Query 026508
Match_columns 237
No_of_seqs 181 out of 1130
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:55:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026508.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026508hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02862 2-C-methyl-D-erythrit 100.0 2.1E-77 4.5E-82 524.7 23.4 181 55-237 36-216 (216)
2 PRK00084 ispF 2-C-methyl-D-ery 100.0 1E-76 2.2E-81 500.8 20.3 159 79-237 1-159 (159)
3 PF02542 YgbB: YgbB family; I 100.0 2.9E-77 6.3E-82 503.3 14.3 157 81-237 1-157 (157)
4 COG0245 IspF 2C-methyl-D-eryth 100.0 7.2E-76 1.6E-80 495.3 18.7 157 81-237 1-157 (159)
5 TIGR00151 ispF 2C-methyl-D-ery 100.0 1.7E-75 3.6E-80 491.7 19.7 155 82-236 1-155 (155)
6 cd00554 MECDP_synthase MECDP_s 100.0 1.2E-74 2.6E-79 485.6 19.3 153 82-234 1-153 (153)
7 PRK09382 ispDF bifunctional 2- 100.0 1.1E-69 2.3E-74 504.0 21.1 157 80-236 217-373 (378)
8 cd08517 PBP2_NikA_DppA_OppA_li 78.4 9.5 0.00021 35.4 7.6 92 115-211 261-369 (480)
9 cd04911 ACT_AKiii-YclM-BS_1 AC 72.2 18 0.00039 27.7 6.4 54 154-209 15-74 (76)
10 cd00995 PBP2_NikA_DppA_OppA_li 68.2 23 0.00049 32.4 7.3 103 102-211 242-358 (466)
11 cd08492 PBP2_NikA_DppA_OppA_li 62.5 39 0.00085 31.5 7.9 52 157-212 316-380 (484)
12 cd08502 PBP2_NikA_DppA_OppA_li 62.3 25 0.00054 33.1 6.6 96 115-214 262-370 (472)
13 cd08501 PBP2_Lpqw The substrat 61.8 17 0.00036 34.1 5.3 53 157-213 320-383 (486)
14 PF00496 SBP_bac_5: Bacterial 61.5 13 0.00029 32.9 4.4 109 98-212 201-330 (374)
15 cd05565 PTS_IIB_lactose PTS_II 61.3 9.9 0.00022 30.1 3.2 56 149-207 9-78 (99)
16 PF08821 CGGC: CGGC domain; I 57.4 42 0.0009 27.0 6.2 53 150-203 48-101 (107)
17 TIGR00853 pts-lac PTS system, 55.6 13 0.00027 28.9 2.9 54 150-206 13-80 (95)
18 cd08496 PBP2_NikA_DppA_OppA_li 55.2 31 0.00067 32.1 5.9 107 99-214 234-352 (454)
19 TIGR00254 GGDEF diguanylate cy 55.0 89 0.0019 23.5 8.4 101 96-200 32-150 (165)
20 cd08513 PBP2_thermophilic_Hb8_ 54.6 51 0.0011 30.9 7.2 91 115-211 258-372 (482)
21 COG1831 Predicted metal-depend 54.3 15 0.00033 34.7 3.7 68 131-207 122-190 (285)
22 PF14359 DUF4406: Domain of un 52.9 30 0.00065 26.9 4.6 44 157-203 18-61 (92)
23 PTZ00397 macrophage migration 52.3 21 0.00045 28.0 3.7 90 116-221 16-112 (116)
24 COG5561 Predicted metal-bindin 52.2 66 0.0014 26.2 6.5 54 149-203 37-92 (101)
25 cd08494 PBP2_NikA_DppA_OppA_li 52.2 57 0.0012 30.0 7.0 101 103-212 239-351 (448)
26 KOG0523 Transketolase [Carbohy 51.1 25 0.00053 36.6 4.8 94 127-231 163-257 (632)
27 COG2081 Predicted flavoprotein 49.7 20 0.00043 35.4 3.8 34 132-171 95-128 (408)
28 cd08497 PBP2_NikA_DppA_OppA_li 49.0 40 0.00088 32.0 5.7 52 157-212 320-382 (491)
29 cd08499 PBP2_Ylib_like The sub 48.8 70 0.0015 29.9 7.1 50 157-211 303-353 (474)
30 PF08345 YscJ_FliF_C: Flagella 48.8 58 0.0013 26.9 6.0 56 155-210 87-156 (160)
31 COG1395 Predicted transcriptio 48.8 88 0.0019 30.1 7.8 63 153-216 3-84 (313)
32 PRK15109 antimicrobial peptide 48.5 70 0.0015 31.3 7.3 90 115-211 310-415 (547)
33 cd08519 PBP2_NikA_DppA_OppA_li 48.1 92 0.002 29.3 7.8 47 157-203 309-358 (469)
34 PF01282 Ribosomal_S24e: Ribos 47.1 37 0.0008 26.1 4.2 34 181-214 6-40 (84)
35 cd08512 PBP2_NikA_DppA_OppA_li 45.4 82 0.0018 29.4 7.0 45 157-203 318-364 (476)
36 PF00691 OmpA: OmpA family; I 45.3 28 0.0006 25.5 3.2 72 140-214 1-80 (97)
37 cd08489 PBP2_NikA The substrat 44.7 48 0.0011 31.1 5.4 51 157-211 306-369 (488)
38 cd08520 PBP2_NikA_DppA_OppA_li 43.9 96 0.0021 29.0 7.3 86 115-203 252-359 (468)
39 PRK03094 hypothetical protein; 43.6 28 0.0006 27.2 3.0 27 157-183 10-45 (80)
40 cd08510 PBP2_Lactococcal_OppA_ 43.6 1E+02 0.0022 29.4 7.5 46 157-203 343-402 (516)
41 PF08541 ACP_syn_III_C: 3-Oxoa 43.2 21 0.00045 26.2 2.2 39 164-208 1-39 (90)
42 TIGR02294 nickel_nikA nickel A 42.5 57 0.0012 30.9 5.6 55 157-215 314-381 (500)
43 COG3978 Acetolactate synthase 42.4 1.4E+02 0.0029 23.9 6.7 54 154-214 14-80 (86)
44 COG0747 DdpA ABC-type dipeptid 42.3 1.1E+02 0.0023 28.6 7.3 98 114-216 310-427 (556)
45 cd08509 PBP2_TmCBP_oligosaccha 42.2 76 0.0016 30.3 6.4 47 156-203 323-382 (509)
46 PRK09755 putative ABC transpor 41.9 1.7E+02 0.0036 28.5 8.7 52 157-211 359-412 (535)
47 PF12685 SpoIIIAH: SpoIIIAH-li 41.8 49 0.0011 28.6 4.6 52 159-210 139-196 (196)
48 PTZ00397 macrophage migration 41.7 97 0.0021 24.2 6.0 43 185-227 17-59 (116)
49 cd02413 40S_S3_KH K homology R 39.7 78 0.0017 24.1 4.9 48 162-209 13-72 (81)
50 COG2004 RPS24A Ribosomal prote 38.7 33 0.00072 28.2 3.0 34 178-211 22-56 (107)
51 cd08493 PBP2_DppA_like The sub 38.7 1.6E+02 0.0034 27.7 7.8 100 100-203 255-369 (482)
52 cd01993 Alpha_ANH_like_II This 38.2 1.4E+02 0.0031 24.0 6.6 60 149-210 8-69 (185)
53 PRK08208 coproporphyrinogen II 36.8 1.2E+02 0.0026 29.1 6.9 58 153-214 175-232 (430)
54 PF07109 Mg-por_mtran_C: Magne 36.7 16 0.00035 29.4 0.9 35 137-175 45-81 (97)
55 cd08490 PBP2_NikA_DppA_OppA_li 36.3 87 0.0019 29.1 5.7 52 157-212 294-357 (470)
56 cd08504 PBP2_OppA The substrat 36.3 1.3E+02 0.0029 28.2 6.9 47 157-203 325-374 (498)
57 PF02338 OTU: OTU-like cystein 36.0 24 0.00051 27.0 1.6 19 115-133 2-20 (121)
58 COG3747 Phage terminase, small 35.5 56 0.0012 28.7 4.0 51 155-205 81-133 (160)
59 PF01187 MIF: Macrophage migra 35.3 31 0.00067 27.1 2.2 35 187-221 74-110 (114)
60 PRK06294 coproporphyrinogen II 35.0 1.5E+02 0.0033 27.8 7.1 60 153-216 137-196 (370)
61 PF09581 Spore_III_AF: Stage I 34.8 39 0.00084 28.3 2.9 28 183-210 160-187 (188)
62 PF07302 AroM: AroM protein; 34.3 48 0.001 30.1 3.5 75 117-203 111-204 (221)
63 cd08503 PBP2_NikA_DppA_OppA_li 33.8 1.1E+02 0.0023 28.7 5.9 51 157-213 307-359 (460)
64 PRK08446 coproporphyrinogen II 33.8 1.4E+02 0.003 27.8 6.6 60 152-215 131-190 (350)
65 cd07044 CofD_YvcK Family of Co 33.7 35 0.00075 32.2 2.6 19 109-127 79-97 (309)
66 cd05564 PTS_IIB_chitobiose_lic 32.7 70 0.0015 24.6 3.8 56 149-207 8-77 (96)
67 cd08518 PBP2_NikA_DppA_OppA_li 32.6 1E+02 0.0022 28.9 5.6 52 157-212 299-362 (464)
68 cd08574 GDPD_GDE_2_3_6 Glycero 32.0 1.9E+02 0.0041 25.6 6.9 85 84-176 32-134 (252)
69 PF13710 ACT_5: ACT domain; PD 31.7 76 0.0016 22.7 3.6 30 155-185 4-33 (63)
70 PTZ00450 macrophage migration 31.6 46 0.001 26.8 2.7 37 186-222 75-111 (113)
71 cd08500 PBP2_NikA_DppA_OppA_li 31.0 1.3E+02 0.0028 28.8 6.0 53 157-213 315-381 (499)
72 PRK05660 HemN family oxidoredu 30.4 2.1E+02 0.0047 26.9 7.3 59 153-215 141-199 (378)
73 PLN02414 glycine dehydrogenase 30.2 86 0.0019 34.2 5.1 100 110-215 38-176 (993)
74 PRK10696 tRNA 2-thiocytidine b 29.9 1.5E+02 0.0033 26.2 6.0 54 149-207 38-93 (258)
75 TIGR01588 citE citrate lyase, 29.8 64 0.0014 29.5 3.6 67 97-170 148-216 (288)
76 cd08507 PBP2_SgrR_like The C-t 29.8 99 0.0021 29.0 5.0 54 157-215 283-336 (448)
77 cd08508 PBP2_NikA_DppA_OppA_li 29.7 1.6E+02 0.0035 27.7 6.4 45 157-203 310-355 (470)
78 PF03776 MinE: Septum formatio 29.7 1E+02 0.0022 22.9 4.1 40 176-215 11-57 (70)
79 smart00267 GGDEF diguanylate c 29.6 2.3E+02 0.005 20.8 7.5 99 97-200 34-149 (163)
80 cd08514 PBP2_AppA_like The sub 29.5 1.6E+02 0.0034 27.6 6.2 46 157-203 311-369 (483)
81 PF03698 UPF0180: Uncharacteri 29.0 45 0.00098 25.9 2.1 26 157-182 10-44 (80)
82 PF06135 DUF965: Bacterial pro 29.0 39 0.00085 26.5 1.8 36 149-184 13-49 (79)
83 PRK07379 coproporphyrinogen II 28.6 2.1E+02 0.0045 27.3 6.9 58 154-215 150-207 (400)
84 cd01713 PAPS_reductase This do 28.6 76 0.0016 24.5 3.4 13 150-162 9-21 (173)
85 PRK12378 hypothetical protein; 28.6 4.6E+02 0.0099 23.9 9.2 62 116-184 143-204 (235)
86 PRK04262 hypothetical protein; 28.4 61 0.0013 29.7 3.3 47 156-208 211-257 (347)
87 cd08498 PBP2_NikA_DppA_OppA_li 28.2 2.4E+02 0.0052 26.5 7.2 91 115-212 263-367 (481)
88 TIGR02432 lysidine_TilS_N tRNA 27.4 2.1E+02 0.0045 23.5 6.0 14 113-126 8-21 (189)
89 PF02594 DUF167: Uncharacteris 27.4 61 0.0013 24.6 2.6 33 179-211 32-64 (77)
90 PRK06816 3-oxoacyl-(acyl carri 27.3 1.4E+02 0.0029 28.0 5.4 56 157-221 275-335 (378)
91 cd08515 PBP2_NikA_DppA_OppA_li 27.0 1.8E+02 0.004 27.1 6.2 52 157-212 308-361 (460)
92 PRK11198 LysM domain/BON super 26.9 57 0.0012 27.1 2.6 42 135-179 8-50 (147)
93 CHL00203 fabH 3-oxoacyl-acyl-c 26.7 66 0.0014 29.0 3.1 43 160-208 232-274 (326)
94 PF08645 PNK3P: Polynucleotide 26.6 95 0.0021 25.9 3.8 64 137-203 16-83 (159)
95 COG0635 HemN Coproporphyrinoge 26.3 2.3E+02 0.0049 27.6 6.8 61 152-216 170-230 (416)
96 cd08516 PBP2_NikA_DppA_OppA_li 25.9 1.8E+02 0.0039 26.9 5.9 51 157-212 302-354 (457)
97 PRK15413 glutathione ABC trans 25.7 2.2E+02 0.0048 27.3 6.6 93 115-213 281-384 (512)
98 PRK15104 oligopeptide ABC tran 25.5 2.5E+02 0.0054 27.3 7.0 88 120-211 319-420 (543)
99 PRK00396 rnpA ribonuclease P; 25.0 1.5E+02 0.0033 24.5 4.8 45 154-201 67-111 (130)
100 TIGR03722 arch_KAE1 universal 24.7 1E+02 0.0023 28.4 4.1 52 153-204 46-100 (322)
101 KOG1759 Macrophage migration i 24.5 2.8E+02 0.0061 23.2 6.1 42 188-229 19-60 (115)
102 PF13740 ACT_6: ACT domain; PD 24.4 2.3E+02 0.0049 20.5 5.1 58 150-210 9-76 (76)
103 PRK05473 hypothetical protein; 24.3 46 0.00099 26.5 1.4 36 150-185 17-53 (86)
104 KOG2891 Surface glycoprotein [ 24.2 53 0.0011 31.9 2.1 51 138-198 159-209 (445)
105 cd08505 PBP2_NikA_DppA_OppA_li 23.7 1.5E+02 0.0033 28.8 5.2 94 115-213 304-417 (528)
106 PRK01178 rps24e 30S ribosomal 23.1 1.5E+02 0.0033 23.7 4.2 32 181-212 24-56 (99)
107 TIGR02845 spore_V_AD stage V s 23.0 1.2E+02 0.0026 29.3 4.2 67 133-204 24-98 (327)
108 cd08506 PBP2_clavulanate_OppA2 23.0 1.9E+02 0.0041 27.0 5.5 99 100-203 235-348 (466)
109 cd01994 Alpha_ANH_like_IV This 22.9 1.9E+02 0.004 25.0 5.1 56 149-209 8-66 (194)
110 PRK05367 glycine dehydrogenase 22.8 93 0.002 33.7 3.8 97 109-211 12-145 (954)
111 cd08495 PBP2_NikA_DppA_OppA_li 22.5 2.1E+02 0.0045 26.9 5.7 106 102-214 253-372 (482)
112 PRK09894 diguanylate cyclase; 22.4 5E+02 0.011 22.3 9.8 102 94-200 155-273 (296)
113 TIGR00268 conserved hypothetic 22.1 2E+02 0.0043 25.5 5.2 17 111-127 19-35 (252)
114 COG0594 RnpA RNase P protein c 22.1 1.7E+02 0.0038 23.6 4.4 46 154-202 62-107 (117)
115 COG4631 XdhB Xanthine dehydrog 22.0 84 0.0018 33.0 3.1 33 188-220 490-522 (781)
116 TIGR02873 spore_ylxY probable 22.0 1.5E+02 0.0032 27.1 4.4 45 124-175 220-264 (268)
117 PRK00194 hypothetical protein; 21.3 1.2E+02 0.0027 22.1 3.2 50 150-199 10-68 (90)
118 PF14516 AAA_35: AAA-like doma 21.3 1.7E+02 0.0036 27.1 4.7 65 138-204 31-97 (331)
119 TIGR00188 rnpA ribonuclease P 21.3 2.1E+02 0.0046 22.2 4.7 44 154-200 61-104 (105)
120 cd08029 LA_like_fungal La-moti 21.1 19 0.0004 27.5 -1.3 47 150-203 16-62 (76)
121 cd04890 ACT_AK-like_1 ACT doma 20.8 2.7E+02 0.006 18.6 5.2 42 154-195 14-60 (62)
122 TIGR00538 hemN oxygen-independ 20.3 3.4E+02 0.0075 26.1 6.8 58 152-213 184-241 (455)
123 PF14330 DUF4387: Domain of un 20.2 1.5E+02 0.0032 24.1 3.6 51 157-207 1-55 (99)
124 PRK05628 coproporphyrinogen II 20.2 4.5E+02 0.0097 24.5 7.3 60 150-213 139-198 (375)
125 PRK08304 stage V sporulation p 20.1 1.5E+02 0.0032 28.7 4.2 68 133-204 30-104 (337)
No 1
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=100.00 E-value=2.1e-77 Score=524.73 Aligned_cols=181 Identities=83% Similarity=1.302 Sum_probs=168.9
Q ss_pred ccccccccccccCcccccCCCCCCCceeEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCC
Q 026508 55 SAAATSSIEVKESSASIQPSKSKSLPFRVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGL 134 (237)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~gl 134 (237)
+++++++.+++... ...+....|+||||+|||+|||++|||||||||+||+++||.||||||||+|||+||||||+|+
T Consensus 36 ~~~~~~~~~~~~~~--~~~~~~~~~~~RvG~G~DvH~~~~gr~LiLGGV~Ip~~~Gl~gHSDgDVllHAi~DALLGA~gl 113 (216)
T PLN02862 36 TAAASTTAEVENAL--TPSKAAPTLPFRVGHGFDLHRLEPGLPLIIGGIDIPHDRGCEAHSDGDVLLHCVVDAILGALGL 113 (216)
T ss_pred cccccceeeeeccc--CCcccCccCceeEEEeEEccccCCCCcEEEeeEEeCCCCCcCccCHHHHHHHHHHHHHHHHccC
Confidence 34444455554433 5556667788999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 135 PDIGQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 135 GDIG~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
||||+||||+||+|||+||.+||++++++++++||+|+|+|+|||+|+|||+||+++||+||+++|++++++|||||||+
T Consensus 114 GDIG~~FPdtd~~~Kg~~S~~lL~~a~~ll~~~G~~I~NvD~tII~q~PKi~p~~~~m~~~La~lL~i~~~~VnIKAtT~ 193 (216)
T PLN02862 114 PDIGQIFPDTDPKWKGADSSVFIKEAVRLMHEAGYEIGNLDATLILQRPKLSPHKEAIRSNLSKLLGADPSVVNLKAKTH 193 (216)
T ss_pred CcccccCCCCChhhCCCCHHHHHHHHHHHHHHcCCEEEEEEEEEEcCCCcchHHHHHHHHHHHHHhCCCcceEEEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccccceEEEEEEEeeeC
Q 026508 215 EKVDSLGENRSIAAHTVILLMKK 237 (237)
Q Consensus 215 E~LG~~Gr~egIaa~Avvll~k~ 237 (237)
|+|||+||+|||+|+|+|+|+++
T Consensus 194 E~LG~~Gr~egIaa~Avvll~~~ 216 (216)
T PLN02862 194 EKVDSLGENRSIAAHTVVLLMKK 216 (216)
T ss_pred CCCCCCccCCcEEEEEEEEEEeC
Confidence 99999999999999999999875
No 2
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=100.00 E-value=1e-76 Score=500.80 Aligned_cols=159 Identities=51% Similarity=0.874 Sum_probs=156.8
Q ss_pred CceeEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHH
Q 026508 79 LPFRVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIK 158 (237)
Q Consensus 79 ~~~RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~ 158 (237)
|++|||+|||+|||+++||||||||+||+++|+.|||||||++|||+||||||+|+||||+||||+||+|||+||.+||+
T Consensus 1 m~~RiG~G~D~H~~~~~r~l~LGGV~i~~~~gl~gHSDgDVl~HAi~DAlLGA~glgDIG~~Fp~td~~~kg~~S~~lL~ 80 (159)
T PRK00084 1 MMMRIGQGFDVHRFGEGRPLILGGVEIPYEKGLLGHSDGDVLLHAICDALLGAAALGDIGKHFPDTDPAFKGADSRVLLR 80 (159)
T ss_pred CCceEEEeEEcccccCCCcEEEEeEEeCCCCCCcccCHHHHHHHHHHHHHHHHccCCchhhhCCCCChhhCCCCHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEEEEEEeeeC
Q 026508 159 EAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAHTVILLMKK 237 (237)
Q Consensus 159 ~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~Avvll~k~ 237 (237)
+++++++++||+|+|+|+|||+|+|||+||+++||+|||++|+++.++|||||||+|+|||+||+|||+|+|+|+|.+.
