Score=17.51 Aligned_cols=28 Identities=14% Similarity=0.077 Sum_probs=23.2 Q ss_pred HHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 32 RVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 32 ~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) .+...++...++|.+-.||..|-+.|.. T Consensus 8 sLadvldriLDKGiVI~adi~VSl~gie 35 (68) T PRK09371 8 SLAEVIDRILDKGIVVDAWVRVSLVGIE 35 (68) T ss_pred cHHHHHHHHccCCeEEEEEEEEEEeeeE Confidence 3566788889999999999999888763 No 166 >PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W. Probab=36.32 E-value=24 Score=17.23 Aligned_cols=17 Identities=35% Similarity=0.522 Sum_probs=10.8 Q ss_pred HHhCCCCCCCCeEEEee Q psy255 40 GRDRKFLNQGDPVIVVT 56 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~ 56 (70) .+..=+++.||.|++-- T Consensus 36 ~r~~iwI~~GD~V~V~~ 52 (65) T PF01176_consen 36 FRKRIWIKRGDFVLVEP 52 (65) T ss_dssp HHTCC---TTEEEEEEE T ss_pred eeeeEecCCCCEEEEEe Confidence 56677999999998754 No 167 >PF14502 HTH_41: Helix-turn-helix domain Probab=36.21 E-value=39 Score=15.88 Aligned_cols=17 Identities=6% Similarity=0.268 Sum_probs=13.7 Q ss_pred HHHHHHHHHHHhCCCCC Q psy255 31 TRVAHGIKYGRDRKFLN 47 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~ 47 (70) -.++.|++++++.|-++ T Consensus 21 GtiQ~Alk~Le~~gaI~ 37 (48) T PF14502_consen 21 GTIQNALKFLEENGAIK 37 (48) T ss_pred hHHHHHHHHHHHCCcEE Confidence 45889999999998653 No 168 >PF03831 PhnA: PhnA protein; InterPro: IPR013988 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the C-terminal domain of PhnA.; PDB: 2AKK_A 2AKL_A. Probab=36.13 E-value=22 Score=17.29 Aligned_cols=15 Identities=33% Similarity=0.530 Sum_probs=10.1 Q ss_pred CCCCCCeEEEeeccc Q psy255 45 FLNQGDPVIVVTGWK 59 (70) Q Consensus 45 ~~~~GD~vv~~~g~~ 59 (70) .++.||.|+++-..+ T Consensus 9 ~L~dGDsV~~iKDLk 23 (56) T PF03831_consen 9 ELQDGDSVTLIKDLK 23 (56) T ss_dssp B--TTEEEEESS-EE T ss_pred CccCCCEEEEEeeee Confidence 678999999987664 No 169 >cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins. Probab=35.99 E-value=57 Score=18.11 Aligned_cols=20 Identities=30% Similarity=0.209 Sum_probs=15.2 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+++.|+ ++||.|.+.+.. T Consensus 37 ~dA~~lgI-~~Gd~V~v~s~~ 56 (143) T cd02780 37 EDAAKLGI-KTGDRVRVVTPG 56 (143) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 45677886 799999987754 No 170 >PF05763 DUF835: Protein of unknown function (DUF835); InterPro: IPR008553 The members of this archaebacterial protein entry are around 250-300 amino acid residues in length. The function of these proteins is not known. Probab=35.83 E-value=85 Score=17.76 Aligned_cols=52 Identities=12% Similarity=0.220 Sum_probs=29.1 Q ss_pred eecC-ChhHHh--hhcccceeeecCC---CCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 2 SSTR-SEEIPK--QVLIGKIEPSPAD---WLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 2 a~t~-~~~~~r--~l~l~~v~~~~~~---~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ++|. +++..+ .--.+|+.....+ ...+.+.+.+.+.+++++. |+.+|++-|. T Consensus 27 ~itR~~Pe~~~~~~~~viWlT~~~~~~~I~Pt~L~~l~~~i~~fl~~~-----~~~vViiD~l 84 (136) T PF05763_consen 27 AITRRNPEEWREKNTPVIWLTKVEGENAISPTNLHKLLDTIVRFLKEN-----GNGVVIIDGL 84 (136) T ss_pred EEEecChhhccccCCcEEEEeccCCCCccCchhhHHHHHHHHHHHHhC-----CCcEEEEecH Confidence 5666 566666 3346672222222 2234466677777887772 3347777765 No 171 >TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter. Probab=35.64 E-value=95 Score=18.22 Aligned_cols=14 Identities=7% Similarity=0.145 Sum_probs=6.9 Q ss_pred HHHHHHHHHhCCCC Q psy255 33 VAHGIKYGRDRKFL 46 (70) Q Consensus 33 ~~~a~~~~~~~g~~ 46 (70) +++|+..|...|++ T Consensus 51 VReAL~~L~~eGlv 64 (212) T TIGR03338 51 VREAFRALEEAGLV 64 (212) T ss_pred HHHHHHHHHHCCCE Confidence 44455555555544 No 172 >PF00994 MoCF_biosynth: Probable molybdopterin binding domain; InterPro: IPR001453 Eukaryotic and prokaryotic molybdoenzymes require a molybdopterin cofactor (MoCF) for their activity. The biosynthesis of this cofactor involves a complex multistep enzymatic pathway. One of the eukaryotic proteins involved in this pathway is the Drosophila protein cinnamon [] which is highly similar to gephyrin, a rat microtubule-associated protein which was thought to anchor the glycine receptor to subsynaptic microtubules. Cinnamon and gephyrin are evolutionary related, in their N-terminal half, to the Escherichia coli MoCF biosynthesis proteins mog/chlG and moaB/chlA2 and, in their C-terminal half, to E. coli moeA/chlE.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 3TCR_B 1O8O_B 1O8Q_G 1EAV_D 1O8N_C 1UUX_A 1UUY_A 2G2C_A 2G4R_C 3K6A_F .... Probab=35.62 E-value=82 Score=17.47 Aligned_cols=27 Identities=26% Similarity=0.331 Sum_probs=16.5 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) |..+.+.++++.+.+. +|.||.+.|.. T Consensus 41 Dd~~~i~~~l~~~~~~-----~D~VittGG~g 67 (144) T PF00994_consen 41 DDPDAIKEALRRALDR-----ADLVITTGGTG 67 (144) T ss_dssp SSHHHHHHHHHHHHHT-----TSEEEEESSSS T ss_pred CCHHHHHHHHHhhhcc-----CCEEEEcCCcC Confidence 3445566666554444 38888888774 No 173 >cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=35.57 E-value=60 Score=18.31 Aligned_cols=20 Identities=20% Similarity=0.064 Sum_probs=14.8 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.+.+.|+ ++||.|.+.+.. T Consensus 38 ~dA~~lgI-~dGd~V~v~~~~ 57 (141) T cd02776 38 KDAAELGI-KDNDWVEVFNDN 57 (141) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 44677785 799999887653 No 174 >cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=35.51 E-value=57 Score=17.79 Aligned_cols=20 Identities=25% Similarity=0.232 Sum_probs=14.7 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-+.+.|+ +.||.|.+.+.. T Consensus 40 ~dA~~~gi-~~Gd~V~v~s~~ 59 (129) T cd02793 40 ADAAARGI-ADGDIVRVFNDR 59 (129) T ss_pred HHHHHcCC-CCCCEEEEEcCC Confidence 44677785 799999887654 No 175 >PF00741 Gas_vesicle: Gas vesicle protein; InterPro: IPR000638 Gas vesicles are small, hollow, gas filled protein structures found in several cyanobacterial and archaebacterial microorganisms []. They allow the positioning of the bacteria at the favourable depth for growth. Gas vesicles are hollow cylindrical tubes, closed by a hollow, conical cap at each end. Both the conical end caps and central cylinder are made up of 4-5 nm wide ribs that run at right angles to the long axis of the structure. Gas vesicles seem to be constituted of two different protein components, GVPa and GVPc. GVPa, a small protein of about 70 amino acid residues, is the main constituent of gas vesicles and form the essential core of the structure. The sequence of GVPa is extremely well conserved. GvpJ and gvpM, two proteins encoded in the cluster of genes required for gas vesicle synthesis in the archaebacteria Halobacterium salinarium and Halobacterium mediterranei (Haloferax mediterranei), have been found [] to be evolutionary related to GVPa. The exact function of these two proteins is not known, although they could be important for determining the shape determination gas vesicles. The N-terminal domain of Aphanizomenon flos-aquae protein gvpA/J is also related to GVPa.; GO: 0005198 structural molecule activity, 0012506 vesicle membrane Probab=35.31 E-value=24 Score=15.87 Aligned_cols=25 Identities=24% Similarity=0.201 Sum_probs=20.7 Q ss_pred HHHHHHHHhCCCCCCCCeEEEeecc Q psy255 34 AHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 34 ~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .+.++.+.++|.+-.||..+-++|. T Consensus 3 ~d~LdriLdkGvVi~gdi~isva~v 27 (39) T PF00741_consen 3 VDLLDRILDKGVVIDGDIRISVAGV 27 (39) T ss_pred HHHHHHHcCCceEEEEEEEEEEcce Confidence 3467788899999999999988875 No 176 >COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only] Probab=35.08 E-value=20 Score=24.96 Aligned_cols=22 Identities=45% Similarity=0.493 Sum_probs=15.0 Q ss_pred CCCCCeEEEeecccCCCCCCceEe Q psy255 46 LNQGDPVIVVTGWKKGAGFTNTLI 69 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~tn~l~ 69 (70) +++||.++++..+ +.|.|+.++ T Consensus 406 ikpGdvvaVvGqS--GaGKttllR 427 (593) T COG2401 406 IKPGDVVAVVGQS--GAGKTTLLR 427 (593) T ss_pred ecCCCeEEEEecC--CCCcchHHH Confidence 6899999988544 236666543 No 177 >TIGR02365 dha_L_ycgS dihydroxyacetone kinase, phosphoprotein-dependent, L subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the subunit homologous to the E. coli YcgS subunit. Probab=35.04 E-value=49 Score=19.73 Aligned_cols=27 Identities=15% Similarity=0.165 Sum_probs=21.8 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) -..+..+.+.++++|..++||+=++.. T Consensus 100 ~~al~~a~~~i~~~g~a~~GdkTmlD~ 126 (194) T TIGR02365 100 AEILQAGLEGIQSRGKATPGEKTMVDV 126 (194) T ss_pred HHHHHHHHHHHHHHcCCCCCCcchhhh Confidence 356888888889999999999876543 No 178 >smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein. Probab=34.95 E-value=45 Score=14.33 Aligned_cols=21 Identities=10% Similarity=0.159 Sum_probs=16.2 Q ss_pred HHHHHHHHHHHHhCCCCCCCC Q psy255 30 DTRVAHGIKYGRDRKFLNQGD 50 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD 50 (70) ...+..+++.+.+.|++.... T Consensus 22 ~~tv~~~l~~L~~~g~l~~~~ 42 (48) T smart00419 22 RETVSRTLKRLEKEGLISREG 42 (48) T ss_pred HHHHHHHHHHHHHCCCEEEeC Confidence 356788899999999987443 No 179 >PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A. Probab=34.84 E-value=52 Score=17.21 Aligned_cols=18 Identities=6% Similarity=0.270 Sum_probs=14.6 Q ss_pred HHHHHHHHHHHHHhCCCC Q psy255 29 VDTRVAHGIKYGRDRKFL 46 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~ 46 (70) +++-++.|+++|.+.|++ T Consensus 78 ~~~~v~~al~~L~~eG~I 95 (102) T PF08784_consen 78 SENEVRKALDFLSNEGHI 95 (102) T ss_dssp -HHHHHHHHHHHHHTTSE T ss_pred CHHHHHHHHHHHHhCCeE Confidence 467789999999999975 No 180 >PRK14483 DhaKLM operon coactivator DhaQ; Provisional Probab=34.77 E-value=1.3e+02 Score=19.93 Aligned_cols=30 Identities=10% Similarity=0.130 Sum_probs=22.4 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) .+.+++++..++.+.+.--+++||.|+++- T Consensus 229 ~~a~~l~~~l~~~ll~~~~~~~gd~v~vlV 258 (329) T PRK14483 229 SSSEILAIELVNKLKSKYRWQKGDNFILLI 258 (329) T ss_pred CCHHHHHHHHHHHHHhhcCcCCCCeEEEEE Confidence 456778888888877765667999888654 No 181 >TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). Probab=34.63 E-value=32 Score=19.79 Aligned_cols=16 Identities=25% Similarity=0.231 Sum_probs=13.4 Q ss_pred CCCCCeEEEeecccCC Q psy255 46 LNQGDPVIVVTGWKKG 61 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~ 61 (70) +++||+|-++.|...+ T Consensus 120 ~~~G~~V~I~~Gpf~G 135 (172) T TIGR00922 120 FEVGEQVRVNDGPFAN 135 (172) T ss_pred CCCCCEEEEeecCCCC Confidence 6799999999997544 No 182 >TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components. Probab=34.61 E-value=81 Score=17.10 Aligned_cols=39 Identities=10% Similarity=-0.047 Sum_probs=23.2 Q ss_pred eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 18 IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 18 v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) +..+......+.++..+...+.+.+. .+||-|++.+... T Consensus 30 i~~i~~~~~~~~~~~~~~l~~~i~~~---~~~~~vivltDl~ 68 (116) T TIGR00824 30 VGAVPFVPGENAETLQEKYNAALADL---DTEEEVLFLVDIF 68 (116) T ss_pred eEEEEcCCCcCHHHHHHHHHHHHHhc---CCCCCEEEEEeCC Confidence 44444444556777666666656553 5677777776553 No 183 >KOG3580|consensus Probab=34.42 E-value=29 Score=25.20 Aligned_cols=26 Identities=23% Similarity=0.351 Sum_probs=19.9 Q ss_pred HHHHHHHhCCCCCCCCeEEEeecccC Q psy255 35 HGIKYGRDRKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 35 ~a~~~~~~~g~~~~GD~vv~~~g~~~ 60 (70) ..+.-.-..|.++.||+||++-|.+. T Consensus 46 DVlpGGPAeG~LQenDrvvMVNGvsM 71 (1027) T KOG3580|consen 46 DVLPGGPAEGLLQENDRVVMVNGVSM 71 (1027) T ss_pred eccCCCCcccccccCCeEEEEcCcch Confidence 34444556899999999999999753 No 184 >TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M. Probab=34.30 E-value=63 Score=21.57 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=15.3 Q ss_pred HHHHHHHhCCCCCCCCeEE-Eeecc Q psy255 35 HGIKYGRDRKFLNQGDPVI-VVTGW 58 (70) Q Consensus 35 ~a~~~~~~~g~~~~GD~vv-~~~g~ 58 (70) .++..+.+.|.+++|++|| +++|. T Consensus 354 Aal~k~~~~g~i~~~~~Vv~vlTG~ 378 (398) T TIGR03844 354 AALVKAVESGFIGPDDDILLNITGG 378 (398) T ss_pred HHHHHHHHhCCCCCCCeEEEEECCc Confidence 3445566777787888755 55564 No 185 >cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho Probab=34.18 E-value=24 Score=17.84 Aligned_cols=16 Identities=25% Similarity=0.364 Sum_probs=12.5 Q ss_pred HhCCCCCCCCeEEEee Q psy255 41 RDRKFLNQGDPVIVVT 56 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~ 56 (70) .+.|.++.||.+.+.- T Consensus 22 v~~G~v~~Gd~v~~~P 37 (81) T cd03695 22 IASGSIRVGDEVVVLP 37 (81) T ss_pred EccceEECCCEEEEcC Confidence 3578899999987764 No 186 >TIGR01916 F420_cofE F420-0:gamma-glutamyl ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates. Probab=33.98 E-value=49 Score=20.86 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=12.1 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +++||.+++.+... T Consensus 28 l~dgDIlvVaeKiV 41 (243) T TIGR01916 28 LEDGDVLVVASTVV 41 (243) T ss_pred CCCCCEEEEeehhh Confidence 89999999988654 No 187 >smart00354 HTH_LACI helix_turn _helix lactose operon repressor. Probab=33.95 E-value=63 Score=15.74 Aligned_cols=42 Identities=5% Similarity=0.037 Sum_probs=25.9 Q ss_pred hhHHhhhcccc--eeeecCCCCCCHHHHHHHHHHHHHhCCCCCC Q psy255 7 EEIPKQVLIGK--IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 7 ~~~~r~l~l~~--v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~ 48 (70) .++++++.++. |.-...+...-.++..+...+.+++.|+..+ T Consensus 4 ~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~ 47 (70) T smart00354 4 KDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPN 47 (70) T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCC Confidence 35677777776 4444333222245667777888888888533 No 188 >KOG4146|consensus Probab=33.93 E-value=41 Score=18.20 Aligned_cols=18 Identities=17% Similarity=0.451 Sum_probs=13.0 Q ss_pred HhCCCCCCCCeEEEeecc Q psy255 41 RDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g~ 58 (70) ++.--++.||.|++++-. T Consensus 81 kedy~ledgD~ivfiSTl 98 (101) T KOG4146|consen 81 KEDYPLEDGDHIVFISTL 98 (101) T ss_pred ccccCcccCCEEEEEEec Confidence 445567888998888754 No 189 >smart00652 eIF1a eukaryotic translation initiation factor 1A. Probab=33.68 E-value=26 Score=18.22 Aligned_cols=17 Identities=29% Similarity=0.475 Sum_probs=13.0 Q ss_pred HHHhCCCCCCCCeEEEe Q psy255 39 YGRDRKFLNQGDPVIVV 55 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~~ 55 (70) ..++.=+++.||.|++- T Consensus 37 K~Rk~iwI~~GD~VlVe 53 (83) T smart00652 37 KMRKKVWIRRGDIVLVD 53 (83) T ss_pred hhcccEEEcCCCEEEEE Confidence 34456789999999984 No 190 >COG0039 Mdh Malate/lactate dehydrogenases [Energy production and conversion] Probab=33.59 E-value=47 Score=21.66 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=16.2 Q ss_pred CCCCCCCeEEEeecccCCCCC Q psy255 44 KFLNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~~~g~ 64 (70) .-++.=|.|++++|.|.++|. T Consensus 65 ~~~~~aDiVvitAG~prKpGm 85 (313) T COG0039 65 EDLKGADIVVITAGVPRKPGM 85 (313) T ss_pred hhhcCCCEEEEeCCCCCCCCC Confidence 345667999999999887773 No 191 >PF12124 Nsp3_PL2pro: Coronavirus polyprotein cleavage domain; InterPro: IPR022733 This domain is found in SARS coronaviruses, and is about 70 amino acids in length. It is found associated with various other coronavirus proteins due to the polyprotein nature of most viral translation. PL2pro is a domain of the non-structural protein nsp3. The domain performs three of the cleavages required to separate the translated polyprotein into its distinct proteins. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity, 0016788 hydrolase activity, acting on ester bonds, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2KAF_A 2KQW_A. Probab=33.33 E-value=15 Score=17.83 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=9.1 Q ss_pred CCCCCCeEEEe Q psy255 45 FLNQGDPVIVV 55 (70) Q Consensus 45 ~~~~GD~vv~~ 55 (70) +++.||++|.- T Consensus 31 flkrgdkivyh 41 (66) T PF12124_consen 31 FLKRGDKIVYH 41 (66) T ss_dssp EEEETTEEEEE T ss_pred HHhcCCEEEEE Confidence 67899999963 No 192 >smart00855 PGAM Phosphoglycerate mutase family. Phosphoglycerate mutase (PGAM) and bisphosphoglycerate mutase (BPGM) are structurally related enzymes that catalyse reactions involving the transfer of phospho groups between the three carbon atoms of phosphoglycerate PUBMED:2847721, PUBMED:2831102, PUBMED:10958932. Both enzymes can catalyse three different reactions with different specificities, the isomerization of 2-phosphoglycerate (2-PGA) to 3-phosphoglycerate (3-PGA) with 2,3-diphosphoglycerate (2,3-DPG) as the primer of the reaction, the synthesis of 2,3-DPG from 1,3-DPG with 3-PGA as a primer and the degradation of 2,3-DPG to 3-PGA (phosphatase activity). In mammals, PGAM is a dimeric protein with two isoforms, the M (muscle) and B (brain) forms. In yeast, PGAM is a tetrameric protein. Probab=33.22 E-value=76 Score=17.53 Aligned_cols=29 Identities=14% Similarity=0.031 Sum_probs=14.1 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ..++..+++.+.+.-.-+.++.