Query 044500
Match_columns 86
No_of_seqs 129 out of 649
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 03:49:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044500hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02279 ent-kaur-16-ene synth 100.0 6.3E-29 1.4E-33 202.2 8.9 84 1-84 527-611 (784)
2 cd00684 Terpene_cyclase_plant_ 99.9 3.8E-25 8.2E-30 173.7 9.4 84 1-84 294-377 (542)
3 PLN02592 ent-copalyl diphospha 99.9 3.6E-25 7.8E-30 180.4 8.9 83 1-83 575-671 (800)
4 cd00868 Terpene_cyclase_C1 Ter 99.5 3.8E-13 8.3E-18 95.8 8.9 83 2-84 61-143 (284)
5 PF03936 Terpene_synth_C: Terp 99.2 4.2E-11 9E-16 84.8 7.8 83 2-84 75-158 (270)
6 cd00687 Terpene_cyclase_nonpla 97.8 6.7E-05 1.4E-09 54.5 6.4 78 2-83 71-149 (303)
7 cd00385 Isoprenoid_Biosyn_C1 I 96.5 0.0057 1.2E-07 40.9 4.6 73 2-84 28-100 (243)
8 PF14165 YtzH: YtzH-like prote 89.6 0.95 2.1E-05 28.5 4.4 39 7-47 19-57 (87)
9 PRK09177 xanthine-guanine phos 78.9 0.67 1.5E-05 31.4 0.1 22 1-22 88-109 (156)
10 PF00156 Pribosyltran: Phospho 78.9 0.67 1.5E-05 28.9 0.1 20 1-20 92-111 (125)
11 PF06883 RNA_pol_Rpa2_4: RNA p 74.6 0.74 1.6E-05 26.7 -0.5 33 10-42 3-35 (58)
12 KOG2099 Glycogen phosphorylase 73.5 3.1 6.6E-05 34.8 2.5 37 19-55 381-418 (843)
13 COG2236 Predicted phosphoribos 70.3 2.2 4.9E-05 30.2 1.0 22 1-22 91-112 (192)
14 TIGR00636 PduO_Nterm ATP:cob(I 67.7 8.7 0.00019 26.7 3.5 48 4-53 22-69 (171)
15 TIGR02710 CRISPR-associated pr 67.7 13 0.00028 29.1 4.7 60 3-81 122-181 (380)
16 PRK05205 bifunctional pyrimidi 66.9 2.2 4.7E-05 29.1 0.4 24 1-27 99-122 (176)
17 PRK09162 hypoxanthine-guanine 66.6 2.2 4.7E-05 29.4 0.3 25 1-28 101-125 (181)
18 PRK11595 DNA utilization prote 65.3 2.6 5.6E-05 29.9 0.5 18 1-18 191-208 (227)
19 TIGR00201 comF comF family pro 64.9 1.7 3.8E-05 29.9 -0.4 19 1-19 156-174 (190)
20 TIGR01203 HGPRTase hypoxanthin 64.0 2.7 5.9E-05 28.5 0.4 20 1-20 88-107 (166)
21 PRK02304 adenine phosphoribosy 63.8 3.3 7.1E-05 28.1 0.8 21 1-21 118-138 (175)
22 TIGR01090 apt adenine phosphor 61.9 3.2 6.9E-05 28.1 0.4 21 1-21 113-133 (169)
23 COG1040 ComFC Predicted amidop 60.7 3.8 8.3E-05 29.3 0.7 19 2-20 189-207 (225)
24 PRK07322 adenine phosphoribosy 59.1 4 8.6E-05 28.0 0.5 20 1-20 124-143 (178)
25 KOG2047 mRNA splicing factor [ 58.0 27 0.00059 29.8 5.2 67 12-78 363-434 (835)
26 TIGR01367 pyrE_Therm orotate p 57.2 4.4 9.6E-05 28.1 0.5 24 1-27 109-132 (187)
27 COG2096 cob(I)alamin adenosylt 55.4 28 0.00061 24.7 4.3 47 5-53 30-76 (184)
28 PRK07199 phosphoribosylpyropho 55.3 5 0.00011 30.0 0.5 19 1-19 215-233 (301)
29 PRK15423 hypoxanthine phosphor 55.3 5 0.00011 27.8 0.5 21 1-21 96-116 (178)
30 PLN02297 ribose-phosphate pyro 53.2 5.4 0.00012 30.4 0.4 20 1-20 234-253 (326)
31 TIGR00336 pyrE orotate phospho 53.1 5.8 0.00013 27.0 0.6 20 1-20 112-131 (173)
32 PRK13812 orotate phosphoribosy 52.3 7.2 0.00016 26.8 0.9 21 1-21 111-131 (176)
33 PF10962 DUF2764: Protein of u 52.0 54 0.0012 24.5 5.5 37 8-45 68-106 (271)
34 PRK09441 cytoplasmic alpha-amy 51.9 14 0.00031 28.9 2.6 20 9-28 76-95 (479)
35 PRK08558 adenine phosphoribosy 50.4 7.5 0.00016 28.1 0.8 22 1-22 180-201 (238)
36 PRK02458 ribose-phosphate pyro 49.7 6.1 0.00013 29.9 0.3 19 1-19 222-240 (323)
37 smart00642 Aamy Alpha-amylase 49.3 19 0.00041 24.4 2.6 30 9-38 65-95 (166)
38 PRK02269 ribose-phosphate pyro 49.0 7.3 0.00016 29.3 0.6 20 1-20 221-240 (320)
39 PLN02238 hypoxanthine phosphor 48.9 6.5 0.00014 27.4 0.3 20 1-20 101-120 (189)
40 PRK04923 ribose-phosphate pyro 48.1 8.5 0.00018 29.1 0.8 19 1-19 221-239 (319)
41 PRK00455 pyrE orotate phosphor 48.0 9 0.00019 26.6 0.9 22 1-22 117-138 (202)
42 PF11433 DUF3198: Protein of u 46.4 54 0.0012 18.5 4.1 27 47-73 21-49 (51)
43 PF09127 Leuk-A4-hydro_C: Leuk 46.3 70 0.0015 21.2 5.0 36 36-71 102-138 (143)
44 PRK05911 RNA polymerase sigma 46.3 1.1E+02 0.0023 21.9 6.3 47 29-76 201-250 (257)
45 PRK02277 orotate phosphoribosy 45.0 9.5 0.00021 26.6 0.6 24 1-27 144-167 (200)
46 PF01923 Cob_adeno_trans: Coba 44.8 95 0.0021 20.9 6.5 47 6-54 25-71 (163)
47 PTZ00149 hypoxanthine phosphor 44.3 8 0.00017 28.3 0.2 20 1-20 154-173 (241)
48 PF02650 HTH_WhiA: WhiA C-term 42.8 79 0.0017 19.5 4.5 51 18-68 21-76 (85)
49 PF00128 Alpha-amylase: Alpha 42.8 18 0.00039 25.2 1.8 22 8-29 46-67 (316)
50 PF02197 RIIa: Regulatory subu 42.5 51 0.0011 17.1 4.8 32 45-76 3-34 (38)
51 PF04545 Sigma70_r4: Sigma-70, 42.2 54 0.0012 17.3 3.7 29 30-58 1-32 (50)
52 PRK00934 ribose-phosphate pyro 41.1 11 0.00023 27.8 0.4 25 1-28 208-232 (285)
53 PF10945 DUF2629: Protein of u 39.6 23 0.00049 19.6 1.5 16 12-27 22-37 (44)
54 COG2342 Predicted extracellula 39.5 7.7 0.00017 29.5 -0.5 78 4-83 54-135 (300)
55 COG0864 NikR Predicted transcr 38.8 97 0.0021 20.8 4.8 30 49-82 16-45 (136)
56 TIGR00684 narJ nitrate reducta 38.8 1.2E+02 0.0027 20.4 5.9 43 14-56 79-122 (152)
57 COG0783 Dps DNA-binding ferrit 38.5 43 0.00094 22.9 3.1 39 25-63 38-78 (156)
58 cd07177 terB_like tellurium re 38.3 83 0.0018 18.3 5.5 35 8-42 13-50 (104)
59 PF08281 Sigma70_r4_2: Sigma-7 37.8 41 0.0009 17.9 2.4 27 30-56 7-36 (54)
60 cd07679 F-BAR_PACSIN2 The F-BA 37.7 1.6E+02 0.0034 21.9 6.1 63 8-79 162-238 (258)
61 COG4572 ChaB Putative cation t 37.5 26 0.00057 21.4 1.6 20 32-51 15-34 (76)
62 PRK12520 RNA polymerase sigma 36.5 54 0.0012 21.9 3.3 49 29-78 127-178 (191)
63 PF13837 Myb_DNA-bind_4: Myb/S 36.2 90 0.0019 18.1 7.7 62 12-81 5-69 (90)
64 PF06394 Pepsin-I3: Pepsin inh 36.0 21 0.00046 21.8 1.1 30 13-42 45-74 (76)
65 COG4755 Uncharacterized protei 35.3 1.5E+02 0.0032 20.3 6.0 35 13-59 10-44 (151)
66 PTZ00271 hypoxanthine-guanine 35.2 15 0.00032 26.3 0.4 20 1-20 122-141 (211)
67 PRK15020 ethanolamine utilizat 34.6 65 0.0014 24.1 3.7 44 7-53 110-153 (267)
68 TIGR03487 cas_csp2 CRISPR-asso 34.3 2E+02 0.0044 22.6 6.4 47 12-58 337-383 (489)
69 PRK03092 ribose-phosphate pyro 34.3 18 0.00039 27.1 0.7 25 1-28 205-229 (304)
70 PRK13811 orotate phosphoribosy 34.2 20 0.00042 24.4 0.8 21 1-21 108-128 (170)
71 PTZ00145 phosphoribosylpyropho 33.6 11 0.00024 30.0 -0.6 19 1-19 339-357 (439)
72 PRK00553 ribose-phosphate pyro 32.9 18 0.0004 27.4 0.6 19 1-19 222-240 (332)
73 PRK06031 phosphoribosyltransfe 32.8 18 0.00039 26.2 0.5 24 1-27 158-181 (233)
74 cd04300 GT1_Glycogen_Phosphory 32.5 36 0.00078 29.2 2.3 32 20-51 350-382 (797)
75 PF00616 RasGAP: GTPase-activa 32.2 1.2E+02 0.0027 20.1 4.6 23 29-51 115-137 (197)
76 PF07739 TipAS: TipAS antibiot 31.9 1.2E+02 0.0027 18.4 4.6 64 9-78 9-72 (118)
77 PF04217 DUF412: Protein of un 31.8 62 0.0013 22.1 2.9 53 30-82 87-143 (143)
78 PTZ00098 phosphoethanolamine N 31.8 1.9E+02 0.0042 20.7 7.8 67 11-78 181-247 (263)
79 KOG4025 Putative apoptosis rel 31.2 1.3E+02 0.0028 21.5 4.5 36 43-79 134-169 (207)
80 TIGR02394 rpoS_proteo RNA poly 31.2 1.2E+02 0.0026 22.0 4.6 46 29-75 218-270 (285)
81 PF00343 Phosphorylase: Carboh 31.2 18 0.00038 30.6 0.2 32 21-52 265-297 (713)
82 PF12881 NUT_N: NUT protein N 31.0 50 0.0011 25.5 2.6 37 12-55 251-287 (328)
83 KOG3231 Predicted assembly/vac 30.3 36 0.00078 24.2 1.6 22 2-23 144-165 (208)
84 COG0503 Apt Adenine/guanine ph 30.1 26 0.00057 24.1 0.9 23 1-26 120-142 (179)
85 PF14629 ORC4_C: Origin recogn 30.0 1.8E+02 0.0039 19.8 5.7 59 12-77 101-165 (203)
86 PF15602 Imm43: Immunity prote 29.8 2E+02 0.0043 20.2 5.3 36 16-54 34-69 (171)
87 PF00249 Myb_DNA-binding: Myb- 29.7 93 0.002 16.3 5.5 18 12-29 5-22 (48)
88 cd05128 RasGAP_GAP1_like The G 29.4 73 0.0016 24.1 3.3 24 29-52 147-170 (315)
89 PRK01250 inorganic pyrophospha 29.3 36 0.00077 23.8 1.5 52 29-80 122-174 (176)
90 smart00595 MADF subfamily of S 29.2 1.2E+02 0.0027 17.6 5.5 53 19-82 2-58 (89)
91 cd05135 RasGAP_RASAL Ras GTPas 28.6 83 0.0018 24.0 3.5 24 28-51 163-186 (333)
92 COG3092 Uncharacterized protei 28.1 1.4E+02 0.003 20.4 4.0 54 29-82 91-148 (149)
93 KOG1539 WD repeat protein [Gen 27.6 2.8E+02 0.006 24.4 6.6 42 8-49 821-864 (910)
94 PRK11923 algU RNA polymerase s 27.5 1.9E+02 0.0041 19.1 5.8 53 29-81 134-191 (193)
95 PRK12531 RNA polymerase sigma 27.3 1.1E+02 0.0024 20.5 3.6 49 29-78 137-188 (194)
96 PRK14985 maltodextrin phosphor 27.2 43 0.00093 28.8 1.8 32 20-51 352-384 (798)
97 cd05392 RasGAP_Neurofibromin_l 26.8 1E+02 0.0022 22.9 3.7 23 29-51 141-163 (323)
98 COG0462 PrsA Phosphoribosylpyr 26.7 19 0.0004 27.6 -0.3 18 1-18 218-235 (314)
99 COG0296 GlgB 1,4-alpha-glucan 26.6 57 0.0012 27.2 2.4 21 9-29 209-229 (628)
100 TIGR02698 CopY_TcrY copper tra 26.6 80 0.0017 20.5 2.7 25 11-35 102-126 (130)
101 cd05130 RasGAP_Neurofibromin N 26.5 92 0.002 23.7 3.4 23 29-51 150-172 (329)
102 PLN02373 soluble inorganic pyr 26.5 66 0.0014 22.8 2.4 53 29-81 128-180 (188)
103 cd05394 RasGAP_RASA2 RASA2 (or 26.4 1E+02 0.0022 23.5 3.6 36 16-51 130-168 (313)
104 PRK12515 RNA polymerase sigma 26.2 1.3E+02 0.0029 19.9 3.9 31 29-59 127-160 (189)
105 PRK12537 RNA polymerase sigma 26.0 94 0.002 20.6 3.1 31 29-59 129-162 (182)
106 cd05395 RasGAP_RASA4 Ras GTPas 25.9 88 0.0019 24.0 3.2 23 29-51 163-185 (337)
107 PRK12530 RNA polymerase sigma 25.7 1E+02 0.0022 20.7 3.2 47 29-76 130-179 (189)
108 smart00323 RasGAP GTPase-activ 25.3 1E+02 0.0022 23.0 3.4 24 29-52 165-188 (344)
109 KOG2792 Putative cytochrome C 25.2 1.2E+02 0.0026 22.9 3.7 24 12-37 155-178 (280)
110 cd05136 RasGAP_DAB2IP The DAB2 25.0 94 0.002 23.4 3.2 23 29-51 142-164 (309)
111 cd05391 RasGAP_p120GAP p120GAP 25.0 99 0.0021 23.4 3.3 23 29-51 141-163 (315)
112 KOG3922 Sulfotransferases [Pos 24.9 1.5E+02 0.0032 23.1 4.2 32 9-51 254-285 (361)
113 PLN02293 adenine phosphoribosy 24.7 32 0.0007 23.9 0.6 21 1-21 129-149 (187)
114 TIGR03001 Sig-70_gmx1 RNA poly 24.6 1.4E+02 0.0031 21.3 3.9 31 29-59 157-190 (244)
115 PRK12522 RNA polymerase sigma 24.3 2.1E+02 0.0045 18.6 5.9 31 29-59 115-148 (173)
116 PRK01816 hypothetical protein; 24.3 1E+02 0.0022 21.1 3.0 53 30-82 86-142 (143)
117 PF12128 DUF3584: Protein of u 24.2 1.6E+02 0.0034 26.1 4.8 41 11-51 1043-1085(1201)
118 PRK01259 ribose-phosphate pyro 24.2 29 0.00064 25.9 0.3 25 1-28 212-236 (309)
119 TIGR02093 P_ylase glycogen/sta 24.2 26 0.00057 30.0 0.1 25 20-44 347-372 (794)
120 PLN02440 amidophosphoribosyltr 24.1 29 0.00063 27.6 0.3 19 1-19 344-362 (479)
121 TIGR03879 near_KaiC_dom probab 24.1 1.3E+02 0.0028 18.1 3.1 28 31-58 13-44 (73)
122 smart00394 RIIa RIIalpha, Regu 23.9 1.2E+02 0.0025 15.4 4.7 30 47-76 5-34 (38)
123 PLN00196 alpha-amylase; Provis 23.9 88 0.0019 24.6 2.9 20 9-28 87-106 (428)
124 PF11794 HpaB_N: 4-hydroxyphen 23.5 2.5E+02 0.0054 20.8 5.1 46 9-54 72-120 (264)
125 PF05772 NinB: NinB protein; 22.9 2E+02 0.0044 19.0 4.1 31 46-80 44-74 (127)
126 PF14572 Pribosyl_synth: Phosp 22.8 16 0.00034 25.9 -1.3 17 1-17 87-103 (184)
127 PF01817 CM_2: Chorismate muta 22.7 1.3E+02 0.0029 17.4 3.0 24 32-55 56-80 (81)
128 PRK06827 phosphoribosylpyropho 22.6 36 0.00078 26.5 0.6 17 1-17 268-284 (382)
129 PF09346 SMI1_KNR4: SMI1 / KNR 22.4 1.2E+02 0.0027 17.9 2.9 28 11-45 2-29 (130)
130 PRK14986 glycogen phosphorylas 22.1 72 0.0016 27.5 2.2 23 20-42 363-386 (815)
131 TIGR03209 P21_Cbot clostridium 22.0 2.1E+02 0.0046 17.9 4.6 30 29-58 103-135 (142)
132 PF04033 DUF365: Domain of unk 21.9 61 0.0013 20.7 1.4 23 6-28 32-59 (97)
133 PF08264 Anticodon_1: Anticodo 21.9 2.2E+02 0.0047 17.9 5.1 6 20-25 16-21 (153)
134 PRK09448 DNA starvation/statio 21.8 1.3E+02 0.0029 20.3 3.2 38 25-62 45-84 (162)
135 TIGR02402 trehalose_TreZ malto 21.7 82 0.0018 25.4 2.4 20 9-28 155-174 (542)
136 cd05133 RasGAP_IQGAP1 IQGAP1 i 21.7 1.4E+02 0.003 23.1 3.6 30 17-50 131-160 (360)
137 COG0634 Hpt Hypoxanthine-guani 21.7 52 0.0011 23.3 1.1 21 1-21 97-117 (178)
138 PF06838 Met_gamma_lyase: Meth 21.5 1.1E+02 0.0025 24.2 3.1 20 10-29 317-336 (403)
139 KOG3991 Uncharacterized conser 20.7 2E+02 0.0043 21.4 4.0 42 12-53 91-134 (256)
140 PF02416 MttA_Hcf106: mttA/Hcf 20.7 1.4E+02 0.0029 16.6 2.6 25 31-55 19-46 (53)
141 TIGR02943 Sig70_famx1 RNA poly 20.6 2.7E+02 0.0059 18.6 5.9 30 30-59 128-160 (188)
142 PF13873 Myb_DNA-bind_5: Myb/S 20.5 1.8E+02 0.004 16.5 7.5 64 12-78 6-71 (78)
143 KOG2669 Regulator of nuclear m 20.1 2.3E+02 0.0051 21.8 4.5 43 31-74 71-113 (325)
144 TIGR02959 SigZ RNA polymerase 20.1 1.7E+02 0.0037 19.1 3.4 31 29-59 96-129 (170)
145 KOG2460 Signal recognition par 20.0 2.3E+02 0.005 23.6 4.6 17 12-28 128-144 (593)
146 PF07477 Glyco_hydro_67C: Glyc 20.0 3.6E+02 0.0079 19.7 5.2 14 70-83 200-213 (225)
No 1
>PLN02279 ent-kaur-16-ene synthase
Probab=99.96 E-value=6.3e-29 Score=202.17 Aligned_cols=84 Identities=19% Similarity=0.213 Sum_probs=80.9
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcCcc-ccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWDTG-AMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGY 79 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD~~-~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ay 79 (86)
|++||+||+|||+|||++||+||||||++ .+++||+|||+||++|++++||++.++.+.||+++++|++++|+++++||
T Consensus 527 tviDD~fD~yGt~eEL~~ft~aVeRWD~~~~~~~lpeymki~f~aL~~t~nei~~~~~~~qGr~v~~~l~~aW~~ll~ay 606 (784)
T PLN02279 527 TVVDDFFDVGGSEEELENLIQLVEKWDVNGSPDFCSEQVEIIFSALRSTISEIGDKAFTWQGRNVTSHIIKIWLDLLKSM 606 (784)
T ss_pred HHHHHHhhccCCHHHHHHHHHHHHHhccccchhhCcHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999998 66899999999999999999999999999999999999999999999999
Q ss_pred HHHHh
Q 044500 80 FEFFL 84 (86)
Q Consensus 80 l~~~~ 84 (86)
++||-
T Consensus 607 l~EAe 611 (784)
T PLN02279 607 LTEAQ 611 (784)
T ss_pred HHHHH
Confidence 99983
No 2
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=99.92 E-value=3.8e-25 Score=173.73 Aligned_cols=84 Identities=38% Similarity=0.586 Sum_probs=81.9
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYF 80 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl 80 (86)
+++||+||+|||+||++.||+||+|||++++++||+|||+||++++++++++++++.+.+|++.+.|+++.|+++++||+
T Consensus 294 ~~iDD~fD~~gt~eEl~~ft~ai~rwd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l 373 (542)
T cd00684 294 TVIDDTYDVYGTLEELELFTEAVERWDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYL 373 (542)
T ss_pred hhhHhhhccCCCHHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHh
Q 044500 81 EFFL 84 (86)
Q Consensus 81 ~~~~ 84 (86)
+||.
