Query 010849
Match_columns 499
No_of_seqs 304 out of 1641
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:16:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010849.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010849hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12315 DUF3633: Protein of u 100.0 1.1E-85 2.4E-90 624.1 20.4 209 287-495 1-212 (212)
2 KOG1703 Adaptor protein Enigma 99.9 9.9E-29 2.1E-33 266.2 5.1 336 133-498 132-479 (479)
3 KOG1701 Focal adhesion adaptor 99.8 2.8E-22 6E-27 206.5 0.1 157 97-267 294-462 (468)
4 KOG4577 Transcription factor L 99.7 4.6E-20 9.9E-25 181.7 -3.7 125 133-269 31-155 (383)
5 KOG2272 Focal adhesion protein 99.7 1.4E-18 2.9E-23 168.8 -2.1 162 89-267 24-193 (332)
6 KOG2272 Focal adhesion protein 99.7 2.7E-18 5.9E-23 166.7 -0.3 148 105-267 165-312 (332)
7 KOG1703 Adaptor protein Enigma 99.7 4.1E-18 8.8E-23 184.1 0.3 154 97-264 322-478 (479)
8 KOG1701 Focal adhesion adaptor 99.7 3.7E-18 8.1E-23 176.2 -2.5 123 131-269 270-394 (468)
9 KOG1044 Actin-binding LIM Zn-f 99.5 1.9E-15 4.1E-20 160.8 3.0 123 131-268 129-251 (670)
10 PF00412 LIM: LIM domain; Int 99.2 8.7E-12 1.9E-16 96.3 4.9 57 138-194 1-58 (58)
11 KOG1044 Actin-binding LIM Zn-f 99.1 1.1E-10 2.4E-15 125.0 4.8 111 135-270 16-126 (670)
12 KOG4577 Transcription factor L 98.6 4.1E-09 8.9E-14 104.9 -2.0 103 97-199 52-159 (383)
13 KOG1700 Regulatory protein MLP 98.6 1.7E-08 3.6E-13 97.9 1.0 121 135-269 7-168 (200)
14 PF00412 LIM: LIM domain; Int 98.3 5.3E-07 1.1E-11 69.4 4.0 57 198-267 1-57 (58)
15 smart00132 LIM Zinc-binding do 98.2 1.2E-06 2.6E-11 61.5 3.1 37 137-173 1-38 (39)
16 PF13485 Peptidase_MA_2: Pepti 97.3 0.00049 1.1E-08 59.5 6.2 108 371-493 18-127 (128)
17 KOG0490 Transcription factor, 96.8 0.00017 3.6E-09 70.1 -1.7 115 140-267 1-119 (235)
18 KOG1700 Regulatory protein MLP 96.6 0.00055 1.2E-08 66.6 0.1 62 134-195 107-168 (200)
19 smart00132 LIM Zinc-binding do 96.5 0.0022 4.7E-08 44.7 2.8 37 197-244 1-37 (39)
20 KOG1702 Nebulin repeat protein 96.4 0.00037 8E-09 67.3 -2.3 59 136-194 5-63 (264)
21 PF10026 DUF2268: Predicted Zn 91.7 0.66 1.4E-05 44.8 7.7 45 376-420 63-113 (195)
22 PF01433 Peptidase_M1: Peptida 86.5 0.5 1.1E-05 49.4 2.8 44 377-420 294-339 (390)
23 PF04450 BSP: Peptidase of pla 82.3 1.5 3.3E-05 42.9 3.9 91 375-484 93-184 (205)
24 PF14891 Peptidase_M91: Effect 81.4 1 2.2E-05 42.7 2.3 20 377-396 102-121 (174)
25 PF13699 DUF4157: Domain of un 81.0 0.94 2E-05 37.7 1.7 18 378-395 61-78 (79)