+|+++|. T Consensus 122 ~~Rv~~~~~~i~~~~~~~~~~vlvVtHg~ 150 (155) T smart00855 122 VERLVRALEELIATHDKSGQNVLIVSHGG 150 (155) T ss_pred HHHHHHHHHHHHHhcccCCCeEEEEECCc Confidence 34445555554444222344556666664 No 193 >TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons. Probab=33.15 E-value=38 Score=19.02 Aligned_cols=18 Identities=33% Similarity=0.532 Sum_probs=14.4 Q ss_pred CCCCCCCeEEEeecccCC Q psy255 44 KFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~~ 61 (70) ..+++||.|-++.|...+ T Consensus 85 ~~~~~Gd~V~I~~GPf~G 102 (145) T TIGR00405 85 ESIKKGDIVEIISGPFKG 102 (145) T ss_pred cccCCCCEEEEeecCCCC Confidence 348899999999997543 No 194 >PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A. Probab=32.99 E-value=52 Score=16.78 Aligned_cols=19 Identities=26% Similarity=0.448 Sum_probs=11.6 Q ss_pred HHHHHhCCCCCCCCeEEEee Q psy255 37 IKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~~~ 56 (70) .++++++++ +.||.+++-. T Consensus 66 ~~Fv~~n~L-~~GD~~~F~~ 84 (100) T PF02362_consen 66 KKFVRDNGL-KEGDVCVFEL 84 (100) T ss_dssp HHHHHHCT---TT-EEEEEE T ss_pred HHHHHHcCC-CCCCEEEEEE Confidence 356667776 6999998764 No 195 >cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a Probab=32.65 E-value=20 Score=21.12 Aligned_cols=21 Identities=38% Similarity=0.490 Sum_probs=12.9 Q ss_pred CCCCCeEEEeecccCCCCCCce Q psy255 46 LNQGDPVIVVTGWKKGAGFTNT 67 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~tn~ 67 (70) +.+|++++++.|.. +.|.|.. T Consensus 24 i~~~~~~~~ltG~N-g~GKStl 44 (200) T cd03280 24 LGENKRVLVITGPN-AGGKTVT 44 (200) T ss_pred ECCCceEEEEECCC-CCChHHH Confidence 45778878777742 3455543 No 196 >KOG1535|consensus Probab=32.62 E-value=77 Score=19.64 Aligned_cols=29 Identities=28% Similarity=0.353 Sum_probs=21.1 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecccCCCC Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGWKKGAG 63 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~~~~~g 63 (70) +...+.++.+.=.+.+||.| +.|.|.+.| T Consensus 164 ip~li~~is~~~tL~~GDvI--LTGTP~GVg 192 (217) T KOG1535|consen 164 IPDLISRLSQIMTLEPGDVI--LTGTPEGVG 192 (217) T ss_pred HHHHHHHHhhheeecCCCEE--EecCCCccc Confidence 56677788888889999964 467775543 No 197 >CHL00142 rps17 ribosomal protein S17; Validated Probab=32.39 E-value=57 Score=17.08 Aligned_cols=17 Identities=24% Similarity=0.204 Sum_probs=13.9 Q ss_pred CCCCCCCeEEEeecccC Q psy255 44 KFLNQGDPVIVVTGWKK 60 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~ 60 (70) +-++.||.|.+..+-|. T Consensus 49 n~~~~GD~V~I~e~RPl 65 (84) T CHL00142 49 NECNIGDQVLIEETRPL 65 (84) T ss_pred CCCCCCCEEEEEEcCCC Confidence 45899999999988764 No 198 >PRK13293 F420-0--gamma-glutamyl ligase; Reviewed Probab=32.31 E-value=67 Score=20.29 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=13.8 Q ss_pred CCCCCCCCeEEEeeccc Q psy255 43 RKFLNQGDPVIVVTGWK 59 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~ 59 (70) .-.+++||.+++++... T Consensus 27 ~~~l~dGDIlvVaeKiV 43 (245) T PRK13293 27 RYDLEDGDIIVIASTIV 43 (245) T ss_pred cCCCCCCCEEEEeehHH Confidence 35799999999998653 No 199 >COG1725 Predicted transcriptional regulators [Transcription] Probab=32.19 E-value=63 Score=18.23 Aligned_cols=24 Identities=25% Similarity=0.227 Sum_probs=18.8 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEE Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~ 54 (70) ..+..-+....-.|-+++||++=- T Consensus 14 ~QI~~qIk~~I~~g~l~pGdkLPS 37 (125) T COG1725 14 EQIANQIKEQIASGELKPGDKLPS 37 (125) T ss_pred HHHHHHHHHHHHhCCcCCCCCCCc Confidence 556666778888999999998643 No 200 >PF11181 YflT: Heat induced stress protein YflT Probab=32.14 E-value=85 Score=16.60 Aligned_cols=26 Identities=12% Similarity=0.240 Sum_probs=19.0 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) ++-+..+++.|+..|+ .+.|..|++. T Consensus 9 ~~E~~~~I~~L~~~Gy-~~ddI~Vva~ 34 (103) T PF11181_consen 9 EEEALSAIEELKAQGY-SEDDIYVVAK 34 (103) T ss_pred HHHHHHHHHHHHHcCC-CcccEEEEEc Confidence 4446668899999998 4667766664 No 201 >cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher Probab=32.05 E-value=43 Score=17.05 Aligned_cols=15 Identities=33% Similarity=0.514 Sum_probs=12.4 Q ss_pred hCCCCCCCCeEEEee Q psy255 42 DRKFLNQGDPVIVVT 56 (70) Q Consensus 42 ~~g~~~~GD~vv~~~ 56 (70) +.|.++.||.+.+.- T Consensus 23 ~~G~v~~gd~v~~~p 37 (87) T cd03697 23 ERGTIKVGDEVEIVG 37 (87) T ss_pred CCCCCccCCEEEEeC Confidence 579999999998753 No 202 >PRK12338 hypothetical protein; Provisional Probab=31.94 E-value=50 Score=21.56 Aligned_cols=24 Identities=8% Similarity=0.061 Sum_probs=20.1 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCe Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDP 51 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~ 51 (70) +.++.++.+.+.|++.|++-++++ T Consensus 294 ~~~e~l~~i~~~L~~~G~L~~~~~ 317 (319) T PRK12338 294 PDEESLNRIIEELEEEGLLYEEER 317 (319) T ss_pred CCHHHHHHHHHHHHHCCccccCcC Confidence 457889999999999999887764 No 203 >COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport] Probab=31.88 E-value=37 Score=18.65 Aligned_cols=13 Identities=23% Similarity=0.399 Sum_probs=10.3 Q ss_pred CCCCCCeEEEeec Q psy255 45 FLNQGDPVIVVTG 57 (70) Q Consensus 45 ~~~~GD~vv~~~g 57 (70) -+++||++++..+ T Consensus 33 ~ik~GD~IiF~~~ 45 (111) T COG4043 33 QIKPGDKIIFNGD 45 (111) T ss_pred CCCCCCEEEEcCC Confidence 3589999998854 No 204 >cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins. Probab=31.85 E-value=49 Score=16.18 Aligned_cols=15 Identities=47% Similarity=0.691 Sum_probs=12.9 Q ss_pred CCCCCCCeEEEeeccc Q psy255 44 KFLNQGDPVIVVTGWK 59 (70) Q Consensus 44 g~~~~GD~vv~~~g~~ 59 (70) | +++||.|+-+.|.+ T Consensus 24 g-L~~GD~I~~Ing~~ 38 (79) T cd00986 24 K-LKAGDHIIAVDGKP 38 (79) T ss_pred C-CCCCCEEEEECCEE Confidence 6 89999999988875 No 205 >TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C Probab=31.62 E-value=29 Score=18.74 Aligned_cols=16 Identities=38% Similarity=0.584 Sum_probs=12.9 Q ss_pred HHHhCCCCCCCCeEEE Q psy255 39 YGRDRKFLNQGDPVIV 54 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~ 54 (70) .++..=|++.||.|++ T Consensus 51 K~Rk~iwI~~GD~VlV 66 (99) T TIGR00523 51 KLKKRIWIREGDVVIV 66 (99) T ss_pred hhcccEEecCCCEEEE Confidence 3445778999999998 No 206 >PLN02569 threonine synthase Probab=31.62 E-value=73 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.306 Sum_probs=15.6 Q ss_pred HHHHHHhCCCCCCCCeEEEe-ecc Q psy255 36 GIKYGRDRKFLNQGDPVIVV-TGW 58 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~-~g~ 58 (70) +...+.+.|.++++|+||++ +|. T Consensus 414 al~kl~~~g~i~~~~~VV~i~Tg~ 437 (484) T PLN02569 414 ALKKLRASGVIGPTDRTVVVSTAH 437 (484) T ss_pred HHHHHHHcCCCCCCCcEEEEeCCC Confidence 44556678888888877654 444 No 207 >cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2. Probab=31.34 E-value=27 Score=18.57 Aligned_cols=17 Identities=18% Similarity=0.165 Sum_probs=13.5 Q ss_pred HHHHhCCCCCCCCeEEE Q psy255 38 KYGRDRKFLNQGDPVIV 54 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~ 54 (70) ..+.++|.++.||.+|. T Consensus 19 tviV~~GtL~~Gd~iv~ 35 (95) T cd03702 19 TVLVQNGTLKVGDVLVA 35 (95) T ss_pred EEEEEcCeEeCCCEEEE Confidence 34567899999999886 No 208 >PRK04012 translation initiation factor IF-1A; Provisional Probab=31.08 E-value=30 Score=18.72 Aligned_cols=17 Identities=35% Similarity=0.583 Sum_probs=13.1 Q ss_pred HHHhCCCCCCCCeEEEe Q psy255 39 YGRDRKFLNQGDPVIVV 55 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~~ 55 (70) ..+..=|++.||.|++- T Consensus 53 K~Rk~IwI~~GD~VlVe 69 (100) T PRK04012 53 KMKKRMWIREGDVVIVA 69 (100) T ss_pred hhcccEEecCCCEEEEE Confidence 34456789999999985 No 209 >PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B .... Probab=31.04 E-value=35 Score=15.19 Aligned_cols=13 Identities=23% Similarity=0.363 Sum_probs=9.6 Q ss_pred CCCCCeEEEeecc Q psy255 46 LNQGDPVIVVTGW 58 (70) Q Consensus 46 ~~~GD~vv~~~g~ 58 (70) +++||.+.++.-. T Consensus 16 ~~~Gd~i~v~~~~ 28 (48) T PF00018_consen 16 FKKGDIIEVLEKS 28 (48) T ss_dssp B-TTEEEEEEEES T ss_pred EECCCEEEEEEec Confidence 6799999998744 No 210 >TIGR03801 asp_4_decarbox aspartate 4-decarboxylase. This enzyme, aspartate 4-decarboxylase (EC 4.1.1.12), removes the side-chain carboxylate from L-aspartate, converting it to L-alanine plus carbon dioxide. It is a PLP-dependent enzyme, homologous to aspartate aminotransferase (EC 2.6.1.1). Probab=31.00 E-value=98 Score=21.58 Aligned_cols=31 Identities=13% Similarity=0.188 Sum_probs=23.0 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ....+.+..+...++...++++||.|++..- T Consensus 162 ~Gat~al~~~~~~l~~~~ll~pGD~Vlv~~P 192 (521) T TIGR03801 162 EGGTAAMCYIFDSLKANELLKKGDKIALMTP 192 (521) T ss_pred CCHHHHHHHHHHHHhHhhcCCCCCEEEEeCC Confidence 3455666777777777788999999988653 No 211 >cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li Probab=30.98 E-value=24 Score=17.78 Aligned_cols=16 Identities=19% Similarity=0.474 Sum_probs=12.1 Q ss_pred HhCCCCCCCCeEEEee Q psy255 41 RDRKFLNQGDPVIVVT 56 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~ 56 (70) .+.|.++.||.+.+.- T Consensus 21 v~~G~i~~G~~v~i~P 36 (82) T cd04089 21 VESGTIKKGDKLLVMP 36 (82) T ss_pred EeeeEEecCCEEEEeC Confidence 3578889999987653 No 212 >cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=30.96 E-value=79 Score=17.86 Aligned_cols=20 Identities=25% Similarity=0.232 Sum_probs=15.0 Q ss_pred HHHHhCCCCCCCCeEEEeecc Q psy255 38 KYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 38 ~~~~~~g~~~~GD~vv~~~g~ 58 (70) +-|.+.|+ ++||.|.+.+.. T Consensus 45 ~dA~~lGI-~dGD~V~V~s~~ 64 (137) T cd02784 45 RTAEALGL-LQGDVVRIRRGG 64 (137) T ss_pred HHHHHcCC-CCCCEEEEEeCC Confidence 45667786 799999988754 No 213 >PRK09620 hypothetical protein; Provisional Probab=30.93 E-value=1.3e+02 Score=18.45 Aligned_cols=43 Identities=7% Similarity=-0.069 Sum_probs=26.9 Q ss_pred ecCChhHHhhhcccc----eeeecCCCCCCHHHHHHHHHHHHHhCCC Q psy255 3 STRSEEIPKQVLIGK----IEPSPADWLRDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 3 ~t~~~~~~r~l~l~~----v~~~~~~~~~~~~~~~~~a~~~~~~~g~ 45 (70) +.++++....+.-.+ +.-|..+...+.+++++.|.+.++++++ T Consensus 129 L~~~pdIl~~l~~~~~~~~~vGFkaEt~~~~~~l~~~A~~kl~~k~~ 175 (229) T PRK09620 129 FQKAPKVLKQIKQWDPETVLVGFKLESDVNEEELFERAKNRMEEAKA 175 (229) T ss_pred EEECcHHHHHHHhhCCCCEEEEEEeccCCCHHHHHHHHHHHHHHcCC Confidence 345666666665322 3444444444467889999998888763 No 214 >cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende Probab=30.83 E-value=47 Score=17.30 Aligned_cols=15 Identities=33% Similarity=0.408 Sum_probs=12.0 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) -.+++||.|++..+. T Consensus 46 ~~l~~Gd~V~v~G~v 60 (91) T cd04482 46 RLLIPGDEVTVYGSV 60 (91) T ss_pred CCCCCCCEEEEEEEE Confidence 457899999988765 No 215 >PF01996 F420_ligase: F420-0:Gamma-glutamyl ligase; InterPro: IPR002847 This entry contains F420-0:gamma-glutamyl ligase and related proteins. F420-0:gamma-glutamyl ligase catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives [, , , ].; PDB: 2G9I_A 2PHN_A. Probab=30.75 E-value=21 Score=21.98 Aligned_cols=29 Identities=24% Similarity=0.248 Sum_probs=12.5 Q ss_pred HHHHHHHHHHHHhCC-CCCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRK-FLNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g-~~~~GD~vv~~~g~ 58 (70) |++.+...+++++.| -+++||.+++.+.. T Consensus 11 DDl~~iI~~~~~~~~~~l~dgDIlvvaeki 40 (228) T PF01996_consen 11 DDLAEIIIEYLKKAGLELRDGDILVVAEKI 40 (228) T ss_dssp --HHHHHHCCS--------TT-EEEEEHHH T ss_pred CCHHHHHHHHHhhhcccCCCCCEEEEehHH Confidence 344444444444443 47999999998754 No 216 >TIGR01835 HMG-CoA-S_prok 3-hydroxy-3-methylglutaryl CoA synthase, prokaryotic clade. This clade of hydroxymethylglutaryl-CoA (HMG-CoA) synthases is found in a limited spectrum of mostly gram-positive bacteria which make isopentenyl pyrophosphate (IPP) via the mevalonate pathway. This pathway is found primarily in eukaryotes and archaea, but the bacterial homologs are distinct, having aparrently diverged after being laterally transferred from an early eukaryote. HMG-CoA synthase is the first step in the pathway and joins acetyl-CoA with acetoacetyl-CoA with the release of one molecule of CoA. The Borellia sequence may have resulted from a separate lateral transfer event. Probab=30.65 E-value=99 Score=20.32 Aligned_cols=24 Identities=13% Similarity=0.087 Sum_probs=17.2 Q ss_pred HHHHHHHHHhCC-CCCCCCeEEEee Q psy255 33 VAHGIKYGRDRK-FLNQGDPVIVVT 56 (70) Q Consensus 33 ~~~a~~~~~~~g-~~~~GD~vv~~~ 56 (70) +-.++..+.+.+ .+++||+|.+.+ T Consensus 279 ~~l~L~~~l~~~~~~~~Gd~ill~s 303 (379) T TIGR01835 279 LYLGLASLLENAFEDTTGDKIGLFS 303 (379) T ss_pred HHHHHHHHHHhcccCCCCCEEEEEE Confidence 444555666665 689999999876 No 217 >PF14338 Mrr_N: Mrr N-terminal domain Probab=30.63 E-value=85 Score=16.15 Aligned_cols=23 Identities=9% Similarity=0.231 Sum_probs=19.5 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCe Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDP 51 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~ 51 (70) -+.++..|..+|+..|+++.-++ T Consensus 53 ~~~ri~Wa~~~L~~aGli~~~~r 75 (92) T PF14338_consen 53 FKNRIRWARSYLKKAGLIERPKR 75 (92) T ss_pred HHHhHHHHHHHHHHCCCccCCCC Confidence 47889999999999999987544 No 218 >TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity. Probab=30.63 E-value=77 Score=17.89 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=13.3 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.+++.+.|...++. +++|+. +.+.|. T Consensus 4 s~~~t~~l~~~l~~~---l~~~~~-i~l~G~ 30 (133) T TIGR00150 4 DEKAMDKFGKAFAKP---LDFGTV-VLLKGD 30 (133) T ss_pred CHHHHHHHHHHHHHh---CCCCCE-EEEEcC Confidence 445555555544433 345554 455554 No 219 >PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A .... Probab=30.58 E-value=70 Score=15.14 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=11.7 Q ss_pred HHHHHHHHHhCCCCCCCCeE Q psy255 33 VAHGIKYGRDRKFLNQGDPV 52 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~v 52 (70) +...+......|-+++||++ T Consensus 5 i~~~l~~~I~~g~~~~g~~l 24 (64) T PF00392_consen 5 IYDQLRQAILSGRLPPGDRL 24 (64) T ss_dssp HHHHHHHHHHTTSS-TTSBE T ss_pred HHHHHHHHHHcCCCCCCCEe Confidence 44455556666767777765 No 220 >cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM Probab=30.49 E-value=26 Score=17.66 Aligned_cols=15 Identities=20% Similarity=0.550 Sum_probs=11.7 Q ss_pred hCCCCCCCCeEEEee Q psy255 42 DRKFLNQGDPVIVVT 56 (70) Q Consensus 42 ~~g~~~~GD~vv~~~ 56 (70) +.|.+++||.|.+.- T Consensus 23 ~~G~i~~Gd~v~i~P 37 (83) T cd03698 23 ESGSIQKGDTLLVMP 37 (83) T ss_pred eeeEEeCCCEEEEeC Confidence 578889999987653 No 221 >PLN02654 acetate-CoA ligase Probab=30.29 E-value=1.2e+02 Score=21.30 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=18.3 Q ss_pred HHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 32 RVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 32 ~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .....-..|++.| +++||+|.+.... T Consensus 129 ~v~~lA~~L~~~G-v~~GdrV~i~~pn 154 (666) T PLN02654 129 RVCQLANYLKDVG-VKKGDAVVIYLPM 154 (666) T ss_pred HHHHHHHHHHHcC-CCCCCEEEEEcCC Confidence 3444445677888 5899999987654 No 222 >PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A. Probab=30.25 E-value=45 Score=16.10 Aligned_cols=16 Identities=25% Similarity=0.287 Sum_probs=8.3 Q ss_pred hCCCCCCCCeEEEeec Q psy255 42 DRKFLNQGDPVIVVTG 57 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g 57 (70) .+|-++.||+|-++-- T Consensus 2 R~Gpf~~GdrVQlTD~ 17 (54) T PF14801_consen 2 RRGPFRAGDRVQLTDP 17 (54) T ss_dssp ---S--TT-EEEEEET T ss_pred CcCCCCCCCEEEEccC Confidence 3577899999998864 No 223 >cd01674 Homoaconitase_Swivel Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. This is the swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. Probab=30.22 E-value=60 Score=18.52 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=20.4 Q ss_pred CHHHHHHHHHHHHHhC--CCCCCCCeEEEeecccCCCCC Q psy255 28 DVDTRVAHGIKYGRDR--KFLNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~--g~~~~GD~vv~~~g~~~~~g~ 64 (70) +.+++-+++++.+... ..+++|| |+++|..++.|+ T Consensus 23 ~~e~la~~~~e~~dp~f~~~v~~gd--ilVaG~nFG~GS 59 (129) T cd01674 23 TPEKMAEVCMENYDSEFSTKTKQGD--ILVSGFNFGTGS 59 (129) T ss_pred CHHHHHHhhcccCCchhhhcCCCCC--EEEeCCccCCCC Confidence 5566666666544321 3478898 455676665554 No 224 >COG1935 Uncharacterized conserved protein [Function unknown] Probab=29.96 E-value=41 Score=18.89 Aligned_cols=14 Identities=29% Similarity=0.408 Sum_probs=11.7 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +++||.|.+|+-.. T Consensus 39 l~~GDlVFlT~~~~ 52 (122) T COG1935 39 LHEGDLVFLTSTSL 52 (122) T ss_pred CCCCCEEEEehhHh Confidence 58999999998654 No 225 >PF13497 DUF4121: Domain of unknown function (DUF4121) Probab=29.91 E-value=92 Score=19.90 Aligned_cols=53 Identities=19% Similarity=0.048 Sum_probs=32.5 Q ss_pred ChhHHhhhcccc--eeeecCCCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 6 SEEIPKQVLIGK--IEPSPADWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 6 ~~~~~r~l~l~~--v~~~~~~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) +.++++.|+-+. -+++.- ...+.-+.+-+.++.-++...=+.||+|..+++.. T Consensus 7 ~~EtL~~lN~~yd~~h~ltq-~DVdkaN~~V~~IE~tRs~~~Pq~GD~v~y~tr~G 61 (262) T PF13497_consen 7 SLETLIELNVSYDREHGLTQ-EDVDKANRLVEHIERTRSERTPQVGDRVEYTTRHG 61 (262) T ss_pred cHHHHHHhhcccccccCccH-HHHHHHHHHHHHHHhhccccCCCCCceEEEEcCCC Confidence 445666666444 444321 11122244555666677788899999999999763 No 226 >KOG2107|consensus Probab=29.72 E-value=26 Score=20.93 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=11.9 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) ++++||.