T Consensus 81 ~~~~~~~~~g~~i~niD~tii~e~PKi~p~~~~m~~~la~~L~i~~~~V~iKatT~E~lg~~Gr~egi~~~avv~l~~~ 159 (159)
T PRK00084 81 EVARLLRAKGYRIGNVDITIIAQRPKMAPHIEEMRANIAEDLGIPLDDVNVKATTTEKLGFTGRGEGIAAQAVVLLVKA 159 (159)
T ss_pred HHHHHHHHcCCEEEEEEEEEEcCCCcchHHHHHHHHHHHHHhCCCcceEEEEEecCCCCCCCcCCCceEEEEEEEEEeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999874
No 3
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=100.00 E-value=2.9e-77 Score=503.27 Aligned_cols=157 Identities=55% Similarity=0.972 Sum_probs=150.3
Q ss_pred eeEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHH
Q 026508 81 FRVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEA 160 (237)
Q Consensus 81 ~RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v 160 (237)
||||+|||+|||+++||||||||+||+++||.||||||||+|||+||||||+|+||||+||||+||+|||+||.+||+++
T Consensus 1 ~RiG~G~D~H~~~~~r~L~LgGV~ip~~~gl~gHSDgDVl~HAi~DAlLGA~glgDIG~~Fpd~d~~~k~~~S~~lL~~~ 80 (157)
T PF02542_consen 1 MRIGIGYDVHRFVEGRPLILGGVEIPSEKGLEGHSDGDVLLHAIIDALLGAAGLGDIGTHFPDTDPKYKGADSRILLKEV 80 (157)
T ss_dssp EEEEEEEEEEEEEETSEEEETTEEEEESEEEESSSS--HHHHHHHHHHHHHTTS-THHHHSTTTSGGGTTCSHHHHHHHH
T ss_pred CeeEeEEEeeeecCCCCEEEeeEEcCCCCCCcccChHHHHHHHHHHHHHHhccCCcccccCCCCChhhCCCCHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEEEEEEeeeC
Q 026508 161 VRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAHTVILLMKK 237 (237)
Q Consensus 161 ~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~Avvll~k~ 237 (237)
+++++++||+|+|+|+|||+|+|||+||+++||+|||++|++++++|||||||+|+|||+||+|||+|+|+|||+|+
T Consensus 81 ~~~~~~~g~~i~niD~tii~e~PKi~p~~~~m~~~la~~L~~~~~~V~iKatT~E~lg~~Gr~egi~a~av~ll~~~ 157 (157)
T PF02542_consen 81 VELLREKGYRIVNIDITIIAERPKISPYRPAMRENLAKLLGIPPDRVNIKATTTEGLGFIGRGEGIAAHAVVLLEKK 157 (157)
T ss_dssp HHHHHHTTEEEEEEEEEEESSSSTTGGGHHHHHHHHHHHHTS-GGGEEEEEE-TTTSHHHHTTSEEEEEEEEEEEE-
T ss_pred HHHHHHcCcEEEEEEEEEEcCCCccHHHHHHHHHHHHHHhCCCcceEEEEEecCCCCCcccCCCcEEEEEEEEEEeC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999986
No 4
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=100.00 E-value=7.2e-76 Score=495.31 Aligned_cols=157 Identities=55% Similarity=0.994 Sum_probs=155.4
Q ss_pred eeEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHH
Q 026508 81 FRVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEA 160 (237)
Q Consensus 81 ~RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v 160 (237)
+|||+|||+|+|+++||||||||+||+++|+.|||||||++|||+||||||+++||||+||||+||+|||+||+.||+++
T Consensus 1 ~RiG~G~DvH~~~~g~p~iLgGV~ip~~~Gl~gHSDgDVllHAi~DAllgA~glGDIG~~Fp~~d~~~kgadS~~lL~~~ 80 (159)
T COG0245 1 IRIGLGFDVHRFGEGRPLILGGVEIPHEKGLLGHSDGDVLLHALTDALLGAAGLGDIGKHFPDTDPRWKGADSRILLKEA 80 (159)
T ss_pred CcccccceeeeecCCCcEEEEEEEecCCCCccccChHHHHHHHHHHHHHHhhccCcchhcCCCCCcccCCCchHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEEEEEEeeeC
Q 026508 161 VRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAHTVILLMKK 237 (237)
Q Consensus 161 ~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~Avvll~k~ 237 (237)
+++++++||+|+|+|+|||+|+|||.||+++||+|||++|++++++|||||||+|+|||+||+|||+|+|||||+|.
T Consensus 81 ~~~v~~~g~~i~Nvd~tii~~~PK~~P~~~amr~~ia~~L~i~~~~invKatT~E~LGf~Gr~eGia~~avvlv~~~ 157 (159)
T COG0245 81 VELVREKGYRIGNVDITIIAQRPKLGPYREAMRANIAELLGIPVDRINVKATTTEKLGFTGRGEGIACQAVVLLVKQ 157 (159)
T ss_pred HHHHHHhCcEEEeEEEEEEEecCcccchHHHHHHHHHHHhCCCchheEEEEeccCccccccccCceEEEEEEEEEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999873
No 5
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=100.00 E-value=1.7e-75 Score=491.73 Aligned_cols=155 Identities=57% Similarity=0.989 Sum_probs=153.8
Q ss_pred eEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHHH
Q 026508 82 RVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEAV 161 (237)
Q Consensus 82 RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~ 161 (237)
|||+|||+|||+++||||||||+||+++||.|||||||++|||+||||||+|+||||+||||+||+|||+||..||++++
T Consensus 1 RvG~G~D~H~~~~~r~l~LgGV~ip~~~Gl~gHSDgDVl~HAi~DAlLGA~glgDIG~~Fpdtd~~~k~~~S~~lL~~~~ 80 (155)
T TIGR00151 1 RIGQGFDVHRFGPGRPLILGGVEIPHEKGLLAHSDGDVLLHALTDALLGALGLGDIGKHFPDTDPRWKGADSRVLLRHAV 80 (155)
T ss_pred CcEeeEeccccCCCCcEEEeeEEeCCCCCCcccCHHHHHHHHHHHHHHHHccCCcCcccCCCCChhhCCCCHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEEEEEEeee
Q 026508 162 RLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAHTVILLMK 236 (237)
Q Consensus 162 ~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~Avvll~k 236 (237)
++++++||+|+|+|+|||+|+|||+||+++||+|||++|+++.++|||||||+|+|||+||+|||+|+|+||++|
T Consensus 81 ~~~~~~g~~i~niD~tii~e~PKi~p~~~~m~~~la~~L~~~~~~V~iKatT~E~lg~~Gr~egia~~av~ll~~ 155 (155)
T TIGR00151 81 ALIKEKGYRIGNVDITIIAQRPKLLPHIPAMRENIAELLGIPLDSVNVKATTTEKLGFTGRGEGIACQAVVLLVK 155 (155)
T ss_pred HHHHHcCCEEEEEEEEEEcCCCcchHHHHHHHHHHHHHhCCCcceEEEEEecCCCCCCCcCCCceEEEEEEEEeC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999975
No 6
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=100.00 E-value=1.2e-74 Score=485.57 Aligned_cols=153 Identities=56% Similarity=1.008 Sum_probs=152.0
Q ss_pred eEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHHH
Q 026508 82 RVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEAV 161 (237)
Q Consensus 82 RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~ 161 (237)
|||+|||+|||+++||||||||+||+++||.|||||||++|||+||||||+|+||||+||||+||+|||+||..||++++
T Consensus 1 RvG~G~D~H~~~~~r~l~LgGV~i~~~~gl~gHSDgDVl~HAl~DAlLGA~glgDIG~~Fp~~d~~~k~~~S~~lL~~~~ 80 (153)
T cd00554 1 RIGIGYDVHRFVEGRPLILGGVEIPHEKGLLGHSDGDVLLHALTDALLGAAGLGDIGEHFPDTDPKWKGADSRILLEEAL 80 (153)
T ss_pred CcEeeEeccccCCCCCEEEeeEEeCCCCCCcccCHHHHHHHHHHHHHHHHccCCcccccCCCCChhhCCCCHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEEEEEEe
Q 026508 162 RLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAHTVILL 234 (237)
Q Consensus 162 ~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~Avvll 234 (237)
++++++||+|+|+|+|||+|+|||+||+++||+|||++|+++.++|||||||+|+|||+||+|||+|+|+||+
T Consensus 81 ~~~~~~g~~i~niD~tii~e~PKi~p~~~~m~~~ls~~L~~~~~~V~iKatT~E~lg~~Gr~egia~~av~ll 153 (153)
T cd00554 81 KLIREKGYEIVNIDITIIAERPKISPYREAMRANLAELLGIPPSRVNIKATTTEGLGFTGRGEGIAAQAVVLL 153 (153)
T ss_pred HHHHHcCCEEEEEEEEEEecCCcchHHHHHHHHHHHHHhCCCCceEEEEEecCCCCCCCcCCCceEEEEEEeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999986
No 7
>PRK09382 ispDF bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional
Probab=100.00 E-value=1.1e-69 Score=504.02 Aligned_cols=157 Identities=45% Similarity=0.768 Sum_probs=155.5
Q ss_pred ceeEEeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHH
Q 026508 80 PFRVGHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKE 159 (237)
Q Consensus 80 ~~RIG~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~ 159 (237)
.+|||+|||+|+|++||+||||||+||+++||.|||||||++|||+||||||+|+||||+||||+||+|||+||..||++
T Consensus 217 ~~~~g~g~d~h~~~~~~~~~lggv~i~~~~g~~~hsd~dv~~ha~~da~lga~~~gdig~~fp~~d~~~k~~~s~~~l~~ 296 (378)
T PRK09382 217 DIRTGNGFDVHAFEEGDPVTLCGVKIPHDFGLKGHSDADVALHALTDALLGAIGAGDIGEHFPDSDPQWKGAASKILLEH 296 (378)
T ss_pred ceEEEEeeeeeeecCCCCEEEeeEEecCCCCCcccChHHHHHHHHHHHHHHHccCCcCcccCCCCChhhCCCCHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEEEEEEeee
Q 026508 160 AVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAHTVILLMK 236 (237)
Q Consensus 160 v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~Avvll~k 236 (237)
++++++++||+|+|+|+|||+|+|||+||+++||+|||++|+++.++|||||||+|+|||+||+|||+|+|+|+|.+
T Consensus 297 ~~~~~~~~~~~~~n~d~~i~~~~pk~~~~~~~~~~~~~~~l~~~~~~v~~ka~t~e~lg~~g~~~gi~~~a~~~~~~ 373 (378)
T PRK09382 297 AADFVREAGGEIINADVTIIAEAPKIGPHKQAMRENLAEILGIPKDRVSVKATTTEKLGFVGRGEGIAAIATATVKY 373 (378)
T ss_pred HHHHHHHcCCEEEEEEEEEEecCCcchHHHHHHHHHHHHHhCCCcceEEEEEecCCCCcCCcCCCceEEEEEEEEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999975
No 8
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=78.44 E-value=9.5 Score=35.44 Aligned_cols=92 Identities=27% Similarity=0.360 Sum_probs=53.6
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCCCH---HHHHHHHHHHHHhCCCeEE----EEEEEEE
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGAPS---SVFIKEAVRLMDEAGYEIG----NLDATLI 179 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~dS---~~lL~~v~~ll~~~G~~I~----NiD~TIi 179 (237)
+|-+| |.||| ++.+++..+..-- .++|...+.|.+.+. ..=++++.++|++.||... .+.++|.
T Consensus 261 ~d~~vR~Al~~aidr~~i~~~~~~g~~~~~~-~~~p~~~~~~~~~~~~~~~~d~~~A~~lL~~aG~~~~~~G~~~~l~l~ 339 (480)
T cd08517 261 KDVRVRQAIAHAIDRQFIVDTVFFGYGKPAT-GPISPSLPFFYDDDVPTYPFDVAKAEALLDEAGYPRGADGIRFKLRLD 339 (480)
T ss_pred CCHHHHHHHHHhcCHHHHHHHHHcCcceecc-cccCCCcccccCCCCCCCCCCHHHHHHHHHHcCCCcCCCCceEEEEEE
Confidence 46554 77765 6777764333222 356666555543211 1126899999999999852 3556664
Q ss_pred c--CCCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 180 L--QRPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 180 ~--q~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
. ..+.....-+.+++++.+ +||+ |+|+.
T Consensus 340 ~~~~~~~~~~~a~~i~~~l~~-iGi~---v~i~~ 369 (480)
T cd08517 340 PLPYGEFWKRTAEYVKQALKE-VGID---VELRS 369 (480)
T ss_pred ecCCCchHHHHHHHHHHHHHH-cCCE---EEEEE
Confidence 4 234334555667777766 5775 55554
No 9
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=72.20 E-value=18 Score=27.72 Aligned_cols=54 Identities=15% Similarity=0.366 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHhCCCeEEEE-----EEEEEcCCCCCch-hHHHHHHHHHHHhCCCCCceeE
Q 026508 154 SVFIKEAVRLMDEAGYEIGNL-----DATLILQRPKLSP-YKETIRTNLSELLGADPTVVNL 209 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~Ni-----D~TIi~q~PKl~p-~~~~mr~~La~lL~i~~~~VnI 209 (237)
.-|++++++.+++.|-.+.++ |++|+.+...+.+ ..+++.+.|.+.|+. +.|.|
T Consensus 15 vGF~rk~L~I~E~~~is~Eh~PSGID~~Siii~~~~~~~~~~~~i~~~i~~~~~p--D~i~v 74 (76)
T cd04911 15 VGFGRKLLSILEDNGISYEHMPSGIDDISIIIRDNQLTDEKEQKILAEIKEELHP--DEIEI 74 (76)
T ss_pred hcHHHHHHHHHHHcCCCEeeecCCCccEEEEEEccccchhhHHHHHHHHHHhcCC--CEEEE
Confidence 458999999999999998876 7899999999999 999999999998864 45544
No 10
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=68.19 E-value=23 Score=32.38 Aligned_cols=103 Identities=25% Similarity=0.403 Sum_probs=54.8
Q ss_pred eeeeCCCCCCCCCChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCC-ccCC-CC-HHHHHHHHHHHHHhCCCe
Q 026508 102 GINVPHERGCEAHSDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDP-KWKG-AP-SSVFIKEAVRLMDEAGYE 170 (237)
Q Consensus 102 GV~Ip~~~GL~gHSDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp-~~Kg-~d-S~~lL~~v~~ll~~~G~~ 170 (237)
.+.+....+. -+|-+| |.||| ++.+++..+..- ..++|...+ .+.. .. -..=++++.++|++.||.
T Consensus 242 ~l~~N~~~~~--~~d~~vR~Al~~aidr~~i~~~~~~g~~~~~-~~~~~~~~~~~~~~~~~~~~~d~~kA~~lL~~ag~~ 318 (466)
T cd00995 242 YLGFNTNKPP--FDDKRVRQAISYAIDREEIIDAVLGGYGTPA-TSPLPPGSWGYYDKDLEPYEYDPEKAKELLAEAGYK 318 (466)
T ss_pred EEEeecCCCC--CCCHHHHHHHHHhcCHHHHHHHHHhCCcccc-cCCCCCcccccCCcccCCCCCCHHHHHHHHHHhCCC
Confidence 3444444332 356554 66664 666666444333 224444433 1111 00 011267999999999997
Q ss_pred EE-EEEEEEEc--CCCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 171 IG-NLDATLIL--QRPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 171 I~-NiD~TIi~--q~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
-. .+.++|.. ..|......+.|++.|.+ +||+ |.|+.
T Consensus 319 ~~~~~~l~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~~~~ 358 (466)
T cd00995 319 DGKGLELTLLYNSDGPTRKEIAEAIQAQLKE-IGIK---VEIEP 358 (466)
T ss_pred CCCceEEEEEeCCCCCcHHHHHHHHHHHHHH-cCce---EEEEE
Confidence 42 24555544 333445566777888877 6876 44444
No 11
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=62.54 E-value=39 Score=31.51 Aligned_cols=52 Identities=31% Similarity=0.509 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCCe-E----------EEEEEEEEcC--CCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 157 IKEAVRLMDEAGYE-I----------GNLDATLILQ--RPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 157 L~~v~~ll~~~G~~-I----------~NiD~TIi~q--~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
++++.++|.+.||. . .-+.+++... .|......+.|++.|.+ +||+ |.|+..
T Consensus 316 ~~~A~~lL~~aG~~~~~~~g~~~~~g~~l~l~~~~~~~~~~~~~~a~~i~~~l~~-iGi~---v~i~~~ 380 (484)
T cd08492 316 PEKAKKLLDEAGWTARGADGIRTKDGKRLTLTFLYSTGQPQSQSVLQLIQAQLKE-VGID---LQLKVL 380 (484)
T ss_pred HHHHHHHHHHcCCCcCCCCceecCCCcEEEEEEecCCCCchHHHHHHHHHHHHHh-hCeE---EEEEEe
Confidence 68999999999997 2 1244555433 23344455666777665 6766 444443
No 12
>cd08502 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=62.27 E-value=25 Score=33.07 Aligned_cols=96 Identities=20% Similarity=0.263 Sum_probs=54.0
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCC-CCcccCCCCCCccCCCCH----HHHHHHHHHHHHhCCCeEEEEEEEEEcC
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLP-DIGQIFPDSDPKWKGAPS----SVFIKEAVRLMDEAGYEIGNLDATLILQ 181 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glG-DIG~~FPdtDp~~Kg~dS----~~lL~~v~~ll~~~G~~I~NiD~TIi~q 181 (237)
+|-.| |.||| ++.+++..+.+ -...+||...+-|...+. ..=++++.++|.+.||+-.-+-+.+-.+
T Consensus 262 ~d~~vR~Ai~~aidr~~i~~~~~~g~~~~~~~~~~~p~~~~~~~~~~~~~~~~~d~~kA~~lL~~aG~~g~~l~l~~~~~ 341 (472)
T cd08502 262 DNPKIRRAVLAALDQEDLLAAAVGDPDFYKVCGSMFPCGTPWYSEAGKEGYNKPDLEKAKKLLKEAGYDGEPIVILTPTD 341 (472)
T ss_pred cCHHHHHHHHHhcCHHHHHHHHhCCCcccccCCccCCCCCcccccccccccCcCCHHHHHHHHHHcCCCCceEEEEECCC
Confidence 56644 66765 45554432210 123466665544432221 1226889999999999643333333334
Q ss_pred CCCCchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 182 RPKLSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 182 ~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
.|....--+.++++|++ +||+ |+|+.-+.
T Consensus 342 ~~~~~~~a~~i~~~l~~-iGI~---v~v~~~~~ 370 (472)
T cd08502 342 YAYLYNAALVAAQQLKA-AGFN---VDLQVMDW 370 (472)
T ss_pred CcchhhHHHHHHHHHHh-cCcE---EEEEEech
Confidence 56555667777888877 6776 55655443
No 13
>cd08501 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to
Probab=61.79 E-value=17 Score=34.12 Aligned_cols=53 Identities=26% Similarity=0.443 Sum_probs=35.3
Q ss_pred HHHHHHHHHhCCCeEE---------EEEEEEEcC--CCCCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 157 IKEAVRLMDEAGYEIG---------NLDATLILQ--RPKLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~---------NiD~TIi~q--~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
++++.++|++.||.-. .+.++|... .+.....-+.++++|.+ +||+ |+|+...
T Consensus 320 ~~kAk~lL~~aG~~~~~~g~~~~g~~~~l~l~~~~~~~~~~~~a~~i~~~l~~-iGi~---v~i~~~~ 383 (486)
T cd08501 320 PEAAKKLLDDAGYTLGGDGIEKDGKPLTLRIAYDGDDPTAVAAAELIQDMLAK-AGIK---VTVVSVP 383 (486)
T ss_pred HHHHHHHHHhcceeccCCccccCCcceEEEEEeCCCCHHHHHHHHHHHHHHHh-cCCE---EEecccC
Confidence 7899999999999752 355666553 34444566667777766 5775 5555543
No 14
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=61.46 E-value=13 Score=32.92 Aligned_cols=109 Identities=19% Similarity=0.188 Sum_probs=64.7
Q ss_pred eEEeeeeeCCCCCCCCCChhHH---HHHHH-HHHHHHhcCCCC---CcccCCCCCCccCCCCHH----HHHHHHHHHHHh
Q 026508 98 LIIGGINVPHERGCEAHSDGDV---LLHCV-VDAILGALGLPD---IGQIFPDSDPKWKGAPSS----VFIKEAVRLMDE 166 (237)
Q Consensus 98 LiLGGV~Ip~~~GL~gHSDGDV---LlHAI-~DALLGA~glGD---IG~~FPdtDp~~Kg~dS~----~lL~~v~~ll~~ 166 (237)
.....+.+....+.. +|-+| |.||| -++|.....-|. .-.++|...+.+...... .=++++.++|++
T Consensus 201 ~~~~~l~fN~~~~~~--~d~~vR~Al~~aidr~~i~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~A~~lL~~ 278 (374)
T PF00496_consen 201 PGYYYLAFNTNNPPF--SDKAVRQALAYAIDREAIVKNIFGGYATPANSPVPPSSPGYDDSFDPEYGEYDPEKARELLEK 278 (374)
T ss_dssp EEEEEEEE-TTSTTT--TSHHHHHHHHHHS-HHHHHHHTTTTSCEEESSSSTTTSTTGTTTSSHHHHHHHHHHHHHHHHH
T ss_pred ccceeeecccccccc--chhhhHHHHHhhhhHHHHHHHHHhhccccccccccccccccccccccccccCCHHHHHHhHHh
Confidence 334445555554433 34443 55554 233333332121 122344444555444333 248899999999
Q ss_pred CCCeEEE----------EEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 167 AGYEIGN----------LDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 167 ~G~~I~N----------iD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
.||.-.+ +-+++....|-...-.+.+++++.+ +||. |+|+..
T Consensus 279 ag~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~-~Gi~---v~i~~~ 330 (374)
T PF00496_consen 279 AGYKKSDGGGWRKDPLPLIILYTSDDPIWKAIAEALQEQLKK-IGIK---VEIKPV 330 (374)
T ss_dssp TTHEESTTSEEEETEEEEEEEEETTSHHHHHHHHHHHHHHHH-TTEE---EEEEEE
T ss_pred hhhhcccccccccccccccccccccccchHHHHHHHHHHHhh-ccee---EEEEEe
Confidence 9999886 6666677888777788888888888 8865 666654
No 15
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=61.32 E-value=9.9 Score=30.13 Aligned_cols=56 Identities=16% Similarity=0.373 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCeE--------------EEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCce
Q 026508 149 KGAPSSVFIKEAVRLMDEAGYEI--------------GNLDATLILQRPKLSPYKETIRTNLSELLGADPTVV 207 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~G~~I--------------~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~V 207 (237)
.|++|..+.+++.+.++++|..+ .+.|+ +.=-|.++-+.+++++.. +-.|++...|
T Consensus 9 ~GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~~~~~~Dv--ill~PQv~~~~~~i~~~~-~~~~ipv~~I 78 (99)
T cd05565 9 GGGTSGLLANALNKGAKERGVPLEAAAGAYGSHYDMIPDYDL--VILAPQMASYYDELKKDT-DRLGIKLVTT 78 (99)
T ss_pred CCCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHHhccCCCE--EEEcChHHHHHHHHHHHh-hhcCCCEEEe
Confidence 47999999999999999999854 44554 344577777777776654 3446765444
No 16
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=57.38 E-value=42 Score=27.02 Aligned_cols=53 Identities=19% Similarity=0.448 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCC-CchhHHHHHHHHHHHhCCC
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPK-LSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PK-l~p~~~~mr~~La~lL~i~ 203 (237)
|-+...++.++.+++ +.|.+.+++-.-+....|. -=||+++|++.|.+..|++
T Consensus 48 GCpg~~~~~~~~~l~-~~~~d~IHlssC~~~~~~~~~CP~~~~~~~~I~~~~gi~ 101 (107)
T PF08821_consen 48 GCPGRKLVRRIKKLK-KNGADVIHLSSCMVKGNPHGPCPHIDEIKKIIEEKFGIE 101 (107)
T ss_pred CCChhHHHHHHHHHH-HCCCCEEEEcCCEecCCCCCCCCCHHHHHHHHHHHhCCC
Confidence 345677787777766 7899999999999887754 7799999999999999875
No 17
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=55.63 E-value=13 Score=28.92 Aligned_cols=54 Identities=17% Similarity=0.365 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCeE--------------EEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCc
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEI--------------GNLDATLILQRPKLSPYKETIRTNLSELLGADPTV 206 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I--------------~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~ 206 (237)
|++|..+++++.+.++++|+.+ .+.|+ |.=-|.++.+.+++++. ++-.|++...
