Query psy8853
Match_columns 242
No_of_seqs 119 out of 1047
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 21:02:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8853.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8853hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0217 Uncharacterized conser 100.0 8E-98 2E-102 650.5 26.5 238 1-241 1-240 (241)
2 PRK00110 hypothetical protein; 100.0 8.1E-94 1.8E-98 635.2 28.1 238 1-242 1-239 (245)
3 TIGR01033 DNA-binding regulato 100.0 5.8E-92 1.3E-96 621.5 28.0 236 1-239 1-238 (238)
4 PRK12378 hypothetical protein; 100.0 6E-90 1.3E-94 607.0 27.1 232 2-239 1-235 (235)
5 PF01709 Transcrip_reg: Transc 100.0 1.6E-88 3.5E-93 598.8 22.5 232 5-239 1-234 (234)
6 KOG2972|consensus 100.0 3E-71 6.5E-76 483.1 20.1 235 1-240 29-275 (276)
7 PRK07562 ribonucleotide-diphos 98.7 1.6E-08 3.5E-13 105.8 7.1 69 7-75 296-371 (1220)
8 cd04888 ACT_PheB-BS C-terminal 93.5 0.23 4.9E-06 35.1 5.4 64 172-235 5-73 (76)
9 PF03927 NapD: NapD protein; 91.9 0.16 3.5E-06 37.7 2.9 67 171-239 7-77 (79)
10 PF13291 ACT_4: ACT domain; PD 88.4 1.2 2.6E-05 32.1 5.0 65 172-236 9-80 (80)
11 PRK10553 assembly protein for 86.7 1.7 3.6E-05 33.1 5.0 67 171-240 9-81 (87)
12 cd04877 ACT_TyrR N-terminal AC 86.5 2.5 5.3E-05 30.2 5.7 59 177-236 10-69 (74)
13 PF09186 DUF1949: Domain of un 86.1 1.1 2.4E-05 29.9 3.4 52 174-225 1-52 (56)
14 cd04878 ACT_AHAS N-terminal AC 85.2 3.9 8.6E-05 27.6 6.0 57 177-234 10-71 (72)
15 PRK04435 hypothetical protein; 83.6 3.7 8E-05 33.8 6.2 63 172-235 74-142 (147)
16 cd04887 ACT_MalLac-Enz ACT_Mal 80.6 8 0.00017 26.9 6.2 58 175-232 7-68 (74)
17 cd04881 ACT_HSDH-Hom ACT_HSDH_ 80.1 6.4 0.00014 27.0 5.6 59 177-235 10-73 (79)
18 COG2605 Predicted kinase relat 78.9 5.5 0.00012 37.1 6.1 46 148-193 267-316 (333)
19 PRK15385 magnesium transport p 78.6 8 0.00017 34.4 6.9 68 171-238 144-222 (225)
20 cd04876 ACT_RelA-SpoT ACT dom 77.3 9.5 0.00021 24.6 5.5 61 174-234 5-69 (71)
21 PF01037 AsnC_trans_reg: AsnC 75.3 6.5 0.00014 27.3 4.5 68 172-240 1-72 (74)
22 COG3062 NapD Uncharacterized p 75.3 6.1 0.00013 30.5 4.5 66 172-239 11-80 (94)
23 TIGR00257 IMPACT_YIGZ uncharac 72.8 17 0.00038 31.7 7.4 72 150-225 118-192 (204)
24 cd04874 ACT_Af1403 N-terminal 72.2 14 0.0003 24.9 5.4 57 177-235 10-70 (72)
25 PRK11152 ilvM acetolactate syn 68.6 5.4 0.00012 29.5 2.8 61 174-234 10-73 (76)
26 PRK09977 putative Mg(2+) trans 67.5 10 0.00022 33.5 4.8 65 171-235 146-213 (215)
27 cd04879 ACT_3PGDH-like ACT_3PG 67.1 8.2 0.00018 25.8 3.4 57 176-235 8-69 (71)
28 PRK06737 acetolactate synthase 66.8 11 0.00024 27.8 4.2 61 176-236 11-75 (76)
29 PRK11568 hypothetical protein; 66.7 29 0.00062 30.4 7.4 73 151-225 119-192 (204)
30 PF13601 HTH_34: Winged helix 65.8 6.9 0.00015 28.9 2.9 52 176-227 26-78 (80)
31 PF00403 HMA: Heavy-metal-asso 65.8 21 0.00045 24.1 5.2 43 152-194 15-62 (62)
32 PRK08577 hypothetical protein; 65.3 15 0.00033 29.4 5.1 57 178-235 67-130 (136)
33 cd04901 ACT_3PGDH C-terminal A 63.3 7.7 0.00017 26.5 2.6 56 177-235 9-67 (69)
34 cd04903 ACT_LSD C-terminal ACT 63.1 11 0.00024 25.2 3.5 56 177-235 9-69 (71)
35 PF13710 ACT_5: ACT domain; PD 62.6 7.1 0.00015 27.4 2.4 57 178-234 3-63 (63)
36 TIGR02717 AcCoA-syn-alpha acet 60.5 29 0.00062 33.6 6.9 139 94-238 205-378 (447)
37 PF01037 AsnC_trans_reg: AsnC 60.3 7.4 0.00016 27.0 2.1 28 208-236 3-30 (74)
38 cd04882 ACT_Bt0572_2 C-termina 59.8 36 0.00079 22.6 5.6 27 100-126 2-28 (65)
39 PF09413 DUF2007: Domain of un 59.1 19 0.00041 25.0 4.1 54 174-227 5-67 (67)
40 PRK08178 acetolactate synthase 58.2 19 0.00042 27.9 4.3 61 176-238 17-82 (96)
41 PF01842 ACT: ACT domain; Int 57.3 9.6 0.00021 25.5 2.3 29 177-205 10-38 (66)
42 PF14257 DUF4349: Domain of un 56.4 34 0.00074 30.4 6.3 28 100-127 54-81 (262)
43 PRK02472 murD UDP-N-acetylmura 56.1 26 0.00056 33.2 5.7 60 48-116 280-340 (447)
44 COG3453 Uncharacterized protei 55.9 30 0.00065 28.2 5.1 74 144-226 13-87 (130)
45 PF07942 N2227: N2227-like pro 55.7 18 0.00038 33.1 4.3 77 88-167 154-241 (270)
46 PRK13562 acetolactate synthase 55.3 23 0.00049 26.8 4.1 60 176-235 11-75 (84)
47 PRK10858 nitrogen regulatory p 55.3 36 0.00077 26.8 5.5 54 172-225 4-81 (112)
48 PRK10665 nitrogen regulatory p 55.1 37 0.00079 26.8 5.5 48 172-219 4-74 (112)
49 PF02662 FlpD: Methyl-viologen 55.1 1.1E+02 0.0023 24.4 8.5 88 138-228 29-123 (124)
50 TIGR01143 murF UDP-N-acetylmur 54.4 38 0.00083 32.0 6.5 61 48-117 259-319 (417)
51 PRK03803 murD UDP-N-acetylmura 53.5 37 0.00081 32.3 6.4 61 48-117 278-339 (448)
52 COG0347 GlnK Nitrogen regulato 53.3 30 0.00065 27.6 4.7 56 171-226 3-82 (112)
53 PRK04663 murD UDP-N-acetylmura 53.0 35 0.00076 32.5 6.1 62 48-118 274-336 (438)
54 cd04880 ACT_AAAH-PDT-like ACT 51.7 43 0.00094 23.5 5.0 52 177-228 9-67 (75)
55 TIGR01087 murD UDP-N-acetylmur 51.1 41 0.0009 31.7 6.2 61 48-117 269-330 (433)
56 PRK01390 murD UDP-N-acetylmura 50.9 41 0.00089 32.1 6.2 60 48-116 292-352 (460)
57 PRK03806 murD UDP-N-acetylmura 50.4 49 0.0011 31.3 6.6 61 48-117 273-334 (438)
58 PRK02705 murD UDP-N-acetylmura 50.0 44 0.00096 31.8 6.3 61 48-117 286-347 (459)
59 PRK12677 xylose isomerase; Pro 49.9 65 0.0014 30.7 7.3 57 147-203 31-91 (384)
60 TIGR01081 mpl UDP-N-acetylmura 49.1 61 0.0013 30.9 7.1 60 48-117 283-343 (448)
61 PRK11930 putative bifunctional 48.3 49 0.0011 34.4 6.7 61 48-117 291-352 (822)
62 TIGR01529 argR_whole arginine 47.4 1.3E+02 0.0029 24.6 7.9 90 103-194 11-113 (146)
63 PRK14106 murD UDP-N-acetylmura 47.0 50 0.0011 31.3 6.1 62 48-117 284-345 (450)
64 CHL00100 ilvH acetohydroxyacid 46.9 27 0.00058 29.8 3.8 60 176-236 11-75 (174)
65 PF08671 SinI: Anti-repressor 45.7 48 0.001 20.3 3.7 25 47-71 4-28 (30)
66 TIGR00119 acolac_sm acetolacta 45.6 58 0.0013 27.3 5.5 60 176-236 10-74 (157)
67 PRK04280 arginine repressor; P 45.6 1.7E+02 0.0036 24.2 8.3 92 101-194 11-115 (148)
68 PRK12338 hypothetical protein; 45.1 38 0.00082 31.7 4.8 129 50-196 173-314 (319)
69 TIGR00705 SppA_67K signal pept 44.5 1.2E+02 0.0027 30.5 8.7 138 59-226 75-217 (584)
70 PRK01710 murD UDP-N-acetylmura 44.4 53 0.0011 31.6 5.9 58 49-116 289-347 (458)
71 PF01612 DNA_pol_A_exo1: 3'-5' 44.4 19 0.00041 28.8 2.4 67 172-240 1-87 (176)
72 PRK10773 murF UDP-N-acetylmura 44.4 61 0.0013 31.1 6.3 62 48-117 287-348 (453)
73 PF01514 YscJ_FliF: Secretory 44.3 1.1E+02 0.0025 26.4 7.4 110 133-242 21-141 (206)
74 PRK01368 murD UDP-N-acetylmura 44.0 61 0.0013 31.3 6.2 61 48-117 280-341 (454)
75 TIGR03190 benz_CoA_bzdN benzoy 43.6 76 0.0016 29.9 6.7 48 175-228 324-374 (377)
76 PF03698 UPF0180: Uncharacteri 43.5 19 0.00042 26.9 2.1 21 179-199 8-28 (80)
77 TIGR00706 SppA_dom signal pept 43.1 2.1E+02 0.0046 24.4 10.8 134 62-226 15-151 (207)
78 PF14502 HTH_41: Helix-turn-he 42.6 20 0.00044 24.3 1.9 44 47-98 5-48 (48)
79 cd04904 ACT_AAAH ACT domain of 41.3 99 0.0021 21.9 5.6 49 177-228 10-66 (74)
80 cd04908 ACT_Bt0572_1 N-termina 41.1 86 0.0019 21.4 5.1 25 101-125 5-29 (66)
81 PRK03094 hypothetical protein; 40.5 24 0.00051 26.5 2.2 19 179-197 8-26 (80)
82 PRK00139 murE UDP-N-acetylmura 40.4 80 0.0017 30.3 6.4 60 48-117 283-343 (460)
83 PF05225 HTH_psq: helix-turn-h 39.7 29 0.00064 22.7 2.3 22 52-73 20-41 (45)
84 PRK14022 UDP-N-acetylmuramoyla 39.2 83 0.0018 30.4 6.3 59 48-117 301-360 (481)
85 PRK11895 ilvH acetolactate syn 38.5 2.4E+02 0.0052 23.7 11.0 123 99-228 4-141 (161)
86 cd04925 ACT_ACR_2 ACT domain-c 38.4 51 0.0011 23.4 3.7 37 99-139 2-38 (74)
87 PRK14093 UDP-N-acetylmuramoyla 38.4 1.2E+02 0.0027 29.2 7.4 65 48-117 296-360 (479)
88 PF02016 Peptidase_S66: LD-car 38.4 30 0.00065 31.4 3.0 56 178-236 13-68 (284)
89 COG4669 EscJ Type III secretor 37.8 1.5E+02 0.0032 26.8 7.2 84 150-233 34-126 (246)
90 cd07062 Peptidase_S66_mccF_lik 37.6 53 0.0011 30.1 4.5 56 178-236 17-72 (308)
91 PRK11895 ilvH acetolactate syn 37.3 70 0.0015 26.9 4.8 60 176-236 11-75 (161)
92 PF14085 DUF4265: Domain of un 37.3 90 0.002 24.5 5.2 56 171-229 54-113 (117)
93 PF01930 Cas_Cas4: Domain of u 37.2 77 0.0017 25.6 5.0 43 186-228 91-136 (162)
94 PF13740 ACT_6: ACT domain; PD 37.1 1E+02 0.0023 21.8 5.2 54 177-230 12-70 (76)
95 PHA03188 UL14 tegument protein 36.9 2.8E+02 0.0061 24.2 8.4 65 1-72 1-68 (199)
96 PRK10949 protease 4; Provision 36.0 4.9E+02 0.011 26.6 12.6 138 59-226 94-236 (618)
97 TIGR01085 murE UDP-N-acetylmur 35.6 1.1E+02 0.0024 29.2 6.6 61 48-117 291-352 (464)
98 PRK00421 murC UDP-N-acetylmura 34.1 79 0.0017 30.3 5.3 61 48-116 284-346 (461)
99 cd04879 ACT_3PGDH-like ACT_3PG 34.1 1.3E+02 0.0029 19.5 6.3 27 101-127 3-29 (71)
100 TIGR01082 murC UDP-N-acetylmur 33.8 74 0.0016 30.4 5.0 46 48-101 278-323 (448)
101 COG3492 Uncharacterized protei 33.7 31 0.00068 26.7 1.9 20 215-234 16-35 (104)
102 PF09682 Holin_LLH: Phage holi 33.6 2.2E+02 0.0049 21.9 7.9 55 20-74 40-102 (108)
103 PRK02006 murD UDP-N-acetylmura 33.3 1.1E+02 0.0025 29.6 6.3 61 48-117 325-386 (498)
104 PF05423 Mycobact_memb: Mycoba 33.2 60 0.0013 26.7 3.7 21 84-104 51-71 (140)
105 PRK11929 putative bifunctional 33.1 98 0.0021 32.7 6.2 62 48-117 796-857 (958)
106 PF00392 GntR: Bacterial regul 33.1 97 0.0021 21.2 4.3 51 24-75 1-51 (64)
107 PRK13209 L-xylulose 5-phosphat 33.0 2.1E+02 0.0046 25.1 7.5 53 147-199 21-77 (283)
108 TIGR00479 rumA 23S rRNA (uraci 32.7 46 0.001 31.7 3.4 34 173-206 393-427 (431)
109 cd04906 ACT_ThrD-I_1 First of 32.2 2E+02 0.0043 20.9 6.1 51 147-197 13-71 (85)
110 cd04886 ACT_ThrD-II-like C-ter 32.1 1.5E+02 0.0033 19.5 5.3 55 174-228 5-67 (73)
111 PRK13168 rumA 23S rRNA m(5)U19 31.9 1.2E+02 0.0027 29.1 6.2 60 140-206 370-431 (443)
112 PF07592 DDE_Tnp_ISAZ013: Rhod 31.8 18 0.00038 33.8 0.4 13 2-14 224-236 (311)
113 PRK13210 putative L-xylulose 5 31.5 2.6E+02 0.0057 24.3 7.8 83 146-228 15-106 (284)
114 PRK05066 arginine repressor; P 30.9 3.1E+02 0.0068 22.8 8.3 92 101-193 16-117 (156)
115 PRK09856 fructoselysine 3-epim 30.9 2.9E+02 0.0062 24.0 8.0 51 147-197 13-65 (275)
116 PF12002 MgsA_C: MgsA AAA+ ATP 30.8 40 0.00088 28.7 2.4 40 26-65 22-64 (168)
117 PRK01438 murD UDP-N-acetylmura 30.6 1.3E+02 0.0028 28.9 6.1 62 48-117 305-366 (480)
118 TIGR00119 acolac_sm acetolacta 30.6 3.2E+02 0.0069 22.8 11.3 122 99-228 3-140 (157)
119 cd04883 ACT_AcuB C-terminal AC 30.3 80 0.0017 21.5 3.5 26 171-196 44-69 (72)
120 PRK00441 argR arginine repress 29.9 1.8E+02 0.0038 24.1 6.0 92 101-194 11-115 (149)
121 cd04905 ACT_CM-PDT C-terminal 29.8 1.4E+02 0.0029 21.2 4.8 56 174-229 8-70 (80)
122 PF04639 Baculo_E56: Baculovir 29.7 1.4E+02 0.003 27.7 5.8 71 34-127 79-149 (305)
123 cd07025 Peptidase_S66 LD-Carbo 29.7 84 0.0018 28.4 4.4 56 179-237 14-69 (282)
124 TIGR00216 ispH_lytB (E)-4-hydr 29.3 95 0.0021 28.5 4.7 81 107-195 14-116 (280)
125 smart00633 Glyco_10 Glycosyl h 29.1 1.3E+02 0.0028 26.5 5.4 80 150-235 139-222 (254)
126 PRK01060 endonuclease IV; Prov 28.9 3.5E+02 0.0075 23.6 8.2 58 137-195 3-63 (281)
127 PRK14700 recombination factor 28.9 60 0.0013 30.2 3.3 39 28-66 162-203 (300)
128 PRK11092 bifunctional (p)ppGpp 28.6 1.5E+02 0.0032 30.7 6.4 62 175-236 634-699 (702)
129 COG0771 MurD UDP-N-acetylmuram 28.4 1.2E+02 0.0025 29.8 5.4 62 48-118 281-343 (448)
130 PRK15348 type III secretion sy 28.4 3.2E+02 0.0068 24.7 7.8 90 151-241 34-132 (249)
131 PF04273 DUF442: Putative phos 27.8 2.8E+02 0.006 21.6 6.5 70 147-225 15-85 (110)
132 PRK03369 murD UDP-N-acetylmura 27.7 1.3E+02 0.0029 29.2 5.7 60 48-115 288-347 (488)
133 TIGR01501 MthylAspMutase methy 27.4 2.6E+02 0.0057 22.7 6.5 43 147-193 39-81 (134)
134 cd02116 ACT ACT domains are co 27.4 1.4E+02 0.003 17.5 4.7 25 177-201 8-32 (60)
135 PF08777 RRM_3: RNA binding mo 27.3 2.7E+02 0.0058 21.5 6.3 59 95-159 1-60 (105)
136 cd04902 ACT_3PGDH-xct C-termin 27.0 98 0.0021 20.9 3.5 58 174-234 6-68 (73)
137 PRK00696 sucC succinyl-CoA syn 26.9 1.8E+02 0.004 27.3 6.3 60 170-238 257-318 (388)
138 smart00685 DM14 Repeats in fly 26.8 1E+02 0.0022 21.7 3.5 27 12-38 17-43 (59)
139 COG1438 ArgR Arginine represso 26.5 2.5E+02 0.0055 23.4 6.3 93 100-194 12-117 (150)
140 PRK04194 hypothetical protein; 25.8 1.5E+02 0.0033 28.5 5.6 41 151-191 265-313 (392)
141 PF01969 DUF111: Protein of un 25.6 79 0.0017 30.3 3.6 41 151-191 267-315 (382)
142 PRK04308 murD UDP-N-acetylmura 25.6 1.8E+02 0.0039 27.6 6.1 61 48-116 280-340 (445)
143 PF13936 HTH_38: Helix-turn-he 25.3 63 0.0014 20.8 2.1 20 53-72 25-44 (44)
144 PF01910 DUF77: Domain of unkn 25.3 45 0.00097 25.3 1.5 52 182-241 20-75 (92)
145 PF12213 Dpoe2NT: DNA polymera 25.2 27 0.00058 25.6 0.3 47 182-228 7-54 (73)
146 TIGR02544 III_secr_YscJ type I 25.2 4E+02 0.0086 22.9 7.6 91 151-241 33-132 (193)
147 TIGR01955 RfaH transcriptional 24.8 1E+02 0.0022 25.0 3.7 23 172-194 2-24 (159)
148 COG2044 Predicted peroxiredoxi 24.8 2.1E+02 0.0045 23.1 5.3 64 95-162 4-77 (120)
149 cd04884 ACT_CBS C-terminal ACT 24.4 1.9E+02 0.0042 19.9 4.6 56 173-228 5-66 (72)
150 PRK11253 ldcA L,D-carboxypepti 24.3 1.4E+02 0.003 27.5 4.9 55 179-236 17-72 (305)
151 PRK11179 DNA-binding transcrip 24.1 1.8E+02 0.0038 23.6 5.0 41 27-75 9-50 (153)
152 TIGR01307 pgm_bpd_ind 2,3-bisp 23.9 1.9E+02 0.0041 28.8 5.9 119 25-163 72-227 (501)
153 cd04927 ACT_ACR-like_2 Second 23.7 95 0.0021 22.2 3.0 29 98-126 1-29 (76)
154 PRK04690 murD UDP-N-acetylmura 23.4 2.3E+02 0.0049 27.4 6.4 59 48-115 283-342 (468)
155 cd04899 ACT_ACR-UUR-like_2 C-t 23.1 1.2E+02 0.0025 20.5 3.3 28 99-126 2-29 (70)
156 PF14258 DUF4350: Domain of un 23.0 2.4E+02 0.0052 19.4 4.9 20 177-196 3-22 (70)
157 COG0858 RbfA Ribosome-binding 23.0 1.2E+02 0.0027 24.1 3.7 69 161-229 36-117 (118)
158 COG2608 CopZ Copper chaperone 22.8 2.3E+02 0.0049 20.0 4.8 45 153-197 20-69 (71)
159 PF15474 MU117: Meiotically up 22.4 3.4E+02 0.0074 20.9 6.0 66 59-131 14-81 (97)
160 PF08544 GHMP_kinases_C: GHMP 22.4 2.1E+02 0.0046 19.9 4.7 45 148-192 35-83 (85)
161 PF11588 DUF3243: Protein of u 22.3 31 0.00067 26.0 0.1 26 47-72 13-38 (81)
162 smart00497 IENR1 Intron encode 22.2 70 0.0015 20.7 1.9 27 47-73 16-42 (53)
163 PRK10872 relA (p)ppGpp synthet 22.1 1.8E+02 0.0039 30.4 5.6 62 175-236 674-740 (743)
164 PRK11929 putative bifunctional 22.1 2.2E+02 0.0049 30.0 6.5 60 48-117 312-375 (958)
165 TIGR01016 sucCoAbeta succinyl- 22.1 2.1E+02 0.0045 26.9 5.7 75 153-238 242-318 (386)
166 TIGR00489 aEF-1_beta translati 22.0 1.5E+02 0.0033 22.4 3.9 55 179-234 17-80 (88)
167 PRK09014 rfaH transcriptional 21.8 1.2E+02 0.0026 24.8 3.6 23 172-194 5-27 (162)
168 TIGR01127 ilvA_1Cterm threonin 21.7 5.5E+02 0.012 23.8 8.5 50 147-196 317-379 (380)
169 PF02829 3H: 3H domain; Inter 21.6 1.7E+02 0.0037 22.5 4.2 84 106-193 6-96 (98)
170 PTZ00065 60S ribosomal protein 21.6 1.2E+02 0.0026 24.9 3.4 22 86-107 13-36 (130)
171 cd06146 mut-7_like_exo DEDDy 3 21.4 1.8E+02 0.0039 24.5 4.7 65 173-239 2-91 (193)
172 PRK00435 ef1B elongation facto 21.3 1.2E+02 0.0027 22.9 3.3 56 178-234 16-80 (88)
173 COG2605 Predicted kinase relat 21.3 2.4E+02 0.0053 26.5 5.7 96 27-142 228-329 (333)
174 TIGR00691 spoT_relA (p)ppGpp s 21.3 2.3E+02 0.005 29.2 6.2 61 175-235 618-682 (683)
175 PF00543 P-II: Nitrogen regula 21.1 1E+02 0.0022 23.3 2.8 23 172-194 1-23 (102)
176 cd04929 ACT_TPH ACT domain of 20.9 2.4E+02 0.0051 20.3 4.6 49 177-228 10-66 (74)
177 PRK00141 murD UDP-N-acetylmura 20.7 2.4E+02 0.0053 27.2 6.0 62 48-117 294-355 (473)
178 KOG2121|consensus 20.6 55 0.0012 34.0 1.5 54 51-107 222-279 (746)
179 PF00488 MutS_V: MutS domain V 20.2 84 0.0018 27.6 2.5 23 50-72 207-229 (235)
180 COG3636 Predicted transcriptio 20.1 2E+02 0.0043 22.5 4.1 39 18-60 45-90 (100)
181 COG4492 PheB ACT domain-contai 20.1 1.7E+02 0.0036 24.4 3.9 55 179-234 84-144 (150)
182 COG1619 LdcA Uncharacterized p 20.1 1.6E+02 0.0034 27.5 4.3 63 171-236 12-80 (313)
183 cd07884 RHD-n_Relish N-termina 20.1 2.8E+02 0.006 23.5 5.4 74 81-155 38-120 (159)
No 1
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=8e-98 Score=650.51 Aligned_cols=238 Identities=47% Similarity=0.752 Sum_probs=232.6
Q ss_pred CCCcchhHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCC
Q psy8853 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNE 79 (242)
Q Consensus 1 maGHsKW~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~ 79 (242)
|||||||+||||+|+++|++|||+|+||+|+|++|||. ||||+.|||||.||++||++|||||+|||||+||+|+ .+
T Consensus 1 MaGHsKw~nIkhrK~a~Dakr~Kif~Kl~keI~vAaK~Gg~dP~~NprLr~aI~kAk~~nmPkd~IerAI~ka~G~--~d 78 (241)
T COG0217 1 MAGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGGPDPESNPRLRTAIEKAKAANMPKDNIERAIKKASGG--KD 78 (241)
T ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHHHcCCCHHHHHHHHHhccCC--CC
Confidence 99999999999999999999999999999999999999 7999999999999999999999999999999999987 47
Q ss_pred CcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-CChhHHHHHHHh
Q psy8853 80 NINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-TKKNTLLDLALE 158 (242)
Q Consensus 80 ~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-~~~d~~~e~Aie 158 (242)
+.+|++++|||||||||+|||||||||+|||+++||++|+|+||+||++|||+|||+|||+|.+.++ .++|++||.|||
T Consensus 79 ~~~~~ei~YEGygP~GvaiiVe~LTDN~NRTas~vR~~F~K~GG~lg~~GSV~~mF~~kGvi~~~~~~~~ed~l~e~~ie 158 (241)
T COG0217 79 GANYEEIRYEGYGPGGVAIIVEALTDNRNRTASNVRSAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIE 158 (241)
T ss_pred ccceEEEEEEeECCCceEEEEEeccCCcchhHHHHHHHHHhcCCccCCCceEEEEEeccEEEEECCCCCCHHHHHHHHHH
Confidence 7899999999999999999999999999999999999999999999999999999999999999987 599999999999
Q ss_pred cCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCcccceecc
Q psy8853 159 KGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 159 ~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~Ni 238 (242)
+|||||+.+ +|.|+|+|+|++|..|+++|+++|+++..+++.|+|+++|++++|+++++++|||+||++||||+||||+
T Consensus 159 agaeDv~~~-~~~~~V~t~p~~~~~V~~~L~~~g~~~~~ael~~iP~~~v~~~~e~a~k~~kLid~LEd~DDVQ~Vy~N~ 237 (241)
T COG0217 159 AGAEDVEED-EGSIEVYTEPEDFNKVKEALEAAGYEIESAELTMIPQNTVELDDEDAEKLEKLIDALEDDDDVQNVYHNA 237 (241)
T ss_pred CCchhhhcC-CCeEEEEEChHHHHHHHHHHHHcCCceeeeeEEEecCCceecCHHHHHHHHHHHHHHhcccchHHHHhcc
Confidence 999999997 5689999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccC
Q psy8853 239 LIF 241 (242)
Q Consensus 239 ~~~ 241 (242)
+++
T Consensus 238 ~~~ 240 (241)
T COG0217 238 EIS 240 (241)
T ss_pred ccC
Confidence 986
No 2
>PRK00110 hypothetical protein; Validated
Probab=100.00 E-value=8.1e-94 Score=635.20 Aligned_cols=238 Identities=48% Similarity=0.777 Sum_probs=229.7
Q ss_pred CCCcchhHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCC
Q psy8853 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNE 79 (242)
Q Consensus 1 maGHsKW~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~ 79 (242)
|||||||+||||+|+++|++||++|+||+|+|++|||. ||||+.|++||++|++||++||||++|||||+||+|. .+
T Consensus 1 maGHskW~~Ikh~K~~~D~kksk~f~kl~reI~vAak~GG~DP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~--~~ 78 (245)
T PRK00110 1 MAGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGGGDPEGNPRLRLAIDKAKAANMPKDNIERAIKKGTGE--LD 78 (245)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCC--CC
Confidence 89999999999999999999999999999999999999 8999999999999999999999999999999999986 36
Q ss_pred CcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCCCChhHHHHHHHhc
Q psy8853 80 NINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPNTKKNTLLDLALEK 159 (242)
Q Consensus 80 ~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~~~~d~~~e~Aie~ 159 (242)
+.+|++++|||||||||+|||||||||+|||+++||++|+|+||+||++|||+|||+|+|+|.+... ++|++||+|||+
T Consensus 79 ~~~~~e~~YEg~gP~GvaiiVe~lTDN~nRt~~~vR~~f~K~gG~l~~~Gsv~~~Fe~kG~i~~~~~-~~d~~~e~aiea 157 (245)
T PRK00110 79 GANYEEIRYEGYGPGGVAIIVEALTDNRNRTAAEVRHAFSKNGGNLGETGSVSYMFDRKGVIVIEPL-DEDELMEAALEA 157 (245)
T ss_pred ccceEEEEEEEEcCCCeEEEEEEecCCHHHHHHHHHHHHHhcCceeCCCcceEEEeccceEEEeCCC-CHHHHHHHHHhC
Confidence 7899999999999999999999999999999999999999999999999999999999999999854 799999999999
Q ss_pred CCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCcccceeccc
Q psy8853 160 GAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNAL 239 (242)
Q Consensus 160 GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~Ni~ 239 (242)
|||||+++ ++.|+|+|+|++|.+|+++|++.||++.++++.|+|+++|+|++++++++.+|+++|+++||||+||||++
T Consensus 158 GaeDv~~e-~~~~~i~~~p~~~~~v~~~L~~~g~~~~~sei~~~P~~~v~l~~e~~~~~~~li~~Led~dDVq~Vy~N~~ 236 (245)
T PRK00110 158 GAEDVETD-DESFEVITAPEDFEAVRDALEAAGLEAESAEVTMIPQNTVELDEETAEKLLKLIDALEDLDDVQNVYHNAE 236 (245)
T ss_pred CCCEeecc-CCeEEEEECHHHHHHHHHHHHHcCCCeeeeEEEEecCCCcccCHHHHHHHHHHHHHHhcCCCcceEeECCC
Confidence 99999774 45799999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cCC
Q psy8853 240 IFD 242 (242)
Q Consensus 240 ~~~ 242 (242)
+++
T Consensus 237 ~~~ 239 (245)
T PRK00110 237 ISD 239 (245)
T ss_pred CCH
Confidence 753
No 3
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=100.00 E-value=5.8e-92 Score=621.50 Aligned_cols=236 Identities=46% Similarity=0.747 Sum_probs=228.0
Q ss_pred CCCcchhHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCC
Q psy8853 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNE 79 (242)
Q Consensus 1 maGHsKW~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~ 79 (242)
|||||||+||||+|+++|++|+++|+||+|+|++|||. ||||+.|++||++|++||++||||++|||||+||+|. .+
T Consensus 1 maGHskw~~Ikh~K~~~D~~ksk~f~kl~r~I~vA~k~GG~DP~~N~~L~~ai~~Ak~~~~Pkd~IerAIkr~~g~--~~ 78 (238)
T TIGR01033 1 MAGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGGGDPESNPRLRTAIEKAKAANMPKDNIERAIKKGAGE--LD 78 (238)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCC--CC
Confidence 89999999999999999999999999999999999999 8999999999999999999999999999999999986 36
Q ss_pred CcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-CChhHHHHHHHh
Q psy8853 80 NINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-TKKNTLLDLALE 158 (242)
Q Consensus 80 ~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-~~~d~~~e~Aie 158 (242)
+.+|++++|||||||||+|||||||||+|||+++||++|+|+||+||++|||+|||+|+|+|.+..+ .++|++||.|||
T Consensus 79 ~~~~~~~~YEg~gP~GvaiiVe~lTDN~nRt~~~ir~~f~K~gg~l~~~gsv~~~Fe~kG~i~~~~~~~~~d~~~e~aie 158 (238)
T TIGR01033 79 GSNYEEITYEGYAPGGVAIIVECLTDNKNRTASEVRSAFNKNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEAAIE 158 (238)
T ss_pred ccceEEEEEEEEcCCceEEEEEEecCCHHhHHHHHHHHHHHcCCeeCCCCceeeeeecceEEEECCCCCCHHHHHHHHHh
Confidence 7799999999999999999999999999999999999999999999999999999999999999854 578999999999
Q ss_pred cCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCcccceecc
Q psy8853 159 KGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 159 ~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~Ni 238 (242)