|++=+|. T Consensus 119 ~vekGDlivlPaGi 132 (179) T KOG2107|consen 119 FVEKGDLIVLPAGI 132 (179) T ss_pred EEecCCEEEecCcc Confidence 57899999998886 No 227 >PRK07591 threonine synthase; Validated Probab=29.70 E-value=83 Score=21.09 Aligned_cols=22 Identities=18% Similarity=0.206 Sum_probs=14.7 Q ss_pred HHHHHHhCCCCCCCCeEEEe-ec Q psy255 36 GIKYGRDRKFLNQGDPVIVV-TG 57 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~-~g 57 (70) ++..+.+.|.++++++||++ +| T Consensus 366 al~~l~~~g~i~~~~~VV~i~tG 388 (421) T PRK07591 366 VLKKLVEAGKIDPDEETVVYITG 388 (421) T ss_pred HHHHHHHhCCCCCCCeEEEEeCC Confidence 44556677778888886654 44 No 228 >smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations. Probab=29.67 E-value=56 Score=14.24 Aligned_cols=13 Identities=23% Similarity=0.416 Sum_probs=10.7 Q ss_pred CCCCCeEEEeecc Q psy255 46 LNQGDPVIVVTGW 58 (70) Q Consensus 46 ~~~GD~vv~~~g~ 58 (70) +++||.|.++... T Consensus 21 ~~~Gd~v~v~~~~ 33 (58) T smart00326 21 FKKGDIITVLEKS 33 (58) T ss_pred CCCCCEEEEEEcC Confidence 6899999998764 No 229 >PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B. Probab=29.63 E-value=67 Score=16.06 Aligned_cols=22 Identities=14% Similarity=0.129 Sum_probs=17.3 Q ss_pred CCHHHHHHHHHHHHHhCCCCCC Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~ 48 (70) .-.+..++.|+..++++|+++. T Consensus 34 Gv~e~avR~alsRl~~~G~L~~ 55 (70) T PF07848_consen 34 GVSESAVRTALSRLVRRGWLES 55 (70) T ss_dssp T--HHHHHHHHHHHHHTTSEEE T ss_pred CCChHHHHHHHHHHHHcCceee Confidence 3457889999999999999864 No 230 >PLN02856 fumarylacetoacetase Probab=29.55 E-value=48 Score=22.58 Aligned_cols=16 Identities=44% Similarity=0.696 Sum_probs=13.3 Q ss_pred hCCCCCCCCeEEEeec Q psy255 42 DRKFLNQGDPVIVVTG 57 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g 57 (70) ++.|+++||.|++..- T Consensus 387 ~r~fL~dGD~V~l~g~ 402 (424) T PLN02856 387 RRKFLEDGDEVVLSGW 402 (424) T ss_pred ccccCCCCCEEEEEEE Confidence 4789999999998753 No 231 >PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional Probab=29.46 E-value=1.1e+02 Score=22.75 Aligned_cols=24 Identities=25% Similarity=0.367 Sum_probs=19.8 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) .+.-+.|++.+..+| ||.||+=.+ T Consensus 308 ~~~A~~aldlAlgRG----GDQvvvk~~ 331 (838) T PRK14538 308 ATYSQNAIELAQKRG----GDQAVVNIE 331 (838) T ss_pred HHHHHHHHHHHhccC----CCEEEEEcC Confidence 456778888888888 999999875 No 232 >cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins. Probab=29.32 E-value=64 Score=15.61 Aligned_cols=17 Identities=35% Similarity=0.855 Sum_probs=13.2 Q ss_pred hCCCCCCCCeEEEeeccc Q psy255 42 DRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g~~ 59 (70) +.| +++||.|+-+-|.+ T Consensus 27 ~aG-l~~GD~I~~Ing~~ 43 (80) T cd00990 27 KAG-LVAGDELVAVNGWR 43 (80) T ss_pred HhC-CCCCCEEEEECCEE Confidence 456 58999999888764 No 233 >cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function. Probab=29.31 E-value=53 Score=16.40 Aligned_cols=16 Identities=25% Similarity=0.138 Sum_probs=12.4 Q ss_pred CCCCCCCeEEEeeccc Q psy255 44 KFLNQGDPVIVVTGWK 59 (70) Q Consensus 44 g~~~~GD~vv~~~g~~ 59 (70) -.+++||.|++..+.. T Consensus 42 ~~l~~Gd~V~v~G~v~ 57 (73) T cd04487 42 PEVEVGDIVRVTGEVE 57 (73) T ss_pred CCCCCCCEEEEEEEEe Confidence 3578999999887653 No 234 >PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A .... Probab=29.28 E-value=63 Score=14.25 Aligned_cols=18 Identities=11% Similarity=0.198 Sum_probs=13.4 Q ss_pred HHHHHHHHHHHHhCCCCC Q psy255 30 DTRVAHGIKYGRDRKFLN 47 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~ 47 (70) ...+...++.+.+.|+++ T Consensus 31 ~~tv~~~l~~L~~~g~I~ 48 (48) T PF13412_consen 31 RSTVNRYLKKLEEKGLIE 48 (48) T ss_dssp HHHHHHHHHHHHHTTSEE T ss_pred HHHHHHHHHHHHHCcCcC Confidence 455777788888888763 No 235 >PF14394 DUF4423: Domain of unknown function (DUF4423) Probab=29.23 E-value=51 Score=19.37 Aligned_cols=29 Identities=3% Similarity=0.101 Sum_probs=21.4 Q ss_pred HHHHHHHHHHHHhCCCCCCCCe--EEEeecc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDP--VIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~--vv~~~g~ 58 (70) .+-++.++++|.+.|++++... .+.+... T Consensus 55 ~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~ 85 (171) T PF14394_consen 55 AEEVRDSLEFLEKLGLIKKDGDGKYVQTDKS 85 (171) T ss_pred HHHHHHHHHHHHHCCCeEECCCCcEEEecce Confidence 3457889999999999987654 5555543 No 236 >PF14080 DUF4261: Domain of unknown function (DUF4261) Probab=29.14 E-value=85 Score=15.72 Aligned_cols=27 Identities=15% Similarity=0.073 Sum_probs=19.2 Q ss_pred HHHHHHHHHHHHhCCC-CCCCCeE-EEee Q psy255 30 DTRVAHGIKYGRDRKF-LNQGDPV-IVVT 56 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~-~~~GD~v-v~~~ 56 (70) -+.+.....++.+.|- +++||.+ -+.. T Consensus 26 ~~~l~~ia~Yil~~~~~l~dGdTi~G~~~ 54 (77) T PF14080_consen 26 YNFLYNIAYYILENGVVLKDGDTISGFSE 54 (77) T ss_pred HHHHHHHHHHHHcCCCccCCCCeeccCCC Confidence 3556666677888875 9999998 4443 No 237 >COG0011 Uncharacterized conserved protein [Function unknown] Probab=29.11 E-value=1e+02 Score=16.71 Aligned_cols=19 Identities=21% Similarity=0.260 Sum_probs=13.8 Q ss_pred CCHHHHHHHHHHHHHhCCC Q psy255 27 RDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~ 45 (70) .+...-+..+++.+++.|+ T Consensus 17 ~svs~yVa~~i~~lk~~gl 35 (100) T COG0011 17 PSVSKYVAEAIEILKESGL 35 (100) T ss_pred CCHHHHHHHHHHHHHHcCC Confidence 3456778888888888775 No 238 >cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin. Probab=29.06 E-value=1.1e+02 Score=16.84 Aligned_cols=27 Identities=15% Similarity=0.165 Sum_probs=15.5 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) |..+.++++++.+.+ .-|.|+.+.|.. T Consensus 43 Dd~~~i~~~i~~~~~-----~~DlvittGG~g 69 (133) T cd00758 43 DDADSIRAALIEASR-----EADLVLTTGGTG 69 (133) T ss_pred CCHHHHHHHHHHHHh-----cCCEEEECCCCC Confidence 444556666665544 257777666653 No 239 >KOG1546|consensus Probab=28.80 E-value=1.4e+02 Score=20.01 Aligned_cols=25 Identities=8% Similarity=0.329 Sum_probs=20.7 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEe Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVV 55 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~ 55 (70) +...+..|+.+|.+.. ++||.+++= T Consensus 120 T~~Nir~Al~wLV~~a--q~gD~LvfH 144 (362) T KOG1546|consen 120 TGKNIRRALRWLVESA--QPGDSLVFH 144 (362) T ss_pred cHHHHHHHHHHHHhcC--CCCCEEEEE Confidence 4577999999999986 699988863 No 240 >TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetase. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown. Probab=28.75 E-value=1.2e+02 Score=20.37 Aligned_cols=22 Identities=27% Similarity=0.501 Sum_probs=12.1 Q ss_pred HHHHHHHHhCCCCCCCCeEEEeecc Q psy255 34 AHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 34 ~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ++|++.+++ .+++||.|+ +.|- T Consensus 425 ~~a~~~~~~--~~~~~d~VL-v~G~ 446 (464) T TIGR01085 425 RQAIRYAIS--NAKAGDVVL-IAGK 446 (464) T ss_pred HHHHHHHHH--hcCCCCEEE-EEEc Confidence 334455544 357898654 4443 No 241 >PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A. Probab=28.66 E-value=71 Score=15.25 Aligned_cols=20 Identities=10% Similarity=0.217 Sum_probs=16.3 Q ss_pred HHHHHHHHHHHHHhCCCCCC Q psy255 29 VDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~ 48 (70) +...+..+++.+.+.|+++. T Consensus 35 ~~~~v~~~L~~L~~~GlV~~ 54 (68) T PF01978_consen 35 SRSTVYRALKSLEEKGLVER 54 (68) T ss_dssp SHHHHHHHHHHHHHTTSEEE T ss_pred CHHHHHHHHHHHHHCCCEEE Confidence 35668889999999999864 No 242 >COG1368 MdoB Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane] Probab=28.57 E-value=1.6e+02 Score=21.04 Aligned_cols=33 Identities=21% Similarity=0.195 Sum_probs=24.9 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeecccCC Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWKKG 61 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~~ 61 (70) ...|+.+...++.+|++|+ .-+.|+++-|.+.+ T Consensus 461 ~y~D~al~~F~~~lkk~~~--~~~sviv~~GDH~~ 493 (650) T COG1368 461 HYADEALGQFIDKLKKSGL--YKNSVIVLYGDHYG 493 (650) T ss_pred hhHHHHHHHHHHHHHhcCC--CCCcEEEEECCCCC Confidence 3467888899999999995 45667777777654 No 243 >PRK05863 sulfur carrier protein ThiS; Provisional Probab=28.51 E-value=58 Score=15.74 Aligned_cols=13 Identities=38% Similarity=0.435 Sum_probs=10.6 Q ss_pred CCCCCeEEEeecc Q psy255 46 LNQGDPVIVVTGW 58 (70) Q Consensus 46 ~~~GD~vv~~~g~ 58 (70) +++||+|-+++-. T Consensus 50 L~~gD~ieIv~~V 62 (65) T PRK05863 50 LRDGARLEVVTAV 62 (65) T ss_pred cCCCCEEEEEeec Confidence 7899999987643 No 244 >PF02073 Peptidase_M29: Thermophilic metalloprotease (M29); InterPro: IPR000787 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M29 (aminopeptidase T family, clan M-). The protein fold of the peptidase domain and the active site residues are not known for any members of the thermophilic metallo-aminopeptidases family.; GO: 0004177 aminopeptidase activity, 0006508 proteolysis; PDB: 2AYI_D 1ZJC_A. Probab=28.39 E-value=1.4e+02 Score=19.99 Aligned_cols=30 Identities=13% Similarity=0.104 Sum_probs=18.5 Q ss_pred HHHHHHHHHHHHHhCC-CCCCCCeEEEeecc Q psy255 29 VDTRVAHGIKYGRDRK-FLNQGDPVIVVTGW 58 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g-~~~~GD~vv~~~g~ 58 (70) .++.++.-.+.+.+.| -+++||.|++.+.. T Consensus 3 ~~~~l~kyA~llV~~glnvq~Gq~v~I~~~~ 33 (398) T PF02073_consen 3 FDERLEKYAELLVKYGLNVQPGQKVLIRAPV 33 (398) T ss_dssp HHHHHHHHHHHHHHTTT---TT-EEEEEEET T ss_pred chHHHHHHHHHHHHhccCCCCCCEEEEEecc Confidence 4555666666767665 58999999998764 No 245 >PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A. Probab=28.34 E-value=17 Score=19.55 Aligned_cols=18 Identities=33% Similarity=0.434 Sum_probs=3.0 Q ss_pred HhCCCCCCCCeEEEeecc Q psy255 41 RDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g~ 58 (70) -+.+.++.||.|++.... T Consensus 6 ~~~~~~~~Gd~V~V~ls~ 23 (94) T PF08980_consen 6 YDLGHLKRGDTVVVRLSH 23 (94) T ss_dssp -------TT-------SS T ss_pred echhccCCCCEEEEEeCC Confidence 467888999999988764 No 246 >smart00098 alkPPc Alkaline phosphatase homologues. Probab=28.32 E-value=1.2e+02 Score=20.56 Aligned_cols=12 Identities=17% Similarity=0.401 Sum_probs=8.4 Q ss_pred CCCeEEEeeccc Q psy255 48 QGDPVIVVTGWK 59 (70) Q Consensus 48 ~GD~vv~~~g~~ 59 (70) .+|.+|+++..+ T Consensus 296 ~~dTLiiVTADH 307 (419) T smart00098 296 EDETLVIVTADH 307 (419) T ss_pred CCCcEEEEEecC Confidence 567777777654 No 247 >PRK10005 dihydroxyacetone kinase subunit DhaL; Provisional Probab=28.24 E-value=75 Score=19.33 Aligned_cols=25 Identities=16% Similarity=0.076 Sum_probs=20.8 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEE Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~ 54 (70) -+.+..+.+-.+++|-.++||+=++ T Consensus 107 ~~al~~~~~~i~~~G~A~~GdkTml 131 (210) T PRK10005 107 YQMFRDGADGVISRGKAEPGDKTMC 131 (210) T ss_pred HHHHHHHHHHHHHHcCCCCCCchhH Confidence 4568888888999999999998654 No 248 >TIGR03417 chol_sulfatase choline-sulfatase. Probab=27.98 E-value=1.7e+02 Score=20.04 Aligned_cols=30 Identities=10% Similarity=0.192 Sum_probs=22.4 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) ..|..+-..++.+++.|+. .+.+|+..+.. T Consensus 261 ~~D~~iG~il~~L~~~g~~--dnTivvf~sDH 290 (500) T TIGR03417 261 YLDDKIGELLQTLEETRQA--DDTIVLFTSDH 290 (500) T ss_pred HHHHHHHHHHHHHHhcCCc--CCcEEEEECCC Confidence 3567788889999999984 46777766654 No 249 >PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A. Probab=27.83 E-value=44 Score=17.98 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=8.8 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) --+++||.|.+++-. T Consensus 79 y~l~~~D~I~FiSTL 93 (96) T PF09138_consen 79 YVLKDGDNITFISTL 93 (96) T ss_dssp SB--TTEEEEEEETT T ss_pred eEcCCCCEEEEEccC Confidence 356778888777644 No 250 >PF02769 AIRS_C: AIR synthase related protein, C-terminal domain; InterPro: IPR010918 This entry includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; PDB: 2Z1F_A 2Z1E_A 2YXZ_D 2V9Y_A 2HS0_A 2HRU_A 2HS3_A 3D54_A 1VK3_A 2HS4_A .... Probab=27.78 E-value=39 Score=18.63 Aligned_cols=12 Identities=33% Similarity=0.520 Sum_probs=9.6 Q ss_pred CCCCeEEEeecc Q psy255 47 NQGDPVIVVTGW 58 (70) Q Consensus 47 ~~GD~vv~~~g~ 58 (70) ++||.|+++... T Consensus 1 k~GD~i~~~g~~ 12 (153) T PF02769_consen 1 KPGDLIIVTGSL 12 (153) T ss_dssp STTEEEEEECSS T ss_pred CCCCEEEEECCC Confidence 689999988754 No 251 >PRK14479 dihydroxyacetone kinase; Provisional Probab=27.75 E-value=1.4e+02 Score=21.15 Aligned_cols=31 Identities=16% Similarity=0.078 Sum_probs=23.4 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ...++++++.++.+.+.--+++||+|+++-. T Consensus 228 ~~a~~~~~~~~~~l~~~~~~~~~d~v~~lvN 258 (568) T PRK14479 228 PTADELADRLVDRILADLPLGAGERVAVLVN 258 (568) T ss_pred CCHHHHHHHHHHHHHhhcCCCCCCeEEEEec Confidence 4567788888888777666789988887543 No 252 >PF06838 Met_gamma_lyase: Methionine gamma-lyase ; InterPro: IPR009651 This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria [].; PDB: 3JZL_A 3I16_C 3GWP_A 3FD0_B 3HT4_F. Probab=27.71 E-value=22 Score=23.98 Aligned_cols=18 Identities=28% Similarity=0.377 Sum_probs=11.8 Q ss_pred CCCCCCCCeEEEeecccC Q psy255 43 RKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~~ 60 (70) .|++++||.++.++|.|. T Consensus 90 fg~LrpGD~ll~~tG~PY 107 (403) T PF06838_consen 90 FGVLRPGDELLSITGKPY 107 (403) T ss_dssp HHH--TT-EEEESSSS-- T ss_pred HhcCCCCCeEEEcCCCch Confidence 578899999999999884 No 253 >PRK06732 phosphopantothenate--cysteine ligase; Validated Probab=27.54 E-value=1.5e+02 Score=18.06 Aligned_cols=43 Identities=2% Similarity=-0.231 Sum_probs=26.6 Q ss_pred ecCChhHHhhhcccc----eeeecCCCCCCHHHHHHHHHHHHHhCCC Q psy255 3 STRSEEIPKQVLIGK----IEPSPADWLRDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 3 ~t~~~~~~r~l~l~~----v~~~~~~~~~~~~~~~~~a~~~~~~~g~ 45 (70) +.+.+++...+.-.+ +.-|..+...+.+++++.|.+.++++|+ T Consensus 135 l~~~p~il~~~~~~~~~~~~vgF~~e~~~~~~~l~~~a~~kl~~~~~ 181 (229) T PRK06732 135 LKKTPKVISYVKKWNPNITLVGFKLLVNVSKEELIKVARASLIKNQA 181 (229) T ss_pred EEEChHHHHHHHhhCCCcEEEEEEeccCCCHHHHHHHHHHHHHHcCC Confidence 456667766665322 2334333333567899999998888774 No 254 >KOG1176|consensus Probab=27.32 E-value=1.3e+02 Score=21.17 Aligned_cols=29 Identities=14% Similarity=0.099 Sum_probs=20.8 Q ss_pred HHHHHHHHHHHHhCCC-CCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRKF-LNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~-~~~GD~vv~~~g~ 58 (70) .++.......+.+.|+ +++||.|.+++.. T Consensus 52 ~~~~~r~A~~L~~~~~~i~~gDvV~i~~pN 81 (537) T KOG1176|consen 52 HDRCRRLASALSELGLGIKKGDVVGILAPN 81 (537) T ss_pred HHHHHHHHHHHHhcCCCCCCCCEEEEEcCC Confidence 3445555566777776 8999999998754 No 255 >cd06259 YdcF-like YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis. Probab=27.27 E-value=1.2e+02 Score=16.71 Aligned_cols=32 Identities=13% Similarity=0.210 Sum_probs=21.9 Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 24 DWLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 24 ~~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +...++.+...++.+.+.+.|+ ...+++++.. T Consensus 74 ~~s~~T~ena~~~~~~~~~~~~---~~i~lVTs~~ 105 (150) T cd06259 74 DRSTNTYENARFSAELLRERGI---RSVLLVTSAY 105 (150) T ss_pred CCCCCHHHHHHHHHHHHHhcCC---CeEEEECCHH Confidence 3456787888888899999988 3344444443 No 256 >cd01579 AcnA_Bact_Swivel Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. This distinct subfamily is found only in bacteria and archea. Its exact characteristics are not known. Probab=27.16 E-value=65 Score=17.96 Aligned_cols=20 Identities=25% Similarity=0.313 Sum_probs=14.2 Q ss_pred CCCCCCeEEEeecccCCCCC Q psy255 45 FLNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~~~g~ 64 (70) .+++||.-|+++|..++.|+ T Consensus 43 ~~~~~~~~iiVaG~nFG~GS 62 (121) T cd01579 43 RAKAAGPGFIVGGENYGQGS 62 (121) T ss_pred hcccCCCeEEEcCCcCCCCc Confidence 67788866777887666554 No 257 >PRK06944 sulfur carrier protein ThiS; Provisional Probab=27.15 E-value=78 Score=14.94 Aligned_cols=14 Identities=29% Similarity=0.254 Sum_probs=10.3 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||+|-++.-. T Consensus 49 ~L~~gD~vei~~~v 62 (65) T PRK06944 49 ALAAGDRLDLVQPV 62 (65) T ss_pred cCCCCCEEEEEeec Confidence 47888888887643 No 258 >cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression. Probab=27.10 E-value=38 Score=17.42 Aligned_cols=16 Identities=19% Similarity=0.189 Sum_probs=12.4 Q ss_pred HhCCCCCCCCeEEEee Q psy255 41 RDRKFLNQGDPVIVVT 56 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~ 56 (70) .+.|.++.||.+.+.- T Consensus 26 v~~G~i~~gd~v~i~P 41 (91) T cd03693 26 VETGVLKPGMVVTFAP 41 (91) T ss_pred EecceeecCCEEEECC Confidence 3578899999987653 No 259 >PRK05638 threonine synthase; Validated Probab=27.08 E-value=99 Score=20.80 Aligned_cols=23 Identities=26% Similarity=0.496 Sum_probs=15.1 Q ss_pred HHHHHHhCCCCCCCCeEEE-eecc Q psy255 36 GIKYGRDRKFLNQGDPVIV-VTGW 58 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~-~~g~ 58 (70) +...+.+.|.+.+|+.||+ ++|. T Consensus 331 a~~~~~~~g~i~~~~~Vv~i~tG~ 354 (442) T PRK05638 331 ALLKLGEEGYIEKGDKVVLVVTGS 354 (442) T ss_pred HHHHHHHcCCCCCCCeEEEEeCCC Confidence 3445667787888888764 4554 No 260 >PRK05659 sulfur carrier protein ThiS; Validated Probab=27.07 E-value=65 Score=15.34 Aligned_cols=16 Identities=31% Similarity=0.414 Sum_probs=11.5 Q ss_pred CCCCCCCCeEEEeecc Q psy255 43 RKFLNQGDPVIVVTGW 58 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~ 58 (70) .