T Consensus 374 ~EA~ 377 (542)
T cd00684 374 VEAK 377 (542)
T ss_pred HHHH
Confidence 9984
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.92 E-value=3.6e-25 Score=180.43 Aligned_cols=83 Identities=13% Similarity=0.007 Sum_probs=80.0
Q ss_pred CcccccccccCCHHHHHHHHHHHH--------hcCccccCcCch------hHHHHHHHHHHHHHHHHHHHHHhccccHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVK--------RWDTGAMVKLPC------YMQICYLAMFNFGNDLAYYDLKIHGLNLLS 66 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~--------RWD~~~~~~Lpe------ymk~~f~~l~~~~~ei~~~~~~~~~~~~~~ 66 (86)
|++||+||+|||+|||++||++|+ |||.+++++||+ |||+||.+|++++||++.++.+.||+++++
T Consensus 575 tviDD~fD~yGt~eEl~~ft~~v~~~~~~~~~rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~ 654 (800)
T PLN02592 575 EAISSYFNKETSSKQRRAFLHEFGYGYKINGRRSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISH 654 (800)
T ss_pred HhhcccccCCCCHHHHHHHHHHHHhcccccccccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHH
Confidence 689999999999999999999997 999999999988 999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q 044500 67 NIKNEVANNVLGYFEFF 83 (86)
Q Consensus 67 ~lk~~~~~l~~ayl~~~ 83 (86)
|++++|.+++++++.++
T Consensus 655 ~L~~~W~~l~~~w~~~g 671 (800)
T PLN02592 655 LLRHAWEMWLLKWLLEG 671 (800)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999998764
No 4
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=99.46 E-value=3.8e-13 Score=95.78 Aligned_cols=83 Identities=35% Similarity=0.566 Sum_probs=79.4
Q ss_pred cccccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHH
Q 044500 2 ANDDMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFE 81 (86)
Q Consensus 2 v~DD~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~ 81 (86)
++||.||.+|+.+|++.++++++||+....+.+|++++.++.+++++.+++...+.+.+|+.....+++.|.++++++..
T Consensus 61 ~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~ 140 (284)
T cd00868 61 VIDDTYDDYGTLEELELFTEAVERWDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLV 140 (284)
T ss_pred HHHhccccCCCHHHHHHHHHHHHhcChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999989989999999999999999999
Q ss_pred HHh
Q 044500 82 FFL 84 (86)
Q Consensus 82 ~~~ 84 (86)
++-
T Consensus 141 e~~ 143 (284)
T cd00868 141 EAK 143 (284)
T ss_pred HHH
Confidence 873
No 5
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=99.23 E-value=4.2e-11 Score=84.76 Aligned_cols=83 Identities=25% Similarity=0.277 Sum_probs=77.5
Q ss_pred cccccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhcccc-HHHHHHHHHHHHHHHHH
Q 044500 2 ANDDMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLN-LLSNIKNEVANNVLGYF 80 (86)
Q Consensus 2 v~DD~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~-~~~~lk~~~~~l~~ayl 80 (86)
++||.||..|+.++++.|+++++||++.....+|+.++.++.++.++++++...+.+.+++. ..+++++.|.+++++++
T Consensus 75 ~~DD~~D~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (270)
T PF03936_consen 75 IFDDFFDDGGSAEELEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYL 154 (270)
T ss_dssp HHHHHHHTTSHHHHHHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eeeeccccccchHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHH
Confidence 68999999999999999999999999988889999999999999999999999999987664 88999999999999999
Q ss_pred HHHh
Q 044500 81 EFFL 84 (86)
Q Consensus 81 ~~~~ 84 (86)
+++-
T Consensus 155 ~e~~ 158 (270)
T PF03936_consen 155 WEAR 158 (270)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 8863
No 6
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=97.82 E-value=6.7e-05 Score=54.48 Aligned_cols=78 Identities=10% Similarity=-0.063 Sum_probs=62.0
Q ss_pred cccccccccC-CHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHH
Q 044500 2 ANDDMYDTYG-SLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYF 80 (86)
Q Consensus 2 v~DD~yD~yg-T~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl 80 (86)
++||.||..| +.++++.+++.+.++.......-|...+.+..++.+....+...+. ......+++.|.+++.|++
T Consensus 71 ~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~d~~~r~~~~~~----~~~~~r~~~~~~~~~~a~~ 146 (303)
T cd00687 71 VFDDLLDRDQKSPEDGEAGVTRLLDILRGDGLDSPDDATPLEFGLADLWRRTLARMS----AEWFNRFAHYTEDYFDAYI 146 (303)
T ss_pred HhcccCCccccCHHHHHHHHHHHHhccCCCCCCCCCCCCHHHHHHHHHHHHhccCCC----HHHHHHHHHHHHHHHHHHH
Confidence 6899999984 9999999999888887643222257888889999999988877643 3335778899999999999
Q ss_pred HHH
Q 044500 81 EFF 83 (86)
Q Consensus 81 ~~~ 83 (86)
.|+
T Consensus 147 ~e~ 149 (303)
T cd00687 147 WEG 149 (303)
T ss_pred HHH
Confidence 886
No 7
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=96.51 E-value=0.0057 Score=40.91 Aligned_cols=73 Identities=19% Similarity=0.109 Sum_probs=57.0
Q ss_pred cccccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHH
Q 044500 2 ANDDMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFE 81 (86)
Q Consensus 2 v~DD~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~ 81 (86)
++||++|..++..+.......+ ...+.|..+...+..+.+.++++..... ......+++.|.+++.++..
T Consensus 28 ~~DDi~D~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~g~~~ 97 (243)
T cd00385 28 VHDDIVDDSGTRRGLPTAHLAV------AIDGLPEAILAGDLLLADAFEELAREGS----PEALEILAEALLDLLEGQLL 97 (243)
T ss_pred HHhhcccCCCCCCCchhhhhhH------HhcCchHHHHHHHHHHHHHHHHHHhCCC----HHHHHHHHHHHHHHHHHHHH
Confidence 6899999999888877665554 3456889998889999998888876422 44567888999999999988
Q ss_pred HHh
Q 044500 82 FFL 84 (86)
Q Consensus 82 ~~~ 84 (86)
++.
T Consensus 98 d~~ 100 (243)
T cd00385 98 DLK 100 (243)
T ss_pred HHH
Confidence 754
No 8
>PF14165 YtzH: YtzH-like protein
Probab=89.61 E-value=0.95 Score=28.54 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=31.9
Q ss_pred ccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHH
Q 044500 7 YDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFN 47 (86)
Q Consensus 7 yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~ 47 (86)
-|.+||..|++.+...|+. .-+-..++..+|-+...+|+
T Consensus 19 ~DccgTvsEcEQieRLvks--Lm~n~~i~~~ik~~L~~Iy~ 57 (87)
T PF14165_consen 19 LDCCGTVSECEQIERLVKS--LMANPNIDADIKQTLEEIYS 57 (87)
T ss_pred hhccCcHHHHHHHHHHHHH--HHcCCCcCHHHHHHHHHHHH
Confidence 4899999999999999987 66666789999877766654
No 9
>PRK09177 xanthine-guanine phosphoribosyltransferase; Validated
Probab=78.93 E-value=0.67 Score=31.38 Aligned_cols=22 Identities=27% Similarity=0.323 Sum_probs=18.6
Q ss_pred CcccccccccCCHHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDA 22 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~a 22 (86)
.|+||+.|+++|+.++..+...
T Consensus 88 LIVDDIiDTG~Tl~~v~~~l~~ 109 (156)
T PRK09177 88 LVVDDLVDTGGTARAVREMYPK 109 (156)
T ss_pred EEEeeeeCCHHHHHHHHHHHhh
Confidence 3789999999999999877653
No 10
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=78.87 E-value=0.67 Score=28.91 Aligned_cols=20 Identities=35% Similarity=0.414 Sum_probs=16.3
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
.++||++|+.+|+.++..+.
T Consensus 92 liVDDvi~tG~Tl~~~~~~L 111 (125)
T PF00156_consen 92 LIVDDVIDTGGTLKEAIELL 111 (125)
T ss_dssp EEEEEEESSSHHHHHHHHHH
T ss_pred EEEeeeEcccHHHHHHHHHH
Confidence 37899999999988876543
No 11
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=74.58 E-value=0.74 Score=26.75 Aligned_cols=33 Identities=24% Similarity=0.352 Sum_probs=28.5
Q ss_pred cCCHHHHHHHHHHHHhcCccccCcCchhHHHHH
Q 044500 10 YGSLDEVELFTDAVKRWDTGAMVKLPCYMQICY 42 (86)
Q Consensus 10 ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f 42 (86)
|.+.++.+.+.+.+.+|..+.-..+|..+.|+|
T Consensus 3 ~~~~~~a~~~~~~LR~~Kv~~~~~vP~~lEI~~ 35 (58)
T PF06883_consen 3 YVSPEEAEQIADQLRYLKVEGEHGVPPTLEIGY 35 (58)
T ss_pred eecHHHHHHHHHHHHHHHHcCCCCCCCceEEEE
Confidence 457899999999999999998778998887665
No 12
>KOG2099 consensus Glycogen phosphorylase [Carbohydrate transport and metabolism]
Probab=73.46 E-value=3.1 Score=34.84 Aligned_cols=37 Identities=30% Similarity=0.458 Sum_probs=29.5
Q ss_pred HHHHHHhcCccccCc-CchhHHHHHHHHHHHHHHHHHH
Q 044500 19 FTDAVKRWDTGAMVK-LPCYMQICYLAMFNFGNDLAYY 55 (86)
Q Consensus 19 ft~av~RWD~~~~~~-Lpeymk~~f~~l~~~~~ei~~~ 55 (86)
+-+|++||-.+.++. ||.+++|+|..=-..++.+...
T Consensus 381 lpEALErWp~~L~e~LLPRHleIIy~In~~~l~~i~~~ 418 (843)
T KOG2099|consen 381 LPEALERWPVSLMEKLLPRHLEIIYEINQRFLQTVAAK 418 (843)
T ss_pred cHHHHHHhhHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence 457999999999987 7999999997666666655544
No 13
>COG2236 Predicted phosphoribosyltransferases [General function prediction only]
Probab=70.26 E-value=2.2 Score=30.23 Aligned_cols=22 Identities=23% Similarity=0.120 Sum_probs=18.5
Q ss_pred CcccccccccCCHHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDA 22 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~a 22 (86)
.|+||+.|+..|++....+.+-
T Consensus 91 LIVDDI~DTG~Tl~~a~~~l~~ 112 (192)
T COG2236 91 LIVDDIVDTGETLELALEELKK 112 (192)
T ss_pred EEEecccCchHhHHHHHHHHHh
Confidence 3799999999999988877654
No 14
>TIGR00636 PduO_Nterm ATP:cob(I)alamin adenosyltransferase. This model represents as ATP:cob(I)alamin adenosyltransferase family corresponding to the N-terminal half of Salmonella PduO, a 1,2-propanediol utilization protein that probably is bifunctional. PduO represents one of at least three families of ATP:corrinoid adenosyltransferase: others are CobA (which partially complements PduO) and EutT. It was not clear originally whether ATP:cob(I)alamin adenosyltransferase activity resides in the N-terminal region of PduO, modeled here, but this has now become clear from the characterization of MeaD from Methylobacterium extorquens.
Probab=67.74 E-value=8.7 Score=26.71 Aligned_cols=48 Identities=25% Similarity=0.344 Sum_probs=27.8
Q ss_pred cccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHH
Q 044500 4 DDMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLA 53 (86)
Q Consensus 4 DD~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~ 53 (86)
|...++|||+|||..++-.+.. ... -+.+-+.+.-+=..|++...+++
T Consensus 22 d~riea~Gt~DElns~iGl~~~-~~~-~~~~~~~L~~iQ~~Lf~l~~~la 69 (171)
T TIGR00636 22 SPRVEAYGTLDELNSFIGVALS-LLK-WEDLKEDLERIQNDLFDIGGDLA 69 (171)
T ss_pred CccceehhhHHHHHHHHHHHHH-hcC-cHHHHHHHHHHHHHHHHHhHHhc
Confidence 4568999999999999887643 110 01123334444445555444444
No 15
>TIGR02710 CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
Probab=67.70 E-value=13 Score=29.09 Aligned_cols=60 Identities=18% Similarity=0.165 Sum_probs=40.2
Q ss_pred ccccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHH
Q 044500 3 NDDMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFE 81 (86)
Q Consensus 3 ~DD~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~ 81 (86)
+.|-|++|| .-|...+.++..|+| |.+-...+.++.....+..++ --.+.++.+|++|+.
T Consensus 122 ~~nP~~v~~-~~e~~~~r~l~n~~d--------------y~aA~~~~~~L~~r~l~~~~~----~~~~~~~~l~~~y~~ 181 (380)
T TIGR02710 122 PSDPYNVEG-NTEQGYARRAINAFD--------------YLFAHARLETLLRRLLSAVNH----TFYEAMIKLTRAYLH 181 (380)
T ss_pred cCCHHHHHH-HHHHHHHHHHHHhcC--------------hHHHHHHHHHHHhcccChhhh----hHHHHHHHHHHHHHH
Confidence 567889998 556667889999998 666666677766553221111 122568888888874
No 16
>PRK05205 bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase; Provisional
Probab=66.91 E-value=2.2 Score=29.11 Aligned_cols=24 Identities=21% Similarity=0.218 Sum_probs=18.2
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcC
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWD 27 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD 27 (86)
+|+||+.|+++|+.++. +.+++..
T Consensus 99 LIVDDIidTG~Tl~~~~---~~L~~~G 122 (176)
T PRK05205 99 ILVDDVLYTGRTIRAAL---DALFDYG 122 (176)
T ss_pred EEEecccCcHHHHHHHH---HHHHhcC
Confidence 47899999999988875 4455543
No 17
>PRK09162 hypoxanthine-guanine phosphoribosyltransferase; Provisional
Probab=66.62 E-value=2.2 Score=29.37 Aligned_cols=25 Identities=16% Similarity=0.153 Sum_probs=19.1
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcCc
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD~ 28 (86)
+++||+.|+..|+.++... +++...
T Consensus 101 LIVDDIidTG~Tl~~~~~~---Lk~~Ga 125 (181)
T PRK09162 101 LVVDDILDEGHTLAAIRDR---CLEMGA 125 (181)
T ss_pred EEEccccCcHHHHHHHHHH---HHhCCC
Confidence 3789999999999988654 555543
No 18
>PRK11595 DNA utilization protein GntX; Provisional
Probab=65.31 E-value=2.6 Score=29.95 Aligned_cols=18 Identities=22% Similarity=0.246 Sum_probs=15.5
Q ss_pred CcccccccccCCHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVEL 18 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ 18 (86)
+++||++++.+|+.|+..