+|||||+.+++ .|+|+|+|++|.+|+++|++.||++.++++.|+|+++|+|++++++++.+|+++|+++||||+||||+
T Consensus 159 aGAedv~~~~~-~~~v~~~~~~~~~v~~~L~~~g~~i~~sei~~~P~~~v~l~~e~~~~~~~li~~Lee~dDVq~Vy~N~ 237 (238)
T TIGR01033 159 AGAEDIDVDDD-EFEVYTAPEELEKVKEALEAKGFPIESAEITMIPLTTVDLDDEQAEKLLKLIDALEDDDDVQEVYHNF 237 (238)
T ss_pred CCCceeeccCC-cEEEEECHHHHHHHHHHHHHcCCCceeeEEEEecCCCcccCHHHHHHHHHHHHHHhcCCCcceeeeCC
Confidence 99999977555 49999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred c
Q psy8853 239 L 239 (242)
Q Consensus 239 ~ 239 (242)
+
T Consensus 238 ~ 238 (238)
T TIGR01033 238 E 238 (238)
T ss_pred C
Confidence 5
No 4
>PRK12378 hypothetical protein; Provisional
Probab=100.00 E-value=6e-90 Score=606.96 Aligned_cols=232 Identities=39% Similarity=0.649 Sum_probs=223.3
Q ss_pred CCcchhHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCC
Q psy8853 2 AGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNEN 80 (242)
Q Consensus 2 aGHsKW~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~ 80 (242)
+|| ||+||||+|+++|++||++|+||+|+|++|||. ||||+.||+||++|++||++||||++||||||||+|. ++
T Consensus 1 ~g~-kW~~Ikh~K~~~Da~ksk~f~kl~reI~vA~k~GG~dP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~---~~ 76 (235)
T PRK12378 1 MGR-AWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGGPDPESNPALRFVIERAKKANVPKDVIERAIKKAKGG---GG 76 (235)
T ss_pred CCc-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHhccCC---CC
Confidence 688 999999999999999999999999999999999 8999999999999999999999999999999999985 56
Q ss_pred cceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCCCChhHHHHHHHhcC
Q psy8853 81 INYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPNTKKNTLLDLALEKG 160 (242)
Q Consensus 81 ~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~~~~d~~~e~Aie~G 160 (242)
.+|++++|||||||||+|||||||||+|||+++||++|+|+||+||++|||+|||+|+|+|.+... ++|++||+|||+|
T Consensus 77 ~~~~e~~YEgygPgGvaiiVe~lTDN~nRt~~~vr~~f~K~gg~l~~~gsv~~~Fe~kG~i~i~~~-~~d~~~e~aieaG 155 (235)
T PRK12378 77 EDYEEVRYEGFGPNGVMVIVECLTDNVNRTVANVRSAFNKNGGNLGTSGSVAFMFDHKGVFVFEGD-DEDELLEALIDAD 155 (235)
T ss_pred CceEEEEEEEEcCCCcEEEEEECCCCHHHHHHHHHHHHhhcCCeECCCCceeeeeecceEEEeCCC-CHHHHHHHHHhCC
Confidence 689999999999999999999999999999999999999999999999999999999999999865 8999999999998
Q ss_pred C--cceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCcccceecc
Q psy8853 161 A--EDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 161 a--eDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~Ni 238 (242)
| +||++++ +.|+|+|+|++|.+|+++|++.||++.++++.|+|+++|+|++++++++.+|+++|+++||||+||||+
T Consensus 156 a~~edv~~~~-~~~~i~t~p~~~~~v~~~L~~~g~~~~~sei~~~P~~~v~l~~e~~~~~~~li~~Led~dDVq~Vy~N~ 234 (235)
T PRK12378 156 VDVEDVEEEE-GTITVYTDPTDFHKVKKALEAAGIEFLVAELEMIPQNPVELSGEDLEQFEKLLDALEDDDDVQNVYHNV 234 (235)
T ss_pred CCcccccccC-CeEEEEECHHHHHHHHHHHHHcCCCceeeEEEEecCCCccCCHHHHHHHHHHHHHHhcCCCccceeeCC
Confidence 8 8886544 579999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred c
Q psy8853 239 L 239 (242)
Q Consensus 239 ~ 239 (242)
+
T Consensus 235 ~ 235 (235)
T PRK12378 235 E 235 (235)
T ss_pred C
Confidence 4
No 5
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=100.00 E-value=1.6e-88 Score=598.82 Aligned_cols=232 Identities=44% Similarity=0.716 Sum_probs=208.5
Q ss_pred chhHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcce
Q psy8853 5 SKWANIKRKKLIVDAKRGKICTRIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINY 83 (242)
Q Consensus 5 sKW~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~ 83 (242)
|||+||||+|+++|++||++|+||+|+|++|||. ||||+.|++||++|++||++||||++|||||+||+|. .++.+|
T Consensus 1 sKW~nIkh~K~~~D~~ksk~f~kl~reI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~IerAIkk~~~~--~~~~~~ 78 (234)
T PF01709_consen 1 SKWSNIKHKKAAQDAKKSKLFTKLSREITVAVKEGGPDPDMNPRLRSAIEKAKKANMPKDNIERAIKKASGK--SDGANY 78 (234)
T ss_dssp -SCGGTSSSTTTTTTSHHHHHHHHHHHHHHHHHCC-S-GGGSHHHHHHHHHHHHTT--HHHHHHHHHHCCST--SST---
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHHHHHhCCCHHHHHHHHHhcCcC--CCCcCc
Confidence 7999999999999999999999999999999999 8999999999999999999999999999999999987 367899
Q ss_pred eEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEEC-CCCChhHHHHHHHhcCCc
Q psy8853 84 IEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFL-PNTKKNTLLDLALEKGAE 162 (242)
Q Consensus 84 ~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~-~~~~~d~~~e~Aie~Gae 162 (242)
++++|||||||||+|||||+|||+|||+++||++|+|+||+|+++|||+|||+|+|+|.++ ...++|++||+|||+|||
T Consensus 79 ~~~~yEg~gP~Gvaiive~lTDN~nRt~~~ir~~~~K~gg~l~~~gsv~~~F~~kG~i~~~~~~~~~d~~~e~aIe~Gae 158 (234)
T PF01709_consen 79 EEITYEGYGPGGVAIIVECLTDNKNRTVSDIRSIFKKNGGSLGPSGSVSFMFERKGVIEVSKKDLDEDELMEDAIEAGAE 158 (234)
T ss_dssp EEEEEEEEETTTEEEEEEEEES-HHHHHHHHHHHHHTTT-EEE-TTSSGGGEEEEEEEEEEHCCS-HHHHHHHHHHHTES
T ss_pred eEEEEEEEcCCCcEEEEEEeCCCHhHHHHHHHHHHHHcCceeCCCCcceeeeeeeEEEEEEeCCCChHHHHHHHHhCCCc
Confidence 9999999999999999999999999999999999999999999999999999999999999 568999999999999999
Q ss_pred ceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCcccceeccc
Q psy8853 163 DFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNAL 239 (242)
Q Consensus 163 Dve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~Ni~ 239 (242)
||+++ ||.|+|+|+|++|.+|+++|++.||++.++++.|+|+++|+|++++++++.+|+++|+++|||++||||++
T Consensus 159 Dve~~-d~~~~~~c~p~~~~~v~~~L~~~g~~i~~~e~~~~P~~~v~l~~e~~~~~~~lie~Lee~dDV~~Vy~Nie 234 (234)
T PF01709_consen 159 DVEED-DGEFEFICDPSDLSAVKKALEKKGYEIESAELEYIPNNPVELSEEDAEKVEKLIEALEELDDVQNVYHNIE 234 (234)
T ss_dssp EEEEC-TSEEEEEEEGGGHHHHHHHHHHTT---SEEEEEEEESS-EE--HHHHHHHHHHHHHHHTSTTEEEEEESEE
T ss_pred Eeeec-CCeEEEEECHHHHHHHHHHHHHcCCCeeEEEEEEeCCCCcccCHHHHHHHHHHHHHHhCCcCcceeeeCCC
Confidence 99965 66899999999999999999999999999999999999999999999999999999999999999999985
No 6
>KOG2972|consensus
Probab=100.00 E-value=3e-71 Score=483.12 Aligned_cols=235 Identities=32% Similarity=0.537 Sum_probs=216.0
Q ss_pred CCCcchhHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCC
Q psy8853 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNE 79 (242)
Q Consensus 1 maGHsKW~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~ 79 (242)
|+||||||||||+|+++|++|++++.||+++|.+|||. |+||..|.+|++.++.||+.+|||+.|||||+||++. +
T Consensus 29 ~sgH~kwskIk~~Kg~nD~~rsk~~nkl~~~i~~aVk~gg~np~lN~~LAtlle~ak~~~vpkd~ien~i~ras~k---~ 105 (276)
T KOG2972|consen 29 MSGHNKWSKIKHKKGANDQARSKQINKLSQGIILAVKQGGANPELNMRLATLLESAKKISVPKDGIENAINRASGK---E 105 (276)
T ss_pred ecccchhhhhcccccccHHHHHHHHHHHHHHHHHHHHhcCCCchhhhHHHHHHHHHHhcCCCHHHHHHHHHHhccC---C
Confidence 78999999999999999999999999999999999999 8999999999999999999999999999999999996 6
Q ss_pred CcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceee-EEEECCC-CChhHHHHHHH
Q psy8853 80 NINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCG-QLLFLPN-TKKNTLLDLAL 157 (242)
Q Consensus 80 ~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG-~i~v~~~-~~~d~~~e~Ai 157 (242)
+...+.+.||+||||||++|||++|||+||+++.||++|+|+||.+. ++++|+|++|| |+.+++. .++|.|.-.+|
T Consensus 106 ~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~nk~GG~s~--~~~r~~FdkKG~Vv~V~~~~~dk~vL~ie~i 183 (276)
T KOG2972|consen 106 GSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIFNKHGGASA--SGVRFLFDKKGVVVNVPPEKRDKDVLNIEAI 183 (276)
T ss_pred CCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHHHHcCCccc--ccceeEEeccceEEecChhhcchhhhhHHHH
Confidence 77889999999999999999999999999999999999999998654 57899999999 6777765 56666666668
Q ss_pred hcCCcceEe--------ecCce-EEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcC
Q psy8853 158 EKGAEDFLI--------DKDNK-ITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 158 e~GaeDve~--------~ed~~-~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~ 228 (242)
|+||+|+.. +++++ |+|+|+|++|++|...|.+.||++.+++++|+|.++|++++..++++++|+++|+|+
T Consensus 184 e~~A~d~~~~~~~e~d~eeer~~fkiv~e~ssl~qV~~~Lr~~G~~i~d~~le~~P~~~vev~~~~lEk~qkL~q~L~e~ 263 (276)
T KOG2972|consen 184 EAGAEDIVAEPVLEIDEEEEREEFKIVTEPSSLNQVAHKLRSKGFEIKDSGLEFIPLEEVEVDVPALEKIQKLIQALYEN 263 (276)
T ss_pred HhcccccccCcccccccccccceeEEEeccchHHHHHHHhhcCCceeeccccccccCCccccCccchHHHHHHHHHHhhc
Confidence 877777644 12334 999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccceecccc
Q psy8853 229 HDVKKVYTNALI 240 (242)
Q Consensus 229 dDV~~Vy~Ni~~ 240 (242)
|||..||+|+.-
T Consensus 264 edV~~iy~ni~~ 275 (276)
T KOG2972|consen 264 EDVMFIYDNILN 275 (276)
T ss_pred hhHHHHhhcccC
Confidence 999999999964
No 7
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.74 E-value=1.6e-08 Score=105.84 Aligned_cols=69 Identities=26% Similarity=0.339 Sum_probs=63.6
Q ss_pred hHHhHHHhHHhHHHHHHHHHHHHHHHHHHHhc--C-----CCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCC
Q psy8853 7 WANIKRKKLIVDAKRGKICTRIMRELRVAINF--G-----NNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSN 75 (242)
Q Consensus 7 W~nIkh~K~~~Da~k~k~f~kl~reI~~Avk~--G-----~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~ 75 (242)
|.+.+..|.+.+..++++++|+.++|..|++. | +||+.|++|+.+|++||+.+||++.|+|+|+++.++
T Consensus 296 ~K~~ee~Kvaalv~gski~~k~lk~I~~A~~~~~G~~~~~~DP~~NpaLk~aI~~Ak~~~vP~~~I~RvI~~A~qg 371 (1220)
T PRK07562 296 WKVKEEQKVAALVTGSKIVSKHLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALVPENYIKRVIQFARQG 371 (1220)
T ss_pred hccchhhhHHhhhhcchHHHHHHHHHHHHHHhccccccccCCccccHHHHHHHHHHHhccCCHHHHHHHHHHhhcc
Confidence 44556789999999999999999999999997 3 699999999999999999999999999999999875
No 8
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=93.50 E-value=0.23 Score=35.15 Aligned_cols=64 Identities=16% Similarity=0.210 Sum_probs=47.1
Q ss_pred EEEEeCcccHHHHHHHHHHCCCceeeceeeeecCc----ceecCHHHHH-HHHHHHHHHhcCCCcccce
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYT----NIVFKDGEAI-KLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~----~v~l~~e~~~-~~~~li~~Lee~dDV~~Vy 235 (242)
++....|.-+..+...|.+.|.++......-.|.. .+.+...+.+ .+.+++++|+.+++|.+|+
T Consensus 5 i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~ 73 (76)
T cd04888 5 LLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELREIDGVEKVE 73 (76)
T ss_pred EEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEE
Confidence 44556688899999999999999866543211221 2234456666 9999999999999999986
No 9
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=91.94 E-value=0.16 Score=37.73 Aligned_cols=67 Identities=13% Similarity=0.214 Sum_probs=47.7
Q ss_pred eEEEEeCcccHHHHHHHHHHC-CCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCccc---ceeccc
Q psy8853 171 KITIITSPSKFIEIKNSLEMT-GFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKK---VYTNAL 239 (242)
Q Consensus 171 ~~~~~c~p~~~~~v~~~L~~~-g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~---Vy~Ni~ 239 (242)
.+.|.|.|..+..|+.+|... |.+|...+-. =+--|.+..+....+..++++|+++|.|.. |||..+
T Consensus 7 s~vV~~~p~~~~~v~~~l~~~~gvEVh~~~~~--GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~lvYh~~e 77 (79)
T PF03927_consen 7 SLVVHARPERLEEVAEALAAIPGVEVHAVDED--GKIVVTIEAESSEEEVDLIDAINALPGVLSASLVYHYFE 77 (79)
T ss_dssp EEEEEE-CCCHHHHHHHHCCSTTEEEEEEETT--TEEEEEEEESSHHHHHHHHHHHCCSTTEEEEEESSEE-S
T ss_pred EEEEEECchhHHHHHHHHHcCCCcEEEeeCCC--CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEEEEec
Confidence 478999999999999999876 6665433211 112345677777889999999999998876 466543
No 10
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=88.44 E-value=1.2 Score=32.10 Aligned_cols=65 Identities=14% Similarity=0.236 Sum_probs=48.4
Q ss_pred EEEEe--CcccHHHHHHHHHHCCCceeeceeeeec-C----cceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 172 ITIIT--SPSKFIEIKNSLEMTGFKAESSGIVMRP-Y----TNIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 172 ~~~~c--~p~~~~~v~~~L~~~g~~v~~sel~~~P-~----~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
+.+.| .|--|..+...+.+.|..+.+....-.- . -.+.+.=.+.+.+..++++|+.+|+|..|+.
T Consensus 9 l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~R 80 (80)
T PF13291_consen 9 LRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVER 80 (80)
T ss_dssp EEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEEE
T ss_pred EEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEEC
Confidence 44444 5777999999999999998877766642 2 2233444677899999999999999999873
No 11
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=86.68 E-value=1.7 Score=33.07 Aligned_cols=67 Identities=15% Similarity=0.269 Sum_probs=50.2
Q ss_pred eEEEEeCcccHHHHHHHHHHC-CCceeeceeeeecC--cceecCHHHHHHHHHHHHHHhcCCCccc---ceecccc
Q psy8853 171 KITIITSPSKFIEIKNSLEMT-GFKAESSGIVMRPY--TNIVFKDGEAIKLQKLLNELKKLHDVKK---VYTNALI 240 (242)
Q Consensus 171 ~~~~~c~p~~~~~v~~~L~~~-g~~v~~sel~~~P~--~~v~l~~e~~~~~~~li~~Lee~dDV~~---Vy~Ni~~ 240 (242)
.+.+.|.|..+..|++.|.+. |.+|.-.+ -+. --|.|..+....+...++.++.+|.|.. |||+++.
T Consensus 9 SlVV~~~Pe~~~~V~~~l~~ipg~Evh~~d---~~~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVYh~~d~ 81 (87)
T PRK10553 9 SLVVQAKSERISDISTQLNAFPGCEVAVSD---APSGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVYHQQDE 81 (87)
T ss_pred EEEEEeChHHHHHHHHHHHcCCCcEEEeec---CCCCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEEEEecc
Confidence 378999999999999999987 55543221 022 2456777788888999999999998765 6888763
No 12
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=86.51 E-value=2.5 Score=30.16 Aligned_cols=59 Identities=22% Similarity=0.180 Sum_probs=44.1
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC-cceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY-TNIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~-~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
.+--+..+...+.+.|+.+.+.+..-- . -.+++.-.+.+.+..++++|+.+++|.+|+.
T Consensus 10 r~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~l~i~v~~~~~L~~li~~L~~i~gV~~V~R 69 (74)
T cd04877 10 RLGITQEVLDLLVEHNIDLRGIEIDPK-GRIYLNFPTIEFEKLQTLMPEIRRIDGVEDVKT 69 (74)
T ss_pred cchHHHHHHHHHHHCCCceEEEEEecC-CeEEEEeEecCHHHHHHHHHHHhCCCCceEEEE
Confidence 344589999999999999877775321 2 2223444567789999999999999999874
No 13
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=86.09 E-value=1.1 Score=29.92 Aligned_cols=52 Identities=15% Similarity=0.208 Sum_probs=35.2
Q ss_pred EEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHH
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNEL 225 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~L 225 (242)
+.|+.+.+..|+..|++.|+.+.+.+-.---.-.+.+++++.+.+.+.+..+
T Consensus 1 i~~~Y~~~~~v~~~l~~~~~~i~~~~y~~~V~~~v~v~~~~~~~f~~~l~~~ 52 (56)
T PF09186_consen 1 ISCDYSQYGKVERLLEQNGIEIVDEDYTDDVTLTVAVPEEEVEEFKAQLTDL 52 (56)
T ss_dssp EEE-CCCHHHHHHHHHHTTTEEEEEEECTTEEEEEEEECCCHHHHHHHHHHH
T ss_pred CEechhhHHHHHHHHHHCCCEEEcceecceEEEEEEECHHHHHHHHHHHHHH
Confidence 5689999999999999988877665533332234556777777766665544
No 14
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=85.20 E-value=3.9 Score=27.56 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=42.0
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC-c----ceecCHHHHHHHHHHHHHHhcCCCcccc
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY-T----NIVFKDGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~-~----~v~l~~e~~~~~~~li~~Lee~dDV~~V 234 (242)
.|.-+..+...|.+.|+.+.+....-.|. . .+.+.... ..+..+++.|+.+++|.+|
T Consensus 10 ~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 10 EPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEGDD-DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred CCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEECCH-HHHHHHHHHHhCCccEEEe
Confidence 45568899999999999987766543322 1 22344445 8899999999999999887
No 15
>PRK04435 hypothetical protein; Provisional
Probab=83.60 E-value=3.7 Score=33.81 Aligned_cols=63 Identities=17% Similarity=0.256 Sum_probs=47.5
Q ss_pred EEEEeCcccHHHHHHHHHHCCCceeeceeeeecCc-----ceecCHHHHH-HHHHHHHHHhcCCCcccce
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYT-----NIVFKDGEAI-KLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~-----~v~l~~e~~~-~~~~li~~Lee~dDV~~Vy 235 (242)
+.....|--|..|.+.|.+.|.++..-... +|.+ .+.++-.+++ .+..|+++|+.+++|.+|.
T Consensus 74 i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~-i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~ 142 (147)
T PRK04435 74 LLLEDRSGTLSKVLNVIAEAGGNILTINQS-IPLQGRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVE 142 (147)
T ss_pred EEEecCCCHHHHHHHHHHHcCCCeEEEEEE-cCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEE
Confidence 445567888999999999999998765532 4432 3344445554 8999999999999999875
No 16
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=80.56 E-value=8 Score=26.94 Aligned_cols=58 Identities=12% Similarity=0.196 Sum_probs=43.2
Q ss_pred EeCcccHHHHHHHHHHCCCceeeceeeeecCc----ceecCHHHHHHHHHHHHHHhcCCCcc
Q psy8853 175 ITSPSKFIEIKNSLEMTGFKAESSGIVMRPYT----NIVFKDGEAIKLQKLLNELKKLHDVK 232 (242)
Q Consensus 175 ~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~----~v~l~~e~~~~~~~li~~Lee~dDV~ 232 (242)
.=.|-.|..|...|.+.|.++.+....-.+.. .+.+.-.+.+.+..++++|+..++|.
T Consensus 7 ~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L~~i~gV~ 68 (74)
T cd04887 7 PNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSEEHAETIVAAVRALPEVK 68 (74)
T ss_pred CCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCHHHHHHHHHHHhcCCCeE
Confidence 34577899999999999999876555443322 23345566778889999999999975
No 17
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=80.14 E-value=6.4 Score=27.01 Aligned_cols=59 Identities=24% Similarity=0.204 Sum_probs=42.7
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC-c----ceecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY-T----NIVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~-~----~v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
.|..+..+...|.+.|..+........+. . .+.+.+.+.+.+..+++.|+..++|+.+.
T Consensus 10 ~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~~~~~~~l~~~i~~L~~~~~V~~~~ 73 (79)
T cd04881 10 KPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTHETSEAALNAALAEIEALDAVQGVP 73 (79)
T ss_pred CCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEccCCHHHHHHHHHHHHcCccccCCc
Confidence 45568999999999999887665433322 1 12234556788999999999999998764
No 18
>COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]
Probab=78.92 E-value=5.5 Score=37.06 Aligned_cols=46 Identities=28% Similarity=0.389 Sum_probs=39.4
Q ss_pred ChhHHHHHHHhcCCcceEeec---CceEEEEeCcccHHHHHHHHHHC-CC
Q psy8853 148 KKNTLLDLALEKGAEDFLIDK---DNKITIITSPSKFIEIKNSLEMT-GF 193 (242)
Q Consensus 148 ~~d~~~e~Aie~GaeDve~~e---d~~~~~~c~p~~~~~v~~~L~~~-g~ 193 (242)
..|.+.+.|++.||---.... .|...|+|+|+....|.++|+.. |+
T Consensus 267 ~IDriy~~A~~~GA~~gKl~GaG~gGFllf~~~p~k~~~l~r~l~~~~~~ 316 (333)
T COG2605 267 AIDRIYELALKNGAYGGKLSGAGGGGFLLFFCDPSKRNELARALEKEQGF 316 (333)
T ss_pred HHHHHHHHHHhcCchhceeeccCCccEEEEEeCccchHHHHHHHHHhcCC
Confidence 368999999999999877743 45788999999999999999987 44
No 19
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=78.59 E-value=8 Score=34.41 Aligned_cols=68 Identities=4% Similarity=-0.019 Sum_probs=48.5
Q ss_pred eEEEEeCccc----HHHHHHHHHHCCCceeeceeeeec-Ccceec------CHHHHHHHHHHHHHHhcCCCcccceecc
Q psy8853 171 KITIITSPSK----FIEIKNSLEMTGFKAESSGIVMRP-YTNIVF------KDGEAIKLQKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 171 ~~~~~c~p~~----~~~v~~~L~~~g~~v~~sel~~~P-~~~v~l------~~e~~~~~~~li~~Lee~dDV~~Vy~Ni 238 (242)
.+.++|.+.+ ...+.+.|++.+|.+.+-+..-.+ .+.+++ ...+-..+++++.+|...|.|.+|+=++
T Consensus 144 ~~~v~~~~~~~~~vr~~L~~~l~~~~~~~~~l~~~~~~~~~~~ei~a~l~~~~~~~~~le~iv~~L~~~pgV~~v~W~~ 222 (225)
T PRK15385 144 ILKVTCNKEDESAVRQWLLNIVKEAAICLQGLGSVPAQEQGYKEIRAELVGHADYRKTRELIISRIGDNDNITAIHWSI 222 (225)
T ss_pred EEEEEEcCcchhHHHHHHHHHHHhCCCceEEeEeeecCCCCeEEEEEEEEecCCchhhHHHHHHHHhCCCCeEEEEEEe
Confidence 3578998877 455566677778988777765554 233333 2334568999999999999999998664
No 20
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=77.28 E-value=9.5 Score=24.58 Aligned_cols=61 Identities=13% Similarity=0.207 Sum_probs=40.6
Q ss_pred EEeCcccHHHHHHHHHHCCCceeeceeeeec-C---cceecCHHHHHHHHHHHHHHhcCCCcccc
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKAESSGIVMRP-Y---TNIVFKDGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P-~---~~v~l~~e~~~~~~~li~~Lee~dDV~~V 234 (242)
+.-.|..+..+...|.+.++.+.+....-.. . -.+.+.......+..+++.|...++|..|
T Consensus 5 ~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~v 69 (71)
T cd04876 5 AIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRDLEHLARIMRKLRQIPGVIDV 69 (71)
T ss_pred EeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCcEEE
Confidence 3445677899999999999988765543221 1 12223322344688999999999998765
No 21
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=75.31 E-value=6.5 Score=27.29 Aligned_cols=68 Identities=15% Similarity=0.283 Sum_probs=47.0
Q ss_pred EEEEeCccc--HHHHHHHHHHCCCceeeceeeeecCc-ceecCHHHHHHHHHHHHH-HhcCCCcccceecccc
Q psy8853 172 ITIITSPSK--FIEIKNSLEMTGFKAESSGIVMRPYT-NIVFKDGEAIKLQKLLNE-LKKLHDVKKVYTNALI 240 (242)
Q Consensus 172 ~~~~c~p~~--~~~v~~~L~~~g~~v~~sel~~~P~~-~v~l~~e~~~~~~~li~~-Lee~dDV~~Vy~Ni~~ 240 (242)
+.|.|+|.. +..+.+.|.+. -+|.+.....=+.+ .+.+--.+.+.+..|+.. |..+|.|.++.+.+-+
T Consensus 1 V~V~~~~~~~~~~~~~~~l~~~-p~V~~~~~vtG~~d~~~~v~~~d~~~l~~~i~~~l~~~~gV~~~~t~ivl 72 (74)
T PF01037_consen 1 VLVKVEPGHDAYDEFAEALAEI-PEVVECYSVTGEYDLILKVRARDMEELEEFIREKLRSIPGVRRTETSIVL 72 (74)
T ss_dssp EEEEESTTGTHHHHHHHHHHTS-TTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTHHTSTTEEEEEEEEEE
T ss_pred CEEEEcCCCchHHHHHHHHHcC-CCEEEEEEEeCCCCEEEEEEECCHHHHHHHHHHHhhcCCCEEEEEEEEEE
Confidence 467889988 99999999875 12333322222222 233444667889999998 9999999999988754
No 22
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=75.31 E-value=6.1 Score=30.49 Aligned_cols=66 Identities=15% Similarity=0.259 Sum_probs=48.9
Q ss_pred EEEEeCcccHHHHHHHHHHC-CCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCccc---ceeccc
Q psy8853 172 ITIITSPSKFIEIKNSLEMT-GFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKK---VYTNAL 239 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~-g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~---Vy~Ni~ 239 (242)
..+.|-|..+.+|+.+|... |.+|.-++-. =+--|-+..+..+.+..=++.++++|.|.+ |||-++
T Consensus 11 lVv~~~pe~l~av~~~L~~ip~~EV~~~d~~--GKlVVVie~~~~~~l~~tie~i~nl~gVlav~lVyhqqd 80 (94)
T COG3062 11 LVVQAKPERLSAVKTALLAIPGCEVYGEDAE--GKLVVVIEAEDSETLLETIESIRNLPGVLAVSLVYHQQD 80 (94)
T ss_pred EeeecCHHHHHHHHHHHhcCCCcEeeccCCC--ceEEEEEEcCchHHHHHHHHHHhcCCceeEEEEEEEEEe
Confidence 67899999999999999887 6666544422 122344577778888889999999998776 466544
No 23
>TIGR00257 IMPACT_YIGZ uncharacterized protein, YigZ family. This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ.