26 PF06114 DUF955: Domain of unk 80.9 2.3 4.9E-05 36.0 4.1 52 365-416 29-86 (122)
27 PF01431 Peptidase_M13: Peptid 80.7 0.67 1.4E-05 44.5 0.8 17 377-393 35-51 (206)
28 PF10263 SprT-like: SprT-like 80.2 1.3 2.8E-05 40.6 2.5 22 373-394 55-76 (157)
29 TIGR02412 pepN_strep_liv amino 80.1 8.3 0.00018 45.3 9.7 42 378-419 287-330 (831)
30 PRK03001 M48 family peptidase; 77.9 0.96 2.1E-05 46.1 1.0 20 372-391 118-137 (283)
31 PRK01345 heat shock protein Ht 76.5 1.2 2.5E-05 46.5 1.2 19 373-391 119-137 (317)
32 PRK02391 heat shock protein Ht 74.7 1.3 2.8E-05 45.8 0.9 21 371-391 126-146 (296)
33 KOG1702 Nebulin repeat protein 74.4 0.57 1.2E-05 45.7 -1.6 97 195-310 4-112 (264)
34 PRK03072 heat shock protein Ht 73.2 1.3 2.8E-05 45.5 0.5 21 370-390 119-139 (288)
35 PF10460 Peptidase_M30: Peptid 72.6 4.8 0.0001 42.9 4.5 44 376-419 137-186 (366)
36 smart00731 SprT SprT homologue 70.8 3.6 7.8E-05 37.8 2.8 22 374-395 55-76 (146)
37 PRK14015 pepN aminopeptidase N 70.5 15 0.00032 43.7 8.3 41 378-419 296-339 (875)
38 PRK02870 heat shock protein Ht 68.6 1.9 4.2E-05 45.3 0.6 18 372-389 167-184 (336)
39 PRK03982 heat shock protein Ht 68.3 1.9 4.1E-05 44.1 0.4 20 372-391 119-138 (288)
40 COG2856 Predicted Zn peptidase 68.1 11 0.00023 37.4 5.6 55 365-419 59-120 (213)
41 PRK04897 heat shock protein Ht 67.5 1.9 4E-05 44.5 0.2 20 371-390 130-149 (298)
42 PRK05457 heat shock protein Ht 67.0 2.3 5E-05 43.6 0.7 21 370-390 126-146 (284)
43 KOG0490 Transcription factor, 66.5 2 4.3E-05 41.6 0.1 94 98-192 16-118 (235)
44 KOG0320 Predicted E3 ubiquitin 65.8 3.5 7.6E-05 39.6 1.7 48 160-207 129-179 (187)
45 PF09768 Peptidase_M76: Peptid 65.4 4.6 0.0001 38.6 2.4 22 374-395 67-88 (173)
46 PRK01265 heat shock protein Ht 65.2 2.5 5.4E-05 44.3 0.6 17 373-389 135-151 (324)
47 PHA02456 zinc metallopeptidase 62.4 4.8 0.0001 35.9 1.7 15 380-394 81-95 (141)
48 PF14835 zf-RING_6: zf-RING of 61.1 8 0.00017 31.2 2.6 46 163-208 8-53 (65)
49 PRK14559 putative protein seri 60.2 7.3 0.00016 44.6 3.2 49 136-206 2-52 (645)
50 PF01447 Peptidase_M4: Thermol 58.4 6.1 0.00013 36.8 1.8 18 374-391 131-148 (150)
51 TIGR02411 leuko_A4_hydro leuko 57.5 8.8 0.00019 43.5 3.2 40 379-418 280-321 (601)
52 cd04270 ZnMc_TACE_like Zinc-de 57.3 6.6 0.00014 39.3 2.0 18 373-390 162-179 (244)
53 PF10083 DUF2321: Uncharacteri 56.7 7.5 0.00016 36.6 2.1 54 182-248 27-82 (158)
54 PRK04351 hypothetical protein; 56.5 9.7 0.00021 35.5 2.8 20 376-395 59-78 (149)
55 PF06524 NOA36: NOA36 protein; 55.7 9.8 0.00021 38.7 2.8 110 105-242 40-179 (314)