T Consensus 191 llvDDv~tTG~Tl~~~~~ 208 (227)
T PRK11595 191 AIVDDVVTTGSTVAEIAQ 208 (227)
T ss_pred EEEeeeecchHHHHHHHH
Confidence 479999999999988754
No 19
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=64.95 E-value=1.7 Score=29.87 Aligned_cols=19 Identities=26% Similarity=0.343 Sum_probs=16.1
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+++||+|.++.|+.|+...
T Consensus 156 llvDDV~TTGaTl~~~~~~ 174 (190)
T TIGR00201 156 VLVDDVVTTGATLHEIARL 174 (190)
T ss_pred EEEeeeeccHHHHHHHHHH
Confidence 4799999999999998654
No 20
>TIGR01203 HGPRTase hypoxanthine phosphoribosyltransferase. Sequence differences as small as a single residue can affect whether members of this family act on hypoxanthine and guanine or hypoxanthine only. The designation of this model as equivalog reflects hypoxanthine specificity and does not reflect whether or not guanine can replace hypoxanthine.
Probab=64.00 E-value=2.7 Score=28.55 Aligned_cols=20 Identities=20% Similarity=0.115 Sum_probs=16.6
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+++||+.|+.+|+.++....
T Consensus 88 livDDii~TG~Tl~~~~~~l 107 (166)
T TIGR01203 88 LIVEDIVDTGLTLQYLLDLL 107 (166)
T ss_pred EEEeeeeCcHHHHHHHHHHH
Confidence 37899999999998886543
No 21
>PRK02304 adenine phosphoribosyltransferase; Provisional
Probab=63.81 E-value=3.3 Score=28.11 Aligned_cols=21 Identities=24% Similarity=0.377 Sum_probs=17.0
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
.++||++++.+|+.++.....
T Consensus 118 LIVDDivtTG~Tl~~~~~~l~ 138 (175)
T PRK02304 118 LIVDDLLATGGTLEAAIKLLE 138 (175)
T ss_pred EEEeCCccccHHHHHHHHHHH
Confidence 379999999999888865543
No 22
>TIGR01090 apt adenine phosphoribosyltransferase. A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this model and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage.
Probab=61.91 E-value=3.2 Score=28.08 Aligned_cols=21 Identities=19% Similarity=0.332 Sum_probs=17.1
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
+++||++++.+|+.++.....
T Consensus 113 LIVDDIitTG~Tl~~a~~~L~ 133 (169)
T TIGR01090 113 LIVDDLLATGGTAEATDELIR 133 (169)
T ss_pred EEEeccccchHHHHHHHHHHH
Confidence 378999999999988865543
No 23
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=60.67 E-value=3.8 Score=29.34 Aligned_cols=19 Identities=32% Similarity=0.399 Sum_probs=16.3
Q ss_pred cccccccccCCHHHHHHHH
Q 044500 2 ANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 2 v~DD~yD~ygT~eEl~~ft 20 (86)
++||+|.++.|+.|+....
T Consensus 189 LvDDV~TTGaTl~~~~~~L 207 (225)
T COG1040 189 LVDDVYTTGATLKEAAKLL 207 (225)
T ss_pred EEecccccHHHHHHHHHHH
Confidence 6899999999999986543
No 24
>PRK07322 adenine phosphoribosyltransferase; Provisional
Probab=59.11 E-value=4 Score=28.00 Aligned_cols=20 Identities=30% Similarity=0.376 Sum_probs=16.2
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
.++||++++.+|+.++....
T Consensus 124 LIVDDiitTG~Tl~aa~~~L 143 (178)
T PRK07322 124 AIVDDVVSTGGTLTALERLV 143 (178)
T ss_pred EEEeccccccHHHHHHHHHH
Confidence 37999999999998776543
No 25
>KOG2047 consensus mRNA splicing factor [RNA processing and modification]
Probab=58.03 E-value=27 Score=29.76 Aligned_cols=67 Identities=13% Similarity=0.176 Sum_probs=49.1
Q ss_pred CHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccc-----cHHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGL-----NLLSNIKNEVANNVLG 78 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~-----~~~~~lk~~~~~l~~a 78 (86)
.-+-+..+|+||++|||.-..+-|.-+-.-|-.+|...+.++..-.-..+. -.++.|-+.|.+++..
T Consensus 363 ~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waem 434 (835)
T KOG2047|consen 363 AAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEM 434 (835)
T ss_pred hHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHH
Confidence 345577899999999999888889999888999998888776543322222 2356777788777643
No 26
>TIGR01367 pyrE_Therm orotate phosphoribosyltransferase, Thermus family. This model represents a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori, Mesorhizobium loti, and related species.
Probab=57.17 E-value=4.4 Score=28.14 Aligned_cols=24 Identities=29% Similarity=0.199 Sum_probs=18.8
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcC
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWD 27 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD 27 (86)
.|+||+.|+.+|+.++... +++..
T Consensus 109 LIVDDIi~TG~Tl~~a~~~---l~~~G 132 (187)
T TIGR01367 109 VAVEDVVTTGGSLLEAIRA---IEGQG 132 (187)
T ss_pred EEEEeeecchHHHHHHHHH---HHHcC
Confidence 3799999999999888755 45544
No 27
>COG2096 cob(I)alamin adenosyltransferase [Coenzyme transport and metabolism]
Probab=55.36 E-value=28 Score=24.70 Aligned_cols=47 Identities=23% Similarity=0.398 Sum_probs=26.5
Q ss_pred ccccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHH
Q 044500 5 DMYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLA 53 (86)
Q Consensus 5 D~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~ 53 (86)
..-..|||+||+..|+-...---. -+.+-..++-+...|++.--+++
T Consensus 30 ~rVeayGtlDElNs~IG~A~~~~~--~~~i~~~L~~IQ~~LF~lG~dLa 76 (184)
T COG2096 30 PRVEAYGTLDELNSFIGLARALLK--DEDIRAILRRIQNDLFDLGADLA 76 (184)
T ss_pred ceeeeeccHHHHHHHHHHHHHhCC--HHHHHHHHHHHHHHHHHhhhhhc
Confidence 345689999999999875543111 02333444445555555444443
No 28
>PRK07199 phosphoribosylpyrophosphate synthetase; Provisional
Probab=55.30 E-value=5 Score=29.99 Aligned_cols=19 Identities=26% Similarity=0.135 Sum_probs=15.6
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+++||+.|+.||+.+....
T Consensus 215 IIVDDIidTG~Tl~~aa~~ 233 (301)
T PRK07199 215 VLVDDIVSTGRTLIEAARQ 233 (301)
T ss_pred EEEecccCcHHHHHHHHHH
Confidence 4799999999998877543
No 29
>PRK15423 hypoxanthine phosphoribosyltransferase; Provisional
Probab=55.26 E-value=5 Score=27.78 Aligned_cols=21 Identities=19% Similarity=0.319 Sum_probs=17.2
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
+++||+.|+..|+..+..+..
T Consensus 96 LlVDDIiDTG~TL~~l~~~l~ 116 (178)
T PRK15423 96 LIVEDIIDSGNTLSKVREILS 116 (178)
T ss_pred EEEeeecCchHHHHHHHHHHH
Confidence 378999999999998776643
No 30
>PLN02297 ribose-phosphate pyrophosphokinase
Probab=53.16 E-value=5.4 Score=30.40 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=16.2
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+++||+.|+.||+.++....
T Consensus 234 lIVDDIidTG~Tl~~aa~~L 253 (326)
T PLN02297 234 VIVDDLVQSGGTLIECQKVL 253 (326)
T ss_pred EEEecccCcHHHHHHHHHHH
Confidence 47999999999988876443
No 31
>TIGR00336 pyrE orotate phosphoribosyltransferase. The conserved Lys (K) residue at position 101 of the seed alignment has been proposed as the active site for the enzyme.
Probab=53.12 E-value=5.8 Score=26.95 Aligned_cols=20 Identities=20% Similarity=0.096 Sum_probs=16.4
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+++||+.++.||+.+.....
T Consensus 112 lIVDDvi~TG~Tl~~a~~~l 131 (173)
T TIGR00336 112 VVVEDVITTGTSILEAVEII 131 (173)
T ss_pred EEEeccccChHHHHHHHHHH
Confidence 47999999999988876544
No 32
>PRK13812 orotate phosphoribosyltransferase; Provisional
Probab=52.29 E-value=7.2 Score=26.85 Aligned_cols=21 Identities=14% Similarity=-0.058 Sum_probs=17.1
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
+|+||+.++.||+.++....+
T Consensus 111 lIVDDvitTG~Tl~~~~~~l~ 131 (176)
T PRK13812 111 VVLEDIATTGQSAVDAVEALR 131 (176)
T ss_pred EEEEEeeCCCHHHHHHHHHHH
Confidence 479999999999988865544
No 33
>PF10962 DUF2764: Protein of unknown function (DUF2764); InterPro: IPR024492 This bacterial family of proteins has no known function.
Probab=52.03 E-value=54 Score=24.51 Aligned_cols=37 Identities=24% Similarity=0.261 Sum_probs=26.0
Q ss_pred cccC--CHHHHHHHHHHHHhcCccccCcCchhHHHHHHHH
Q 044500 8 DTYG--SLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAM 45 (86)
Q Consensus 8 D~yg--T~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l 45 (86)
+.+| |-+|+.....+. +|.......+|+||+-+...-
T Consensus 68 ~~~g~~~~~el~~~~~~~-~~~~~~~~~lP~y~~~Fl~~y 106 (271)
T PF10962_consen 68 DPRGNYSEEELEELIKAQ-KEGDEPDKGLPSYLKDFLEDY 106 (271)
T ss_pred CcccCcCHHHHHHHHHHH-HhcccccccccHHHHHHHHHH
Confidence 4455 678888888765 566555778999997655443
No 34
>PRK09441 cytoplasmic alpha-amylase; Reviewed
Probab=51.85 E-value=14 Score=28.91 Aligned_cols=20 Identities=25% Similarity=0.320 Sum_probs=17.9
Q ss_pred ccCCHHHHHHHHHHHHhcCc
Q 044500 9 TYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~ 28 (86)
.|||.+|++.|+++..+=.+
T Consensus 76 ~fGt~~dl~~Li~~~H~~Gi 95 (479)
T PRK09441 76 KYGTKEELLNAIDALHENGI 95 (479)
T ss_pred CcCCHHHHHHHHHHHHHCCC
Confidence 78999999999999997654
No 35
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=50.35 E-value=7.5 Score=28.09 Aligned_cols=22 Identities=9% Similarity=0.064 Sum_probs=17.7
Q ss_pred CcccccccccCCHHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDA 22 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~a 22 (86)
.|+||+.++.||+..+..+.+.
T Consensus 180 LIVDDvi~TG~Tl~~~~~ll~~ 201 (238)
T PRK08558 180 LIVDDIIRSGETQRALLDLARQ 201 (238)
T ss_pred EEEecccccCHHHHHHHHHHHH
Confidence 3799999999998887665543
No 36
>PRK02458 ribose-phosphate pyrophosphokinase; Provisional
Probab=49.67 E-value=6.1 Score=29.86 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=15.9
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+|+||+.|+.||+-+....
T Consensus 222 iIVDDIidTG~Tl~~aa~~ 240 (323)
T PRK02458 222 ILIDDILNTGKTFAEAAKI 240 (323)
T ss_pred EEEcceeCcHHHHHHHHHH
Confidence 4799999999998887644
No 37
>smart00642 Aamy Alpha-amylase domain.
Probab=49.26 E-value=19 Score=24.44 Aligned_cols=30 Identities=10% Similarity=0.205 Sum_probs=22.7
Q ss_pred ccCCHHHHHHHHHHHHhcCcccc-CcCchhH
Q 044500 9 TYGSLDEVELFTDAVKRWDTGAM-VKLPCYM 38 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~~~~-~~Lpeym 38 (86)
.|||.+|++.|+++..+-.+..+ |-.|.++
T Consensus 65 ~~Gt~~d~~~lv~~~h~~Gi~vilD~V~NH~ 95 (166)
T smart00642 65 RFGTMEDFKELVDAAHARGIKVILDVVINHT 95 (166)
T ss_pred ccCCHHHHHHHHHHHHHCCCEEEEEECCCCC
Confidence 68999999999999999877533 3344443
No 38
>PRK02269 ribose-phosphate pyrophosphokinase; Provisional
Probab=48.98 E-value=7.3 Score=29.34 Aligned_cols=20 Identities=30% Similarity=0.287 Sum_probs=16.1
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+|+||+.|+.||+.++....
T Consensus 221 iIVDDIidTG~Tl~~aa~~L 240 (320)
T PRK02269 221 ILIDDMIDTAGTICHAADAL 240 (320)
T ss_pred EEEeeecCcHHHHHHHHHHH
Confidence 47999999999988875443
No 39
>PLN02238 hypoxanthine phosphoribosyltransferase
Probab=48.89 E-value=6.5 Score=27.35 Aligned_cols=20 Identities=20% Similarity=0.253 Sum_probs=16.1
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+++||+.|+.+|+..+....
T Consensus 101 liVDDIidTG~Tl~~~~~~l 120 (189)
T PLN02238 101 LLVEDIVDTGNTLSALVAHL 120 (189)
T ss_pred EEEecccchHHHHHHHHHHH
Confidence 37899999999988876443
No 40
>PRK04923 ribose-phosphate pyrophosphokinase; Provisional
Probab=48.12 E-value=8.5 Score=29.08 Aligned_cols=19 Identities=32% Similarity=0.349 Sum_probs=15.4
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+|+||+.|+.||+-+....
T Consensus 221 iIVDDIidTG~Tl~~aa~~ 239 (319)
T PRK04923 221 VLVDDLVDTAGTLCAAAAA 239 (319)
T ss_pred EEEecccCchHHHHHHHHH
Confidence 4799999999998777533
No 41
>PRK00455 pyrE orotate phosphoribosyltransferase; Validated
Probab=47.97 E-value=9 Score=26.58 Aligned_cols=22 Identities=27% Similarity=0.188 Sum_probs=17.7
Q ss_pred CcccccccccCCHHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTDA 22 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~a 22 (86)
+++||+-|+.+|+.++....+.
T Consensus 117 liVDDvi~tG~Tl~~~~~~l~~ 138 (202)
T PRK00455 117 LVVEDVITTGGSVLEAVEAIRA 138 (202)
T ss_pred EEEecccCCcHHHHHHHHHHHH
Confidence 3789999999999998655443
No 42
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=46.41 E-value=54 Score=18.52 Aligned_cols=27 Identities=11% Similarity=0.008 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHhccccH--HHHHHHHHH
Q 044500 47 NFGNDLAYYDLKIHGLNL--LSNIKNEVA 73 (86)
Q Consensus 47 ~~~~ei~~~~~~~~~~~~--~~~lk~~~~ 73 (86)
+..+|+|+-..+-+++|. +...|+.|+
T Consensus 21 ~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 21 RNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 445566666566677764 578888886
No 43
>PF09127 Leuk-A4-hydro_C: Leukotriene A4 hydrolase, C-terminal; InterPro: IPR015211 This C-terminal domain is found in peptidases belonging to MEROPS peptidase family M1, particularly: aminopeptidase-1 of Caenorhabditis elegans, aminopeptidase O, aminopeptidase B and the bifunctional leukotriene A4 hydrolase/aminopeptidase. The domain adopts a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. It is required for the formation of a deep cleft harbouring the catalytic Zn2+ site in leukotriene A4 hydrolase []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0019370 leukotriene biosynthetic process; PDB: 3FUJ_A 3FU3_A 3FTX_A 3FTS_A 3B7R_L 2VJ8_A 3FTW_A 3FUF_A 3FU0_A 3CHO_A ....
Probab=46.33 E-value=70 Score=21.20 Aligned_cols=36 Identities=17% Similarity=0.097 Sum_probs=24.9
Q ss_pred hhHHHHHHHHHH-HHHHHHHHHHHhccccHHHHHHHH
Q 044500 36 CYMQICYLAMFN-FGNDLAYYDLKIHGLNLLSNIKNE 71 (86)
Q Consensus 36 eymk~~f~~l~~-~~~ei~~~~~~~~~~~~~~~lk~~ 71 (86)
.+++.+|++|.. .-.+++.+...+.+....+-.+..
T Consensus 102 KfvrPlYr~L~~~~~~~~A~~~F~~~k~~YHpi~~~~ 138 (143)
T PF09127_consen 102 KFVRPLYRALAKPEGRDLAKETFEKAKPFYHPITRQM 138 (143)
T ss_dssp HHHHHHHHHHHTTTCHHHHHHHHHHHGGGS-HHHHHH
T ss_pred hhHHHHHHHHHccchHHHHHHHHHHHHHhcCHHHHHH
Confidence 466678999998 777888888887776544444333
No 44
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=46.27 E-value=1.1e+02 Score=21.95 Aligned_cols=47 Identities=4% Similarity=-0.116 Sum_probs=29.2
Q ss_pred cccCcCchhHHHHHHHHHH---HHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFN---FGNDLAYYDLKIHGLNLLSNIKNEVANNV 76 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~---~~~ei~~~~~~~~~~~~~~~lk~~~~~l~ 76 (86)
.+++.||+.-+.++...+- +++||++.+....+ .+-....++.++|-
T Consensus 201 ~al~~L~~~er~vi~l~y~e~~t~~EIA~~lgis~~-~V~~~~~ral~kLr 250 (257)
T PRK05911 201 EAILALEEKERKVMALYYYEELVLKEIGKILGVSES-RVSQIHSKALLKLR 250 (257)
T ss_pred HHHHcCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHH-HHHHHHHHHHHHHH
Confidence 3677899988877777653 68999988655322 22334444444433
No 45
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=44.96 E-value=9.5 Score=26.63 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=18.4
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcC
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWD 27 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD 27 (86)
+++||+.++.+|+.++... +++-.
T Consensus 144 lIVDDVitTG~Tl~~ai~~---l~~~G 167 (200)
T PRK02277 144 VIVDDVITSGTTMKETIEY---LKEHG 167 (200)
T ss_pred EEEeeccCchHHHHHHHHH---HHHcC
Confidence 3789999999999888644 55543
No 46
>PF01923 Cob_adeno_trans: Cobalamin adenosyltransferase; InterPro: IPR002779 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation [], while EutT produces AdoCbl for ethanolamine utilisation []. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 2ZHY_A 2ZHZ_B 3KE5_C 3KE4_B 2AH6_C 1NOG_A 2IDX_C 3GAH_A 3CI1_A 3CI3_A ....