Probab=72.81 E-value=17 Score=31.72 Aligned_cols=72 Identities=13% Similarity=0.072 Sum_probs=48.0
Q ss_pred hHHHHHHHh-cCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecC--cceecCHHHHHHHHHHHHHH
Q psy8853 150 NTLLDLALE-KGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPY--TNIVFKDGEAIKLQKLLNEL 225 (242)
Q Consensus 150 d~~~e~Aie-~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~--~~v~l~~e~~~~~~~li~~L 225 (242)
-.....||+ ++..+..... .+.|.|+.+.+..|...|.+.++.+.+.+ |--. -.+.++.++.+.+...+..|
T Consensus 118 ~~aa~~al~~a~~~~~~~~~--~~~~~~~y~~~~~v~~~l~~~~~~i~~~~--y~~~V~~~~~v~~~~~~~~~~~l~~~ 192 (204)
T TIGR00257 118 GKSVLEALNNIQKEEKLELE--ILSLHCDYKQLDALERELKKFQLEIIKSN--FSNNVVLVEISGTKENLAFSEQLTEI 192 (204)
T ss_pred HHHHHHHHHhCCeEEEEEEE--EEEEEechhHHHHHHHHHHHCCCEEEeeE--ecCCEEEEEEECHHHHHHHHHHHHHH
Confidence 344555665 4555554432 58999999999999999999988765544 4333 24445777777766655544
No 24
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=72.17 E-value=14 Score=24.92 Aligned_cols=57 Identities=14% Similarity=0.197 Sum_probs=40.1
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC----cceecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY----TNIVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~----~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
.|-.+..+...|.+.++++.+....--+. -.+.++.. ..+..+++.|++.++|..|+
T Consensus 10 ~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~--~~~~~~~~~L~~~~~v~~v~ 70 (72)
T cd04874 10 KPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYMELEGV--GDIEELVEELRSLPIVREVE 70 (72)
T ss_pred CCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEEEecc--ccHHHHHHHHhCCCCeEEEE
Confidence 45678999999999999987554321111 12334432 57779999999999998875
No 25
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=68.61 E-value=5.4 Score=29.47 Aligned_cols=61 Identities=21% Similarity=0.240 Sum_probs=43.9
Q ss_pred EEeCcccHHHHHHHHHHCCCceeeceeeeecC---cceecCHHHHHHHHHHHHHHhcCCCcccc
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKAESSGIVMRPY---TNIVFKDGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~---~~v~l~~e~~~~~~~li~~Lee~dDV~~V 234 (242)
+-=.|.-|..|...++..||+|.+-....... ..+.+.-++-..++.++..|+-+.||.+|
T Consensus 10 v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~~~~~i~ql~kQL~KL~dV~~V 73 (76)
T PRK11152 10 ARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVASERPIDLLSSQLNKLVDVAHV 73 (76)
T ss_pred EECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEECCCchHHHHHHHHhcCcCeEEE
Confidence 34467889999999999999998877666433 23333222445677888888888898876
No 26
>PRK09977 putative Mg(2+) transport ATPase; Provisional
Probab=67.53 E-value=10 Score=33.46 Aligned_cols=65 Identities=12% Similarity=0.138 Sum_probs=46.5
Q ss_pred eEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCc---ceecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 171 KITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYT---NIVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 171 ~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~---~v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
.+.+.|++.+...+.+.|.+.++.+.+.++...... .+++.-........+++.|.+.|+|..|-
T Consensus 146 ~~~i~~~~~~~~~i~~~l~~~~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~~~~V~~v~ 213 (215)
T PRK09977 146 HLQLTLVNGNVVSMLDWFKQQKIKTDLVSLQENEDHEVVAIDITLHATTSIEDLYRLLKGIAGVKGVS 213 (215)
T ss_pred EEEEEEccccHHHHHHHHHHcCceEEEEEEEecCCCcEEEEEEEECCCCCHHHHHHHHhcCCCceEEE
Confidence 477889999999999999999998877665543321 12221112345778899999999998873
No 27
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=67.15 E-value=8.2 Score=25.78 Aligned_cols=57 Identities=16% Similarity=0.166 Sum_probs=40.3
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeeeec-C----cceecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVMRP-Y----TNIVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~~P-~----~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
-.|--+..+...|.+.|+++.+....--. . -.+.++.. ....+++.|++.++|.+|.
T Consensus 8 d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~~~---~~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 8 DVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSP---VPEEVLEELKALPGIIRVR 69 (71)
T ss_pred CCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcCCC---CCHHHHHHHHcCCCeEEEE
Confidence 35667899999999999998766543321 1 12334332 3679999999999999885
No 28
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=66.82 E-value=11 Score=27.82 Aligned_cols=61 Identities=21% Similarity=0.277 Sum_probs=42.6
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeeeecC---cceecC-HHHHHHHHHHHHHHhcCCCccccee
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVMRPY---TNIVFK-DGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~~P~---~~v~l~-~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
=.|.-|..+...+...||++.+-.....-. ..+.+. ..+-..+..++..|+-+.||.+|-+
T Consensus 11 n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~~~sriti~~~~~~~~i~qi~kQL~KLidV~~V~~ 75 (76)
T PRK06737 11 NDPSVLLRISGIFARRGYYISSLNLNERDTSGVSEMKLTAVCTENEATLLVSQLKKLINVLQVNK 75 (76)
T ss_pred cCCCHHHHHHHHHhccCcceEEEEecccCCCCeeEEEEEEECCHHHHHHHHHHHhCCcCEEEEEe
Confidence 357789999999999999998755543322 222331 2233577788889999999988753
No 29
>PRK11568 hypothetical protein; Provisional
Probab=66.74 E-value=29 Score=30.37 Aligned_cols=73 Identities=11% Similarity=0.009 Sum_probs=46.8
Q ss_pred HHHHHHHh-cCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHH
Q psy8853 151 TLLDLALE-KGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNEL 225 (242)
Q Consensus 151 ~~~e~Aie-~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~L 225 (242)
.....||+ ++..+.... ..+.|.|+...+..|...|.+.++.+.+.+..=--.-.+.++.++.+.+...+..+
T Consensus 119 ~aa~~al~~a~~~~~~~~--~~~~i~~~y~~~~~v~~~l~~~~~~i~~~~y~~~V~~~~~v~~~~~~~~~~~l~~~ 192 (204)
T PRK11568 119 GGVQQALRQLTTQRKVPL--TEYTLQCEYAQLAGIEALLGQFDGKIVNSEYQAFVTLRVALPAAKVAEFSAKLADF 192 (204)
T ss_pred HHHHHHHHhCCeEEEEEe--EEEEEEECcchHHHHHHHHHHCCCEEEcceecCCEEEEEEECHHHHHHHHHHHHHH
Confidence 44444554 454444332 25899999999999999999998877555432111223556777777777655544
No 30
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=65.81 E-value=6.9 Score=28.86 Aligned_cols=52 Identities=17% Similarity=0.217 Sum_probs=35.8
Q ss_pred eCcccHHHHHHHHHHCCC-ceeeceeeeecCcceecCHHHHHHHHHHHHHHhc
Q psy8853 176 TSPSKFIEIKNSLEMTGF-KAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKK 227 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~-~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee 227 (242)
+++..+.+--+.|++.|| ++...-..-.|.+.+.|++.=.+.+.+-++.|++
T Consensus 26 lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L~~ 78 (80)
T PF13601_consen 26 LTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAALRE 78 (80)
T ss_dssp --HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHHHH
Confidence 356677788888999998 3444444456999999999888888888888765
No 31
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=65.76 E-value=21 Score=24.10 Aligned_cols=43 Identities=26% Similarity=0.515 Sum_probs=30.7
Q ss_pred HHHHHHhc--CCcceEee-cCceEEEEeCccc--HHHHHHHHHHCCCc
Q psy8853 152 LLDLALEK--GAEDFLID-KDNKITIITSPSK--FIEIKNSLEMTGFK 194 (242)
Q Consensus 152 ~~e~Aie~--GaeDve~~-ed~~~~~~c~p~~--~~~v~~~L~~~g~~ 194 (242)
-++.+|.. |+.++..+ ..+...|..+|.. ..++.++|++.||+
T Consensus 15 ~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 15 KVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp HHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred HHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 34555553 88888775 3456777666655 79999999999985
No 32
>PRK08577 hypothetical protein; Provisional
Probab=65.27 E-value=15 Score=29.43 Aligned_cols=57 Identities=26% Similarity=0.321 Sum_probs=41.0
Q ss_pred cccHHHHHHHHHHCCCceeeceeeeecC-c------ceecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 178 PSKFIEIKNSLEMTGFKAESSGIVMRPY-T------NIVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 178 p~~~~~v~~~L~~~g~~v~~sel~~~P~-~------~v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
|--|+.+.+.|.+.|+++.+....-.+. . .+++++.+ ..+..+++.|+.+++|.+|+
T Consensus 67 ~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~~~-~~l~~l~~~L~~l~~V~~V~ 130 (136)
T PRK08577 67 PGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSKSD-IDLEELEEELKKLEEVKEVE 130 (136)
T ss_pred CCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCCch-hhHHHHHHHHHcCCCEEEEE
Confidence 4468899999999999987665544441 1 12334321 56899999999999999886
No 33
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=63.27 E-value=7.7 Score=26.51 Aligned_cols=56 Identities=16% Similarity=0.188 Sum_probs=38.5
Q ss_pred CcccHHHHHHHHHHCCCceeeceeee---ecCcceecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVM---RPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~---~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
.|--+..+...|...|+++......- .....++++.. .+..++++|...++|.+|+
T Consensus 9 ~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~~~---~l~~li~~l~~~~~V~~v~ 67 (69)
T cd04901 9 VPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDIDSE---VSEELLEALRAIPGTIRVR 67 (69)
T ss_pred CCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcCCC---CCHHHHHHHHcCCCeEEEE
Confidence 46778999999999998874432211 11122334433 6779999999999999885
No 34
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=63.09 E-value=11 Score=25.20 Aligned_cols=56 Identities=13% Similarity=0.210 Sum_probs=39.1
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC---cc--eecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY---TN--IVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~---~~--v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
.|..+..+...|.+.|+++.+....-... .. +.+++. .+..++++|++.++|.+|.
T Consensus 9 ~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v~~~---~~~~~i~~l~~~~~v~~v~ 69 (71)
T cd04903 9 KPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQP---IDEEVIEEIKKIPNIHQVI 69 (71)
T ss_pred CCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEeCCC---CCHHHHHHHHcCCCceEEE
Confidence 45568999999999999987654322111 11 333333 6779999999999999875
No 35
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=62.61 E-value=7.1 Score=27.43 Aligned_cols=57 Identities=30% Similarity=0.464 Sum_probs=39.8
Q ss_pred cccHHHHHHHHHHCCCceeeceeee--ecC-cceecC-HHHHHHHHHHHHHHhcCCCcccc
Q psy8853 178 PSKFIEIKNSLEMTGFKAESSGIVM--RPY-TNIVFK-DGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 178 p~~~~~v~~~L~~~g~~v~~sel~~--~P~-~~v~l~-~e~~~~~~~li~~Lee~dDV~~V 234 (242)
|--|..+..-+...||++.+-.+.. .|. ..+.+. ..+...+..|+..|+-+.||.+|
T Consensus 3 ~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~~~~i~~l~~Ql~KlidV~~V 63 (63)
T PF13710_consen 3 PGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGDDREIEQLVKQLEKLIDVVKV 63 (63)
T ss_dssp TTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES-CCHHHHHHHHHHCSTTEEEE
T ss_pred cHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeCchhHHHHHHHHhccCCeEeC
Confidence 5668899999999999998887777 333 233331 12234677788899999999876
No 36
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=60.47 E-value=29 Score=33.59 Aligned_cols=139 Identities=17% Similarity=0.166 Sum_probs=82.3
Q ss_pred CCeEEEEEEecCCcchhHHHHHHHh-------hhcCcc-------ccCCCccc-------cccceeeEEEECCCCChhHH
Q psy8853 94 NGAAIIVDCITNNRMRTVSNIRNIF-------NKNGGN-------LSKEGSVL-------FMFKHCGQLLFLPNTKKNTL 152 (242)
Q Consensus 94 gGv~iive~lTdN~nRt~~~vr~~f-------~K~gg~-------l~~~gsv~-------~~F~~kG~i~v~~~~~~d~~ 152 (242)
..+.+.+|.+.| ..|...-+|.+- =|.|-+ ++.+|++. -+|.+-|++.+. +.|++
T Consensus 205 ~~I~ly~E~~~~-~~~f~~aa~~a~~~KPVv~~k~Grs~~g~~aa~sHtgalag~~~~~~a~~~~~Gv~~~~---~~~el 280 (447)
T TIGR02717 205 KVILLYLEGIKD-GRKFLKTAREISKKKPIVVLKSGTSEAGAKAASSHTGALAGSDEAYDAAFKQAGVIRAD---SIEEL 280 (447)
T ss_pred CEEEEEecCCCC-HHHHHHHHHHHcCCCCEEEEecCCChhhhhhhhhccccccChHHHHHHHHHHCCeEEeC---CHHHH
Confidence 456677776655 345666666552 122211 22223222 378888998886 77888
Q ss_pred HHHHHhcCCcceEeecCceEEEEeCcccH-HHHHHHHHHCCCceeec--e----------eeeecCcceecCH-HHHHHH
Q psy8853 153 LDLALEKGAEDFLIDKDNKITIITSPSKF-IEIKNSLEMTGFKAESS--G----------IVMRPYTNIVFKD-GEAIKL 218 (242)
Q Consensus 153 ~e~Aie~GaeDve~~ed~~~~~~c~p~~~-~~v~~~L~~~g~~v~~s--e----------l~~~P~~~v~l~~-e~~~~~ 218 (242)
++.+-=..-.-.-. .+ .+-|++..--. .-+.+.++..|+++-.- + -.+.+.||+++.. .+-+.+
T Consensus 281 ~~~~~~l~~~~~~~-g~-rvaivs~sGG~g~l~aD~~~~~Gl~lp~ls~~t~~~L~~~lp~~~~~~NPlDl~~~~~~~~~ 358 (447)
T TIGR02717 281 FDLARLLSNQPLPK-GN-RVAIITNAGGPGVIATDACEENGLELAELSEATKNKLRNILPPEASIKNPVDVLGDATPERY 358 (447)
T ss_pred HHHHHHHhcCCCCC-CC-eEEEEECCchHHHHHHHHHHHcCCCcCCCCHHHHHHHHHhCccccccCCCEecCCCCCHHHH
Confidence 87765333222111 12 36666665555 44577788778775310 0 0123468999843 456789
Q ss_pred HHHHHHHhcCCCcccceecc
Q psy8853 219 QKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 219 ~~li~~Lee~dDV~~Vy~Ni 238 (242)
.+.++.|.++|+|.-|.-++
T Consensus 359 ~~al~~l~~dp~vd~Vlv~~ 378 (447)
T TIGR02717 359 AKALKTVAEDENVDGVVVVL 378 (447)
T ss_pred HHHHHHHHcCCCCCEEEEEc
Confidence 99999999999998887554
No 37
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=60.29 E-value=7.4 Score=27.00 Aligned_cols=28 Identities=14% Similarity=0.359 Sum_probs=23.8
Q ss_pred eecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 208 IVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 208 v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
|.+++.. +.+.+|.+.|.++|+|..+|.
T Consensus 3 V~~~~~~-~~~~~~~~~l~~~p~V~~~~~ 30 (74)
T PF01037_consen 3 VKVEPGH-DAYDEFAEALAEIPEVVECYS 30 (74)
T ss_dssp EEESTTG-THHHHHHHHHHTSTTEEEEEE
T ss_pred EEEcCCC-chHHHHHHHHHcCCCEEEEEE
Confidence 5566666 789999999999999999986
No 38
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=59.84 E-value=36 Score=22.57 Aligned_cols=27 Identities=15% Similarity=0.263 Sum_probs=21.5
Q ss_pred EEEecCCcchhHHHHHHHhhhcCcccc
Q psy8853 100 VDCITNNRMRTVSNIRNIFNKNGGNLS 126 (242)
Q Consensus 100 ve~lTdN~nRt~~~vr~~f~K~gg~l~ 126 (242)
+.+..+++....+++-.+|.++|+++.
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~ 28 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIE 28 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChh
Confidence 456677888888888888988888774
No 39
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=59.09 E-value=19 Score=24.98 Aligned_cols=54 Identities=20% Similarity=0.231 Sum_probs=32.7
Q ss_pred EEeCcccHHHHHHHHHHCCCce-----eecee-eeecC---cceecCHHHHHHHHHHHHHHhc
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKA-----ESSGI-VMRPY---TNIVFKDGEAIKLQKLLNELKK 227 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v-----~~sel-~~~P~---~~v~l~~e~~~~~~~li~~Lee 227 (242)
-..+|-+..-++..|++.|++. ..+.. .+.|. ..|-+.+++.++...+++.+++
T Consensus 5 ~~~~~~ea~~i~~~L~~~gI~~~v~~~~~~~~~g~~g~~~~~~v~V~~~d~~~A~~il~~~~~ 67 (67)
T PF09413_consen 5 TAGDPIEAELIKGLLEENGIPAFVKNEHMSGYAGEPGTGGQVEVYVPEEDYERAREILEEFEN 67 (67)
T ss_dssp EE--HHHHHHHHHHHHHTT--EE--S----SS---S--SSSEEEEEEGGGHHHHHHHHHHTT-
T ss_pred EcCCHHHHHHHHHHHHhCCCcEEEECCccchhhcccCccCceEEEECHHHHHHHHHHHHHhcC
Confidence 3456778899999999999974 11222 33455 3445688999999999988763
No 40
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=58.18 E-value=19 Score=27.87 Aligned_cols=61 Identities=21% Similarity=0.323 Sum_probs=43.9
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeee--ecC-ccee--cCHHHHHHHHHHHHHHhcCCCcccceecc
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVM--RPY-TNIV--FKDGEAIKLQKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~--~P~-~~v~--l~~e~~~~~~~li~~Lee~dDV~~Vy~Ni 238 (242)
=.|--|..|...+...||+|++-.... .|. +.+. +.+ + ..+++++..|+.+.||.+|++.-
T Consensus 17 N~pGVL~RIaglFsRRgyNIeSLtvg~te~~~iSRmtivv~~-~-~~i~Qi~kQL~KLidVikV~~l~ 82 (96)
T PRK08178 17 NHPGVMSHVCGLFARRAFNVEGILCLPIQDGDKSRIWLLVND-D-QRLEQMISQIEKLEDVLKVRRNQ 82 (96)
T ss_pred CCcCHHHHHHHHHhcCCcCeeeEEEeecCCCCceEEEEEEcC-c-hHHHHHHHHHhCCcCEEEEEECC
Confidence 367789999999999999987643322 333 2233 343 2 58889999999999999998743
No 41
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=57.29 E-value=9.6 Score=25.49 Aligned_cols=29 Identities=14% Similarity=0.182 Sum_probs=24.1
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY 205 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~ 205 (242)
.|--|..|...|.+.|++|......-...
T Consensus 10 rpG~l~~v~~~la~~~inI~~~~~~~~~~ 38 (66)
T PF01842_consen 10 RPGILADVTEILADHGINIDSISQSSDKD 38 (66)
T ss_dssp STTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred CCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence 46778999999999999998887766655
No 42
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=56.42 E-value=34 Score=30.35 Aligned_cols=28 Identities=18% Similarity=0.362 Sum_probs=24.5
Q ss_pred EEEecCCcchhHHHHHHHhhhcCccccC
Q psy8853 100 VDCITNNRMRTVSNIRNIFNKNGGNLSK 127 (242)
Q Consensus 100 ve~lTdN~nRt~~~vr~~f~K~gg~l~~ 127 (242)
+...|++...+...|+.+..++||-+..
T Consensus 54 l~lev~d~~~a~~~i~~~~~~~gG~i~~ 81 (262)
T PF14257_consen 54 LSLEVKDVEKAVKKIENLVESYGGYIES 81 (262)
T ss_pred EEEEECCHHHHHHHHHHHHHHcCCEEEE
Confidence 5677899999999999999999997653
No 43
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=56.07 E-value=26 Score=33.20 Aligned_cols=60 Identities=15% Similarity=0.149 Sum_probs=44.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRN 116 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~ 116 (242)
+..||.-|...++|.+.|.++|+...+- .+ ++|..+ .+|+.+|.|+.-.|+.-+.+-++.
T Consensus 280 a~aAia~~~~lgi~~~~i~~~L~~f~~~---~~------R~e~~~~~~g~~vi~D~~a~N~~s~~~al~~ 340 (447)
T PRK02472 280 ALAAIAAAKLLGVSNEAIREVLSTFSGV---KH------RLQYVGTIDGRKFYNDSKATNILATQKALSG 340 (447)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------cceEEEEECCeEEEECCCCCCHHHHHHHHHh
Confidence 4577788888999999999999987754 22 344333 367889999977788877666655
No 44
>COG3453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.91 E-value=30 Score=28.17 Aligned_cols=74 Identities=16% Similarity=0.241 Sum_probs=48.6
Q ss_pred CCCCChhHHHHHHHhcCCcceEee-cCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHH
Q psy8853 144 LPNTKKNTLLDLALEKGAEDFLID-KDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLL 222 (242)
Q Consensus 144 ~~~~~~d~~~e~Aie~GaeDve~~-ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li 222 (242)
++-.+.+++-+++ ..|---|... .||. = ..--.+.+++.+++..|+. ..|+|.+.-.+++++.+.+...+
T Consensus 13 sgQi~~~D~~~ia-a~GFksiI~nRPDgE--e-~~QP~~~~i~~aa~~aGl~-----y~~iPV~~~~iT~~dV~~f~~Al 83 (130)
T COG3453 13 SGQISPADIASIA-ALGFKSIICNRPDGE--E-PGQPGFAAIAAAAEAAGLT-----YTHIPVTGGGITEADVEAFQRAL 83 (130)
T ss_pred cCCCCHHHHHHHH-HhccceecccCCCCC--C-CCCCChHHHHHHHHhcCCc-----eEEeecCCCCCCHHHHHHHHHHH
Confidence 3335666765555 3444443331 1110 0 0123589999999999986 57999999999999988888877
Q ss_pred HHHh
Q psy8853 223 NELK 226 (242)
Q Consensus 223 ~~Le 226 (242)
+.++
T Consensus 84 ~eae 87 (130)
T COG3453 84 DEAE 87 (130)
T ss_pred HHhC
Confidence 7664
No 45
>PF07942 N2227: N2227-like protein; InterPro: IPR012901 This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (P53934 from SWISSPROT). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions [].
Probab=55.68 E-value=18 Score=33.06 Aligned_cols=77 Identities=18% Similarity=0.285 Sum_probs=55.4
Q ss_pred EEEeccC---C------eEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEEC--CCCChhHHHHHH
Q psy8853 88 YEGYSVN---G------AAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFL--PNTKKNTLLDLA 156 (242)
Q Consensus 88 yEg~gPg---G------v~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~--~~~~~d~~~e~A 156 (242)
-|.|+|. + +.+.|++ ..|.-.-+..|.++++ -||-.-.-|++.|-|...+ +.-. -.++.|++..++
T Consensus 154 ~e~y~~~~~~~~~d~VvT~FFIDT-A~Ni~~Yi~tI~~lLk-pgG~WIN~GPLlyh~~~~~-~~~~~sveLs~eEi~~l~ 230 (270)
T PF07942_consen 154 LEVYGPDENKGSFDVVVTCFFIDT-AENIIEYIETIEHLLK-PGGYWINFGPLLYHFEPMS-IPNEMSVELSLEEIKELI 230 (270)
T ss_pred EEecCCcccCCcccEEEEEEEeec-hHHHHHHHHHHHHHhc-cCCEEEecCCccccCCCCC-CCCCcccCCCHHHHHHHH
Confidence 4556666 3 3455555 5677788888888875 5777777789999999875 1111 136889999999
Q ss_pred HhcCCcceEee
Q psy8853 157 LEKGAEDFLID 167 (242)
Q Consensus 157 ie~GaeDve~~ 167 (242)
...|-+++.++
T Consensus 231 ~~~GF~~~~~~ 241 (270)
T PF07942_consen 231 EKLGFEIEKEE 241 (270)
T ss_pred HHCCCEEEEEE
Confidence 99999998763
No 46
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=55.33 E-value=23 Score=26.84 Aligned_cols=60 Identities=17% Similarity=0.214 Sum_probs=43.2
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeeee--cC-ccee--cCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVMR--PY-TNIV--FKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~~--P~-~~v~--l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
=.|--|.++...+...||+|.+-.+... |. +.+. ++..+-..++.++..|+-+.||.+|+
T Consensus 11 N~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~ 75 (84)
T PRK13562 11 DQVSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVE 75 (84)
T ss_pred CCCCHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEE
Confidence 3577899999999999999876544433 32 2333 33234467888888999999999998
No 47
>PRK10858 nitrogen regulatory protein P-II 1; Provisional
Probab=55.25 E-value=36 Score=26.84 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=36.4
Q ss_pred EEEEeCcccHHHHHHHHHHCCCc---e------------------eeceeeeecCcceec--CHHHHHHH-HHHHHHH
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFK---A------------------ESSGIVMRPYTNIVF--KDGEAIKL-QKLLNEL 225 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~---v------------------~~sel~~~P~~~v~l--~~e~~~~~-~~li~~L 225 (242)
++.+.-|..+..|+++|.+.|+. + ......|+|+..+++ ++++.+.+ ..+++..
T Consensus 4 I~AIIRp~kl~~v~~aL~~~G~~g~Tv~~V~G~G~q~g~~~~~~~~~~~~~~~pK~~ieivv~D~~v~~vv~~I~~~a 81 (112)
T PRK10858 4 IDAIIKPFKLDDVREALAEVGITGMTVTEVKGFGRQKGHTELYRGAEYMVDFLPKVKIEIVVPDDIVDTCVDTIIRTA 81 (112)
T ss_pred EEEEECHHHHHHHHHHHHHCCCCeEEEEEeEecCCCCCCceeeecceeeccceeeEEEEEEEChHhHHHHHHHHHHHh
Confidence 66788899999999999998775 2 011245888888775 66666543 3344333
No 48
>PRK10665 nitrogen regulatory protein P-II 2; Provisional
Probab=55.06 E-value=37 Score=26.77 Aligned_cols=48 Identities=19% Similarity=0.349 Sum_probs=33.1
Q ss_pred EEEEeCcccHHHHHHHHHHCCCc---ee------------------eceeeeecCcceec--CHHHHHHHH
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFK---AE------------------SSGIVMRPYTNIVF--KDGEAIKLQ 219 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~---v~------------------~sel~~~P~~~v~l--~~e~~~~~~ 219 (242)
++.+.-|..|..|+++|.+.|+. +. ...+.|+|+..+++ ++++.+.+-
T Consensus 4 I~AIIRp~kl~~v~~AL~~~G~~g~Tv~~V~G~G~q~g~~~~~rg~~~~~~~~~k~~ieivv~de~ve~vv 74 (112)
T PRK10665 4 VTVIIKPFKLEDVREALSSIGIQGLTVTEVKGFGRQKGHAELYRGAEYSVNFLPKVKIDVAIADDQLDEVI 74 (112)
T ss_pred EEEEECHHHHHHHHHHHHHCCCCcEEEEeeEecCCCCCCcceeccceeeecccceEEEEEEEChHhHHHHH
Confidence 56778888999999999888765 10 12245778887775 676665433
No 49
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=55.06 E-value=1.1e+02 Score=24.42 Aligned_cols=88 Identities=16% Similarity=0.157 Sum_probs=52.9
Q ss_pred eeEEEECCCCC-hhHHHHHHHhcCCcceEeec--CceEEE-E---eCcccHHHHHHHHHHCCCceeeceeeeecCcceec
Q psy8853 138 CGQLLFLPNTK-KNTLLDLALEKGAEDFLIDK--DNKITI-I---TSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVF 210 (242)
Q Consensus 138 kG~i~v~~~~~-~d~~~e~Aie~GaeDve~~e--d~~~~~-~---c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l 210 (242)
.-+|.++.... ....+..|++.||+-|-.-. .|...+ . --...+..+++.|++.|++.+--.+.|+.....
T Consensus 29 vriIrvpC~Grv~~~~il~Af~~GADGV~V~gC~~g~Ch~~~Gn~~a~~Rv~~~k~~L~~~Gi~~eRv~~~~~~~~~~-- 106 (124)
T PF02662_consen 29 VRIIRVPCSGRVDPEFILRAFEKGADGVLVAGCHPGDCHYREGNYRAEKRVERLKKLLEELGIEPERVRLYWISAPEG-- 106 (124)
T ss_pred eEEEEccCCCccCHHHHHHHHHcCCCEEEEeCCCCCCCCcchhhHHHHHHHHHHHHHHHHcCCChhHeEEEEeCcccH--
Confidence 45566665422 23557778999998886621 111111 1 122456788899999999877777666654321
Q ss_pred CHHHHHHHHHHHHHHhcC
Q psy8853 211 KDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 211 ~~e~~~~~~~li~~Lee~ 228 (242)
+.-.+.+..|.+.|+++
T Consensus 107 -~~fa~~~~~f~~~i~~l 123 (124)
T PF02662_consen 107 -KRFAEIVNEFTERIKEL 123 (124)
T ss_pred -HHHHHHHHHHHHHHHHc
Confidence 12245677777777654
No 50
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ.
Probab=54.38 E-value=38 Score=32.00 Aligned_cols=61 Identities=20% Similarity=0.214 Sum_probs=45.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- .+ -+ |....+|+.+|+++.-.|+.-+.+-+..+
T Consensus 259 ~laAia~~~~lGi~~~~i~~~l~~~~~~---~g-R~-----e~~~~~~~~vidDsya~np~s~~~al~~l 319 (417)
T TIGR01143 259 ALAAAALALELGIPLEEIAEGLAELKLV---KG-RF-----EIQTKNGLTLIDDTYNANPDSMRAALDAL 319 (417)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC-ce-----eEEcCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 4567788889999999999999988764 22 23 32235789999998887887666666554
No 51
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=53.48 E-value=37 Score=32.29 Aligned_cols=61 Identities=21% Similarity=0.222 Sum_probs=45.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- .+ |+|..+ .+|+.+|.++--.|+.-+.+-++.+
T Consensus 278 alaAia~a~~lgi~~~~i~~~L~~f~g~---~~------R~e~v~~~~gv~~idDs~atN~~a~~~al~~l 339 (448)
T PRK03803 278 ALAALALGEAAGLPKEAMLEVLRTFTGL---PH------RCEWVREVAGVDYYNDSKGTNVGATVAAIEGL 339 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCC---CC------ceEEEEEeCCeEEEEcCCcCCHHHHHHHHHhh
Confidence 4578888999999999999999987764 22 334333 2568888888677887777777765
No 52
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=53.29 E-value=30 Score=27.60 Aligned_cols=56 Identities=21% Similarity=0.344 Sum_probs=39.1
Q ss_pred eEEEEeCcccHHHHHHHHHHCCCc---e------------------eeceeeeecCcceec--CHHHHHH-HHHHHHHHh
Q psy8853 171 KITIITSPSKFIEIKNSLEMTGFK---A------------------ESSGIVMRPYTNIVF--KDGEAIK-LQKLLNELK 226 (242)
Q Consensus 171 ~~~~~c~p~~~~~v~~~L~~~g~~---v------------------~~sel~~~P~~~v~l--~~e~~~~-~~~li~~Le 226 (242)
.++.+.-|..|..|+++|++.|+. + ..-+..|+|...+++ ++++.+. ++.+...++
T Consensus 3 ~I~aIiRP~kl~~vkeaL~~~G~~gmTv~~V~G~G~Qkg~~e~yrg~~~~~~~lpK~~ieIvV~de~ve~vie~I~~~a~ 82 (112)
T COG0347 3 KIEAIIRPFKLDDVKEALEKAGVPGMTVTEVKGRGRQKGHTELYRGAEYEVDFLPKVKIEIVVSDEDVDEVIEAIKKAAR 82 (112)
T ss_pred EEEEEeCHHHhHHHHHHHHHcCCCceEEEeeeeecccCCccccccchhhhhhcccceEEEEEEChHHHHHHHHHHHHHHh
Confidence 367888999999999999999865 1 112456788877765 7777655 445555554
No 53
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=53.04 E-value=35 Score=32.54 Aligned_cols=62 Identities=11% Similarity=0.131 Sum_probs=47.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHHh
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNIF 118 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~f 118 (242)
..+|+.-|...++|.+.|.++|+.-++- .+ |+|..+ .+|+.+|-++.-.|+.-+.+-++.+.