56 PF01435 Peptidase_M48: Peptid 54.6 9 0.00019 36.6 2.4 23 373-395 84-106 (226)
57 smart00726 UIM Ubiquitin-inter 54.3 7 0.00015 25.9 1.0 20 77-96 2-21 (26)
58 smart00504 Ubox Modified RING 54.1 15 0.00032 28.1 3.1 44 163-207 2-47 (63)
59 PF02809 UIM: Ubiquitin intera 53.6 7.1 0.00015 23.7 0.9 16 76-91 2-17 (18)
60 PF04298 Zn_peptidase_2: Putat 53.1 12 0.00027 37.2 3.0 29 371-399 82-110 (222)
61 PRK11827 hypothetical protein; 52.4 9.5 0.00021 30.4 1.7 18 287-304 33-50 (60)
62 PF14471 DUF4428: Domain of un 52.3 8.5 0.00018 29.5 1.4 30 236-267 1-30 (51)
63 PF11781 RRN7: RNA polymerase 51.6 9.8 0.00021 27.1 1.5 25 235-265 9-33 (36)
64 KOG1813 Predicted E3 ubiquitin 51.2 8 0.00017 39.9 1.4 46 162-208 241-288 (313)
65 PF02163 Peptidase_M50: Peptid 49.9 15 0.00032 34.7 3.0 20 377-396 6-26 (192)
66 PF01421 Reprolysin: Reprolysi 49.6 17 0.00038 34.6 3.5 24 366-389 119-142 (199)
67 PF10367 Vps39_2: Vacuolar sor 49.3 11 0.00024 31.9 1.8 30 134-163 77-107 (109)
68 KOG3931 Uncharacterized conser 48.8 9.5 0.00021 40.3 1.6 22 373-394 100-121 (484)
69 PRK04860 hypothetical protein; 48.8 19 0.00042 34.0 3.5 28 374-402 59-89 (160)
70 PF13920 zf-C3HC4_3: Zinc fing 48.2 22 0.00048 26.3 3.1 42 164-206 4-48 (50)
71 PF12773 DZR: Double zinc ribb 47.4 22 0.00048 26.3 3.0 11 197-207 31-41 (50)
72 cd06158 S2P-M50_like_1 Unchara 46.1 18 0.00039 34.6 2.9 18 377-394 8-25 (181)
73 smart00235 ZnMc Zinc-dependent 45.8 10 0.00023 33.9 1.2 11 380-390 88-98 (140)
74 PF10463 Peptidase_U49: Peptid 45.8 27 0.00059 34.4 4.2 50 372-421 95-145 (206)
75 cd04267 ZnMc_ADAM_like Zinc-de 45.2 13 0.00028 35.2 1.7 24 366-390 122-145 (192)
76 TIGR02414 pepN_proteo aminopep 44.5 79 0.0017 37.6 8.4 36 378-418 283-325 (863)
77 PF01863 DUF45: Protein of unk 43.6 15 0.00032 35.0 1.9 25 366-390 152-176 (205)
78 PRK14890 putative Zn-ribbon RN 43.5 25 0.00054 28.0 2.8 28 135-171 7-34 (59)
79 cd04268 ZnMc_MMP_like Zinc-dep 43.0 13 0.00029 33.9 1.5 14 377-390 93-106 (165)
80 COG5152 Uncharacterized conser 42.0 9.2 0.0002 37.4 0.2 45 162-207 196-242 (259)
81 PF10367 Vps39_2: Vacuolar sor 42.0 24 0.00051 29.8 2.8 28 164-191 80-108 (109)
82 PF00645 zf-PARP: Poly(ADP-rib 41.5 6.9 0.00015 32.2 -0.6 18 132-149 4-21 (82)
83 KOG3624 M13 family peptidase [ 40.5 13 0.00029 42.5 1.3 15 377-391 517-531 (687)
84 COG4357 Zinc finger domain con 40.2 4.2 9E-05 35.3 -2.1 49 138-186 38-86 (105)
85 cd00203 ZnMc Zinc-dependent me 40.0 19 0.00041 32.8 2.0 16 375-390 93-108 (167)
86 PF00413 Peptidase_M10: Matrix 39.8 19 0.00041 32.4 1.9 17 373-389 100-116 (154)