-.+++||+|-+++-. T Consensus 48 ~~~l~~gD~vei~~~v 63 (66) T PRK05659 48 STALREGDVVEIVHAL 63 (66) T ss_pred cccCCCCCEEEEEEEe Confidence 3457899999887643 No 261 >PRK10886 DnaA initiator-associating protein DiaA; Provisional Probab=26.98 E-value=44 Score=20.09 Aligned_cols=15 Identities=13% Similarity=0.319 Sum_probs=12.9 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) ...++||.+++++++ T Consensus 105 ~~~~~gDvli~iS~S 119 (196) T PRK10886 105 ALGHAGDVLLAISTR 119 (196) T ss_pred HcCCCCCEEEEEeCC Confidence 457899999999987 No 262 >TIGR02703 carboxysome_A carboxysome peptide A. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to Pfam family pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. Probab=26.96 E-value=54 Score=17.11 Aligned_cols=14 Identities=29% Similarity=0.254 Sum_probs=12.0 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +..||.|.+++|+. T Consensus 44 AG~Ge~Vlv~~Gs~ 57 (81) T TIGR02703 44 CKPGDWVLCVGSSA 57 (81) T ss_pred CCCCCEEEEeCCHH Confidence 56899999999875 No 263 >cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution. Probab=26.89 E-value=38 Score=17.29 Aligned_cols=16 Identities=13% Similarity=0.341 Sum_probs=12.5 Q ss_pred HhCCCCCCCCeEEEee Q psy255 41 RDRKFLNQGDPVIVVT 56 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~ 56 (70) .+.|.+++||.+.+.- T Consensus 22 v~~G~v~~g~~v~~~P 37 (87) T cd03694 22 VSKGVIRLGDTLLLGP 37 (87) T ss_pred EecCEEeCCCEEEECC Confidence 3678899999988753 No 264 >COG1817 Uncharacterized protein conserved in archaea [Function unknown] Probab=26.87 E-value=72 Score=21.19 Aligned_cols=43 Identities=19% Similarity=0.073 Sum_probs=27.0 Q ss_pred eecCChhHHhhhcccc--------eeeecCCCCC-C-HHHHHHHHHHHHHhCC Q psy255 2 SSTRSEEIPKQVLIGK--------IEPSPADWLR-D-VDTRVAHGIKYGRDRK 44 (70) Q Consensus 2 a~t~~~~~~r~l~l~~--------v~~~~~~~~~-~-~~~~~~~a~~~~~~~g 44 (70) .|+||+++.+.|.+.- ..|....... + ..+.....++.+++.| T Consensus 165 ~f~pd~evlkeLgl~~~~~yIVmRpe~~~A~y~~g~~~~~~~~~li~~l~k~g 217 (346) T COG1817 165 GFVPDPEVLKELGLEEGETYIVMRPEPWGAHYDNGDRGISVLPDLIKELKKYG 217 (346) T ss_pred cCCCCHHHHHHcCCCCCCceEEEeeccccceeeccccchhhHHHHHHHHHhCc Confidence 4789999999997644 2332222111 1 2345777888888888 No 265 >cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. Probab=26.84 E-value=67 Score=13.78 Aligned_cols=12 Identities=25% Similarity=0.484 Sum_probs=10.1 Q ss_pred CCCCCeEEEeec Q psy255 46 LNQGDPVIVVTG 57 (70) Q Consensus 46 ~~~GD~vv~~~g 57 (70) +++||.|.++.. T Consensus 18 ~~~Gd~v~v~~~ 29 (54) T cd00174 18 FKKGDIIEVLEK 29 (54) T ss_pred CCCCCEEEEEEc Confidence 678999998876 No 266 >TIGR02704 carboxysome_B carboxysome peptide B. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to Pfam family pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. Probab=26.77 E-value=57 Score=16.99 Aligned_cols=14 Identities=21% Similarity=0.254 Sum_probs=11.9 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +..||.|.+++|+. T Consensus 43 AG~Ge~Vlv~~Gsa 56 (80) T TIGR02704 43 APEGKWVFTASGSA 56 (80) T ss_pred CCCCCEEEEeCCHH Confidence 46899999999974 No 267 >TIGR02828 putative membrane fusion protein. Members of this family show similarity to the members of TIGR00999, the membrane fusion protein (MFP) cluster 2 family, which is linked to RND transport systems. Probab=26.74 E-value=43 Score=19.37 Aligned_cols=12 Identities=8% Similarity=0.069 Sum_probs=8.2 Q ss_pred CCCCCCCCeEEEe Q psy255 43 RKFLNQGDPVIVV 55 (70) Q Consensus 43 ~g~~~~GD~vv~~ 55 (70) .| +++||+||++ T Consensus 176 ~G-L~~GD~Vv~~ 187 (188) T TIGR02828 176 EG-DKPPDAQLLT 187 (188) T ss_pred ec-CCCCCEEEec Confidence 35 4788888764 No 268 >PTZ00237 acetyl-CoA synthetase; Provisional Probab=26.62 E-value=1.4e+02 Score=20.87 Aligned_cols=28 Identities=11% Similarity=0.062 Sum_probs=19.4 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .+.....-..+++.|+ ++||+|.+.... T Consensus 99 ~~~v~~lA~~L~~~Gv-~~GDrV~i~~~n 126 (647) T PTZ00237 99 YEKVCEFSRVLLNLNI-SKNDNVLIYMAN 126 (647) T ss_pred HHHHHHHHHHHHHcCC-CCCCEEEEECCC Confidence 3445555566778885 899999987643 No 269 >PRK06488 sulfur carrier protein ThiS; Validated Probab=26.59 E-value=83 Score=15.02 Aligned_cols=14 Identities=21% Similarity=0.515 Sum_probs=10.0 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||.|-++.-. T Consensus 49 ~L~dgD~Ieiv~~V 62 (65) T PRK06488 49 VLHEGDRIEILSPM 62 (65) T ss_pred ccCCCCEEEEEEec Confidence 46788888877643 No 270 >COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism] Probab=26.53 E-value=69 Score=15.98 Aligned_cols=17 Identities=29% Similarity=0.364 Sum_probs=12.1 Q ss_pred hCCCCCCCCeEEEeecc Q psy255 42 DRKFLNQGDPVIVVTGW 58 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g~ 58 (70) +...++.||+|-+++-. T Consensus 49 ~~~~l~~gD~ievv~~v 65 (68) T COG2104 49 ADTILKEGDRIEVVRVV 65 (68) T ss_pred hhccccCCCEEEEEEee Confidence 34557889999887643 No 271 >PRK06437 hypothetical protein; Provisional Probab=26.47 E-value=64 Score=15.79 Aligned_cols=15 Identities=13% Similarity=0.273 Sum_probs=10.9 Q ss_pred CCCCCCCCeEEEeec Q psy255 43 RKFLNQGDPVIVVTG 57 (70) Q Consensus 43 ~g~~~~GD~vv~~~g 57 (70) .-.+++||+|-++.- T Consensus 49 ~~~L~dgD~Veiv~~ 63 (67) T PRK06437 49 DHNVKKEDDVLILEV 63 (67) T ss_pred ceEcCCCCEEEEEec Confidence 335789999888754 No 272 >PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A. Probab=26.21 E-value=56 Score=15.97 Aligned_cols=16 Identities=6% Similarity=0.198 Sum_probs=10.5 Q ss_pred HHHHHHHHhCCCCCCC Q psy255 34 AHGIKYGRDRKFLNQG 49 (70) Q Consensus 34 ~~a~~~~~~~g~~~~G 49 (70) .+..++++++||+-+- T Consensus 30 ~eV~~YC~~~GWIip~ 45 (57) T PF08727_consen 30 PEVREYCEEQGWIIPA 45 (57) T ss_dssp HHHHHHHHHHT--TT- T ss_pred HHHHHHHHHCCccccC Confidence 4577899999998764 No 273 >COG4738 Predicted transcriptional regulator [Transcription] Probab=26.15 E-value=65 Score=18.13 Aligned_cols=16 Identities=19% Similarity=0.569 Sum_probs=13.7 Q ss_pred HHHHHHHHHhCCCCCC Q psy255 33 VAHGIKYGRDRKFLNQ 48 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~ 48 (70) +.-|++++++.||+.. T Consensus 58 VSiAMr~Lre~gWV~~ 73 (124) T COG4738 58 VSIAMRYLRENGWVDE 73 (124) T ss_pred hHHHHHHHHHccccch Confidence 5678999999999864 No 274 >COG5471 Uncharacterized conserved protein [Function unknown] Probab=26.06 E-value=84 Score=17.25 Aligned_cols=15 Identities=27% Similarity=0.587 Sum_probs=8.6 Q ss_pred CCCCCCCCeEEEeec Q psy255 43 RKFLNQGDPVIVVTG 57 (70) Q Consensus 43 ~g~~~~GD~vv~~~g 57 (70) ++++++|+.|-++.. T Consensus 3 kNfv~~gktveiva~ 17 (107) T COG5471 3 KNFVEPGKTVEIVAP 17 (107) T ss_pred ccccCCCCEEEEecc Confidence 355666666665554 No 275 >PRK13759 arylsulfatase; Provisional Probab=26.03 E-value=1.7e+02 Score=19.84 Aligned_cols=29 Identities=10% Similarity=0.256 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) .|..+-..++.+++.|+.+ +.+|+..+.. T Consensus 277 ~D~~iG~l~~~l~~~g~~d--nTiiv~tsDH 305 (485) T PRK13759 277 IDHQIGRFLQALKEFGLLD--NTIILFVSDH 305 (485) T ss_pred HHHHHHHHHHHHHhcCCcc--CeEEEEECCC Confidence 4567777889999999854 6777766554 No 276 >PRK00358 pyrH uridylate kinase; Provisional Probab=26.01 E-value=1e+02 Score=18.54 Aligned_cols=26 Identities=15% Similarity=0.133 Sum_probs=14.8 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +.+....+.+++ +.+.|..+++++|. T Consensus 23 ~~i~~~~~~i~~--~~~~g~~vvlV~gG 48 (231) T PRK00358 23 EVLDRIAEEIKE--VVELGVEVAIVVGG 48 (231) T ss_pred HHHHHHHHHHHH--HHHCCCeEEEEECC Confidence 445555555553 33466777777773 No 277 >COG4100 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism] Probab=25.94 E-value=53 Score=21.90 Aligned_cols=18 Identities=28% Similarity=0.395 Sum_probs=16.3 Q ss_pred CCCCCCCCeEEEeecccC Q psy255 43 RKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~~ 60 (70) .|++++||-+..+.|.|. T Consensus 101 fg~LRpgDell~i~G~PY 118 (416) T COG4100 101 FGILRPGDELLYITGSPY 118 (416) T ss_pred HhccCCCCeEEEecCCcc Confidence 689999999999999884 No 278 >TIGR02114 coaB_strep phosphopantothenate--cysteine ligase, streptococcal. In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the C-terminal region of TIGR00521, corresponding to phosphopantothenate--cysteine ligase activity. Probab=25.92 E-value=1.6e+02 Score=17.89 Aligned_cols=43 Identities=5% Similarity=-0.235 Sum_probs=27.2 Q ss_pred ecCChhHHhhhcccc----eeeecCCCCCCHHHHHHHHHHHHHhCCC Q psy255 3 STRSEEIPKQVLIGK----IEPSPADWLRDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 3 ~t~~~~~~r~l~l~~----v~~~~~~~~~~~~~~~~~a~~~~~~~g~ 45 (70) +.+.+++...+.-.+ +.-|..+...+.+++++.|.+.++++|+ T Consensus 134 l~~~p~il~~~~~~~~~~~~vgF~~e~~~~~~~l~~~a~~kl~~~~~ 180 (227) T TIGR02114 134 LKKTPKVISLVKEWNPQIHLVGFKLLVNVTQEELVKVARASLIKNQA 180 (227) T ss_pred EEEChHHHHHHHhhCCCcEEEEEEeccCCCHHHHHHHHHHHHHHcCC Confidence 556777777665322 3334333333567889999998888774 No 279 >PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional Probab=25.86 E-value=1.3e+02 Score=16.89 Aligned_cols=25 Identities=12% Similarity=-0.048 Sum_probs=21.8 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCe Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDP 51 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~ 51 (70) .+.+.+++..-+.+.+.|++..||. T Consensus 16 ~d~~~Ll~~l~~~l~~sglF~~~~I 40 (126) T PRK15031 16 ADLPGLFAKVNQALAATGIFPLGGI 40 (126) T ss_pred CCHHHHHHHHHHHHHhCCCCCcccc Confidence 4677889999999999999999984 No 280 >PTZ00471 60S ribosomal protein L27; Provisional Probab=25.72 E-value=48 Score=19.02 Aligned_cols=15 Identities=47% Similarity=0.714 Sum_probs=12.5 Q ss_pred CCCCCCeEEEeeccc Q psy255 45 FLNQGDPVIVVTGWK 59 (70) Q Consensus 45 ~~~~GD~vv~~~g~~ 59 (70) ++++|-.||+++|-- T Consensus 4 ~~kpgkVVivL~GR~ 18 (134) T PTZ00471 4 FLKPGKVVIVTSGRY 18 (134) T ss_pred cccCCEEEEEEcccc Confidence 678999999999864 No 281 >PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A. Probab=25.72 E-value=1.3e+02 Score=16.58 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=18.9 Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 25 WLRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 25 ~~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ...+..+++..|.+.+ ..| .+.||++.+. T Consensus 41 ~g~dLG~Rm~~a~~~~-~~g----~~~vvliGsD 69 (122) T PF09837_consen 41 QGGDLGERMANAFQQA-ARG----YEPVVLIGSD 69 (122) T ss_dssp -SSSHHHHHHHHHHHH-HTT-----SEEEEE-SS T ss_pred CCCCHHHHHHHHHHHH-HcC----CCcEEEEcCC Confidence 4567888899998888 433 3477777655 No 282 >PLN00208 translation initiation factor (eIF); Provisional Probab=25.65 E-value=41 Score=19.52 Aligned_cols=16 Identities=25% Similarity=0.486 Sum_probs=12.5 Q ss_pred HHhCCCCCCCCeEEEe Q psy255 40 GRDRKFLNQGDPVIVV 55 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~ 55 (70) ++.+=|+++||.|++- T Consensus 65 mRKrIWI~~GD~VlVe 80 (145) T PLN00208 65 MRKKVWIAAGDIILVG 80 (145) T ss_pred ceeeEEecCCCEEEEE Confidence 3446789999999985 No 283 >PRK10846 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional Probab=25.59 E-value=1.1e+02 Score=20.25 Aligned_cols=23 Identities=26% Similarity=0.202 Sum_probs=13.8 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .+.|++.+.+ ..++||.|++ +|+ T Consensus 381 ~~~Ai~~a~~--~a~~gD~VLi-~GS 403 (416) T PRK10846 381 VAQAWDAAMA--DAKPEDTVLV-CGS 403 (416) T ss_pred HHHHHHHHHH--hcCCCCEEEE-ECc Confidence 3455555554 4578997666 454 No 284 >PRK15448 ethanolamine catabolic microcompartment shell protein EutN; Provisional Probab=25.56 E-value=60 Score=17.43 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=12.1 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +..||.|.+++|+. T Consensus 49 AG~Ge~Vlv~~Gss 62 (95) T PRK15448 49 AGTGEWVLLVSGSS 62 (95) T ss_pred CCCCCEEEEeCChH Confidence 56899999999875 No 285 >PRK09990 DNA-binding transcriptional regulator GlcC; Provisional Probab=25.56 E-value=1.4e+02 Score=18.04 Aligned_cols=15 Identities=20% Similarity=0.383 Sum_probs=11.5 Q ss_pred HHHHHHHHHHhCCCC Q psy255 32 RVAHGIKYGRDRKFL 46 (70) Q Consensus 32 ~~~~a~~~~~~~g~~ 46 (70) -+++|+..|...|++ T Consensus 47 pVREAL~~L~~eGlV 61 (251) T PRK09990 47 ALREGLTVLRGRGII 61 (251) T ss_pred HHHHHHHHHHHCCCE Confidence 377788888888876 No 286 >cd01614 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, Probab=25.55 E-value=63 Score=16.86 Aligned_cols=14 Identities=36% Similarity=0.408 Sum_probs=11.8 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +..||.|.+++|.. T Consensus 49 AG~Ge~Vlv~~Gs~ 62 (83) T cd01614 49 AGVGEWVLVATGSA 62 (83) T ss_pred CCCCCEEEEeCChH Confidence 46899999999974 No 287 >PF09691 PulS_OutS: Bacterial chaperone lipoprotein (PulS_OutS); InterPro: IPR019114 This family comprises lipoproteins from gamma proteobacterial species: pullulanase secretion protein PulS protein of Klebsiella pneumoniae (P20440 from SWISSPROT), the lipoprotein OutS protein of Erwinia chrysanthemi (Q01567 from SWISSPROT) and the functionally uncharacterised type II secretion protein EtpO (Q7BSV3 from SWISSPROT) from Escherichia coli O157:H7. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. In addition to the PulS/OutS proteins this entry also includes other functionally uncharacterised proteins, such as YacC from Escherischia coli (P0AA95 from SWISSPROT).; PDB: 3SOL_A 3UYM_A 3UTK_A 4A56_A. Probab=25.52 E-value=1.3e+02 Score=16.58 Aligned_cols=19 Identities=11% Similarity=0.275 Sum_probs=13.9 Q ss_pred CHHHHHHHHHHHHHhCCCC Q psy255 28 DVDTRVAHGIKYGRDRKFL 46 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~ 46 (70) +...++..|+.+++++||- T Consensus 47 ~~~~I~~~a~~~A~~~gWd 65 (109) T PF09691_consen 47 DEQEIIRAAVIFAQQRGWD 65 (109) T ss_dssp -HHHHHHHHHHHHHHTT-- T ss_pred CHHHHHHHHHHHHHHcCCC Confidence 4457899999999999984 No 288 >PRK05473 hypothetical protein; Provisional Probab=25.49 E-value=63 Score=17.12 Aligned_cols=32 Identities=13% Similarity=0.209 Sum_probs=22.1 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEE--EeecccC Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVI--VVTGWKK 60 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv--~~~g~~~ 60 (70) +..+.+..+-+.++++|. .|=+.+| +++|.|. T Consensus 19 ~v~eiL~~Vy~AL~EKGY-NPinQiVGYllSGDPa 52 (86) T PRK05473 19 DVREILTTVYDALEEKGY-NPINQIVGYLLSGDPA 52 (86) T ss_pred HHHHHHHHHHHHHHHcCC-ChHHHHHhhhccCCCC Confidence 456778888888999997 4555555 4666654 No 289 >PF03079 ARD: ARD/ARD' family; InterPro: IPR004313 The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7 from SWISSPROT, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ []. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions []. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [, ]. This family also contains other proteins, whose functions are not well characterised.; GO: 0010309 acireductone dioxygenase [iron(II)-requiring] activity, 0055114 oxidation-reduction process; PDB: 1VR3_A 1ZRR_A 2HJI_A. Probab=25.49 E-value=24 Score=20.55 Aligned_cols=13 Identities=31% Similarity=0.549 Sum_probs=6.6 Q ss_pred CCCCCeEEEeecc Q psy255 46 LNQGDPVIVVTGW 58 (70) Q Consensus 46 ~~~GD~vv~~~g~ 58 (70) +++||.+++=+|. T Consensus 119 ~e~GDli~vP~g~ 131 (157) T PF03079_consen 119 CEKGDLIVVPAGT 131 (157) T ss_dssp EETTCEEEE-TT- T ss_pred EcCCCEEecCCCC Confidence 4566666665554 No 290 >PTZ00414 10 kDa heat shock protein; Provisional Probab=25.46 E-value=50 Score=17.91 Aligned_cols=10 Identities=30% Similarity=0.610 Sum_probs=8.4 Q ss_pred CCCCCCeEEE Q psy255 45 FLNQGDPVIV 54 (70) Q Consensus 45 ~~~~GD~vv~ 54 (70) -++.||+|++ T Consensus 62 ~Vk~GD~Vl~ 71 (100) T PTZ00414 62 TVKVGDTVLL 71 (100) T ss_pred eecCCCEEEE Confidence 4899999986 No 291 >PRK06260 threonine synthase; Validated Probab=25.45 E-value=1.2e+02 Score=20.09 Aligned_cols=23 Identities=17% Similarity=0.395 Sum_probs=14.8 Q ss_pred HHHHHHhCCCCCCCCeEE-Eeecc Q psy255 36 GIKYGRDRKFLNQGDPVI-VVTGW 58 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv-~~~g~ 58 (70) +...+.+.|.+.+|+.|| +++|. T Consensus 343 a~~~l~~~g~i~~~~~VV~i~tG~ 366 (397) T PRK06260 343 GLIKLVEEGVIDKDERVVCITTGH 366 (397) T ss_pred HHHHHHHcCCCCCCCeEEEEeCCC Confidence 344566778778888766 45554 No 292 >PRK07445 O-succinylbenzoic acid--CoA ligase; Reviewed Probab=25.45 E-value=1.7e+02 Score=19.43 Aligned_cols=30 Identities=0% Similarity=-0.236 Sum_probs=22.3 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ..+......+.+++.|..+.||+|.+.... T Consensus 25 l~~~~~~~a~~L~~~g~~~~~~~V~i~~~n 54 (452) T PRK07445 25 FYQLAQQLYLQLQQLATPRTPPKILLAESD 54 (452) T ss_pred HHHHHHHHHHHHHHhcCCCCCCeEEEecCC Confidence 345565666778888988889999887654 No 293 >PF14453 ThiS-like: ThiS-like ubiquitin Probab=25.45 E-value=63 Score=15.70 Aligned_cols=14 Identities=29% Similarity=0.487 Sum_probs=9.7 Q ss_pred CCCCCCCCeEEEee Q psy255 43 RKFLNQGDPVIVVT 56 (70) Q Consensus 43 ~g~~~~GD~vv~~~ 56 (70) .-.+++||.|+++. T Consensus 42 d~~L~e~D~v~~Ik 55 (57) T PF14453_consen 42 DIELKEGDEVFLIK 55 (57) T ss_pred ccccCCCCEEEEEe Confidence 34577888888763 No 294 >PRK02268 hypothetical protein; Provisional Probab=25.40 E-value=53 Score=18.94 Aligned_cols=11 Identities=27% Similarity=0.489 Sum_probs=9.3 Q ss_pred CCCCCeEEEee Q psy255 46 LNQGDPVIVVT 56 (70) Q Consensus 46 ~~~GD~vv~~~ 56 (70) +++||.