T Consensus 13 G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~~~~~~Dv--ill~pqi~~~~~~i~~~-~~~~~ipv~~ 80 (95)
T TIGR00853 13 GMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGEKLDDADV--VLLAPQVAYMLPDLKKE-TDKKGIPVEV 80 (95)
T ss_pred chhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHhhcCCCCE--EEECchHHHHHHHHHHH-hhhcCCCEEE
Confidence 6788889999999999999954 23343 33456677777777665 4555666433
No 18
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=55.16 E-value=31 Score=32.15 Aligned_cols=107 Identities=22% Similarity=0.260 Sum_probs=61.4
Q ss_pred EEeeeeeCCCCCCCCCChhHH---HHHHH-----HHHHHHhcCCCCC-cccCCCCCCccCCCC---HHHHHHHHHHHHHh
Q 026508 99 IIGGINVPHERGCEAHSDGDV---LLHCV-----VDAILGALGLPDI-GQIFPDSDPKWKGAP---SSVFIKEAVRLMDE 166 (237)
Q Consensus 99 iLGGV~Ip~~~GL~gHSDGDV---LlHAI-----~DALLGA~glGDI-G~~FPdtDp~~Kg~d---S~~lL~~v~~ll~~ 166 (237)
-..++.+...... .+|-.| |.||| ++.+++ |.+.. ..++|...+.|...- -..=++++.++|.+
T Consensus 234 ~~~~l~fN~~~~~--~~d~~vRkAl~~aidr~~i~~~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~A~~lL~~ 309 (454)
T cd08496 234 AATLLLLNITGAP--FDDPKVRQAINYAIDRKAFVDALLF--GLGEPASQPFPPGSWAYDPSLENTYPYDPEKAKELLAE 309 (454)
T ss_pred ceEEEEecCCCCC--CCCHHHHHHHHhhcCHHHHHHHHhc--CCCccccCCCCCCCccccccccccCCCCHHHHHHHHHH
Confidence 3455666655543 456554 77775 344443 22222 234555444332110 01126789999999
Q ss_pred CCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 167 AGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 167 ~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
.||+ ..+.++|....|......+.+++++.+ +|++ |+++....
T Consensus 310 aG~~-~g~~l~i~~~~~~~~~~a~~i~~~l~~-iGi~---v~~~~~~~ 352 (454)
T cd08496 310 AGYP-NGFSLTIPTGAQNADTLAEIVQQQLAK-VGIK---VTIKPLTG 352 (454)
T ss_pred cCCC-CCceEEEEecCCchhHHHHHHHHHHHH-cCce---EEEEEech
Confidence 9997 445666655555555667777788766 6876 66666543
No 19
>TIGR00254 GGDEF diguanylate cyclase (GGDEF) domain. The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein.
Probab=55.02 E-value=89 Score=23.53 Aligned_cols=101 Identities=13% Similarity=0.125 Sum_probs=61.4
Q ss_pred CCeEEeeeeeCCCC---CCCCCChhHHHHHHHHHHHHHhcCCC---------CCcccCCCCCCccCCCCHHHHHHHHHHH
Q 026508 96 YPLIIGGINVPHER---GCEAHSDGDVLLHCVVDAILGALGLP---------DIGQIFPDSDPKWKGAPSSVFIKEAVRL 163 (237)
Q Consensus 96 r~LiLGGV~Ip~~~---GL~gHSDGDVLlHAI~DALLGA~glG---------DIG~~FPdtDp~~Kg~dS~~lL~~v~~l 163 (237)
+++.+--|.|+.-. ...|+.-+|-+++.+++.|-..+.-+ +++-++|+.++ .....+.++..+.
T Consensus 32 ~~~~l~~i~i~~~~~i~~~~G~~~~~~ll~~~a~~l~~~~~~~~~i~r~~~~~f~il~~~~~~----~~~~~l~~~i~~~ 107 (165)
T TIGR00254 32 RSFSVLMIDIDNFKKINDTLGHDVGDEVLREVARILQSSVRGSDVVGRYGGEEFVVILPGTPL----EDALSKAERLRDA 107 (165)
T ss_pred CceEEEEEeccchhHHHHhhChhhHHHHHHHHHHHHHHhcCcCCEEEEecCCeEEEEeCCCCh----HHHHHHHHHHHHH
Confidence 44555556665422 35778889999999999987766544 44455555432 2345666777776
Q ss_pred HHhCCCeE-----EEEEEEE-EcCCCCCchhHHHHHHHHHHHh
Q 026508 164 MDEAGYEI-----GNLDATL-ILQRPKLSPYKETIRTNLSELL 200 (237)
Q Consensus 164 l~~~G~~I-----~NiD~TI-i~q~PKl~p~~~~mr~~La~lL 200 (237)
+.+..+.+ .++++.+ ++..|.-....+++.++...+|
T Consensus 108 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~a~~al 150 (165)
T TIGR00254 108 INSKPIEVAGSETLTVTVSIGVACYPGHGLTLEELLKRADEAL 150 (165)
T ss_pred HHhCeeccCCCceEEEEEEEEEEEcCCCCCCHHHHHHHHHHHH
Confidence 66544433 3477666 4555554345666666666655
No 20
>cd08513 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporter
Probab=54.59 E-value=51 Score=30.85 Aligned_cols=91 Identities=25% Similarity=0.344 Sum_probs=50.4
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCCCH---HHHHHHHHHHHHhCCCeEE-----------
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGAPS---SVFIKEAVRLMDEAGYEIG----------- 172 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~dS---~~lL~~v~~ll~~~G~~I~----------- 172 (237)
+|-.| |.||| ++++++..+..- ..++|...+-| ..+. ..=++++.++|++.||...
T Consensus 258 ~d~~vR~Al~~aiDr~~i~~~~~~g~~~~~-~~~~p~~~~~~-~~~~~~~~~d~~kAk~lL~eaG~~~~~~g~~~~~~g~ 335 (482)
T cd08513 258 ADVRVRQALAYAIDRDAIVKTLYGGKATPA-PTPVPPGSWAD-DPLVPAYEYDPEKAKQLLDEAGWKLGPDGGIREKDGT 335 (482)
T ss_pred CCHHHHHHHHhhcCHHHHHHHHhcCcccee-ccCCCCCcccc-CCCcccCCCCHHHHHHHHHHcCCccCCCCcEEcCCCc
Confidence 46554 77775 667766332221 22455443211 1111 1126799999999999731
Q ss_pred EEEEEEEcCC--CCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 173 NLDATLILQR--PKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 173 NiD~TIi~q~--PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
.+.++++... |......+.|++.|++ +||+ |+|+.
T Consensus 336 ~l~l~l~~~~~~~~~~~~a~~i~~~l~~-iGi~---v~~~~ 372 (482)
T cd08513 336 PLSFTLLTTSGNAVRERVAELIQQQLAK-IGID---VEIEN 372 (482)
T ss_pred EEEEEEEeCCCChHHHHHHHHHHHHHHH-cCCE---EEEee
Confidence 2556665432 4444556667777776 6875 55554
No 21
>COG1831 Predicted metal-dependent hydrolase (urease superfamily) [General function prediction only]
Probab=54.28 E-value=15 Score=34.68 Aligned_cols=68 Identities=21% Similarity=0.396 Sum_probs=53.9
Q ss_pred hcCCCCCcc-cCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCce
Q 026508 131 ALGLPDIGQ-IFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVV 207 (237)
Q Consensus 131 A~glGDIG~-~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~V 207 (237)
|.|+|.+|. |||-+...|+- |-.+|++++++.+ ++||-|+.-.++..+---+=...+|+.-|+++.+|
T Consensus 122 avaiGEvGrPHypVs~~v~~~--~n~vl~~a~elA~-------dvdc~vqLHtes~~~~~~~~i~~~ak~~G~~~~~V 190 (285)
T COG1831 122 AVAIGEVGRPHYPVSEEVWEA--SNEVLEYAMELAK-------DVDCAVQLHTESLDEETYEEIAEMAKEAGIKPYRV 190 (285)
T ss_pred eeeeeccCCCCCCCCHHHHHH--HHHHHHHHHHHhh-------cCCCcEEEecCCCChHHHHHHHHHHHHhCCCccee
Confidence 668999995 88888877753 6788999999987 58899999999999833333467788899987776
No 22
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=52.89 E-value=30 Score=26.91 Aligned_cols=44 Identities=25% Similarity=0.350 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
..++.+.|+++||.+.|=-.. ..|.=.+|.+-|+..|+.+..+|
T Consensus 18 f~~~a~~L~~~G~~vvnPa~~---~~~~~~~~~~ym~~~l~~L~~cD 61 (92)
T PF14359_consen 18 FNAAAKRLRAKGYEVVNPAEL---GIPEGLSWEEYMRICLAMLSDCD 61 (92)
T ss_pred HHHHHHHHHHCCCEEeCchhh---CCCCCCCHHHHHHHHHHHHHhCC
Confidence 456788889999999986544 56777789999999999998776
No 23
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=52.32 E-value=21 Score=27.98 Aligned_cols=90 Identities=18% Similarity=0.076 Sum_probs=59.6
Q ss_pred hhHHHHHHHHHHHHHhcCCCCC---cccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCC--chhHH
Q 026508 116 DGDVLLHCVVDAILGALGLPDI---GQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKL--SPYKE 190 (237)
Q Consensus 116 DGDVLlHAI~DALLGA~glGDI---G~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl--~p~~~ 190 (237)
+-+.++-++.++|..++|.+.= -.+-|+.+=-|. ...=...-|.++.+..+.+= ..+..
T Consensus 16 ~~~~~~~~~~~~l~~~lgkPe~~~~v~~~~~~~m~f~----------------g~~~p~a~v~i~~~g~~~~e~k~~l~~ 79 (116)
T PTZ00397 16 QADAALSDIENAIADVLGKPLSYIMSGYDYQKHMRFG----------------GSHDGCCFVRVTSIGGISRSNNSSIAA 79 (116)
T ss_pred cHHHHHHHHHHHHHHHhCCChHHEEEEEeCCceEEEC----------------CCCCceEEEEEEEecCCCHHHHHHHHH
Confidence 3677888888888888887651 111122222222 12225566777777665432 35778
Q ss_pred HHHHHHHHHhCCCCCceeEEeEcCCC--CCCcc
Q 026508 191 TIRTNLSELLGADPTVVNLKAKTHEK--VDSLG 221 (237)
Q Consensus 191 ~mr~~La~lL~i~~~~VnIKAtT~E~--LG~~G 221 (237)
+|-+.|++.||+++++|-|.-...+. .|+-|
T Consensus 80 ~i~~~l~~~lgi~~~rv~I~f~~~~~~~w~~~G 112 (116)
T PTZ00397 80 AITKILASHLKVKSERVYIEFKDCSAQNWAFNG 112 (116)
T ss_pred HHHHHHHHHhCcCcccEEEEEEECChhheeEcc
Confidence 89999999999999999999987776 55544
No 24
>COG5561 Predicted metal-binding protein [Function unknown]
Probab=52.22 E-value=66 Score=26.25 Aligned_cols=54 Identities=24% Similarity=0.426 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhH--HHHHHHHHHHhCCC
Q 026508 149 KGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYK--ETIRTNLSELLGAD 203 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~--~~mr~~La~lL~i~ 203 (237)
.|.+.+.++..+..+....|-+.+++.....+++|| -||+ ++|-+..-+.++|+
T Consensus 37 GgCpGrlvpn~~k~lk~~egaeaihfasCml~~~Pk-Cpy~~~eei~Kk~ie~~~i~ 92 (101)
T COG5561 37 GGCPGRLVPNQIKQLKGKEGAEAIHFASCMLAFKPK-CPYASAEEIAKKEIEKMGIK 92 (101)
T ss_pred CCCCcchhHHHHHHHhhccccceeeeeeeeeccCCC-CCccCHHHHHHHHHHHhCCc
Confidence 466778888888888888899999999999999997 4899 99977777888876
No 25
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=52.16 E-value=57 Score=30.04 Aligned_cols=101 Identities=26% Similarity=0.335 Sum_probs=52.9
Q ss_pred eeeCCCCCCCCCChhHH---HHHHH-----HHHHHHhcCCCCC-cccCCCCCCccCCCCH--HHHHHHHHHHHHhCCCeE
Q 026508 103 INVPHERGCEAHSDGDV---LLHCV-----VDAILGALGLPDI-GQIFPDSDPKWKGAPS--SVFIKEAVRLMDEAGYEI 171 (237)
Q Consensus 103 V~Ip~~~GL~gHSDGDV---LlHAI-----~DALLGA~glGDI-G~~FPdtDp~~Kg~dS--~~lL~~v~~ll~~~G~~I 171 (237)
+.+....+. -+|-+| |.||| ++.+++ |.+.. ..+||...+.|.+... ..=++++.++|++.||+-
T Consensus 239 l~~N~~~~~--~~d~~vR~Al~~aidr~~i~~~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~d~~kA~~lL~~aG~~~ 314 (448)
T cd08494 239 LAMNNARAP--FDDVRVRQAIRYAIDRKALIDAAWD--GYGTPIGGPISPLDPGYVDLTGLYPYDPDKARQLLAEAGAAY 314 (448)
T ss_pred EEecCCCCC--CCCHHHHHHHHHhcCHHHHHHHHhc--CcceecccccCCCccccccccccCCCCHHHHHHHHHHcCCCC
Confidence 334444332 356554 66665 344443 23332 4567777766654321 122789999999999964
Q ss_pred EEEEEEEEcC-CCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 172 GNLDATLILQ-RPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 172 ~NiD~TIi~q-~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
. ..++|... .+-...--+.|++.|.+ +||+ |+++..
T Consensus 315 g-~~l~l~~~~~~~~~~~a~~i~~~l~~-~GI~---v~i~~~ 351 (448)
T cd08494 315 G-LTLTLTLPPLPYARRIGEIIASQLAE-VGIT---VKIEVV 351 (448)
T ss_pred C-eEEEEEecCCcchhHHHHHHHHHHHh-cCcE---EEEEEe
Confidence 1 23444322 22122233456666666 6775 555544
No 26
>KOG0523 consensus Transketolase [Carbohydrate transport and metabolism]
Probab=51.11 E-value=25 Score=36.58 Aligned_cols=94 Identities=19% Similarity=0.215 Sum_probs=68.2
Q ss_pred HHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHHHH-HHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCC
Q 026508 127 AILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEAVR-LMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPT 205 (237)
Q Consensus 127 ALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~~-ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~ 205 (237)
++.|=..++.|-.+|.++.----++.|.-+=+.+.+ ....-||++..||= ...++|++.+.+..-..--
T Consensus 163 s~Ag~l~ldnLVai~D~n~is~~g~t~~~~~~dV~~~r~ea~g~~~~~V~~----------~d~d~i~ka~~~a~~~k~k 232 (632)
T KOG0523|consen 163 SLAGHLKLDNLVAIYDNNKISIDGATSLGFDEDVYQLRFEAFGWNVIIVDG----------GDVDEIRKAIGKAKSVKGK 232 (632)
T ss_pred hhhhhcccCCEEEEEccccccCCCCCcccccccHHHHHHHHhCceEEEEcC----------cCHHHHHHHHhhhhhccCC
Confidence 344567788888899888666667778777778888 77788999887762 2289999999998632211
Q ss_pred ceeEEeEcCCCCCCcccccceEEEEE
Q 026508 206 VVNLKAKTHEKVDSLGENRSIAAHTV 231 (237)
Q Consensus 206 ~VnIKAtT~E~LG~~Gr~egIaa~Av 231 (237)
-=-||+||.|+.|+.+-+ -...|..
T Consensus 233 pt~i~~~t~~g~G~~~ig-~~~~Hg~ 257 (632)
T KOG0523|consen 233 PTAIKATTFIGRGSPYIG-SESVHGA 257 (632)
T ss_pred ceeeeeeeeeecCccccc-cccccCC
Confidence 245899999999998766 4444443
No 27
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=49.73 E-value=20 Score=35.42 Aligned_cols=34 Identities=32% Similarity=0.624 Sum_probs=28.6
Q ss_pred cCCCCCcccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeE
Q 026508 132 LGLPDIGQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEI 171 (237)
Q Consensus 132 ~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I 171 (237)
.-.+|.|++||++|. +..+|+..++.+++.|-+|
T Consensus 95 ~~e~~~Gr~Fp~sdk------A~~Iv~~ll~~~~~~gV~i 128 (408)
T COG2081 95 LKEEDLGRMFPDSDK------ASPIVDALLKELEALGVTI 128 (408)
T ss_pred eEEccCceecCCccc------hHHHHHHHHHHHHHcCcEE
Confidence 346899999999884 8899999999999888664
No 28
>cd08497 PBP2_NikA_DppA_OppA_like_14 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=49.05 E-value=40 Score=32.02 Aligned_cols=52 Identities=27% Similarity=0.500 Sum_probs=35.4
Q ss_pred HHHHHHHHHhCCCeEEE-----------EEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 157 IKEAVRLMDEAGYEIGN-----------LDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~N-----------iD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
++++.++|++.||.-.+ +.+++....+....--+.|+++|.+ +||. |+++..
T Consensus 320 ~~kAk~lL~~aG~~~~~g~~~~~~~G~~l~l~~~~~~~~~~~~a~~i~~~l~~-iGi~---v~i~~~ 382 (491)
T cd08497 320 LRKALELLAEAGWTVRGGDILVNADGEPLSFEILLDSPTFERVLLPYVRNLKK-LGID---ASLRLV 382 (491)
T ss_pred HHHHHHHHHHcCCccCCCCEEECCCCCEEEEEEEeCCCcHHHHHHHHHHHHHh-cCce---EEEeec
Confidence 67899999999997532 5677776666444455667777766 6765 444443
No 29
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=48.83 E-value=70 Score=29.92 Aligned_cols=50 Identities=28% Similarity=0.456 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcC-CCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQ-RPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q-~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
++++.++|++.||. ..+.++|+.. .+....--+.|+++|.+ +||+ |+|+.
T Consensus 303 ~~~A~~lL~eaG~~-~~~~l~l~~~~~~~~~~~a~~i~~~l~~-~GI~---v~i~~ 353 (474)
T cd08499 303 PEKAKELLAEAGYP-DGFETTLWTNDNRERIKIAEFIQQQLAQ-IGID---VEIEV 353 (474)
T ss_pred HHHHHHHHHHcCCC-CCceEEEEecCCCchhHHHHHHHHHHHH-cCce---EEEEe
Confidence 67899999999996 2356666543 23223345667777766 6876 55554
No 30
>PF08345 YscJ_FliF_C: Flagellar M-ring protein C-terminal; InterPro: IPR013556 This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (IPR006182 from INTERPRO).
Probab=48.82 E-value=58 Score=26.94 Aligned_cols=56 Identities=20% Similarity=0.327 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHhCCCeEEEEEEEEEcCC-----------CCCchhHHHHHHHHHHHhCCCCC---ceeEE
Q 026508 155 VFIKEAVRLMDEAGYEIGNLDATLILQR-----------PKLSPYKETIRTNLSELLGADPT---VVNLK 210 (237)
Q Consensus 155 ~lL~~v~~ll~~~G~~I~NiD~TIi~q~-----------PKl~p~~~~mr~~La~lL~i~~~---~VnIK 210 (237)
+-+.+..+..+...++|.++-+.|+... |.-..-+.+|++-++.+.|++.+ +|+|.
T Consensus 87 Yev~~~v~~~~~~~g~I~rlsVaV~vd~~~~~~~~~~~~~~~~~~~~~i~~lV~~A~G~~~~RGD~v~V~ 156 (160)
T PF08345_consen 87 YEVNKTVTQTEKAPGKIKRLSVAVVVDGKYVTAKAANYVPRSPEELAQIRDLVASAIGIDPDRGDQVTVS 156 (160)
T ss_pred ecCCeEEEEEEcCCcEEEEEEEEEEEcCcccccccccccCCCHHHHHHHHHHHHHHhCCCcccCCEEEEE
Confidence 3445666677778999999999998888 77777999999999999999976 44443
No 31
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=48.79 E-value=88 Score=30.05 Aligned_cols=63 Identities=25% Similarity=0.477 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHhCCCeEEEEE-----EEEEcCCC-------------CCch-hHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 153 SSVFIKEAVRLMDEAGYEIGNLD-----ATLILQRP-------------KLSP-YKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 153 S~~lL~~v~~ll~~~G~~I~NiD-----~TIi~q~P-------------Kl~p-~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
...|+.++.+.|+.+||++..++ ..|++.++ +|++ -.++| +.||+.|+.++-.|..|.++
T Consensus 3 re~li~~vi~iL~~~gf~v~~i~~~~~~fDivar~~~~~~iiKVL~NiD~l~~e~a~eL-kkla~~l~aspivVg~r~~~ 81 (313)
T COG1395 3 REELISEVIEILRRNGFEVSDIEYRSRSFDIVARRDLRLLIIKVLYNIDGLSRETAEEL-KKLAKSLLASPIVVGLRTKN 81 (313)
T ss_pred HHHHHHHHHHHHHhCCceEEeecccccceEEEEecccceeeeeeeecccccCHHHHHHH-HHHHHHhCCCceEEEEecCC
Confidence 46799999999999999998875 45666666 4444 34455 46899999999999999987
Q ss_pred CCC
Q 026508 214 HEK 216 (237)
Q Consensus 214 ~E~ 216 (237)
.+-
T Consensus 82 ~~L 84 (313)
T COG1395 82 EPL 84 (313)
T ss_pred Ccc
Confidence 764
No 32
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=48.47 E-value=70 Score=31.29 Aligned_cols=90 Identities=17% Similarity=0.239 Sum_probs=52.0
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCCCH--HHHHHHHHHHHHhCCCeEEEEEEEEEcC---
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGAPS--SVFIKEAVRLMDEAGYEIGNLDATLILQ--- 181 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~dS--~~lL~~v~~ll~~~G~~I~NiD~TIi~q--- 181 (237)
+|-.| |.||| ++++++..+.. .-.++|.+.+.|..... ..=++++.++|.+.||+- ..++|+..