87 PF04228 Zn_peptidase: Putativ 39.8 23 0.0005 36.6 2.8 21 375-395 167-187 (292)
88 KOG3714 Meprin A metalloprotea 39.7 14 0.0003 40.0 1.1 14 380-393 161-174 (411)
89 PRK14873 primosome assembly pr 39.6 18 0.0004 41.5 2.2 55 338-393 501-558 (665)
90 PF14634 zf-RING_5: zinc-RING 38.8 30 0.00064 25.1 2.5 39 165-203 2-44 (44)
91 cd00162 RING RING-finger (Real 38.7 25 0.00054 24.1 2.0 40 165-204 2-44 (45)
92 COG5504 Predicted Zn-dependent 38.3 39 0.00085 34.4 4.0 39 379-418 141-186 (280)
93 PF14247 DUF4344: Domain of un 38.2 51 0.0011 32.8 4.8 39 377-417 91-129 (220)
94 cd06159 S2P-M50_PDZ_Arch Uncha 38.1 26 0.00056 35.7 2.8 27 370-397 111-138 (263)
95 cd06162 S2P-M50_PDZ_SREBP Ster 37.5 23 0.0005 36.4 2.3 18 377-394 134-151 (277)
96 cd06161 S2P-M50_SpoIVFB SpoIVF 36.9 32 0.00068 33.5 3.1 21 376-396 36-57 (208)
97 PF10235 Cript: Microtubule-as 36.3 23 0.00051 30.4 1.8 36 164-207 46-81 (90)
98 PHA00527 hypothetical protein 36.2 1.3E+02 0.0029 26.7 6.4 47 364-415 64-113 (129)
99 PRK09672 phage exclusion prote 35.9 50 0.0011 34.4 4.4 50 371-420 158-208 (305)
100 PRK04023 DNA polymerase II lar 35.9 40 0.00087 40.4 4.1 52 134-208 625-676 (1121)
101 cd05709 S2P-M50 Site-2 proteas 35.9 26 0.00057 32.8 2.3 20 377-396 7-27 (180)
102 COG1451 Predicted metal-depend 35.8 21 0.00045 35.5 1.6 27 364-390 161-187 (223)
103 COG0501 HtpX Zn-dependent prot 35.3 22 0.00047 35.8 1.7 19 372-390 151-169 (302)
104 TIGR02289 M3_not_pepF oligoend 35.2 46 0.001 37.2 4.4 45 376-420 335-389 (549)
105 PF13688 Reprolysin_5: Metallo 34.9 25 0.00053 33.2 2.0 20 374-393 138-157 (196)
106 cd06164 S2P-M50_SpoIVFB_CBS Sp 34.7 33 0.00072 34.0 2.9 21 376-396 51-72 (227)
107 PF13240 zinc_ribbon_2: zinc-r 34.3 25 0.00054 22.5 1.3 9 138-146 2-10 (23)
108 PF05299 Peptidase_M61: M61 gl 33.6 14 0.0003 33.4 0.0 41 378-418 4-57 (122)
109 cd04281 ZnMc_BMP1_TLD Zinc-dep 33.5 22 0.00047 34.8 1.3 11 380-390 89-99 (200)
110 PF14471 DUF4428: Domain of un 32.7 29 0.00063 26.5 1.6 29 164-193 1-30 (51)
111 COG1645 Uncharacterized Zn-fin 32.4 24 0.00052 32.4 1.3 28 237-271 31-58 (131)
112 cd04279 ZnMc_MMP_like_1 Zinc-d 32.4 26 0.00057 32.0 1.6 16 375-390 101-116 (156)
113 KOG2199 Signal transducing ada 32.3 22 0.00047 38.3 1.2 25 73-97 161-185 (462)
114 COG0308 PepN Aminopeptidase N 32.1 55 0.0012 38.8 4.6 115 379-498 308-466 (859)
115 PF05572 Peptidase_M43: Pregna 31.7 27 0.00059 32.6 1.6 20 374-394 65-84 (154)
116 KOG1280 Uncharacterized conser 31.6 33 0.00071 36.3 2.3 16 228-243 73-88 (381)