Probab=44.82 E-value=95 Score=20.90 Aligned_cols=47 Identities=23% Similarity=0.384 Sum_probs=27.8
Q ss_pred cccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHH
Q 044500 6 MYDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAY 54 (86)
Q Consensus 6 ~yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~ 54 (86)
..+.|||+|||..++-.++. .-.-..+.+.++-+-..|++...+++.
T Consensus 25 rie~~G~lDEl~a~igla~~--~~~~~~~~~~L~~iq~~L~~l~~~la~ 71 (163)
T PF01923_consen 25 RIEAYGTLDELNAFIGLARS--EIKEEELREILERIQNELFDLGAELAT 71 (163)
T ss_dssp HHHHHHHHHHHHHHHHHHHT--HCTTHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred eeeeeeeHHHHHHHHHHHHH--HcCchhHHHHHHHHHHHHHHHHHHHcC
Confidence 46889999999999877764 111122334444555555555544443
No 47
>PTZ00149 hypoxanthine phosphoribosyltransferase; Provisional
Probab=44.28 E-value=8 Score=28.28 Aligned_cols=20 Identities=20% Similarity=0.243 Sum_probs=16.2
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+++||+.|+.+|+.++....
T Consensus 154 LIVDDIidTG~Tl~~~~~~L 173 (241)
T PTZ00149 154 LIVEDIIDTGNTLVKFCEYL 173 (241)
T ss_pred EEEEeEeChHHHHHHHHHHH
Confidence 47999999999988876443
No 48
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=42.80 E-value=79 Score=19.48 Aligned_cols=51 Identities=10% Similarity=-0.061 Sum_probs=30.5
Q ss_pred HHHHHHHhcCc-cccCcCchhHHHHHHHHHH----HHHHHHHHHHHhccccHHHHH
Q 044500 18 LFTDAVKRWDT-GAMVKLPCYMQICYLAMFN----FGNDLAYYDLKIHGLNLLSNI 68 (86)
Q Consensus 18 ~ft~av~RWD~-~~~~~Lpeymk~~f~~l~~----~~~ei~~~~~~~~~~~~~~~l 68 (86)
.-.++|++... ...+.||+..+.++..=++ +.+|+++.+.+.=.++.++|-
T Consensus 21 ~qi~~I~~i~~~~~~~~l~~~l~~~a~lRl~~Pd~SL~EL~~~~~~~iSKSgvnhr 76 (85)
T PF02650_consen 21 KQIEAIEFIEENNGLDKLPEKLREFAELRLENPDASLKELGELLEPPISKSGVNHR 76 (85)
T ss_dssp HHHHHHHHHHHHT-GGGS-HHHHHHHHHHHH-TTS-HHHHHHTT--T--HHHHHHH
T ss_pred HHHHHHHHHHHhcccccCCHHHHHHHHHHHHCccccHHHHHHHHcCcCcHHHHHHH
Confidence 34556666654 4678899999887776665 689999887664444555443
No 49
>PF00128 Alpha-amylase: Alpha amylase, catalytic domain; InterPro: IPR006047 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Enzymes containing this domain, such as alpha-amylase, belong to family 13 (GH13 from CAZY) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins. This entry represents the catalytic domain found in several protein members of this family. It has a structure consisting of an 8 stranded alpha/beta barrel that contains the active site, interrupted by a ~70 amino acid calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain []. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0003824 catalytic activity, 0043169 cation binding, 0005975 carbohydrate metabolic process; PDB: 3FAX_A 3FAW_A 2DH3_B 2DH2_A 1CIU_A 1A47_A 3BMW_A 3BMV_A 2FH8_A 2FH6_A ....
Probab=42.79 E-value=18 Score=25.16 Aligned_cols=22 Identities=14% Similarity=0.430 Sum_probs=18.7
Q ss_pred cccCCHHHHHHHHHHHHhcCcc
Q 044500 8 DTYGSLDEVELFTDAVKRWDTG 29 (86)
Q Consensus 8 D~ygT~eEl~~ft~av~RWD~~ 29 (86)
..|||.+|++.|+++..+=.+.
T Consensus 46 ~~~Gt~~d~~~Lv~~~h~~gi~ 67 (316)
T PF00128_consen 46 PRFGTMEDFKELVDAAHKRGIK 67 (316)
T ss_dssp TTTBHHHHHHHHHHHHHHTTCE
T ss_pred cccchhhhhhhhhhccccccce
Confidence 4789999999999999876653
No 50
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=42.47 E-value=51 Score=17.14 Aligned_cols=32 Identities=6% Similarity=-0.024 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 044500 45 MFNFGNDLAYYDLKIHGLNLLSNIKNEVANNV 76 (86)
Q Consensus 45 l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~ 76 (86)
+-+.++++..++...+-.+++.+..+-+.+|.
T Consensus 3 l~~lL~~~~~~vl~~qP~Di~~F~a~yF~~L~ 34 (38)
T PF02197_consen 3 LQELLKEFTREVLREQPDDILQFAADYFEKLE 34 (38)
T ss_dssp HHHHHHHHHHHHHHH--S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 34567788888888888888888877776654
No 51
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=42.18 E-value=54 Score=17.30 Aligned_cols=29 Identities=14% Similarity=-0.104 Sum_probs=20.0
Q ss_pred ccCcCchhHHHHHHHHHH---HHHHHHHHHHH
Q 044500 30 AMVKLPCYMQICYLAMFN---FGNDLAYYDLK 58 (86)
Q Consensus 30 ~~~~Lpeymk~~f~~l~~---~~~ei~~~~~~ 58 (86)
++++||+.-+-+....|- ++.||++.+.-
T Consensus 1 Al~~L~~~er~vi~~~y~~~~t~~eIa~~lg~ 32 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEGLTLEEIAERLGI 32 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-SHHHHHHHHTS
T ss_pred ChhhCCHHHHHHHHHHhcCCCCHHHHHHHHCC
Confidence 467888777777666664 68888887544
No 52
>PRK00934 ribose-phosphate pyrophosphokinase; Provisional
Probab=41.09 E-value=11 Score=27.83 Aligned_cols=25 Identities=20% Similarity=0.282 Sum_probs=19.4
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcCc
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD~ 28 (86)
+++||+.|+.||+.++. +++++...
T Consensus 208 lIVDDIi~TG~Tl~~aa---~~Lk~~GA 232 (285)
T PRK00934 208 LIVDDIISTGGTMATAI---KILKEQGA 232 (285)
T ss_pred EEEcCccccHHHHHHHH---HHHHHCCC
Confidence 37899999999987765 55667654
No 53
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=39.61 E-value=23 Score=19.60 Aligned_cols=16 Identities=25% Similarity=0.646 Sum_probs=12.0
Q ss_pred CHHHHHHHHHHHHhcC
Q 044500 12 SLDEVELFTDAVKRWD 27 (86)
Q Consensus 12 T~eEl~~ft~av~RWD 27 (86)
.+---+.++++++||=
T Consensus 22 DIsr~e~l~~~~~RWP 37 (44)
T PF10945_consen 22 DISREERLNQALQRWP 37 (44)
T ss_pred HHHHHHHHHHHHHHCh
Confidence 3444567899999995
No 54
>COG2342 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]
Probab=39.53 E-value=7.7 Score=29.46 Aligned_cols=78 Identities=10% Similarity=0.039 Sum_probs=53.1
Q ss_pred cccccccCCHHHHHHHHHHHHhcCcc--ccCcCchhHHHHHHH--HHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHH
Q 044500 4 DDMYDTYGSLDEVELFTDAVKRWDTG--AMVKLPCYMQICYLA--MFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGY 79 (86)
Q Consensus 4 DD~yD~ygT~eEl~~ft~av~RWD~~--~~~~Lpeymk~~f~~--l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ay 79 (86)
++.+++-.|.|||+...++= ||=+. ++.+--+ .|..... .-+.-+.+.++-..+.|.+.+.|=-.+|++.+++|
T Consensus 54 ~g~~~~~~~~eelr~~~~gg-~~pIAYlsIg~ae~-yR~Ywd~~w~~~~p~wLg~edP~W~Gny~VkYW~~eWkdii~~~ 131 (300)
T COG2342 54 CGPFNTPWTIEELRTKADGG-VKPIAYLSIGEAES-YRFYWDKYWLTGRPDWLGEEDPEWPGNYAVKYWEPEWKDIIRSY 131 (300)
T ss_pred cCCCCCcCcHHHHHHHhcCC-eeEEEEEechhhhh-hhhHhhhhhhcCCcccccCCCCCCCCCceeeccCHHHHHHHHHH
Confidence 45677778999999999887 76543 1221112 2211111 11345667777777899999999999999999999
Q ss_pred HHHH
Q 044500 80 FEFF 83 (86)
Q Consensus 80 l~~~ 83 (86)
+..-
T Consensus 132 l~rL 135 (300)
T COG2342 132 LDRL 135 (300)
T ss_pred HHHH
Confidence 9763
No 55
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=38.83 E-value=97 Score=20.79 Aligned_cols=30 Identities=10% Similarity=-0.093 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Q 044500 49 GNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFEF 82 (86)
Q Consensus 49 ~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~~ 82 (86)
++|+.+-+.+.+.+++... ..+.+|.|+++
T Consensus 16 l~elD~~i~~rg~~sRSE~----IrdAir~yl~e 45 (136)
T COG0864 16 LEELDELIEERGYSSRSEL----IRDALREYLEE 45 (136)
T ss_pred HHHHHHHHHHcCCCcHHHH----HHHHHHHHHHH
Confidence 4555544444566677644 55556666665
No 56
>TIGR00684 narJ nitrate reductase molybdenum cofactor assembly chaperone. This protein is termed NarJ in most species that have a single copy, and has been called the delta subunit of nitrate reductase. However, although it is required for correct assembly of active enzyme, it dissociates and is not part of the enzyme. Two hits to this model are found each in E. coli and in Mycobacterium tuberculosis, but in each case duplication to create paralogs appears to be recent. The NarX protein of Mycobacterium tuberculosis includes one of these paralogs as a domain, fused to structural domains of nitrate reductases before and after the NarJ-homologous region.
Probab=38.78 E-value=1.2e+02 Score=20.44 Aligned_cols=43 Identities=12% Similarity=0.023 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhcCccc-cCcCchhHHHHHHHHHHHHHHHHHHH
Q 044500 14 DEVELFTDAVKRWDTGA-MVKLPCYMQICYLAMFNFGNDLAYYD 56 (86)
Q Consensus 14 eEl~~ft~av~RWD~~~-~~~Lpeymk~~f~~l~~~~~ei~~~~ 56 (86)
..+..|.+.-+++.... ..+||+|+=.+...+...-.+.+...
T Consensus 79 ~al~~l~~~Y~~~G~~~~~~ELPDyLp~~LEFla~~~~~~~~~~ 122 (152)
T TIGR00684 79 QEMLELKSHYEQQGDMPVDRELPDYLPLMLEYLALVDPEAARRF 122 (152)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Confidence 34666777778887764 46899999655555543323434443
No 57
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=38.47 E-value=43 Score=22.93 Aligned_cols=39 Identities=13% Similarity=0.153 Sum_probs=33.8
Q ss_pred hcCccccCc--CchhHHHHHHHHHHHHHHHHHHHHHhcccc
Q 044500 25 RWDTGAMVK--LPCYMQICYLAMFNFGNDLAYYDLKIHGLN 63 (86)
Q Consensus 25 RWD~~~~~~--Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~ 63 (86)
-|++.+.+. |=+.+.-.|..+-..+.++++.+..-||..
T Consensus 38 HWnV~G~~F~~lHe~~ee~y~el~~~~DeiAERi~~LGg~p 78 (156)
T COG0783 38 HWNVKGPNFFALHEKLEELYEELAEHVDEIAERIRALGGVP 78 (156)
T ss_pred ccceeCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 599998886 558888999999999999999999988864
No 58
>cd07177 terB_like tellurium resistance terB-like protein. This family consists of tellurium resistance terB proteins, N-terminal domain of heat shock DnaJ-like proteins, N-terminal domain of Mo-dependent nitrogenase-like proteins, C-terminal domain of ABC transporter ATP-binding proteins, C-terminal domain of serine/threonine protein kinase, and many hypothetical bacterial proteins. The function of this family is unknown.
Probab=38.34 E-value=83 Score=18.32 Aligned_cols=35 Identities=11% Similarity=0.095 Sum_probs=26.2
Q ss_pred cccCCHHHHHHHHHHHHhcCc---cccCcCchhHHHHH
Q 044500 8 DTYGSLDEVELFTDAVKRWDT---GAMVKLPCYMQICY 42 (86)
Q Consensus 8 D~ygT~eEl~~ft~av~RWD~---~~~~~Lpeymk~~f 42 (86)
|..-+.+|.+.+.+.+++|.. ...+.+++.++...
T Consensus 13 DG~i~~~E~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (104)
T cd07177 13 DGRVDEEEIAAIEALLRRLPLLDAEERAELIALLEEPL 50 (104)
T ss_pred cCCCCHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 777899999999999999875 44555665555444
No 59
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=37.75 E-value=41 Score=17.89 Aligned_cols=27 Identities=19% Similarity=0.149 Sum_probs=18.1
Q ss_pred ccCcCchhHHHHHHHHHH---HHHHHHHHH
Q 044500 30 AMVKLPCYMQICYLAMFN---FGNDLAYYD 56 (86)
Q Consensus 30 ~~~~Lpeymk~~f~~l~~---~~~ei~~~~ 56 (86)
++..||+..+.+|.-.+- ++.||++.+
T Consensus 7 ~l~~L~~~~r~i~~l~~~~g~s~~eIa~~l 36 (54)
T PF08281_consen 7 ALAQLPERQREIFLLRYFQGMSYAEIAEIL 36 (54)
T ss_dssp HHHCS-HHHHHHHHHHHTS---HHHHHHHC
T ss_pred HHHCCCHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 455699999988877654 577887764
No 60
>cd07679 F-BAR_PACSIN2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons 2 (PACSIN2). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSIN 2 or Syndapin II is expressed ubiquitously and is involved in the regulation of tubulin polymerization. It associates with Golgi membranes and forms a complex with dynamin II which is crucial in promoting vesicle formation from the trans-Golgi network. PACSIN 2 contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave su
Probab=37.68 E-value=1.6e+02 Score=21.95 Aligned_cols=63 Identities=13% Similarity=0.117 Sum_probs=38.4
Q ss_pred cccCCHHHHHHHHHHHHhcC-------------ccccCcC-chhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHH
Q 044500 8 DTYGSLDEVELFTDAVKRWD-------------TGAMVKL-PCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVA 73 (86)
Q Consensus 8 D~ygT~eEl~~ft~av~RWD-------------~~~~~~L-peymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~ 73 (86)
|.-++.++++.+.+-+++-- +..++.. |.|| --....++.+.++|.+ ++.++|+...
T Consensus 162 d~~~~~~q~~K~~~k~~k~~~~~~k~~~~Y~~~l~~L~~~~~~y~-e~m~~~fe~~Q~~E~e--------Ri~F~K~~l~ 232 (258)
T cd07679 162 DPALNPEQLKKLQDKVEKCKQDVLKTKEKYEKSLKELDQTTPQYM-ENMEQVFEQCQQFEEK--------RLRFFREVLL 232 (258)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH-HHHHHHHHHHHHHHHH--------HHHHHHHHHH
Confidence 55678888888876666432 2333332 5555 2344455555555554 6888998888
Q ss_pred HHHHHH
Q 044500 74 NNVLGY 79 (86)
Q Consensus 74 ~l~~ay 79 (86)
.+++..
T Consensus 233 ~~~~~l 238 (258)
T cd07679 233 EVQKHL 238 (258)
T ss_pred HHHHHc
Confidence 877653
No 61
>COG4572 ChaB Putative cation transport regulator [General function prediction only]
Probab=37.49 E-value=26 Score=21.38 Aligned_cols=20 Identities=35% Similarity=0.353 Sum_probs=16.1
Q ss_pred CcCchhHHHHHHHHHHHHHH
Q 044500 32 VKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 32 ~~Lpeymk~~f~~l~~~~~e 51 (86)
.+||+..+++|.+.++.--+
T Consensus 15 ~~lp~haqdiy~~afnsA~e 34 (76)
T COG4572 15 HQLPSHAQDIYKAAFNSAWE 34 (76)
T ss_pred HHhHHHHHHHHHHHHHHHHh
Confidence 46999999999999986433
No 62
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=36.49 E-value=54 Score=21.87 Aligned_cols=49 Identities=6% Similarity=-0.149 Sum_probs=30.4
Q ss_pred cccCcCchhHHHHHHHHH---HHHHHHHHHHHHhccccHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMF---NFGNDLAYYDLKIHGLNLLSNIKNEVANNVLG 78 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~---~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~a 78 (86)
.++++||+..|.+|.--+ -++.||++.+....+ .+-..+..+-+.+-++
T Consensus 127 ~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~-tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 127 ACVDRLPPRTGRVFMMREWLELETEEICQELQITAT-NAWVLLYRARMRLREC 178 (191)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHHHHHH
Confidence 467789999998887654 268999988655332 2334444444444333
No 63
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=36.20 E-value=90 Score=18.13 Aligned_cols=62 Identities=11% Similarity=-0.077 Sum_probs=32.9
Q ss_pred CHHHHHHHHHHHHhcCc-c-ccCc-CchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDT-G-AMVK-LPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFE 81 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~-~-~~~~-Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~ 81 (86)
|.+|...|.+++.. +. . ..+. -..-. ....++|++++...|-.......+.-|+.|.+.|-.
T Consensus 5 t~~et~~Li~~~~~-~~~~~~~~~~~~~~~-------~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 5 TDEETKLLIELWKE-NLMELRFDNGGKKRN-------KKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp -HHHHHHHHHHHHH---HHHHHHH--SS---------HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHH-HHHHHHHhhhccccc-------hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 56788888888876 31 1 0110 00011 124666777766433223357788889999998854
No 64
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=35.97 E-value=21 Score=21.84 Aligned_cols=30 Identities=7% Similarity=0.185 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHhcCccccCcCchhHHHHH
Q 044500 13 LDEVELFTDAVKRWDTGAMVKLPCYMQICY 42 (86)
Q Consensus 13 ~eEl~~ft~av~RWD~~~~~~Lpeymk~~f 42 (86)
..||+.|.+-+.+|....-+.+.+.++.+|
T Consensus 45 ~~eL~~y~~~v~~y~~~l~~~iq~~~~~~~ 74 (76)
T PF06394_consen 45 QQELKTYQKKVAAYKEQLQQQIQEQVESLF 74 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHTT----------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 468899999999999877777777776655
No 65
>COG4755 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.25 E-value=1.5e+02 Score=20.30 Aligned_cols=35 Identities=11% Similarity=0.045 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHh
Q 044500 13 LDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKI 59 (86)
Q Consensus 13 ~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~ 59 (86)
++-+..|+..+++|= .+=+.++.+++.+++.+...