T Consensus 310 ~d~~vRkAl~~AIDr~~i~~~~~~g~~~~-a~~~~p~~~~~~~~~~~~~~yd~~kAk~lL~eAG~~~--~~l~i~~~~~~ 386 (547)
T PRK15109 310 NNPAVRHALALAINNQRLMQSIYYGTAET-AASILPRASWAYDNEAKITEYNPEKSREQLKALGLEN--LTLKLWVPTAS 386 (547)
T ss_pred CCHHHHHHHHHhcCHHHHHHHHhcCcccc-ccccCCCCccccCCccCCCCCCHHHHHHHHHHcCCCC--ceEEEEEecCC
Confidence 46554 77764 56655432211 12356665554432111 122689999999999975 44455432
Q ss_pred ---CCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 182 ---RPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 182 ---~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
.|......+.+++.+.+ +||+ |+|+.
T Consensus 387 ~~~~~~~~~~a~~iq~~l~~-iGI~---v~i~~ 415 (547)
T PRK15109 387 QAWNPSPLKTAELIQADLAQ-VGVK---VVIVP 415 (547)
T ss_pred CCCCCCHHHHHHHHHHHHHH-cCCE---EEEEE
Confidence 35566666778888877 4776 55554
No 33
>cd08519 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=48.11 E-value=92 Score=29.26 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=32.2
Q ss_pred HHHHHHHHHhCCCeEE-EEEEEEEc--CCCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIG-NLDATLIL--QRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~-NiD~TIi~--q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
++++.++|++.||.-+ .+.++|+. ..|....-.+.+++.++++.+++
T Consensus 309 ~~kA~~lL~~aG~~~G~~l~l~~~~~~~~~~~~~~a~~i~~~l~~~G~i~ 358 (469)
T cd08519 309 VEKARQLLQQAGYSAENPLKLELWYRSNHPADKLEAATLKAQLEADGLFK 358 (469)
T ss_pred HHHHHHHHHHhCCCCCCCceEEEEecCCCCchhHHHHHHHHHHHhccceE
Confidence 6899999999999642 34555544 45666666677777777764344
No 34
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=47.11 E-value=37 Score=26.15 Aligned_cols=34 Identities=24% Similarity=0.469 Sum_probs=25.2
Q ss_pred CCCC-CchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 181 QRPK-LSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 181 q~PK-l~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
..|. =.|=+.+|++.||+.|+++++.|-|.-=-+
T Consensus 6 ~h~g~~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t 40 (84)
T PF01282_consen 6 LHPGKPTPSRKEIREKLAAMLNVDPDLIVVFGIKT 40 (84)
T ss_dssp E-SSSSS--HHHHHHHHHHHHTSTGCCEEEEEEEE
T ss_pred ECCCCCCCCHHHHHHHHHHHhCCCCCeEEEeccEe
Confidence 3444 468899999999999999999998875433
No 35
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=45.40 E-value=82 Score=29.44 Aligned_cols=45 Identities=22% Similarity=0.416 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEc--CCCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLIL--QRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~--q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
++++.++|++.||. ....++|.. ..|......+.|++.|.+ +||+
T Consensus 318 ~~~A~~lL~eaG~~-~g~~l~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~ 364 (476)
T cd08512 318 LEKAKELLAEAGYP-NGFKLTLSYNSGNEPREDIAQLLQASLAQ-IGIK 364 (476)
T ss_pred HHHHHHHHHHcCCC-CCcEEEEEeCCCCcchHHHHHHHHHHHHH-hCCe
Confidence 67899999999996 123344432 333444556667777766 5775
No 36
>PF00691 OmpA: OmpA family; InterPro: IPR006665 This entry represents domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins [], such as porin-like integral membrane proteins (such as ompA) [], small lipid-anchored proteins (such as pal) [], and MotB proton channels []. The N-terminal half is variable although some of the proteins in this group have the OmpA-like transmembrane domain IPR000498 from INTERPRO at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules []. MotB (and MotA) serves two functions in E. coli, the MotA(4)-MotB(2) complex attaches to the cell wall via MotB to form the stator of the flagellar motor, and the MotA-MotB complex couples the flow of ions across the cell membrane to movement of the rotor [].; GO: 0009279 cell outer membrane; PDB: 1OAP_A 2W8B_G 2HQS_C 4ERH_A 2ZF8_A 2ZOV_A 2ZVZ_B 2ZVY_A 3TD4_B 3TD5_D ....
Probab=45.31 E-value=28 Score=25.55 Aligned_cols=72 Identities=15% Similarity=0.222 Sum_probs=50.5
Q ss_pred cCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCC-------CCch-hHHHHHHHHHHHhCCCCCceeEEe
Q 026508 140 IFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRP-------KLSP-YKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 140 ~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~P-------Kl~p-~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
+|+.++.+.. .+....|.++.+.|+..++.. .|.+.=.+... +|+- +-.++++.|-+ .|+++++|.+++
T Consensus 1 ~F~~~s~~l~-~~~~~~L~~l~~~l~~~~~~~-~i~I~G~td~~g~~~~n~~LS~~RA~~V~~~L~~-~gi~~~ri~~~~ 77 (97)
T PF00691_consen 1 YFDPNSSELS-PESQEQLDELAKILKYPGNKD-QIEIEGHTDSTGSAEYNQELSQRRAEAVKQYLVE-NGIPPERISVVG 77 (97)
T ss_dssp HBSTTSSSBH-HHHHHHHHHHHHHHHSTTSTT-EEEEEEEEESSSSHHHHHHHHHHHHHHHHHHHHH-TTSSGGGEEEEE
T ss_pred CCCcCcceeC-HHHHHHHHHHHHHHhCcCCCC-eEEEEEEEcCcchhhHHhHHHHHHHHHHHHHHHH-cCCChHhEEEEE
Confidence 4777666663 567888999999999667776 66666655553 3332 44566677777 899999999887
Q ss_pred EcC
Q 026508 212 KTH 214 (237)
Q Consensus 212 tT~ 214 (237)
.-.
T Consensus 78 ~G~ 80 (97)
T PF00691_consen 78 YGE 80 (97)
T ss_dssp ETT
T ss_pred Ecc
Confidence 644
No 37
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=44.72 E-value=48 Score=31.11 Aligned_cols=51 Identities=27% Similarity=0.489 Sum_probs=34.0
Q ss_pred HHHHHHHHHhCCCeEEE-----------EEEEEEcC--CCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 157 IKEAVRLMDEAGYEIGN-----------LDATLILQ--RPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~N-----------iD~TIi~q--~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
++++.++|++.||...| +.++++.. .|....--..+++++++ +||+ |+++.
T Consensus 306 ~~~A~~lL~~aG~~~~~~~g~~~~~g~~~~~~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~~~~ 369 (488)
T cd08489 306 PEKANALLDEAGWTLNEGDGIREKDGKPLSLELVYQTDNALQKSIAEYLQSELKK-IGID---LNIIG 369 (488)
T ss_pred HHHHHHHHHHcCCCcCCCCceEccCCceEEEEEEecCCCchHHHHHHHHHHHHHH-cCcE---EEEee
Confidence 78999999999997542 56777653 34444555666677666 5775 55554
No 38
>cd08520 PBP2_NikA_DppA_OppA_like_21 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=43.89 E-value=96 Score=29.03 Aligned_cols=86 Identities=20% Similarity=0.303 Sum_probs=46.2
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCc--ccCCCCCCccCCCCH--HHHHHHHHHHHHhCCCeEE---------E
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIG--QIFPDSDPKWKGAPS--SVFIKEAVRLMDEAGYEIG---------N 173 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG--~~FPdtDp~~Kg~dS--~~lL~~v~~ll~~~G~~I~---------N 173 (237)
+|-.| |.||| ++.+++ |.|... .+||...+-|..... ..=++++.++|++.||.-. -
T Consensus 252 ~d~~vR~Al~~aiDr~~i~~~~~~--g~~~~a~~~~~~~~~~~~~~~~~~~~~d~~kAk~lL~eaG~~~~~~~~~~~g~~ 329 (468)
T cd08520 252 SDKEFRQAIAYAIDRQELVEKAAR--GAAALGSPGYLPPDSPWYNPNVPKYPYDPEKAKELLKGLGYTDNGGDGEKDGEP 329 (468)
T ss_pred cCHHHHHHHHHhcCHHHHHHHHhc--CCccccccCCCCCccccccccccccCCCHHHHHHHHHHcCCcccCCCCCcCCce
Confidence 45444 66665 666665 344442 367766544421100 1126899999999999531 2
Q ss_pred EEEEEEcC-CCCCchhHHHHHHHHHHHhCCC
Q 026508 174 LDATLILQ-RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 174 iD~TIi~q-~PKl~p~~~~mr~~La~lL~i~ 203 (237)
+.++++.. .+....-.+.+++.|++ +||+
T Consensus 330 l~l~l~~~~~~~~~~~a~~i~~~l~~-iGi~ 359 (468)
T cd08520 330 LSLELLTSSSGDEVRVAELIKEQLER-VGIK 359 (468)
T ss_pred EEEEEEecCCchHHHHHHHHHHHHHH-cCce
Confidence 45555432 23333344556666665 4654
No 39
>PRK03094 hypothetical protein; Provisional
Probab=43.63 E-value=28 Score=27.24 Aligned_cols=27 Identities=15% Similarity=0.420 Sum_probs=20.4
Q ss_pred HHHHHHHHHhCCCeEE---------EEEEEEEcCCC
Q 026508 157 IKEAVRLMDEAGYEIG---------NLDATLILQRP 183 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~---------NiD~TIi~q~P 183 (237)
|..+.+.|+++||+++ ++|+.|+.-+.
T Consensus 10 Ls~i~~~L~~~GYeVv~l~~~~~~~~~Da~VitG~d 45 (80)
T PRK03094 10 LTDVQQALKQKGYEVVQLRSEQDAQGCDCCVVTGQD 45 (80)
T ss_pred cHHHHHHHHHCCCEEEecCcccccCCcCEEEEeCCC
Confidence 5567889999999995 36777776543
No 40
>cd08510 PBP2_Lactococcal_OppA_like The substrate binding component of an ABC-type lactococcal OppA-like transport system contains. This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in sev
Probab=43.62 E-value=1e+02 Score=29.45 Aligned_cols=46 Identities=22% Similarity=0.345 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCCeEEE------------EEEEEEc--CCCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIGN------------LDATLIL--QRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~N------------iD~TIi~--q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
++++.++|++.||...+ +.+++.. ..|....-.+.|++.+.+ +||.
T Consensus 343 ~~~Ak~lL~eaG~~~~~~dg~~~~~~G~~l~i~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~ 402 (516)
T cd08510 343 PEKAKKLLDEAGYKDVDGDGFREDPDGKPLTINFAAMSGSETAEPIAQYYIQQWKK-IGLN 402 (516)
T ss_pred HHHHHHHHHHcCCEEcCCCeeEECCCCcEEEEEEEecCCCccHHHHHHHHHHHHHH-cCce
Confidence 67899999999997533 4455543 344444445556777665 5764
No 41
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=43.20 E-value=21 Score=26.25 Aligned_cols=39 Identities=21% Similarity=0.350 Sum_probs=27.3
Q ss_pred HHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCcee
Q 026508 164 MDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVN 208 (237)
Q Consensus 164 l~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~Vn 208 (237)
|++.|++...||..|.-|-- ..|.+.+++.||++.+++.
T Consensus 1 L~~~g~~~~did~~i~hq~~------~~~~~~~~~~lgi~~~~~~ 39 (90)
T PF08541_consen 1 LERAGLSPDDIDHFIPHQAS------KKILDSIAKRLGIPPERFP 39 (90)
T ss_dssp HHHTT--GGGESEEEE-SSS------HHHHHHHHHHHTS-GGGBE
T ss_pred CccccCCHHHCCEEEeCCCC------HHHHHHHHHHcCCcHHHHH
Confidence 57889999999999987743 3456668899999988764
No 42
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=42.54 E-value=57 Score=30.95 Aligned_cols=55 Identities=24% Similarity=0.474 Sum_probs=36.4
Q ss_pred HHHHHHHHHhCCCeEEE-----------EEEEEEc--CCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCC
Q 026508 157 IKEAVRLMDEAGYEIGN-----------LDATLIL--QRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~N-----------iD~TIi~--q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E 215 (237)
++++.++|.+.||...+ +.++|.. +.|....-.+.+++.+++ +||. |+|+..+..
T Consensus 314 ~~kAk~lL~~aG~~~~~g~~~~~~~G~~l~l~l~~~~~~~~~~~~a~~l~~~l~~-~GI~---v~i~~~~~~ 381 (500)
T TIGR02294 314 VKKANALLDEAGWKLGKGKDVREKDGKPLELELYYDKTSALQKSLAEYLQAEWRK-IGIK---LSLIGEEED 381 (500)
T ss_pred HHHHHHHHHHcCCcccCCCceEcCCCceEEEEEEEcCCChhhHHHHHHHHHHHHH-cCCe---EEEeecChh
Confidence 77899999999997532 4456653 445555566777777777 5765 555554443
No 43
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=42.36 E-value=1.4e+02 Score=23.92 Aligned_cols=54 Identities=15% Similarity=0.318 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHhCCCeEE-------------EEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 154 SVFIKEAVRLMDEAGYEIG-------------NLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~-------------NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
...|+.+++..+.+||.+. ||+.|+=.++| .+-.+..|.++.. ...|.|..-++
T Consensus 14 pe~leRVLrvtrhRGF~vcamnmt~~~da~~~nie~tV~s~R~-----~~lL~~QLeKl~D--v~~V~i~~~~~ 80 (86)
T COG3978 14 PETLERVLRVTRHRGFRVCAMNMTAAVDAGNANIELTVDSDRS-----VDLLTSQLEKLYD--VAHVEITQSET 80 (86)
T ss_pred hHHHHHHHHHhhhcCeEEEEeecccccccccceEEEEEcCCCC-----hHHHHHHHHHHcc--ceeEEEeehhh
Confidence 5789999999999999874 77888888887 6778888888874 44677665443
No 44
>COG0747 DdpA ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]
Probab=42.33 E-value=1.1e+02 Score=28.60 Aligned_cols=98 Identities=24% Similarity=0.266 Sum_probs=56.4
Q ss_pred CChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCC-CCH----HHHHHHHHHHHHhCCCeEE------EE
Q 026508 114 HSDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKG-APS----SVFIKEAVRLMDEAGYEIG------NL 174 (237)
Q Consensus 114 HSDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg-~dS----~~lL~~v~~ll~~~G~~I~------Ni 174 (237)
.+|-+| |.||| +|.+++..+--.-+..||...+-|.. ... ..=++++.++|.+.||.-. ..
T Consensus 310 ~~d~~vRqAl~~aidr~~i~~~~~~G~~~~~~~~~~~~~~~~y~~~~~~~~~~~~d~~~Ak~lL~eaG~~~~~g~~~~~~ 389 (556)
T COG0747 310 LDDVRVRQALAYAIDRDAIVDTVLKGLGAVPADGPVPPLVPGYNPDIEKYAADAYDPEKAKALLDEAGYKDNDGFGGGPL 389 (556)
T ss_pred CCChHHHHHHHHhcCHHHHHHHHhcccccccCCCCCCCcccccccccccccccCCCHHHHHHHHHHcCCCCCCCCcceeE
Confidence 778887 77776 44454443334667888887555554 111 2357889999999999984 34
Q ss_pred EEEEEcCCCCCchhHHHHHHHHHHHhC-CCCCceeEEeEcCCC
Q 026508 175 DATLILQRPKLSPYKETIRTNLSELLG-ADPTVVNLKAKTHEK 216 (237)
Q Consensus 175 D~TIi~q~PKl~p~~~~mr~~La~lL~-i~~~~VnIKAtT~E~ 216 (237)
.+++.. ..- .+...+|-+-|++-|. +- |+|+.++.|.
T Consensus 390 ~~~~~~-~~~-~~~~~~~a~~i~~~l~~iG---I~v~~~~~~~ 427 (556)
T COG0747 390 TLTLES-AGY-NPGARAIAELIQAQLAKIG---IKVELQTLDW 427 (556)
T ss_pred EEeccc-CCC-CcchHHHHHHHHHHHHHcC---CeeEEEEeeH
Confidence 444443 111 3444455555554442 11 4455555444
No 45
>cd08509 PBP2_TmCBP_oligosaccharides_like The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. L
Probab=42.22 E-value=76 Score=30.29 Aligned_cols=47 Identities=26% Similarity=0.369 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhCCCeE-----------EEEEEEEEcC--CCCCchhHHHHHHHHHHHhCCC
Q 026508 156 FIKEAVRLMDEAGYEI-----------GNLDATLILQ--RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 156 lL~~v~~ll~~~G~~I-----------~NiD~TIi~q--~PKl~p~~~~mr~~La~lL~i~ 203 (237)
=++++.++|.+.||.. .-+.++++.. .+......+.+++.|++ +|++
T Consensus 323 d~~~A~~lL~~aG~~~~~~G~~~~~~g~~l~l~l~~~~~~~~~~~~a~~lq~~l~~-iGi~ 382 (509)
T cd08509 323 DPDKAKKLLESAGFKKDKDGKWYTPDGTPLKFTIIVPSGWTDWMAAAQIIAEQLKE-FGID 382 (509)
T ss_pred CHHHHHHHHHHcCCeECCCCeEECCCCceEEEEEEccCCchHHHHHHHHHHHHHHh-cCeE
Confidence 3789999999999975 2256666543 34444556677777766 6754
No 46
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=41.89 E-value=1.7e+02 Score=28.53 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=31.6
Q ss_pred HHHHHHHHHhCCCeEE-EEEEEEEcC-CCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 157 IKEAVRLMDEAGYEIG-NLDATLILQ-RPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~-NiD~TIi~q-~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
++++.++|.+.||.-+ .+-+++... .+......+.|++.+.+.+||+ |.|+.
T Consensus 359 ~~kAk~LL~eAG~~~g~~~~l~l~~~~~~~~~~~a~~iq~~l~~~iGI~---v~i~~ 412 (535)
T PRK09755 359 VAMAKALLKQAGYDASHPLRFELFYNKYDLHEKTAIALSSEWKKWLGAQ---VTLRT 412 (535)
T ss_pred HHHHHHHHHHcCCcCCCCceEEEEeCCCchHHHHHHHHHHHHHHHhCCe---eEEEe
Confidence 8899999999999632 122344322 2222344566777777756875 55554
No 47
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=41.76 E-value=49 Score=28.60 Aligned_cols=52 Identities=17% Similarity=0.223 Sum_probs=36.3
Q ss_pred HHHHHHHhCCCeE--EEE---EEEEEcCCCCCch-hHHHHHHHHHHHhCCCCCceeEE
Q 026508 159 EAVRLMDEAGYEI--GNL---DATLILQRPKLSP-YKETIRTNLSELLGADPTVVNLK 210 (237)
Q Consensus 159 ~v~~ll~~~G~~I--~Ni---D~TIi~q~PKl~p-~~~~mr~~La~lL~i~~~~VnIK 210 (237)
.+-.+|+.+||.= +.+ -++|+.+.++|.+ -..+|+.-+.+.+|++.++|.|+
T Consensus 139 ~iE~llkakGf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V~ 196 (196)
T PF12685_consen 139 EIENLLKAKGFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISVT 196 (196)
T ss_dssp HHHHHHHTTS-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEEE
T ss_pred HHHHHHHhCCCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEeC
Confidence 3567899999953 322 3667778888997 88999999999999999999986
No 48
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=41.73 E-value=97 Score=24.17 Aligned_cols=43 Identities=9% Similarity=0.117 Sum_probs=38.1
Q ss_pred CchhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceE
Q 026508 185 LSPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIA 227 (237)
Q Consensus 185 l~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIa 227 (237)
......++-+.|++.||.|.+.+-|-....+.|-|-||.+-.+
T Consensus 17 ~~~~~~~~~~~l~~~lgkPe~~~~v~~~~~~~m~f~g~~~p~a 59 (116)
T PTZ00397 17 ADAALSDIENAIADVLGKPLSYIMSGYDYQKHMRFGGSHDGCC 59 (116)
T ss_pred HHHHHHHHHHHHHHHhCCChHHEEEEEeCCceEEECCCCCceE
Confidence 5678888999999999999999999999999999999998543
No 49
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=39.70 E-value=78 Score=24.11 Aligned_cols=48 Identities=15% Similarity=0.172 Sum_probs=38.8
Q ss_pred HHHHhCCCe-------EEEEEEEEEcCCCCC-----chhHHHHHHHHHHHhCCCCCceeE
Q 026508 162 RLMDEAGYE-------IGNLDATLILQRPKL-----SPYKETIRTNLSELLGADPTVVNL 209 (237)
Q Consensus 162 ~ll~~~G~~-------I~NiD~TIi~q~PKl-----~p~~~~mr~~La~lL~i~~~~VnI 209 (237)
+.+...||. ...+-++|-+.+|.+ +.-++++++.|.+.++++..+|.|
T Consensus 13 k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v 72 (81)
T cd02413 13 RELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVEL 72 (81)
T ss_pred HHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEE
Confidence 456667763 234678899999985 378999999999999999999888
No 50
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=38.73 E-value=33 Score=28.17 Aligned_cols=34 Identities=24% Similarity=0.485 Sum_probs=26.5
Q ss_pred EEcCCCC-CchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 178 LILQRPK-LSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 178 Ii~q~PK-l~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
+++-.|- =.|-+.++|+.||+.|+.+.+.|-|=-
T Consensus 22 ~~v~h~g~~TPSr~evrekla~~l~~d~e~VvV~~ 56 (107)
T COG2004 22 FVVYHEGSPTPSRKEVREKLAAMLGADKELVVVDY 56 (107)
T ss_pred EEEEeCCCCCCCHHHHHHHHHHHHCCCcceEEEEe
Confidence 3333443 358999999999999999999998743
No 51
>cd08493 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their li
Probab=38.72 E-value=1.6e+02 Score=27.70 Aligned_cols=100 Identities=20% Similarity=0.258 Sum_probs=51.9
Q ss_pred EeeeeeCCCCCCCCCChhH---HHHHHH-----HHHHHHhcCCCCCcccCCCCCCccCC-CCH-HHHHHHHHHHHHhCCC
Q 026508 100 IGGINVPHERGCEAHSDGD---VLLHCV-----VDAILGALGLPDIGQIFPDSDPKWKG-APS-SVFIKEAVRLMDEAGY 169 (237)
Q Consensus 100 LGGV~Ip~~~GL~gHSDGD---VLlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg-~dS-~~lL~~v~~ll~~~G~ 169 (237)
.+++.+.+..+.. +|-. +|.||| ++++++..+...-+ ++|...+.|.. ... ..=++++.++|++.||
T Consensus 255 ~~~l~~N~~~~~~--~d~~vR~Al~~aidr~~i~~~~~~g~~~~~~~-~~p~~~~~~~~~~~~~~~d~~~A~~lL~~aG~ 331 (482)
T cd08493 255 VGYLAFNTQKPPF--DDPKVRQAIAHAINKEAIVDAVYQGTATVAKN-PLPPTSWGYNDDVPDYEYDPEKAKALLAEAGY 331 (482)
T ss_pred EEEEEEecCCCcc--CCHHHHHHHHHhcCHHHHHHHHhcCceeeccC-ccCCCccccCCCCccCCCCHHHHHHHHHHcCC
Confidence 4566676655543 3433 466654 56666533333322 45544433321 110 1117889999999999
Q ss_pred eE-EEEEEEEEcC----CCCCchhHHHHHHHHHHHhCCC
Q 026508 170 EI-GNLDATLILQ----RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 170 ~I-~NiD~TIi~q----~PKl~p~~~~mr~~La~lL~i~ 203 (237)
.- .-+.+.+..+ .|......+.|++.+.+ +||.