117 PF06689 zf-C4_ClpX: ClpX C4-t 31.6 38 0.00082 24.6 2.0 32 236-267 3-34 (41)
118 PRK14559 putative protein seri 31.6 40 0.00088 38.7 3.2 37 164-207 3-39 (645)
119 PF13574 Reprolysin_2: Metallo 31.5 28 0.0006 32.9 1.7 18 378-395 111-128 (173)
120 cd06461 M2_ACE Peptidase famil 31.5 50 0.0011 36.6 3.8 33 381-414 250-290 (477)
121 cd04327 ZnMc_MMP_like_3 Zinc-d 31.4 31 0.00068 33.1 2.0 16 377-392 91-106 (198)
122 PF08394 Arc_trans_TRASH: Arch 31.4 23 0.0005 25.5 0.8 22 138-159 1-23 (37)
123 COG4784 Putative Zn-dependent 31.2 66 0.0014 34.3 4.4 107 367-497 108-220 (479)
124 COG2738 Predicted Zn-dependent 30.8 28 0.00061 34.2 1.5 28 370-397 84-111 (226)
125 PLN03208 E3 ubiquitin-protein 30.3 48 0.001 32.4 3.1 30 162-192 18-47 (193)
126 PF10391 DNA_pol_lambd_f: Fing 30.3 53 0.0011 25.2 2.7 27 466-494 6-32 (52)
127 cd04282 ZnMc_meprin Zinc-depen 30.2 26 0.00056 35.1 1.3 12 379-390 121-132 (230)
128 TIGR03826 YvyF flagellar opero 29.9 26 0.00056 32.4 1.1 36 236-286 5-40 (137)
129 COG2191 Formylmethanofuran deh 29.8 21 0.00047 35.0 0.6 18 176-193 186-203 (206)
130 cd04269 ZnMc_adamalysin_II_lik 29.8 52 0.0011 31.1 3.2 16 375-390 128-143 (194)
131 cd06160 S2P-M50_like_2 Unchara 29.7 50 0.0011 31.7 3.1 22 376-397 39-61 (183)
132 PF01258 zf-dskA_traR: Prokary 29.7 10 0.00022 26.6 -1.2 28 165-192 6-33 (36)
133 COG2835 Uncharacterized conser 29.4 40 0.00086 26.9 1.9 16 288-303 34-49 (60)
134 PRK00420 hypothetical protein; 29.3 28 0.0006 31.1 1.2 30 237-272 26-55 (112)
135 COG1645 Uncharacterized Zn-fin 28.8 29 0.00063 31.8 1.2 21 165-190 31-51 (131)
136 PF13834 DUF4193: Domain of un 28.7 18 0.00039 31.6 -0.1 30 234-264 70-99 (99)
137 COG2888 Predicted Zn-ribbon RN 28.7 51 0.0011 26.3 2.4 29 135-172 9-37 (61)
138 cd04283 ZnMc_hatching_enzyme Z 28.3 31 0.00067 33.2 1.4 12 379-390 78-89 (182)
139 KOG3314 Ku70-binding protein [ 28.0 35 0.00075 32.6 1.6 20 375-394 88-107 (194)
140 TIGR00181 pepF oligoendopeptid 27.6 30 0.00065 38.8 1.4 17 375-391 375-391 (591)
141 cd04272 ZnMc_salivary_gland_MP 27.6 37 0.0008 33.1 1.9 15 376-390 143-157 (220)
142 PF01400 Astacin: Astacin (Pep 27.3 36 0.00077 32.7 1.6 13 378-390 79-91 (191)
143 COG4783 Putative Zn-dependent 27.0 36 0.00079 37.5 1.8 18 376-393 128-145 (484)
144 PRK14873 primosome assembly pr 26.7 38 0.00082 39.0 2.0 58 234-310 410-468 (665)
145 PF13583 Reprolysin_4: Metallo 26.5 34 0.00074 33.3 1.4 15 380-394 139-153 (206)
146 KOG4739 Uncharacterized protei 26.5 43 0.00092 33.7 2.0 34 174-207 15-49 (233)