+|+=+ T Consensus 36 mkpGD~ivyYs 46 (141) T PRK02268 36 MKPGDWIIYYS 46 (141) T ss_pred CCCCCEEEEEe Confidence 58999999855 No 295 >PRK08559 nusG transcription antitermination protein NusG; Validated Probab=25.35 E-value=1.4e+02 Score=17.08 Aligned_cols=16 Identities=38% Similarity=0.590 Sum_probs=13.4 Q ss_pred CCCCCeEEEeecccCC Q psy255 46 LNQGDPVIVVTGWKKG 61 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~ 61 (70) +++||.|-++.|...+ T Consensus 95 ~~~G~~V~I~~Gpf~g 110 (153) T PRK08559 95 IKEGDIVELIAGPFKG 110 (153) T ss_pred CCCCCEEEEeccCCCC Confidence 7899999999997543 No 296 >COG0309 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones] Probab=25.35 E-value=50 Score=21.87 Aligned_cols=12 Identities=42% Similarity=0.531 Sum_probs=8.8 Q ss_pred CCCCCeEEEeec Q psy255 46 LNQGDPVIVVTG 57 (70) Q Consensus 46 ~~~GD~vv~~~g 57 (70) +++||.|+++.+ T Consensus 161 ~~~GD~vI~tg~ 172 (339) T COG0309 161 ARPGDAVIVTGT 172 (339) T ss_pred CCCCCEEEEcCC Confidence 678888887654 No 297 >PF13406 SLT_2: Transglycosylase SLT domain; PDB: 1LTM_A 1D0L_A 1QDT_A 1D0K_A 1D0M_A 1QDR_A 1QUT_A 1QUS_A 4ANR_A. Probab=25.27 E-value=1.1e+02 Score=19.37 Aligned_cols=27 Identities=15% Similarity=0.211 Sum_probs=17.9 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEE Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~ 54 (70) .+.++.+..+-++++++|| ++|..+.. T Consensus 183 ~s~~DAiaS~ANyL~~~GW-~~g~~~~~ 209 (262) T PF13406_consen 183 NSPADAIASIANYLKKHGW-QPGEPWGR 209 (262) T ss_dssp T-HHHHHHHHHHHHHHTT---TT--SEE T ss_pred CCHHHHHHHHHHHHHHcCC-CCCCceeE Confidence 3577889999999999999 56655554 No 298 >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=25.25 E-value=1.3e+02 Score=19.04 Aligned_cols=21 Identities=14% Similarity=0.207 Sum_probs=13.2 Q ss_pred HHHHHHhCCCCCCCCeEEEee Q psy255 36 GIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~~ 56 (70) +...+.+.+.+.+|++||+++ T Consensus 284 a~~~~~~~~~~~~~~~vv~i~ 304 (307) T cd06449 284 GMIDLVRNGEFKEGSKVLFIH 304 (307) T ss_pred HHHHHHhcCCCCCCCeEEEEe Confidence 333455566667777887665 No 299 >cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. Probab=25.16 E-value=40 Score=16.91 Aligned_cols=15 Identities=20% Similarity=0.211 Sum_probs=11.6 Q ss_pred hCCCCCCCCeEEEee Q psy255 42 DRKFLNQGDPVIVVT 56 (70) Q Consensus 42 ~~g~~~~GD~vv~~~ 56 (70) +.|.+++||.+.+.- T Consensus 23 ~sG~i~~g~~v~~~p 37 (83) T cd03696 23 LSGSVKVGDKVEILP 37 (83) T ss_pred eecEEeCCCEEEECC Confidence 578889999987653 No 300 >COG4079 Uncharacterized protein conserved in archaea [Function unknown] Probab=25.09 E-value=65 Score=20.63 Aligned_cols=17 Identities=29% Similarity=0.403 Sum_probs=12.2 Q ss_pred hCCCCCCCCeEEEeecc Q psy255 42 DRKFLNQGDPVIVVTGW 58 (70) Q Consensus 42 ~~g~~~~GD~vv~~~g~ 58 (70) ..|-++|||+|++--|. T Consensus 258 ~~g~~~pGd~vvv~dg~ 274 (293) T COG4079 258 GNGEVEPGDRVVVKDGV 274 (293) T ss_pred cCCccCCCCEEEEecCc Confidence 35667888888877665 No 301 >PRK07768 long-chain-fatty-acid--CoA ligase; Validated Probab=25.09 E-value=1.6e+02 Score=19.68 Aligned_cols=28 Identities=21% Similarity=0.133 Sum_probs=20.7 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ..........+.+.|+ ++||+|++.... T Consensus 36 ~~~v~~~a~~L~~~g~-~~gd~V~l~~~~ 63 (545) T PRK07768 36 HERARRIAGGLAAAGV-GPGDAVAVLAGA 63 (545) T ss_pred HHHHHHHHHHHHHhCC-CCCCEEEEECCC Confidence 4556666677788885 899999988654 No 302 >cd04259 AAK_AK-DapDC AAK_AK-DapDC: Amino Acid Kinase Superfamily (AAK), AK-DapDC; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the bifunctional enzyme AK - DAP decarboxylase (DapDC) found in some bacteria. Aspartokinase is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. DapDC, which is the lysA gene product, catalyzes the decarboxylation of DAP to lysine. Probab=25.01 E-value=2e+02 Score=18.49 Aligned_cols=35 Identities=26% Similarity=0.392 Sum_probs=20.6 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCC-eEEEeecccCCCCCCce Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGD-PVIVVTGWKKGAGFTNT 67 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD-~vv~~~g~~~~~g~tn~ 67 (70) .+. +.++.+.+..+++. +.|+ .||+++... |.||. T Consensus 12 ~~~-~~~~~v~~ii~~~~--~~~~~~vVVVSA~~---gvTd~ 47 (295) T cd04259 12 SSR-ARWDTIAKLAQKHL--NTGGQPLIVCSALS---GISNK 47 (295) T ss_pred CCH-HHHHHHHHHHHHHh--hcCCCEEEEEeCCC---CCchH Confidence 344 46777777776542 3454 666676653 56664 No 303 >cd01337 MDH_glyoxysomal_mitochondrial Glyoxysomal and mitochondrial malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are localized to the glycosome and mitochondria. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Probab=24.99 E-value=84 Score=20.30 Aligned_cols=19 Identities=26% Similarity=0.511 Sum_probs=14.4 Q ss_pred CCCCCeEEEeecccCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~ 64 (70) ++.=|.||+++|.+..+|. T Consensus 66 ~~daDivvitaG~~~k~g~ 84 (310) T cd01337 66 LKGADVVVIPAGVPRKPGM 84 (310) T ss_pred cCCCCEEEEeCCCCCCCCC Confidence 5566889999998866654 No 304 >PLN03174 Chalcone-flavanone isomerase-related; Provisional Probab=24.96 E-value=2e+02 Score=18.54 Aligned_cols=30 Identities=10% Similarity=0.018 Sum_probs=22.0 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) +.++.++......++...+++||.+.+..- T Consensus 195 e~~e~IekF~~~F~~~~~l~kGdvI~~~~~ 224 (278) T PLN03174 195 DNKELLQSFTSLFKDEYKIPKGSVIDLSRE 224 (278) T ss_pred chHHHHHHHHHHHhccccCCCCCEEEEEEc Confidence 344567777777777777899999887754 No 305 >TIGR02283 MltB_2 lytic murein transglycosylase. Members of this family are closely related to the MltB family lytic murein transglycosylases described by TIGR02282 and are likewise all proteobacterial, although that family and this one form clearly distinct clades. Several species have one member of each family. Many members of this family (unlike the MltB family) contain an additional C-terminal domain, a putative peptidoglycan binding domain (pfam01471), not included in region described by this model. Many sequences appear to contain N-terminal lipoprotein attachment sites, as does E. coli MltB in TIGR02282. Probab=24.95 E-value=1.7e+02 Score=18.98 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=21.4 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEE Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~ 54 (70) .+.++.+..+-++++++|| ++|..+.+ T Consensus 184 ~~~~Da~~S~AnyL~~~GW-~~g~pw~~ 210 (300) T TIGR02283 184 NSVPDALASTANYLVNGGW-KRGEPWGY 210 (300) T ss_pred CCHHHHHHHHHHHHHHcCC-CCCCceEE Confidence 3567888899999999998 67766655 No 306 >cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr Probab=24.84 E-value=75 Score=16.48 Aligned_cols=33 Identities=9% Similarity=0.196 Sum_probs=20.1 Q ss_pred hhHHhhhcccc--eeeecCCCCCCHHHHHHHHHHH Q psy255 7 EEIPKQVLIGK--IEPSPADWLRDVDTRVAHGIKY 39 (70) Q Consensus 7 ~~~~r~l~l~~--v~~~~~~~~~~~~~~~~~a~~~ 39 (70) +.++|+|.|.. +..+..+...+..+.+.+.+.. T Consensus 17 ~~Lar~Lgls~~~I~~i~~~~p~~l~eQv~~mL~~ 51 (83) T cd08319 17 EQVLLDLGLSQTDIYRCKENHPHNVQSQIVEALVK 51 (83) T ss_pred HHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHH Confidence 34677777777 6666555555665555555543 No 307 >COG2144 Selenophosphate synthetase-related proteins [General function prediction only] Probab=24.76 E-value=52 Score=21.57 Aligned_cols=21 Identities=19% Similarity=0.029 Sum_probs=16.9 Q ss_pred HHHHHhCCCCCCCCeEEEeec Q psy255 37 IKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~~~g 57 (70) .+.+...+-.++||++|++.- T Consensus 151 ~e~Ii~s~~Ak~GD~lI~~~d 171 (324) T COG2144 151 EEPIITSGTAKPGDLLIFVGD 171 (324) T ss_pred cccccccCCCCcCCEEEEEec Confidence 355667888999999999875 No 308 >PRK14533 groES co-chaperonin GroES; Provisional Probab=24.64 E-value=54 Score=17.37 Aligned_cols=12 Identities=33% Similarity=0.321 Sum_probs=9.4 Q ss_pred CCCCCCCeEEEe Q psy255 44 KFLNQGDPVIVV 55 (70) Q Consensus 44 g~~~~GD~vv~~ 55 (70) .-++.||+|++- T Consensus 52 ~~Vk~GD~Vl~~ 63 (91) T PRK14533 52 FDIKVGDKVIFS 63 (91) T ss_pred ccccCCCEEEEc Confidence 348999999873 No 309 >PRK12297 obgE GTPase CgtA; Reviewed Probab=24.64 E-value=98 Score=20.98 Aligned_cols=17 Identities=24% Similarity=0.212 Sum_probs=12.7 Q ss_pred HHHHHhCCCCCCCCeEEE Q psy255 37 IKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~ 54 (70) .+.|++.|. ++||.|.+ T Consensus 399 ~~~l~~~g~-~~gd~v~i 415 (424) T PRK12297 399 DDALREAGA-KDGDTVRI 415 (424) T ss_pred HHHHHHCCC-CCCCEEEE Confidence 345677774 89999987 No 310 >cd03782 MATH_Meprin_Beta Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for f Probab=24.61 E-value=92 Score=18.54 Aligned_cols=20 Identities=25% Similarity=0.380 Sum_probs=15.6 Q ss_pred HHHHHhCCCCCCCCeEEEee Q psy255 37 IKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~~~ 56 (70) .+.++.+.+++.+|.++++. T Consensus 146 h~~L~~r~yikdD~ifi~~~ 165 (167) T cd03782 146 HLRLRSRDFIKGDDVIFLLT 165 (167) T ss_pred HHHHhhcCcccCCeEEEEEe Confidence 45678899998888888763 No 311 >KOG0744|consensus Probab=24.61 E-value=33 Score=23.07 Aligned_cols=20 Identities=25% Similarity=0.310 Sum_probs=13.5 Q ss_pred CCCeEEEeecccCCCCCCceE Q psy255 48 QGDPVIVVTGWKKGAGFTNTL 68 (70) Q Consensus 48 ~GD~vv~~~g~~~~~g~tn~l 68 (70) .-.++++++|.| |.|.|..+ T Consensus 175 t~NRliLlhGPP-GTGKTSLC 194 (423) T KOG0744|consen 175 TWNRLILLHGPP-GTGKTSLC 194 (423) T ss_pred eeeeEEEEeCCC-CCChhHHH Confidence 457889999954 55666543 No 312 >cd05290 LDH_3 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of some bacterial LDHs from firmicutes, gammaproteobacteria, and actinobacteria. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Probab=24.56 E-value=71 Score=20.51 Aligned_cols=20 Identities=20% Similarity=0.295 Sum_probs=14.6 Q ss_pred CCCCCeEEEeecccCCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGFT 65 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~t 65 (70) ++.=|.||+++|.+..+|.| T Consensus 66 ~~~aDivvitaG~~~kpg~t 85 (307) T cd05290 66 CADADIIVITAGPSIDPGNT 85 (307) T ss_pred hCCCCEEEECCCCCCCCCCC Confidence 45568899999987666654 No 313 >TIGR02316 propion_prpE propionate--CoA ligase. This family contains one of three readily separable clades of proteins in the group of acetate and propionate--CoA ligases. Characterized members of this family act on propionate. From propionyl-CoA, there is a cyclic degradation pathway: it is ligated by PrpC to the TCA cycle intermediate oxaloacetate, acted upon further by PrpD and an aconitase, then cleaved by PrpB to pyruvate and the TCA cycle intermediate succinate. Probab=24.44 E-value=1.8e+02 Score=20.14 Aligned_cols=27 Identities=19% Similarity=0.092 Sum_probs=19.6 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +........+++.|+ ++||+|.+.... T Consensus 91 ~~v~~lA~~L~~~Gv-~~Gd~V~i~~~n 117 (628) T TIGR02316 91 REVNVFASALRALGV-GRGDRVLIYMPM 117 (628) T ss_pred HHHHHHHHHHHHcCC-CCCCEEEEEcCC Confidence 445555567788885 799999987654 No 314 >PRK04984 fatty acid metabolism regulator; Provisional Probab=24.38 E-value=1.4e+02 Score=17.96 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=15.3 Q ss_pred HHHHHHHHHHhCCCCC--CCCeEEE Q psy255 32 RVAHGIKYGRDRKFLN--QGDPVIV 54 (70) Q Consensus 32 ~~~~a~~~~~~~g~~~--~GD~vv~ 54 (70) .+++|+..|...|++. +|.-..| T Consensus 47 ~VReAL~~L~~eGlv~~~~g~G~~V 71 (239) T PRK04984 47 TLREVLQRLARDGWLTIQHGKPTKV 71 (239) T ss_pred HHHHHHHHHHHCCCEEEeCCCeeEe Confidence 4788888888888775 4443333 No 315 >PRK00561 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=24.33 E-value=2e+02 Score=18.25 Aligned_cols=31 Identities=16% Similarity=0.187 Sum_probs=21.4 Q ss_pred CHHHHHHHHHHHHHhCCCCCCC-CeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQG-DPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~G-D~vv~~~g~ 58 (70) ...+......+.+++.++...+ |.|+++.|. T Consensus 12 ~s~~~~~~l~~~~~~~~~~~~~~D~vi~iGGD 43 (259) T PRK00561 12 QTEPVLPKLKKVLKKKLAVEDGADYLFVLGGD 43 (259) T ss_pred HHHHHHHHHHHHHhhCCCccCCCCEEEEECCc Confidence 3445566666777778876555 888888776 No 316 >PF00056 Ldh_1_N: lactate/malate dehydrogenase, NAD binding domain Prosite entry for lactate dehydrogenase Prosite entry for malate dehydrogenase; InterPro: IPR001236 L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis []. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate []. The enzyme participates in the citric acid cycle. This entry represents the N-terminal, and is thought to be a Rossmann NAD-binding fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1IB6_B 3HHP_C 1IE3_A 2PWZ_A 1EMD_A 2CMD_A 1EZ4_D 9LDT_B 9LDB_B 2D4A_C .... Probab=24.29 E-value=54 Score=18.39 Aligned_cols=19 Identities=26% Similarity=0.562 Sum_probs=13.8 Q ss_pred CCCCCeEEEeecccCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~ 64 (70) ++.=|.||+++|.+..+|. T Consensus 67 ~~~aDivvitag~~~~~g~ 85 (141) T PF00056_consen 67 LKDADIVVITAGVPRKPGM 85 (141) T ss_dssp GTTESEEEETTSTSSSTTS T ss_pred cccccEEEEeccccccccc Confidence 4566889999998765554 No 317 >cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery. Probab=24.29 E-value=79 Score=16.80 Aligned_cols=16 Identities=25% Similarity=0.522 Sum_probs=13.2 Q ss_pred CCCCCCCCeEEEeecc Q psy255 43 RKFLNQGDPVIVVTGW 58 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~ 58 (70) ....++||.+++..|. T Consensus 28 ~~~~k~Gd~~i~~~~~ 43 (105) T cd06541 28 EQLPKAGDYLIILDGQ 43 (105) T ss_pred ccCCCCCCEEEEecCC Confidence 4678999999998764 No 318 >KOG0024|consensus Probab=24.26 E-value=52 Score=21.89 Aligned_cols=24 Identities=29% Similarity=0.378 Sum_probs=19.5 Q ss_pred HHHHHHhCCCCCCCCeEEEeeccc Q psy255 36 GIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) ..+...+-..++.||+|++-.|.+ T Consensus 73 V~evG~~Vk~LkVGDrVaiEpg~~ 96 (354) T KOG0024|consen 73 VEEVGDEVKHLKVGDRVAIEPGLP 96 (354) T ss_pred hhhhcccccccccCCeEEecCCCc Confidence 345667777899999999988876 No 319 >cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos Probab=24.24 E-value=69 Score=14.96 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=12.9 Q ss_pred CCCCCCCeEEEeeccc Q psy255 44 KFLNQGDPVIVVTGWK 59 (70) Q Consensus 44 g~~~~GD~vv~~~g~~ 59 (70) .-+++||.++-+-|.+ T Consensus 29 ~gl~~GD~I~~Ing~~ 44 (70) T cd00136 29 AGLQAGDVILAVNGTD 44 (70) T ss_pred cCCCCCCEEEEECCEE Confidence 3468999999888775 No 320 >COG1243 ELP3 Histone acetyltransferase [Transcription / Chromatin structure and dynamics] Probab=24.23 E-value=1.3e+02 Score=21.06 Aligned_cols=48 Identities=13% Similarity=0.241 Sum_probs=32.7 Q ss_pred hhHHhhhcccc-eeeecCC---CC--CCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 7 EEIPKQVLIGK-IEPSPAD---WL--RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 7 ~~~~r~l~l~~-v~~~~~~---~~--~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ....|.|..|- ..|+--. |. .--..++++|.+.+++.| -+++.+++|. T Consensus 440 ~aivrelhvyg~~vpig~~~~~~QH~G~G~~L~~~AE~ia~ee~----~~ki~viSgi 493 (515) T COG1243 440 TAIVRELHVYGSEVPIGKREDEWQHRGYGRELLEEAERIAREEG----AKKILVISGI 493 (515) T ss_pred hhhhhhhhccccccccccCcchhhcccHHHHHHHHHHHHHHhhc----cccEEEEecc Confidence 44557777666 5554221 11 124688999999999999 4678999987 No 321 >TIGR03270 methan_mark_4 putative methanogen marker protein 4. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely linked to it. Some members have been suggested to be a methyltransferase, based on the proximity of its gene to genes of the multi-subunit complex, N5-methyl-tetrahydromethanopterin--coenzyme M methyltransferase. That context is not conserved, however. The family shows similarity to various phosphate acyltranferases. Probab=24.22 E-value=1.8e+02 Score=17.84 Aligned_cols=27 Identities=15% Similarity=0.116 Sum_probs=22.7 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) -++++++.++++..|+ +| +|.++++.. T Consensus 74 ~~Ii~nav~~a~~lGi-~P--KVAvLsa~E 100 (202) T TIGR03270 74 VKIIELASEFLRRLGR-EP--KVAVLSGGR 100 (202) T ss_pred HHHHHHHHHHHHHcCC-CC--cEEEEeeee Confidence 4679999999999999 66 888888764 No 322 >TIGR01293 Kv_beta voltage-dependent potassium channel beta subunit, animal. Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs. Probab=24.18 E-value=2e+02 Score=18.26 Aligned_cols=14 Identities=7% Similarity=0.162 Sum_probs=10.5 Q ss_pred HHHHHHHHhCCCCC Q psy255 34 AHGIKYGRDRKFLN 47 (70) Q Consensus 34 ~~a~~~~~~~g~~~ 47 (70) -.+++.+++.|.++ T Consensus 132 ~~aL~~l~~~G~ir 145 (317) T TIGR01293 132 VRAMTYVINQGMAM 145 (317) T ss_pred HHHHHHHHHcCCee Confidence 35778888888764 No 323 >PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X .... Probab=24.06 E-value=1.1e+02 Score=15.17 Aligned_cols=25 Identities=16% Similarity=0.182 Sum_probs=17.3 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEE Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~ 54 (70) +..+...+....-.|-+++|+.|.| T Consensus 57 ~~~i~~~la~~il~~~~~~g~~v~v 81 (81) T PF10431_consen 57 EREIEPPLADAILSGKIKEGDTVRV 81 (81) T ss_dssp HHHHHHHHHHHHHHSCSCTTCEEEE T ss_pred HHHHHHHHHHHHHcCCCCCcCEeeC Confidence 4445556666666788889998865 No 324 >PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown. Probab=24.04 E-value=73 Score=15.77 Aligned_cols=15 Identities=27% Similarity=0.153 Sum_probs=11.4 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) .-+++|.+|++.