T Consensus 274 alaAia~a~~lGi~~~~i~~~L~~f~g~---~~------R~e~v~~~~g~~~idDs~~tn~~s~~~Al~~~~ 336 (438)
T PRK04663 274 VLVVLALLDAAGVDYRKALDALKSYTGL---TH------RCQVVADNHGIKWVNDSKATNVASTLAALSGLE 336 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------ceEEeeeeCCcEEEeCCCcCCHHHHHHHHHhcc
Confidence 4567788899999999999999988765 22 333332 36888999988788888888888653
No 54
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=51.66 E-value=43 Score=23.48 Aligned_cols=52 Identities=13% Similarity=0.187 Sum_probs=37.5
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecCcc------eecCHH-HHHHHHHHHHHHhcC
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPYTN------IVFKDG-EAIKLQKLLNELKKL 228 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~------v~l~~e-~~~~~~~li~~Lee~ 228 (242)
.|-.|..|-+.+.+.|+.+.+-+-...+... ++++.. +...+..+++.|++.
T Consensus 9 ~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~ 67 (75)
T cd04880 9 KPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRV 67 (75)
T ss_pred cCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHh
Confidence 5888999999999999987766544444321 556543 457888888888874
No 55
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase.
Probab=51.11 E-value=41 Score=31.74 Aligned_cols=61 Identities=20% Similarity=0.193 Sum_probs=46.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- .+ |+|..+ .+|+.+|.+.--.|+.-|..-++.+
T Consensus 269 a~aAia~a~~lgi~~~~i~~~L~~f~g~---~~------R~e~v~~~~g~~~idD~~atn~~a~~~al~~~ 330 (433)
T TIGR01087 269 ILAAIALAKSLGLNLEAILEALRSFKGL---PH------RLEYVGQKNGVHFYNDSKATNVHATLAALSAF 330 (433)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------ceEEEEEECCEEEEEcCCCCCHHHHHHHHHhC
Confidence 4578888999999999999999988764 22 344332 3688899997778888777777764
No 56
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.86 E-value=41 Score=32.13 Aligned_cols=60 Identities=13% Similarity=0.115 Sum_probs=44.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRN 116 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~ 116 (242)
+..|+..|...++|.+.|.++|+...+- .+ |+|..+ .+|+.+|.++...|+.-+.+.|+.
T Consensus 292 a~aAiaa~~~lgi~~~~i~~gL~~~~~~---~g------R~e~i~~~~g~~vIdDs~ahNp~s~~~aL~~ 352 (460)
T PRK01390 292 AAAAYAAARALGLSPEEIAAGLASFPGL---AH------RMEQVGRRGGVLFVNDSKATNADAAAKALSS 352 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------ceEEEeeeCCcEEEEcCCCCCHHHHHHHHHh
Confidence 4566777788899999999999987654 22 344333 357888889988999888876664
No 57
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.39 E-value=49 Score=31.33 Aligned_cols=61 Identities=20% Similarity=0.205 Sum_probs=45.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- .+ |+|-.+ .+|+.+|.++.-.|+.-+..-++.+
T Consensus 273 a~aAia~a~~lgi~~~~i~~~L~~f~~~---~g------R~E~v~~~~~~~~i~Ds~a~n~~a~~~al~~l 334 (438)
T PRK03806 273 ALAALALADAVGIPRASSLKALTTFTGL---PH------RFQLVLEHNGVRWINDSKATNVGSTEAALNGL 334 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------eEEEEEeeCCEEEEEcCCCCCHHHHHHHHHhC
Confidence 4578888899999999999999987654 22 344333 3678888888778887777766664
No 58
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.00 E-value=44 Score=31.76 Aligned_cols=61 Identities=23% Similarity=0.263 Sum_probs=44.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+..|+..|...++|.+.|.++|++..+- .+ ++|..+ .+|+.+|.|+--.|+.-+..-++.+
T Consensus 286 alaAia~a~~lgv~~~~i~~~L~~f~~~---~g------R~e~~~~~~~~~ii~Ds~a~N~~s~~~al~~l 347 (459)
T PRK02705 286 LLLAVAAARLAGLSAEAIAEALRSFPGV---PH------RLERIGTINGIDFINDSKATNYDAAEVGLKAV 347 (459)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------ceEEEEeeCCcEEEEeCCCCCHHHHHHHHHhC
Confidence 4567788888899999999999987654 22 344333 2578899998778887666666554
No 59
>PRK12677 xylose isomerase; Provisional
Probab=49.91 E-value=65 Score=30.67 Aligned_cols=57 Identities=14% Similarity=0.112 Sum_probs=40.9
Q ss_pred CChhHHHHHHHhcCCcceEeecCceEEEEeCcc----cHHHHHHHHHHCCCceeeceeeee
Q psy8853 147 TKKNTLLDLALEKGAEDFLIDKDNKITIITSPS----KFIEIKNSLEMTGFKAESSGIVMR 203 (242)
Q Consensus 147 ~~~d~~~e~Aie~GaeDve~~ed~~~~~~c~p~----~~~~v~~~L~~~g~~v~~sel~~~ 203 (242)
.+.++.++.+-++|++-|+...+..+-+-.++. .+..+++.|++.|+.|......+.
T Consensus 31 ~~~~E~v~~~a~~Gf~gVElh~~~l~p~~~~~~~~~~~~~~lk~~l~~~GL~v~~v~~n~f 91 (384)
T PRK12677 31 LDPVEAVHKLAELGAYGVTFHDDDLVPFGATDAERDRIIKRFKKALDETGLVVPMVTTNLF 91 (384)
T ss_pred CCHHHHHHHHHHhCCCEEEecccccCCCCCChhhhHHHHHHHHHHHHHcCCeeEEEecCCC
Confidence 588999999999999999885443232322222 378999999999999766544433
No 60
>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase. Alternate name: murein tripeptide ligase
Probab=49.09 E-value=61 Score=30.92 Aligned_cols=60 Identities=15% Similarity=0.179 Sum_probs=44.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+..|+..|...++|.+.|.++|+...+- . -|+|..+ .+|+.+|.|+ -.|+.-+.+-++.+
T Consensus 283 a~~A~a~~~~lgi~~~~i~~~L~~~~~~---~------~R~e~~~~~~g~~ii~D~-ahNp~s~~~~l~~l 343 (448)
T TIGR01081 283 ALMAIAAARHVGVAIEDACEALGSFVNA---K------RRLELKGEANGITVYDDF-AHHPTAIEATLQGL 343 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---C------cceEEEEecCCeEEEEeC-CCCHHHHHHHHHHH
Confidence 4567788888899999999999877653 1 2344443 3678999998 88888776666655
No 61
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=48.31 E-value=49 Score=34.42 Aligned_cols=61 Identities=15% Similarity=0.134 Sum_probs=46.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- . -++|..+ .+|+.+|.++.-.|+.-+.+-|+.+
T Consensus 291 alaAia~a~~lGi~~~~i~~~L~~f~~~---~------gR~e~~~~~~g~~vIdDSyn~nP~s~~aaL~~l 352 (822)
T PRK11930 291 LIHCIAVLLYLGYSADQIQERMARLEPV---A------MRLEVKEGINNCTLINDSYNSDLQSLDIALDFL 352 (822)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---C------CeeEEEEcCCCcEEEECCCCCCHHHHHHHHHHH
Confidence 3467788999999999999999987764 2 2445444 4789999998888887777777666
No 62
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=47.35 E-value=1.3e+02 Score=24.61 Aligned_cols=90 Identities=18% Similarity=0.168 Sum_probs=65.3
Q ss_pred ecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-------C---C---hhHHHHHHHhcCCcceEeecC
Q psy8853 103 ITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-------T---K---KNTLLDLALEKGAEDFLIDKD 169 (242)
Q Consensus 103 lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-------~---~---~d~~~e~Aie~GaeDve~~ed 169 (242)
+..|.-.|..+|...+++.|-.++ ..+|+.+|.+.|++.+..+ . . ..+-+...+.-.+.+++-.+
T Consensus 11 i~~~~i~tqeeL~~~L~~~G~~vs-qaTIsRdL~elglvk~~~~~g~~~Y~~~~~~~~~~~~~l~~~~~~~v~~v~~~~- 88 (146)
T TIGR01529 11 ITEEKISTQEELVALLKAEGIEVT-QATVSRDLRELGAVKVRDEDGSYVYSLPADGVSDPTSKLKRLLKNLVLSIDRAG- 88 (146)
T ss_pred HHcCCCCCHHHHHHHHHHhCCCcC-HHHHHHHHHHcCCEEEECCCCcEEEeeccccccchhHHHHHHHHHHeeEeeccC-
Confidence 356677899999999999987753 4578889999999876422 0 0 11234555555555555544
Q ss_pred ceEEEEeCcccHHHHHHHHHHCCCc
Q psy8853 170 NKITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 170 ~~~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
..+.+.|.|-.-..|...|...+++
T Consensus 89 ~~vvikT~pG~A~~va~~iD~~~~~ 113 (146)
T TIGR01529 89 NLIVIRTKPGEASVIANLLDRLDKD 113 (146)
T ss_pred CEEEEEeCCCcHHHHHHHHHhCCCC
Confidence 3788999999999999999998764
No 63
>PRK14106 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=46.99 E-value=50 Score=31.28 Aligned_cols=62 Identities=18% Similarity=0.136 Sum_probs=44.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+..|+.-|...++|.+.|..+|+...+- .+ -++.+. ..+|+.+|+++.-.|+.-+.+-++.+
T Consensus 284 a~aAia~~~~lgi~~~~i~~~L~~~~~~---~g-R~e~i~----~~~~~~vi~D~~ahNP~s~~~~l~~l 345 (450)
T PRK14106 284 ALAATAAAYLLGISPDVIANTLKTFKGV---EH-RIEFVA----EINGVKFINDSKGTNPDAAIKALEAY 345 (450)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---Cc-ceEEEe----eECCEEEEeCCCccCHHHHHHHHHhC
Confidence 5678888899999999999999887654 22 333221 13467899998888987666655544
No 64
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=46.93 E-value=27 Score=29.81 Aligned_cols=60 Identities=20% Similarity=0.277 Sum_probs=41.8
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeeeecCc-----ceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVMRPYT-----NIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~-----~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
=.|--+..|...|...||++.+-...-.+.. ++.++.++.. ++.|...|+.+-||.+|..
T Consensus 11 n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~~sr~TIvv~~~~~~-ieqL~kQL~KLidVl~V~~ 75 (174)
T CHL00100 11 DESGVLTRIAGLFARRGFNIESLAVGPAEQKGISRITMVVPGDDRT-IEQLTKQLYKLVNILKVQD 75 (174)
T ss_pred CcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCCccEEEEEEECCHHH-HHHHHHHHHHHhHhhEEEe
Confidence 3577899999999999999988776443332 2234443322 7778888888888887765
No 65
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=45.68 E-value=48 Score=20.26 Aligned_cols=25 Identities=16% Similarity=0.185 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Q psy8853 47 KLRLAIEKALDANIPKNNIFRAIQK 71 (242)
Q Consensus 47 ~L~~ai~~Ak~~nmPk~~Ie~AIkk 71 (242)
-.-.+|..|+..|++++-|..-++.
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3567899999999999999988864
No 66
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=45.57 E-value=58 Score=27.26 Aligned_cols=60 Identities=23% Similarity=0.309 Sum_probs=44.3
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeeeecC---cce--ecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVMRPY---TNI--VFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~~P~---~~v--~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
=.|--|..|...+...||++.+--+..... ..+ .++. +-..+..+...|+.+.||.+|++
T Consensus 10 n~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~-d~~~i~qi~kQl~Kli~V~~V~~ 74 (157)
T TIGR00119 10 NEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVG-DDKVLEQITKQLNKLVDVIKVSD 74 (157)
T ss_pred CCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEEC-CHHHHHHHHHHHhcCccEEEEEe
Confidence 367889999999999999998765544431 122 2333 34578888999999999999987
No 67
>PRK04280 arginine repressor; Provisional
Probab=45.57 E-value=1.7e+02 Score=24.17 Aligned_cols=92 Identities=17% Similarity=0.107 Sum_probs=69.1
Q ss_pred EEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-------C------ChhHHHHHHHhcCCcceEee
Q psy8853 101 DCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-------T------KKNTLLDLALEKGAEDFLID 167 (242)
Q Consensus 101 e~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-------~------~~d~~~e~Aie~GaeDve~~ 167 (242)
+.+++|.=+|..+|...+.+.|-. .+..+++....+.|++.++.+ . +...-++.++.-.+.+|+-.
T Consensus 11 ~iI~~~~I~tQeeL~~~L~~~Gi~-vTQATiSRDikeL~lvKv~~~~G~~~Y~lp~~~~~~~~~~l~~~~~~~v~sv~~~ 89 (148)
T PRK04280 11 EIITNNEIETQDELVDRLREEGFN-VTQATVSRDIKELHLVKVPLPDGRYKYSLPADQRFNPLQKLKRALMDSFVKIDGA 89 (148)
T ss_pred HHHHhCCCCCHHHHHHHHHHcCCC-eehHHHHHHHHHcCCEEeecCCCcEEEeeccccccchHHHHHHHHHHHEEEEeee
Confidence 456788889999999999999876 456788999999999987532 1 12234555555555555554
Q ss_pred cCceEEEEeCcccHHHHHHHHHHCCCc
Q psy8853 168 KDNKITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 168 ed~~~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
+ ..+.|.|.|-.-..|...|...+++
T Consensus 90 ~-~~vvikT~pG~A~~va~~iD~~~~~ 115 (148)
T PRK04280 90 G-NLLVLKTLPGNANSIGALIDNLDWD 115 (148)
T ss_pred C-CEEEEEcCCChHHHHHHHHHhCCCC
Confidence 4 3788999999999999999988764
No 68
>PRK12338 hypothetical protein; Provisional
Probab=45.08 E-value=38 Score=31.65 Aligned_cols=129 Identities=16% Similarity=0.130 Sum_probs=75.8
Q ss_pred HHHHHHHHcCCC---HHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCcccc
Q psy8853 50 LAIEKALDANIP---KNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLS 126 (242)
Q Consensus 50 ~ai~~Ak~~nmP---k~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~ 126 (242)
..++.|+..++| +.++++++++.-.. =.++.. +-+.-.....+..++..++-++||.+-
T Consensus 173 ~l~~~A~e~~VpvI~N~did~Tv~~ile~----I~e~s~--------------~i~~~H~~~~~~~El~~I~vd~Gg~v~ 234 (319)
T PRK12338 173 HLVEQAREHNVPVIKNDDIDCTVKKMLSY----IREVCV--------------TVTLQHSVDDLDEVIEIIIKRHGGRIT 234 (319)
T ss_pred HHHHhHhhCCCceeCCCcHHHHHHHHHHH----HHhheE--------------EEEEeCCHHHHHHHHHeEEecCCCEEE
Confidence 567789999999 67778887766542 011211 113345678888899888789999876
Q ss_pred CCCcccccc--ceeeEEEECCCCChhHHHHHHHhcC-----CcceEeecCc--eEEEEe-CcccHHHHHHHHHHCCCcee
Q psy8853 127 KEGSVLFMF--KHCGQLLFLPNTKKNTLLDLALEKG-----AEDFLIDKDN--KITIIT-SPSKFIEIKNSLEMTGFKAE 196 (242)
Q Consensus 127 ~~gsv~~~F--~~kG~i~v~~~~~~d~~~e~Aie~G-----aeDve~~ed~--~~~~~c-~p~~~~~v~~~L~~~g~~v~ 196 (242)
+.--=-|=| .=+|-+.++...+-+..++..=+.. ++-.-.-.+| ...|.| +.+.|..+.++|+++||=+.
T Consensus 235 dV~h~iyG~~~~i~~~l~i~s~~dv~~Fi~~~~~~~~~~~~~~~L~~lT~gvH~Hti~a~~~e~l~~i~~~L~~~G~L~~ 314 (319)
T PRK12338 235 DISYPIPGFKDPLKREVNVSDPDEAEKFIKRLNENPKKKEDLKRLYSLSNNVHSHRICAPDEESLNRIIEELEEEGLLYE 314 (319)
T ss_pred EecccCCCCCceeEEEEccCCHHHHHHHHHHHhhCCccccchhhHHHHhCCeeEEEEEeCCHHHHHHHHHHHHHCCcccc
Confidence 432001111 1233333432234455555443333 2333222345 355655 56788999999999998653
No 69
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both.
Probab=44.50 E-value=1.2e+02 Score=30.47 Aligned_cols=138 Identities=12% Similarity=0.146 Sum_probs=83.1
Q ss_pred CCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCcccccccee
Q psy8853 59 NIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHC 138 (242)
Q Consensus 59 nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~k 138 (242)
.++-..|-++|++|... ...+-+..+.-+|+|.. --..++||..+.+..-+ | .+
T Consensus 75 ~~~l~~i~~~i~~A~~D-----~~IkgIvL~i~~~~g~~----------~~~~~ei~~ai~~fk~s-g--Kp-------- 128 (584)
T TIGR00705 75 AISLFDIVNAIRQAADD-----RRIEGLVFDLSNFSGWD----------SPHLVEIGSALSEFKDS-G--KP-------- 128 (584)
T ss_pred CcCHHHHHHHHHHHhcC-----CCceEEEEEccCCCCCC----------HHHHHHHHHHHHHHHhc-C--Ce--------
Confidence 56778999999999864 35566666665543311 11456788887654211 0 01
Q ss_pred eEEEECCCCChhHHHHHHHhcCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceee-----eecCcceecCHH
Q psy8853 139 GQLLFLPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIV-----MRPYTNIVFKDG 213 (242)
Q Consensus 139 G~i~v~~~~~~d~~~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~-----~~P~~~v~l~~e 213 (242)
|+.+......- ..-|-..|+.|-....|.+.++.-.....-++..|++.|++++.-... .-|-+.-+++++
T Consensus 129 -VvA~~~~~~s~---~YylAs~AD~I~~~p~G~v~~~G~~~~~~~~k~~ldKlGV~~~v~r~G~yKsa~epf~r~~mS~e 204 (584)
T TIGR00705 129 -VYAYGTNYSQG---QYYLASFADEIILNPMGSVDLHGFYTETLFYKGMLDKLGVRWHXFRVGTYKGAVEPFSRKDMSPE 204 (584)
T ss_pred -EEEEEccccch---hhhhhhhCCEEEECCCceEEeeceecccccHHHHHHHcCCeEEEeeccccccccCcccCCCCCHH
Confidence 11111011111 123446688887766676666555555455889999999986433221 224444578999
Q ss_pred HHHHHHHHHHHHh
Q psy8853 214 EAIKLQKLLNELK 226 (242)
Q Consensus 214 ~~~~~~~li~~Le 226 (242)
+.+.++.+++.|-
T Consensus 205 ~re~~~~~l~~l~ 217 (584)
T TIGR00705 205 ARRNYQRWLGELW 217 (584)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998874
No 70
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=44.41 E-value=53 Score=31.55 Aligned_cols=58 Identities=19% Similarity=0.230 Sum_probs=42.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHH
Q psy8853 49 RLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRN 116 (242)
Q Consensus 49 ~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~ 116 (242)
.+|+.-|... +|.+.|.++|+...+. .+ +.|-++ .+|+.+|.|+.--|+..+.+-|+.
T Consensus 289 laA~a~a~~~-i~~~~i~~~L~~f~~~---~~------R~e~~~~~~g~~~i~Dsy~~np~s~~~al~~ 347 (458)
T PRK01710 289 LAAFCAVNDD-VSIESMKKVATTFSGV---EH------RCEFVREINGVKYYNDSIASSPTRTLAGLKA 347 (458)
T ss_pred HHHHHHHHhC-CCHHHHHHHHHhCCCC---Cc------ceEEEEEECCEEEecccccCCHHHHHHHHHh
Confidence 3455556666 9999999999988865 22 344433 478999999999999977777754
No 71
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=44.40 E-value=19 Score=28.83 Aligned_cols=67 Identities=16% Similarity=0.086 Sum_probs=40.0
Q ss_pred EEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcc---------eec---------CHHHHHH--HHHHHHHHhcCCCc
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTN---------IVF---------KDGEAIK--LQKLLNELKKLHDV 231 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~---------v~l---------~~e~~~~--~~~li~~Lee~dDV 231 (242)
|+++++++++..+.+.|.+.+ +..-.+++.|..+ +.+ ..-.... +...+..+-++++|
T Consensus 1 y~~v~~~~~l~~~~~~l~~~~--~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i 78 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNAK--VLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI 78 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTTS--EEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred CEecCCHHHHHHHHHHHcCCC--eEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence 467778888888888887653 3333333333322 111 1111111 45666777789999
Q ss_pred ccceecccc
Q psy8853 232 KKVYTNALI 240 (242)
Q Consensus 232 ~~Vy~Ni~~ 240 (242)
..|.||+..
T Consensus 79 ~kv~~n~~~ 87 (176)
T PF01612_consen 79 IKVGHNAKF 87 (176)
T ss_dssp EEEESSHHH
T ss_pred cEEEEEEec
Confidence 999999864
No 72
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=44.37 E-value=61 Score=31.09 Aligned_cols=62 Identities=8% Similarity=0.088 Sum_probs=44.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+..||.-|...++|.+.|.++|+...+- .+ -++.+. .++|+.||-++.-.|+.-...-+..+
T Consensus 287 alaAia~a~~lGi~~~~i~~~L~~~~~~---~g-R~e~v~----~~~g~~iIDDsYn~nP~s~~aaL~~l 348 (453)
T PRK10773 287 ALAAAALAMSVGATLDAVKAGLANLKAV---PG-RLFPIQ----LAEGQLLLDDSYNANVGSMTAAAQVL 348 (453)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC-ceeEEE----CCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence 4567888999999999999999988764 22 233322 24678788788888877665555554
No 73
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=44.27 E-value=1.1e+02 Score=26.38 Aligned_cols=110 Identities=13% Similarity=0.160 Sum_probs=56.0
Q ss_pred cccceeeEEEECCCCCh---hHHHHHHHhcCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeec-ee-eeecCcc
Q psy8853 133 FMFKHCGQLLFLPNTKK---NTLLDLALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESS-GI-VMRPYTN 207 (242)
Q Consensus 133 ~~F~~kG~i~v~~~~~~---d~~~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~s-el-~~~P~~~ 207 (242)
+++.+..+..+-.++++ .++++..-+.|..--...+.+.|.|..+..++.+.+-.|.+.|++-... .. .+.++..
T Consensus 21 ~~~~~~~y~~L~~~l~~~da~~i~~~L~~~gI~y~~~~~g~~~~I~Vp~~~~~~ar~~La~~glp~~~~~g~~~~~~~~~ 100 (206)
T PF01514_consen 21 LWSSRPDYVVLYSGLDEEDANEIVAALDENGIPYKLSDDGGTWTILVPEDQVARARMLLASQGLPKSGFSGFEELFDNSS 100 (206)
T ss_dssp -----E--EEEEEEE-HHHHHHHHHHHHHTT--EEEEE-TTSEEEEEEGGGHHHHHHHHHHTT-S------CCHHTTT-S
T ss_pred HHhcCCCceecccCCCHHHHHHHHHHHHHCCCCcEecCCCCeeEEEeCHHHHHHHHHHHHHcCCCCCCCCCHHHHhccCC
Confidence 44444433333223443 3455555567776544433335889999999999999999999975432 34 4466655
Q ss_pred eecCHHH-HHHH-----HHHHHHHhcCCCcccceeccccCC
Q psy8853 208 IVFKDGE-AIKL-----QKLLNELKKLHDVKKVYTNALIFD 242 (242)
Q Consensus 208 v~l~~e~-~~~~-----~~li~~Lee~dDV~~Vy~Ni~~~~ 242 (242)
.-.++.+ ...+ ..|-..|+.+|.|...-=++.+|+
T Consensus 101 ~~~T~~~~~~~~~~ale~eL~~tI~~i~gV~~A~V~l~~Pe 141 (206)
T PF01514_consen 101 FGTTDFEEKVNYQRALEGELERTIESIDGVESARVHLVLPE 141 (206)
T ss_dssp ---SHHHHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEE--
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHcCCCeeEEEEEEecCC
Confidence 5555533 2333 234556788899987766665553
No 74
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=43.96 E-value=61 Score=31.33 Aligned_cols=61 Identities=16% Similarity=0.202 Sum_probs=46.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+..|+.-|...++|.+.|.++|+...+- . -++|..+ .+|+.+|.|+--.|+.-+..-++.+
T Consensus 280 a~aAia~~~~lgi~~~~i~~~L~~F~~~---~------~Rle~v~~~~gv~~i~DS~atN~~a~~~al~~~ 341 (454)
T PRK01368 280 IAASYAVAKIIGVEPKKILESISSFQSL---P------HRMQYIGSINNISFYNDSKATNAISAVQSIKAL 341 (454)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---C------cceEEEEEECCeEEEECCCCCCHHHHHHHHHhc
Confidence 4567788888899999999999987764 2 2333333 2689999998888998888877776
No 75
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=43.62 E-value=76 Score=29.93 Aligned_cols=48 Identities=19% Similarity=0.215 Sum_probs=37.9
Q ss_pred EeCcccHHH--HHHHHHHCCCceeeceeeeecCcceecCHHH-HHHHHHHHHHHhcC
Q psy8853 175 ITSPSKFIE--IKNSLEMTGFKAESSGIVMRPYTNIVFKDGE-AIKLQKLLNELKKL 228 (242)
Q Consensus 175 ~c~p~~~~~--v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~-~~~~~~li~~Lee~ 228 (242)
.|+|..+.. +++.|++.|+++..-+..|. . +.++ ..+++.|+|.|++-
T Consensus 324 fC~~~~~e~~~lk~~l~e~GIP~L~iE~D~~-~-----~~gQi~TRlEAFlEml~~~ 374 (377)
T TIGR03190 324 FCDPHEGDYPDLKRHLEANGIPTLFLEFDIT-N-----PIGPFRIRIEAFLETLSEE 374 (377)
T ss_pred CCCcchhhhHHHHHHHHHCCCCEEEEecCCC-C-----chHHHHHHHHHHHHHHhhc
Confidence 699998866 89999999999888887775 1 2334 56899999999753
No 76
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=43.45 E-value=19 Score=26.94 Aligned_cols=21 Identities=14% Similarity=0.314 Sum_probs=17.7
Q ss_pred ccHHHHHHHHHHCCCceeece
Q psy8853 179 SKFIEIKNSLEMTGFKAESSG 199 (242)
Q Consensus 179 ~~~~~v~~~L~~~g~~v~~se 199 (242)
..|..|+++|+++||+|..-+
T Consensus 8 ~~Ls~v~~~L~~~GyeVv~l~ 28 (80)
T PF03698_consen 8 EGLSNVKEALREKGYEVVDLE 28 (80)
T ss_pred CCchHHHHHHHHCCCEEEecC
Confidence 568999999999999986544
No 77
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=43.12 E-value=2.1e+02 Score=24.39 Aligned_cols=134 Identities=13% Similarity=0.057 Sum_probs=72.4
Q ss_pred HHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEE
Q psy8853 62 KNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQL 141 (242)
Q Consensus 62 k~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i 141 (242)
-+.|.++|+++... .....+...+-.|||... ...+|+..+.++.. .|=++
T Consensus 15 ~~~l~~~l~~a~~d-----~~i~~vvl~~~s~Gg~~~-----------~~~~l~~~i~~~~~-------------~kpvi 65 (207)
T TIGR00706 15 PEDFDKKIKRIKDD-----KSIKALLLRINSPGGTVV-----------ASEEIYEKLKKLKA-------------KKPVV 65 (207)
T ss_pred HHHHHHHHHHHhhC-----CCccEEEEEecCCCCCHH-----------HHHHHHHHHHHhcC-------------CCCEE
Confidence 45677888888743 244567777778877432 34667776666530 11122
Q ss_pred EECCCCChhHHHHHHHhcCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceee---ceeeeecCcceecCHHHHHHH
Q psy8853 142 LFLPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAES---SGIVMRPYTNIVFKDGEAIKL 218 (242)
Q Consensus 142 ~v~~~~~~d~~~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~---sel~~~P~~~v~l~~e~~~~~ 218 (242)
.+-.+....--..+|+ .|+-+--.+.+.+-.+.-.......++.|++.|+++.. .+..=.+...-++++++.+.+
T Consensus 66 a~v~g~a~s~g~~la~--aaD~i~a~p~a~vg~iGv~~~~~~~~~~l~k~Gv~~~~~~~g~~K~~~~~~~~~s~~~~e~~ 143 (207)
T TIGR00706 66 ASMGGVAASGGYYIAM--AADEIVANPGTITGSIGVILQGANVEKLYEKLGIEFEVIKSGEYKDIGSPTRELTPEERDIL 143 (207)
T ss_pred EEECCccchHHHHHHh--cCCEEEECCCCeEEeeeEEEecCCHHHHHHhCCceEEEEEcCCCcCCCCCCCCCCHHHHHHH
Confidence 2222212223344444 45555555543333322222334478889999987522 222222222236788888888
Q ss_pred HHHHHHHh
Q psy8853 219 QKLLNELK 226 (242)
Q Consensus 219 ~~li~~Le 226 (242)
+.+++.+.
T Consensus 144 ~~~l~~~~ 151 (207)
T TIGR00706 144 QNLVNESY 151 (207)
T ss_pred HHHHHHHH
Confidence 88887664
No 78
>PF14502 HTH_41: Helix-turn-helix domain
Probab=42.59 E-value=20 Score=24.31 Aligned_cols=44 Identities=16% Similarity=0.161 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEE
Q psy8853 47 KLRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAI 98 (242)
Q Consensus 47 ~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~i 98 (242)
||..+-+-+.+.++..-+|++||+.-... ..|..|-.|.-|.+|
T Consensus 5 Ri~tI~e~~~~~~vs~GtiQ~Alk~Le~~--------gaI~Le~rGh~GTfi 48 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSRGTIQNALKFLEEN--------GAIKLESRGHLGTFI 48 (48)
T ss_pred ccCCHHHHHHHhCcchhHHHHHHHHHHHC--------CcEEeeecCcCcccC
Confidence 66778888999999999999999977643 256788888777653
No 79
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=41.26 E-value=99 Score=21.93 Aligned_cols=49 Identities=16% Similarity=0.250 Sum_probs=33.3
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC--cc------eecCHHHHHHHHHHHHHHhcC
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY--TN------IVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~--~~------v~l~~e~~~~~~~li~~Lee~ 228 (242)
.|-.|..|-+.+...|+++.. |+-+|. .+ |+++. +.+.+.++++.|+..