147 PF06677 Auto_anti-p27: Sjogre 26.3 44 0.00094 24.6 1.5 21 237-263 20-40 (41)
148 PF14446 Prok-RING_1: Prokaryo 26.0 70 0.0015 25.0 2.7 12 135-146 5-16 (54)
149 PF08219 TOM13: Outer membrane 25.9 47 0.001 27.7 1.8 23 375-398 49-71 (77)
150 COG1381 RecO Recombinational D 25.9 64 0.0014 32.4 3.2 31 232-264 152-182 (251)
151 cd06459 M3B_Oligoendopeptidase 25.1 74 0.0016 33.7 3.7 38 376-413 220-260 (427)
152 PF07607 DUF1570: Protein of u 25.0 80 0.0017 28.8 3.4 33 380-412 3-39 (128)
153 PF12674 Zn_ribbon_2: Putative 24.9 34 0.00074 28.7 0.9 29 164-192 2-35 (81)
154 PF13582 Reprolysin_3: Metallo 24.8 37 0.0008 29.4 1.2 12 379-390 108-119 (124)
155 PF01432 Peptidase_M3: Peptida 24.7 1.5E+02 0.0033 32.0 6.1 18 377-394 241-258 (458)
156 cd06163 S2P-M50_PDZ_RseP-like 23.3 59 0.0013 31.2 2.3 21 376-396 7-28 (182)
157 KOG2932 E3 ubiquitin ligase in 23.2 39 0.00084 35.3 1.1 42 165-206 93-134 (389)
158 PRK14714 DNA polymerase II lar 23.1 90 0.002 38.5 4.2 51 235-291 693-743 (1337)
159 cd04278 ZnMc_MMP Zinc-dependen 22.8 40 0.00087 30.9 1.0 19 374-393 103-121 (157)
160 cd02249 ZZ Zinc finger, ZZ typ 22.7 69 0.0015 23.5 2.1 11 182-192 22-32 (46)
161 PF13203 DUF2201_N: Putative m 22.6 57 0.0012 33.1 2.2 23 371-393 53-75 (292)
162 PF13248 zf-ribbon_3: zinc-rib 22.6 53 0.0011 21.4 1.3 9 137-145 4-12 (26)
163 COG2191 Formylmethanofuran deh 22.5 36 0.00077 33.5 0.6 31 235-267 173-203 (206)
164 PF13923 zf-C3HC4_2: Zinc fing 22.5 60 0.0013 22.7 1.7 37 165-201 1-39 (39)
165 cd04280 ZnMc_astacin_like Zinc 22.4 43 0.00094 31.8 1.2 10 380-389 76-85 (180)
166 TIGR00595 priA primosomal prot 22.1 61 0.0013 36.0 2.5 27 367-393 374-401 (505)
167 KOG1046 Puromycin-sensitive am 21.8 1.7E+02 0.0037 34.9 6.2 39 375-418 321-366 (882)
168 PF09471 Peptidase_M64: IgA Pe 21.3 50 0.0011 33.7 1.4 19 377-395 215-233 (264)
169 cd06258 Peptidase_M3_like The 21.2 1.5E+02 0.0033 30.8 5.1 37 376-412 152-196 (365)
170 PRK04439 S-adenosylmethionine 21.0 86 0.0019 33.9 3.1 22 380-402 104-125 (399)
171 PF09943 DUF2175: Uncharacteri 20.8 25 0.00054 30.9 -0.7 28 137-164 4-32 (101)
172 KOG3579 Predicted E3 ubiquitin 20.7 46 0.001 34.4 1.0 29 138-166 271-299 (352)
173 smart00291 ZnF_ZZ Zinc-binding 20.4 86 0.0019 22.9 2.2 11 182-192 26-36 (44)
174 KOG0978 E3 ubiquitin ligase in 20.3 38 0.00081 39.1 0.3 27 183-209 663-692 (698)
No 1
>PF12315 DUF3633: Protein of unknown function (DUF3633); InterPro: IPR022087 This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with PF00412 from PFAM.