T Consensus 10 ~~~~~sf~~~Le~Wv------------klQk~~l~~lk~~~~~~k~~ 44 (151)
T COG4755 10 LEYLESFMERLEQWV------------KLQKRQLKELKSHGEHMKVA 44 (151)
T ss_pred HHHHHHHHHHHHHHH------------HHHHHHHHHHHhHHHHhhHH
Confidence 566788999999985 23455555666665554443
No 66
>PTZ00271 hypoxanthine-guanine phosphoribosyltransferase; Provisional
Probab=35.20 E-value=15 Score=26.28 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=15.9
Q ss_pred CcccccccccCCHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFT 20 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft 20 (86)
+++||+.|+.-|+..+....
T Consensus 122 LIVDDIvDTG~TL~~v~~~l 141 (211)
T PTZ00271 122 LIVEDIVDSAITLQYLMRFM 141 (211)
T ss_pred EEEecccCCHHHHHHHHHHH
Confidence 47999999999987776543
No 67
>PRK15020 ethanolamine utilization cobalamin adenosyltransferase; Provisional
Probab=34.56 E-value=65 Score=24.08 Aligned_cols=44 Identities=9% Similarity=-0.087 Sum_probs=26.2
Q ss_pred ccccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHH
Q 044500 7 YDTYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLA 53 (86)
Q Consensus 7 yD~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~ 53 (86)
...|||+|||..++=.++ +... +.+.+.+.-+-+.|++...+++
T Consensus 110 Ie~~GtlDELnA~IGl~~-~~~~--~~~~~~L~~Iq~~Lf~i~~~la 153 (267)
T PRK15020 110 LGFRAVLDSTIALAVWLQ-IELA--EPWQPWLADIRSRLGNIMRADA 153 (267)
T ss_pred eeeeehHHHHHHHHHHHH-Hhcc--HHHHHHHHHHHHHHHHHHHHHc
Confidence 578999999998887653 4321 1344445555555555444443
No 68
>TIGR03487 cas_csp2 CRISPR-associated protein, Csp2 family. Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pging (Porphyromonas gingivalis) subtype.
Probab=34.33 E-value=2e+02 Score=22.64 Aligned_cols=47 Identities=13% Similarity=0.038 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLK 58 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~ 58 (86)
|-.=|++|+++-=.==.|.-...|+.+|++|.-.+.-++.+..++..
T Consensus 337 t~rflq~f~k~af~df~s~raeypeqikil~ni~f~kmeki~adiia 383 (489)
T TIGR03487 337 TNRFLQLFNKAAFDDFFSFRAEYPEQIKILFNIFFTKMEKIDADIIA 383 (489)
T ss_pred HHHHHHHhhhHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhHHHHH
Confidence 44456667665322112444568999999999998888888766543
No 69
>PRK03092 ribose-phosphate pyrophosphokinase; Provisional
Probab=34.26 E-value=18 Score=27.06 Aligned_cols=25 Identities=32% Similarity=0.361 Sum_probs=18.3
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcCc
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD~ 28 (86)
+++||+.|+.||+-++. +.+++...
T Consensus 205 iIVDDIi~TG~Tl~~aa---~~Lk~~Ga 229 (304)
T PRK03092 205 VLVDDMIDTGGTIAGAV---RALKEAGA 229 (304)
T ss_pred EEEccccCcHHHHHHHH---HHHHhcCC
Confidence 47899999999987664 55555443
No 70
>PRK13811 orotate phosphoribosyltransferase; Provisional
Probab=34.15 E-value=20 Score=24.44 Aligned_cols=21 Identities=14% Similarity=-0.126 Sum_probs=16.5
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
+|+||+-++.||+.++....+
T Consensus 108 lIVDDvi~TG~T~~~~~~~l~ 128 (170)
T PRK13811 108 LLVEDVTTSGGSALYGIEQLR 128 (170)
T ss_pred EEEEecccccHHHHHHHHHHH
Confidence 479999999999888754443
No 71
>PTZ00145 phosphoribosylpyrophosphate synthetase; Provisional
Probab=33.59 E-value=11 Score=30.02 Aligned_cols=19 Identities=42% Similarity=0.452 Sum_probs=15.8
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+|+||+.|+.||+-+....
T Consensus 339 IIVDDIIdTG~Tl~~aa~~ 357 (439)
T PTZ00145 339 IIVDDMIDTSGTLCEAAKQ 357 (439)
T ss_pred EEEcceeCcHHHHHHHHHH
Confidence 4799999999998887544
No 72
>PRK00553 ribose-phosphate pyrophosphokinase; Provisional
Probab=32.93 E-value=18 Score=27.42 Aligned_cols=19 Identities=32% Similarity=0.389 Sum_probs=15.4
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+|+||+.|+.||+-+....
T Consensus 222 IIVDDIi~TG~Tl~~aa~~ 240 (332)
T PRK00553 222 LIVDDMIDTGGTVIAAAKL 240 (332)
T ss_pred EEEeccccchHHHHHHHHH
Confidence 4799999999998777533
No 73
>PRK06031 phosphoribosyltransferase; Provisional
Probab=32.75 E-value=18 Score=26.19 Aligned_cols=24 Identities=13% Similarity=-0.000 Sum_probs=18.5
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcC
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWD 27 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD 27 (86)
.|+||+.++.||+.++..+ +++-.
T Consensus 158 LIVDDVitTG~Tl~aa~~l---L~~~G 181 (233)
T PRK06031 158 ALIDDVISSGASIVAGLRL---LAACG 181 (233)
T ss_pred EEEEeEccccHHHHHHHHH---HHHcC
Confidence 3799999999998887654 55543
No 74
>cd04300 GT1_Glycogen_Phosphorylase This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. The allosteric control mechanisms of yeast and mammalian members of this family are different from that of bacterial members. The members of this family belong to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=32.51 E-value=36 Score=29.17 Aligned_cols=32 Identities=22% Similarity=0.476 Sum_probs=24.6
Q ss_pred HHHHHhcCccccCc-CchhHHHHHHHHHHHHHH
Q 044500 20 TDAVKRWDTGAMVK-LPCYMQICYLAMFNFGND 51 (86)
Q Consensus 20 t~av~RWD~~~~~~-Lpeymk~~f~~l~~~~~e 51 (86)
-+|.++|+++.++. ||.+++|++.-=.....+
T Consensus 350 pealE~wp~~l~~~~lpr~~~II~~In~~~~~~ 382 (797)
T cd04300 350 PEALEKWPVDLFERLLPRHLEIIYEINRRFLEE 382 (797)
T ss_pred hHHhCccCHHHHHHHChHHHHHHHHHHHHHHHH
Confidence 46889999999998 699999988764444443
No 75
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=32.16 E-value=1.2e+02 Score=20.15 Aligned_cols=23 Identities=4% Similarity=0.176 Sum_probs=18.2
Q ss_pred cccCcCchhHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
+.++.+|..+|.+.+.++..+.+
T Consensus 115 ~s~~~~P~~lr~i~~~i~~~~~~ 137 (197)
T PF00616_consen 115 SSIDQIPPSLRYICKQIYEAVEK 137 (197)
T ss_dssp GGGGGS-HHHHHHHHHHHHHHHH
T ss_pred HhHHHhhHHHHHHHHHHHHHHHH
Confidence 58889999999999998876554
No 76
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=31.89 E-value=1.2e+02 Score=18.40 Aligned_cols=64 Identities=5% Similarity=-0.025 Sum_probs=20.4
Q ss_pred ccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHH
Q 044500 9 TYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLG 78 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~a 78 (86)
.||+ +......+-...|.......+.....-++..|-..+++ .+ .-.+.-++-+.+.|..+++.
T Consensus 9 ~yg~-~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~l~~~~~~---g~--~p~s~evq~l~~~~~~~~~~ 72 (118)
T PF07739_consen 9 RYGD-EAYAESEERLASLSKEEWQELQKEWDELFAELAALMEE---GV--DPDSPEVQELAERWMELINQ 72 (118)
T ss_dssp H------------------------TTHHHHHHHHHHHHHHHH---T----TT-HHHHHHHHHHHHHHHH
T ss_pred HHCh-HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHc---CC--CcCCHHHHHHHHHHHHHHHH
Confidence 3555 44443333334444455555555554444444433322 00 12344567777778877764
No 77
>PF04217 DUF412: Protein of unknown function, DUF412; InterPro: IPR007334 This family consists of bacterial uncharacterised proteins.
Probab=31.84 E-value=62 Score=22.10 Aligned_cols=53 Identities=13% Similarity=0.051 Sum_probs=38.9
Q ss_pred ccCcCchhHHHHHHHHHHHHHHHHHHHHHhccc----cHHHHHHHHHHHHHHHHHHH
Q 044500 30 AMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGL----NLLSNIKNEVANNVLGYFEF 82 (86)
Q Consensus 30 ~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~----~~~~~lk~~~~~l~~ayl~~ 82 (86)
+...||..+..-|..+.+-+.+.+..+...+++ +...-|+.+++++=++|++|
T Consensus 87 a~tpLPp~l~~Wy~ei~~Kl~~~g~~~~~~~~~P~Y~dLA~lL~~Af~~LDk~f~~e 143 (143)
T PF04217_consen 87 ANTPLPPSLLSWYHEIRQKLQEQGIALQPVKSKPRYQDLAELLKRAFKQLDKSFWEE 143 (143)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHhHHHHhcC
Confidence 456699999888888888777776555444332 23477899999999999865
No 78
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=31.82 E-value=1.9e+02 Score=20.66 Aligned_cols=67 Identities=7% Similarity=-0.012 Sum_probs=45.9
Q ss_pred CCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHH
Q 044500 11 GSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLG 78 (86)
Q Consensus 11 gT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~a 78 (86)
.|.+++....++. -+..-....++++....+......+..-.+++.+..|....+.++..|..++.+
T Consensus 181 ~~~~~~~~~l~~a-GF~~v~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (263)
T PTZ00098 181 IPIQEYGDLIKSC-NFQNVVAKDISDYWLELLQVELKKLEEKKEEFLKLYSEKEYNSLKDGWTRKIKD 247 (263)
T ss_pred CCHHHHHHHHHHC-CCCeeeEEeCcHHHHHHHHHHHHHHHHhHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 3556655444332 233333445788888888888888888888888877777777788878777654
No 79
>KOG4025 consensus Putative apoptosis related protein [Function unknown]
Probab=31.24 E-value=1.3e+02 Score=21.50 Aligned_cols=36 Identities=8% Similarity=0.023 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHH
Q 044500 43 LAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGY 79 (86)
Q Consensus 43 ~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ay 79 (86)
+.|++++|++..... -+++-.+.+-|+++....+.+
T Consensus 134 KkLLd~vN~v~~~~p-~t~~~AvE~rKkEFVkYSK~F 169 (207)
T KOG4025|consen 134 KKLLDAVNAVYRIVP-LTAQPAVEKRKKEFVKYSKRF 169 (207)
T ss_pred HHHHHHHHHHHhhcc-ccccHHHHHHHHHHHHHHHHH
Confidence 445677777766544 455666666677766666554
No 80
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=31.21 E-value=1.2e+02 Score=21.98 Aligned_cols=46 Identities=7% Similarity=-0.141 Sum_probs=30.3
Q ss_pred cccCcCchhHHHHHHHHH-------HHHHHHHHHHHHhccccHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMF-------NFGNDLAYYDLKIHGLNLLSNIKNEVANN 75 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~-------~~~~ei~~~~~~~~~~~~~~~lk~~~~~l 75 (86)
.+++.||+..|.++...| -++.||++.+.-..+ .+-..+..+.+.|
T Consensus 218 ~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~-tVk~~l~rAlkkL 270 (285)
T TIGR02394 218 AWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRE-RVRQIQVEALKKL 270 (285)
T ss_pred HHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHH-HHHHHHHHHHHHH
Confidence 578889999998887654 289999988654332 2334444444444
No 81
>PF00343 Phosphorylase: Carbohydrate phosphorylase; InterPro: IPR000811 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 35 GT35 from CAZY comprises enzymes with only one known activity; glycogen and starch phosphorylase (2.4.1.1 from EC). The main role of glycogen phosphorylase (GPase) is to provide phosphorylated glucose molecules (G-1-P) []. GPase is a highly regulated allosteric enzyme. The net effect of the regulatory site allows the enzyme to operate at a variety of rates; the enzyme is not simply regulated as "on" or "off", but rather it can be thought of being set to operate at an ideal rate based on changing conditions at in the cell. The most important allosteric effector is the phosphate molecule covalently attached to Ser14. This switches GPase from the b (inactive) state to the a (active) state. Upon phosphorylation, GPase attains about 80% of its Vmax. When the enzyme is not phosphorylated, GPase activity is practically non-existent at low AMP levels. There is some apparent controversy as to the structure of GPase. All sources agree that the enzyme is multimeric, but there is apparent controversy as to the enzyme being a tetramer or a dimer. Apparently, GPase (in the a form) forms tetramers in the crystal form. The consensus seems to be that `regardless of the a or b form, GPase functions as a dimer in vivo []. The GPase monomer is best described as consisting of two domains, an N-terminal domain and a C-terminal domain []. The C-terminal domain is often referred to as the catalytic domain. It consists of a beta-sheet core surrounded by layers of helical segments []. The vitamin cofactor pyridoxal phosphate (PLP) is covalently attached to the amino acid backbone. The N-terminal domain also consists of a central beta-sheet core and is surrounded by layers of helical segments. The N-terminal domain contains different allosteric effector sites to regulate the enzyme. Bacterial phosphorylases follow the same catalytic mechanisms as their plant and animal counterparts, but differ considerably in terms of their substrate specificity and regulation. The catalytic domains are highly conserved while the regulatory sites are only poorly conserved. For maltodextrin phosphorylase from Escherichia coli the physiological role of the enzyme in the utilisation of maltidextrins is known in detail; that of all the other bacterial phosphorylases is still unclear. Roles in regulatuon of endogenous glycogen metabolism in periods of starvation, and sporulation, stress response or quick adaptation to changing environments are possible [].; GO: 0004645 phosphorylase activity, 0005975 carbohydrate metabolic process; PDB: 1YGP_B 2AW3_B 2AV6_B 1AHP_B 1QM5_A 1L5W_A 2ECP_A 2ASV_A 1L5V_B 1E4O_B ....
Probab=31.20 E-value=18 Score=30.63 Aligned_cols=32 Identities=25% Similarity=0.530 Sum_probs=23.1
Q ss_pred HHHHhcCccccCc-CchhHHHHHHHHHHHHHHH
Q 044500 21 DAVKRWDTGAMVK-LPCYMQICYLAMFNFGNDL 52 (86)
Q Consensus 21 ~av~RWD~~~~~~-Lpeymk~~f~~l~~~~~ei 52 (86)
+|.+||+++.++. ||.++++++..=-....++
T Consensus 265 ealE~wp~~l~~~~Lpr~~~ii~ein~~f~~~~ 297 (713)
T PF00343_consen 265 EALEKWPVDLFERYLPRHLEIIYEINRRFLDEL 297 (713)
T ss_dssp GGS-EEEHHHHHHHSHHHHHHHHHHHHHHHHHH
T ss_pred ccccccCHHHHHHHChHHHHHHHHHhHHHHHHH
Confidence 5779999999987 7999999876544444443
No 82
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. It is also found in FAM22, which are a family of uncharacterised mammalian proteins.
Probab=30.97 E-value=50 Score=25.47 Aligned_cols=37 Identities=16% Similarity=0.259 Sum_probs=28.5
Q ss_pred CHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYY 55 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~ 55 (86)
|+||- +-.|||.|+- -+.+=|++|..+-.-|.|+|.+
T Consensus 251 tlEeG--l~ra~qEW~~-----~SnfdRmifyemaekFmEFEae 287 (328)
T PF12881_consen 251 TLEEG--LWRAVQEWQH-----TSNFDRMIFYEMAEKFMEFEAE 287 (328)
T ss_pred cHHHH--HHHHHHHhhc-----cccccHHHHHHHHHHHccCCcH
Confidence 56665 6789999985 3456678888888888888764
No 83
>KOG3231 consensus Predicted assembly/vacuolar sorting protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.25 E-value=36 Score=24.22 Aligned_cols=22 Identities=27% Similarity=0.421 Sum_probs=18.8
Q ss_pred cccccccccCCHHHHHHHHHHH
Q 044500 2 ANDDMYDTYGSLDEVELFTDAV 23 (86)
Q Consensus 2 v~DD~yD~ygT~eEl~~ft~av 23 (86)
.+||++|..|.-||....++-|
T Consensus 144 TLDdild~sgDeeEs~aiVNqV 165 (208)
T KOG3231|consen 144 TLDDILDGSGDEEESQAIVNQV 165 (208)
T ss_pred hHHHHhcCCCcHHHHHHHHHHH
Confidence 3799999999999998877755
No 84
>COG0503 Apt Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]
Probab=30.07 E-value=26 Score=24.10 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=17.1
Q ss_pred CcccccccccCCHHHHHHHHHHHHhc
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRW 26 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RW 26 (86)
.|+||+-++.||..-+. +.+++=
T Consensus 120 lIVDDllaTGgT~~a~~---~Ll~~~ 142 (179)
T COG0503 120 LIVDDLLATGGTALALI---ELLEQA 142 (179)
T ss_pred EEEecchhcChHHHHHH---HHHHHC
Confidence 37999999999976655 445553
No 85
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=30.02 E-value=1.8e+02 Score=19.78 Aligned_cols=59 Identities=8% Similarity=-0.109 Sum_probs=36.4
Q ss_pred CHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHHHHHHh------ccccHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKI------HGLNLLSNIKNEVANNVL 77 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~------~~~~~~~~lk~~~~~l~~ 77 (86)
|.-||-.++. ..||. ..-+ -| +=|..+|+.+.++.+..... .....-+-++++|..|.+
T Consensus 101 S~LEL~LLIa-~~rl~-~~~~-~~----~NF~~vy~EY~~~~~~~~~~~~~~~~~~~~~k~v~~~a~E~L~~ 165 (203)
T PF14629_consen 101 SVLELCLLIA-AARLI-KGYE-ET----FNFEMVYDEYKKFAKSYNSSSAIVGTIKVWSKPVALKAWEHLLS 165 (203)
T ss_pred CHHHHHHHHH-HHHHH-hccC-CC----ccHHHHHHHHHHHHHhhccccccccccccCCHHHHHHHHHHHHH
Confidence 5567766665 45777 3333 12 23677777777777665443 233445778899988875
No 86
>PF15602 Imm43: Immunity protein 43
Probab=29.78 E-value=2e+02 Score=20.17 Aligned_cols=36 Identities=17% Similarity=0.419 Sum_probs=23.0
Q ss_pred HHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHHHHH
Q 044500 16 VELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGNDLAY 54 (86)
Q Consensus 16 l~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ei~~ 54 (86)
+..+-.+|++|..+..+.+|+.- |..+++....+|+
T Consensus 34 ~~~~E~~v~~~p~~d~~~~~~~~---~~~il~~La~~e~ 69 (171)
T PF15602_consen 34 ADAYERAVRTWPENDPEEMPADD---YVRILNILAHMER 69 (171)
T ss_pred HHHHHHHHhcCCCCCcccCcHHH---HHHHHHHHHHHHH
Confidence 44577888999988777777544 4444444444444
No 87
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=29.68 E-value=93 Score=16.30 Aligned_cols=18 Identities=28% Similarity=0.429 Sum_probs=14.1
Q ss_pred CHHHHHHHHHHHHhcCcc
Q 044500 12 SLDEVELFTDAVKRWDTG 29 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~ 29 (86)
|.+|-..|.+||.....+
T Consensus 5 t~eE~~~l~~~v~~~g~~ 22 (48)
T PF00249_consen 5 TEEEDEKLLEAVKKYGKD 22 (48)
T ss_dssp -HHHHHHHHHHHHHSTTT
T ss_pred CHHHHHHHHHHHHHhCCc
Confidence 789999999999985544
No 88
>cd05128 RasGAP_GAP1_like The GAP1 family of Ras GTPase-activating proteins includes GAP1(m) (or RASA2), GAP1_IP4BP (or RASA3), Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), and Ras GTPase activating-like proteins (RASAL) or RASAL1. The members are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin homology domain that is associated with a Bruton's tyrosine kinase motif. While this domain structure is conserved, a small change in the function of each individual domain and the interaction between domains has a marked effect on the regulation of each protein.