T Consensus 10 ~pG~L~~vL~~f~~~~iNlt~--IeSRP~~~~~~~y~Ffvd~~~-~~~~~~~~l~~L~~~ 66 (74)
T cd04904 10 EVGALARALKLFEEFGVNLTH--IESRPSRRNGSEYEFFVDCEV-DRGDLDQLISSLRRV 66 (74)
T ss_pred CCcHHHHHHHHHHHCCCcEEE--EECCCCCCCCceEEEEEEEEc-ChHHHHHHHHHHHHh
Confidence 478888999999888876544 444554 22 56654 334588888888764
No 80
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=41.08 E-value=86 Score=21.38 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=20.7
Q ss_pred EEecCCcchhHHHHHHHhhhcCccc
Q psy8853 101 DCITNNRMRTVSNIRNIFNKNGGNL 125 (242)
Q Consensus 101 e~lTdN~nRt~~~vr~~f~K~gg~l 125 (242)
.+..+|.....++|-.+|.++|.++
T Consensus 5 ~v~v~d~pG~La~v~~~l~~~~inI 29 (66)
T cd04908 5 SVFLENKPGRLAAVTEILSEAGINI 29 (66)
T ss_pred EEEEcCCCChHHHHHHHHHHCCCCE
Confidence 4467888889999999999998876
No 81
>PRK03094 hypothetical protein; Provisional
Probab=40.48 E-value=24 Score=26.51 Aligned_cols=19 Identities=11% Similarity=0.464 Sum_probs=16.6
Q ss_pred ccHHHHHHHHHHCCCceee
Q psy8853 179 SKFIEIKNSLEMTGFKAES 197 (242)
Q Consensus 179 ~~~~~v~~~L~~~g~~v~~ 197 (242)
+.|..|++.|+++||+|..
T Consensus 8 ~~Ls~i~~~L~~~GYeVv~ 26 (80)
T PRK03094 8 QSLTDVQQALKQKGYEVVQ 26 (80)
T ss_pred cCcHHHHHHHHHCCCEEEe
Confidence 5788999999999999854
No 82
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=40.37 E-value=80 Score=30.31 Aligned_cols=60 Identities=20% Similarity=0.256 Sum_probs=44.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
...|+.-|...++|.+.|..+|+...+- .+ ++|... .+|+.+|+| .-.|+.-+.+-++.+
T Consensus 283 alaAia~a~~lgi~~~~i~~~L~~~~~~---~g------R~e~~~~~~~~~iI~D-yahNP~s~~aal~~l 343 (460)
T PRK00139 283 LLAALAALLALGVPLEDALAALAKLQGV---PG------RMERVDAGQGPLVIVD-YAHTPDALEKVLEAL 343 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC------CcEEEEcCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 4467778888999999999999988754 22 344443 368899999 788887777666665
No 83
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=39.70 E-value=29 Score=22.74 Aligned_cols=22 Identities=14% Similarity=0.289 Sum_probs=16.1
Q ss_pred HHHHHHcCCCHHHHHHHHHhcC
Q psy8853 52 IEKALDANIPKNNIFRAIQKNN 73 (242)
Q Consensus 52 i~~Ak~~nmPk~~Ie~AIkk~~ 73 (242)
-+.|+..|||+.+|.+-++...
T Consensus 20 r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 20 RKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp HHHHHHHT--HHHHHHHHHHTT
T ss_pred HHHHHHHCcCHHHHHHHHcCCC
Confidence 3558899999999998887654
No 84
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=39.17 E-value=83 Score=30.42 Aligned_cols=59 Identities=20% Similarity=0.180 Sum_probs=42.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+. .+- .+ ++|..+ .+|+.+|+| .-.|+.-..+-+..+
T Consensus 301 alaAia~a~~lgi~~~~i~~~L~~-~~~---~g------R~e~i~~~~g~~vi~D-yahNP~s~~aal~~l 360 (481)
T PRK14022 301 AMAAGLACLRLGASLEDIQKGIAQ-TPV---PG------RMEVLTQSNGAKVFID-YAHNGDSLNKLIDVV 360 (481)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcc-CCC---CC------CeEEEECCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 456778888899999999999988 543 22 344444 368889999 677776665555554
No 85
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=38.47 E-value=2.4e+02 Score=23.68 Aligned_cols=123 Identities=13% Similarity=0.154 Sum_probs=69.7
Q ss_pred EEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeE--EEECCCCChhHHHHHHH-h-cCCcceEe----ec-C
Q psy8853 99 IVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQ--LLFLPNTKKNTLLDLAL-E-KGAEDFLI----DK-D 169 (242)
Q Consensus 99 ive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~--i~v~~~~~~d~~~e~Ai-e-~GaeDve~----~e-d 169 (242)
++.++.+|.....+.|-.+|.++|.++-. -++..- +..|+ +.+.-..+.+ .++..+ . .-..||-. .+ +
T Consensus 4 ~IsV~veN~pGvL~rI~~lf~rrg~NI~S-l~v~~t-e~~~~sriti~V~~~~~-~i~qi~kQl~KLidV~~V~~~~~~~ 80 (161)
T PRK11895 4 TLSVLVENEPGVLSRVAGLFSRRGYNIES-LTVGPT-EDPGLSRMTIVTSGDEQ-VIEQITKQLNKLIDVLKVVDLTEEA 80 (161)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCcEEE-EEeeec-CCCCEEEEEEEEECCHH-HHHHHHHHHhccccEEEEEecCCcc
Confidence 56779999999999999999999997731 112111 11233 3332222332 233222 1 13333322 11 1
Q ss_pred ------ceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcC
Q psy8853 170 ------NKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 170 ------~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~ 228 (242)
-.+.|.|++..-..+.+-.+..+-.+....-.++ .++++... +++..|++.|+..
T Consensus 81 ~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivdv~~~~~---~iE~tG~~-~ki~~~~~~l~~~ 141 (161)
T PRK11895 81 HVERELALVKVRASGENRAEILRLADIFRAKIVDVTPESL---TIEVTGDS-DKIDAFIDLLRPY 141 (161)
T ss_pred hhheEEEEEEEECCcccHHHHHHHHHHhCCEEEEecCCEE---EEEEeCCH-HHHHHHHHHhhhc
Confidence 1478899998888888888877666654432221 45664322 4566666666554
No 86
>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=38.43 E-value=51 Score=23.39 Aligned_cols=37 Identities=14% Similarity=0.210 Sum_probs=30.2
Q ss_pred EEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceee
Q psy8853 99 IVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCG 139 (242)
Q Consensus 99 ive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG 139 (242)
++|+.|.++....++|-.+|..+|.++-. +.+|..-|
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~----A~i~t~~~ 38 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVE----ARAWTHNG 38 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEE----EEEEEECC
Confidence 68999999999999999999999998863 35554433
No 87
>PRK14093 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional
Probab=38.37 E-value=1.2e+02 Score=29.24 Aligned_cols=65 Identities=11% Similarity=-0.032 Sum_probs=45.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+||.-|...++|.+.|.++|++.... .+ -++..+++.. .+++.||=||.-.|+.-..+-|+.+
T Consensus 296 alaAia~a~~lGi~~~~i~~~l~~~~~~---~g-R~~~~r~~~~-~~~~~iIDDsYahnP~s~~aaL~~l 360 (479)
T PRK14093 296 SLAVLAAAELAGADLALAALALSQVQPA---AG-RGVRHTLEVG-GGEATLIDESYNANPASMAAALGVL 360 (479)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCc---CC-cceEEEeecC-CCCEEEEECCCCCCHHHHHHHHHHH
Confidence 3467888999999999999999988754 22 3456667733 3556666567777776666666554
No 88
>PF02016 Peptidase_S66: LD-carboxypeptidase; InterPro: IPR003507 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature is found in the Escherichia coli microcin C7 self-immunity protein mccF and in muramoyltetrapeptide carboxypeptidase (3.4.17.13 from EC, LD-carboxypeptidase A). LD-carboxypeptidase A belongs to MEROPS peptidase family S66 (clan SS). The entry also contains uncharacterised proteins including hypothetical proteins from various bacteria archaea.; PDB: 1ZRS_A 1ZL0_B 2AUM_B 2AUN_B 3TLG_A 3TLC_A 3TLZ_B 3TLY_B 3TLE_A 3TLB_B ....
Probab=38.36 E-value=30 Score=31.41 Aligned_cols=56 Identities=14% Similarity=0.242 Sum_probs=39.3
Q ss_pred cccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 178 PSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 178 p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
++.+..-.+.|++.||+|......+-.... +...+.++...|.+++.+ |+|..|+.
T Consensus 13 ~~~l~~~~~~L~~~G~~v~~~~~~~~~~~~--~ags~~~Ra~dL~~a~~d-~~i~aI~~ 68 (284)
T PF02016_consen 13 PERLERGIKRLESWGFKVVVGPHVFKRDGY--LAGSDEERAEDLNEAFAD-PEIDAIWC 68 (284)
T ss_dssp HHHHHHHHHHHHHTTEEEEE-TTTTS-BTT--BSS-HHHHHHHHHHHHHS-TTEEEEEE
T ss_pred HHHHHHHHHHHHhCCCEEEECCcccccCCC--cCCCHHHHHHHHHHHhcC-CCCCEEEE
Confidence 356778888999999998887766666443 344555688888888865 88888875
No 89
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=37.81 E-value=1.5e+02 Score=26.82 Aligned_cols=84 Identities=24% Similarity=0.286 Sum_probs=56.8
Q ss_pred hHHHHHHHhcCCcceEe-ecCceEEEEeCcccHHHHHHHHHHCCCceee--ceeeeecCc-ceecCHHHHHHH-----HH
Q psy8853 150 NTLLDLALEKGAEDFLI-DKDNKITIITSPSKFIEIKNSLEMTGFKAES--SGIVMRPYT-NIVFKDGEAIKL-----QK 220 (242)
Q Consensus 150 d~~~e~Aie~GaeDve~-~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~--sel~~~P~~-~v~l~~e~~~~~-----~~ 220 (242)
.+++-+....|.+=.+. +++|.+.+..++++|..--+-|...||+-.. .=..+.|.+ .|.=+-++..++ ++
T Consensus 34 NemlAlL~~~gI~A~K~~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP~eEkaR~~~~~eQ~ 113 (246)
T COG4669 34 NEMLALLMSHGINAEKKADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSPTEEKARLNYAKEQQ 113 (246)
T ss_pred HHHHHHHHHcCCcceeeccCCCceEEEEcHHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCcHHHHHHHHHHHHHH
Confidence 35566666777776665 4567899999999999999999999997432 113445554 444444555444 34
Q ss_pred HHHHHhcCCCccc
Q psy8853 221 LLNELKKLHDVKK 233 (242)
Q Consensus 221 li~~Lee~dDV~~ 233 (242)
|=..|..+|.|..
T Consensus 114 le~tLs~mDGVi~ 126 (246)
T COG4669 114 LEQTLSKMDGVIS 126 (246)
T ss_pred HHHHHHhcCceEE
Confidence 5556788888754
No 90
>cd07062 Peptidase_S66_mccF_like Microcin C7 self-immunity protein determines resistance to exogenous microcin C7. Microcin C7 self-immunity protein (mccF): MccF, a homolog of the LD-carboxypeptidase family, mediates resistance against exogenously added microcin C7 (MccC7), a ribosomally-encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. The plasmid-encoded mccF gene is transcribed in the opposite direction to the other five genes (mccA-E) and is required for the full expression of immunity but not for production. The catalytic triad residues (Ser, His, Glu) of LD-carboxypeptidase are also conserved in MccF, strongly suggesting that MccF shares the hydrolytic activity with LD-carboxypeptidases. Substrates of MccF have not been deduced, but could likely be microcin C7 precursors. The possible role of MccF is to defend producer cells against exogenous microcin from re-entering after having been exported. It is suggested that M
Probab=37.61 E-value=53 Score=30.08 Aligned_cols=56 Identities=14% Similarity=0.248 Sum_probs=41.5
Q ss_pred cccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 178 PSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 178 p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
+..+....+.|++.||+|......|..... +...+.++...|.+++. +|+|..|+.
T Consensus 17 ~~~~~~~~~~L~~~G~~v~~~~~~~~~~~~--~ag~~~~Ra~dL~~a~~-Dp~i~aI~~ 72 (308)
T cd07062 17 PHRLERAKKRLENLGFEVVEGPNALKGDKY--LSASPEERAEELMAAFA-DPSIKAIIP 72 (308)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccccccc--ccCCHHHHHHHHHHHhc-CCCCCEEEE
Confidence 345778888999999999888877776553 44444558888888884 677888775
No 91
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=37.33 E-value=70 Score=26.91 Aligned_cols=60 Identities=18% Similarity=0.272 Sum_probs=41.9
Q ss_pred eCcccHHHHHHHHHHCCCceeeceeeeec--C-ccee--cCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 176 TSPSKFIEIKNSLEMTGFKAESSGIVMRP--Y-TNIV--FKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 176 c~p~~~~~v~~~L~~~g~~v~~sel~~~P--~-~~v~--l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
=.|--|..|...+...||++.+--+...- . ..+. ++. +-..+++++..|+.+.||.+|++
T Consensus 11 N~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~-~~~~i~qi~kQl~KLidV~~V~~ 75 (161)
T PRK11895 11 NEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSG-DEQVIEQITKQLNKLIDVLKVVD 75 (161)
T ss_pred CCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEEC-CHHHHHHHHHHHhccccEEEEEe
Confidence 36788999999999999999775544332 1 1233 232 33467777788888899998876
No 92
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=37.26 E-value=90 Score=24.54 Aligned_cols=56 Identities=14% Similarity=0.131 Sum_probs=39.1
Q ss_pred eEEEEeCccc---HHHHHHHHHHCCCceeeceeeeecCcceecCH-HHHHHHHHHHHHHhcCC
Q psy8853 171 KITIITSPSK---FIEIKNSLEMTGFKAESSGIVMRPYTNIVFKD-GEAIKLQKLLNELKKLH 229 (242)
Q Consensus 171 ~~~~~c~p~~---~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~-e~~~~~~~li~~Lee~d 229 (242)
++.|+-.+.. +.+|.+.|++.|..++-..-.|+ .+.+++ -++..+..+++.+++..
T Consensus 54 TiRv~~~~~~~~~~~~v~~~l~~lG~~~E~~~~~~l---av~VP~~~~~~~i~~~L~~~~e~g 113 (117)
T PF14085_consen 54 TIRVIFDDPGPDDIEAVREELEALGCTVEGFSERML---AVDVPPSVDFDAIKDYLDRGEEQG 113 (117)
T ss_pred EEEEEEcCCcchhHHHHHHHHHHcCCeEEccCCCEE---EEEECCCCCHHHHHHHHHhhhhcC
Confidence 6776665554 59999999999987765554333 445544 46788888888887754
No 93
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=37.22 E-value=77 Score=25.65 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=33.7
Q ss_pred HHHHHCCCceeeceeeeecC---cceecCHHHHHHHHHHHHHHhcC
Q psy8853 186 NSLEMTGFKAESSGIVMRPY---TNIVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 186 ~~L~~~g~~v~~sel~~~P~---~~v~l~~e~~~~~~~li~~Lee~ 228 (242)
-.|+..|+++....|.|++. -.|++++++...+.++++.+.++
T Consensus 91 ~lL~~~g~~v~~G~i~y~~~~~~~~v~~~~~~~~~v~~~i~~i~~~ 136 (162)
T PF01930_consen 91 LLLEEFGIPVKRGYIYYIEDRKRVRVEITEELRRKVEKLIEEIRKI 136 (162)
T ss_pred HHHHhcCccceeEEEEEecCCeEEEEeCCHHHHHHHHHHHHHHHHH
Confidence 34666699998888888886 36778899989999998888654
No 94
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=37.07 E-value=1e+02 Score=21.84 Aligned_cols=54 Identities=17% Similarity=0.167 Sum_probs=38.9
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecCc-----ceecCHHHHHHHHHHHHHHhcCCC
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPYT-----NIVFKDGEAIKLQKLLNELKKLHD 230 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~~-----~v~l~~e~~~~~~~li~~Lee~dD 230 (242)
.|--++.|...|.+.|.++..++...+... .|+++++..+++.+-+..|....+
T Consensus 12 rpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~l~~~~~ 70 (76)
T PF13740_consen 12 RPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEELAEELG 70 (76)
T ss_dssp -TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHHHHHHTT
T ss_pred CCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHHHHHHCC
Confidence 366678999999999999988887777653 345677777778777777754444
No 95
>PHA03188 UL14 tegument protein; Provisional
Probab=36.88 E-value=2.8e+02 Score=24.18 Aligned_cols=65 Identities=20% Similarity=0.253 Sum_probs=40.0
Q ss_pred CCCcchhHHh---HHHhHHhHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhc
Q psy8853 1 MAGHSKWANI---KRKKLIVDAKRGKICTRIMRELRVAINFGNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKN 72 (242)
Q Consensus 1 maGHsKW~nI---kh~K~~~Da~k~k~f~kl~reI~~Avk~G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~ 72 (242)
|+||..++-- ++..-+.--.|..+|--=.-+ -++.|.||+ +|.+..+.-.||.+ -..+++.|...
T Consensus 1 ~~~~~~~~~~~RrrR~~L~Ea~~Re~iyK~RTLd---Lir~GVd~~-dP~FV~AFTsAK~A---~~dl~rqLrs~ 68 (199)
T PHA03188 1 MSGHTPLSAAHRRNRVHLLEAHHRAGLFKERTLD---LIRGGASTQ-DPAFVHAFTAAKDA---CADLNNNIRSA 68 (199)
T ss_pred CCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHcCCCCC-ChHHHHHHHHHHHH---HHHHHHHHHHH
Confidence 8999887532 222333444455555321111 123388885 99999999999998 56677777533
No 96
>PRK10949 protease 4; Provisional
Probab=36.02 E-value=4.9e+02 Score=26.57 Aligned_cols=138 Identities=10% Similarity=0.067 Sum_probs=88.1
Q ss_pred CCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCcccccccee
Q psy8853 59 NIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHC 138 (242)
Q Consensus 59 nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~k 138 (242)
.++-..|-.+|++|... ...+-+..+.-+|+|..+ -+.++||..+.+...+ |. +
T Consensus 94 ~~~l~div~~i~~Aa~D-----~rIkgivL~i~s~gG~~~----------a~~~eI~~ai~~fk~s-GK--p-------- 147 (618)
T PRK10949 94 ENSLFDIVNTIRQAKDD-----RNITGIVLDLKNFAGADQ----------PSMQYIGKALREFRDS-GK--P-------- 147 (618)
T ss_pred cccHHHHHHHHHHHhcC-----CCceEEEEEeCCCCCccH----------HHHHHHHHHHHHHHHh-CC--e--------
Confidence 35667899999999864 356677777777766321 2467888887765321 00 1
Q ss_pred eEEEECCCCChhHHHHHHHhcCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeeceeee-----ecCcceecCHH
Q psy8853 139 GQLLFLPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVM-----RPYTNIVFKDG 213 (242)
Q Consensus 139 G~i~v~~~~~~d~~~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~-----~P~~~v~l~~e 213 (242)
++.+....+.... -|-..|+.|-....|.+.++.-.....-++..|++.|++++.-...= -|-+.-+.+++
T Consensus 148 -VvA~~~~~~s~~Y---yLASaAD~I~l~P~G~v~~~G~~~~~~~~k~lLdKlGV~~~v~r~G~yKsA~epf~r~~mS~e 223 (618)
T PRK10949 148 -VYAVGDSYSQGQY---YLASFANKIYLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPA 223 (618)
T ss_pred -EEEEecCccchhh---hhhhhCCEEEECCCceEEEeeeecchhhHHHHHHHcCCeEEEEEecCCCCCCCcccCCCCCHH
Confidence 1111111111121 23456888877777777777777777788999999999865322211 24444567999
Q ss_pred HHHHHHHHHHHHh
Q psy8853 214 EAIKLQKLLNELK 226 (242)
Q Consensus 214 ~~~~~~~li~~Le 226 (242)
+.+.++.+++.|-
T Consensus 224 ~Re~~~~ll~~l~ 236 (618)
T PRK10949 224 AREADSRWIGELW 236 (618)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999884
No 97
>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetase. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown.
Probab=35.63 E-value=1.1e+02 Score=29.22 Aligned_cols=61 Identities=20% Similarity=0.177 Sum_probs=44.0
Q ss_pred HHHHHHHHHHcC-CCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDAN-IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~n-mPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
..+|+.-|...+ +|.+.|..+|+...+. .+ -++.+. ..+|+.+|.+ ...|+.-+.+-+..+
T Consensus 291 alaAia~a~~lg~i~~e~i~~~L~~~~~~---~g-R~e~~~----~~~g~~vi~D-y~~NP~s~~aal~~l 352 (464)
T TIGR01085 291 LLAALATLLHLGGIDLEDIVAALEKFRGV---PG-RMELVD----GGQKFLVIVD-YAHTPDALEKALRTL 352 (464)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHhCCCC---CC-CcEEEE----cCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 346777788888 9999999999988864 22 333322 1368889999 788887776666665
No 98
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=34.08 E-value=79 Score=30.27 Aligned_cols=61 Identities=23% Similarity=0.242 Sum_probs=39.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEe--cCCcchhHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCI--TNNRMRTVSNIRN 116 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~l--TdN~nRt~~~vr~ 116 (242)
+.+|+..|...++|.+.|.++|+...+- .+ -++.+. ..+|+.+|.+.- -+|...+...++.
T Consensus 284 ~~aA~a~~~~lgv~~~~i~~~l~~f~~~---~~-R~e~~~----~~~g~~~i~D~aHnp~~~~a~~~al~~ 346 (461)
T PRK00421 284 ALAAIAVALELGIDDEAIREALATFKGV---KR-RFEEKG----EVGGVVLIDDYAHHPTEIKATLKAARQ 346 (461)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---Cc-ccEEEE----ecCCcEEEEeCCCCHHHHHHHHHHHHh
Confidence 4467778888999999999999988764 22 233221 135788998841 3334445555553
No 99
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=34.07 E-value=1.3e+02 Score=19.52 Aligned_cols=27 Identities=11% Similarity=0.254 Sum_probs=23.3
Q ss_pred EEecCCcchhHHHHHHHhhhcCccccC
Q psy8853 101 DCITNNRMRTVSNIRNIFNKNGGNLSK 127 (242)
Q Consensus 101 e~lTdN~nRt~~~vr~~f~K~gg~l~~ 127 (242)
.+.++|..+..++|-.+|.++|.++..
T Consensus 3 ~v~~~d~~g~l~~i~~~l~~~~~nI~~ 29 (71)
T cd04879 3 LIVHKDVPGVIGKVGTILGEHGINIAA 29 (71)
T ss_pred EEEecCCCCHHHHHHHHHHhcCCCeee
Confidence 457889999999999999999998753
No 100
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (murein tripeptide ligase) is described by TIGR01081.
Probab=33.80 E-value=74 Score=30.36 Aligned_cols=46 Identities=26% Similarity=0.283 Sum_probs=32.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEE
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVD 101 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive 101 (242)
+.+|+..|...++|.+.|..+|+...+- .. -++.+ .+ .+|+.+|.+
T Consensus 278 ~~aA~a~~~~lgi~~~~i~~~l~~f~~~---~~-R~e~~-~~---~~gv~~i~D 323 (448)
T TIGR01082 278 ALAAIAVALELGIDFEAILRALANFQGV---KR-RFEIL-GE---FGGVLLIDD 323 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---Cc-cceEE-EE---eCCeEEEEc
Confidence 4577788888999999999999988864 21 23322 11 357888887
No 101
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.65 E-value=31 Score=26.66 Aligned_cols=20 Identities=25% Similarity=0.539 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHhcCCCcccc
Q psy8853 215 AIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 215 ~~~~~~li~~Lee~dDV~~V 234 (242)
...+.+|++-|.+..|||+|
T Consensus 16 AAaFRrLv~HL~~rsdvQNI 35 (104)
T COG3492 16 AAAFRRLVEHLQERSDVQNI 35 (104)
T ss_pred HHHHHHHHHHHHHhcccchh
Confidence 45789999999999999987
No 102
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=33.60 E-value=2.2e+02 Score=21.93 Aligned_cols=55 Identities=16% Similarity=0.071 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHHhc--CCCCCCCHHHHHHHHHHHHc------CCCHHHHHHHHHhcCC
Q psy8853 20 KRGKICTRIMRELRVAINF--GNNPDTNIKLRLAIEKALDA------NIPKNNIFRAIQKNNS 74 (242)
Q Consensus 20 ~k~k~f~kl~reI~~Avk~--G~dP~~N~~L~~ai~~Ak~~------nmPk~~Ie~AIkk~~g 74 (242)
+..+++.-+++.-..||-+ +...+..-++..|+...+.. +++-+.|+.+|..|-.
T Consensus 40 ~~~~~~~~vak~Av~aveq~~~~~~~G~~K~~~A~~~v~~~L~~~gi~~t~~~i~~~IEaAV~ 102 (108)
T PF09682_consen 40 KLVKILEIVAKIAVNAVEQVAKEGGKGEEKKAEAVQYVKERLKKKGIKVTDEQIEGAIEAAVK 102 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 4455566677888888777 34447777888887776665 8889999999987753
No 103
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=33.26 E-value=1.1e+02 Score=29.56 Aligned_cols=61 Identities=16% Similarity=0.229 Sum_probs=43.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- .+ |+|-.+ .+|+.+|-++--.|+.-+.+-++.+
T Consensus 325 alaAia~~~~lgi~~~~i~~aL~~f~~~---~g------R~e~~~~~~g~~~idDs~~tn~~s~~~al~~~ 386 (498)
T PRK02006 325 ALAALALARAIGLPAAPLLHGLREYRGE---PH------RVELVATIDGVDYYDDSKGTNVGATVAALDGL 386 (498)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCC---CC------ceEEEEEECCEEEEEcCCCCCHHHHHHHHHhC
Confidence 3567788888999999999999987764 22 344433 2677777777656776666666653
No 104
>PF05423 Mycobact_memb: Mycobacterium membrane protein; InterPro: IPR008693 This family contains several membrane proteins from Mycobacterium species [].
Probab=33.17 E-value=60 Score=26.69 Aligned_cols=21 Identities=19% Similarity=0.283 Sum_probs=16.8
Q ss_pred eEEEEEEeccCCeEEEEEEec
Q psy8853 84 IEVRYEGYSVNGAAIIVDCIT 104 (242)
Q Consensus 84 ~~~~yEg~gPgGv~iive~lT 104 (242)
..++||..||.|...-|.-+.
T Consensus 51 k~V~YEV~G~~G~~~~I~Y~D 71 (140)
T PF05423_consen 51 KTVTYEVTGPPGSTATISYLD 71 (140)
T ss_pred cEEEEEEEcCCCCeEEEEEEc
Confidence 689999999988766666653
No 105
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=33.07 E-value=98 Score=32.67 Aligned_cols=62 Identities=21% Similarity=0.148 Sum_probs=45.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+...+- .+ -++.+.. ++|+.+|.++.-.|+.-+.+-|..+
T Consensus 796 alaAia~a~~lGi~~~~i~~~L~~f~~~---~g-R~e~~~~----~~~~~iidDsya~np~s~~aaL~~l 857 (958)
T PRK11929 796 ALAAIACALAAGASLKQIRAGLERFQPV---AG-RMQRRRL----SCGTRIIDDTYNANPDSMRAAIDVL 857 (958)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCC---CC-CceEEEc----CCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 4568888999999999999999988764 22 2332221 4788999999888887666656544
No 106
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=33.06 E-value=97 Score=21.16 Aligned_cols=51 Identities=20% Similarity=0.227 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCC
Q psy8853 24 ICTRIMRELRVAINFGNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSN 75 (242)
Q Consensus 24 ~f~kl~reI~~Avk~G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~ 75 (242)
++.++...|...+..|. ...+.+|=+.-+-|+..+++..++.+|+++-...
T Consensus 1 l~~~i~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp HHHHHHHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 35677788888888742 2234566666677899999999999999987643
No 107
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=33.01 E-value=2.1e+02 Score=25.05 Aligned_cols=53 Identities=21% Similarity=0.139 Sum_probs=39.6
Q ss_pred CChhHHHHHHHhcCCcceEeecCc--eEE--EEeCcccHHHHHHHHHHCCCceeece
Q psy8853 147 TKKNTLLDLALEKGAEDFLIDKDN--KIT--IITSPSKFIEIKNSLEMTGFKAESSG 199 (242)
Q Consensus 147 ~~~d~~~e~Aie~GaeDve~~ed~--~~~--~~c~p~~~~~v~~~L~~~g~~v~~se 199 (242)
.+.++.+..+-++|.+-||..-.+ .+. .-.++..+..+++.|++.|+++....
T Consensus 21 ~~~~e~~~~~~~~G~~~iEl~~~~~~~~~~~~~~~~~~~~~l~~~l~~~gl~i~~~~ 77 (283)
T PRK13209 21 ECWLEKLAIAKTAGFDFVEMSVDESDERLARLDWSREQRLALVNALVETGFRVNSMC 77 (283)
T ss_pred CCHHHHHHHHHHcCCCeEEEecCccccchhccCCCHHHHHHHHHHHHHcCCceeEEe
Confidence 578899999999999999984221 111 12267789999999999999986543
No 108
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=32.68 E-value=46 Score=31.67 Aligned_cols=34 Identities=18% Similarity=0.154 Sum_probs=15.6
Q ss_pred EEEeCcccHHHHHHHHHHCCCceeece-eeeecCc
Q psy8853 173 TIITSPSKFIEIKNSLEMTGFKAESSG-IVMRPYT 206 (242)
Q Consensus 173 ~~~c~p~~~~~v~~~L~~~g~~v~~se-l~~~P~~ 206 (242)
-|.|+|..|..-...|.+.||.+.... +.|.|+|
T Consensus 393 yvsc~p~tlard~~~l~~~gy~~~~~~~~DmFP~T 427 (431)
T TIGR00479 393 YVSCNPATLARDLEFLCKEGYGITWVQPVDMFPHT 427 (431)
T ss_pred EEcCCHHHHHHHHHHHHHCCeeEEEEEEeccCCCC
Confidence 344555555444444544455443322 4444443
No 109
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=32.20 E-value=2e+02 Score=20.87 Aligned_cols=51 Identities=18% Similarity=0.272 Sum_probs=31.9
Q ss_pred CChhHHHHHHHhcCCcceEee----cCceEEEEeC----cccHHHHHHHHHHCCCceee
Q psy8853 147 TKKNTLLDLALEKGAEDFLID----KDNKITIITS----PSKFIEIKNSLEMTGFKAES 197 (242)
Q Consensus 147 ~~~d~~~e~Aie~GaeDve~~----ed~~~~~~c~----p~~~~~v~~~L~~~g~~v~~ 197 (242)
..+-.+++..-.++..++.-. +.+.+.|.++ ++++..+.+.|++.||.+..