Probab=100.00 E-value=1.1e-85 Score=624.07 Aligned_cols=209 Identities=74% Similarity=1.172 Sum_probs=198.1
Q ss_pred hcccccccccccccccHHHHHHHHhccccCCCCCCcccceeecccceeeeeeccccC-CCCeeeeeeccccccccceeEE
Q 010849 287 GMNMKLDQQIPMLLVERQALNEAIVGEKNGYHHMPETRGLCLSEEQTVTSILRRPRI-GGNRLVGMRTQPQKLTRKCEVT 365 (499)
Q Consensus 287 g~~m~~~~~~p~~lv~~~~ln~a~~~e~~g~~~~~~trglclse~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~r~~~v~ 365 (499)
+|||||+|+|||+|||++|||+|+++||+|+||+|+||||||||||||+||.|+|++ +++++++|.|+|++++|+|+||
T Consensus 1 ~lnmki~q~~PllLVe~~aLN~a~~~Ek~~~~~~~~tRGLclseeq~v~sv~~~p~~~~~~~~~~~~~e~~~~~~~~eV~ 80 (212)
T PF12315_consen 1 GLNMKIEQEIPLLLVERQALNEAEEGEKIGHHHMPETRGLCLSEEQTVTSVLRRPRMGPGNQLIDMSTEPQRLTRGCEVT 80 (212)
T ss_pred CCCCcccCCCCeEEecHHHHHHHHhhccCCCCCCeeeeeeeeeeeEEEEEEEecCCcCCCCccceeeecceeeccceeEE
Confidence 689999999999999999999999999999999999999999999999999999999 5779999999999999999999
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhhcccCCCCCCCCC--CCCCCCCCCCCCCC
Q 010849 366 AILVLYGLPRLLTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPS--TSSASTSSSSSKKG 443 (499)
Q Consensus 366 ~Ilvl~gLPrl~~g~ilAHE~mHa~l~l~g~~~l~~~veEG~Cq~~a~~wl~~~~~~~~~~~~~--~~~~~~~~~~~~~g 443 (499)
+|||||||||++||||||||||||||||+||++|+++|||||||||||+||++|++++..+.++ ++++++++++||||
T Consensus 81 ~Ilvl~GLPrll~gsiLAHE~mHa~Lrl~g~~~L~~~vEEGiCqvla~~wL~~~~~~~~~~~~~~s~~~s~~~~~~skkg 160 (212)
T PF12315_consen 81 AILVLYGLPRLLTGSILAHELMHAWLRLNGFPNLSPEVEEGICQVLAYLWLESELASGSGSSSSSSSSSSSSASSSSKKG 160 (212)
T ss_pred EEEEECCCCHHHHhhHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHHHHHhhhhhcccCCcccccCCCCCCcccccccc
Confidence 9999999999999999999999999999999999999999999999999999999987664442 23345666778999
Q ss_pred CchHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHhCHHHHHHHHHhhC
Q 010849 444 GKSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKYGLRRTLEHIRLTG 495 (499)
Q Consensus 444 ~~~~~e~~l~~~~~~qi~~d~s~vYGdGfR~~~~a~~~~gl~~~l~~i~~~g 495 (499)
++++||+||++||+||||+|+|||||||||+|++||++|||++||+|||+||
T Consensus 161 ~~s~~E~kL~~f~~~qIe~D~SpvYGdGFRaa~~av~~~GL~~tLdhir~tg 212 (212)
T PF12315_consen 161 AKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANEAVEKYGLRRTLDHIRRTG 212 (212)
T ss_pred cccHHHHHHHHHHHHHhccCCCcccchHHHHHHHHHHHhCHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999998
No 2
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.95 E-value=9.9e-29 Score=266.23 Aligned_cols=336 Identities=41% Similarity=0.664 Sum_probs=284.6
Q ss_pred CCCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhh-hccccccccCCccCCCCcc
Q 010849 133 RSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKE-LTHPKCEVCHQYIPTNGAG 211 (499)
Q Consensus 133 ~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~-~f~pkC~~C~~~I~~~~~g 211 (499)
....+|.+|+..|..+..+ ||.|..|..++.+ +...||.. ...+.|.+|...|..+..+
T Consensus 132 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~p~~~----------~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 191 (479)
T KOG1703|consen 132 PLDSICGGCNSAIEHGRSV----------CFQCKRCSEPLSG----------FPKPSYHESGRSKNEDVEEASSPSSRAG 191 (479)
T ss_pred cccccccCCCcccccccch----------hhhhcccccccCC----------cccccccccccccccccccccccccccc
Confidence 3457899999999766655 9999999988822 23344444 3677899999999988888
Q ss_pred eEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHhhcccc
Q 010849 212 LIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYEGMNMK 291 (499)
Q Consensus 212 ~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~g~~m~ 291 (499)
.+.++.++||.+.||+.|.+..+..|+.|.+.++++..+..+.+++.+|.+|...+++++..+||++..+..++....|+
T Consensus 192 ~~~~~~~~~~~~~~~~~~e~~~tp~~~~~~r~e~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~p~~~~~~~~~~~~~~~ 271 (479)