T Consensus 332 ~~g~~l~i~~~~~~~~~~~~~~~~a~~i~~~l~~-~Gi~ 369 (482)
T cd08493 332 PDGFELTLWYPPVSRPYNPNPKKMAELIQADLAK-VGIK 369 (482)
T ss_pred CCCceEEEEEeCCcccCCCcHHHHHHHHHHHHHH-hCCE
Confidence 63 1333333332 24444455556666655 6775
No 52
>cd01993 Alpha_ANH_like_II This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=38.15 E-value=1.4e+02 Score=23.96 Aligned_cols=60 Identities=23% Similarity=0.292 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHHhC--CCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEE
Q 026508 149 KGAPSSVFIKEAVRLMDEA--GYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLK 210 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~--G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIK 210 (237)
.|.||..+|.-+.+..+.. ++++.- +++--......+.-.+..+.+++.+|++...+++.
T Consensus 8 GG~DS~~ll~~l~~~~~~~~~~~~~~~--~~~d~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~ 69 (185)
T cd01993 8 GGKDSLVLLHVLKKLQRRYPYGFELEA--LTVDEGIPGYRDESLEVVERLAEELGIELEIVSFK 69 (185)
T ss_pred CCHHHHHHHHHHHHHHhhcCCCeEEEE--EEEECCCCCCcHHHHHHHHHHHHHcCCceEEEehh
Confidence 5889999998777766544 444321 22221222233344456678899999987766664
No 53
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=36.79 E-value=1.2e+02 Score=29.09 Aligned_cols=58 Identities=21% Similarity=0.222 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 153 SSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 153 S~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
+..-..++++.+++.|+...|+|+ |.--|. .-.+.+++.+..++.+.++.|++-.-+-
T Consensus 175 ~~~~~~~ai~~l~~~g~~~i~~dl--I~GlP~--qt~e~~~~~l~~~~~l~~~~is~y~L~~ 232 (430)
T PRK08208 175 KRADVHQALEWIRAAGFPILNIDL--IYGIPG--QTHASWMESLDQALVYRPEELFLYPLYV 232 (430)
T ss_pred CHHHHHHHHHHHHHcCCCeEEEEe--ecCCCC--CCHHHHHHHHHHHHhCCCCEEEEccccc
Confidence 344556889999999998888884 556664 3457888888888888888888876443
No 54
>PF07109 Mg-por_mtran_C: Magnesium-protoporphyrin IX methyltransferase C-terminus; InterPro: IPR010940 This entry represents the C terminus (approximately 100 residues) of bacterial and eukaryotic Magnesium-protoporphyrin IX methyltransferase (2.1.1.11 from EC). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX metylester using S-adenosyl-L-methionine as a cofactor [].; GO: 0046406 magnesium protoporphyrin IX methyltransferase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process
Probab=36.71 E-value=16 Score=29.37 Aligned_cols=35 Identities=31% Similarity=0.615 Sum_probs=23.2
Q ss_pred CcccCCCCCCccCCCCHHHHH--HHHHHHHHhCCCeEEEEE
Q 026508 137 IGQIFPDSDPKWKGAPSSVFI--KEAVRLMDEAGYEIGNLD 175 (237)
Q Consensus 137 IG~~FPdtDp~~Kg~dS~~lL--~~v~~ll~~~G~~I~NiD 175 (237)
||++||-.|-. ...+.. +.+.+.+.+.||++.+..
T Consensus 45 iG~lFP~~dRs----p~i~~~~e~~l~~~l~~~g~~~~r~~ 81 (97)
T PF07109_consen 45 IGKLFPRPDRS----PRIYPHREEDLRRALAAAGWRIGRTE 81 (97)
T ss_pred HhccCCCCCCC----CcEEEeCHHHHHHHHHhCCCeeeecc
Confidence 79999987742 222222 246677777999998754
No 55
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=36.34 E-value=87 Score=29.05 Aligned_cols=52 Identities=37% Similarity=0.653 Sum_probs=35.7
Q ss_pred HHHHHHHHHhCCCeEE----------EEEEEEEc--CCCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 157 IKEAVRLMDEAGYEIG----------NLDATLIL--QRPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~----------NiD~TIi~--q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
++++.++|++.||.-. -+.++|+. ..|.....-+.+++.|.+ +||. |+++..
T Consensus 294 ~~~A~~lL~~aG~~~~~~~~~~~~G~~~~l~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~~~~~ 357 (470)
T cd08490 294 PEKAKELLAEAGWTDGDGDGIEKDGEPLELTLLTYTSRPELPPIAEAIQAQLKK-IGID---VEIRVV 357 (470)
T ss_pred HHHHHHHHHHcCCCCCCCcccccCCceEEEEEEecCCCCchHHHHHHHHHHHHH-cCce---EEEEEe
Confidence 7789999999999763 24566654 335555666777888776 6876 555543
No 56
>cd08504 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which
Probab=36.33 E-value=1.3e+02 Score=28.17 Aligned_cols=47 Identities=32% Similarity=0.486 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCCeEE--EEEEEEEcC-CCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIG--NLDATLILQ-RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~--NiD~TIi~q-~PKl~p~~~~mr~~La~lL~i~ 203 (237)
++++.++|.+.||.-. -+.++|+.. .|......+.+++.|++.+||+
T Consensus 325 ~~kA~~lL~~aG~~~~~~~~~l~i~~~~~~~~~~~a~~i~~~l~~~iGI~ 374 (498)
T cd08504 325 PEKAKKLLAEAGYELGKNPLKLTLLYNTSENHKKIAEAIQQMWKKNLGVK 374 (498)
T ss_pred HHHHHHHHHHcCcccCCCCceEEEEecCchhHHHHHHHHHHHHHHcCCCe
Confidence 7899999999999643 145555433 2444445555666665556665
No 57
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=36.04 E-value=24 Score=26.97 Aligned_cols=19 Identities=37% Similarity=0.688 Sum_probs=15.3
Q ss_pred ChhHHHHHHHHHHHHHhcC
Q 026508 115 SDGDVLLHCVVDAILGALG 133 (237)
Q Consensus 115 SDGDVLlHAI~DALLGA~g 133 (237)
.||+.++|||++++.+-..
T Consensus 2 gDGnClF~Avs~~l~~~~~ 20 (121)
T PF02338_consen 2 GDGNCLFRAVSDQLYGDGG 20 (121)
T ss_dssp SSTTHHHHHHHHHHCTT-S
T ss_pred CCccHHHHHHHHHHHHhcC
Confidence 4999999999999875433
No 58
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=35.52 E-value=56 Score=28.65 Aligned_cols=51 Identities=24% Similarity=0.405 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHH--HHHHHhCCCCC
Q 026508 155 VFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRT--NLSELLGADPT 205 (237)
Q Consensus 155 ~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~--~La~lL~i~~~ 205 (237)
.+.+.+++.++++|+-|.|-=--.+--.|-++-|.++++. .|+..||+++.
T Consensus 81 siY~~av~~lkk~G~ii~~~~~g~~krNPav~~~sdA~~~l~klaSeLGltP~ 133 (160)
T COG3747 81 SIYRNAVAHLKKHGFIITNQFSGRVKRNPAVQAASDAIRNLLKLASELGLTPS 133 (160)
T ss_pred HHHHHHHHHHHHcceeeeccccceecCChHHHHHHHHHHHHHHHHHHhCCChH
Confidence 3567788999999999998766667788888888888875 57888998764
No 59
>PF01187 MIF: Macrophage migration inhibitory factor (MIF); InterPro: IPR001398 Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response []. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis []. The MIF homologue D-dopachrome tautomerase (4.1.1.84 from EC) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [, ].; PDB: 1UIZ_C 3FWT_A 1HFO_F 2WKB_D 3RF4_B 2OS5_A 3RF5_A 2XCZ_A 3FWU_A 3B64_A ....
Probab=35.30 E-value=31 Score=27.11 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=25.2
Q ss_pred hhHHHHHHHHHHHhCCCCCceeEEeE--cCCCCCCcc
Q 026508 187 PYKETIRTNLSELLGADPTVVNLKAK--THEKVDSLG 221 (237)
Q Consensus 187 p~~~~mr~~La~lL~i~~~~VnIKAt--T~E~LG~~G 221 (237)
.|-.++.+-|.+.||++++||-|+-. ..+.+|+-|
T Consensus 74 ~~s~~i~~~l~~~LgIp~~Riyi~f~d~~~~~~g~nG 110 (114)
T PF01187_consen 74 KYSAAITEFLEEELGIPPDRIYINFHDLPAWNVGWNG 110 (114)
T ss_dssp HHHHHHHHHHHHHHT--GGGEEEEEEEETGGGEEETT
T ss_pred HHHHHHHHHHHHHhCCCcCceEEEEEECCHHHeeeCc
Confidence 47788899999999999999999987 334445444
No 60
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=34.98 E-value=1.5e+02 Score=27.82 Aligned_cols=60 Identities=23% Similarity=0.208 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCC
Q 026508 153 SSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEK 216 (237)
Q Consensus 153 S~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~ 216 (237)
+..-..++++.+++.|+..+|+| +|.--|- .=.+.+++.|..++.+.++.|++=.-|-|.
T Consensus 137 ~~~~~~~ai~~~~~~g~~~v~~D--li~GlPg--qt~~~~~~~l~~~~~l~~~~is~y~l~~~~ 196 (370)
T PRK06294 137 SSSKAIDAVQECSEHGFSNLSID--LIYGLPT--QSLSDFIVDLHQAITLPITHISLYNLTIDP 196 (370)
T ss_pred CHHHHHHHHHHHHHcCCCeEEEE--eecCCCC--CCHHHHHHHHHHHHccCCCeEEEeeeEecC
Confidence 34445578889999999988888 5666663 356788899999999999999987766554
No 61
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=34.84 E-value=39 Score=28.31 Aligned_cols=28 Identities=25% Similarity=0.471 Sum_probs=23.4
Q ss_pred CCCchhHHHHHHHHHHHhCCCCCceeEE
Q 026508 183 PKLSPYKETIRTNLSELLGADPTVVNLK 210 (237)
Q Consensus 183 PKl~p~~~~mr~~La~lL~i~~~~VnIK 210 (237)
+.-..-..+|++.||+.+|+++++|.|-
T Consensus 160 ~~~~~~~~~i~~~la~~~~i~~~~I~V~ 187 (188)
T PF09581_consen 160 PEDSEEEEEIKQYLADFYGISPEQIKVY 187 (188)
T ss_pred ccchHHHHHHHHHHHHHhCCCHHHeEEe
Confidence 3345678899999999999999999873
No 62
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=34.35 E-value=48 Score=30.10 Aligned_cols=75 Identities=27% Similarity=0.436 Sum_probs=60.9
Q ss_pred hHHHHHHHHHHHHHhcCCCCCcccCCCCC------CccCCC-------------CHHHHHHHHHHHHHhCCCeEEEEEEE
Q 026508 117 GDVLLHCVVDAILGALGLPDIGQIFPDSD------PKWKGA-------------PSSVFIKEAVRLMDEAGYEIGNLDAT 177 (237)
Q Consensus 117 GDVLlHAI~DALLGA~glGDIG~~FPdtD------p~~Kg~-------------dS~~lL~~v~~ll~~~G~~I~NiD~T 177 (237)
-|-+++.++.|+.+. +-+|-+.|..+ .+|+.. .+..=|.++.+.|+++|-++.=+||.
T Consensus 111 P~ril~~lV~al~~~---~~vGVivP~~eQ~~~~~~kW~~l~~~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCm 187 (221)
T PF07302_consen 111 PDRILPPLVAALVGG---HQVGVIVPLPEQIAQQAEKWQPLGNPVVVAAASPYEGDEEELAAAARELAEQGADLIVLDCM 187 (221)
T ss_pred hHHhHHHHHHHhcCC---CeEEEEecCHHHHHHHHHHHHhcCCCeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECC
Confidence 577899999998775 66787787732 466665 45677888999999999999999984
Q ss_pred EEcCCCCCchhHHHHHHHHHHHhCCC
Q 026508 178 LILQRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 178 Ii~q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
-|-.+||+.+++.+|.+
T Consensus 188 ---------GYt~~~r~~~~~~~g~P 204 (221)
T PF07302_consen 188 ---------GYTQEMRDIVQRALGKP 204 (221)
T ss_pred ---------CCCHHHHHHHHHHhCCC
Confidence 58899999999999987
No 63
>cd08503 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=33.85 E-value=1.1e+02 Score=28.68 Aligned_cols=51 Identities=20% Similarity=0.237 Sum_probs=34.9
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcCCC--CCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQRP--KLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q~P--Kl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
++++.++|++.||.- +.++|+.... -.....+.+++.|++ +||. |.++..+
T Consensus 307 ~~~A~~lL~eaG~~~--~~l~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~i~~~~ 359 (460)
T cd08503 307 PDKAKALLAEAGLPD--LEVELVTSDAAPGAVDAAVLFAEQAAQ-AGIN---INVKRVP 359 (460)
T ss_pred HHHHHHHHHHcCCCC--ceEEEEecCCCccHHHHHHHHHHHHHh-hCCE---EEEEEeC
Confidence 678999999999974 5666665333 244456677777777 6876 6666543
No 64
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=33.75 E-value=1.4e+02 Score=27.80 Aligned_cols=60 Identities=22% Similarity=0.183 Sum_probs=43.2
Q ss_pred CHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCC
Q 026508 152 PSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 152 dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E 215 (237)
.+..-..++++.+++.|+.-+|+|. |.--|. .=.+.+++.|..++.+.++.|++=.=|-|
T Consensus 131 ~~~~~~~~ai~~lr~~g~~~v~iDl--i~GlPg--qt~~~~~~~l~~~~~l~~~~is~y~L~~~ 190 (350)
T PRK08446 131 HSQKQIIKAIENAKKAGFENISIDL--IYDTPL--DNKKLLKEELKLAKELPINHLSAYSLTIE 190 (350)
T ss_pred CCHHHHHHHHHHHHHcCCCEEEEEe--ecCCCC--CCHHHHHHHHHHHHhcCCCEEEeccceec
Confidence 3455566789999999998777776 444454 23678888888888888999887554443
No 65
>cd07044 CofD_YvcK Family of CofD-like proteins and proteins related to YvcK. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but ha
Probab=33.71 E-value=35 Score=32.19 Aligned_cols=19 Identities=16% Similarity=0.155 Sum_probs=15.8
Q ss_pred CCCCCCChhHHHHHHHHHH
Q 026508 109 RGCEAHSDGDVLLHCVVDA 127 (237)
Q Consensus 109 ~GL~gHSDGDVLlHAI~DA 127 (237)
..+.||||||.++|++..-
T Consensus 79 ~~l~gh~~GNL~l~~l~~~ 97 (309)
T cd07044 79 NEGLGHSLGNLAIAGXTSI 97 (309)
T ss_pred CCccCCcHHHHHHHHHHHh
Confidence 4599999999999996543
No 66
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=32.70 E-value=70 Score=24.56 Aligned_cols=56 Identities=18% Similarity=0.431 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCeE--------------EEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCce
Q 026508 149 KGAPSSVFIKEAVRLMDEAGYEI--------------GNLDATLILQRPKLSPYKETIRTNLSELLGADPTVV 207 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~G~~I--------------~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~V 207 (237)
-|++|..+++++-+.++++|+.+ .+.| +|.=.|-++.+.+++++...+ .+++...|
T Consensus 8 ~G~sTS~~~~ki~~~~~~~~~~~~v~~~~~~~~~~~~~~~D--iil~~Pqv~~~~~~i~~~~~~-~~~pv~~I 77 (96)
T cd05564 8 AGMSTSILVKKMKKAAEKRGIDAEIEAVPESELEEYIDDAD--VVLLGPQVRYMLDEVKKKAAE-YGIPVAVI 77 (96)
T ss_pred CCchHHHHHHHHHHHHHHCCCceEEEEecHHHHHHhcCCCC--EEEEChhHHHHHHHHHHHhcc-CCCcEEEc
Confidence 36788889999999999999842 2334 334456677777777665433 45554433
No 67
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=32.58 E-value=1e+02 Score=28.88 Aligned_cols=52 Identities=23% Similarity=0.391 Sum_probs=33.8
Q ss_pred HHHHHHHHHhCCCeEE----------EEEEEEEc--CCCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 157 IKEAVRLMDEAGYEIG----------NLDATLIL--QRPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~----------NiD~TIi~--q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
++++.++|.+.||.-. .+.++|+. ..|.....-+.|++.|++ +||+ |.|+..
T Consensus 299 ~~~Ak~lL~eaG~~~~~~g~~~~~g~~l~l~l~~~~~~~~~~~~a~~i~~~l~~-iGi~---v~i~~~ 362 (464)
T cd08518 299 PEKAKKILEEAGWKDGDDGGREKDGQKAEFTLYYPSGDQVRQDLAVAVASQAKK-LGIE---VKLEGK 362 (464)
T ss_pred HHHHHHHHHHcCCCcCCCCeeccCCcEEEEEEEeCCCCHHHHHHHHHHHHHHHH-hCCe---EEEEEe
Confidence 6899999999999743 25566654 333334455667777766 6876 555543
No 68
>cd08574 GDPD_GDE_2_3_6 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2, GDE3, GDE6-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase domain-containing protein subtype 5 (GDE2), subtype 2 (GDE3), subtype 1 (GDE6), and their eukaryotic homologs. Mammalian GDE2, GDE3, and GDE6 show very high sequence similarity to each other and have been classified into the same family. Although they are all transmembrane proteins, based on different pattern of tissue distribution, these enzymes might display diverse cellular functions. Mammalian GDE2 is primarily expressed in mature neurons. It selectively hydrolyzes glycerophosphocholine (GPC) and mainly functions in a complex with an antioxidant scavenger peroxiredoxin1 (Prdx1) to control motor neuron differentiation in the spinal cord. Mammalian GDE3 is specifically expressed in bo
Probab=31.97 E-value=1.9e+02 Score=25.60 Aligned_cols=85 Identities=20% Similarity=0.184 Sum_probs=50.0
Q ss_pred EeeeeeeecCCCCCeEEeeeeeCCCCCCCCCChhHHHH-----HHHHHHHHHhcCCCCCcccCCCCCCc-----------
Q 026508 84 GHGFDLHRLEPGYPLIIGGINVPHERGCEAHSDGDVLL-----HCVVDAILGALGLPDIGQIFPDSDPK----------- 147 (237)
Q Consensus 84 G~G~DvHr~~~gr~LiLGGV~Ip~~~GL~gHSDGDVLl-----HAI~DALLGA~glGDIG~~FPdtDp~----------- 147 (237)
|+=+|||.-..|.++++ |+.-|.-=+++.-.+ ..|.|-=+.-+..=|.|.||.+++|.
T Consensus 32 ~iE~DV~lTkDg~lVV~------HD~~l~Rtt~~~g~~~~~~~~~v~~~T~~eL~~ld~g~~f~~~~~~~~~~~~~~~~~ 105 (252)
T cd08574 32 GLETDVTISYDGVPFLM------HDRTLRRTTNVADVFPERAHERASMFTWTDLQQLNAGQWFLKDDPFWTASSLSESDR 105 (252)
T ss_pred EEEEEEeEccCCcEEEe------CCCcccccCCCCcccccccccchhcCCHHHHhhCCCCCcccCCCccchhcccccchh
Confidence 67789999888887766 444443333333210 01223333333444788999776663
Q ss_pred --cCCCCHHHHHHHHHHHHHhCCCeEEEEEE
Q 026508 148 --WKGAPSSVFIKEAVRLMDEAGYEIGNLDA 176 (237)
Q Consensus 148 --~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~ 176 (237)
|++. ..-.|+++++++++.+. -.||++
T Consensus 106 ~~~~~~-~IPtL~evl~~~~~~~~-~l~iEi 134 (252)
T cd08574 106 EEAGNQ-SIPSLAELLRLAKKHNK-SVIFDL 134 (252)
T ss_pred hhcCCC-CCCCHHHHHHHHHHcCC-eEEEEe
Confidence 3332 23468899999987554 356665
No 69
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=31.72 E-value=76 Score=22.75 Aligned_cols=30 Identities=13% Similarity=0.326 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhCCCeEEEEEEEEEcCCCCC
Q 026508 155 VFIKEAVRLMDEAGYEIGNLDATLILQRPKL 185 (237)
Q Consensus 155 ~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl 185 (237)
-.|.++..+++.+||.|..+.+.- .+.|.+
T Consensus 4 GvL~Ri~~vf~rRg~nI~sl~v~~-~~~~~~ 33 (63)
T PF13710_consen 4 GVLNRITGVFRRRGFNIESLSVGP-TEDPGI 33 (63)
T ss_dssp THHHHHHHHHHTTT-EECEEEEEE--SSTTE
T ss_pred HHHHHHHHHHhcCCeEEeeEEeee-cCCCCE
Confidence 368899999999999999998887 566655
No 70
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=31.58 E-value=46 Score=26.80 Aligned_cols=37 Identities=8% Similarity=0.045 Sum_probs=0.0
Q ss_pred chhHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCccc
Q 026508 186 SPYKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGE 222 (237)
Q Consensus 186 ~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr 222 (237)
..|-.++-+-|.+-|||+++||-|+-.-....|+-|+
T Consensus 75 ~~~s~~i~~~l~~~LgIp~dRiYI~f~d~~~~G~nG~ 111 (113)
T PTZ00450 75 KMMTPRITAAITKECGIPAERIYVFYYSTKHCGWNGT 111 (113)
T ss_pred HHHHHHHHHHHHHHcCCCcccEEEEEEcHHHcccCcE
No 71
>cd08500 PBP2_NikA_DppA_OppA_like_4 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=31.02 E-value=1.3e+02 Score=28.80 Aligned_cols=53 Identities=28% Similarity=0.378 Sum_probs=36.7
Q ss_pred HHHHHHHHHhCCCeE------------EEEEEEEEc--CCCCCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 157 IKEAVRLMDEAGYEI------------GNLDATLIL--QRPKLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 157 L~~v~~ll~~~G~~I------------~NiD~TIi~--q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
++++.++|.+.||.. .-+.++|+. ..|......+.|+++|.+ +||. |+++...