T Consensus 13 G~L~~ll~~l~~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~ 71 (85)
T cd04906 13 GSFKKFCELIGPRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71 (85)
T ss_pred cHHHHHHHHhCCCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEE
Confidence 345666664444444444332 2334556555 56699999999999998643
No 110
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=32.13 E-value=1.5e+02 Score=19.47 Aligned_cols=55 Identities=7% Similarity=0.152 Sum_probs=34.8
Q ss_pred EEeCcccHHHHHHHHHHCCCceeeceeeeec----Ccc----eecCHHHHHHHHHHHHHHhcC
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKAESSGIVMRP----YTN----IVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P----~~~----v~l~~e~~~~~~~li~~Lee~ 228 (242)
+.-.|-.|..+.+.|.+.|.++.+....+.. ... +.++-...+.+..+++.|+..
T Consensus 5 ~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~~ 67 (73)
T cd04886 5 LPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALREA 67 (73)
T ss_pred eCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHHc
Confidence 3346788999999999999998765544331 111 223323345567777777653
No 111
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=31.91 E-value=1.2e+02 Score=29.05 Aligned_cols=60 Identities=17% Similarity=0.315 Sum_probs=42.9
Q ss_pred EEEECCC-CChhHHHHHHHhcCCcceEeecCceEEEEeCcccHHHHHHHHHHCCCceeece-eeeecCc
Q psy8853 140 QLLFLPN-TKKNTLLDLALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSG-IVMRPYT 206 (242)
Q Consensus 140 ~i~v~~~-~~~d~~~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~se-l~~~P~~ 206 (242)
+|.+.++ ...+++++...... .++.+-|.|+|..|..=-..|.+.||.+.... +.+.|+|
T Consensus 370 ~Vi~dPPr~g~~~~~~~l~~~~-------~~~ivyvSCnp~tlaRDl~~L~~~gY~l~~i~~~DmFP~T 431 (443)
T PRK13168 370 KVLLDPPRAGAAEVMQALAKLG-------PKRIVYVSCNPATLARDAGVLVEAGYRLKRAGMLDMFPHT 431 (443)
T ss_pred EEEECcCCcChHHHHHHHHhcC-------CCeEEEEEeChHHhhccHHHHhhCCcEEEEEEEeccCCCC
Confidence 4555544 33455555555432 24467899999999888888988899997765 8899987
No 112
>PF07592 DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE domain; InterPro: IPR011518 These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.77 E-value=18 Score=33.81 Aligned_cols=13 Identities=38% Similarity=0.805 Sum_probs=11.2
Q ss_pred CCcchhHHhHHHh
Q psy8853 2 AGHSKWANIKRKK 14 (242)
Q Consensus 2 aGHsKW~nIkh~K 14 (242)
-|||||..|-|+-
T Consensus 224 P~tSKwN~IEHRl 236 (311)
T PF07592_consen 224 PGTSKWNPIEHRL 236 (311)
T ss_pred CCcccccchhhhH
Confidence 4899999999964
No 113
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=31.52 E-value=2.6e+02 Score=24.32 Aligned_cols=83 Identities=14% Similarity=0.053 Sum_probs=51.1
Q ss_pred CCChhHHHHHHHhcCCcceEeecCc--eEEEE--eCcccHHHHHHHHHHCCCceeeceee-eecCcceecCH----HHHH
Q psy8853 146 NTKKNTLLDLALEKGAEDFLIDKDN--KITII--TSPSKFIEIKNSLEMTGFKAESSGIV-MRPYTNIVFKD----GEAI 216 (242)
Q Consensus 146 ~~~~d~~~e~Aie~GaeDve~~ed~--~~~~~--c~p~~~~~v~~~L~~~g~~v~~sel~-~~P~~~v~l~~----e~~~ 216 (242)
..+.++.++.|-++|.+-||..-.. ..... -++.++..+++.|++.|+.+.+.... +.+.+....++ +..+
T Consensus 15 ~~~~~e~~~~~~~~G~~~iEl~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gl~i~~~~~~~~~~~~~~~~d~~~r~~~~~ 94 (284)
T PRK13210 15 HLSWEERLVFAKELGFDFVEMSVDESDERLARLDWSKEERLSLVKAIYETGVRIPSMCLSGHRRFPFGSRDPATRERALE 94 (284)
T ss_pred CCCHHHHHHHHHHcCCCeEEEecCCcccccccccCCHHHHHHHHHHHHHcCCCceEEecccccCcCCCCCCHHHHHHHHH
Confidence 3688999999999999999884211 00111 14567899999999999988754321 11111111222 2345
Q ss_pred HHHHHHHHHhcC
Q psy8853 217 KLQKLLNELKKL 228 (242)
Q Consensus 217 ~~~~li~~Lee~ 228 (242)
.+.+.++.-..+
T Consensus 95 ~~~~~i~~a~~l 106 (284)
T PRK13210 95 IMKKAIRLAQDL 106 (284)
T ss_pred HHHHHHHHHHHh
Confidence 566777666655
No 114
>PRK05066 arginine repressor; Provisional
Probab=30.92 E-value=3.1e+02 Score=22.80 Aligned_cols=92 Identities=16% Similarity=0.106 Sum_probs=66.4
Q ss_pred EEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-------C---ChhHHHHHHHhcCCcceEeecCc
Q psy8853 101 DCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-------T---KKNTLLDLALEKGAEDFLIDKDN 170 (242)
Q Consensus 101 e~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-------~---~~d~~~e~Aie~GaeDve~~ed~ 170 (242)
+.+++|.-+|..+|...+.+.|-.-.+..+++..-.+.|++.++.+ + ....-+...+.-.+.+|+..+ .
T Consensus 16 ~iI~~~~I~tQeeL~~~L~~~Gi~~vTQATiSRDikeL~lvKv~~~~G~~~Y~l~~~~~~~~l~~~l~~~v~~v~~~~-~ 94 (156)
T PRK05066 16 ALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKFGAVRTRNAKMEMVYCLPAELGVPTTSSPLKNLVLDIDHND-A 94 (156)
T ss_pred HHHhhCCCCCHHHHHHHHHHCCCCeecHHHHHHHHHHcCCEEeeCCCCCEEEEeCCCCcchHHHHHHHHHeeeeeecC-C
Confidence 3457788889999999999998772356788888899999987532 1 111223445544445555533 4
Q ss_pred eEEEEeCcccHHHHHHHHHHCCC
Q psy8853 171 KITIITSPSKFIEIKNSLEMTGF 193 (242)
Q Consensus 171 ~~~~~c~p~~~~~v~~~L~~~g~ 193 (242)
.+.|.|.|-.-..|...|.+.++
T Consensus 95 ~ivIkT~pG~A~~va~~iD~~~~ 117 (156)
T PRK05066 95 LIVIHTSPGAAQLIARLLDSLGK 117 (156)
T ss_pred EEEEEcCCChHHHHHHHHHcCCC
Confidence 78899999999999999998876
No 115
>PRK09856 fructoselysine 3-epimerase; Provisional
Probab=30.87 E-value=2.9e+02 Score=24.01 Aligned_cols=51 Identities=12% Similarity=-0.029 Sum_probs=37.0
Q ss_pred CChhHHHHHHHhcCCcceEeecCceEEEE--eCcccHHHHHHHHHHCCCceee
Q psy8853 147 TKKNTLLDLALEKGAEDFLIDKDNKITII--TSPSKFIEIKNSLEMTGFKAES 197 (242)
Q Consensus 147 ~~~d~~~e~Aie~GaeDve~~ed~~~~~~--c~p~~~~~v~~~L~~~g~~v~~ 197 (242)
.+.++.+..+-++|.+-||...+....+. ....++..+++.+++.|+++.+
T Consensus 13 ~~l~~~l~~~~~~G~~~vEl~~~~~~~~~~~~~~~~~~~l~~~~~~~gl~v~s 65 (275)
T PRK09856 13 LPIEHAFRDASELGYDGIEIWGGRPHAFAPDLKAGGIKQIKALAQTYQMPIIG 65 (275)
T ss_pred CCHHHHHHHHHHcCCCEEEEccCCccccccccCchHHHHHHHHHHHcCCeEEE
Confidence 47889999999999999987422111111 2345789999999999998754
No 116
>PF12002 MgsA_C: MgsA AAA+ ATPase C terminal; InterPro: IPR021886 The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities []. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication []. Additionally, MgsA may play a role in chromosomal segregation []. This is consistent with a report that MgsA co-localises with the replisome and affects chromosome segregation []. This domain represents the C-terminal region of MgsA. ; PDB: 2R9G_A 2QW6_D 3CTD_B 3PVS_B 3BGE_A.
Probab=30.79 E-value=40 Score=28.66 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhc--C-CCCCCCHHHHHHHHHHHHcCCCHHHH
Q psy8853 26 TRIMRELRVAINF--G-NNPDTNIKLRLAIEKALDANIPKNNI 65 (242)
Q Consensus 26 ~kl~reI~~Avk~--G-~dP~~N~~L~~ai~~Ak~~nmPk~~I 65 (242)
..+.|.+.+.+-+ | +||..-..--++.+.++..+||-..|
T Consensus 22 ~~i~RRL~i~AsEDIGlAdP~Al~~a~aa~~a~~~iG~PE~~i 64 (168)
T PF12002_consen 22 RFIARRLIIIASEDIGLADPQALSIAVAAYQAVERIGMPEARI 64 (168)
T ss_dssp HHHHHHHHHHHHHCTGGGSTCHHHHHHHHHHHHHHH-CCCCHH
T ss_pred HHHHHHHHHHHHHhhhccCccHHHHHHHHHHHHHHHCCcHHHH
Confidence 3456666666665 8 89998888889999999999998765
No 117
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=30.64 E-value=1.3e+02 Score=28.87 Aligned_cols=62 Identities=11% Similarity=0.142 Sum_probs=42.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+..||..|...++|.+.|.++|++..+- .+ -+|.+ ++ .+|+.+|-++.-.|+.-+.+-|+.+
T Consensus 305 a~aAia~~~~lgi~~~~i~~~L~~~~~~---~g-R~E~i-~~---~~~~~iiDDs~ahNp~a~~aaL~~l 366 (480)
T PRK01438 305 ALAAAALARSFGVPPAAVRDGLRAFRPD---AH-RIEHV-AD---ADGVTWVDDSKATNPHAAAASLAAY 366 (480)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC-ceEEE-EE---ECCEEEEecCccCCHHHHHHHHHhC
Confidence 3456667778899999999999988764 22 23322 11 3466666677888888877766654
No 118
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=30.59 E-value=3.2e+02 Score=22.78 Aligned_cols=122 Identities=12% Similarity=0.122 Sum_probs=70.5
Q ss_pred EEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeE--EEECCCCChhHHHHHHHh--cCCcce---Eee-cC-
Q psy8853 99 IVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQ--LLFLPNTKKNTLLDLALE--KGAEDF---LID-KD- 169 (242)
Q Consensus 99 ive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~--i~v~~~~~~d~~~e~Aie--~GaeDv---e~~-ed- 169 (242)
++.++.+|....++.|-.+|+++|.++-.- ++..- +..|+ +.+.-..+ |+.++.... .-..|| .+- ++
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl-~v~~t-~~~~~sriti~V~~d-~~~i~qi~kQl~Kli~V~~V~~~~~~~ 79 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESL-TVGPT-EDPDLSRMTIVVVGD-DKVLEQITKQLNKLVDVIKVSDLTESA 79 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEE-EEeec-CCCCEEEEEEEEECC-HHHHHHHHHHHhcCccEEEEEecCCCc
Confidence 467899999999999999999999977311 11111 11333 32222223 233333222 133333 221 11
Q ss_pred ------ceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCc-ceecCHHHHHHHHHHHHHHhcC
Q psy8853 170 ------NKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYT-NIVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 170 ------~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~-~v~l~~e~~~~~~~li~~Lee~ 228 (242)
-.+.|.|++++-..+.+-.+..+-.+.... |.+ .++++... +++..|++.|+..
T Consensus 80 ~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivdv~----~~~~~ie~tG~~-~ki~~~~~~l~~~ 140 (157)
T TIGR00119 80 IVERELCLVKVSAPGEGRDEIIRLTNIFRGRIVDVS----PDSYTVEVTGDS-DKIDAFLELLRPF 140 (157)
T ss_pred ceeeEEEEEEEECCccCHHHHHHHHHHhCCEEEEec----CCEEEEEEcCCH-HHHHHHHHHhhhc
Confidence 147899999988888888887766655443 332 45665432 4566666666654
No 119
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=30.32 E-value=80 Score=21.49 Aligned_cols=26 Identities=12% Similarity=0.119 Sum_probs=19.5
Q ss_pred eEEEEeCcccHHHHHHHHHHCCCcee
Q psy8853 171 KITIITSPSKFIEIKNSLEMTGFKAE 196 (242)
Q Consensus 171 ~~~~~c~p~~~~~v~~~L~~~g~~v~ 196 (242)
.+.|..+..+...+.+.|++.||++.
T Consensus 44 ~v~i~v~~~~~~~~~~~L~~~G~~v~ 69 (72)
T cd04883 44 ILVFRVQTMNPRPIIEDLRRAGYEVL 69 (72)
T ss_pred EEEEEEecCCHHHHHHHHHHCCCeee
Confidence 35666666666799999999998764
No 120
>PRK00441 argR arginine repressor; Provisional
Probab=29.90 E-value=1.8e+02 Score=24.06 Aligned_cols=92 Identities=15% Similarity=0.140 Sum_probs=65.5
Q ss_pred EEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-------C------ChhHHHHHHHhcCCcceEee
Q psy8853 101 DCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-------T------KKNTLLDLALEKGAEDFLID 167 (242)
Q Consensus 101 e~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-------~------~~d~~~e~Aie~GaeDve~~ 167 (242)
+.+..+.-.+..+|...|.+.|-... .-+++..+..-|++.++.. . ....-++..+.-.+..|+-.
T Consensus 11 ~ll~~~~~~~q~eL~~~L~~~G~~vS-qaTisRDl~~L~lvKv~~~~G~~~Y~l~~~~~~~~~~~l~~~~~~~v~~v~~~ 89 (149)
T PRK00441 11 EIINSKEIETQEELAEELKKMGFDVT-QATVSRDIKELKLIKVLSNDGKYKYATISKTESNLSDRLVNIFSNTVISVENV 89 (149)
T ss_pred HHHHHcCCCcHHHHHHHHHhcCCCcC-HHHHHHHHHHcCcEEeECCCCCEEEEeCcccccchHHHHHHHHHHHeeeEeec
Confidence 34455666788899999999886643 4578888999998877522 0 11234455565566666654
Q ss_pred cCceEEEEeCcccHHHHHHHHHHCCCc
Q psy8853 168 KDNKITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 168 ed~~~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
+. .+.|.|.|-.-..|...|...+++
T Consensus 90 ~~-lvvIkT~pG~A~~va~~iD~~~~~ 115 (149)
T PRK00441 90 DN-MIVIKTISGSASAAAEAIDTLNFD 115 (149)
T ss_pred CC-EEEEEeCCCcHHHHHHHHHhCCCC
Confidence 43 788999999999999999988764
No 121
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=29.78 E-value=1.4e+02 Score=21.22 Aligned_cols=56 Identities=18% Similarity=0.212 Sum_probs=36.8
Q ss_pred EEeCcccHHHHHHHHHHCCCceeeceeeeecCcc------eecCHH-HHHHHHHHHHHHhcCC
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTN------IVFKDG-EAIKLQKLLNELKKLH 229 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~------v~l~~e-~~~~~~~li~~Lee~d 229 (242)
+--.|-.|..+.+.+.+.|+++.+-+....+... |+++.. +.+.+.++++.|+++.
T Consensus 8 ~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~~ 70 (80)
T cd04905 8 LPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRLT 70 (80)
T ss_pred ECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhC
Confidence 3346788999999999999988766533333211 233332 3567888888888743
No 122
>PF04639 Baculo_E56: Baculoviral E56 protein, specific to ODV envelope; InterPro: IPR006733 This family represents the E56 protein, which is localized to the occlusion derived virus (ODV) envelope, but not to the budded virus (BV) envelope []. Signals necessary for transport and/or retention into this structure are believed to be found within the C-terminal portion of ODV-E56.; GO: 0019031 viral envelope
Probab=29.72 E-value=1.4e+02 Score=27.72 Aligned_cols=71 Identities=24% Similarity=0.334 Sum_probs=43.2
Q ss_pred HHHhcCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHH
Q psy8853 34 VAINFGNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSN 113 (242)
Q Consensus 34 ~Avk~G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~ 113 (242)
.|||. .+|++|.|=+.=|+.|..+|=- +..-+ |..| |=+.--.||.+++.+ .-.+++
T Consensus 79 ~aVk~-n~Pet~tRt~~GV~~aL~~nPr---L~~yL-K~aG-------------~~~L~G~gvyLv~~~-----a~Lvqd 135 (305)
T PF04639_consen 79 NAVKQ-NFPETNTRTPEGVENALNQNPR---LNDYL-KTAG-------------YVTLLGVGVYLVFSA-----ATLVQD 135 (305)
T ss_pred HHhhh-cCcccccCCHHHHHHHHHhCcc---HHHHH-hhCC-------------eEEEEeeEEEEEEEH-----HHHHHH
Confidence 34553 5677777777777766666532 23333 2222 222233566666655 448999
Q ss_pred HHHHhhhcCccccC
Q psy8853 114 IRNIFNKNGGNLSK 127 (242)
Q Consensus 114 vr~~f~K~gg~l~~ 127 (242)
|..++++.||++-.
T Consensus 136 Ii~AlNrTGGSyy~ 149 (305)
T PF04639_consen 136 IIDALNRTGGSYYY 149 (305)
T ss_pred HHHHHHhCCCeeEE
Confidence 99999999997643
No 123
>cd07025 Peptidase_S66 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein. LD-carboxypeptidase (Muramoyltetrapeptide carboxypeptidase; EC 3.4.17.13; Merops family S66; initially described as Carboxypeptidase II) family also includes the microcin c7 self-immunity protein (MccF) as well as uncharacterized proteins including hypothetical proteins. LD-carboxypeptidase hydrolyzes the amide bond that links the dibasic amino acids to C-terminal D-amino acids. The physiological substrates of LD-carboxypeptidase are tetrapeptide fragments (such as UDP-MurNAc-tetrapeptides) that are produced when bacterial cell walls are degraded; they contain an L-configured residue (L-lysine or meso-diaminopimelic acid residue) as the penultimate residue and D-alanine as the ultimate residue. A possible role of LD-carboxypeptidase is in peptidoglycan recycling whereby the resulting tripeptide (precursor for murein synthesis) can be reconverted into peptidoglycan by attachment o
Probab=29.71 E-value=84 Score=28.37 Aligned_cols=56 Identities=11% Similarity=0.158 Sum_probs=41.3
Q ss_pred ccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCcccceec
Q psy8853 179 SKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTN 237 (242)
Q Consensus 179 ~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~N 237 (242)
+.+....+.|++.||+|......+.+... ++..+.++.+.|.+++.+ |+|..|+..
T Consensus 14 ~~~~~~~~~L~~~G~~v~~~~~~~~~~~~--~a~s~~~Ra~dL~~a~~d-~~i~aI~~~ 69 (282)
T cd07025 14 ERLERAIARLESLGLEVVVGPHVLARDGY--LAGTDEERAADLNAAFAD-PEIKAIWCA 69 (282)
T ss_pred HHHHHHHHHHHhCCCEEEeccchhhhcCc--cCCCHHHHHHHHHHHhhC-CCCCEEEEc
Confidence 66788899999999999888877776653 444455577777777764 568777753
No 124
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=29.31 E-value=95 Score=28.48 Aligned_cols=81 Identities=12% Similarity=0.173 Sum_probs=46.7
Q ss_pred cchhHHHHHHHhhhcCccccCCCcccc------ccceeeE-EEECCC--------------CChhHHHHHHHhcCCcceE
Q psy8853 107 RMRTVSNIRNIFNKNGGNLSKEGSVLF------MFKHCGQ-LLFLPN--------------TKKNTLLDLALEKGAEDFL 165 (242)
Q Consensus 107 ~nRt~~~vr~~f~K~gg~l~~~gsv~~------~F~~kG~-i~v~~~--------------~~~d~~~e~Aie~GaeDve 165 (242)
+.|++.-+.....+.|+.+-.-|++-| .|.++|+ +.+..- .-..+..+.|-+.|.+=
T Consensus 14 V~rAi~~a~~~~~~~~~~iy~lG~iIHN~~Vv~~L~~~Gv~~~v~~~~~v~~~~~ViirAHGv~~~~~~~~~~~gl~v-- 91 (280)
T TIGR00216 14 VKRAIQMAEEALKESGKPVYTLGPIVHNPQVVERLRERGVFFFLEDLDEVAAGDTVIIRAHGVPPEVREELEKKGLEV-- 91 (280)
T ss_pred HHHHHHHHHHHHhhcCCCeEEecCCccCHHHHHHHHHCCCEEeecCcccCCCCCEEEEeCCCCCHHHHHHHHHCCCeE--
Confidence 457777777766666666555566555 6788885 443310 01234455555555442
Q ss_pred eecCceEEEEeCc-ccHHHHHHHHHHCCCce
Q psy8853 166 IDKDNKITIITSP-SKFIEIKNSLEMTGFKA 195 (242)
Q Consensus 166 ~~ed~~~~~~c~p-~~~~~v~~~L~~~g~~v 195 (242)
+--+||. ...++.-..+.+.||.+
T Consensus 92 ------iDaTCP~V~kv~~~v~~~~~~Gy~i 116 (280)
T TIGR00216 92 ------IDATCPLVTKVHNAVKKYAKEGYHV 116 (280)
T ss_pred ------EeCCCcccHHHHHHHHHHHhCCCEE
Confidence 2245664 34466666777789986
No 125
>smart00633 Glyco_10 Glycosyl hydrolase family 10.
Probab=29.06 E-value=1.3e+02 Score=26.52 Aligned_cols=80 Identities=10% Similarity=0.099 Sum_probs=52.1
Q ss_pred hHHHHHHHhcCCcceEeecCc-eEEEE---eCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHH
Q psy8853 150 NTLLDLALEKGAEDFLIDKDN-KITII---TSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNEL 225 (242)
Q Consensus 150 d~~~e~Aie~GaeDve~~ed~-~~~~~---c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~L 225 (242)
-++++...+.|+. +. .=| ...+. -++..+.+.-+.|.+.|.+|.-+|+.+.-.. -++.+.+.+..++..+
T Consensus 139 ~~~v~~l~~~g~~-iD--giGlQ~H~~~~~~~~~~~~~~l~~~~~~g~pi~iTE~dv~~~~---~~~~qA~~~~~~l~~~ 212 (254)
T smart00633 139 YELVKKLKAKGVP-ID--GIGLQSHLSLGSPNIAEIRAALDRFASLGLEIQITELDISGYP---NPQAQAADYEEVFKAC 212 (254)
T ss_pred HHHHHHHHHCCCc-cc--eeeeeeeecCCCCCHHHHHHHHHHHHHcCCceEEEEeecCCCC---cHHHHHHHHHHHHHHH
Confidence 4566666777773 21 111 11121 2355677777777777999998888764332 1156778899999999
Q ss_pred hcCCCcccce
Q psy8853 226 KKLHDVKKVY 235 (242)
Q Consensus 226 ee~dDV~~Vy 235 (242)
-++|.|..|+
T Consensus 213 ~~~p~v~gi~ 222 (254)
T smart00633 213 LAHPAVTGVT 222 (254)
T ss_pred HcCCCeeEEE
Confidence 9999887774
No 126
>PRK01060 endonuclease IV; Provisional
Probab=28.90 E-value=3.5e+02 Score=23.63 Aligned_cols=58 Identities=17% Similarity=0.101 Sum_probs=39.2
Q ss_pred eeeEEEECCCCChhHHHHHHHhcCCcceEeecC--ceEEE-EeCcccHHHHHHHHHHCCCce
Q psy8853 137 HCGQLLFLPNTKKNTLLDLALEKGAEDFLIDKD--NKITI-ITSPSKFIEIKNSLEMTGFKA 195 (242)
Q Consensus 137 ~kG~i~v~~~~~~d~~~e~Aie~GaeDve~~ed--~~~~~-~c~p~~~~~v~~~L~~~g~~v 195 (242)
+.|..+... .+.+++++.+-++|.+=||..-. ..+.. .-++..+..+++.|++.|+.+
T Consensus 3 ~~g~~~~~~-~~~~~~l~~~~~~G~d~vEl~~~~p~~~~~~~~~~~~~~~lk~~~~~~gl~~ 63 (281)
T PRK01060 3 LIGAHVSAA-GGLEGAVAEAAEIGANAFMIFTGNPQQWKRKPLEELNIEAFKAACEKYGISP 63 (281)
T ss_pred eEEEeeecC-CCHHHHHHHHHHcCCCEEEEECCCCCCCcCCCCCHHHHHHHHHHHHHcCCCC
Confidence 345544432 35888999999999999988422 11211 124557888999999999874
No 127
>PRK14700 recombination factor protein RarA; Provisional
Probab=28.88 E-value=60 Score=30.18 Aligned_cols=39 Identities=15% Similarity=0.162 Sum_probs=31.4
Q ss_pred HHHHHHHHHhc--C-CCCCCCHHHHHHHHHHHHcCCCHHHHH
Q psy8853 28 IMRELRVAINF--G-NNPDTNIKLRLAIEKALDANIPKNNIF 66 (242)
Q Consensus 28 l~reI~~Avk~--G-~dP~~N~~L~~ai~~Ak~~nmPk~~Ie 66 (242)
++|.+.+.+-+ | +||..=+.--++.+.+...|||-..|-
T Consensus 162 IaRRLii~AsEDIGlAdP~al~~a~aa~~A~~~iG~PEa~i~ 203 (300)
T PRK14700 162 IARRMLCIASEDIGNADPQALRVAMDAWNAYEKLGMPEGRLV 203 (300)
T ss_pred HHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHhCChHHHHH
Confidence 56666666666 8 899877777889999999999998873
No 128
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=28.58 E-value=1.5e+02 Score=30.73 Aligned_cols=62 Identities=15% Similarity=0.248 Sum_probs=48.3
Q ss_pred EeCcccHHHHHHHHHHCCCceeeceeeeecCcc----eecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 175 ITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTN----IVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 175 ~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~----v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
.=.+.-|..|...+.+.+..+.+....--+... +.+.=.+.+.+..++..|+..++|.+|+.
T Consensus 634 ~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ieV~~~~~L~~i~~~Lr~i~~V~~V~R 699 (702)
T PRK11092 634 FNHQGALANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLTARDRVHLANIMRKIRVMPDVIKVTR 699 (702)
T ss_pred eCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCcceEEE
Confidence 345566899999999999999887765444322 23445677899999999999999999986
No 129
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=28.44 E-value=1.2e+02 Score=29.81 Aligned_cols=62 Identities=19% Similarity=0.164 Sum_probs=50.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEecc-CCeEEEEEEecCCcchhHHHHHHHh
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSV-NGAAIIVDCITNNRMRTVSNIRNIF 118 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gP-gGv~iive~lTdN~nRt~~~vr~~f 118 (242)
.-++++-|+..++|.+.|-.+|....|- +.+.|-+|- +|+-++=+.=..|..+|.+-|+.+=
T Consensus 281 ~lAa~a~a~~~gv~~e~i~~~L~~F~gl---------~HR~e~v~~~~gv~f~NDSKATN~~At~~AL~~~~ 343 (448)
T COG0771 281 ALAALALARALGVPPEAILEALSSFTGL---------PHRLEFVGEKDGVLFINDSKATNVDATLAALSGFD 343 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---------CcceEEEEecCCEEEecCCCCCCHHHHHHHHHcCC
Confidence 4578899999999999999999999875 334555554 7899999999999999998887543
No 130
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=28.37 E-value=3.2e+02 Score=24.70 Aligned_cols=90 Identities=19% Similarity=0.279 Sum_probs=55.8
Q ss_pred HHHHHHHhcCCcce-EeecCceEEEEeCcccHHHHHHHHHHCCCceeec-eee-eecCcceecCH-HHHHHH-----HHH
Q psy8853 151 TLLDLALEKGAEDF-LIDKDNKITIITSPSKFIEIKNSLEMTGFKAESS-GIV-MRPYTNIVFKD-GEAIKL-----QKL 221 (242)
Q Consensus 151 ~~~e~Aie~GaeDv-e~~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~s-el~-~~P~~~v~l~~-e~~~~~-----~~l 221 (242)
++....-+.|..-- ...++| +.|..+.+++...+..|.+.|++-... ... ..|.+..-.++ |...++ ..|
T Consensus 34 ~I~a~L~~~gI~y~~~~~~~G-~tI~Vp~~~~~~Ar~~La~~GLP~~g~~~~~~lFd~~~l~~t~te~~qki~y~regEL 112 (249)
T PRK15348 34 QMLALLMQHHIDAEKKQEEDG-VTLRVEQSQFINAVELLRLNGYPHRQFTTADKMFPANQLVVSPQEEQQKINFLKEQRI 112 (249)
T ss_pred HHHHHHHHcCCCceEeeCCCC-eEEEecHHHHHHHHHHHHHcCCCCCCCccHHHhCCccccccChhHHHHHHHHHHHHHH
Confidence 45555556777642 223455 899999999999999999999875432 222 34544433322 222222 235
Q ss_pred HHHHhcCCCcccceeccccC
Q psy8853 222 LNELKKLHDVKKVYTNALIF 241 (242)
Q Consensus 222 i~~Lee~dDV~~Vy~Ni~~~ 241 (242)
=..|+.+|+|..--=++.+|
T Consensus 113 arTI~~idgV~~ArVhL~lP 132 (249)
T PRK15348 113 EGMLSQMEGVINAKVTIALP 132 (249)
T ss_pred HHHHHhCCCeeEeEEEEECC
Confidence 55678888888765555554
No 131
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=27.82 E-value=2.8e+02 Score=21.60 Aligned_cols=70 Identities=17% Similarity=0.186 Sum_probs=33.8
Q ss_pred CChhHHHHHHHhcCCcceEee-cCceEEEEeCcccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHH
Q psy8853 147 TKKNTLLDLALEKGAEDFLID-KDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNEL 225 (242)
Q Consensus 147 ~~~d~~~e~Aie~GaeDve~~-ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~L 225 (242)
.+.+++-.++ +.|..-|... .|+.= .+.-.+..++.+.++.|+.. .|+|...-.+++++.+.+.++++.+
T Consensus 15 ~~~~d~~~la-~~GfktVInlRpd~E~---~~qp~~~~~~~~a~~~Gl~y-----~~iPv~~~~~~~~~v~~f~~~l~~~ 85 (110)
T PF04273_consen 15 PSPEDLAQLA-AQGFKTVINLRPDGEE---PGQPSSAEEAAAAEALGLQY-----VHIPVDGGAITEEDVEAFADALESL 85 (110)
T ss_dssp --HHHHHHHH-HCT--EEEE-S-TTST---TT-T-HHCHHHHHHHCT-EE-----EE----TTT--HHHHHHHHHHHHTT
T ss_pred CCHHHHHHHH-HCCCcEEEECCCCCCC---CCCCCHHHHHHHHHHcCCeE-----EEeecCCCCCCHHHHHHHHHHHHhC
Confidence 5667765444 6777776551 11100 01125567888999999864 6788877677777766666665554
No 132
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=27.72 E-value=1.3e+02 Score=29.18 Aligned_cols=60 Identities=17% Similarity=0.111 Sum_probs=40.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIR 115 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr 115 (242)
...|+.-|+..++|.+.|.++|+...+. .+ -+|.+ . ..+|+.+|=|+.-.|+.-+.+-++
T Consensus 288 alaAla~a~~lGi~~e~i~~~L~~f~~~---~g-R~E~v-~---~~~gv~iIDDS~AhNp~s~~aal~ 347 (488)
T PRK03369 288 ALAAAALARAVGVPAGAIADALASFRVG---RH-RAEVV-A---VADGITYVDDSKATNPHAARASIL 347 (488)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---CC-ccEEE-E---cCCCEEEEECCCCCCHHHHHHHHH
Confidence 4567778888999999999999988864 22 23322 1 246776665666667666665554
No 133
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=27.42 E-value=2.6e+02 Score=22.70 Aligned_cols=43 Identities=12% Similarity=0.230 Sum_probs=29.3
Q ss_pred CChhHHHHHHHhcCCcceEeecCceEEEEeCcccHHHHHHHHHHCCC
Q psy8853 147 TKKNTLLDLALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGF 193 (242)
Q Consensus 147 ~~~d~~~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~~~L~~~g~ 193 (242)
.+.|++.+.|++.+|+=|-.+ ....+....+..+.+.|++.|+
T Consensus 39 v~~e~~v~aa~~~~adiVglS----~l~~~~~~~~~~~~~~l~~~gl 81 (134)
T TIGR01501 39 SPQEEFIKAAIETKADAILVS----SLYGHGEIDCKGLRQKCDEAGL 81 (134)
T ss_pred CCHHHHHHHHHHcCCCEEEEe----cccccCHHHHHHHHHHHHHCCC
Confidence 567899999998887665442 2234444557777777777776
No 134
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=27.42 E-value=1.4e+02 Score=17.52 Aligned_cols=25 Identities=16% Similarity=0.199 Sum_probs=20.1
Q ss_pred CcccHHHHHHHHHHCCCceeeceee
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIV 201 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~ 201 (242)
.|..+.++...|...|+.+......