Probab=29.37 E-value=73 Score=24.08 Aligned_cols=24 Identities=13% Similarity=0.050 Sum_probs=20.0
Q ss_pred cccCcCchhHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGNDL 52 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~ei 52 (86)
++++.+|.-++.+++.+.+.+++-
T Consensus 147 ~S~~~~P~~lr~i~~~l~~~v~~k 170 (315)
T cd05128 147 KSSVSCPTVMCDIFYQLRERVGER 170 (315)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHH
Confidence 678899999999999998876553
No 89
>PRK01250 inorganic pyrophosphatase; Provisional
Probab=29.26 E-value=36 Score=23.83 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=32.9
Q ss_pred cccCcCchhHHHHHHHHHHHHHHHH-HHHHHhccccHHHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGNDLA-YYDLKIHGLNLLSNIKNEVANNVLGYF 80 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~ei~-~~~~~~~~~~~~~~lk~~~~~l~~ayl 80 (86)
..++.||..+.---...+.+++..+ .+-.+.+|..-...+++...+-.+.|-
T Consensus 122 ~dl~dl~~~~l~eI~~fF~~YK~le~gk~~~v~g~~~~~~A~~~I~~~~~~y~ 174 (176)
T PRK01250 122 KDVNDLPELLKAQIKHFFEHYKDLEKGKWVKVEGWGGAEEAKAEIVEAIERAK 174 (176)
T ss_pred CChHHCCHHHHHHHHHHHHHhcCCCCCCCEEecCccCHHHHHHHHHHHHHHHh
Confidence 4556677766666666667777765 333334555556777777777777764
No 90
>smart00595 MADF subfamily of SANT domain.
Probab=29.22 E-value=1.2e+02 Score=17.60 Aligned_cols=53 Identities=17% Similarity=0.045 Sum_probs=29.6
Q ss_pred HHHHHHh----cCccccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Q 044500 19 FTDAVKR----WDTGAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFEF 82 (86)
Q Consensus 19 ft~av~R----WD~~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~~ 82 (86)
|+++|++ ||.+ .|+|-.--.+ -....+|+.++.. .+.-++.-|+.|-..|..+
T Consensus 2 LI~~v~~~p~Lwd~~----~~~y~~~~~r--~~aW~~Ia~~l~~-----~~~~~~~kw~~LR~~y~~e 58 (89)
T smart00595 2 LIELVRERPCLWDRR----HPDYRNKEEK--RKAWEEIAEELGL-----SVEECKKRWKNLRDRYRRE 58 (89)
T ss_pred hHHHHHhCccccCCC----ChhhcChHHH--HHHHHHHHHHHCc-----CHHHHHHHHHHHHHHHHHH
Confidence 5666664 7765 3444422111 1245566655422 3556777788887777665
No 91
>cd05135 RasGAP_RASAL Ras GTPase activating-like protein (RASAL) or RASAL1 is a member of the GAP1 family, and a Ca2+ sensor responding in-phase to repetitive Ca2+ signals by associating with the plasma membrane and deactivating Ras. It contains a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL, like Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to receptor-mediated elevation in the concentration of intracellular free Ca2+, a translocation that activates its ability to function as a RasGAP. However, unlike RASAL4, RASAL undergoes an oscillatory translocation to the plasma membrane that occurs in synchrony with repetitive Ca2+ spikes.
Probab=28.56 E-value=83 Score=24.02 Aligned_cols=24 Identities=13% Similarity=0.324 Sum_probs=19.7
Q ss_pred ccccCcCchhHHHHHHHHHHHHHH
Q 044500 28 TGAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 28 ~~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
.++++.+|.-++.+++.++..+.+
T Consensus 163 ~~S~~~~P~~lR~i~~~l~~~v~~ 186 (333)
T cd05135 163 VGSVSQCPPVMRLTFKQLHKRVEE 186 (333)
T ss_pred HhhHHhCCHHHHHHHHHHHHHHHH
Confidence 368889999999999999876654
No 92
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.10 E-value=1.4e+02 Score=20.40 Aligned_cols=54 Identities=9% Similarity=0.057 Sum_probs=42.0
Q ss_pred cccCcCchhHHHHHHHHHHHHHHHHHHHHHhccc----cHHHHHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGL----NLLSNIKNEVANNVLGYFEF 82 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~----~~~~~lk~~~~~l~~ayl~~ 82 (86)
.++..||...-.-|..+..-+.|..+.+...++. ...+-+|++.++|=++++++
T Consensus 91 raiTpl~p~la~Wfyev~~kl~e~g~al~pv~~kP~Yq~LAdvLkrAf~qLdktfl~~ 148 (149)
T COG3092 91 RAITPLPPQLAVWFYEVREKLKEAGQALAPVEEKPTYQALADVLKRAFKQLDKTFLDD 148 (149)
T ss_pred ccCCCCChHHHHHHHHHHHHHHHhCCCCCcCCCCCcHHHHHHHHHHHHHHHHHHHHhc
Confidence 4778899888888888888888888777666554 23477888999998888765
No 93
>KOG1539 consensus WD repeat protein [General function prediction only]
Probab=27.57 E-value=2.8e+02 Score=24.37 Aligned_cols=42 Identities=14% Similarity=0.184 Sum_probs=28.5
Q ss_pred cccCCHHHHHHHHHHHHhc-Ccc-ccCcCchhHHHHHHHHHHHH
Q 044500 8 DTYGSLDEVELFTDAVKRW-DTG-AMVKLPCYMQICYLAMFNFG 49 (86)
Q Consensus 8 D~ygT~eEl~~ft~av~RW-D~~-~~~~Lpeymk~~f~~l~~~~ 49 (86)
|++||++|...|.+.+.+= +.. .-+..--||..+++.=..++
T Consensus 821 d~~~~~~~~~~Fi~~l~~~l~~k~nFEL~qa~~slf~K~H~~~l 864 (910)
T KOG1539|consen 821 DAGETIEEMVIFIKMLTQMLKTKRNFELVQAYMSLFLKSHGLVL 864 (910)
T ss_pred ccCcchHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhhhhhh
Confidence 8999999999999888642 211 22224567777777665555
No 94
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=27.54 E-value=1.9e+02 Score=19.14 Aligned_cols=53 Identities=11% Similarity=0.118 Sum_probs=29.7
Q ss_pred cccCcCchhHHHHHHH-HHH--HHHHHHHHHHHhccc--cHHHHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLA-MFN--FGNDLAYYDLKIHGL--NLLSNIKNEVANNVLGYFE 81 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~-l~~--~~~ei~~~~~~~~~~--~~~~~lk~~~~~l~~ayl~ 81 (86)
.+++.||+--+.+|.- .+. +++||++.+....+. ..+.-+++..++.++-|++
T Consensus 134 ~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~~ 191 (193)
T PRK11923 134 RTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLLQ 191 (193)
T ss_pred HHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3566699877766654 333 588999886554332 2233344444444444444
No 95
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.26 E-value=1.1e+02 Score=20.52 Aligned_cols=49 Identities=12% Similarity=-0.095 Sum_probs=30.7
Q ss_pred cccCcCchhHHHHHHHHH---HHHHHHHHHHHHhccccHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMF---NFGNDLAYYDLKIHGLNLLSNIKNEVANNVLG 78 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~---~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~a 78 (86)
.++.+||+--+.+|.-.+ -+++||++.+.-. .+.+-..+..+-+.+-++
T Consensus 137 ~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis-~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 137 KFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIP-LGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcC-HHHHHHHHHHHHHHHHHH
Confidence 367889998888887644 2799999886543 223334444554444443
No 96
>PRK14985 maltodextrin phosphorylase; Provisional
Probab=27.18 E-value=43 Score=28.76 Aligned_cols=32 Identities=28% Similarity=0.337 Sum_probs=24.4
Q ss_pred HHHHHhcCccccCc-CchhHHHHHHHHHHHHHH
Q 044500 20 TDAVKRWDTGAMVK-LPCYMQICYLAMFNFGND 51 (86)
Q Consensus 20 t~av~RWD~~~~~~-Lpeymk~~f~~l~~~~~e 51 (86)
-+|.++|+++.++. ||.++++++..=....++
T Consensus 352 pealE~w~~~l~~~~Lpr~~~ii~~in~~fl~~ 384 (798)
T PRK14985 352 PEALECWDEKLVKSLLPRHMQIIKEINTRFKTL 384 (798)
T ss_pred hhhhCCCCHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 36889999999998 599999888664444433
No 97
>cd05392 RasGAP_Neurofibromin_like Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In yeast Ras proteins are activated by GEFs, and inhibited by two GAPs, Ira1 and Ira2. Ras proteins activate the cAMP/protein kinase A (PKA) pathway, which controls metabolism, stress resistance, growth, and meiosis. Recent studies showed that the kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with Ira1 and Ira2. Gpb1/2 bind to a conserved C-terminal domain of Ira1/2, and loss of Gpb1/2 results in a destabilization of Ira1 and Ira2, leading to elevated levels of Ras2-GTP and uninhibited cAMP-PKA signaling. Since the Gpb1/2 binding domain on Ira1/2 is conserved in the human neurofibromin prote
Probab=26.81 E-value=1e+02 Score=22.90 Aligned_cols=23 Identities=4% Similarity=0.206 Sum_probs=19.8
Q ss_pred cccCcCchhHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
++++.+|..+|.+++.+++.+.+
T Consensus 141 ~s~~~~P~~lr~i~~~l~~~v~~ 163 (323)
T cd05392 141 SSLDRFPPELREICHHIYEVVSE 163 (323)
T ss_pred HhHHhCCHHHHHHHHHHHHHHHH
Confidence 68889999999999999877664
No 98
>COG0462 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]
Probab=26.66 E-value=19 Score=27.58 Aligned_cols=18 Identities=28% Similarity=0.423 Sum_probs=14.4
Q ss_pred CcccccccccCCHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVEL 18 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ 18 (86)
+++||+-|+.||+=+.-.
T Consensus 218 iiVDDiIdTgGTi~~Aa~ 235 (314)
T COG0462 218 VIVDDIIDTGGTIAKAAK 235 (314)
T ss_pred EEEeccccccHHHHHHHH
Confidence 378999999999766543
No 99
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=26.64 E-value=57 Score=27.23 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=18.2
Q ss_pred ccCCHHHHHHHHHHHHhcCcc
Q 044500 9 TYGSLDEVELFTDAVKRWDTG 29 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~~ 29 (86)
.|||+|+++.|+++-..=.+.
T Consensus 209 ryGtPedfk~fVD~aH~~GIg 229 (628)
T COG0296 209 RYGTPEDFKALVDAAHQAGIG 229 (628)
T ss_pred cCCCHHHHHHHHHHHHHcCCE
Confidence 699999999999999986553
No 100
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=26.62 E-value=80 Score=20.53 Aligned_cols=25 Identities=16% Similarity=0.230 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHhcCccccCcCc
Q 044500 11 GSLDEVELFTDAVKRWDTGAMVKLP 35 (86)
Q Consensus 11 gT~eEl~~ft~av~RWD~~~~~~Lp 35 (86)
-|.+|++.+-+.|+.|...+++..|
T Consensus 102 ls~eele~L~~li~~~~~~~~~~~~ 126 (130)
T TIGR02698 102 LSQTDIEKLEKLLSEKKSTAVEEVP 126 (130)
T ss_pred CCHHHHHHHHHHHHhcccCCCcccc
Confidence 3778888888888888887777665
No 101
>cd05130 RasGAP_Neurofibromin Neurofibromin is the product of the neurofibromatosis type 1 gene (NF1) and shares a region of similarity with catalytic domain of the mammalian p120RasGAP protein and an extended similarity with the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2. Neurofibromin has been shown to function as a GAP (GTPase-activating protein) which inhibits low molecular weight G proteins such as Ras by stimulating their intrinsic GTPase activity. NF1 is a common genetic disorder characterized by various symptoms ranging from predisposition for the development of tumors to learning disability or mental retardation. Loss of neurofibromin activity can be correlated to the increase in Ras-GTP concentration in neurofibromas of NF1 of patients, supporting the notion that unregulated Ras signaling may contribute to their development.
Probab=26.54 E-value=92 Score=23.69 Aligned_cols=23 Identities=4% Similarity=0.189 Sum_probs=19.3
Q ss_pred cccCcCchhHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
++++.+|..+|.+++.+++.+.+
T Consensus 150 ~S~~~~P~~lR~i~~~l~~~v~~ 172 (329)
T cd05130 150 NSSSEFPPQLRSVCHCLYQVVSQ 172 (329)
T ss_pred HhHHhCCHHHHHHHHHHHHHHHH
Confidence 67889999999999999876643
No 102
>PLN02373 soluble inorganic pyrophosphatase
Probab=26.47 E-value=66 Score=22.76 Aligned_cols=53 Identities=9% Similarity=-0.006 Sum_probs=32.9
Q ss_pred cccCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYFE 81 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl~ 81 (86)
..++.||..+.---...+.+++..+.+-.+.+|..-...+++..++-.+.|-+
T Consensus 128 ~dl~Dl~~~~l~~I~~fF~~YK~legK~v~v~g~~~~~~A~~~I~~~~~~y~~ 180 (188)
T PLN02373 128 TDIKELPPHRLAEIRRFFEDYKKNENKEVAVNDFLPAEAAIEAIQYSMDLYAE 180 (188)
T ss_pred CChHHCCHHHHHHHHHHHHHhcccCCCeEEeCCccCHHHHHHHHHHHHHHHHH
Confidence 44556777776666667777777765433445555556666666666666644
No 103
>cd05394 RasGAP_RASA2 RASA2 (or GAP1(m)) is a member of the GAP1 family of Ras GTPase-activating proteins that includes GAP1_IP4BP (or RASA3), CAPRI, and RASAL. In vitro, RASA2 has been shown to bind inositol 1,3,4,5-tetrakisphosphate (IP4), the water soluble inositol head group of the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate (PIP3). In vivo studies also demonstrated that RASA2 binds PIP3, and it is recruited to the plasma membrane following agonist stimulation of PI 3-kinase. Furthermore, the membrane translocation is a consequence of the ability of its pleckstrin homology (PH) domain to bind PIP3.
Probab=26.41 E-value=1e+02 Score=23.50 Aligned_cols=36 Identities=11% Similarity=0.096 Sum_probs=25.6
Q ss_pred HHHHHHHHHh-cCc--cccCcCchhHHHHHHHHHHHHHH
Q 044500 16 VELFTDAVKR-WDT--GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 16 l~~ft~av~R-WD~--~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
.++|...+++ ||- ++.+.+|.-++.+|+.+...+++
T Consensus 130 ~~~L~~~~~~~~~~I~~S~~~~P~~lr~i~~~lr~~v~~ 168 (313)
T cd05394 130 KENLRYYVDKVFFCIVKSSMSCPTVMCDIFYSLRHMAVK 168 (313)
T ss_pred HHHHHHHHHHHHHHHHhCcccCcHHHHHHHHHHHHHHHH
Confidence 3555555553 663 78889999999999888866543
No 104
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.18 E-value=1.3e+02 Score=19.91 Aligned_cols=31 Identities=6% Similarity=-0.115 Sum_probs=22.6
Q ss_pred cccCcCchhHHHHHHHHH-H--HHHHHHHHHHHh
Q 044500 29 GAMVKLPCYMQICYLAMF-N--FGNDLAYYDLKI 59 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~-~--~~~ei~~~~~~~ 59 (86)
.++++||+..+.+|.--+ . .++||++.+...
T Consensus 127 ~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis 160 (189)
T PRK12515 127 ACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIP 160 (189)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence 467889999998885433 2 689999886553
No 105
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=26.03 E-value=94 Score=20.56 Aligned_cols=31 Identities=13% Similarity=0.026 Sum_probs=23.5
Q ss_pred cccCcCchhHHHHHHHHH---HHHHHHHHHHHHh
Q 044500 29 GAMVKLPCYMQICYLAMF---NFGNDLAYYDLKI 59 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~---~~~~ei~~~~~~~ 59 (86)
.+++.||+..|.+|..-+ -+++||++.+...