T Consensus 315 ~e~Ak~lL~~aG~~~~~~dG~~~~~~G~~l~l~i~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~~~~~~ 381 (499)
T cd08500 315 PDKANKLLDEAGLKKKDADGFRLDPDGKPVEFTLITNAGNSIREDIAELIKDDWRK-IGIK---VNLQPID 381 (499)
T ss_pred HHHHHHHHHHcCCcccCCCCcEECCCCcEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCc---eEEEecc
Confidence 689999999999972 123555544 345666777888888877 6876 5555443
No 72
>PRK05660 HemN family oxidoreductase; Provisional
Probab=30.42 E-value=2.1e+02 Score=26.93 Aligned_cols=59 Identities=22% Similarity=0.184 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCC
Q 026508 153 SSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 153 S~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E 215 (237)
+..-..++++.+++.|+..+|+|... --|. .=.+.+++.|..++.+.++.|++=.-|-|
T Consensus 141 ~~~~~~~ai~~~~~~G~~~v~~dli~--Glpg--qt~~~~~~~l~~~~~l~p~~is~y~l~~~ 199 (378)
T PRK05660 141 GPDEAKRAAKLAQGLGLRSFNLDLMH--GLPD--QSLEEALDDLRQAIALNPPHLSWYQLTIE 199 (378)
T ss_pred CHHHHHHHHHHHHHcCCCeEEEEeec--CCCC--CCHHHHHHHHHHHHhcCCCeEEeeccEec
Confidence 44445677899999999887888744 4454 34567888888888888999987655543
No 73
>PLN02414 glycine dehydrogenase (decarboxylating)
Probab=30.19 E-value=86 Score=34.22 Aligned_cols=100 Identities=16% Similarity=0.240 Sum_probs=67.6
Q ss_pred CCCCCChhHHHHHHHHHHHHHhcCCCCCcccC----CCCC-------C-ccCCCCHHHHHHHHHHHHHhCCCeEEEEEEE
Q 026508 110 GCEAHSDGDVLLHCVVDAILGALGLPDIGQIF----PDSD-------P-KWKGAPSSVFIKEAVRLMDEAGYEIGNLDAT 177 (237)
Q Consensus 110 GL~gHSDGDVLlHAI~DALLGA~glGDIG~~F----PdtD-------p-~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~T 177 (237)
--.||++.| ..++|.++|..+|-++| |.+= | -+++.+-..++++..++..++....+.+..-
T Consensus 38 r~i~~~~~~------~~~ML~~ig~~s~d~l~~~~iP~~i~~~~l~lp~~~~~~sE~e~~~~~~~la~kN~~~~~fiG~G 111 (993)
T PLN02414 38 RHNSATPEE------QKAMAEYCGFDSLDALIDATVPKSIRLDSMKLSKYDEGLTESQMLEHMKSLASKNKVFKSYIGMG 111 (993)
T ss_pred ccCCcCHHH------HHHHHHhcCccCHHHHhhccCCHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHhcCCccccccCCC
Confidence 457788876 47889999999998888 5321 2 1346788888888777766532223444433
Q ss_pred E------------EcCCCC----CchhHHH-----------HHHHHHHHhCCCCCceeEEeEcCC
Q 026508 178 L------------ILQRPK----LSPYKET-----------IRTNLSELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 178 I------------i~q~PK----l~p~~~~-----------mr~~La~lL~i~~~~VnIKAtT~E 215 (237)
. +.++|. ..||-.+ .|..||+++|++++++++=--+++
T Consensus 112 ~y~~~~P~~v~~~i~~~~~~~TaytPYqaEisQG~lqal~~~Qt~ia~LtG~~~anaSL~d~aTA 176 (993)
T PLN02414 112 YYNTHVPPVILRNILENPGWYTQYTPYQAEIAQGRLESLLNYQTMITDLTGLPMSNASLLDEGTA 176 (993)
T ss_pred CCCccCCHHHHHHHHhChHHHhhcCCCchHHHHHHHHHHHHHHHHHHHHhCCChhhEeecCChHH
Confidence 3 456664 3566544 688899999999999887655554
No 74
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=29.87 E-value=1.5e+02 Score=26.24 Aligned_cols=54 Identities=19% Similarity=0.244 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHHHHhCC--CeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCce
Q 026508 149 KGAPSSVFIKEAVRLMDEAG--YEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVV 207 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~G--~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~V 207 (237)
.|.||..||.-..++-++.+ |++.-+.+. - .+..+.++..+.+++.+|++...+
T Consensus 38 GG~DS~~LL~ll~~l~~~~~~~~~l~av~vd--~---g~~~~~~~~~~~~~~~lgI~~~v~ 93 (258)
T PRK10696 38 GGKDSYTLLDILLNLQKRAPINFELVAVNLD--Q---KQPGFPEHVLPEYLESLGVPYHIE 93 (258)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCeEEEEEEec--C---CCCCCCHHHHHHHHHHhCCCEEEE
Confidence 57888888876666544433 444333221 1 122344455677888888875433
No 75
>TIGR01588 citE citrate lyase, beta subunit. This is a model of the beta subunit of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff.
Probab=29.82 E-value=64 Score=29.50 Aligned_cols=67 Identities=13% Similarity=0.284 Sum_probs=49.8
Q ss_pred CeEEeeeeeCCCCCCCCCChhHHHHHHHHHHHHHh--cCCCCCcccCCCCCCccCCCCHHHHHHHHHHHHHhCCCe
Q 026508 97 PLIIGGINVPHERGCEAHSDGDVLLHCVVDAILGA--LGLPDIGQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYE 170 (237)
Q Consensus 97 ~LiLGGV~Ip~~~GL~gHSDGDVLlHAI~DALLGA--~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~ 170 (237)
-|++|...+-.+.|+.+..|++.+.++....++-| +|+.=|+..|+| |++. .=|++-.+.-+..||.
T Consensus 148 ~l~~G~~Dls~~lG~~~~~~~~~~~~ar~~iv~aaraag~~~id~v~~~----~~d~---~~l~~~~~~~~~~Gf~ 216 (288)
T TIGR01588 148 GIALGAEDYVTDMKTSRSPDGTELFYARCAILHAARAAGIAAFDTVYSD----VNNE---EGFLAEAQLIKQLGFD 216 (288)
T ss_pred EEEeCHHHHHHHcCCCcCCCchHHHHHHHHHHHHHHHcCCCcccCCccC----cCCH---HHHHHHHHHHHHcCCC
Confidence 48888888888899988888888999888877776 566667776665 3333 3366666778889985
No 76
>cd08507 PBP2_SgrR_like The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold. A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery f
Probab=29.76 E-value=99 Score=29.04 Aligned_cols=54 Identities=20% Similarity=0.242 Sum_probs=36.4
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCC
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E 215 (237)
++++.++|.+.||.-..+-+++..+.| ...-.+.|++.+.+ +|+. |+|+.-..+
T Consensus 283 ~~~Ak~lL~eaG~~~~~~~l~~~~~~~-~~~~a~~l~~~l~~-~Gi~---v~l~~~~~~ 336 (448)
T cd08507 283 REKIRRLLKESEYPGEELTLATYNQHP-HREDAKWIQQRLAK-HGIR---LEIHILSYE 336 (448)
T ss_pred HHHHHhhccccCCCCceEEEEEcCCCc-hHHHHHHHHHHHHH-cCcE---EEEEeeccc
Confidence 678999999999976555555555666 55666677777665 5765 666654443
No 77
>cd08508 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=29.75 E-value=1.6e+02 Score=27.68 Aligned_cols=45 Identities=22% Similarity=0.371 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEc-CCCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLIL-QRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~-q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
++++.++|++.||.- .+-+++.. +.+.....-+.|++.|.+ +||+
T Consensus 310 ~~kA~~lL~eaG~~~-g~~l~~~~~~~~~~~~~a~~l~~~l~~-~Gi~ 355 (470)
T cd08508 310 PAKAKALLAEAGFPN-GLTLTFLVSPAAGQQSIMQVVQAQLAE-AGIN 355 (470)
T ss_pred HHHHHHHHHHcCCCC-CceEEEEecCCchHHHHHHHHHHHHHh-cCcE
Confidence 789999999999963 24455543 334344455566666665 5765
No 78
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=29.70 E-value=1e+02 Score=22.88 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=24.0
Q ss_pred EEEEcCCCCCch---hHHHHHHHH----HHHhCCCCCceeEEeEcCC
Q 026508 176 ATLILQRPKLSP---YKETIRTNL----SELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 176 ~TIi~q~PKl~p---~~~~mr~~L----a~lL~i~~~~VnIKAtT~E 215 (237)
+.+..+|-.+.| |.++||+-| ++-..++.+.|.|+.+..+
T Consensus 11 ~iL~~dR~~~~~~~~~l~~lk~eil~viskYv~i~~~~v~v~l~~~~ 57 (70)
T PF03776_consen 11 LILAHDRGGLSPQPDYLEQLKKEILEVISKYVEIDEEDVEVQLERDD 57 (70)
T ss_dssp EEEEEECCSC-CTTSSHHHHHHHHHHHHHHHS---CCCEEEEEEECT
T ss_pred HHHHHHccCCCCcHHHHHHHHHHHHHHHHhheecCcccEEEEEEECC
Confidence 345556666666 666666555 5556788999999998554
No 79
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=29.64 E-value=2.3e+02 Score=20.81 Aligned_cols=99 Identities=17% Similarity=0.237 Sum_probs=60.2
Q ss_pred CeEEeeeeeCCCC---CCCCCChhHHHHHHHHHHHHHhcCCCC---------CcccCCCCCCccCCCCHHHHHHHHHHHH
Q 026508 97 PLIIGGINVPHER---GCEAHSDGDVLLHCVVDAILGALGLPD---------IGQIFPDSDPKWKGAPSSVFIKEAVRLM 164 (237)
Q Consensus 97 ~LiLGGV~Ip~~~---GL~gHSDGDVLlHAI~DALLGA~glGD---------IG~~FPdtDp~~Kg~dS~~lL~~v~~ll 164 (237)
++.+.-+.|+.-. ...|+..+|-++..+++.|--...-.| ++-+++.++. .....++++..+.+
T Consensus 34 ~~~l~~i~i~~~~~~~~~~g~~~~~~~l~~i~~~l~~~~~~~~~~~r~~~~~f~ii~~~~~~----~~~~~~~~~l~~~~ 109 (163)
T smart00267 34 PFALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSSCLRPGDLLARLGGDEFALLLPETSL----EEAIALAERILQQL 109 (163)
T ss_pred eEEEEEEEccccchhhhccCchhHHHHHHHHHHHHHHhcCCCCEEEEecCceEEEEecCCCH----HHHHHHHHHHHHHH
Confidence 3777788887543 358999999999999999977665533 3444444322 12355666666666
Q ss_pred HhCCCeE----EEEEEEE-EcCCCCCchhHHHHHHHHHHHh
Q 026508 165 DEAGYEI----GNLDATL-ILQRPKLSPYKETIRTNLSELL 200 (237)
Q Consensus 165 ~~~G~~I----~NiD~TI-i~q~PKl~p~~~~mr~~La~lL 200 (237)
+. -+.. ..+++.+ ++..|......+++.++....|
T Consensus 110 ~~-~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ll~~a~~al 149 (163)
T smart00267 110 RE-PIIIHGIPLYLTISIGVAAYPNPGEDAEDLLKRADTAL 149 (163)
T ss_pred hC-ccccCCcEEEEEEEEEEEeCCCCCCCHHHHHHHHHHHH
Confidence 53 2222 2345445 4444555555666666655555
No 80
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains correspondin
Probab=29.48 E-value=1.6e+02 Score=27.64 Aligned_cols=46 Identities=30% Similarity=0.437 Sum_probs=30.4
Q ss_pred HHHHHHHHHhCCCeEE-----------EEEEEEEcC--CCCCchhHHHHHHHHHHHhCCC
Q 026508 157 IKEAVRLMDEAGYEIG-----------NLDATLILQ--RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~-----------NiD~TIi~q--~PKl~p~~~~mr~~La~lL~i~ 203 (237)
++++.++|++.||.-. .+.++|+.. .|-...-.+.+++.|++ +|+.
T Consensus 311 ~~~Ak~lL~eaG~~~~~~~~~~~~~G~~l~l~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~ 369 (483)
T cd08514 311 PDKAKELLAEAGWVDGDDDGILDKDGKPFSFTLLTNQGNPVREQAATIIQQQLKE-IGID 369 (483)
T ss_pred HHHHHHHHHHcCCCcCCCCceecCCCCEEEEEEEecCCCchHHHHHHHHHHHHHh-cCcE
Confidence 6889999999999752 345556543 24444455667777766 5765
No 81
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=28.97 E-value=45 Score=25.91 Aligned_cols=26 Identities=23% Similarity=0.507 Sum_probs=19.9
Q ss_pred HHHHHHHHHhCCCeEEE---------EEEEEEcCC
Q 026508 157 IKEAVRLMDEAGYEIGN---------LDATLILQR 182 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~N---------iD~TIi~q~ 182 (237)
|..+.+.|+++||++++ +|+.|+.-.
T Consensus 10 Ls~v~~~L~~~GyeVv~l~~~~~~~~~daiVvtG~ 44 (80)
T PF03698_consen 10 LSNVKEALREKGYEVVDLENEQDLQNVDAIVVTGQ 44 (80)
T ss_pred chHHHHHHHHCCCEEEecCCccccCCcCEEEEECC
Confidence 56788999999999974 666666543
No 82
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=28.96 E-value=39 Score=26.50 Aligned_cols=36 Identities=22% Similarity=0.269 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCeEEEE-EEEEEcCCCC
Q 026508 149 KGAPSSVFIKEAVRLMDEAGYEIGNL-DATLILQRPK 184 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~G~~I~Ni-D~TIi~q~PK 184 (237)
+..+-...|+.|++-|+|+||...|= ==-|+...|-
T Consensus 13 ~~~~~~~iL~~Vy~AL~EKGYnPinQivGYllSGDPa 49 (79)
T PF06135_consen 13 KEKEIREILKQVYAALEEKGYNPINQIVGYLLSGDPA 49 (79)
T ss_pred chhhHHHHHHHHHHHHHHcCCChHHHHHhheecCCCc
Confidence 35577899999999999999987662 2223444554
No 83
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=28.64 E-value=2.1e+02 Score=27.31 Aligned_cols=58 Identities=28% Similarity=0.238 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCC
Q 026508 154 SVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHE 215 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E 215 (237)
..-..++++.+++.|+...|+|. |.--|- .=.+.+++.|..++.+.++.|++=.-|-|
T Consensus 150 ~~~~~~ai~~l~~~G~~~v~~dl--I~GlPg--qt~e~~~~tl~~~~~l~p~~is~y~L~~~ 207 (400)
T PRK07379 150 VKDIFAAVDLIHQAGIENFSLDL--ISGLPH--QTLEDWQASLEAAIALNPTHLSCYDLVLE 207 (400)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEe--ecCCCC--CCHHHHHHHHHHHHcCCCCEEEEecceec
Confidence 33455788899999998777775 555553 35678888999999999999988655543
No 84
>cd01713 PAPS_reductase This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase acti
Probab=28.64 E-value=76 Score=24.54 Aligned_cols=13 Identities=31% Similarity=0.567 Sum_probs=6.4
Q ss_pred CCCHHHHHHHHHH
Q 026508 150 GAPSSVFIKEAVR 162 (237)
Q Consensus 150 g~dS~~lL~~v~~ 162 (237)
|.||..+|.-+.+
T Consensus 9 GkDS~~ll~l~~~ 21 (173)
T cd01713 9 GKDSTVLLHLALK 21 (173)
T ss_pred ChHHHHHHHHHHH
Confidence 4455555544444
No 85
>PRK12378 hypothetical protein; Provisional
Probab=28.55 E-value=4.6e+02 Score=23.93 Aligned_cols=62 Identities=21% Similarity=0.291 Sum_probs=44.0
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCC
Q 026508 116 DGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPK 184 (237)
Q Consensus 116 DGDVLlHAI~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PK 184 (237)
|-|-++=..+|| || +.=|+ ..+ +..|.-.-...-|..+.+.|++.||.+.+.+++.+.+.+.
T Consensus 143 ~~d~~~e~aiea--Ga-~~edv---~~~-~~~~~i~t~p~~~~~v~~~L~~~g~~~~~sei~~~P~~~v 204 (235)
T PRK12378 143 DEDELLEALIDA--DV-DVEDV---EEE-EGTITVYTDPTDFHKVKKALEAAGIEFLVAELEMIPQNPV 204 (235)
T ss_pred CHHHHHHHHHhC--CC-Ccccc---ccc-CCeEEEEECHHHHHHHHHHHHHcCCCceeeEEEEecCCCc
Confidence 555555555554 33 22333 122 3367777778888999999999999999999999998874
No 86
>PRK04262 hypothetical protein; Provisional
Probab=28.39 E-value=61 Score=29.75 Aligned_cols=47 Identities=21% Similarity=0.326 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCcee
Q 026508 156 FIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVN 208 (237)
Q Consensus 156 lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~Vn 208 (237)
+.+.+.+.|++.|+...+||.-++-|- -..|.+.+++.||++.+++-
T Consensus 211 ~~~~i~~~L~~~gl~~~dId~~v~Hq~------n~~~~~~~~~~Lgl~~ek~~ 257 (347)
T PRK04262 211 IISAAKGLMEKLGLKPSDYDYAVFHQP------NGKFPLRVAKMLGFTKEQVK 257 (347)
T ss_pred HHHHHHHHHHHhCcCHHHhceeecCCC------chHHHHHHHHHcCCCHHHhh
Confidence 334455778889999999998777532 23466677888899888774
No 87
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=28.25 E-value=2.4e+02 Score=26.55 Aligned_cols=91 Identities=26% Similarity=0.345 Sum_probs=48.0
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCCCH---HHHHHHHHHHHHhCCCeEEEEEEEEEcCC-
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGAPS---SVFIKEAVRLMDEAGYEIGNLDATLILQR- 182 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~dS---~~lL~~v~~ll~~~G~~I~NiD~TIi~q~- 182 (237)
+|-+| |.||| ++.+++..+.. .-.++|...+ |-+.+. ..=++++.++|.+.||.-+ ..++|....
T Consensus 263 ~d~~vR~Ai~~aidr~~i~~~~~~g~~~~-~~~~~p~~~~-~~~~~~~~~~~d~~kAk~lL~~aG~~~g-~~l~l~~~~~ 339 (481)
T cd08498 263 KDPRVRQALSLAIDREAIVDRVMRGLATP-AGQLVPPGVF-GGEPLDKPPPYDPEKAKKLLAEAGYPDG-FELTLHCPND 339 (481)
T ss_pred CCHHHHHHHHHhcCHHHHHHHHhcCceee-cCCccCCCcc-ccCcccCCCCCCHHHHHHHHHHcCCCCC-ceEEEEEcCC
Confidence 46555 77776 55555433222 1234555433 211111 1127899999999999522 345554332
Q ss_pred --CCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 183 --PKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 183 --PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
+.-....+.|++.|.+ +||+ |.|+..
T Consensus 340 ~~~~~~~~a~~i~~~l~~-~Gi~---v~i~~~ 367 (481)
T cd08498 340 RYVNDEAIAQAVAGMLAR-IGIK---VNLETM 367 (481)
T ss_pred CCCcchHHHHHHHHHHHH-hCce---EEEEEe
Confidence 2223445666777665 5775 555543
No 88
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).
Probab=27.42 E-value=2.1e+02 Score=23.49 Aligned_cols=14 Identities=29% Similarity=0.404 Sum_probs=6.2
Q ss_pred CCChhHHHHHHHHH
Q 026508 113 AHSDGDVLLHCVVD 126 (237)
Q Consensus 113 gHSDGDVLlHAI~D 126 (237)
|=-|.=|++|.+.+
T Consensus 8 GG~DS~~ll~ll~~ 21 (189)
T TIGR02432 8 GGVDSMALLHLLLK 21 (189)
T ss_pred CCHHHHHHHHHHHH
Confidence 33344444444444
No 89
>PF02594 DUF167: Uncharacterised ACR, YggU family COG1872; InterPro: IPR003746 This entry describes proteins of unknown function. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer alpha/beta structure consisting of beta(2)-loop-alpha-beta(2)-alpha [, ].; PDB: 1YH5_A 1N91_A 1JRM_A.
Probab=27.40 E-value=61 Score=24.60 Aligned_cols=33 Identities=12% Similarity=0.196 Sum_probs=25.4
Q ss_pred EcCCCCCchhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 179 ILQRPKLSPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 179 i~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
+.+-|.=+.==+++.+.||+.|+++.++|.|..