T Consensus 8 ~~~~l~~i~~~l~~~~~~i~~~~~~ 32 (60)
T cd02116 8 RPGLLAKVLSVLAEAGINITSIEQR 32 (60)
T ss_pred CCchHHHHHHHHHHCCCcEEEEEeE
Confidence 3667999999999999998766643
No 135
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=27.32 E-value=2.7e+02 Score=21.46 Aligned_cols=59 Identities=17% Similarity=0.197 Sum_probs=24.7
Q ss_pred CeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCcccccc-ceeeEEEECCCCChhHHHHHHHhc
Q psy8853 95 GAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMF-KHCGQLLFLPNTKKNTLLDLALEK 159 (242)
Q Consensus 95 Gv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F-~~kG~i~v~~~~~~d~~~e~Aie~ 159 (242)
|+.|-++.+.+-.. ..+|+..|+.+| +..-|.|.- +..|+|.+..+.+...+++.+-+.
T Consensus 1 G~il~~~g~~~~~~--re~iK~~f~~~g----~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 1 GCILKFSGLGEPTS--REDIKEAFSQFG----EVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp --EEEEEE--SS----HHHHHHHT-SS------EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred CeEEEEecCCCCcC--HHHHHHHHHhcC----CcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 44555555444444 788888888865 111223332 445666665443344445555444
No 136
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=26.99 E-value=98 Score=20.91 Aligned_cols=58 Identities=12% Similarity=0.129 Sum_probs=37.6
Q ss_pred EEeCcccHHHHHHHHHHCCCceeeceeeeecC-----cceecCHHHHHHHHHHHHHHhcCCCcccc
Q psy8853 174 IITSPSKFIEIKNSLEMTGFKAESSGIVMRPY-----TNIVFKDGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 174 ~~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~-----~~v~l~~e~~~~~~~li~~Lee~dDV~~V 234 (242)
..-.|..+..+.+.|.+.|+.+.+.....-+. -.+.++... -..+++.|.+.++|..|
T Consensus 6 ~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~~~---~~~~~~~l~~~~~v~~v 68 (73)
T cd04902 6 NTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPV---PDEVLEELRALPGILSA 68 (73)
T ss_pred eCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCCCC---CHHHHHHHHcCCCccEE
Confidence 34467788999999999999886554322111 122344321 24788889999988765
No 137
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=26.91 E-value=1.8e+02 Score=27.27 Aligned_cols=60 Identities=12% Similarity=0.143 Sum_probs=48.3
Q ss_pred ceEEEEeCcccHHHH-HHHHHHCCCceeeceeeeecCcceecCH-HHHHHHHHHHHHHhcCCCcccceecc
Q psy8853 170 NKITIITSPSKFIEI-KNSLEMTGFKAESSGIVMRPYTNIVFKD-GEAIKLQKLLNELKKLHDVKKVYTNA 238 (242)
Q Consensus 170 ~~~~~~c~p~~~~~v-~~~L~~~g~~v~~sel~~~P~~~v~l~~-e~~~~~~~li~~Lee~dDV~~Vy~Ni 238 (242)
|.+-+++.--=+.-+ .+.|...|+ .|.||+++.. .+.+.+...++.+.++|+|..|.-|+
T Consensus 257 ~~i~ii~ng~G~~~~~~D~l~~~g~---------~~~NPvDl~g~~~~e~~~~aL~~l~~d~~vd~vlv~~ 318 (388)
T PRK00696 257 GNIGCMVNGAGLAMATMDIIKLYGG---------EPANFLDVGGGATAERVAEAFKIILSDPNVKAILVNI 318 (388)
T ss_pred CcEEEEECCchHHHHHHHHHHHcCC---------CcCCeEEecCCCCHHHHHHHHHHHhcCCCCCEEEEEe
Confidence 468888888888774 489998887 7889999843 45678889999999999998888664
No 138
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=26.81 E-value=1e+02 Score=21.74 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=23.7
Q ss_pred HHhHHhHHHHHHHHHHHHHHHHHHHhc
Q psy8853 12 RKKLIVDAKRGKICTRIMRELRVAINF 38 (242)
Q Consensus 12 h~K~~~Da~k~k~f~kl~reI~~Avk~ 38 (242)
+-|...|..+++.|.|+++.+..+++.
T Consensus 17 ~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 17 QAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 458888999999999999999888886
No 139
>COG1438 ArgR Arginine repressor [Transcription]
Probab=26.49 E-value=2.5e+02 Score=23.45 Aligned_cols=93 Identities=17% Similarity=0.144 Sum_probs=66.6
Q ss_pred EEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC-------C------ChhHHHHHHHhcCCcceEe
Q psy8853 100 VDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN-------T------KKNTLLDLALEKGAEDFLI 166 (242)
Q Consensus 100 ve~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~-------~------~~d~~~e~Aie~GaeDve~ 166 (242)
-+.+|.|.=.|..+|...+.++|.. .+..+|+..-.+-|.+.++.+ + .........+..=+.++.-
T Consensus 12 k~iI~~~~i~TQ~Elv~~L~~~Gi~-vTQaTvSRDlkelglvKv~~~~g~~~Y~l~~~~~~~~~~~~~~~~~~~v~~vd~ 90 (150)
T COG1438 12 KEIITEEKISTQEELVELLQEEGIE-VTQATVSRDLKELGLVKVRNEKGTYVYSLPAELGVPPTSKLKRYLKDLVLSIDR 90 (150)
T ss_pred HHHHHhCCCCCHHHHHHHHHHcCCe-EehHHHHHHHHHcCCEEecCCCCcEEEEeCCccCCCchhhHHHHHHHHheeecc
Confidence 3456888889999999999999998 467799999999999998743 0 1111111223222344433
Q ss_pred ecCceEEEEeCcccHHHHHHHHHHCCCc
Q psy8853 167 DKDNKITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 167 ~ed~~~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
.+ ..+.+.|.|-.-..+...|...+.+
T Consensus 91 ~~-~~ivlkT~PG~A~~ia~~lD~~~~~ 117 (150)
T COG1438 91 NG-NLIVLKTSPGAAQLIARLLDSLAKD 117 (150)
T ss_pred CC-cEEEEEeCCchHHHHHHHHHhcCch
Confidence 22 3788999999888888888888765
No 140
>PRK04194 hypothetical protein; Provisional
Probab=25.76 E-value=1.5e+02 Score=28.50 Aligned_cols=41 Identities=32% Similarity=0.383 Sum_probs=34.1
Q ss_pred HHHHHHHhcCCcceEeec----C---c-eEEEEeCcccHHHHHHHHHHC
Q psy8853 151 TLLDLALEKGAEDFLIDK----D---N-KITIITSPSKFIEIKNSLEMT 191 (242)
Q Consensus 151 ~~~e~Aie~GaeDve~~e----d---~-~~~~~c~p~~~~~v~~~L~~~ 191 (242)
-++|..+++||-||-... . | .+.++|.|.+...+.+.|-..
T Consensus 265 ~~~e~L~~~GAlDV~~tPi~MKK~RPg~~L~vl~~~~~~~~l~~~if~e 313 (392)
T PRK04194 265 YLFERLLEAGALDVFITPITMKKNRPGHLLTVICPPEKAEELARILFRE 313 (392)
T ss_pred HHHHHHHHCCCceeeeccceecCCCceeEEEEEeCHHHHHHHHHHHHhc
Confidence 478999999999997732 1 2 689999999999999999765
No 141
>PF01969 DUF111: Protein of unknown function DUF111; InterPro: IPR002822 The proteins in this family have no known function.; PDB: 3C19_A.
Probab=25.64 E-value=79 Score=30.31 Aligned_cols=41 Identities=24% Similarity=0.350 Sum_probs=34.1
Q ss_pred HHHHHHHhcCCcceEee----cCc----eEEEEeCcccHHHHHHHHHHC
Q psy8853 151 TLLDLALEKGAEDFLID----KDN----KITIITSPSKFIEIKNSLEMT 191 (242)
Q Consensus 151 ~~~e~Aie~GaeDve~~----ed~----~~~~~c~p~~~~~v~~~L~~~ 191 (242)
-++|..+++||-||-.. ..| .+.++|.|.+..++.+.|-..
T Consensus 267 ~~~e~L~~~GAlDV~~~Pi~MKK~RPg~~l~Vl~~~~~~~~l~~~if~e 315 (382)
T PF01969_consen 267 YLIERLLEAGALDVFFTPIQMKKNRPGYLLTVLCRPEDAEALAELIFRE 315 (382)
T ss_dssp HHHHHHTTSTEEEEEEEEEEETTTEEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCceeEEccceEEcCceeEEEEEEeCHHHHHHHHHHHHHh
Confidence 57999999999999773 222 589999999999999998754
No 142
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=25.60 E-value=1.8e+02 Score=27.60 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=40.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRN 116 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~ 116 (242)
+.+|+..|...++|.+.|..+|+...+- .+ -++.+ .+ -+|+.+|-++--.|+.-+..-++.
T Consensus 280 alaAia~a~~lgi~~~~i~~~L~~f~~~---~~-R~e~~-~~---~~~~~~iDDs~~~n~~s~~~al~~ 340 (445)
T PRK04308 280 VMAAVALCEAVGLPREALLEHVKTFQGL---PH-RVEKI-GE---KNGVVFIDDSKGTNVGATAAAIAG 340 (445)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCC---CC-ceEEE-Ee---eCCeEEEEcCCCCCHHHHHHHHHh
Confidence 4678888889999999999999988764 22 23322 22 146777777755666544444444
No 143
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.32 E-value=63 Score=20.84 Aligned_cols=20 Identities=20% Similarity=0.311 Sum_probs=14.7
Q ss_pred HHHHHcCCCHHHHHHHHHhc
Q psy8853 53 EKALDANIPKNNIFRAIQKN 72 (242)
Q Consensus 53 ~~Ak~~nmPk~~Ie~AIkk~ 72 (242)
+-|+..|+++.+|-+-|+|+
T Consensus 25 ~IA~~lg~s~sTV~relkR~ 44 (44)
T PF13936_consen 25 EIAKRLGRSRSTVSRELKRN 44 (44)
T ss_dssp HHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHCcCcHHHHHHHhcC
Confidence 45788899999999998874
No 144
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=25.27 E-value=45 Score=25.30 Aligned_cols=52 Identities=19% Similarity=0.096 Sum_probs=31.1
Q ss_pred HHHHHHHHHCCCceeeceeeeecC---cceecC-HHHHHHHHHHHHHHhcCCCcccceeccccC
Q psy8853 182 IEIKNSLEMTGFKAESSGIVMRPY---TNIVFK-DGEAIKLQKLLNELKKLHDVKKVYTNALIF 241 (242)
Q Consensus 182 ~~v~~~L~~~g~~v~~sel~~~P~---~~v~l~-~e~~~~~~~li~~Lee~dDV~~Vy~Ni~~~ 241 (242)
..+.+.|++.| +.|.++ |.++-+ ++-++.+.++.+.+.+ ..+.+|++++.++
T Consensus 20 ~~~i~~i~~sg-------l~y~v~pm~T~iEGe~dev~~~i~~~~e~~~~-~G~~Rv~t~ikId 75 (92)
T PF01910_consen 20 AEAIEVIKESG-------LKYEVGPMGTTIEGELDEVMALIKEAHEALFE-AGAKRVVTVIKID 75 (92)
T ss_dssp HHHHHHHHTSS-------SEEEEETTEEEEEEEHHHHHHHHHHHHHHHHC-TTSSEEEEEEEEE
T ss_pred HHHHHHHHHcC-------CceEEcCCccEEEecHHHHHHHHHHHHHHHHH-cCCCeEEEEEEEE
Confidence 34445555545 455554 555555 3335556666666655 4688999998874
No 145
>PF12213 Dpoe2NT: DNA polymerases epsilon N terminal; InterPro: IPR024639 This domain is found in the N-terminal of DNA polymerase epsilon subunit B proteins. It contains a single completely conserved phenylalanine residue that may be functionally important. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. The N-terminal domain has close structural relation to AAA+ protein C-terminal domains [].; PDB: 2V6Z_M.
Probab=25.18 E-value=27 Score=25.60 Aligned_cols=47 Identities=15% Similarity=0.196 Sum_probs=35.2
Q ss_pred HHHHHHHHHCCCceeeceeeeecCcceecCHHHHH-HHHHHHHHHhcC
Q psy8853 182 IEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAI-KLQKLLNELKKL 228 (242)
Q Consensus 182 ~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~-~~~~li~~Lee~ 228 (242)
..|.++++=.||.+..-...|+......+++++++ -+.++++.++--
T Consensus 7 k~I~~~FkL~Gl~Lr~eA~~~l~~~l~~~~~~e~e~~l~~Ii~~v~kq 54 (73)
T PF12213_consen 7 KKIVKAFKLRGLSLRSEASKYLAEQLQSLSEEEREDWLDKIIDAVQKQ 54 (73)
T ss_dssp HHHHHHHHHTT-EE-HHHHHHHHHHTTTS-TTTHHHHHHHHHHHHTTS
T ss_pred HHHHHHhhhccceecHHHHHHHHHHHccCCHHHHHHHHHHHHHHHhcC
Confidence 45677777779999888899998888888887766 499999998754
No 146
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=25.16 E-value=4e+02 Score=22.86 Aligned_cols=91 Identities=15% Similarity=0.205 Sum_probs=57.3
Q ss_pred HHHHHHHhcCCcceEe-ecCceEEEEeCcccHHHHHHHHHHCCCceee-cee-eeecCcceecCH-HHHHHHH-----HH
Q psy8853 151 TLLDLALEKGAEDFLI-DKDNKITIITSPSKFIEIKNSLEMTGFKAES-SGI-VMRPYTNIVFKD-GEAIKLQ-----KL 221 (242)
Q Consensus 151 ~~~e~Aie~GaeDve~-~ed~~~~~~c~p~~~~~v~~~L~~~g~~v~~-sel-~~~P~~~v~l~~-e~~~~~~-----~l 221 (242)
++....-+.|..--.+ ..++.+.|..+..++..++..|.+.|+.-.. ..+ +..++...-.++ ++...+. .|
T Consensus 33 ~I~~~L~~~gI~y~~~~~~~~g~~I~Vp~~~~~~ar~~La~~glp~~~~~~~~elf~~~~lg~T~~~e~~~~~~ale~EL 112 (193)
T TIGR02544 33 EMLAVLMRHGIDAEKEGSGKGGYTISVEESDFARAVELLRQYGLPRQRFVNLGELFPKDGLVSSPQEERARYLYAIEQRL 112 (193)
T ss_pred HHHHHHHHCCCCeEEeecCCCCeEEEEcHHHHHHHHHHHHHcCCCCCCCCCHHHHccCCCCcCCHHHHHHHHHHHHHHHH
Confidence 4555555677765442 2223489999999999999999999986432 333 566776555554 3333333 34
Q ss_pred HHHHhcCCCcccceeccccC
Q psy8853 222 LNELKKLHDVKKVYTNALIF 241 (242)
Q Consensus 222 i~~Lee~dDV~~Vy~Ni~~~ 241 (242)
-..|+.+|.|.+--=++-+|
T Consensus 113 ~rtI~~i~~V~~ArVhl~~P 132 (193)
T TIGR02544 113 EQTLSQIDGVISARVHVVLP 132 (193)
T ss_pred HHHHHhcCCeeeeEEEEECC
Confidence 45677888888544444443
No 147
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=24.82 E-value=1e+02 Score=24.96 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=20.3
Q ss_pred EEEEeCcccHHHHHHHHHHCCCc
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
|.+.|-|..-..+.+.|+++|++
T Consensus 2 Yvl~~~~~~E~~v~~~L~~~gi~ 24 (159)
T TIGR01955 2 YLLYCKPRQEQRAQEHLERQAVE 24 (159)
T ss_pred EEEEEcCchHHHHHHHHHHCCCE
Confidence 67889999999999999999974
No 148
>COG2044 Predicted peroxiredoxins [General function prediction only]
Probab=24.77 E-value=2.1e+02 Score=23.10 Aligned_cols=64 Identities=20% Similarity=0.224 Sum_probs=43.5
Q ss_pred CeEEEEEEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC----------CChhHHHHHHHhcCCc
Q psy8853 95 GAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN----------TKKNTLLDLALEKGAE 162 (242)
Q Consensus 95 Gv~iive~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~----------~~~d~~~e~Aie~Gae 162 (242)
-+.+++-.=++|.-|+-+-+=....- .++|. -|..+|.=.|+-.+.++ ..+++++..|+|.|++
T Consensus 4 ~v~i~~t~G~~~~~r~ya~f~~A~~a--~smg~--dV~iF~t~dG~~l~~K~~~ekik~~~~~~l~~~~~~a~e~GVk 77 (120)
T COG2044 4 KVLIVVTSGPNNPERAYAPFVMATAA--ASMGY--DVTIFFTMDGVTLVKKKVAEKIKHPNFPPLEELIKQAIEAGVK 77 (120)
T ss_pred eEEEEEecCCCCHHHHHhHHHHHHHH--HhCCC--ceEEEEEeccceeeeecchhhhcCCCCCCHHHHHHHHHHcCCE
Confidence 35666667778888987654333321 24443 56777888888777643 3679999999999964
No 149
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.35 E-value=1.9e+02 Score=19.86 Aligned_cols=56 Identities=16% Similarity=0.111 Sum_probs=36.4
Q ss_pred EEEeCcccHHHHHHHHHHCCCceeeceeeee----cC--cceecCHHHHHHHHHHHHHHhcC
Q psy8853 173 TIITSPSKFIEIKNSLEMTGFKAESSGIVMR----PY--TNIVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 173 ~~~c~p~~~~~v~~~L~~~g~~v~~sel~~~----P~--~~v~l~~e~~~~~~~li~~Lee~ 228 (242)
.+--.|-.|..+.+.|.+.|.+|.+-..... +. ..+.++-+....++.+++.|++.
T Consensus 5 ~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~e~~~~~~~i~~~L~~~ 66 (72)
T cd04884 5 LLEDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTPMDRSKENELIEELKAK 66 (72)
T ss_pred EecCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEEecchHHHHHHHHHhCc
Confidence 3444688999999999999999876543332 11 22333323333478888888765
No 150
>PRK11253 ldcA L,D-carboxypeptidase A; Provisional
Probab=24.28 E-value=1.4e+02 Score=27.46 Aligned_cols=55 Identities=16% Similarity=0.182 Sum_probs=37.9
Q ss_pred ccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHH-hcCCCccccee
Q psy8853 179 SKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNEL-KKLHDVKKVYT 236 (242)
Q Consensus 179 ~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~L-ee~dDV~~Vy~ 236 (242)
+.+....+.|++.||+|......+.... -+...+.++...|.+++ ..+| |..|+.
T Consensus 17 ~~~~~~i~~L~~~G~~v~~~~~~~~~~~--~~agtd~~Ra~dL~~a~a~~dp-i~aI~~ 72 (305)
T PRK11253 17 AAALRGVQRLTDAGHQVENVEVIARRYQ--RFAGTDGERLADLNSLADLTTP-NTIVLA 72 (305)
T ss_pred HHHHHHHHHHHhCCCEEeeccccccccC--ccCCCHHHHHHHHHHHHhcCCC-ccEEEE
Confidence 3577777889999999877776664333 34445556888888887 3444 887775
No 151
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=24.05 E-value=1.8e+02 Score=23.58 Aligned_cols=41 Identities=12% Similarity=0.088 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhc-CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCC
Q psy8853 27 RIMRELRVAINF-GNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSN 75 (242)
Q Consensus 27 kl~reI~~Avk~-G~dP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~ 75 (242)
.+=++|..+.+. |- ..+.. -|+..|++..++.+-|+|-...
T Consensus 9 ~~D~~Il~~Lq~d~R--~s~~e------iA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALMENAR--TPYAE------LAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHHcCC--CCHHH------HHHHHCcCHHHHHHHHHHHHHC
Confidence 344556666665 32 12333 3556688888888888887753
No 152
>TIGR01307 pgm_bpd_ind 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This protein is about double in length of, and devoid of homology to the form of phosphoglycerate mutase that uses 2,3-bisphosphoglycerate as a cofactor.
Probab=23.86 E-value=1.9e+02 Score=28.85 Aligned_cols=119 Identities=15% Similarity=0.190 Sum_probs=70.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCCH---------------HHHHHHHHhcCCCCCCCCcceeEEEEE
Q psy8853 25 CTRIMRELRVAINFGNNPDTNIKLRLAIEKALDANIPK---------------NNIFRAIQKNNSNIKNENINYIEVRYE 89 (242)
Q Consensus 25 f~kl~reI~~Avk~G~dP~~N~~L~~ai~~Ak~~nmPk---------------~~Ie~AIkk~~g~~~~~~~~~~~~~yE 89 (242)
...-...|..|++.| +-..|+.|..++++||+.|=.- +-|..-|+-|..
T Consensus 72 v~q~~~ri~~ai~~g-~~~~n~~l~~~~~~~~~~~~~lHl~GL~SdGgVHsh~~hl~~l~~~a~~--------------- 135 (501)
T TIGR01307 72 VYQDLVRISQAIKDG-EFFANPALLGAIDRAKDNNGKLHLMGLVSDGGVHSHIDHLIALIELAAE--------------- 135 (501)
T ss_pred eccchHHHHHHHhcC-CcccCHHHHHHHHHHHhcCCceEEEEeccCCCCcchHHHHHHHHHHHHH---------------
Confidence 333345578888875 5678999999999998765332 334444444432
Q ss_pred EeccCCe-EEEEEEecCCc-------chhHHHHHHHhhhcC-ccccCCCccccccceeeEEEE-C--------CC----C
Q psy8853 90 GYSVNGA-AIIVDCITNNR-------MRTVSNIRNIFNKNG-GNLSKEGSVLFMFKHCGQLLF-L--------PN----T 147 (242)
Q Consensus 90 g~gPgGv-~iive~lTdN~-------nRt~~~vr~~f~K~g-g~l~~~gsv~~~F~~kG~i~v-~--------~~----~ 147 (242)
.|+ -+.|.|+||=+ ..-+.++...+.+.| |+++..+.=-|-+||-..-.- . .. .
T Consensus 136 ----~g~~~v~vH~~~DGRD~~p~s~~~~~~~l~~~~~~~~~~~iasv~GRyyaMDRd~rw~rv~~ay~~~~~g~~~~~~ 211 (501)
T TIGR01307 136 ----RGIEKVVLHAFTDGRDTAPKSAESYLEQLQAFLKEIGNGRIATISGRYYAMDRDQRWDRVEIAYKAITGGDGFEFS 211 (501)
T ss_pred ----cCCCeEEEEEecCCCCCCchhHHHHHHHHHHHHHHhCCEEEEEEeCcceeecCccchHHHHHHHHHHhcCCCCCCC
Confidence 133 47788999853 345667777777766 777654333466676543210 0 00 2
Q ss_pred ChhHHHHHHHhcCCcc
Q psy8853 148 KKNTLLDLALEKGAED 163 (242)
Q Consensus 148 ~~d~~~e~Aie~GaeD 163 (242)
+..++++.+-+.|..|
T Consensus 212 ~~~~ai~~~y~~~~~D 227 (501)
T TIGR01307 212 DPVAYIQDAYARDITD 227 (501)
T ss_pred CHHHHHHHHHhCCCCC
Confidence 4445566666667655
No 153
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.68 E-value=95 Score=22.21 Aligned_cols=29 Identities=3% Similarity=0.197 Sum_probs=26.5
Q ss_pred EEEEEecCCcchhHHHHHHHhhhcCcccc
Q psy8853 98 IIVDCITNNRMRTVSNIRNIFNKNGGNLS 126 (242)
Q Consensus 98 iive~lTdN~nRt~~~vr~~f~K~gg~l~ 126 (242)
+++|+.|.++.+..+.+-.+|..+|.++-
T Consensus 1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~ 29 (76)
T cd04927 1 FLLKLFCSDRKGLLHDVTEVLYELELTIE 29 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHCCCeEE
Confidence 47899999999999999999999998774
No 154
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=23.41 E-value=2.3e+02 Score=27.41 Aligned_cols=59 Identities=10% Similarity=0.098 Sum_probs=42.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec-cCCeEEEEEEecCCcchhHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS-VNGAAIIVDCITNNRMRTVSNIR 115 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g-PgGv~iive~lTdN~nRt~~~vr 115 (242)
...|+..|...+++.+.|.++|+...+- . .++|-.+ .+|+.+|-++.-.|+.-+..-|+
T Consensus 283 a~~A~a~~~~lgi~~~~i~~~l~~~~~~---~------gR~e~~~~~~g~~iidDs~ahNp~a~~~al~ 342 (468)
T PRK04690 283 LCAVLAALEALGLDAVALAPAAAGFRPL---P------NRLQELGSRDGITYVNDSISTTPHASLAALD 342 (468)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC---C------CCcEEEEccCCeEEEEeCCCCCHHHHHHHHH
Confidence 4567777778899999999999987643 2 2344433 35788888877888887776554
No 155
>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.14 E-value=1.2e+02 Score=20.50 Aligned_cols=28 Identities=11% Similarity=0.301 Sum_probs=25.1
Q ss_pred EEEEecCCcchhHHHHHHHhhhcCcccc
Q psy8853 99 IVDCITNNRMRTVSNIRNIFNKNGGNLS 126 (242)
Q Consensus 99 ive~lTdN~nRt~~~vr~~f~K~gg~l~ 126 (242)
++.+.+.++....++|-.+|+.+|.++-
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~ 29 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIH 29 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEE
Confidence 4677899999999999999999999875
No 156
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=22.96 E-value=2.4e+02 Score=19.42 Aligned_cols=20 Identities=30% Similarity=0.403 Sum_probs=13.8
Q ss_pred CcccHHHHHHHHHHCCCcee
Q psy8853 177 SPSKFIEIKNSLEMTGFKAE 196 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~ 196 (242)
.|.=+.++.+.|++.|++|.
T Consensus 3 ~p~G~~a~~~~L~~~g~~v~ 22 (70)
T PF14258_consen 3 APNGTYALYQLLEEQGVKVE 22 (70)
T ss_pred CchHHHHHHHHHHHCCCeeE
Confidence 35556677777777777765
No 157
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]
Probab=22.96 E-value=1.2e+02 Score=24.06 Aligned_cols=69 Identities=29% Similarity=0.407 Sum_probs=47.4
Q ss_pred CcceEeecCc-----eEEEEe-CcccHHHHHHHHHHC-CCc----eeeceeeeecCcceecCH--HHHHHHHHHHHHHhc
Q psy8853 161 AEDFLIDKDN-----KITIIT-SPSKFIEIKNSLEMT-GFK----AESSGIVMRPYTNIVFKD--GEAIKLQKLLNELKK 227 (242)
Q Consensus 161 aeDve~~ed~-----~~~~~c-~p~~~~~v~~~L~~~-g~~----v~~sel~~~P~~~v~l~~--e~~~~~~~li~~Lee 227 (242)
+.||+...|- +|.++| +..+...+.++|.+. |+= .....+.|+|.=.-..|+ +....+..|++.|..
T Consensus 36 Vt~V~vS~Dl~~A~Vyvt~l~~~~~~~~~~~~~L~~A~g~ir~~l~~~~~lr~~PeL~F~~D~s~~~~~ki~~Ll~~l~~ 115 (118)
T COG0858 36 VTDVEVSKDLSHAKVYVTVLGDEESSKAEILAALNKAKGFIRSELGKRLRLRKTPELHFVYDDSIENGNKIDALLNDLKK 115 (118)
T ss_pred EEEEEEcCCCceEEEEEEecCCchhhHHHHHHHHHHhHHHHHHHHHHhCCeEeCCeEEEEeCcccchHHHHHHHHHHhhh
Confidence 4556665552 567778 555788888888877 542 355678888886666654 667789999998876
Q ss_pred CC
Q psy8853 228 LH 229 (242)
Q Consensus 228 ~d 229 (242)
-+
T Consensus 116 ~~ 117 (118)
T COG0858 116 AD 117 (118)
T ss_pred cC
Confidence 54
No 158
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=22.78 E-value=2.3e+02 Score=20.04 Aligned_cols=45 Identities=24% Similarity=0.382 Sum_probs=27.8
Q ss_pred HHHHHh-c-CCcceEee-cCceEEEEeCc--ccHHHHHHHHHHCCCceee
Q psy8853 153 LDLALE-K-GAEDFLID-KDNKITIITSP--SKFIEIKNSLEMTGFKAES 197 (242)
Q Consensus 153 ~e~Aie-~-GaeDve~~-ed~~~~~~c~p--~~~~~v~~~L~~~g~~v~~ 197 (242)
.+-||+ . |+.++..+ +.+...+..++ .+..++.+++++.||.+..