T Consensus 129 ~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis 162 (182)
T PRK12537 129 RCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAP 162 (182)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence 578889999998776654 3689999886553
No 106
>cd05395 RasGAP_RASA4 Ras GTPase activating-like 4 protein (RASAL4), also known as Ca2+ -promoted Ras inactivator (CAPRI), is a member of the GAP1 family. Members of the GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL4, like RASAL, is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to a receptor-mediated elevation in the concentration of intracellular free Ca2+ ([Ca2+]i). However, unlike RASAL, RASAL4 does not sense oscillations in [Ca2+]i.
Probab=25.88 E-value=88 Score=24.00 Aligned_cols=23 Identities=9% Similarity=0.138 Sum_probs=19.4
Q ss_pred cccCcCchhHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
++++.+|..+|.+++.++..+.+
T Consensus 163 ~S~~~~P~~iR~i~~~l~~~v~~ 185 (337)
T cd05395 163 QSASYCPLVIRAVFRQLFLRVQE 185 (337)
T ss_pred HHHHhCcHHHHHHHHHHHHHHHH
Confidence 67889999999999998877654
No 107
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.66 E-value=1e+02 Score=20.65 Aligned_cols=47 Identities=9% Similarity=-0.051 Sum_probs=28.9
Q ss_pred cccCcCchhHHHHHHHHHH---HHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFN---FGNDLAYYDLKIHGLNLLSNIKNEVANNV 76 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~---~~~ei~~~~~~~~~~~~~~~lk~~~~~l~ 76 (86)
.++++||+..|.+|..-+- ++.||++.+.-.-| .+-.++..+-+.|-
T Consensus 130 ~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~-tVk~~l~RAr~~Lr 179 (189)
T PRK12530 130 ACLNHLPAQQARVFMMREYLELSSEQICQECDISTS-NLHVLLYRARLQLQ 179 (189)
T ss_pred HHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHHHH
Confidence 3667799988888877542 68999888644322 23344444444433
No 108
>smart00323 RasGAP GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
Probab=25.29 E-value=1e+02 Score=23.03 Aligned_cols=24 Identities=8% Similarity=0.021 Sum_probs=20.4
Q ss_pred cccCcCchhHHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGNDL 52 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~ei 52 (86)
++++.+|..+|.+++.++..+.+-
T Consensus 165 ~s~~~~P~~lr~i~~~l~~~~~~k 188 (344)
T smart00323 165 NSSDRLPYGLRDICKQLRQAAEKR 188 (344)
T ss_pred HhHHhCcHHHHHHHHHHHHHHHHH
Confidence 578899999999999998877663
No 109
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=25.25 E-value=1.2e+02 Score=22.94 Aligned_cols=24 Identities=29% Similarity=0.289 Sum_probs=18.2
Q ss_pred CHHHHHHHHHHHHhcCccccCcCchh
Q 044500 12 SLDEVELFTDAVKRWDTGAMVKLPCY 37 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~~Lpey 37 (86)
-+|||+.++.+|.. +++..++|..
T Consensus 155 CPdELeKm~~~Vd~--i~~~~~~~~~ 178 (280)
T KOG2792|consen 155 CPDELEKMSAVVDE--IEAKPGLPPV 178 (280)
T ss_pred ChHHHHHHHHHHHH--HhccCCCCcc
Confidence 47999999999997 5555666544
No 110
>cd05136 RasGAP_DAB2IP The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated signal pathways, and mediates TNF-induced activation of ASK1-JNK signaling pathways. The mechanism by which TNF signaling is coupled to DAB2IP is not known.
Probab=25.04 E-value=94 Score=23.41 Aligned_cols=23 Identities=9% Similarity=0.141 Sum_probs=19.4
Q ss_pred cccCcCchhHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
++++.+|..+|.+|+.+.+.+.+
T Consensus 142 ~S~~~~P~~lR~i~~~lr~~~~~ 164 (309)
T cd05136 142 NSHCVFPAELREVFASWRERCED 164 (309)
T ss_pred HhHHhCCHHHHHHHHHHHHHHhh
Confidence 67889999999999999877654
No 111
>cd05391 RasGAP_p120GAP p120GAP is a negative regulator of Ras that stimulates hydrolysis of bound GTP to GDP. Once the Ras regulator p120GAP, a member of the GAP protein family, is recruited to the membrane, it is transiently immobilized to interact with Ras-GTP. The down regulation of Ras by p120GAP is a critical step in the regulation of many cellular processes, which is disrupted in approximately 30% of human cancers. p120GAP contains SH2, SH3, PH, calcium- and lipid-binding domains, suggesting its involvement in a complex network of cellular interactions in vivo.
Probab=24.95 E-value=99 Score=23.42 Aligned_cols=23 Identities=17% Similarity=0.039 Sum_probs=19.1
Q ss_pred cccCcCchhHHHHHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
++++.+|..+|.+++.+++.+.+
T Consensus 141 ~S~~~~P~~lr~i~~~l~~~v~~ 163 (315)
T cd05391 141 MAAEILPPTLRYIYGCLQKSVQA 163 (315)
T ss_pred HhHHhCCHHHHHHHHHHHHHHHH
Confidence 57889999999999999876643
No 112
>KOG3922 consensus Sulfotransferases [Posttranslational modification, protein turnover, chaperones]
Probab=24.88 E-value=1.5e+02 Score=23.12 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=22.8
Q ss_pred ccCCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHHHHHHHH
Q 044500 9 TYGSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGND 51 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~e 51 (86)
.-|.+|||+.|...+|| .||. +|+.+.+.+..
T Consensus 254 LVGvtEel~d~l~LLE~-------~lPr----fFkGv~~iY~~ 285 (361)
T KOG3922|consen 254 LVGVTEELEDFLSLLER-------YLPR----FFKGVREIYAT 285 (361)
T ss_pred eeeeHHHHHHHHHHHHH-------HhHH----HHHHHHHHHhh
Confidence 45899999999999999 3444 45555555543
No 113
>PLN02293 adenine phosphoribosyltransferase
Probab=24.65 E-value=32 Score=23.91 Aligned_cols=21 Identities=24% Similarity=0.264 Sum_probs=17.2
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
+++||+..+.||+.++....+
T Consensus 129 lIVDDvitTG~T~~~~~~~l~ 149 (187)
T PLN02293 129 LVIDDLIATGGTLCAAINLLE 149 (187)
T ss_pred EEEeccccchHHHHHHHHHHH
Confidence 378999999999988875544
No 114
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=24.60 E-value=1.4e+02 Score=21.32 Aligned_cols=31 Identities=10% Similarity=-0.128 Sum_probs=23.9
Q ss_pred cccCcCchhHHHHHHHHHH---HHHHHHHHHHHh
Q 044500 29 GAMVKLPCYMQICYLAMFN---FGNDLAYYDLKI 59 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~---~~~ei~~~~~~~ 59 (86)
.++++||+..|.+|..-+- +++||++.+...
T Consensus 157 ~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis 190 (244)
T TIGR03001 157 EALAALSERERHLLRLHFVDGLSMDRIGAMYQVH 190 (244)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence 4688899998888777653 799999886554
No 115
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.34 E-value=2.1e+02 Score=18.58 Aligned_cols=31 Identities=3% Similarity=-0.118 Sum_probs=22.0
Q ss_pred cccCcCchhHHHHHHHHH-H--HHHHHHHHHHHh
Q 044500 29 GAMVKLPCYMQICYLAMF-N--FGNDLAYYDLKI 59 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~-~--~~~ei~~~~~~~ 59 (86)
.++..||+..+.+|.-.+ + .++||++.+.-.
T Consensus 115 ~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis 148 (173)
T PRK12522 115 EVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIP 148 (173)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCC
Confidence 367779998887776544 3 589998886543
No 116
>PRK01816 hypothetical protein; Provisional
Probab=24.32 E-value=1e+02 Score=21.07 Aligned_cols=53 Identities=9% Similarity=0.043 Sum_probs=39.2
Q ss_pred ccCcCchhHHHHHHHHHHHHHHHHHHHHHhccc----cHHHHHHHHHHHHHHHHHHH
Q 044500 30 AMVKLPCYMQICYLAMFNFGNDLAYYDLKIHGL----NLLSNIKNEVANNVLGYFEF 82 (86)
Q Consensus 30 ~~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~----~~~~~lk~~~~~l~~ayl~~ 82 (86)
+...||..+..-|..+.+-+.+.+..+...+++ +...-++.+++.+=++|+++
T Consensus 86 a~tpLPpsL~~Wy~el~~Kl~~~g~~~~p~~~~P~Y~dLA~lLk~Af~~ld~~f~~~ 142 (143)
T PRK01816 86 SVTPLPPALLNWFYEVREKLQEAGQALAPVEGKPTYQALADLLKRAFKQLDKTFLDD 142 (143)
T ss_pred cCCCCChHHHHHHHHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHcCHHHHhh
Confidence 456689999888888888888877665543322 23477899999999998865
No 117
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=24.24 E-value=1.6e+02 Score=26.15 Aligned_cols=41 Identities=12% Similarity=0.236 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHhc-CccccCcCchh-HHHHHHHHHHHHHH
Q 044500 11 GSLDEVELFTDAVKRW-DTGAMVKLPCY-MQICYLAMFNFGND 51 (86)
Q Consensus 11 gT~eEl~~ft~av~RW-D~~~~~~Lpey-mk~~f~~l~~~~~e 51 (86)
+..++|+.|.++...| +-+.-+.+|.. .=....-+.+.+..
T Consensus 1043 ~~w~~Lk~F~~~~~~w~~~~~~~~lP~e~~~~~l~~l~~~l~~ 1085 (1201)
T PF12128_consen 1043 EFWKPLKQFSDEYELWRSSDGSRELPSEEYVNALRELLDILPS 1085 (1201)
T ss_pred ccHHHHHHHHHHHHHHhcccCcccCCCHHHHHHHHHHHHHHhh
Confidence 5789999999999999 77788889855 43444444444443
No 118
>PRK01259 ribose-phosphate pyrophosphokinase; Provisional
Probab=24.19 E-value=29 Score=25.92 Aligned_cols=25 Identities=36% Similarity=0.493 Sum_probs=18.8
Q ss_pred CcccccccccCCHHHHHHHHHHHHhcCc
Q 044500 1 MANDDMYDTYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~av~RWD~ 28 (86)
+++||+.|+.||+.+.. +.+++...
T Consensus 212 liVDDii~TG~T~~~a~---~~l~~~Ga 236 (309)
T PRK01259 212 ILVDDMIDTAGTLCKAA---EALKERGA 236 (309)
T ss_pred EEEecccCcHHHHHHHH---HHHHccCC
Confidence 37899999999987764 55666544
No 119
>TIGR02093 P_ylase glycogen/starch/alpha-glucan phosphorylases. This family consists of phosphorylases. Members use phosphate to break alpha 1,4 linkages between pairs of glucose residues at the end of long glucose polymers, releasing alpha-D-glucose 1-phosphate. The nomenclature convention is to preface the name according to the natural substrate, as in glycogen phosphorylase, starch phosphorylase, maltodextrin phosphorylase, etc. Name differences among these substrates reflect differences in patterns of branching with alpha 1,6 linkages. Members include allosterically regulated and unregulated forms. A related family, TIGR02094, contains examples known to act well on particularly small alpha 1,4 glucans, as may be found after import from exogenous sources.
Probab=24.18 E-value=26 Score=29.99 Aligned_cols=25 Identities=28% Similarity=0.606 Sum_probs=21.4
Q ss_pred HHHHHhcCccccCc-CchhHHHHHHH
Q 044500 20 TDAVKRWDTGAMVK-LPCYMQICYLA 44 (86)
Q Consensus 20 t~av~RWD~~~~~~-Lpeymk~~f~~ 44 (86)
-+|.++|+++.++. ||.+++|++..
T Consensus 347 pealE~wp~~l~~~~Lpr~~~iI~~I 372 (794)
T TIGR02093 347 PEALEKWPVDLFQKLLPRHLEIIYEI 372 (794)
T ss_pred hHHhCCcCHHHHHHHHhHHHHHHHHH
Confidence 46899999999998 89999988755
No 120
>PLN02440 amidophosphoribosyltransferase
Probab=24.08 E-value=29 Score=27.63 Aligned_cols=19 Identities=11% Similarity=0.008 Sum_probs=15.9
Q ss_pred CcccccccccCCHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELF 19 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~f 19 (86)
+++||++++..|+.++...
T Consensus 344 lLVDDiittGtTl~~i~~~ 362 (479)
T PLN02440 344 VVVDDSIVRGTTSSKIVRM 362 (479)
T ss_pred EEEeceeCcHHHHHHHHHH
Confidence 4799999999999887643
No 121
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=24.07 E-value=1.3e+02 Score=18.13 Aligned_cols=28 Identities=4% Similarity=-0.121 Sum_probs=21.4
Q ss_pred cCcCchhHHHHHHHHHH----HHHHHHHHHHH
Q 044500 31 MVKLPCYMQICYLAMFN----FGNDLAYYDLK 58 (86)
Q Consensus 31 ~~~Lpeymk~~f~~l~~----~~~ei~~~~~~ 58 (86)
++.||+..+-.|.-... ++.||++.+.-
T Consensus 13 l~~l~~~~r~af~L~R~~eGlS~kEIAe~LGI 44 (73)
T TIGR03879 13 LTWVDSLAEAAAALAREEAGKTASEIAEELGR 44 (73)
T ss_pred HhcCCHHHHHHHHHHHHHcCCCHHHHHHHHCc
Confidence 56799999988877643 68888887544
No 122
>smart00394 RIIa RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).
Probab=23.87 E-value=1.2e+02 Score=15.45 Aligned_cols=30 Identities=13% Similarity=0.042 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 044500 47 NFGNDLAYYDLKIHGLNLLSNIKNEVANNV 76 (86)
Q Consensus 47 ~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~ 76 (86)
..++++..++...+..+++++..+-+.++.
T Consensus 5 ~~L~~~~~~vl~~qP~d~~~f~~~yF~kL~ 34 (38)
T smart00394 5 ALLEDLTVEVLRAQPSDLVQFAADYFEKLE 34 (38)
T ss_pred HHHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 345566667777788888877777765554
No 123
>PLN00196 alpha-amylase; Provisional
Probab=23.86 E-value=88 Score=24.57 Aligned_cols=20 Identities=15% Similarity=0.297 Sum_probs=17.4
Q ss_pred ccCCHHHHHHHHHHHHhcCc
Q 044500 9 TYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~ 28 (86)
.|||.+|++.|+++.++=.+
T Consensus 87 ~fGt~~elk~Lv~~aH~~GI 106 (428)
T PLN00196 87 KYGNEAQLKSLIEAFHGKGV 106 (428)
T ss_pred cCCCHHHHHHHHHHHHHCCC
Confidence 48999999999999997554
No 124
>PF11794 HpaB_N: 4-hydroxyphenylacetate 3-hydroxylase N terminal; InterPro: IPR024674 This domain is found in the N terminus of HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. The domain is also found in pyoverdin chromophore biosynthetic protein (PvcC), which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=23.52 E-value=2.5e+02 Score=20.83 Aligned_cols=46 Identities=17% Similarity=0.274 Sum_probs=32.9
Q ss_pred ccCCHHHHHHHHHHHHhcCc---cccCcCchhHHHHHHHHHHHHHHHHH
Q 044500 9 TYGSLDEVELFTDAVKRWDT---GAMVKLPCYMQICYLAMFNFGNDLAY 54 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~---~~~~~Lpeymk~~f~~l~~~~~ei~~ 54 (86)
.--|.|+|..=-++++.|-- ..+..-|+||-.+..+++..-+.++.
T Consensus 72 ~p~s~eDL~~rr~~~~~~a~~t~G~~gR~pD~~n~~~~~~~~~~~~~~~ 120 (264)
T PF11794_consen 72 IPRSKEDLVKRRKAIREWARYTGGCMGRSPDYMNALLAGLAAAADFFGT 120 (264)
T ss_dssp ---SHHHHHHHHHHHHHHHHHCCC--STCHHHHHHHHHHHHHCCHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHcCceeecChhHHHHHHHHHHHHHHHHhH
Confidence 44589999999999999954 56666899998888888876555544
No 125
>PF05772 NinB: NinB protein; InterPro: IPR008711 The ninR region of Bacteriophage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of Escherichia coli, respectively, operate on phage lambda []. Genetic recombination in phage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, NinB (Orf), which participates in the early stages of recombination by supplying a function equivalent to the E. coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. NinB has two structural domains with unusual folds, and exists as an intertwined dimer [].; PDB: 1PC6_B.
Probab=22.92 E-value=2e+02 Score=19.01 Aligned_cols=31 Identities=10% Similarity=-0.065 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHH
Q 044500 46 FNFGNDLAYYDLKIHGLNLLSNIKNEVANNVLGYF 80 (86)
Q Consensus 46 ~~~~~ei~~~~~~~~~~~~~~~lk~~~~~l~~ayl 80 (86)
...+.+|++.+.-. |+ .+-.+.||+++.+-+
T Consensus 44 wa~l~dIs~qv~~~-G~---k~~~e~WK~~~~~~~ 74 (127)
T PF05772_consen 44 WAMLGDISRQVEWN-GR---KLDPEDWKELFTAAF 74 (127)
T ss_dssp HHHHHHHHHH--BT-TB------HHHHHHHHHHHH
T ss_pred HHHHHHHHHHhHhc-Cc---cCCHHHHHHHHHHHH
Confidence 34678888886553 43 345588999998877
No 126
>PF14572 Pribosyl_synth: Phosphoribosyl synthetase-associated domain; PDB: 2H07_B 2H06_B 3S5J_B 2HCR_A 3EFH_A 2H08_A 1DKR_B 1DKU_B 1IBS_B 2JI4_A ....
Probab=22.84 E-value=16 Score=25.90 Aligned_cols=17 Identities=35% Similarity=0.462 Sum_probs=13.7
Q ss_pred CcccccccccCCHHHHH
Q 044500 1 MANDDMYDTYGSLDEVE 17 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~ 17 (86)
+++||+-|+.||+-..-
T Consensus 87 IIvDDiIdtg~Tl~~aA 103 (184)
T PF14572_consen 87 IIVDDIIDTGGTLIKAA 103 (184)
T ss_dssp EEEEEEESSTHHHHHHH
T ss_pred eeecccccchHHHHHHH
Confidence 47899999999976654
No 127
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=22.74 E-value=1.3e+02 Score=17.39 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.1
Q ss_pred CcC-chhHHHHHHHHHHHHHHHHHH
Q 044500 32 VKL-PCYMQICYLAMFNFGNDLAYY 55 (86)
Q Consensus 32 ~~L-peymk~~f~~l~~~~~ei~~~ 55 (86)
.++ |++++-+|..+++....++.+
T Consensus 56 ~~l~~~~i~~if~~ii~~s~~~Q~~ 80 (81)
T PF01817_consen 56 GGLDPEFIERIFRAIIEESRAIQYE 80 (81)
T ss_dssp TTSEHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 456 499999999999988777654
No 128
>PRK06827 phosphoribosylpyrophosphate synthetase; Provisional
Probab=22.62 E-value=36 Score=26.52 Aligned_cols=17 Identities=29% Similarity=0.405 Sum_probs=14.0
Q ss_pred CcccccccccCCHHHHH
Q 044500 1 MANDDMYDTYGSLDEVE 17 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~ 17 (86)
+++||+.|+.||+-+..