T Consensus 32 v~app~~GkAN~ali~~La~~l~v~ks~i~i~~ 64 (77)
T PF02594_consen 32 VTAPPVDGKANKALIRFLAKALGVPKSDIEIVS 64 (77)
T ss_dssp BSTTCCCCCHHHHHHHHHHHHCT--TTCEEECC
T ss_pred EecCCCcChhHHHHHHHHHHHhCCCcccEEEEe
Confidence 345566666778999999999999999999976
No 90
>PRK06816 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=27.33 E-value=1.4e+02 Score=28.03 Aligned_cols=56 Identities=23% Similarity=0.237 Sum_probs=37.8
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHh-----CCCCCceeEEeEcCCCCCCcc
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELL-----GADPTVVNLKAKTHEKVDSLG 221 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL-----~i~~~~VnIKAtT~E~LG~~G 221 (237)
-+.+.+.|++.|+.+..||..+.-|-- ..|.+.+++.| |++++++- .+-+++|-+|
T Consensus 275 ~~~i~~~L~~~gl~~~DId~~v~Hq~n------~~~~~~v~~~l~~~~~gl~~~k~~---~~~~~~GNt~ 335 (378)
T PRK06816 275 IKPLLELVDKRNLDPDDIDYFLPHYSS------EYFREKIVELLAKAGFMIPEEKWF---TNLATVGNTG 335 (378)
T ss_pred HHHHHHHHHHcCCChhhCCEEeeCccc------HHHHHHHHHHHHhccCCCChhheE---Eecccccccc
Confidence 334445678899999999988876642 23444555554 89988864 4556777655
No 91
>cd08515 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=27.04 E-value=1.8e+02 Score=27.10 Aligned_cols=52 Identities=25% Similarity=0.280 Sum_probs=32.7
Q ss_pred HHHHHHHHHhCCC-eEEEEEEEEEcC-CCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 157 IKEAVRLMDEAGY-EIGNLDATLILQ-RPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 157 L~~v~~ll~~~G~-~I~NiD~TIi~q-~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
++++.++|++.|| .-..+.+.+... .|....--+.++++|.+ +||. |+|...
T Consensus 308 ~~~A~~lL~~aG~~~g~~l~l~~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~i~~~ 361 (460)
T cd08515 308 PEKAKALLAEAGYPDGFEIDYYAYRGYYPNDRPVAEAIVGMWKA-VGIN---AELNVL 361 (460)
T ss_pred HHHHHHHHHHcCCCCCceEEEEecCCCCCchHHHHHHHHHHHHH-hCce---EEEEEe
Confidence 6789999999999 333444444322 24444555667777766 6876 555555
No 92
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=26.86 E-value=57 Score=27.08 Aligned_cols=42 Identities=10% Similarity=0.192 Sum_probs=31.4
Q ss_pred CCCcc-cCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEE
Q 026508 135 PDIGQ-IFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLI 179 (237)
Q Consensus 135 GDIG~-~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi 179 (237)
.|+|+ +|.-.+++ .+-..+-+.+.+.++++||...++++++-
T Consensus 8 ~~~~~~~~~~~~~~---~~~~~~~~~i~~~i~~~~~~~~~i~V~v~ 50 (147)
T PRK11198 8 KEAGEKLFDAVTAQ---ADNEDAADALKEHISKQGLGDADVNVQVE 50 (147)
T ss_pred HHHHHHhcCCCCcc---cchHHHHHHHHHHHHhcCCCcCCceEEEe
Confidence 35564 67766665 44477777889999999999998887765
No 93
>CHL00203 fabH 3-oxoacyl-acyl-carrier-protein synthase 3; Provisional
Probab=26.75 E-value=66 Score=29.05 Aligned_cols=43 Identities=12% Similarity=0.190 Sum_probs=34.1
Q ss_pred HHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCcee
Q 026508 160 AVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVN 208 (237)
Q Consensus 160 v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~Vn 208 (237)
+.+.|++.||.+.+||..++-|-- ..|.+.+++.||++.+++.
T Consensus 232 i~~~L~~~g~~~~did~~~~hq~~------~~~~~~~~~~lgl~~~k~~ 274 (326)
T CHL00203 232 IIKCLNALNISIDEVDWFILHQAN------KRILEAIANRLSVPNSKMI 274 (326)
T ss_pred HHHHHHHcCCCHHHCCEEEECCCC------HHHHHHHHHHhCCCHHHhh
Confidence 556678899999999998887654 3456678899999988874
No 94
>PF08645 PNK3P: Polynucleotide kinase 3 phosphatase; InterPro: IPR013954 Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin []. ; PDB: 2FPW_A 2FPR_A 2FPX_A 2FPS_A 2FPU_B 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B 3U7G_A ....
Probab=26.57 E-value=95 Score=25.89 Aligned_cols=64 Identities=28% Similarity=0.485 Sum_probs=38.1
Q ss_pred CcccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcC----CCCCchhHHHHHHHHHHHhCCC
Q 026508 137 IGQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQ----RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 137 IG~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q----~PKl~p~~~~mr~~La~lL~i~ 203 (237)
-|..|+.+-.+|+=.+.. .-++++.+.+.||.|+=+.=+=-.. ...+..+++.|+ ++.+.|+++
T Consensus 16 s~~~f~~~~~D~~~~~~~--v~~~L~~l~~~Gy~IvIvTNQ~gi~~~~~~~~~~~~~~ki~-~il~~l~ip 83 (159)
T PF08645_consen 16 SGKKFPKDPDDWKFFPPG--VPEALRELHKKGYKIVIVTNQSGIGRGMGEKDLENFHEKIE-NILKELGIP 83 (159)
T ss_dssp TSTTS-SSTCGGEEC-TT--HHHHHHHHHHTTEEEEEEEE-CCCCCTBTCCHHHHHHHHHH-HHHHHCTS-
T ss_pred CCCcCcCCHHHhhhcchh--HHHHHHHHHhcCCeEEEEeCccccccccccchHHHHHHHHH-HHHHHcCCc
Confidence 477788755566555422 4466777789999997666554322 244556677774 566777877
No 95
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=26.30 E-value=2.3e+02 Score=27.60 Aligned_cols=61 Identities=26% Similarity=0.311 Sum_probs=47.7
Q ss_pred CHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEcCCC
Q 026508 152 PSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKTHEK 216 (237)
Q Consensus 152 dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~E~ 216 (237)
-+.....++++.+++.|+.-.|+|... ..|. .-.+.+++.|..++.+.+++|++=.=|-|.
T Consensus 170 h~~~~~~~a~~~~~~~g~~~in~DLIy--glP~--QT~~~~~~~l~~a~~l~pdhis~y~L~~~p 230 (416)
T COG0635 170 HDEEEAKEAVELARKAGFTSINIDLIY--GLPG--QTLESLKEDLEQALELGPDHLSLYSLAIEP 230 (416)
T ss_pred CCHHHHHHHHHHHHHcCCCcEEEEeec--CCCC--CCHHHHHHHHHHHHhCCCCEEEEeeeecCC
Confidence 345667788999999999999999765 4442 346788899999999999999986666554
No 96
>cd08516 PBP2_NikA_DppA_OppA_like_11 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=25.86 E-value=1.8e+02 Score=26.85 Aligned_cols=51 Identities=24% Similarity=0.397 Sum_probs=33.0
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcC--CCCCchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQ--RPKLSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q--~PKl~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
++++.++|++.||. ....++++.. .|......+.|++.+.+ +|++ |.++..
T Consensus 302 ~~kA~~lL~~aG~~-~g~~l~l~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~~~~~ 354 (457)
T cd08516 302 PEKAKALLAEAGYP-NGFDFTILVTSQYGMHVDTAQVIQAQLAA-IGIN---VEIELV 354 (457)
T ss_pred HHHHHHHHHhcCCC-CCceEEEEeCCCCccHHHHHHHHHHHHHH-cCce---EEEEEe
Confidence 67899999999996 2356666542 34444555667777766 5875 555543
No 97
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=25.75 E-value=2.2e+02 Score=27.30 Aligned_cols=93 Identities=19% Similarity=0.243 Sum_probs=50.2
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCCCH-HHHHHHHHHHHHhCCCeEEEEEEEEEcC--CC
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGAPS-SVFIKEAVRLMDEAGYEIGNLDATLILQ--RP 183 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~dS-~~lL~~v~~ll~~~G~~I~NiD~TIi~q--~P 183 (237)
+|-+| |.||| ++.+++..+..= -.++|..-+-+.+... ..=++++.++|.+.||.-. +.+++... .|
T Consensus 281 ~d~~vRqAi~~AiDr~~i~~~~~~g~~~~~-~~~~p~~~~~~~~~~~~~~D~ekAk~lL~~aG~~~g-~~~~~~~~~~~~ 358 (512)
T PRK15413 281 DNPKVREALNYAINRQALVKVAFAGYATPA-TGVVPPSIAYAQSYKPWPYDPAKARELLKEAGYPNG-FSTTLWSSHNHS 358 (512)
T ss_pred CCHHHHHHHHHhcCHHHHHHHHhcCCcccc-cCCCCCCcccccccCCCCCCHHHHHHHHHHcCCCCC-eeEEEEecCCCc
Confidence 56554 77775 777765433221 1244543221111110 1128899999999999632 45555432 23
Q ss_pred CCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 184 KLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 184 Kl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
.....-+.++++|.+ +||. |+|+...
T Consensus 359 ~~~~~a~~iq~~l~~-iGI~---v~i~~~d 384 (512)
T PRK15413 359 TAQKVLQFTQQQLAQ-VGIK---AQVTAMD 384 (512)
T ss_pred cHHHHHHHHHHHHHh-cCcE---EEEEEec
Confidence 334455566777766 5765 5555443
No 98
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=25.53 E-value=2.5e+02 Score=27.34 Aligned_cols=88 Identities=24% Similarity=0.298 Sum_probs=45.4
Q ss_pred HHHHH-----HHHHHHhcCCCCCcccCCCCC-------CccCCCCHHHHHHHHHHHHHhCCCeEE-EEEEEEEcCC-CCC
Q 026508 120 LLHCV-----VDAILGALGLPDIGQIFPDSD-------PKWKGAPSSVFIKEAVRLMDEAGYEIG-NLDATLILQR-PKL 185 (237)
Q Consensus 120 LlHAI-----~DALLGA~glGDIG~~FPdtD-------p~~Kg~dS~~lL~~v~~ll~~~G~~I~-NiD~TIi~q~-PKl 185 (237)
|.||| ++++++..+..- ..++|... +.|...+...=++++.++|.+.||.-+ -+.+++.... +.-
T Consensus 319 i~~AiDr~~iv~~~~~g~~~~~-~~~~p~~~~~~~~~~~~~~~~~~~~d~~kAk~LL~eAG~~~g~~l~i~l~~~~~~~~ 397 (543)
T PRK15104 319 LKLGLDRDIIVNKVKNQGDLPA-YGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTFNLLYNTSDLH 397 (543)
T ss_pred HHHhhCHHHHHHHHHcCCcccc-ccccCCCCCCCCccccchhhcccccCHHHHHHHHHhcCCCCCCCceEEEEeCCCCch
Confidence 66654 677776444332 33455533 222111112347899999999999632 2345554322 111
Q ss_pred chhHHHHHHHHHHHhCCCCCceeEEe
Q 026508 186 SPYKETIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 186 ~p~~~~mr~~La~lL~i~~~~VnIKA 211 (237)
..-.+.|++.+.+.+||+ |+|+.
T Consensus 398 ~~~a~~i~~~~~~~iGI~---v~l~~ 420 (543)
T PRK15104 398 KKLAIAAASIWKKNLGVN---VKLEN 420 (543)
T ss_pred HHHHHHHHHHHHHhcCce---EEEEe
Confidence 223345556666556765 55544
No 99
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=25.01 E-value=1.5e+02 Score=24.46 Aligned_cols=45 Identities=13% Similarity=0.236 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhC
Q 026508 154 SVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLG 201 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~ 201 (237)
..+|+|++++.+. .+...|+.|++...-...-..++++.|-.+|.
T Consensus 67 KR~lRE~fR~~~~---~l~g~DiVviaR~~~~~~~~~~l~~~l~~ll~ 111 (130)
T PRK00396 67 KRLIRESFRLNQH---SLAGWDIVVVARKGLGELENPELHQQFGKLWK 111 (130)
T ss_pred HHHHHHHHHHhhc---cCCCeeEEEEeCCCcccCCHHHHHHHHHHHHH
Confidence 5678888877753 34689999999887666666677777777764
No 100
>TIGR03722 arch_KAE1 universal archaeal protein Kae1. This family represents the archaeal protein Kae1. Its partner Bud32 is fused with it in about half of the known archaeal genomes. The pair, which appears universal in the archaea, corresponds to EKC/KEOPS complex in eukaryotes. A recent characterization of the member from Pyrococcus abyssi, as an iron-binding, atypical DNA-binding protein with an apurinic lyase activity, challenges the common annotation of close homologs as O-sialoglycoprotein endopeptidase. The latter annotation is based on a characterized protein from the bacterium Pasteurella haemolytica.
Probab=24.73 E-value=1e+02 Score=28.36 Aligned_cols=52 Identities=27% Similarity=0.295 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHH---HHHHHHHHHhCCCC
Q 026508 153 SSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKE---TIRTNLSELLGADP 204 (237)
Q Consensus 153 S~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~---~mr~~La~lL~i~~ 204 (237)
+..|...+-+.+++.|.++.++|...+...|-+.+..- .+.+.|+..++++.
T Consensus 46 ~~~l~~~i~~~l~~~~~~~~did~Iavt~gPg~~~~l~vg~~~ak~la~~~~~p~ 100 (322)
T TIGR03722 46 AEVAPKLIKEALEEAGVSLEDIDAVAFSQGPGLGPCLRVGATAARALALKLNKPL 100 (322)
T ss_pred HHHHHHHHHHHHHHcCCCHHHCCEEEEecCCchHHhHHHHHHHHHHHHHHhCCCe
Confidence 45577778888889999999999999999997776332 34788888888764
No 101
>KOG1759 consensus Macrophage migration inhibitory factor [Defense mechanisms]
Probab=24.54 E-value=2.8e+02 Score=23.18 Aligned_cols=42 Identities=10% Similarity=0.226 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCcccccceEEE
Q 026508 188 YKETIRTNLSELLGADPTVVNLKAKTHEKVDSLGENRSIAAH 229 (237)
Q Consensus 188 ~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~Gr~egIaa~ 229 (237)
+-.+.-.++|+++|-|.++|.|--.-.-+|.|-|..|-.|-.
T Consensus 19 fe~elt~~lAkimgkP~~~i~V~l~~~~~i~fggt~eP~A~~ 60 (115)
T KOG1759|consen 19 FEKELTKALAKIMGKPEDYIMVELAGGVRIAFGGTTEPAAYA 60 (115)
T ss_pred HHHHHHHHHHHHhCCChhhEEEEecCCceEeccCCCCccEEE
Confidence 788889999999999999999999999999999988865543
No 102
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=24.40 E-value=2.3e+02 Score=20.46 Aligned_cols=58 Identities=24% Similarity=0.371 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCC-------chhHHHHHHHHHHH---hCCCCCceeEE
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKL-------SPYKETIRTNLSEL---LGADPTVVNLK 210 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl-------~p~~~~mr~~La~l---L~i~~~~VnIK 210 (237)
|.|..-++..+.+.+.+.|-.|.++..+.+..+--+ ....+++++.|.++ +|++ |.+|
T Consensus 9 G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~l~~~~~l~---v~v~ 76 (76)
T PF13740_consen 9 GPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEELAEELGLD---VSVQ 76 (76)
T ss_dssp EE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHHHHHHTT-E---EEEE
T ss_pred ecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHHHHHHCCcE---EEEC
Confidence 445666889999999999999999887766543211 44667777777766 6654 5554
No 103
>PRK05473 hypothetical protein; Provisional
Probab=24.34 E-value=46 Score=26.54 Aligned_cols=36 Identities=17% Similarity=0.200 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCeEEEE-EEEEEcCCCCC
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEIGNL-DATLILQRPKL 185 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I~Ni-D~TIi~q~PKl 185 (237)
..+-...|+.|++-|+|+||...|= ==-|+...|--
T Consensus 17 ~~~v~eiL~~Vy~AL~EKGYNPinQiVGYllSGDPaY 53 (86)
T PRK05473 17 KKDVREILTTVYDALEEKGYNPINQIVGYLLSGDPAY 53 (86)
T ss_pred HHHHHHHHHHHHHHHHHcCCChHHHHHhhhccCCCCc
Confidence 3367899999999999999987762 22234455543
No 104
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=24.24 E-value=53 Score=31.91 Aligned_cols=51 Identities=24% Similarity=0.354 Sum_probs=39.7
Q ss_pred cccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHH
Q 026508 138 GQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSE 198 (237)
Q Consensus 138 G~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~ 198 (237)
-.||--...-|.+..|..-|+.+++..- +|-|||+ |...||+++|...++.
T Consensus 159 ~kwf~lkedg~~dlpse~rlr~a~eafg----~ir~vdi------picdplr~~mn~kisg 209 (445)
T KOG2891|consen 159 CKWFALKEDGSEDLPSEDRLRKAFEAFG----EIRNVDI------PICDPLREEMNGKISG 209 (445)
T ss_pred ceeeeecccccccCChHHHHHHHHHHhc----cceecCC------cccchhHHHhcCcccc
Confidence 4677755556788999999999988763 6889987 5568999999877653
No 105
>cd08505 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=23.70 E-value=1.5e+02 Score=28.81 Aligned_cols=94 Identities=20% Similarity=0.257 Sum_probs=52.3
Q ss_pred ChhHH---HHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCC----CHHHHHHHHHHHHHhCCCeEEE-------EE
Q 026508 115 SDGDV---LLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGA----PSSVFIKEAVRLMDEAGYEIGN-------LD 175 (237)
Q Consensus 115 SDGDV---LlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~----dS~~lL~~v~~ll~~~G~~I~N-------iD 175 (237)
+|-.| |.||| ++.+++..+.. ...++|...+.|... .-..=++++.++|.+.||.-.. +.
T Consensus 304 ~d~~vR~Ai~~AiDr~~i~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~d~~kA~~lL~~AG~~~~~~g~~G~~l~ 382 (528)
T cd08505 304 EKRKLRQAISIAFDWEEYISIFRNGRAVP-AQGPIPPGIFGYRPGEDGKPVRYDLELAKALLAEAGYPDGRDGPTGKPLV 382 (528)
T ss_pred chHHHHHHHHHhcCHHHHHHHHhcCccee-cccccCCcccCCCcccccCCCCCCHHHHHHHHHHcCCCCCCCCCCCceEE
Confidence 46544 78876 77777532221 223444443333211 0122378999999999997421 23
Q ss_pred EEEEcC-CCCCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 176 ATLILQ-RPKLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 176 ~TIi~q-~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
+++... .|......+.|++++++ +||+ |+|+..+
T Consensus 383 i~~~~~~~~~~~~~a~~iq~~l~~-iGI~---v~i~~~d 417 (528)
T cd08505 383 LNYDTQATPDDKQRLEWWRKQFAK-LGIQ---LNVRATD 417 (528)
T ss_pred EEEecCCCchHHHHHHHHHHHHHH-cCce---EEEEecc
Confidence 333322 24455667777888877 6876 5565543
No 106
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=23.13 E-value=1.5e+02 Score=23.74 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=26.6
Q ss_pred CCCC-CchhHHHHHHHHHHHhCCCCCceeEEeE
Q 026508 181 QRPK-LSPYKETIRTNLSELLGADPTVVNLKAK 212 (237)
Q Consensus 181 q~PK-l~p~~~~mr~~La~lL~i~~~~VnIKAt 212 (237)
.+|- =.|=+.++|+.||+.++.+++.|-|..=
T Consensus 24 ~h~g~~tpsr~eirekLa~~~~~~~~~vvv~~~ 56 (99)
T PRK01178 24 YHEGSATPSRKDVRKKLAAMLNADKELVVVRKI 56 (99)
T ss_pred EeCCCCCCCHHHHHHHHHHHHCcCCCEEEEEcc
Confidence 4454 3689999999999999999999988653
No 107
>TIGR02845 spore_V_AD stage V sporulation protein AD. Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation.
Probab=23.04 E-value=1.2e+02 Score=29.26 Aligned_cols=67 Identities=15% Similarity=0.169 Sum_probs=41.6
Q ss_pred CCCCCcccCCC--CCCccCCCC-----HHHHHHH-HHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCC
Q 026508 133 GLPDIGQIFPD--SDPKWKGAP-----SSVFIKE-AVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADP 204 (237)
Q Consensus 133 glGDIG~~FPd--tDp~~Kg~d-----S~~lL~~-v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~ 204 (237)
+.|-+|.+|.- .|+ |-|.+ -+.|..+ +.+.|++.|.+...||..|++..+. .+. .-..+++.||++.
T Consensus 24 ~~gpl~~~fd~~~~d~-~~g~ks~EkAe~eLa~eAa~~ALekAGL~~~DID~IIvGdl~~-Q~~---~As~vA~~LGIP~ 98 (327)
T TIGR02845 24 GEGPLGDYFDKIYDDL-YCGEDSWEKAERKLMEDAVNLALKKANLKKDDVDFFLAGDLLN-QII---TANFVARDLGIPF 98 (327)
T ss_pred ccCCChhhCCEEEecc-ccCCcCcchhHHHHHHHHHHHHHHHcCCCHHHCCEEEEeCCCC-ccc---HHHHHHHHhCCCE
Confidence 34666777754 232 22333 2445555 5556678899999999999987542 111 2445778888754
No 108
>cd08506 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains cor
Probab=23.01 E-value=1.9e+02 Score=27.02 Aligned_cols=99 Identities=21% Similarity=0.214 Sum_probs=51.1
Q ss_pred EeeeeeCCCCCCCCCChhHH---HHHHH-HHHHHHhcC---CCCC-cccCCCCCCccCCCC------HHHHHHHHHHHHH
Q 026508 100 IGGINVPHERGCEAHSDGDV---LLHCV-VDAILGALG---LPDI-GQIFPDSDPKWKGAP------SSVFIKEAVRLMD 165 (237)
Q Consensus 100 LGGV~Ip~~~GL~gHSDGDV---LlHAI-~DALLGA~g---lGDI-G~~FPdtDp~~Kg~d------S~~lL~~v~~ll~ 165 (237)
..++.+-...+.. +|-+| |.||| -|+|+.... .+.- -.++|...+.|.+.. -..=++++.++|+
T Consensus 235 ~~~l~~N~~~~~~--~d~~vRkAl~~aidr~~i~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~d~ekAk~lL~ 312 (466)
T cd08506 235 VYYLAINTNVPPF--DDVKVRQAVAYAVDRAALVRAFGGPAGGEPATTILPPGIPGYEDYDPYPTKGPKGDPDKAKELLA 312 (466)
T ss_pred EEEEEecCCCCCC--CCHHHHHHHHHhcCHHHHHHHhcCCccccccccccCCCCCCCcccccccCCCCCCCHHHHHHHHH
Confidence 3445555555433 35443 77765 344443322 2221 234555444333221 1123589999999
Q ss_pred hCCCeEEEEEEEEEcC-CCCCchhHHHHHHHHHHHhCCC
Q 026508 166 EAGYEIGNLDATLILQ-RPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 166 ~~G~~I~NiD~TIi~q-~PKl~p~~~~mr~~La~lL~i~ 203 (237)
+.||. .+.++++.. .+....-.+.|++++.+ +||.