--. T Consensus 36 ~~L~~G~kV~V~yd~ 50 (61) T PF07076_consen 36 DGLKPGMKVVVFYDE 50 (61) T ss_pred cccCCCCEEEEEEEc Confidence 346899999987654 No 325 >TIGR01756 LDH_protist lactate dehydrogenase. This model represents a family of protist lactate dehydrogenases which have aparrently evolved from a recent protist malate dehydrogenase ancestor. Lactate dehydrogenase converts the hydroxyl at C-2 of lactate to a carbonyl in the product, pyruvate. The preference of this enzyme for NAD or NADP has not been determined. A critical residue in malate dehydrogenase, arginine-91 (T. vaginalis numbering) has been mutated to a leucine, eliminating the positive charge which complemeted the carboxylate in malate which is absent in lactate. Several other more subtle changes are proposed to make the active site smaller to accomadate the less bulky lactate molecule. Probab=23.96 E-value=77 Score=20.48 Aligned_cols=19 Identities=16% Similarity=0.085 Sum_probs=13.2 Q ss_pred CCCCCeEEEeecccCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~ 64 (70) ++.=|.||+++|.+..+|. T Consensus 58 ~~daDiVVitaG~~~k~g~ 76 (313) T TIGR01756 58 FKDIDCAFLVASVPLKPGE 76 (313) T ss_pred hCCCCEEEECCCCCCCcCC Confidence 3455778999998765553 No 326 >TIGR02282 MltB lytic murein transglycosylase B. This family consists of lytic murein transglycosylases (murein hydrolases) in the family of MltB, which is a membrane-bound lipoprotein in Escherichia coli. The N-terminal lipoprotein modification motif is conserved in about half the members of this family. The term Slt35 describes a naturally occurring soluble fragment of MltB. Members of this family never contain the putative peptidoglycan binding domain described by Pfam model pfam01471, which is associated with several classes of bacterial cell wall lytic enzymes. Probab=23.92 E-value=1.6e+02 Score=19.09 Aligned_cols=26 Identities=27% Similarity=0.425 Sum_probs=21.4 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEE Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIV 54 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~ 54 (70) ++.+.+..+-++++++|| ++|..+.+ T Consensus 180 s~~Dai~S~anyl~~~GW-~~g~p~~~ 205 (290) T TIGR02282 180 SPDDAIGSVANYFHAHGW-VRGDPVAV 205 (290) T ss_pred CHHHHHHHHHHHHHHhCC-CCCCCceE Confidence 467888899999999998 67777665 No 327 >PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ]. Probab=23.90 E-value=88 Score=18.08 Aligned_cols=10 Identities=40% Similarity=0.445 Sum_probs=8.6 Q ss_pred CCCCCCeEEE Q psy255 45 FLNQGDPVIV 54 (70) Q Consensus 45 ~~~~GD~vv~ 54 (70) -++.||.+|. T Consensus 75 ~~q~GDI~I~ 84 (145) T PF05382_consen 75 NLQRGDIFIW 84 (145) T ss_pred cccCCCEEEE Confidence 6799999986 No 328 >PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional Probab=23.72 E-value=1.3e+02 Score=20.20 Aligned_cols=22 Identities=18% Similarity=0.249 Sum_probs=13.2 Q ss_pred HHHHHHHHHhCCCCCCCCeEEEee Q psy255 33 VAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 33 ~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) +.+|.+.+++ ..++||.|+++. T Consensus 420 ~~~a~~~a~~--~a~~gD~vlv~G 441 (461) T PRK00421 420 LEDLAELLAE--VLKPGDLVLTMG 441 (461) T ss_pred HHHHHHHHHH--hcCCCCEEEEEC Confidence 3445555544 457999766654 No 329 >PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A. Probab=23.71 E-value=49 Score=18.40 Aligned_cols=14 Identities=29% Similarity=0.320 Sum_probs=8.4 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) -+++||.+++=+.. T Consensus 39 ~mk~GD~vifY~s~ 52 (143) T PF01878_consen 39 RMKPGDKVIFYHSG 52 (143) T ss_dssp C--TT-EEEEEETS T ss_pred cCCCCCEEEEEEcC Confidence 57899999986554 No 330 >PF11899 DUF3419: Protein of unknown function (DUF3419); InterPro: IPR021829 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 398 to 802 amino acids in length. Probab=23.66 E-value=52 Score=21.96 Aligned_cols=13 Identities=23% Similarity=0.399 Sum_probs=10.5 Q ss_pred CCCCCeEEEeecc Q psy255 46 LNQGDPVIVVTGW 58 (70) Q Consensus 46 ~~~GD~vv~~~g~ 58 (70) +.+||.|+.+++. T Consensus 33 i~~~d~vl~ItSa 45 (380) T PF11899_consen 33 IGPDDRVLTITSA 45 (380) T ss_pred CCCCCeEEEEccC Confidence 5799999988774 No 331 >cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart Probab=23.64 E-value=72 Score=16.10 Aligned_cols=14 Identities=36% Similarity=0.520 Sum_probs=11.3 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||.|.+..-. T Consensus 61 ~~~kG~~V~v~G~l 74 (100) T cd04496 61 YLKKGDLVYVEGRL 74 (100) T ss_pred HhCCCCEEEEEEEE Confidence 57899999987654 No 332 >PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm Probab=23.61 E-value=1e+02 Score=14.81 Aligned_cols=20 Identities=35% Similarity=0.433 Sum_probs=15.3 Q ss_pred HHHHHHhCCCCCCCCeEEEee Q psy255 36 GIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~~ 56 (70) .=++|.+.|| ..||.|-+.. T Consensus 29 ~G~WL~~aGF-~~G~~v~V~v 48 (57) T PF08845_consen 29 KGKWLEEAGF-TIGDPVKVRV 48 (57) T ss_pred chhhhHHhCC-CCCCEEEEEE Confidence 3578888997 6899887654 No 333 >TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). Probab=23.57 E-value=51 Score=16.60 Aligned_cols=15 Identities=27% Similarity=0.115 Sum_probs=11.4 Q ss_pred CCCCCCCCeEEEeec Q psy255 43 RKFLNQGDPVIVVTG 57 (70) Q Consensus 43 ~g~~~~GD~vv~~~g 57 (70) +=++.+||+|.+--. T Consensus 42 rI~I~~GD~V~Ve~s 56 (68) T TIGR00008 42 YIRILPGDKVKVELS 56 (68) T ss_pred cEEECCCCEEEEEEC Confidence 557889999987643 No 334 >PRK14137 recX recombination regulator RecX; Provisional Probab=23.57 E-value=90 Score=18.84 Aligned_cols=20 Identities=5% Similarity=0.097 Sum_probs=16.8 Q ss_pred HHHHHHHHHHHHHhCCCCCC Q psy255 29 VDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~ 48 (70) .++.+..+++.+++.|++.+ T Consensus 70 ~~e~Ie~vI~rL~e~gyLDD 89 (195) T PRK14137 70 DEALVTEVLERVQELGYQDD 89 (195) T ss_pred CHHHHHHHHHHHHHcCCCCH Confidence 46789999999999999854 No 335 >cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre Probab=23.50 E-value=86 Score=13.84 Aligned_cols=38 Identities=5% Similarity=0.039 Sum_probs=20.8 Q ss_pred hHHhhhcccc--eeeecCCCCCCHHHHHHHHHHHHHhCCC Q psy255 8 EIPKQVLIGK--IEPSPADWLRDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 8 ~~~r~l~l~~--v~~~~~~~~~~~~~~~~~a~~~~~~~g~ 45 (70) ++++++.+.+ |.-+......-.........+.+++.|+ T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~ 41 (52) T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGY 41 (52) T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCC Confidence 3566666666 4433332222234556666677777776 No 336 >TIGR01759 MalateDH-SF1 malate dehydrogenase. This model represents a family of malate dehydrogenases in bacteria and eukaryotes which utilize either NAD or NADP depending on the species and context. MDH interconverts malate and oxaloacetate and is a part of the citric acid cycle as well as the C4 cycle in certain photosynthetic organisms. Probab=23.46 E-value=86 Score=20.33 Aligned_cols=19 Identities=16% Similarity=0.457 Sum_probs=13.7 Q ss_pred CCCCCeEEEeecccCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~ 64 (70) ++.=|.||+++|.+..+|. T Consensus 77 ~~daDvVVitAG~~~k~g~ 95 (323) T TIGR01759 77 FKDVDAALLVGAFPRKPGM 95 (323) T ss_pred hCCCCEEEEeCCCCCCCCC Confidence 4455889999998765553 No 337 >PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A. Probab=23.42 E-value=1.2e+02 Score=15.27 Aligned_cols=17 Identities=18% Similarity=0.429 Sum_probs=13.9 Q ss_pred HHHHHHHHHHHHHhCCC Q psy255 29 VDTRVAHGIKYGRDRKF 45 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~ 45 (70) -..+++.++++++++|+ T Consensus 40 a~~L~~~~l~~a~~~~~ 56 (78) T PF14542_consen 40 AKKLVEAALDYARENGL 56 (78) T ss_dssp HHHHHHHHHHHHHHTT- T ss_pred HHHHHHHHHHHHHHCCC Confidence 36889999999999885 No 338 >PRK08053 sulfur carrier protein ThiS; Provisional Probab=23.40 E-value=1e+02 Score=14.79 Aligned_cols=14 Identities=14% Similarity=0.434 Sum_probs=10.3 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||.|-+++-. T Consensus 50 ~L~~gD~Ieii~~v 63 (66) T PRK08053 50 IVQDGDQILLFQVI 63 (66) T ss_pred ccCCCCEEEEEEEc Confidence 47788888887643 No 339 >COG3494 Uncharacterized protein conserved in bacteria [Function unknown] Probab=23.33 E-value=2.1e+02 Score=18.53 Aligned_cols=32 Identities=22% Similarity=0.250 Sum_probs=27.5 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) +....++.+++.++..|-+.-|.-+|+..|.. T Consensus 151 ~d~~dI~~g~~aA~~lg~lDVGQ~aV~~~g~v 182 (279) T COG3494 151 EDLRDIELGIEAANALGALDVGQGAVVVGGRV 182 (279) T ss_pred hhHHHHHHHHHHHHHhccccccceeEEeCCeE Confidence 34466999999999999999999999998864 No 340 >KOG1712|consensus Probab=23.24 E-value=85 Score=18.86 Aligned_cols=20 Identities=20% Similarity=0.307 Sum_probs=15.8 Q ss_pred HHhCCCCCCCCeEEEeeccc Q psy255 40 GRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g~~ 59 (70) -.+.|-+++|++|+++-... T Consensus 113 Emq~~Ai~~g~rvvvVDDll 132 (183) T KOG1712|consen 113 EMQKGAIKPGQRVVVVDDLL 132 (183) T ss_pred eeeccccCCCCeEEEEechh Confidence 35678889999999987653 No 341 >PLN00135 malate dehydrogenase Probab=23.10 E-value=90 Score=20.16 Aligned_cols=19 Identities=16% Similarity=0.372 Sum_probs=13.6 Q ss_pred CCCCCeEEEeecccCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~ 64 (70) ++.=|.||+++|.+..+|. T Consensus 56 ~~daDiVVitAG~~~k~g~ 74 (309) T PLN00135 56 CKGVNIAVMVGGFPRKEGM 74 (309) T ss_pred hCCCCEEEEeCCCCCCCCC Confidence 3455789999998766553 No 342 >PLN02860 o-succinylbenzoate-CoA ligase Probab=23.07 E-value=1.9e+02 Score=19.60 Aligned_cols=27 Identities=15% Similarity=-0.095 Sum_probs=19.1 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +........+.+.|+ ++||+|.+.... T Consensus 40 ~~~~~la~~L~~~Gv-~~gd~V~v~~~n 66 (563) T PLN02860 40 DGVLSLAAGLLRLGL-RNGDVVAIAALN 66 (563) T ss_pred HHHHHHHHHHHHhCC-CCCCEEEEEcCC Confidence 444445556777884 899999988754 No 343 >cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases. Probab=23.05 E-value=73 Score=15.31 Aligned_cols=16 Identities=31% Similarity=0.383 Sum_probs=12.8 Q ss_pred CCCCCCeEEEeecccC Q psy255 45 FLNQGDPVIVVTGWKK 60 (70) Q Consensus 45 ~~~~GD~vv~~~g~~~ 60 (70) -+++||.++-+-|.+. T Consensus 43 gl~~GD~I~~ing~~i 58 (82) T cd00992 43 GLRVGDRILEVNGVSV 58 (82) T ss_pred CCCCCCEEEEECCEEc Confidence 3689999998888753 No 344 >PRK13938 phosphoheptose isomerase; Provisional Probab=23.03 E-value=91 Score=18.70 Aligned_cols=15 Identities=13% Similarity=0.213 Sum_probs=13.4 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) ..+++||.+++++.+ T Consensus 109 ~~~~~~DllI~iS~S 123 (196) T PRK13938 109 GSARPGDTLFAISTS 123 (196) T ss_pred hcCCCCCEEEEEcCC Confidence 678999999999876 No 345 >PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A .... Probab=22.94 E-value=61 Score=14.70 Aligned_cols=12 Identities=25% Similarity=0.565 Sum_probs=9.0 Q ss_pred CCCCCeEEEeec Q psy255 46 LNQGDPVIVVTG 57 (70) Q Consensus 46 ~~~GD~vv~~~g 57 (70) +++||.|.++.. T Consensus 15 ~~~Gd~i~v~~~ 26 (49) T PF14604_consen 15 FKKGDVITVLEK 26 (49) T ss_dssp B-TTEEEEEEEE T ss_pred EcCCCEEEEEEe Confidence 679999998854 No 346 >TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function. Probab=22.93 E-value=1.3e+02 Score=18.04 Aligned_cols=15 Identities=7% Similarity=0.051 Sum_probs=9.0 Q ss_pred HHHHHHHHHhCCCCC Q psy255 33 VAHGIKYGRDRKFLN 47 (70) Q Consensus 33 ~~~a~~~~~~~g~~~ 47 (70) +++|+..|...|+++ T Consensus 47 VREAL~~Le~eGlV~ 61 (235) T TIGR02812 47 LREVLQRLARDGWLT 61 (235) T ss_pred HHHHHHHHHHCCCEE Confidence 556666666666653 No 347 >TIGR01004 PulS_OutS lipoprotein, PulS/OutS family. This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae, the OutS protein of Erwinia chrysanthemi and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. Probab=22.88 E-value=1.6e+02 Score=16.78 Aligned_cols=19 Identities=5% Similarity=0.038 Sum_probs=15.9 Q ss_pred CCHHHHHHHHHHHHHhCCC Q psy255 27 RDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~ 45 (70) .+.+.+.+.|+.+++.+|| T Consensus 62 Pd~~~I~raai~~A~~~gW 80 (128) T TIGR01004 62 PDDGSILKTANNVAIGKGW 80 (128) T ss_pred CcHHHHHHHHHHHHHHcCC Confidence 4555688999999999999 No 348 >PRK03837 transcriptional regulator NanR; Provisional Probab=22.82 E-value=1.8e+02 Score=17.36 Aligned_cols=17 Identities=6% Similarity=0.186 Sum_probs=12.2 Q ss_pred HHHHHHHHHHHhCCCCC Q psy255 31 TRVAHGIKYGRDRKFLN 47 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~ 47 (70) ..+++|+..|...|+++ T Consensus 52 t~VREAL~~L~~eGlv~ 68 (241) T PRK03837 52 PAVREALQALKRKGLVQ 68 (241) T ss_pred HHHHHHHHHHHHCCCEE Confidence 44777777788887764 No 349 >PF12212 PAZ_siRNAbind: Piwi/Argonaute/Zwille siRNA-binding domain; InterPro: IPR021103 This entry represents a siRNA binding repeat found in bacterial and archaeal proteins, which is approximately 50 amino acids in length. There is a conserved LKDIL sequence motif and a single completely conserved residue L that may be functionally important []. ; PDB: 1Z26_A 1Z25_A 1U04_A 3DA5_B. Probab=22.79 E-value=23 Score=16.61 Aligned_cols=19 Identities=11% Similarity=0.277 Sum_probs=14.9 Q ss_pred HHHHHHHHHHHHhCCCCCC Q psy255 30 DTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~ 48 (70) ...++..++.+++.|++++ T Consensus 9 ~kaie~iL~~akEN~iLKD 27 (47) T PF12212_consen 9 SKAIEEILKVAKENGILKD 27 (47) T ss_dssp HHHHHHHHHHTTTTEEEEE T ss_pred hHHHHHHHHHHHhhcHHHH Confidence 3567888888999998765 No 350 >PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional Probab=22.71 E-value=1.3e+02 Score=20.36 Aligned_cols=22 Identities=36% Similarity=0.513 Sum_probs=12.5 Q ss_pred HHHHHHHHhCCCCC-CCCeEEEeecc Q psy255 34 AHGIKYGRDRKFLN-QGDPVIVVTGW 58 (70) Q Consensus 34 ~~a~~~~~~~g~~~-~GD~vv~~~g~ 58 (70) +.|++.+++ .++ +||.|++ +|- T Consensus 432 ~~Ai~~a~~--~a~~~gD~VLi-~G~ 454 (481) T PRK14022 432 AEAIKHAMS--ITEGPGDAVII-AGK 454 (481) T ss_pred HHHHHHHHH--hcCCCCCEEEE-Eec Confidence 334444443 456 8997776 553 No 351 >PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM. Probab=22.69 E-value=2.1e+02 Score=17.93 Aligned_cols=36 Identities=8% Similarity=-0.109 Sum_probs=22.3 Q ss_pred HHhhhcccc--eeeecCCCCCCHHHHHHHHHHHHHhCCC Q psy255 9 IPKQVLIGK--IEPSPADWLRDVDTRVAHGIKYGRDRKF 45 (70) Q Consensus 9 ~~r~l~l~~--v~~~~~~~~~~~~~~~~~a~~~~~~~g~ 45 (70) .+|.+.-.| +..+.++...+ -+.+...+..+.+.|+ T Consensus 173 mvrGl~~~WKQpi~~~f~t~m~-~~~l~~iI~~l~~~g~ 210 (236) T PF12017_consen 173 MVRGLFKSWKQPIYFDFDTSMD-ADILKNIIEKLHEIGY 210 (236) T ss_pred HHHHHHhcCCccEEEEecCcCC-HHHHHHHHHHHHHCCC Confidence 457777788 44444443333 3556777777777776 No 352 >PF11580 DUF3239: Protein of unknown function (DUF3239); InterPro: IPR021632 This entry contains possible membrane proteins, however this cannot be confirmed. Currently they have no known function. ; PDB: 3C8I_B. Probab=22.57 E-value=80 Score=17.93 Aligned_cols=22 Identities=18% Similarity=0.305 Sum_probs=15.3 Q ss_pred eeeecCCCCCCHHHHHHHHHHH Q psy255 18 IEPSPADWLRDVDTRVAHGIKY 39 (70) Q Consensus 18 v~~~~~~~~~~~~~~~~~a~~~ 39 (70) +.|..+.|.....+.++.|.+. T Consensus 89 ~sPmPIaW~T~D~~Vi~~A~~a 110 (128) T PF11580_consen 89 FSPMPIAWGTRDAKVIRRAEKA 110 (128) T ss_dssp EEEEEGGGT---HHHHHHHHHH T ss_pred ccceeeeecCCCHHHHHHHHhh Confidence 9999888988877888877654 No 353 >PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional Probab=22.56 E-value=82 Score=21.29 Aligned_cols=28 Identities=11% Similarity=0.198 Sum_probs=17.8 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .++.+++|++.+++. .++||.|++.=+. T Consensus 416 ~~~~l~~Av~~a~~~--a~~gd~VllsPa~ 443 (473) T PRK00141 416 PEEAMEEAVSAAVSL--AEPGDTVLLAPAA 443 (473) T ss_pred cccCHHHHHHHHHHh--CCCCCEEEeChhh Confidence 333467777777764 5799976665443 No 354 >PTZ00329 eukaryotic translation initiation factor 1A; Provisional Probab=22.48 E-value=53 Score=19.30 Aligned_cols=16 Identities=38% Similarity=0.625 Sum_probs=12.5 Q ss_pred HHhCCCCCCCCeEEEe Q psy255 40 GRDRKFLNQGDPVIVV 55 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~ 55 (70) ++.+=|+.+||.|++- T Consensus 65 mRK~IWI~~GD~VlVe 80 (155) T PTZ00329 65 MRKRVWINIGDIILVS 80 (155) T ss_pred ceeeEEecCCCEEEEe Confidence 3446789999999984 No 355 >PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A .... Probab=22.48 E-value=27 Score=16.85 Aligned_cols=15 Identities=33% Similarity=0.379 Sum_probs=12.4 Q ss_pred hCCCCCCCCeEEEee Q psy255 42 DRKFLNQGDPVIVVT 56 (70) Q Consensus 42 ~~g~~~~GD~vv~~~ 56 (70) ..|.+++||.|.+.. T Consensus 9 ~sG~l~~gd~v~~~~ 23 (74) T PF03144_consen 9 YSGTLKKGDKVRVLP 23 (74) T ss_dssp EESEEETTEEEEEES T ss_pred EEeEEcCCCEEEECc Confidence 468899999999865 No 356 >PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A .... Probab=22.42 E-value=2e+02 Score=17.57 Aligned_cols=39 Identities=5% Similarity=-0.162 Sum_probs=21.5 Q ss_pred Hhhhcccc--eeeecCCC-CCCHHHHHHHHHHHHHhCCCCCC Q psy255 10 PKQVLIGK--IEPSPADW-LRDVDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 10 ~r~l~l~~--v~~~~~~~-~~~~~~~~~~a~~~~~~~g~~~~ 48 (70) +++|.+-+ +.-+..+. ......-.-.+++.+++.|+++. T Consensus 92 L~~L~~d~iDl~~lH~~~~~~~~~~~~~~~l~~l~~~G~ir~ 133 (283) T PF00248_consen 92 LERLGTDYIDLLLLHWPDPSEDALEEVWEALEELKKEGKIRH 133 (283) T ss_dssp HHHHTSSSEEEEEESSSSTTSSHHHHHHHHHHHHHHTTSEEE T ss_pred cccccccchhccccccccccccccchhhhhhhhccccccccc Confidence 44555555 33333222 23324445677888999998753 No 357 >PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B .... Probab=22.40 E-value=94 Score=13.87 Aligned_cols=17 Identities=24% Similarity=0.259 Sum_probs=11.2 Q ss_pred HHhCCCCCCCCeEEEeec Q psy255 40 GRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~g 57 (70) +++.| +++||.|.+.-. T Consensus 16 ~~~l~-l~~Gd~v~i~~~ 32 (47) T PF04014_consen 16 REKLG-LKPGDEVEIEVE 32 (47) T ss_dssp HHHTT-SSTTTEEEEEEE T ss_pred HHHcC-CCCCCEEEEEEe Confidence 34444 588999887643 No 358 >PF08240 ADH_N: Alcohol dehydrogenase GroES-like domain; InterPro: IPR013154 This is the catalytic domain of alcohol dehydrogenases (1.1.1.1 from EC). Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; a name derived from the superfamily of proteins with a GroES fold. Proteins with a GroES fold structure have a highly conserved hydrophobic core and a glycyl-aspartate dipeptide which is thought to maintain the fold [, ].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1YKF_D 2NVB_A 3FSR_D 1BXZ_B 3FTN_A 3MEQ_D 3UOG_B 3HZZ_B 4DVJ_A 1P0F_A .... Probab=22.38 E-value=58 Score=16.99 Aligned_cols=12 Identities=33% Similarity=0.587 Sum_probs=8.8 Q ss_pred CCCCCeEEEeec Q psy255 46 LNQGDPVIVVTG 57 (70) Q Consensus 46 ~~~GD~vv~~~g 57 (70) ++.||+|++... T Consensus 53 ~~~Gd~V~~~~~ 64 (109) T PF08240_consen 53 FKVGDRVVVSPN 64 (109) T ss_dssp SGTT-EEEEESE T ss_pred ccccceeeeecc Confidence 799999998543 No 359 >PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A. Probab=22.36 E-value=97 Score=16.68 Aligned_cols=23 Identities=9% Similarity=0.030 Sum_probs=18.4 Q ss_pred HHHHHHHHhCCCCCCCCeEEEee Q psy255 34 AHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 34 ~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) ..|.+.|.+.|.+-.|..++.+- T Consensus 65 ~~A~rAL~~NG~i~~g~~mvGV~ 87 (100) T PF05172_consen 65 LSAQRALQKNGTIFSGSLMVGVK 87 (100) T ss_dssp HHHHHHHTTTTEEETTCEEEEEE T ss_pred HHHHHHHHhCCeEEcCcEEEEEE Confidence 45888999999998888887553 No 360 >smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor. Probab=22.33 E-value=93 Score=13.82 Aligned_cols=18 Identities=11% Similarity=0.119 Sum_probs=15.0 Q ss_pred HHHHHHHHHHHHhCCCCC Q psy255 30 DTRVAHGIKYGRDRKFLN 47 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~ 47 (70) ...+..+++.+.+.|++. T Consensus 34 ~~tv~~~l~~L~~~g~i~ 51 (60) T smart00345 34 RTTVREALSRLEAEGLVQ 51 (60) T ss_pred HHHHHHHHHHHHHCCCEE Confidence 466888999999999875 No 361 >PF00245 Alk_phosphatase: Alkaline phosphatase; InterPro: IPR001952 This entry represents alkaline phosphatases (3.1.3.1 from EC) (ALP), which act as non-specific phosphomonoesterases to hydrolyse phosphate esters, optimally at high pH. The reaction mechanism involves the attack of a serine alkoxide on a phosphorus of the substrate to form a transient covalent enzyme-phosphate complex, followed by the hydrolysis of the serine phosphate. Alkaline phosphatases are found in all kingdoms of life, with the exception of some plants. Alkaline phosphatases are metalloenzymes that exist as a dimer, each monomer binding metal ions. The metal ions they carry can differ, although zinc and magnesium are the most common. For example, Escherichia coli alkaline phosphatase (encoded by phoA) requires the presence of two zinc ions bound at the M1 and M2 metal sites, and one magnesium ion bound at the M3 site []. However, alkaline phosphatases from Thermotoga maritima and Bacillus subtilis require cobalt for maximal activity []. In mammals, there are four alkaline phosphatase isozymes: placental, placental-like (germ cell), intestinal and tissue-nonspecific (liver/bone/kidney). All four isozymes are anchored to the outer surface of the plasma membrane by a covalently attached glycosylphosphatidylinositol (GPI) anchor []. Human alkaline phosphatases have four metal binding sites: two for zinc, one for magnesium, and one for calcium ion. Placental alkaline phosphatase (ALPP or PLAP) is highly polymorphic, with at least three common alleles []. Its activity is down-regulated by a number of effectors such as l-phenylalanine, 5'-AMP, and by p-nitrophenyl-phosphonate (PNPPate) []. The placental-like isozyme (ALPPL or PLAP-like) is elevated in germ cell tumours. The intestinal isozyme (ALPI or IAP) has the ability to detoxify lipopolysaccharide and prevent bacterial invasion across the gut mucosal barrier []. The tissue-nonspecific isozyme (ALPL) is, and may play a role in skeletal mineralisation. Defects in ALPL are a cause of hypophosphatasia, including infantile-type (OMIM:241500), childhood-type (OMIM:241510) and adult-type (OMIM:146300). Hhypophosphatasia is an inherited metabolic bone disease characterised by defective skeletal mineralisation []. This entry also contains the related enzyme streptomycin-6-phosphate phosphatase (3.1.3.39 from EC) (encoded by strK) from Streptomyces species. This enzyme is involved in the synthesis of the antibiotic streptomycin, specifically cleaving both streptomycin-6-phosphate and, more slowly, streptomycin-3-phosphate [].; GO: 0016791 phosphatase activity, 0008152 metabolic process; PDB: 1AJD_B 1ALH_B 2ANH_B 3BDF_A 1ELZ_B 1ELX_B 1B8J_B 2GA3_A 1ANJ_B 1Y6V_B .... Probab=22.26 E-value=1.5e+02 Score=20.10 Aligned_cols=26 Identities=23% Similarity=0.415 Sum_probs=17.8 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) -++.+..|+++++ +.+|.+||+++.+ T Consensus 285 fD~AV~~a~~~~~-----~~~~TLiIVTADH 310 (421) T PF00245_consen 285 FDDAVKVALDFAE-----KDDDTLIIVTADH 310 (421) T ss_dssp HHHHHHHHHHHHH-----HCSSEEEEEEESS T ss_pred HHHHHHHHHHHhc-----cCCCeEEEEEecc Confidence 3455667777776 4588888887654 No 362 >PF13700 DUF4158: Domain of unknown function (DUF4158) Probab=22.22 E-value=1.4e+02 Score=17.01 Aligned_cols=24 Identities=25% Similarity=0.230 Sum_probs=19.5 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCC Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGD 50 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD 50 (70) .++..++..++++++++.++-||- T Consensus 132 ~~~~~l~~~~~~~L~~~rI~lP~~ 155 (166) T PF13700_consen 132 DDPDDLFNALIEWLRQRRIELPGY 155 (166) T ss_pred CCHHHHHHHHHHHHHHCCeeCCCH Confidence 456678999999999999887763 No 363 >PRK00414 gmhA phosphoheptose isomerase; Reviewed Probab=22.21 E-value=97 Score=18.35 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=12.4 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) ..+++||.+++++.+ T Consensus 107 ~~~~~~Dv~I~iS~S 121 (192) T PRK00414 107 AVGREGDVLLGISTS 121 (192) T ss_pred HhCCCCCEEEEEeCC Confidence 345899999999976 No 364 >PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A. Probab=22.18 E-value=17 Score=21.47 Aligned_cols=20 Identities=40% Similarity=0.522 Sum_probs=14.0 Q ss_pred CCCCeEEEeecccCCCCCCce Q psy255 47 NQGDPVIVVTGWKKGAGFTNT 67 (70) Q Consensus 47 ~~GD~vv~~~g~~~~~g~tn~ 67 (70) ..+|++.++.|.+ |.|.|-. T Consensus 15 ~~~~~~~~l~G~a-GtGKT~~ 34 (196) T PF13604_consen 15 TSGDRVSVLQGPA-GTGKTTL 34 (196) T ss_dssp HCTCSEEEEEEST-TSTHHHH T ss_pred hcCCeEEEEEECC-CCCHHHH Confidence 4789999998864 4565543 No 365 >PRK11468 dihydroxyacetone kinase subunit DhaK; Provisional Probab=22.17 E-value=2.3e+02 Score=19.00 Aligned_cols=17 Identities=12% Similarity=0.053 Sum_probs=12.6 Q ss_pred CCHHHHHHHHHHHHHhC Q psy255 27 RDVDTRVAHGIKYGRDR 43 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~ 43 (70) .+.+++++..++.+.+. T Consensus 229 ~~a~elv~~l~~~ll~~ 245 (356) T PRK11468 229 SSLDQTVDEMFDTLLEN 245 (356) T ss_pred CCHHHHHHHHHHHHHcC Confidence 45677888888887775 No 366 >COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism] Probab=22.17 E-value=34 Score=21.54 Aligned_cols=18 Identities=22% Similarity=0.573 Sum_probs=11.9 Q ss_pred CCCCCeEEEeecccCCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGFT 65 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~t 65 (70) +++|+.|+++..+ |+|.+ T Consensus 25 v~~Gevv~iiGpS--GSGKS 42 (240) T COG1126 25 VEKGEVVVIIGPS--GSGKS 42 (240) T ss_pred EcCCCEEEEECCC--CCCHH Confidence 5789998887543 34544 No 367 >PRK14136 recX recombination regulator RecX; Provisional Probab=22.11 E-value=94 Score=20.38 Aligned_cols=20 Identities=10% Similarity=0.032 Sum_probs=17.1 Q ss_pred HHHHHHHHHHHHHhCCCCCC Q psy255 29 VDTRVAHGIKYGRDRKFLNQ 48 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~ 48 (70) .++.|+.+++.|++.|++.. T Consensus 192 ~ee~IE~VIerLke~gYLDD 211 (309) T PRK14136 192 ESDSVEPLLDALEREGWLSD 211 (309) T ss_pred CHHHHHHHHHHHHHcCCcCH Confidence 45789999999999999865 No 368 >PF03319 EutN_CcmL: Ethanolamine utilisation protein EutN/carboxysome; InterPro: IPR004992 The ethanolamine utilization protein EutN is involved in the cobalamin-dependent degradation of ethanolamine []. The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB: 2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the centre. This suggests that EutN forms a pore, with an opening of 26 Amstrong in diameter on one face and 14 Amstrong on the other face []. This entry represents a family of related bacterial proteins with roles in ethanolamine and carbon dioxide metabolism.; PDB: 2QW7_F 2RCF_E 2HD3_F 2Z9H_D. Probab=22.10 E-value=70 Score=16.66 Aligned_cols=14 Identities=29% Similarity=0.394 Sum_probs=9.8 Q ss_pred CCCCCeEEEeeccc Q psy255 46 LNQGDPVIVVTGWK 59 (70) Q Consensus 46 ~~~GD~vv~~~g~~ 59 (70) +..||.|.+++|.. T Consensus 49 AG~Ge~Vlv~~Gs~ 62 (83) T PF03319_consen 49 AGVGEWVLVTSGSS 62 (83) T ss_dssp --TT-EEEEEETHH T ss_pred CCCCCEEEEECCHH Confidence 45899999999874 No 369 >TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. Probab=22.10 E-value=1.7e+02 Score=16.62 Aligned_cols=28 Identities=7% Similarity=-0.046 Sum_probs=20.8 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .+...+.+..+.++++|+ .|.++++.|. T Consensus 64 ~~~~~~~~~~~~l~~~gl---~~~~vivGG~ 91 (134) T TIGR01501 64 HGEIDCKGLRQKCDEAGL---EGILLYVGGN 91 (134) T ss_pred cCHHHHHHHHHHHHHCCC---CCCEEEecCC Confidence 445568888899999997 3566778775 No 370 >cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers. Probab=22.09 E-value=1.6e+02 Score=16.57 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=14.9 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeeccc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) |..+.+.++++.+.+. ..-|.|+.+.|.. T Consensus 44 Dd~~~i~~~l~~~~~~---~~~DlVittGG~s 72 (152) T cd00886 44 DDKDEIREALIEWADE---DGVDLILTTGGTG 72 (152) T ss_pred CCHHHHHHHHHHHHhc---CCCCEEEECCCcC Confidence 3344566666555431 1456666665543 No 371 >COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis] Probab=22.04 E-value=1.2e+02 Score=18.56 Aligned_cols=24 Identities=13% Similarity=0.112 Sum_probs=19.1 Q ss_pred HHHHHHhCCCCCCCCeEEEeeccc Q psy255 36 GIKYGRDRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~~g~~ 59 (70) -++...+.+++++|+.||=+...| T Consensus 33 L~el~~k~~i~~~~~~ViDLGAAP 56 (205) T COG0293 33 LLELNEKFKLFKPGMVVVDLGAAP 56 (205) T ss_pred HHHHHHhcCeecCCCEEEEcCCCC Confidence 345667789999999999887665 No 372 >PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A. Probab=22.01 E-value=83 Score=17.07 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=9.1 Q ss_pred HHHHHHHHHhCCC Q psy255 33 VAHGIKYGRDRKF 45 (70) Q Consensus 33 ~~~a~~~~~~~g~ 45 (70) .+.|+.+++++|+ T Consensus 58 kE~Ai~yaer~G~ 70 (101) T PF04800_consen 58 KEDAIAYAERNGW 70 (101) T ss_dssp HHHHHHHHHHCT- T ss_pred HHHHHHHHHHcCC Confidence 4567888888886 No 373 >PRK00364 groES co-chaperonin GroES; Reviewed Probab=21.98 E-value=67 Score=17.01 Aligned_cols=11 Identities=27% Similarity=0.314 Sum_probs=9.0 Q ss_pred CCCCCCeEEEe Q psy255 45 FLNQGDPVIVV 55 (70) Q Consensus 45 ~~~~GD~vv~~ 55 (70) -++.||+|++- T Consensus 58 ~vk~GD~Vlf~ 68 (95) T PRK00364 58 DVKVGDKVLFG 68 (95) T ss_pred ccCCCCEEEEc Confidence 37899999974 No 374 >cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits. Probab=21.97 E-value=90 Score=17.38 Aligned_cols=16 Identities=19% Similarity=0.243 Sum_probs=12.5 Q ss_pred CCCCCCCCeEEEeecc Q psy255 43 RKFLNQGDPVIVVTGW 58 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~ 58 (70) .|.++.||.++++.-. T Consensus 72 ~G~l~vGe~~v~i~v~ 87 (124) T cd00756 72 VGRLPPGEAIVLVAVS 87 (124) T ss_pred EcccCCCCEEEEEEEe Confidence 4889999999876543 No 375 >PRK07440 hypothetical protein; Provisional Probab=21.96 E-value=91 Score=15.40 Aligned_cols=15 Identities=27% Similarity=0.251 Sum_probs=10.9 Q ss_pred CCCCCCCeEEEeecc Q psy255 44 KFLNQGDPVIVVTGW 58 (70) Q Consensus 44 g~~~~GD~vv~~~g~ 58 (70) -.+++||+|-+++-. T Consensus 53 ~~L~~gD~IEIv~~v 67 (70) T PRK07440 53 TQVQPGDRLEIVTIV 67 (70) T ss_pred eecCCCCEEEEEEEe Confidence 347899998887643 No 376 >smart00350 MCM minichromosome maintenance proteins. Probab=21.76 E-value=77 Score=21.79 Aligned_cols=14 Identities=29% Similarity=0.133 Sum_probs=11.0 Q ss_pred CCCCCCCeEEEeec Q psy255 44 KFLNQGDPVIVVTG 57 (70) Q Consensus 44 g~~~~GD~vv~~~g 57 (70) +.+++||+|.++.= T Consensus 116 d~~~PGD~V~i~Gi 129 (509) T smart00350 116 DKAKPGDRVEVTGI 129 (509) T ss_pred CcccCCCEEEEEEE Confidence 45799999998753 No 377 >COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism] Probab=21.75 E-value=2e+02 Score=19.51 Aligned_cols=33 Identities=9% Similarity=0.096 Sum_probs=24.2 Q ss_pred CCHHHHHHHHHHHHH-hCCCCCCCCeEEEeeccc Q psy255 27 RDVDTRVAHGIKYGR-DRKFLNQGDPVIVVTGWK 59 (70) Q Consensus 27 ~~~~~~~~~a~~~~~-~~g~~~~GD~vv~~~g~~ 59 (70) .....+.+...+++. .+|+-..-|.|++|+|.. T Consensus 132 ~G~~~LR~~ia~~l~~~~g~~~~~~~IiiT~G~q 165 (459) T COG1167 132 AGLPELREAIAAYLLARRGISCEPEQIVITSGAQ 165 (459) T ss_pred CCcHHHHHHHHHHHHHhcCCccCcCeEEEeCCHH Confidence 344556656666666 899888888999999874 No 378 >TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis. Probab=21.74 E-value=94 Score=14.80 Aligned_cols=14 Identities=36% Similarity=0.465 Sum_probs=10.6 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||.|-++.-. T Consensus 48 ~L~~gD~veii~~V 61 (64) T TIGR01683 48 ILKEGDRIEIVTFV 61 (64) T ss_pred ecCCCCEEEEEEec Confidence 47899999887643 No 379 >PF00501 AMP-binding: AMP-binding enzyme; InterPro: IPR000873 A number of prokaryotic and eukaryotic enzymes, which appear to act via an ATP-dependent covalent binding of AMP to their substrate, share a region of sequence similarity [, , ]. This region is a Ser/Thr/Gly-rich domain that is further characterised by a conserved Pro-Lys-Gly triplet. The family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2V7B_A 2Y4O_B 2VSQ_A 3L8C_B 1RY2_A 3KXW_A 3LNV_A 3ETC_B 3A9U_A 3A9V_A .... Probab=21.71 E-value=2.3e+02 Score=18.04 Aligned_cols=29 Identities=21% Similarity=0.123 Sum_probs=20.9 Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 29 VDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 29 ~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ..+.+......+++.|+ ++||.|++.... T Consensus 27 l~~~v~~la~~L~~~g~-~~~~~V~i~~~n 55 (417) T PF00501_consen 27 LYERVRKLAAALRKLGV-KKGDRVAILLPN 55 (417) T ss_dssp HHHHHHHHHHHHHHTTS-STTSEEEEEESS T ss_pred HHHHHHHHhhHHHHhCC-CccccccccCCc Confidence 34556666667777786 899999987654 No 380 >COG0503 Apt Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism] Probab=21.59 E-value=63 Score=19.05 Aligned_cols=17 Identities=29% Similarity=0.509 Sum_probs=12.9 Q ss_pred CCCCCCCCeEEEeeccc Q psy255 43 RKFLNQGDPVIVVTGWK 59 (70) Q Consensus 43 ~g~~~~GD~vv~~~g~~ 59 (70) .+.+++||+|+++-... T Consensus 110 ~~~l~~G~rVlIVDDll 126 (179) T COG0503 110 KDALKPGDRVLIVDDLL 126 (179) T ss_pred hhhCCCCCEEEEEecch Confidence 44567999999997653 No 381 >PRK01215 competence damage-inducible protein A; Provisional Probab=21.46 E-value=2e+02 Score=18.14 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=16.6 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) |..+.+..+++.+.+ ..|.|+.+.|. T Consensus 47 Dd~~~I~~~l~~a~~-----~~DlVIttGG~ 72 (264) T PRK01215 47 DDIEEIVSAFREAID-----RADVVVSTGGL 72 (264) T ss_pred CCHHHHHHHHHHHhc-----CCCEEEEeCCC Confidence 444556777776654 34887777665 No 382 >PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A .... Probab=21.44 E-value=1.1e+02 Score=14.62 Aligned_cols=25 Identities=16% Similarity=0.246 Sum_probs=18.1 Q ss_pred HHHHHHHHHHHHhCCCCCCC-CeEEE Q psy255 30 DTRVAHGIKYGRDRKFLNQG-DPVIV 54 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~G-D~vv~ 54 (70) ...+...++.+++.|+++.. ..+.+ T Consensus 42 r~tv~r~l~~l~~~g~I~~~~~~i~I 67 (76) T PF13545_consen 42 RETVSRILKRLKDEGIIEVKRGKIII 67 (76) T ss_dssp HHHHHHHHHHHHHTTSEEEETTEEEE T ss_pred HHHHHHHHHHHHHCCCEEEcCCEEEE Confidence 35588899999999999743 34433 No 383 >PRK03670 competence damage-inducible protein A; Provisional Probab=21.40 E-value=1.9e+02 Score=18.16 Aligned_cols=27 Identities=7% Similarity=0.044 Sum_probs=16.0 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) |..+.+..+++.+.+ +..|.|+++.|. T Consensus 44 Dd~~~I~~~l~~a~~----~~~DlVIttGGl 70 (252) T PRK03670 44 DDVEEIKSVVLEILS----RKPEVLVISGGL 70 (252) T ss_pred CCHHHHHHHHHHHhh----CCCCEEEECCCc Confidence 444556666665543 235877777665 No 384 >COG1526 FdhD Uncharacterized protein required for formate dehydrogenase activity [Energy production and conversion] Probab=21.30 E-value=2.3e+02 Score=18.19 Aligned_cols=31 Identities=16% Similarity=0.074 Sum_probs=26.0 Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 27 RDVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) -..++.++..+-.+...| ....+.|++++|- T Consensus 178 VGRHNAvDKliG~~~~~G-~~~~~~vl~tSGR 208 (266) T COG1526 178 VGRHNAVDKLIGRALLEG-IPLSGKVLVTSGR 208 (266) T ss_pred ccchhHHHHHHHHHHHCC-CCcCCeEEEEcCC Confidence 356788899999999999 7888999999974 No 385 >PRK05579 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated Probab=21.13 E-value=2.5e+02 Score=18.92 Aligned_cols=30 Identities=17% Similarity=0.324 Sum_probs=22.3 Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCCCeEEEeec Q psy255 26 LRDVDTRVAHGIKYGRDRKFLNQGDPVIVVTG 57 (70) Q Consensus 26 ~~~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g 57 (70) ..