T Consensus 268 IIVDDII~TG~Tl~~aa 284 (382)
T PRK06827 268 LIVDDMIASGGSMIDAA 284 (382)
T ss_pred EEEeCCcCcHHHHHHHH
Confidence 47899999999977654
No 129
>PF09346 SMI1_KNR4: SMI1 / KNR4 family (SUKH-1); InterPro: IPR018958 Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [, ]. Yeast members of this family are involved in the regulation of cell wall assembly. Saccharomyces cerevisiae (Baker's yeast) protein KNR4 (SMI1) has a regulatory role in chitin deposition and in cell wall assembly []. It was originally identified as a regulator of chitin synthase expression (acting as a repressor) [] and of 1,3-beta-glucan synthase levels []. It was shown to localise in patches at presumptive bud sites in unbudded cells and at the incipient bud site during bud emergence []. KNR4 is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with BCK2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [, ]. PKC1 plays an essential role in cell wall integrity and cell proliferation through a bifurcated PKC1/mitogen-activated protein (MAP) kinase pathway. KNR4 also interacts with the tyrosine-tRNA synthetase protein encoded by TYS1 and is involved in sporulation process []. Note: previously reported evidence that KNR4 may interact with nuclear matrix-association region [] may be due to an artefact [].; PDB: 3D5P_A 2ICG_A.
Probab=22.38 E-value=1.2e+02 Score=17.93 Aligned_cols=28 Identities=11% Similarity=0.158 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHHHhcCccccCcCchhHHHHHHHH
Q 044500 11 GSLDEVELFTDAVKRWDTGAMVKLPCYMQICYLAM 45 (86)
Q Consensus 11 gT~eEl~~ft~av~RWD~~~~~~Lpeymk~~f~~l 45 (86)
.|.+|++.|-+.+.- .||+.+|-+++..
T Consensus 2 ~t~~~I~~~E~~lg~-------~LP~~yk~fl~~~ 29 (130)
T PF09346_consen 2 ATEEEIQELEEKLGV-------RLPDDYKEFLKEH 29 (130)
T ss_dssp --HHHHHHHHHHHTS----------HHHHHHHH--
T ss_pred CCHHHHHHHHHHhCC-------CCcHHHHHHHHhh
Confidence 366777666554432 5999998888754
No 130
>PRK14986 glycogen phosphorylase; Provisional
Probab=22.07 E-value=72 Score=27.52 Aligned_cols=23 Identities=30% Similarity=0.663 Sum_probs=20.2
Q ss_pred HHHHHhcCccccCc-CchhHHHHH
Q 044500 20 TDAVKRWDTGAMVK-LPCYMQICY 42 (86)
Q Consensus 20 t~av~RWD~~~~~~-Lpeymk~~f 42 (86)
-+|.++|+++.++. ||.+++|++
T Consensus 363 pealE~w~~~l~~~~lpr~l~Ii~ 386 (815)
T PRK14986 363 SEALETWPVDMLGKILPRHLQIIF 386 (815)
T ss_pred hHHhCcCCHHHHHHHccHhhhHHH
Confidence 36889999999998 699999988
No 131
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=21.99 E-value=2.1e+02 Score=17.86 Aligned_cols=30 Identities=17% Similarity=-0.051 Sum_probs=22.6
Q ss_pred cccCcCchhHHHHHHHHHH---HHHHHHHHHHH
Q 044500 29 GAMVKLPCYMQICYLAMFN---FGNDLAYYDLK 58 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~~---~~~ei~~~~~~ 58 (86)
.++++||+..|.+|.--+- +++||++.+..
T Consensus 103 ~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~i 135 (142)
T TIGR03209 103 DLISILPNKQKKIIYMKFFEDMKEIDIAKKLHI 135 (142)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc
Confidence 4788899999988777542 78999887543
No 132
>PF04033 DUF365: Domain of unknown function (DUF365); InterPro: IPR007176 This is an archaeal family of unknown function.; PDB: 2KKU_A.
Probab=21.95 E-value=61 Score=20.68 Aligned_cols=23 Identities=26% Similarity=0.758 Sum_probs=17.8
Q ss_pred cccccC-----CHHHHHHHHHHHHhcCc
Q 044500 6 MYDTYG-----SLDEVELFTDAVKRWDT 28 (86)
Q Consensus 6 ~yD~yg-----T~eEl~~ft~av~RWD~ 28 (86)
++-.|| |.||++.....=+||.-
T Consensus 32 i~ekygd~lFLT~eE~r~Y~~~~~Rwg~ 59 (97)
T PF04033_consen 32 IIEKYGDRLFLTKEELRKYERSRKRWGS 59 (97)
T ss_dssp HHHHTSTTBSS-HHHHHHHHHHHHHTSS
T ss_pred HHHHhCcceecCHHHHHHHHhhHHhhcc
Confidence 444555 99999999999999975
No 133
>PF08264 Anticodon_1: Anticodon-binding domain of tRNA; InterPro: IPR013155 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found valyl, leucyl and isoleucyl tRNA synthetases. It binds to the anticodon of the tRNA.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 4DLP_A 1RQG_A 4ARI_A 4AQ7_D 4ARC_A 4AS1_A 1IVS_B 1GAX_B 2CT8_B 2CSX_A ....
Probab=21.89 E-value=2.2e+02 Score=17.93 Aligned_cols=6 Identities=33% Similarity=0.446 Sum_probs=2.5
Q ss_pred HHHHHh
Q 044500 20 TDAVKR 25 (86)
Q Consensus 20 t~av~R 25 (86)
+++++.
T Consensus 16 ~~~~e~ 21 (153)
T PF08264_consen 16 TEAYEN 21 (153)
T ss_dssp HHHHHT
T ss_pred HHHHHC
Confidence 344444
No 134
>PRK09448 DNA starvation/stationary phase protection protein Dps; Provisional
Probab=21.79 E-value=1.3e+02 Score=20.29 Aligned_cols=38 Identities=11% Similarity=0.161 Sum_probs=31.5
Q ss_pred hcCccccCcC--chhHHHHHHHHHHHHHHHHHHHHHhccc
Q 044500 25 RWDTGAMVKL--PCYMQICYLAMFNFGNDLAYYDLKIHGL 62 (86)
Q Consensus 25 RWD~~~~~~L--peymk~~f~~l~~~~~ei~~~~~~~~~~ 62 (86)
-|++.+.... -+.+.-.|..+..-++++++.+...||.
T Consensus 45 hW~v~G~~f~~lH~~lee~~~~~~~~~D~iAERi~~lGg~ 84 (162)
T PRK09448 45 HWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGV 84 (162)
T ss_pred hhhccCCCHHHHHHHHHHHHHHHHHHhHHHHHHHHHcCCC
Confidence 6999888764 4778888889999999999998887775
No 135
>TIGR02402 trehalose_TreZ malto-oligosyltrehalose trehalohydrolase. Members of this family are the trehalose biosynthetic enzyme malto-oligosyltrehalose trehalohydrolase, formally known as 4-alpha-D-{(1-4)-alpha-D-glucano}trehalose trehalohydrolase (EC 3.2.1.141). It is the TreZ protein of the TreYZ pathway for trehalose biosynthesis, and alternative to the OtsAB system.
Probab=21.75 E-value=82 Score=25.40 Aligned_cols=20 Identities=25% Similarity=0.488 Sum_probs=17.8
Q ss_pred ccCCHHHHHHHHHHHHhcCc
Q 044500 9 TYGSLDEVELFTDAVKRWDT 28 (86)
Q Consensus 9 ~ygT~eEl~~ft~av~RWD~ 28 (86)
.|||.+|++.|+++..+=.+
T Consensus 155 ~~G~~~e~k~lV~~aH~~Gi 174 (542)
T TIGR02402 155 AYGGPDDLKALVDAAHGLGL 174 (542)
T ss_pred ccCCHHHHHHHHHHHHHCCC
Confidence 68999999999999998655
No 136
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=21.72 E-value=1.4e+02 Score=23.12 Aligned_cols=30 Identities=17% Similarity=0.192 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCccccCcCchhHHHHHHHHHHHHH
Q 044500 17 ELFTDAVKRWDTGAMVKLPCYMQICYLAMFNFGN 50 (86)
Q Consensus 17 ~~ft~av~RWD~~~~~~Lpeymk~~f~~l~~~~~ 50 (86)
..|.++|. ++++.+|-.+|.+.+.++....
T Consensus 131 ~~fl~~I~----~S~~~~P~~iR~ick~i~~~~~ 160 (360)
T cd05133 131 DKFLSAIV----SSVDKIPYGMRFIAKVLKDSLH 160 (360)
T ss_pred HHHHHHHH----HhHHhCCHHHHHHHHHHHHHHH
Confidence 34555553 5788999999999999887653
No 137
>COG0634 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=21.66 E-value=52 Score=23.28 Aligned_cols=21 Identities=19% Similarity=0.240 Sum_probs=17.7
Q ss_pred CcccccccccCCHHHHHHHHH
Q 044500 1 MANDDMYDTYGSLDEVELFTD 21 (86)
Q Consensus 1 tv~DD~yD~ygT~eEl~~ft~ 21 (86)
.++||+.|+.=|+..++.+..
T Consensus 97 LiVeDIiDsG~TLs~i~~~l~ 117 (178)
T COG0634 97 LIVEDIIDSGLTLSKVRDLLK 117 (178)
T ss_pred EEEecccccChhHHHHHHHHH
Confidence 378999999999999887755
No 138
>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=21.54 E-value=1.1e+02 Score=24.24 Aligned_cols=20 Identities=15% Similarity=0.233 Sum_probs=17.3
Q ss_pred cCCHHHHHHHHHHHHhcCcc
Q 044500 10 YGSLDEVELFTDAVKRWDTG 29 (86)
Q Consensus 10 ygT~eEl~~ft~av~RWD~~ 29 (86)
.|+.|.+..|.++||++.+-
T Consensus 317 l~~~e~l~~FC~~iQ~~sPV 336 (403)
T PF06838_consen 317 LGSPEKLIAFCQGIQAASPV 336 (403)
T ss_dssp -SSHHHHHHHHHHHHHTSSS
T ss_pred CCCHHHHHHHHHHHHhcCCc
Confidence 58999999999999998763
No 139
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.71 E-value=2e+02 Score=21.44 Aligned_cols=42 Identities=14% Similarity=0.222 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHhcCccccC-cCchh-HHHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDTGAMV-KLPCY-MQICYLAMFNFGNDLA 53 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~-~Lpey-mk~~f~~l~~~~~ei~ 53 (86)
.-.|++.|+.+++.|....+. +.|+. ..-++.+.++.++.++
T Consensus 91 d~~~l~~fka~~~kt~~~L~~~gf~e~t~~dFh~~Fievle~v~ 134 (256)
T KOG3991|consen 91 DRAELQKFKAAVEKTKETLVLLGFPEFTFEDFHDTFIEVLEDVE 134 (256)
T ss_pred chHHHHHHHHHHHhhhHHHHHcCCCccchhhHHHHHHHHHHHHc
Confidence 356899999999999987554 36764 3344444455555544
No 140
>PF02416 MttA_Hcf106: mttA/Hcf106 family; InterPro: IPR003369 Members of this protein family are involved in a sec-independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts []. Members of this family in Escherichia coli are involved in export of redox proteins with a "twin arginine" leader motif (S/T-R-R-X-F-L-K) []. This sec-independent pathway is termed TAT for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export.; GO: 0008565 protein transporter activity, 0015031 protein transport; PDB: 2L16_A.
Probab=20.70 E-value=1.4e+02 Score=16.64 Aligned_cols=25 Identities=16% Similarity=-0.120 Sum_probs=14.6
Q ss_pred cCcCchhHHHHH---HHHHHHHHHHHHH
Q 044500 31 MVKLPCYMQICY---LAMFNFGNDLAYY 55 (86)
Q Consensus 31 ~~~Lpeymk~~f---~~l~~~~~ei~~~ 55 (86)
.+.||+.+|-+= +.+-+..++..++
T Consensus 19 p~kLP~~~r~lG~~ir~fk~~~~~~~~~ 46 (53)
T PF02416_consen 19 PKKLPELARSLGKAIREFKKAINEAKEE 46 (53)
T ss_dssp TTTHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 356888888763 3444455555554
No 141
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.64 E-value=2.7e+02 Score=18.55 Aligned_cols=30 Identities=7% Similarity=-0.057 Sum_probs=22.6
Q ss_pred ccCcCchhHHHHHHHHH---HHHHHHHHHHHHh
Q 044500 30 AMVKLPCYMQICYLAMF---NFGNDLAYYDLKI 59 (86)
Q Consensus 30 ~~~~Lpeymk~~f~~l~---~~~~ei~~~~~~~ 59 (86)
++.+||+..|-+|...+ -.++||++++...
T Consensus 128 ~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis 160 (188)
T TIGR02943 128 CLYHLPEQTARVFMMREVLGFESDEICQELEIS 160 (188)
T ss_pred HHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCC
Confidence 56679998888887765 4799999886543
No 142
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=20.47 E-value=1.8e+02 Score=16.54 Aligned_cols=64 Identities=11% Similarity=-0.020 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHHhcCccccCc-CchhHHHHHHHHHHHHHHHHHHHHHhccc-cHHHHHHHHHHHHHHH
Q 044500 12 SLDEVELFTDAVKRWDTGAMVK-LPCYMQICYLAMFNFGNDLAYYDLKIHGL-NLLSNIKNEVANNVLG 78 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~~~~~~-Lpeymk~~f~~l~~~~~ei~~~~~~~~~~-~~~~~lk~~~~~l~~a 78 (86)
|.+|...|.+.|++= .+.+.+ -+... . -..--..-.+|...+-..++. -...-+++-|.++...
T Consensus 6 s~~E~~~Lv~~v~~~-~~il~~k~~~~~-~-~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 6 SEEEKEILVELVEKH-KDILENKFSDSV-S-NKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CHHHHHHHHHHHHHh-HHHHhcccccHH-H-HHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 789999999998872 121211 11111 0 111133455555555554442 2357788888887654
No 143
>KOG2669 consensus Regulator of nuclear mRNA [RNA processing and modification]
Probab=20.14 E-value=2.3e+02 Score=21.83 Aligned_cols=43 Identities=9% Similarity=-0.059 Sum_probs=32.9
Q ss_pred cCcCchhHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHH
Q 044500 31 MVKLPCYMQICYLAMFNFGNDLAYYDLKIHGLNLLSNIKNEVAN 74 (86)
Q Consensus 31 ~~~Lpeymk~~f~~l~~~~~ei~~~~~~~~~~~~~~~lk~~~~~ 74 (86)
....|++.+-|+..+.+.+..+.++.... +...+..+.++|++
T Consensus 71 krk~~ef~~ef~~v~~~a~~~i~~~~~~~-~k~~l~Rl~nIw~e 113 (325)
T KOG2669|consen 71 KRKGPEFVDEFWPVVLKAFAHIVEETDVK-CKKKLGRLINIWEE 113 (325)
T ss_pred hhcCchhHHHHHHHHHHHHHHHHHhcchh-hhHHHHHHHHHHHH
Confidence 45689999999999999999988774443 34557777888875
No 144
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=20.10 E-value=1.7e+02 Score=19.13 Aligned_cols=31 Identities=10% Similarity=-0.205 Sum_probs=23.3
Q ss_pred cccCcCchhHHHHHHHHH---HHHHHHHHHHHHh
Q 044500 29 GAMVKLPCYMQICYLAMF---NFGNDLAYYDLKI 59 (86)
Q Consensus 29 ~~~~~Lpeymk~~f~~l~---~~~~ei~~~~~~~ 59 (86)
.+++.||+..+.+|.-.+ -+++||++++...
T Consensus 96 ~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis 129 (170)
T TIGR02959 96 PMIKELPDEYREAIRLTELEGLSQQEIAEKLGLS 129 (170)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence 367789999988887654 2689999887553
No 145
>KOG2460 consensus Signal recognition particle, subunit Srp68 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.04 E-value=2.3e+02 Score=23.64 Aligned_cols=17 Identities=29% Similarity=0.429 Sum_probs=14.8
Q ss_pred CHHHHHHHHHHHHhcCc
Q 044500 12 SLDEVELFTDAVKRWDT 28 (86)
Q Consensus 12 T~eEl~~ft~av~RWD~ 28 (86)
+-+||+.||++.+|||.
T Consensus 128 ~A~eL~~~~q~~e~~Da 144 (593)
T KOG2460|consen 128 HADELVNLTQNEERFDA 144 (593)
T ss_pred HHHHHHHHHhhHhhhhh
Confidence 35799999999999994
No 146
>PF07477 Glyco_hydro_67C: Glycosyl hydrolase family 67 C-terminus; InterPro: IPR011099 Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C-terminal region of alpha-glucuronidase, which is mainly alpha-helical. It wraps around the catalytic domain (IPR011100 from INTERPRO), making additional interactions both with the N-terminal domain (IPR005154 from INTERPRO) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer [].; GO: 0046559 alpha-glucuronidase activity, 0045493 xylan catabolic process, 0005576 extracellular region; PDB: 1GQL_A 1GQI_B 1GQJ_B 1GQK_A 1H41_A 1MQR_A 1K9F_A 1K9E_A 1L8N_A 1K9D_A ....
Probab=20.01 E-value=3.6e+02 Score=19.75 Aligned_cols=14 Identities=21% Similarity=0.273 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHH
Q 044500 70 NEVANNVLGYFEFF 83 (86)
Q Consensus 70 ~~~~~l~~ayl~~~ 83 (86)
+.|.+.|..|++.+
T Consensus 200 ~~WRD~~~~YF~~~ 213 (225)
T PF07477_consen 200 KWWRDACNTYFQRF 213 (225)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 44889999888765
Done!