T Consensus 20 V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 20 VEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred HHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 344554 2 56666663 33334444444 5788888889999988654
No 159
>PF15474 MU117: Meiotically up-regulated gene family
Probab=22.42 E-value=3.4e+02 Score=20.87 Aligned_cols=66 Identities=17% Similarity=0.234 Sum_probs=50.5
Q ss_pred CCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhc--CccccCCCcc
Q psy8853 59 NIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKN--GGNLSKEGSV 131 (242)
Q Consensus 59 nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~--gg~l~~~gsv 131 (242)
.++.+.=++||.+-.. ..-| -.|.+++-|+..++.+|--++-.++-++|+..+... ++.-..=|++
T Consensus 14 ~~~~~~C~~A~~~~~~-----~~~Y--~~~~~~~~g~C~a~~~~~g~~~~~sG~~i~~~~~~i~~~~~c~~CGs~ 81 (97)
T PF15474_consen 14 RGNVDACDRAINQFDD-----DTIY--TDYTGFGSGNCWAFYTCDGDGCGMSGKDIIDAYQDIYRNGGCKRCGSK 81 (97)
T ss_pred CccHHHHHHHHHhcCC-----CceE--eccccccccceEEEEEecCCCcCccHHHHHHHHHHHHhcCCCcccCCE
Confidence 4678888999998743 2334 578888889999999999999999999999999887 4443333443
No 160
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=22.39 E-value=2.1e+02 Score=19.93 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=34.3
Q ss_pred ChhHHHHHHHhcCCcceEeecC--c-eEEEEe-CcccHHHHHHHHHHCC
Q psy8853 148 KKNTLLDLALEKGAEDFLIDKD--N-KITIIT-SPSKFIEIKNSLEMTG 192 (242)
Q Consensus 148 ~~d~~~e~Aie~GaeDve~~ed--~-~~~~~c-~p~~~~~v~~~L~~~g 192 (242)
..+++.+.+.+.||-=.....- | ++-.+| ++....+|.+.|++.+
T Consensus 35 ~i~~~~~~~~~~Ga~~~~~sGsG~G~~v~~l~~~~~~~~~v~~~l~~~~ 83 (85)
T PF08544_consen 35 EIDELKEAAEENGALGAKMSGSGGGPTVFALCKDEDDAERVAEALREHY 83 (85)
T ss_dssp HHHHHHHHHHHTTESEEEEETTSSSSEEEEEESSHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHCCCCceecCCCCCCCeEEEEECCHHHHHHHHHHHHHhC
Confidence 3578888998899666655443 3 777888 8888899999998764
No 161
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=22.28 E-value=31 Score=25.98 Aligned_cols=26 Identities=15% Similarity=0.068 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhc
Q psy8853 47 KLRLAIEKALDANIPKNNIFRAIQKN 72 (242)
Q Consensus 47 ~L~~ai~~Ak~~nmPk~~Ie~AIkk~ 72 (242)
-|...|+.|++.||+.++|.....+.
T Consensus 13 ~Lg~~v~~ae~~Gms~e~i~~~A~~i 38 (81)
T PF11588_consen 13 FLGDRVEQAEKLGMSEETIANLAYQI 38 (81)
T ss_dssp HHHHHHHHHHHHHHHTT----HHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 48889999999999999999877654
No 162
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.19 E-value=70 Score=20.69 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcC
Q psy8853 47 KLRLAIEKALDANIPKNNIFRAIQKNN 73 (242)
Q Consensus 47 ~L~~ai~~Ak~~nmPk~~Ie~AIkk~~ 73 (242)
...+.-+.||..|++..+|-++++...
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~~~ 42 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNTGK 42 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhCCC
Confidence 367888999999999999999998744
No 163
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=22.12 E-value=1.8e+02 Score=30.43 Aligned_cols=62 Identities=11% Similarity=0.065 Sum_probs=47.2
Q ss_pred EeCcccHHHHHHHHHHCCCceeeceeeeec-C----cceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 175 ITSPSKFIEIKNSLEMTGFKAESSGIVMRP-Y----TNIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 175 ~c~p~~~~~v~~~L~~~g~~v~~sel~~~P-~----~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
.=.+--|..|...|.+.+..|.+....--+ . -.+.|.=.+.+.+..++.+|+..++|.+|+.
T Consensus 674 ~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ieV~~~~~L~~l~~~L~~i~~V~~v~R 740 (743)
T PRK10872 674 NDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIEIYNLQVLGRVLGKLNQVPDVIDARR 740 (743)
T ss_pred cCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEEECCHHHHHHHHHHHhcCCCcCeEEe
Confidence 334556899999999999998777665433 1 2233444678899999999999999999986
No 164
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=22.08 E-value=2.2e+02 Score=30.03 Aligned_cols=60 Identities=18% Similarity=0.255 Sum_probs=43.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEec----cCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYS----VNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~g----PgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|..+|+...+- .+ ++|..+ .+|..+|+| .-.|+.-+.+-++.+
T Consensus 312 alaAia~a~~lgi~~~~I~~~L~~~~~~---~g------R~e~i~~~~~~~~~~vi~D-yahnP~s~~a~l~~l 375 (958)
T PRK11929 312 LLLVAAALKKLGLPLAQIARALAAVSPV---PG------RMERVGPTAGAQGPLVVVD-YAHTPDALAKALTAL 375 (958)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCCCC---CC------CcEEeccccCCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 4567788888999999999999987754 22 344442 367889999 677777665555554
No 165
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit. This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G
Probab=22.06 E-value=2.1e+02 Score=26.90 Aligned_cols=75 Identities=17% Similarity=0.183 Sum_probs=56.5
Q ss_pred HHHHHhcCCcceEeecCceEEEEeCcccHHHHH-HHHHHCCCceeeceeeeecCcceecCH-HHHHHHHHHHHHHhcCCC
Q psy8853 153 LDLALEKGAEDFLIDKDNKITIITSPSKFIEIK-NSLEMTGFKAESSGIVMRPYTNIVFKD-GEAIKLQKLLNELKKLHD 230 (242)
Q Consensus 153 ~e~Aie~GaeDve~~ed~~~~~~c~p~~~~~v~-~~L~~~g~~v~~sel~~~P~~~v~l~~-e~~~~~~~li~~Lee~dD 230 (242)
...|-..|..-|+. +|.+-+++.-.-+.-+. +.+...|.+ |.+++++.. .+.+.+...++.+-++|+
T Consensus 242 e~~~~~~~l~~v~l--~G~i~~i~nG~Gl~~~t~D~~~~~g~~---------~aNplDlgg~a~~~~~~~al~~l~~dp~ 310 (386)
T TIGR01016 242 EVLAKQWGLNYVAL--DGNIGCMVNGAGLAMATMDIIKLYGGE---------PANFLDVGGGASAERVREALKLVLSDKS 310 (386)
T ss_pred hhHHHHcCCcEEcc--CCcEEEEECCccHHHHHHHHHHHcCCC---------CCCcEEecCCCCHHHHHHHHHHHHcCCC
Confidence 34555567666655 46688888888887655 888888764 799999843 456788889999999999
Q ss_pred cccceecc
Q psy8853 231 VKKVYTNA 238 (242)
Q Consensus 231 V~~Vy~Ni 238 (242)
|.-|.-|+
T Consensus 311 vd~ilv~i 318 (386)
T TIGR01016 311 VKVVFINI 318 (386)
T ss_pred CCEEEEEC
Confidence 99888765
No 166
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=21.99 E-value=1.5e+02 Score=22.40 Aligned_cols=55 Identities=15% Similarity=0.171 Sum_probs=31.9
Q ss_pred ccHHHHHHHHHHC---CCceeeceeeeecCc------ceecCHHHHHHHHHHHHHHhcCCCcccc
Q psy8853 179 SKFIEIKNSLEMT---GFKAESSGIVMRPYT------NIVFKDGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 179 ~~~~~v~~~L~~~---g~~v~~sel~~~P~~------~v~l~~e~~~~~~~li~~Lee~dDV~~V 234 (242)
.++..+.+.+++. |+.+...+.+-++=- .+.++++. .....+-+.+...++|+.|
T Consensus 17 vDle~L~~~ik~~~~~g~~~~~~~~ePiaFGLkaL~~~~vv~D~~-g~td~lee~i~~ve~V~sv 80 (88)
T TIGR00489 17 VDLEALKEKIKERIPEGVEIRKIDEEPIAFGLVAINVMVVMGDAE-GGTEAAEESLSGIEGVESV 80 (88)
T ss_pred cCHHHHHHHHHHhCcCCcEEeeeEEEeeeccceeeEEEEEEecCC-cChHHHHHHHhcCCCccEE
Confidence 4566777776655 666554443333321 22234433 4557777788888888876
No 167
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=21.76 E-value=1.2e+02 Score=24.76 Aligned_cols=23 Identities=13% Similarity=0.239 Sum_probs=20.2
Q ss_pred EEEEeCcccHHHHHHHHHHCCCc
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
|.+.|-|..-..+.+.|++.|++
T Consensus 5 Yvl~t~~~~E~~v~~~L~~~gi~ 27 (162)
T PRK09014 5 YLLYCKRGQLQRAQEHLERQGVE 27 (162)
T ss_pred EEEEecCchHHHHHHHHHHCCCE
Confidence 77889999999999999998875
No 168
>TIGR01127 ilvA_1Cterm threonine dehydratase, medium form. A form of threonine dehydratase with two copies of the C-terminal domain Pfam:PF00585 is described by TIGR01124. This model describes a phylogenetically distinct form with a single copy of pfam00585. This form branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any pfam00585 domain. Many members of this model are found in species with other Ile biosynthetic enzymes.
Probab=21.72 E-value=5.5e+02 Score=23.83 Aligned_cols=50 Identities=20% Similarity=0.125 Sum_probs=32.2
Q ss_pred CChhHHHHHHHhcCC--cceEee------cCc--eEEEEe---CcccHHHHHHHHHHCCCcee
Q psy8853 147 TKKNTLLDLALEKGA--EDFLID------KDN--KITIIT---SPSKFIEIKNSLEMTGFKAE 196 (242)
Q Consensus 147 ~~~d~~~e~Aie~Ga--eDve~~------ed~--~~~~~c---~p~~~~~v~~~L~~~g~~v~ 196 (242)
..+-++++..-+.|+ -+|.-. ..+ .+.|.+ ++.++..+.+.|++.||++.
T Consensus 317 G~L~~v~~~i~~~~~NI~~i~~~r~~~~~~~~~~~v~v~vet~~~~~~~~i~~~L~~~G~~v~ 379 (380)
T TIGR01127 317 GALYHLLESIAEARANIVKIDHDRLSKEIPPGFAMVEITLETRGKEHLDEILKILRDMGYNFY 379 (380)
T ss_pred CHHHHHHHHHhcCCCcEEEEEeeccccCCCCceEEEEEEEEeCCHHHHHHHHHHHHHcCCccc
Confidence 456777777777776 344221 112 344433 45788899999999999864
No 169
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=21.64 E-value=1.7e+02 Score=22.54 Aligned_cols=84 Identities=17% Similarity=0.196 Sum_probs=44.6
Q ss_pred CcchhHHHHHHHhhhcCccccCCCccccccceeeEEEECCC----CChhHHHHHHHhcCCcceEeecCc--eEEEEeCc-
Q psy8853 106 NRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPN----TKKNTLLDLALEKGAEDFLIDKDN--KITIITSP- 178 (242)
Q Consensus 106 N~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~v~~~----~~~d~~~e~Aie~GaeDve~~ed~--~~~~~c~p- 178 (242)
...++..++..+.. +||++- .|.+-..=.|.|...-. .|.+..++..=+..+.-.-.-.+| ...|.|+-
T Consensus 6 ~~~~~~~EL~~IVd-~Gg~V~---DV~veHp~YG~i~~~L~i~sr~Dv~~Fi~~l~~~~~~~Ls~LT~GvH~HtI~a~~~ 81 (98)
T PF02829_consen 6 TPDEIEDELEIIVD-NGGRVL---DVIVEHPVYGEITGNLNISSRRDVDKFIEKLEKSKAKPLSSLTGGVHYHTIEAPDE 81 (98)
T ss_dssp -GGGHHHHHHHHHH-TT-EEE---EEEEEETTTEEEEEEEEE-SHHHHHHHHHHHHH--S--STTGGGGEEEEEEEESSH
T ss_pred CHHHHHHHHHHHHH-CCCEEE---EEEEeCCCCcEEEEEEecCCHHHHHHHHHHHhccCCcchHHhcCCEeeEEEEECCH
Confidence 45567777887776 888775 34444444454543322 234444444444455543332345 34555543
Q ss_pred ccHHHHHHHHHHCCC
Q psy8853 179 SKFIEIKNSLEMTGF 193 (242)
Q Consensus 179 ~~~~~v~~~L~~~g~ 193 (242)
+.|..+.++|+++||
T Consensus 82 e~l~~I~~~L~~~G~ 96 (98)
T PF02829_consen 82 EDLDKIEEALKKKGF 96 (98)
T ss_dssp HHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHCCC
Confidence 478999999999887
No 170
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=21.60 E-value=1.2e+02 Score=24.86 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=18.8
Q ss_pred EEEEEecc--CCeEEEEEEecCCc
Q psy8853 86 VRYEGYSV--NGAAIIVDCITNNR 107 (242)
Q Consensus 86 ~~yEg~gP--gGv~iive~lTdN~ 107 (242)
+.|--||| |-+++|||++..|+
T Consensus 13 Vvli~~Gp~~GKL~vIVDIID~nR 36 (130)
T PTZ00065 13 LCLIQYGPDAGKLCFIVDIVTPTR 36 (130)
T ss_pred EEEEecCCCCCCEEEEEEEEcCCe
Confidence 56777898 67999999999985
No 171
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=21.40 E-value=1.8e+02 Score=24.53 Aligned_cols=65 Identities=18% Similarity=0.152 Sum_probs=39.4
Q ss_pred EEEeCcccHHHHHHH--HHHCCCceeeceeeeecC---------cceecCHH--------------HHHHHHHHHHHHhc
Q psy8853 173 TIITSPSKFIEIKNS--LEMTGFKAESSGIVMRPY---------TNIVFKDG--------------EAIKLQKLLNELKK 227 (242)
Q Consensus 173 ~~~c~p~~~~~v~~~--L~~~g~~v~~sel~~~P~---------~~v~l~~e--------------~~~~~~~li~~Lee 227 (242)
-|+..|+++..+... |.+. .+..-+.+|.|. ..++|..+ ..+.+..++..|-+
T Consensus 2 ~~i~~~~el~~~~~~~~l~~~--~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~ 79 (193)
T cd06146 2 HIVDSEEELEALLLALSLEAG--RVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFE 79 (193)
T ss_pred eEecCHHHHHHHHHHHhhccC--CEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhC
Confidence 467778888888877 4433 333333334322 22233211 13456677888888
Q ss_pred CCCcccceeccc
Q psy8853 228 LHDVKKVYTNAL 239 (242)
Q Consensus 228 ~dDV~~Vy~Ni~ 239 (242)
+++|.+|.+++.
T Consensus 80 d~~i~KVg~~~~ 91 (193)
T cd06146 80 DPDVLKLGFGFK 91 (193)
T ss_pred CCCeeEEEechH
Confidence 999999999875
No 172
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=21.33 E-value=1.2e+02 Score=22.94 Aligned_cols=56 Identities=13% Similarity=0.195 Sum_probs=34.0
Q ss_pred cccHHHHHHHHHHC---CCceeeceeeeecCcc------eecCHHHHHHHHHHHHHHhcCCCcccc
Q psy8853 178 PSKFIEIKNSLEMT---GFKAESSGIVMRPYTN------IVFKDGEAIKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 178 p~~~~~v~~~L~~~---g~~v~~sel~~~P~~~------v~l~~e~~~~~~~li~~Lee~dDV~~V 234 (242)
-.++..+.+.+++. |+....++..-++--. +.++++ .-....+-+.+.+.+|||.|
T Consensus 16 e~Dl~~L~~~ik~~~~~g~~~~~~~~ePIaFGLkaL~i~~vv~D~-~~~td~lee~i~~~e~Vqsv 80 (88)
T PRK00435 16 EVDLDELKEKIKEVLPEGYKINGIEEEPIAFGLKALKLYVIMPDE-EGGTEPVEEAFANVEGVESV 80 (88)
T ss_pred CcCHHHHHHHHHHhCcCCcEEeEeEEEEeeccceeEEEEEEEEcC-CcCcHHHHHHHhccCCCcEE
Confidence 34566666666654 6766655555554321 223333 34557788888888888876
No 173
>COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]
Probab=21.32 E-value=2.4e+02 Score=26.47 Aligned_cols=96 Identities=17% Similarity=0.183 Sum_probs=56.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHH---H---HcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEE
Q psy8853 27 RIMRELRVAINFGNNPDTNIKLRLAIEKA---L---DANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIV 100 (242)
Q Consensus 27 kl~reI~~Avk~G~dP~~N~~L~~ai~~A---k---~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iiv 100 (242)
.++.++.-|+-. .| =+.+..+|.+. | ...++++-|||.++.|.... .- --..-|=|-|| ++++
T Consensus 228 ~~A~~~~~al~~-nd---~~~f~~~l~~gW~~KK~ls~~ISN~~IDriy~~A~~~G-A~-----~gKl~GaG~gG-Fllf 296 (333)
T COG2605 228 ALAYEMKDALVR-ND---IPEFGQILDRGWEAKKKLSSRISNDAIDRIYELALKNG-AY-----GGKLSGAGGGG-FLLF 296 (333)
T ss_pred HHHHHHHHHHHh-cc---hHHHHHHHHhHHHhhhhhccCcCcHHHHHHHHHHHhcC-ch-----hceeeccCCcc-EEEE
Confidence 345555555543 33 35677777643 3 37899999999999887541 11 11233445444 3444
Q ss_pred EEecCCcchhHHHHHHHhhhcCccccCCCccccccceeeEEE
Q psy8853 101 DCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLL 142 (242)
Q Consensus 101 e~lTdN~nRt~~~vr~~f~K~gg~l~~~gsv~~~F~~kG~i~ 142 (242)
=|--.++++ |-..|.+..| .+|.|.|+..|.-.
T Consensus 297 ~~~p~k~~~----l~r~l~~~~~-----~~~~~~Fd~~Gsr~ 329 (333)
T COG2605 297 FCDPSKRNE----LARALEKEQG-----FVVDTSFDKEGSRI 329 (333)
T ss_pred EeCccchHH----HHHHHHHhcC-----CeEEEEecCCCeEE
Confidence 455555544 4455566655 36679999999754
No 174
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=21.25 E-value=2.3e+02 Score=29.21 Aligned_cols=61 Identities=13% Similarity=0.091 Sum_probs=47.6
Q ss_pred EeCcccHHHHHHHHHHCCCceeeceeeeecCcc----eecCHHHHHHHHHHHHHHhcCCCcccce
Q psy8853 175 ITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTN----IVFKDGEAIKLQKLLNELKKLHDVKKVY 235 (242)
Q Consensus 175 ~c~p~~~~~v~~~L~~~g~~v~~sel~~~P~~~----v~l~~e~~~~~~~li~~Lee~dDV~~Vy 235 (242)
.=.+.-|..|...|.+.+..|.+....-.+... +.|.=.+...+.+++..|...++|.+|+
T Consensus 618 ~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~~~~~~~~~ieV~~~~~L~~ii~~L~~i~~V~~v~ 682 (683)
T TIGR00691 618 VDRKGVLSDLTTAISENDSNIVSISTKTYGKREAILNITVEIKNYKHLLKIMLKIKTKNDVIVVK 682 (683)
T ss_pred ecCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCceEEe
Confidence 445667999999999999998877766554332 3344577889999999999999999886
No 175
>PF00543 P-II: Nitrogen regulatory protein P-II members of this family.; InterPro: IPR002187 In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity []. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein []. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome. Other proteins highly similar to glnB are: Bacillus subtilis protein nrgB []. Escherichia coli hypothetical protein ybaI []. ; GO: 0030234 enzyme regulator activity, 0006808 regulation of nitrogen utilization; PDB: 1V3S_B 1V3R_C 2XZW_A 2XUL_A 2V5H_J 2XG8_C 2JJ4_F 1QY7_C 4AFF_A 2XBP_A ....
Probab=21.13 E-value=1e+02 Score=23.32 Aligned_cols=23 Identities=30% Similarity=0.469 Sum_probs=19.8
Q ss_pred EEEEeCcccHHHHHHHHHHCCCc
Q psy8853 172 ITIITSPSKFIEIKNSLEMTGFK 194 (242)
Q Consensus 172 ~~~~c~p~~~~~v~~~L~~~g~~ 194 (242)
++.+..|..+..|.++|.+.|+.
T Consensus 1 I~aIir~~~~~~v~~aL~~~G~~ 23 (102)
T PF00543_consen 1 IEAIIRPEKLEEVIEALREAGVP 23 (102)
T ss_dssp EEEEEEGGGHHHHHHHHHHTTGS
T ss_pred CEEEEChhHHHHHHHHHHHCCCC
Confidence 46788999999999999998654
No 176
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.93 E-value=2.4e+02 Score=20.29 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=32.4
Q ss_pred CcccHHHHHHHHHHCCCceeeceeeeecC--cc------eecCHHHHHHHHHHHHHHhcC
Q psy8853 177 SPSKFIEIKNSLEMTGFKAESSGIVMRPY--TN------IVFKDGEAIKLQKLLNELKKL 228 (242)
Q Consensus 177 ~p~~~~~v~~~L~~~g~~v~~sel~~~P~--~~------v~l~~e~~~~~~~li~~Lee~ 228 (242)
.|..|..+-+.++..|+++. .|+-+|. .. |+++... ..+.++++.|++.
T Consensus 10 ~~g~L~~iL~~f~~~~inl~--~IeSRP~~~~~~~y~F~id~e~~~-~~i~~~l~~l~~~ 66 (74)
T cd04929 10 EVGGLAKALKLFQELGINVV--HIESRKSKRRSSEFEIFVDCECDQ-RRLDELVQLLKRE 66 (74)
T ss_pred CCcHHHHHHHHHHHCCCCEE--EEEeccCCCCCceEEEEEEEEcCH-HHHHHHHHHHHHh
Confidence 36778888888888787654 4555664 22 5554433 3788888888763
No 177
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=20.66 E-value=2.4e+02 Score=27.20 Aligned_cols=62 Identities=16% Similarity=0.075 Sum_probs=42.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHH
Q psy8853 48 LRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNI 117 (242)
Q Consensus 48 L~~ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~ 117 (242)
+.+|+.-|...++|.+.|.++|+..... .+ -++.+. + .+|+.+|-++.-.|+.-+.+-++.+
T Consensus 294 a~aA~a~~~~lgi~~~~i~~~l~~~~~~---~~-R~e~~~-~---~~~~~iiDdsyahNp~s~~~~l~~l 355 (473)
T PRK00141 294 ALAAAAVARSQGVAPEAIARALSSFEVA---GH-RGQVVA-E---HGGVTWIDNSKATNPHAADAALAGH 355 (473)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCC---CC-ceEEEE-E---eCCEEEEEcCCCCCHHHHHHHHHhc
Confidence 4577788888999999999999988864 21 233221 1 2466555555677887776666653
No 178
>KOG2121|consensus
Probab=20.64 E-value=55 Score=33.96 Aligned_cols=54 Identities=20% Similarity=0.281 Sum_probs=40.2
Q ss_pred HHHHHHHcCCCHHHHHHHHHhcCCCCCCCCcceeEEEE-EEecc---CCeEEEEEEecCCc
Q psy8853 51 AIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRY-EGYSV---NGAAIIVDCITNNR 107 (242)
Q Consensus 51 ai~~Ak~~nmPk~~Ie~AIkk~~g~~~~~~~~~~~~~y-Eg~gP---gGv~iive~lTdN~ 107 (242)
-+++|++.|+|+--+-..+++++... .+ +-..+++ |..|| |-+.+|++|-+++.
T Consensus 222 ~~~kA~~lGvp~Gp~~~~L~~G~~vt-~~--~g~i~~~~ev~gp~~~~~~f~il~cp~e~~ 279 (746)
T KOG2121|consen 222 DVEKAKELGVPKGPLIGKLKSGESVT-LD--DGTIVVPSEVVGPSRPGASFLILDCPDESY 279 (746)
T ss_pred cHHHHHHhCCCCCcchhhhcCCCcee-cc--CCcEEehhhhcCCCCCccEEEEecCCcHHH
Confidence 36788999999999999999988652 12 2223344 78887 56889999988764
No 179
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=20.16 E-value=84 Score=27.64 Aligned_cols=23 Identities=39% Similarity=0.268 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhc
Q psy8853 50 LAIEKALDANIPKNNIFRAIQKN 72 (242)
Q Consensus 50 ~ai~~Ak~~nmPk~~Ie~AIkk~ 72 (242)
-+|.-|+..|+|++.|+||-+..
T Consensus 207 ~ai~iA~~~g~p~~II~rA~~i~ 229 (235)
T PF00488_consen 207 YAIEIAKLAGLPEEIIERAKEIL 229 (235)
T ss_dssp CHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHHhCcCHHHHHHHHHHH
Confidence 48899999999999999997643
No 180
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=20.12 E-value=2e+02 Score=22.53 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHH-------HHHHHhcCCCCCCCHHHHHHHHHHHHcCC
Q psy8853 18 DAKRGKICTRIMRE-------LRVAINFGNNPDTNIKLRLAIEKALDANI 60 (242)
Q Consensus 18 Da~k~k~f~kl~re-------I~~Avk~G~dP~~N~~L~~ai~~Ak~~nm 60 (242)
+.+|++=.++++|+ ++.|.. |..||++.+++.-+|+.|+
T Consensus 45 ~var~~GMsqvA~~aGlsRe~LYkaLS----~~GNPtf~Til~V~kAlG~ 90 (100)
T COG3636 45 VVARSRGMSQVARKAGLSREGLYKALS----PGGNPTFDTILAVLKALGL 90 (100)
T ss_pred HHHHhcCHHHHHHHhCccHHHHHHHhC----CCCCCcHHHHHHHHHHcCc
Confidence 44555556666654 334443 4558888888888888776
No 181
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=20.10 E-value=1.7e+02 Score=24.36 Aligned_cols=55 Identities=13% Similarity=0.264 Sum_probs=37.9
Q ss_pred ccHHHHHHHHHHCCCceeeceeeeecC-----cceecCHHHH-HHHHHHHHHHhcCCCcccc
Q psy8853 179 SKFIEIKNSLEMTGFKAESSGIVMRPY-----TNIVFKDGEA-IKLQKLLNELKKLHDVKKV 234 (242)
Q Consensus 179 ~~~~~v~~~L~~~g~~v~~sel~~~P~-----~~v~l~~e~~-~~~~~li~~Lee~dDV~~V 234 (242)
-.|+.|-+.+.+.+.+|..-- +-+|. -++.++-..+ ..+.+++++|+..+.|.+|
T Consensus 84 G~LS~vLd~iA~~~~nvLTI~-Q~ipl~g~Anvtlsi~~ssm~~~V~~ii~kl~k~e~V~kV 144 (150)
T COG4492 84 GILSDVLDVIAREEINVLTIH-QTIPLQGRANVTLSIDTSSMEKDVDKIIEKLRKVEGVEKV 144 (150)
T ss_pred hhHHHHHHHHHHhCCcEEEEe-cccccCceeeEEEEEEchhhhhhHHHHHHHHhcccceeEE
Confidence 347888888888888764432 33453 3444444343 5799999999999998876
No 182
>COG1619 LdcA Uncharacterized proteins, homologs of microcin C7 resistance protein MccF [Defense mechanisms]
Probab=20.10 E-value=1.6e+02 Score=27.51 Aligned_cols=63 Identities=21% Similarity=0.307 Sum_probs=44.0
Q ss_pred eEEEEeCc------ccHHHHHHHHHHCCCceeeceeeeecCcceecCHHHHHHHHHHHHHHhcCCCccccee
Q psy8853 171 KITIITSP------SKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYT 236 (242)
Q Consensus 171 ~~~~~c~p------~~~~~v~~~L~~~g~~v~~sel~~~P~~~v~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 236 (242)
++.|+++. ..+.+..+.|+..||+|...+..+.=... ++....+++..|.++.. +|+|.-|+.
T Consensus 12 ~I~iIaPSs~~~~~~~~~~a~~~L~~~G~~v~~~~~i~~~~~~--~a~s~~~R~~dL~~af~-d~~vk~Il~ 80 (313)
T COG1619 12 EIGIIAPSSGATATDALKRAIQRLENLGFEVVFGEHILRRDQY--FAGSDEERAEDLMSAFS-DPDVKAILC 80 (313)
T ss_pred EEEEEecCcccchHHHHHHHHHHHHHcCCEEEechhhhhcccc--ccCCHHHHHHHHHHHhc-CCCCeEEEE
Confidence 56666654 44557778888999999888766554433 33334668888888887 788887765
No 183
>cd07884 RHD-n_Relish N-terminal sub-domain of the Rel homology domain (RHD) of the arthropod protein Relish. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the arthropod Relish protein, in which the RHD domain co-occurs with C-terminal ankyrin repeats. Family members are sometimes referred to as p110 or p68 (proteolytically processed form). Relish is an NF-kappa B-like transcription factor, which plays a role in mediating innate immunity in Drosophila. It is activated via the Imd (immune deficiency) pathway, which triggers phosphorylation of Relish. IKK-dependent proteolytic cleavage of Relish (which involves Dredd) results in a smaller active form (without the C-terminal ankyrin repeats), which is transported into the nucleus and functions as a transactivator.
Probab=20.07 E-value=2.8e+02 Score=23.49 Aligned_cols=74 Identities=19% Similarity=0.304 Sum_probs=42.6
Q ss_pred cceeEEEEEEeccCCeEEEEEEecCCcchhHHHHHHHhhhcC--c--c-----ccCCCccccccceeeEEEECCCCChhH
Q psy8853 81 INYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNG--G--N-----LSKEGSVLFMFKHCGQLLFLPNTKKNT 151 (242)
Q Consensus 81 ~~~~~~~yEg~gPgGv~iive~lTdN~nRt~~~vr~~f~K~g--g--~-----l~~~gsv~~~F~~kG~i~v~~~~~~d~ 151 (242)
..|=++..-+|- |-+.|.|.|.|.+..+-..---.+.-|.+ | . .++.......|...|++.+.+..-.|.
T Consensus 38 KT~Ptv~i~ny~-G~a~I~vslvT~d~p~~~pHpH~LVgK~c~~g~c~~~~~~~~pe~~~~~~F~nLGIqcv~Kk~v~~~ 116 (159)
T cd07884 38 KTFPTVKLCNYR-GQAVIRCSLYQADDNRRKPHVHKLVGKQGDDDVCDPHDIEVSPEGDYVAMFQNMGIIHTAKKNIPEE 116 (159)
T ss_pred CcCCeEEEecCc-CCEEEEEEEEECCCCCCCCCCcccccccccCCCceeeccccCCCCccEEEeCCcceEEEEecchHHH
Confidence 345555444443 23678899999998633333334444442 2 1 112224467899999999987644445
Q ss_pred HHHH
Q psy8853 152 LLDL 155 (242)
Q Consensus 152 ~~e~ 155 (242)
|+.-
T Consensus 117 L~~r 120 (159)
T cd07884 117 LYKK 120 (159)
T ss_pred Hhhh
Confidence 4444
Done!