++++.+....+.+..+.+ .|-+|++++| T Consensus 167 ~~~~~~I~~~~~~~~~~~~l--~gk~vlITgG 196 (399) T PRK05579 167 MAEPEEIVAAAERALSPKDL--AGKRVLITAG 196 (399) T ss_pred CCCHHHHHHHHHHHhhhccc--CCCEEEEeCC Confidence 45788888888877765544 6778888887 No 386 >PRK02866 cyanate hydratase; Validated Probab=21.05 E-value=71 Score=18.59 Aligned_cols=12 Identities=25% Similarity=0.429 Sum_probs=8.6 Q ss_pred CCCCeEEEeecc Q psy255 47 NQGDPVIVVTGW 58 (70) Q Consensus 47 ~~GD~vv~~~g~ 58 (70) .+||+|+++-.. T Consensus 128 p~Gdrv~it~~G 139 (147) T PRK02866 128 PKGDRVVITLDG 139 (147) T ss_pred CCCCEEEEEecc Confidence 359998887643 No 387 >PF14258 DUF4350: Domain of unknown function (DUF4350) Probab=21.04 E-value=44 Score=16.14 Aligned_cols=11 Identities=9% Similarity=0.661 Sum_probs=7.3 Q ss_pred CCCCCCeEEEe Q psy255 45 FLNQGDPVIVV 55 (70) Q Consensus 45 ~~~~GD~vv~~ 55 (70) |++.|.++|++ T Consensus 59 ~v~~G~~lvl~ 69 (70) T PF14258_consen 59 WVEAGNTLVLA 69 (70) T ss_pred HHHcCCEEEEe Confidence 44577777765 No 388 >TIGR01217 ac_ac_CoA_syn acetoacetyl-CoA synthase. This enzyme catalyzes the first step of the mevalonate pathway of IPP biosynthesis. Most bacteria do not use this pathway, but rather the deoxyxylulose pathway. Probab=21.02 E-value=2.3e+02 Score=19.87 Aligned_cols=27 Identities=22% Similarity=-0.033 Sum_probs=18.5 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ..+...-..+++.|+ ++||+|.+.... T Consensus 122 ~~v~~lA~~L~~~Gv-~~GdrV~i~~~n 148 (652) T TIGR01217 122 RQVASLAAALRALGV-RPGDRVSGYLPN 148 (652) T ss_pred HHHHHHHHHHHHcCC-CCCCEEEEEcCC Confidence 334444556778885 899999987543 No 389 >PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A. Probab=21.01 E-value=67 Score=18.53 Aligned_cols=13 Identities=31% Similarity=0.549 Sum_probs=6.2 Q ss_pred EEEeecccCCCCCC Q psy255 52 VIVVTGWKKGAGFT 65 (70) Q Consensus 52 vv~~~g~~~~~g~t 65 (70) +.++.|.| |.|.| T Consensus 19 ~~~i~GpP-GTGKT 31 (236) T PF13086_consen 19 ITLIQGPP-GTGKT 31 (236) T ss_dssp -EEEE-ST-TSSHH T ss_pred CEEEECCC-CCChH Confidence 66666743 45554 No 390 >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=21.00 E-value=1.9e+02 Score=18.46 Aligned_cols=14 Identities=21% Similarity=0.318 Sum_probs=11.4 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+.++|.+|+++.+ T Consensus 123 ~l~~~DvvI~IS~S 136 (291) T TIGR00274 123 HLTKNDVVVGIAAS 136 (291) T ss_pred CCCCCCEEEEEeCC Confidence 46899999988876 No 391 >PF00742 Homoserine_dh: Homoserine dehydrogenase; InterPro: IPR001342 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Homoserine dehydrogenase (1.1.1.3 from EC) catalyses the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine [, ]. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116 from SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain []. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet. This entry represents the catalytic domain of homoserine dehydrogenase.; GO: 0006520 cellular amino acid metabolic process, 0055114 oxidation-reduction process; PDB: 2EJW_E 3ING_A 3JSA_A 3C8M_A 1TVE_A 1EBU_D 1EBF_B 1Q7G_A 3DO5_A 3MTJ_A. Probab=20.98 E-value=1.2e+02 Score=18.01 Aligned_cols=19 Identities=5% Similarity=0.177 Sum_probs=14.1 Q ss_pred HHHHHHHHHHHhCCCCCCC Q psy255 31 TRVAHGIKYGRDRKFLNQG 49 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~G 49 (70) .-+++|++.+++.|+.++. T Consensus 38 ~~f~~al~eAq~lGyaE~D 56 (179) T PF00742_consen 38 LSFSEALKEAQELGYAEAD 56 (179) T ss_dssp --HHHHHHHHHHTTSS-SS T ss_pred CCHHHHHHHHHHcCCCCCC Confidence 4588899999999998873 No 392 >PRK09464 pdhR transcriptional regulator PdhR; Reviewed Probab=20.98 E-value=1.7e+02 Score=17.74 Aligned_cols=14 Identities=14% Similarity=0.218 Sum_probs=8.2 Q ss_pred HHHHHHHHHhCCCC Q psy255 33 VAHGIKYGRDRKFL 46 (70) Q Consensus 33 ~~~a~~~~~~~g~~ 46 (70) +++|+..|...|++ T Consensus 51 VREAL~~L~~eGlv 64 (254) T PRK09464 51 LREAIQRLEAKGLL 64 (254) T ss_pred HHHHHHHHHHCCCE Confidence 55566666666655 No 393 >TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi. Probab=20.97 E-value=96 Score=17.53 Aligned_cols=14 Identities=14% Similarity=0.259 Sum_probs=11.7 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) ..++||.+++++.+ T Consensus 76 ~~~~~D~~i~iS~s 89 (154) T TIGR00441 76 LGQKGDVLLGISTS 89 (154) T ss_pred hCCCCCEEEEEcCC Confidence 35899999999876 No 394 >PLN00165 hypothetical protein; Provisional Probab=20.97 E-value=36 Score=18.11 Aligned_cols=12 Identities=17% Similarity=0.329 Sum_probs=8.5 Q ss_pred HHHHHHhCCCCC Q psy255 36 GIKYGRDRKFLN 47 (70) Q Consensus 36 a~~~~~~~g~~~ 47 (70) |++.+|++|+++ T Consensus 16 aVEalkDQG~cR 27 (88) T PLN00165 16 AVEALKDQGFCR 27 (88) T ss_pred HHhhccccCeee Confidence 567788888743 No 395 >PRK11414 colanic acid/biofilm transcriptional regulator; Provisional Probab=20.97 E-value=2e+02 Score=17.07 Aligned_cols=21 Identities=19% Similarity=0.213 Sum_probs=9.9 Q ss_pred HHHHHHHHHHhCCCCCCCCeE Q psy255 32 RVAHGIKYGRDRKFLNQGDPV 52 (70) Q Consensus 32 ~~~~a~~~~~~~g~~~~GD~v 52 (70) .+...++..+-.|-+++||++ T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L 35 (221) T PRK11414 15 QVENDLKHQLSIGALKPGARL 35 (221) T ss_pred HHHHHHHHHHHhCCCCCCCcc Confidence 344444444444555555554 No 396 >PF02560 Cyanate_lyase: Cyanate lyase C-terminal domain; InterPro: IPR003712 Some bacteria can overcome the toxicity of environmental cyanate by hydrolysis of cyanate. This reaction is catalyzed by cyanate lyase (also known as cyanase) []. Cyanate lyase is found in bacteria and plants and catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. The cyanate lyase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer []. ; GO: 0008824 cyanate hydratase activity, 0009439 cyanate metabolic process; PDB: 2IV1_B 2IUO_A 2IVQ_B 1DW9_A 1DWK_E 2IVG_G 2IU7_J 2IVB_A. Probab=20.97 E-value=63 Score=16.58 Aligned_cols=11 Identities=27% Similarity=0.619 Sum_probs=7.5 Q ss_pred CCCCeEEEeec Q psy255 47 NQGDPVIVVTG 57 (70) Q Consensus 47 ~~GD~vv~~~g 57 (70) .+||+|+++-. T Consensus 54 ~~GdRv~it~~ 64 (73) T PF02560_consen 54 PKGDRVVITMN 64 (73) T ss_dssp TTSEEEEEEEE T ss_pred CCCCEEEEEEe Confidence 36888887653 No 397 >cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface. Probab=20.93 E-value=73 Score=16.76 Aligned_cols=12 Identities=25% Similarity=0.379 Sum_probs=9.4 Q ss_pred CCCCCCeEEEee Q psy255 45 FLNQGDPVIVVT 56 (70) Q Consensus 45 ~~~~GD~vv~~~ 56 (70) -++.||.|++-. T Consensus 57 ~vk~GD~Vl~~~ 68 (93) T cd00320 57 SVKVGDKVLFPK 68 (93) T ss_pred cccCCCEEEECC Confidence 478999998654 No 398 >PRK13294 F420-0--gamma-glutamyl ligase; Provisional Probab=20.84 E-value=1.7e+02 Score=20.04 Aligned_cols=17 Identities=24% Similarity=0.452 Sum_probs=13.6 Q ss_pred CCCCCCCeEEEeecccC Q psy255 44 KFLNQGDPVIVVTGWKK 60 (70) Q Consensus 44 g~~~~GD~vv~~~g~~~ 60 (70) -.+++||.+|+.+.... T Consensus 38 ~~l~dgdv~vv~~k~vs 54 (448) T PRK13294 38 PWLRDGDVLVVTSKIVS 54 (448) T ss_pred CCCCCCCEEEEeeeeee Confidence 46899999999987643 No 399 >cd03783 MATH_Meprin_Alpha Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The alpha subunit is synthesized as a membrane spanning protein, however, it is cleaved during biosynthesis and loses its transmembrane domain. It oligomerizes into large complexes, containing 10-100 subunits (dimers that associate noncovalently), which are secreted as latent proteases and can move through extracellular spaces in a nondestructive manner. This allows delivery of the concentrated protease to sites containing activating enzymes, such as sites of inflammation, infection or cancerous growth. Meprin alpha shows preference for small or hydrophobic residues at the P1 and P1' sites of its substrate. Both Probab=20.66 E-value=1.4e+02 Score=17.75 Aligned_cols=19 Identities=37% Similarity=0.468 Sum_probs=13.9 Q ss_pred HHHHHhCCCCCCCCeEEEe Q psy255 37 IKYGRDRKFLNQGDPVIVV 55 (70) Q Consensus 37 ~~~~~~~g~~~~GD~vv~~ 55 (70) .+.++.+++++.++.+|.+ T Consensus 146 h~~L~~r~yikdDtlfI~~ 164 (167) T cd03783 146 HSQLRRRSFLKNDDLIIFV 164 (167) T ss_pred HHHHhhCCcccCCeEEEEE Confidence 4678889999876666654 No 400 >PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A. Probab=20.65 E-value=63 Score=16.77 Aligned_cols=9 Identities=33% Similarity=0.504 Sum_probs=5.6 Q ss_pred CCCCCeEEE Q psy255 46 LNQGDPVIV 54 (70) Q Consensus 46 ~~~GD~vv~ 54 (70) ++.||.||. T Consensus 2 f~~GD~VVh 10 (98) T PF02559_consen 2 FKIGDYVVH 10 (98) T ss_dssp --TTSEEEE T ss_pred CCCCCEEEE Confidence 578888875 No 401 >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=20.64 E-value=1.8e+02 Score=18.08 Aligned_cols=22 Identities=18% Similarity=0.137 Sum_probs=13.8 Q ss_pred HHHHHHhCCCCCCCCeEEEeecc Q psy255 36 GIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 36 a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) ....+...++ .++|.++.++.+ T Consensus 107 ~~~~l~a~~l-~~~DvvI~IS~S 128 (257) T cd05007 107 GAADLQAINL-TERDVVIGIAAS 128 (257) T ss_pred HHHHHHHcCC-CCCCEEEEEeCC Confidence 3344444443 788888888765 No 402 >PRK11523 DNA-binding transcriptional repressor ExuR; Provisional Probab=20.61 E-value=2.1e+02 Score=17.36 Aligned_cols=24 Identities=21% Similarity=0.235 Sum_probs=16.5 Q ss_pred HHHHHHHHHHHhCCCC--CCCCeEEE Q psy255 31 TRVAHGIKYGRDRKFL--NQGDPVIV 54 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~--~~GD~vv~ 54 (70) .-+++|+..|...|++ .+|--..| T Consensus 47 tpVREAL~~L~~eGlV~~~~~~G~~V 72 (253) T PRK11523 47 TVVREAIIMLEVEGYVEVRKGSGIHV 72 (253) T ss_pred HHHHHHHHHHHHCCCEEEecCCeeEE Confidence 3488888889999987 44544433 No 403 >KOG0479|consensus Probab=20.57 E-value=93 Score=22.77 Aligned_cols=14 Identities=29% Similarity=0.363 Sum_probs=11.1 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) -+||||+|-++.-. T Consensus 226 ~~KPGDRV~ivG~y 239 (818) T KOG0479|consen 226 RVKPGDRVNIVGIY 239 (818) T ss_pred cCCCCCeeEEEEEE Confidence 36899999988654 No 404 >PLN02736 long-chain acyl-CoA synthetase Probab=20.55 E-value=2.3e+02 Score=19.77 Aligned_cols=28 Identities=11% Similarity=-0.294 Sum_probs=19.7 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) .......-..+.+.|+ ++||+|.+.... T Consensus 85 ~~~v~~lA~~L~~~Gv-~~gd~Vai~~~n 112 (651) T PLN02736 85 GTARTAIGSGLVQHGI-PKGACVGLYFIN 112 (651) T ss_pred HHHHHHHHHHHHHhCC-CCCCEEEEEcCC Confidence 3445555566778885 899999887654 No 405 >cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. Probab=20.53 E-value=48 Score=17.13 Aligned_cols=18 Identities=28% Similarity=0.373 Sum_probs=14.0 Q ss_pred HHHhCCCCCCCCeEEEee Q psy255 39 YGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 39 ~~~~~g~~~~GD~vv~~~ 56 (70) ..++.=|++.||-|++.. T Consensus 32 KfRk~iWIkrGd~VlV~p 49 (78) T cd05792 32 KFRKNIWIKRGDFVLVEP 49 (78) T ss_pred hhcccEEEEeCCEEEEEe Confidence 355677899999999853 No 406 >PLN00415 3-ketoacyl-CoA synthase Probab=20.51 E-value=1.9e+02 Score=20.11 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=20.4 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEee Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVT 56 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~ 56 (70) ..+-+.++++..+|-.++||+++.++ T Consensus 400 sSV~yvL~~~~~~~~~~~Gdrvl~ia 425 (466) T PLN00415 400 SSLWYELAYVEAKCRVKRGDRVWQLA 425 (466) T ss_pred hhHHHHHHHHHhhccCCCCCEEEEEE Confidence 44666777888888889999988765 No 407 >PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I .... Probab=20.41 E-value=75 Score=16.58 Aligned_cols=13 Identities=23% Similarity=0.204 Sum_probs=9.2 Q ss_pred CCCCCCeEEEeec Q psy255 45 FLNQGDPVIVVTG 57 (70) Q Consensus 45 ~~~~GD~vv~~~g 57 (70) .++.||+|++-.. T Consensus 57 ~vk~GD~Vl~~~~ 69 (93) T PF00166_consen 57 DVKVGDKVLFPKY 69 (93) T ss_dssp SS-TTSEEEEETT T ss_pred eeeeccEEecccc Confidence 4678999998654 No 408 >cd01338 MDH_choloroplast_like Chloroplast-like malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are bacterial MDHs, and plant MDHs localized to the choloroplasts. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Probab=20.41 E-value=1.1e+02 Score=19.82 Aligned_cols=19 Identities=21% Similarity=0.442 Sum_probs=14.2 Q ss_pred CCCCCeEEEeecccCCCCC Q psy255 46 LNQGDPVIVVTGWKKGAGF 64 (70) Q Consensus 46 ~~~GD~vv~~~g~~~~~g~ 64 (70) ++.=|.||+++|.+..+|. T Consensus 76 ~~daDivvitaG~~~k~g~ 94 (322) T cd01338 76 FKDADWALLVGAKPRGPGM 94 (322) T ss_pred hCCCCEEEEeCCCCCCCCC Confidence 4566899999998765553 No 409 >PRK07696 sulfur carrier protein ThiS; Provisional Probab=20.40 E-value=1e+02 Score=15.00 Aligned_cols=14 Identities=29% Similarity=0.228 Sum_probs=10.4 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||+|-+++-. T Consensus 51 ~L~~gD~iEIv~~V 64 (67) T PRK07696 51 SVFDGDQIEIVTFV 64 (67) T ss_pred ecCCCCEEEEEEEe Confidence 46899998887643 No 410 >TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Probab=20.39 E-value=93 Score=20.78 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=19.2 Q ss_pred HhCCCCCCCCeEEEeecccCC-CCCC Q psy255 41 RDRKFLNQGDPVIVVTGWKKG-AGFT 65 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g~~~~-~g~t 65 (70) -.+-++.||+.|-.++++..| +|.- T Consensus 36 y~~alv~PGeaVG~IAAQSIGEP~TQ 61 (367) T TIGR02389 36 YLRSLIDPGEAVGIVAAQSIGEPGTQ 61 (367) T ss_pred HHHhcCCCccccchhhhhhcCCcccc Confidence 345679999999999988766 5543 No 411 >COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis] Probab=20.35 E-value=1.1e+02 Score=18.14 Aligned_cols=17 Identities=29% Similarity=0.407 Sum_probs=13.3 Q ss_pred HhCCCCCCCCeEEEeec Q psy255 41 RDRKFLNQGDPVIVVTG 57 (70) Q Consensus 41 ~~~g~~~~GD~vv~~~g 57 (70) ...+-+++||.|+++.- T Consensus 102 ~~~~~ik~Gd~VvV~~e 118 (161) T COG2016 102 SADGEIKEGDIVVVVDE 118 (161) T ss_pred ecCCCccCCCEEEEEEc Confidence 45677889999998763 No 412 >PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional Probab=20.33 E-value=2.7e+02 Score=19.38 Aligned_cols=32 Identities=22% Similarity=0.125 Sum_probs=23.3 Q ss_pred CCHHHHHHHHHHHHHhC--CCCCCCCeEEEeeccc Q psy255 27 RDVDTRVAHGIKYGRDR--KFLNQGDPVIVVTGWK 59 (70) Q Consensus 27 ~~~~~~~~~a~~~~~~~--g~~~~GD~vv~~~g~~ 59 (70) .++++.+..+.+.+... .-+ .|-+|++|+|.- T Consensus 233 ~e~~~I~~~v~~~~~~~~~~~l-~gkkvLITaGpT 266 (475) T PRK13982 233 AEPLEIAAAAEALLRPPQPKPL-AGRRVLITAGPT 266 (475) T ss_pred CCHHHHHHHHHHHHhhcccccc-CCCEEEEecCCc Confidence 46788888887777542 223 899999999963 No 413 >PF03283 PAE: Pectinacetylesterase Probab=20.32 E-value=2e+02 Score=19.08 Aligned_cols=29 Identities=14% Similarity=0.056 Sum_probs=19.9 Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEEEeecccC Q psy255 30 DTRVAHGIKYGRDRKFLNQGDPVIVVTGWKK 60 (70) Q Consensus 30 ~~~~~~a~~~~~~~g~~~~GD~vv~~~g~~~ 60 (70) ...++.+++.++++|+-++ +.|+ ++|... T Consensus 137 ~~i~~avl~~l~~~gl~~a-~~vl-ltG~SA 165 (361) T PF03283_consen 137 YRILRAVLDDLLSNGLPNA-KQVL-LTGCSA 165 (361) T ss_pred HHHHHHHHHHHHHhcCccc-ceEE-EeccCh Confidence 4668889999999988555 4444 455543 No 414 >cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin. Probab=20.21 E-value=2e+02 Score=16.76 Aligned_cols=26 Identities=27% Similarity=0.500 Sum_probs=16.0 Q ss_pred CHHHHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 28 DVDTRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 28 ~~~~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) |..+.+..+++.+.+ .-|.|+.+.|. T Consensus 43 Dd~~~I~~~l~~~~~-----~~dlVIttGG~ 68 (170) T cd00885 43 DDEDRIAEALRRASE-----RADLVITTGGL 68 (170) T ss_pred CCHHHHHHHHHHHHh-----CCCEEEECCCC Confidence 444556677766653 45777777665 No 415 >PRK10524 prpE propionyl-CoA synthetase; Provisional Probab=20.19 E-value=2.4e+02 Score=19.43 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=18.7 Q ss_pred HHHHHHHHHHHhCCCCCCCCeEEEeecc Q psy255 31 TRVAHGIKYGRDRKFLNQGDPVIVVTGW 58 (70) Q Consensus 31 ~~~~~a~~~~~~~g~~~~GD~vv~~~g~ 58 (70) +........+++.|. ++||+|.+.... T Consensus 92 ~~v~~lA~~L~~~Gv-~~gd~V~i~~~n 118 (629) T PRK10524 92 DEVNRMAAMLRSLGV-QRGDRVLIYMPM 118 (629) T ss_pred HHHHHHHHHHHHcCC-CCCCEEEEECCC Confidence 334445566778884 899999987643 No 416 >TIGR01266 fum_ac_acetase fumarylacetoacetase. This enzyme catalyzes the final step in the breakdown of tyrosine or phenylalanine to fumarate and acetoacetate. Probab=20.19 E-value=93 Score=21.19 Aligned_cols=17 Identities=47% Similarity=0.814 Sum_probs=13.5 Q ss_pred HHhCCCCCCCCeEEEee Q psy255 40 GRDRKFLNQGDPVIVVT 56 (70) Q Consensus 40 ~~~~g~~~~GD~vv~~~ 56 (70) ..++.+++.||.|++.. T Consensus 377 g~~r~fL~dGD~V~~~~ 393 (415) T TIGR01266 377 GETRTFLEDGDEVILRG 393 (415) T ss_pred CCCCCCCCCCCEEEEEE Confidence 34568999999999854 No 417 >PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D .... Probab=20.17 E-value=65 Score=15.17 Aligned_cols=14 Identities=29% Similarity=0.356 Sum_probs=9.0 Q ss_pred CCCCCCeEEEeecc Q psy255 45 FLNQGDPVIVVTGW 58 (70) Q Consensus 45 ~~~~GD~vv~~~g~ 58 (70) .+++||.|++-... T Consensus 10 ~i~~Gd~v~v~~~~ 23 (70) T PF00717_consen 10 TIKDGDIVLVDPSS 23 (70) T ss_dssp TSSTTEEEEEEETS T ss_pred CeeCCCEEEEEEcC Confidence 35678887776544 No 418 >cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain. Probab=20.07 E-value=86 Score=15.90 Aligned_cols=11 Identities=27% Similarity=0.419 Sum_probs=8.4 Q ss_pred CCCeEEEeecc Q psy255 48 QGDPVIVVTGW 58 (70) Q Consensus 48 ~GD~vv~~~g~ 58 (70) .||+|+++-.. T Consensus 51 ~gdRvvit~~G 61 (69) T cd00559 51 GGDRVVITLDG 61 (69) T ss_pred CCCEEEEEEcc Confidence 68999987643 Done!