T Consensus 313 ~aG~~--g~~l~~~~~~~~~~~~~a~~i~~~l~~-iGI~ 348 (466)
T cd08506 313 EAGVP--GLKLTLAYRDTAVDKKIAEALQASLAR-AGID 348 (466)
T ss_pred HcCCC--CceEEEEeCCCchHHHHHHHHHHHHHH-cCCe
Confidence 99998 456666543 33323344455566544 5765
No 109
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=22.90 E-value=1.9e+02 Score=25.05 Aligned_cols=56 Identities=14% Similarity=0.111 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCC-Cchh--HHHHHHHHHHHhCCCCCceeE
Q 026508 149 KGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPK-LSPY--KETIRTNLSELLGADPTVVNL 209 (237)
Q Consensus 149 Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PK-l~p~--~~~mr~~La~lL~i~~~~VnI 209 (237)
.|.||...|..+.+ +||++.-+=++. .+.+. ...| -.+.-+.+|+.||++...|.+
T Consensus 8 GGkDS~~al~~a~~----~G~~v~~l~~~~-~~~~~~~~~h~~~~e~~~~~A~~lgipl~~i~~ 66 (194)
T cd01994 8 GGKDSCYALYRALE----EGHEVVALLNLT-PEEGSSMMYHTVNHELLELQAEAMGIPLIRIEI 66 (194)
T ss_pred CCHHHHHHHHHHHH----cCCEEEEEEEEe-cCCCCcccccccCHHHHHHHHHHcCCcEEEEeC
Confidence 47788888776655 588775554332 22221 1111 234446789999998766655
No 110
>PRK05367 glycine dehydrogenase; Provisional
Probab=22.82 E-value=93 Score=33.66 Aligned_cols=97 Identities=22% Similarity=0.354 Sum_probs=64.5
Q ss_pred CCCCCCChhHHHHHHHHHHHHHhcCCCCCcccCCCCCC---------cc-CCCCHHHHHHHHHHHHHhC---------CC
Q 026508 109 RGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDP---------KW-KGAPSSVFIKEAVRLMDEA---------GY 169 (237)
Q Consensus 109 ~GL~gHSDGDVLlHAI~DALLGA~glGDIG~~FPdtDp---------~~-Kg~dS~~lL~~v~~ll~~~---------G~ 169 (237)
.--.||++.| ..++|.++|..+|-++|.++=| .. +..+-..+|++..++.+++ ||
T Consensus 12 ~~~i~~~~~~------~~~ml~~~g~~s~~~l~~~~iP~~i~~~~~l~lp~~~sE~e~~~~~~~la~~N~~~~~~ig~G~ 85 (954)
T PRK05367 12 RRHIGPSAAD------QQAMLAALGADSLDALIDQAVPASIRLAEPLDLPAALSEAEALAELRAIASKNKVFRSYIGQGY 85 (954)
T ss_pred ccCCCcCHHH------HHHHHHhcCCCCHHHHhhhhCCHHHhcCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCcccCCCC
Confidence 3457888877 4788999999999999877422 22 2567788888877765542 22
Q ss_pred eEEEEEEEE---EcCCCC----CchhHH-----------HHHHHHHHHhCCCCCceeEEe
Q 026508 170 EIGNLDATL---ILQRPK----LSPYKE-----------TIRTNLSELLGADPTVVNLKA 211 (237)
Q Consensus 170 ~I~NiD~TI---i~q~PK----l~p~~~-----------~mr~~La~lL~i~~~~VnIKA 211 (237)
.---+=.+| ++++|- .-||-+ +.|+.||+++|+++.++++=-
T Consensus 86 y~~~~P~vi~~~i~~~~~~~t~ytPyQ~EisQG~Leal~~~Qt~la~LtG~~~anaSl~d 145 (954)
T PRK05367 86 YGTHTPPVILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMVADLTGLEIANASLLD 145 (954)
T ss_pred CCCcCcHHHHHHHHhCcchhhccCCCChHHHHHHHHHHHHHHHHHHHHHCCChhhccccc
Confidence 211122234 567775 346654 457889999999998877743
No 111
>cd08495 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=22.46 E-value=2.1e+02 Score=26.92 Aligned_cols=106 Identities=26% Similarity=0.358 Sum_probs=55.1
Q ss_pred eeeeCCCCCCCCCChhH---HHHHHH-----HHHHHHhcCCCCCcccCCCCCCccCCCC--HHHHHHHHHHHHHhCCCeE
Q 026508 102 GINVPHERGCEAHSDGD---VLLHCV-----VDAILGALGLPDIGQIFPDSDPKWKGAP--SSVFIKEAVRLMDEAGYEI 171 (237)
Q Consensus 102 GV~Ip~~~GL~gHSDGD---VLlHAI-----~DALLGA~glGDIG~~FPdtDp~~Kg~d--S~~lL~~v~~ll~~~G~~I 171 (237)
++.+....+. -.|-. +|.+|| ++.+++..+..-- .++|+..+.|.... -..=++++.++|++.||+-
T Consensus 253 ~l~~N~~~~~--~~d~~vRkAi~~aidr~~i~~~~~~g~~~pa~-~~~~~~~~~~~~~~~~~~~d~~~Ak~lL~~aG~~~ 329 (482)
T cd08495 253 IYQLNMAEGP--LSDPRVRQALNLAIDREGLVDLLLGGLAAPAT-GPVPPGHPGFGKPTFPYKYDPDKARALLKEAGYGP 329 (482)
T ss_pred EEEecCCCCc--ccCHHHHHHHHHhcCHHHHHHHHhcCCceecc-cccCCCCcCccCCCCCCCCCHHHHHHHHHHcCCCC
Confidence 4555554432 24544 366664 4444432222211 24565555443210 0112689999999999964
Q ss_pred E-EEEEEEEcCC---CCCchhHHHHHHHHHHHhCCCCCceeEEeEcC
Q 026508 172 G-NLDATLILQR---PKLSPYKETIRTNLSELLGADPTVVNLKAKTH 214 (237)
Q Consensus 172 ~-NiD~TIi~q~---PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT~ 214 (237)
. -+-+++.... +.-..-.+.++++|.+ +||. |+++..+.
T Consensus 330 ~~~l~l~~~~~~~~~~~~~~~a~~i~~~l~~-~Gi~---v~~~~~~~ 372 (482)
T cd08495 330 GLTLKLRVSASGSGQMQPLPMNEFIQQNLAE-IGID---LDIEVVEW 372 (482)
T ss_pred CCceEEEEecCCCCCCcHHHHHHHHHHHHHH-cCce---EEEEEccH
Confidence 2 1223333221 3334556677777777 6886 66766553
No 112
>PRK09894 diguanylate cyclase; Provisional
Probab=22.44 E-value=5e+02 Score=22.30 Aligned_cols=102 Identities=10% Similarity=0.027 Sum_probs=61.3
Q ss_pred CCCCeEEeeeeeCCCCC---CCCCChhHHHHHHHHHHHHHhcCCCC---------CcccCCCCCCccCCCCHHHHHHHHH
Q 026508 94 PGYPLIIGGINVPHERG---CEAHSDGDVLLHCVVDAILGALGLPD---------IGQIFPDSDPKWKGAPSSVFIKEAV 161 (237)
Q Consensus 94 ~gr~LiLGGV~Ip~~~G---L~gHSDGDVLlHAI~DALLGA~glGD---------IG~~FPdtDp~~Kg~dS~~lL~~v~ 161 (237)
.++++.|--+.|+.=+- ..||.=||.++..+++.|-..+.-+| +.-++|+++.+ ....++++..
T Consensus 155 ~~~~~~l~~i~id~f~~in~~~G~~~gd~~L~~ia~~l~~~~~~~~~~~R~~g~~F~ill~~~~~~----~~~~~~~~l~ 230 (296)
T PRK09894 155 EPQNLYLALLDIDRFKLVNDTYGHLIGDVVLRTLATYLASWTRDYETVYRYGGEEFIICLKAATDE----EACRAGERIR 230 (296)
T ss_pred cCCcEEEEEEECccccHHHHccCcHHHHHHHHHHHHHHHHhCCCCCEEEEEcCCeEEEEeCCCCHH----HHHHHHHHHH
Confidence 35677777788876443 58999999999999999987775544 34445554321 2355666666
Q ss_pred HHHHhCCCeE----EEEEEEE-EcCCCCCchhHHHHHHHHHHHh
Q 026508 162 RLMDEAGYEI----GNLDATL-ILQRPKLSPYKETIRTNLSELL 200 (237)
Q Consensus 162 ~ll~~~G~~I----~NiD~TI-i~q~PKl~p~~~~mr~~La~lL 200 (237)
+.+.+..+.+ ..+.+++ ++..|. ..-.+++.++...+|
T Consensus 231 ~~~~~~~~~~~~~~~~~~~siGv~~~~~-~~~~~~ll~~A~~Al 273 (296)
T PRK09894 231 QLIANHAITHSDGRINITATFGVSRAFP-EETLDVVIGRADRAM 273 (296)
T ss_pred HHHHhCCcccCCceEEEEEEEEEEEcCC-CCCHHHHHHHHHHHH
Confidence 6666554443 3455555 444443 233444444444444
No 113
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=22.12 E-value=2e+02 Score=25.54 Aligned_cols=17 Identities=24% Similarity=0.263 Sum_probs=9.6
Q ss_pred CCCCChhHHHHHHHHHH
Q 026508 111 CEAHSDGDVLLHCVVDA 127 (237)
Q Consensus 111 L~gHSDGDVLlHAI~DA 127 (237)
+.|--|-=+++|.+.++
T Consensus 19 ~SGGvDSs~ll~la~~~ 35 (252)
T TIGR00268 19 YSGGVDSSLLAAVCSDA 35 (252)
T ss_pred ecCcHHHHHHHHHHHHh
Confidence 44555666666665553
No 114
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=22.06 E-value=1.7e+02 Score=23.59 Aligned_cols=46 Identities=26% Similarity=0.279 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCC
Q 026508 154 SVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGA 202 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i 202 (237)
..+++++++. . ....-+.|++||+...-...--.++.+.|..+|..
T Consensus 62 KR~iRe~~r~-~--~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~ 107 (117)
T COG0594 62 KRLIREAFRL-L--QHLLPGFDIVIIARKGFLELDFSELEKELSQLLKR 107 (117)
T ss_pred HHHHHHHHHh-h--hhhCCCceEEEEECCCCCCCCHHHHHHHHHHHHHH
Confidence 4566666666 3 37788999999999998876566668999988863
No 115
>COG4631 XdhB Xanthine dehydrogenase, molybdopterin-binding subunit B [Nucleotide transport and metabolism]
Probab=22.02 E-value=84 Score=33.02 Aligned_cols=33 Identities=21% Similarity=0.235 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHhCCCCCceeEEeEcCCCCCCc
Q 026508 188 YKETIRTNLSELLGADPTVVNLKAKTHEKVDSL 220 (237)
Q Consensus 188 ~~~~mr~~La~lL~i~~~~VnIKAtT~E~LG~~ 220 (237)
.--++.+..|+.++++.++|.|.|||+.|+.-+
T Consensus 490 L~tKvaQVvA~~fqvd~~rVkitaT~T~KVpNT 522 (781)
T COG4631 490 LYTKVAQVVAEEFQVDIDRVKITATTTDKVPNT 522 (781)
T ss_pred hhHHHHHHHHHHhCcccceEEEeccccCCCCCC
Confidence 345778899999999999999999999998643
No 116
>TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family. Members of this protein family are most closely related to TIGR02764, a subset of polysaccharide deacetylase family proteins found in a species if and only if the species forms endospores like those of Bacillus subtilis or Clostridium tetani. This family is likewise restricted to spore-formers, but is not universal among them in having sequences with full-length matches to the model.
Probab=22.00 E-value=1.5e+02 Score=27.08 Aligned_cols=45 Identities=20% Similarity=0.440 Sum_probs=31.9
Q ss_pred HHHHHHHhcCCCCCcccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEE
Q 026508 124 VVDAILGALGLPDIGQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLD 175 (237)
Q Consensus 124 I~DALLGA~glGDIG~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD 175 (237)
+.+.++..+.-|+|= ++=|+. .+...|..+++.++++||+++.++
T Consensus 220 i~~~v~~~~~~G~II-LmHd~~------~T~~aL~~iI~~Lk~kGy~fvtl~ 264 (268)
T TIGR02873 220 MVNRVLSKIHPGAMV-LMHPTA------SSTEGLEEMITIIKEKGYKIGTIT 264 (268)
T ss_pred HHHHHHhcCCCCcEE-EEcCCc------cHHHHHHHHHHHHHHCCCEEEeHH
Confidence 345555556667764 454442 367789999999999999998875
No 117
>PRK00194 hypothetical protein; Validated
Probab=21.33 E-value=1.2e+02 Score=22.10 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCeEEEEEEEE---------EcCCCCCchhHHHHHHHHHHH
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEIGNLDATL---------ILQRPKLSPYKETIRTNLSEL 199 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I~NiD~TI---------i~q~PKl~p~~~~mr~~La~l 199 (237)
+.|..=++.++.+.+.+.|..|.+++..+ ..+-|....-++++++.|.++
T Consensus 10 g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~~~~~~~~~l~~~l~~l 68 (90)
T PRK00194 10 GKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDISESKKDFAELKEELEEL 68 (90)
T ss_pred cCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEecCCCCCHHHHHHHHHHH
Confidence 34455688999999999999999988654 446665332356666554443
No 118
>PF14516 AAA_35: AAA-like domain
Probab=21.29 E-value=1.7e+02 Score=27.13 Aligned_cols=65 Identities=17% Similarity=0.242 Sum_probs=49.8
Q ss_pred cccCCCCCCccCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCC--CCchhHHHHHHHHHHHhCCCC
Q 026508 138 GQIFPDSDPKWKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRP--KLSPYKETIRTNLSELLGADP 204 (237)
Q Consensus 138 G~~FPdtDp~~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~P--Kl~p~~~~mr~~La~lL~i~~ 204 (237)
|++|--..|+.-|.+| +|..+.+.+++.||..+.+|+.-+.... .+..+...+-..|++.|+++.
T Consensus 31 G~~~~I~apRq~GKTS--ll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~ 97 (331)
T PF14516_consen 31 GSYIRIKAPRQMGKTS--LLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDE 97 (331)
T ss_pred CCEEEEECcccCCHHH--HHHHHHHHHHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCCh
Confidence 5566666777777765 5778899999999999999999875432 244577788899999998873
No 119
>TIGR00188 rnpA ribonuclease P protein component, eubacterial. The yeast mitochondrial RNase P protein component gene RPM2 has no obvious sequence similarity to rnpA, but resembles eukaryotic nuclear RNase P instead.
Probab=21.28 E-value=2.1e+02 Score=22.24 Aligned_cols=44 Identities=23% Similarity=0.237 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHh
Q 026508 154 SVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELL 200 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL 200 (237)
...|+|+++.... .+.+.|+.+++..+....=.+++++.+-+++
T Consensus 61 KR~lRe~~R~~~~---~l~~~d~v~i~r~~~~~~~~~~l~~~l~~l~ 104 (105)
T TIGR00188 61 KRLIREVFRERQE---LLKALDVVVIVRKGFSELTYEAFLKLLLQLF 104 (105)
T ss_pred HHHHHHHHHHhhc---ccCCccEEEEECCCcCcCCHHHHHHHHHHHh
Confidence 5567777776653 3448999999988877766678888877765
No 120
>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen. This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=21.14 E-value=19 Score=27.48 Aligned_cols=47 Identities=13% Similarity=0.231 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCC
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGAD 203 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~ 203 (237)
|.....||++-++. ...|| |++.+|+.-+||..+... +.|+++|.-+
T Consensus 16 NL~~D~fLr~~~~~-~~~G~----Vpl~~i~~F~rmk~l~~~--~~i~~Al~~S 62 (76)
T cd08029 16 NLPTDKFLWTLTGG-SNNGW----VPIKTIASFKRMRRFQPL--EAVVEALRES 62 (76)
T ss_pred hhccCHHHHHHhcc-CCCCc----EehHHHhCchHHHHcCCH--HHHHHHHHhC
Confidence 45566777665543 45688 999999999999988754 7777777643
No 121
>cd04890 ACT_AK-like_1 ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, threonine, methionine, and isoleucine. This CD, includes the first ACT domain of the Escherichia coli (EC) isoenzyme, AKIII (LysC) and the Arabidopsis isoenzyme, asparate kinase 1, both enzymes monofunctional and involved in lysine synthesis, as well as the the first ACT domain of Bacillus subtilis (BS) isoenzyme, AKIII (YclM), and of the Saccharomyces cerevisiae AK (Hom3). Also included are the first ACT domains of the Methylomicrobium alcaliphilum AK, the first enzyme of the ectoine biosynthetic pathway. Members of this CD bel
Probab=20.80 E-value=2.7e+02 Score=18.65 Aligned_cols=42 Identities=14% Similarity=0.310 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhCCCeEEEE-----EEEEEcCCCCCchhHHHHHHH
Q 026508 154 SVFIKEAVRLMDEAGYEIGNL-----DATLILQRPKLSPYKETIRTN 195 (237)
Q Consensus 154 ~~lL~~v~~ll~~~G~~I~Ni-----D~TIi~q~PKl~p~~~~mr~~ 195 (237)
..+..++.+.+.+.|..+.-+ ++++.....+.....+++.+.
T Consensus 14 ~~~~~~if~~l~~~~i~v~~i~t~~~~is~~v~~~~~~~~~~~l~~~ 60 (62)
T cd04890 14 VGFLRKIFEILEKHGISVDLIPTSENSVTLYLDDSLLPKKLKRLLAE 60 (62)
T ss_pred cCHHHHHHHHHHHcCCeEEEEecCCCEEEEEEehhhhhHHHHHHHHh
Confidence 448889999999999988777 678877776665555544443
No 122
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=20.32 E-value=3.4e+02 Score=26.15 Aligned_cols=58 Identities=24% Similarity=0.295 Sum_probs=42.6
Q ss_pred CHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 152 PSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 152 dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
.+..-..++++.+++.|++.+|+|+ |.--|.- =.+.+++.+..++.+.++.|++-.-+
T Consensus 184 ~~~~~~~~ai~~l~~~G~~~v~~dl--i~GlPgq--t~e~~~~tl~~~~~l~~~~is~y~L~ 241 (455)
T TIGR00538 184 QPEEMIFELMNHAREAGFTSINIDL--IYGLPKQ--TKESFAKTLEKVAELNPDRLAVFNYA 241 (455)
T ss_pred CCHHHHHHHHHHHHhcCCCcEEEeE--EeeCCCC--CHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 3445566899999999998777775 4344543 46778888888888889998876543
No 123
>PF14330 DUF4387: Domain of unknown function (DUF4387)
Probab=20.20 E-value=1.5e+02 Score=24.11 Aligned_cols=51 Identities=12% Similarity=0.201 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHH----HHHHHHHHhCCCCCce
Q 026508 157 IKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKET----IRTNLSELLGADPTVV 207 (237)
Q Consensus 157 L~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~----mr~~La~lL~i~~~~V 207 (237)
|.++.+.+|.||-=.-++-.=|+...+..=....+ =++.+|++.++++++|
T Consensus 1 L~dla~vIRSKNAGPf~lT~DI~F~~~e~Y~~vk~s~~l~~~~ia~Ly~i~~~~I 55 (99)
T PF14330_consen 1 LSDLAKVIRSKNAGPFELTFDIIFKDKEAYERVKASGVLTPELIARLYGIDPEDI 55 (99)
T ss_pred CHHHHHHHhccCCCCcEEEEEEEECCHHHHHHHHHcCccCHHHHHHHHCCCHHHE
Confidence 45677888888877777777777766533222222 1567999999999999
No 124
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=20.16 E-value=4.5e+02 Score=24.51 Aligned_cols=60 Identities=25% Similarity=0.179 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCCCceeEEeEc
Q 026508 150 GAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADPTVVNLKAKT 213 (237)
Q Consensus 150 g~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~~~VnIKAtT 213 (237)
...+..-..++++.+++.|+.-+|+|.. .-.|.- =.+.+++.|..++.+.++.|++=.-+
T Consensus 139 R~~s~~~~~~a~~~l~~~g~~~v~~dli--~GlPgq--t~~~~~~tl~~~~~l~~~~i~~y~l~ 198 (375)
T PRK05628 139 RTHTPGRAVAAAREARAAGFEHVNLDLI--YGTPGE--SDDDWRASLDAALEAGVDHVSAYALI 198 (375)
T ss_pred CCCCHHHHHHHHHHHHHcCCCcEEEEEe--ccCCCC--CHHHHHHHHHHHHhcCCCEEEeeeee
Confidence 3345555668899999999875566654 444533 34778888888888889999875444
No 125
>PRK08304 stage V sporulation protein AD; Validated
Probab=20.13 E-value=1.5e+02 Score=28.74 Aligned_cols=68 Identities=16% Similarity=0.192 Sum_probs=40.6
Q ss_pred CCCCCcccCCC--CCCc-----cCCCCHHHHHHHHHHHHHhCCCeEEEEEEEEEcCCCCCchhHHHHHHHHHHHhCCCC
Q 026508 133 GLPDIGQIFPD--SDPK-----WKGAPSSVFIKEAVRLMDEAGYEIGNLDATLILQRPKLSPYKETIRTNLSELLGADP 204 (237)
Q Consensus 133 glGDIG~~FPd--tDp~-----~Kg~dS~~lL~~v~~ll~~~G~~I~NiD~TIi~q~PKl~p~~~~mr~~La~lL~i~~ 204 (237)
+.|-+|.+|.- .|+. |.-+-+....+-+.+.|++.|.+...||..|.+..+. +. ---..+++.||++.
T Consensus 30 ~~gpl~~~fd~~~~d~~~Ge~swEkAeseLa~eAa~~ALekAGI~~~DID~lI~Gdll~---Q~-~sAs~vA~~LGIPa 104 (337)
T PRK08304 30 GEGPLGKYFDKILDDDYCGEKSWEKAERKMMEDAIQQALQKANLKKSDIDYLLAGDLLN---QI-ISANFAARELGIPF 104 (337)
T ss_pred cCCCChhhCCeEecccccCCcCccccHHHHHHHHHHHHHHHcCCCHHHCCEEEEECCCC---Cc-chHHHHHHHhCCcE
Confidence 34556666654 2222 3333333444446666778899999999999987641 11 12334667788753
Done!