T KOG1703|consen 192 LILSRSHPFWKQKYCPSHENDGTPKCCSCERLEPLDTRYVELADGRALCLECMGSASMDSPECQPLVSAPRPASEGLHMK 271 (479)
T ss_pred ccccccchhhhhcccccccCCCCCCcccccccccccccceecccchhhhhhccCCcccCCCccCcceecccccccccccc
Confidence 89999999999999999999999999999998878999999999999999999999999999999999999999999999
Q ss_pred cccccccccccHHHHHHHHhccccCCCCCCcccceeecccceeeeeeccccCCCCeeeeeeccccccccceeEEEEEEEc
Q 010849 292 LDQQIPMLLVERQALNEAIVGEKNGYHHMPETRGLCLSEEQTVTSILRRPRIGGNRLVGMRTQPQKLTRKCEVTAILVLY 371 (499)
Q Consensus 292 ~~~~~p~~lv~~~~ln~a~~~e~~g~~~~~~trglclse~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~v~~Ilvl~ 371 (499)
+.+..+++++++++++.+.+.++...++. .++++|++++++|+++ ..++++.++..+....|+|.+|++++
T Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~p~c~~c~~~i~~~--------~~i~~~~~~~h~~~~~c~~~~~~~~~ 342 (479)
T KOG1703|consen 272 VEKELPLLLVESEALKKLREEEKPAEYHN-VTRPLCLSCNQKIRSV--------KVIVALGKEWHPEHFSCEVCAIVILD 342 (479)
T ss_pred cccccchhhcccccccccccccccccccc-cccccccccccCcccc--------eeEeeccccccccceeeccccccccC
Confidence 99999999999999999988877665443 8999999999999775 34668888888888899999999999
Q ss_pred CCchhHHHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhhcccCCCCCCCC-CCCCC------CCCCCCCCCCC
Q 010849 372 GLPRLLTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMP-STSSA------STSSSSSKKGG 444 (499)
Q Consensus 372 gLPrl~~g~ilAHE~mHa~l~l~g~~~l~~~veEG~Cq~~a~~wl~~~~~~~~~~~~-~~~~~------~~~~~~~~~g~ 444 (499)
|+|+...|.|++||+||+|++.++++.+.+.+||+||++ +.+|+...-.-..-... ...+. .......+++.
T Consensus 343 ~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~-~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~ 421 (479)
T KOG1703|consen 343 GGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCAL-GRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLF 421 (479)
T ss_pred CCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhc-cCeechhceeeecccCCCCCCcccccCCccchhhhHhhhc
Confidence 999999999999999999999999999999999999999 99999998654311111 11111 11112223433
Q ss_pred --chHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHh--CHHHHHHHHHhhCCCC
Q 010849 445 --KSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKY--GLRRTLEHIRLTGNFP 498 (499)
Q Consensus 445 --~~~~e~~l~~~~~~qi~~d~s~vYGdGfR~~~~a~~~~--gl~~~l~~i~~~g~~p 498 (499)
+..++++.++|+.++|+.|.+++||+|||.++.+++.. ++..+++++.....|+
T Consensus 422 ~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~~ 479 (479)
T KOG1703|consen 422 TTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHFP 479 (479)
T ss_pred cccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCCC
Confidence 77889999999999999999999999999999998777 7999998888776654
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.84 E-value=2.8e-22 Score=206.45 Aligned_cols=157 Identities=24% Similarity=0.432 Sum_probs=131.8
Q ss_pred CCCccccc--chHHHHHHhh--cccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCC
Q 010849 97 NGQRWRSN--TDEDYAWALQ--DSQLNPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPI 172 (499)
Q Consensus 97 ~~~~wh~e--~ce~c~r~Lq--~~l~~~~~~pyC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L 172 (499)
.++.+|.+ +|.+|.+.|. .+++.+. +|||+.||.. ...+|..|++.|. .++|.|+|+.||+.||+|..|++.|
T Consensus 294 m~~~fHv~CFtC~~C~r~L~Gq~FY~v~~-k~~CE~cyq~-tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~l 370 (468)
T KOG1701|consen 294 MDQLFHVQCFTCRTCRRQLAGQSFYQVDG-KPYCEGCYQD-TLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCL 370 (468)
T ss_pred hhhhhcccceehHhhhhhhccccccccCC-cccchHHHHH-HHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEecccc
Confidence 34468988 9999999994 6667776 9999999854 4678999999996 6899999999999999999999999
Q ss_pred CCCceEee-CCcccchhhhhhhccccccccCCccCCCC----cceEEeeccCccccccCCCCcCCCCcccCCCCCcccc-
Q 010849 173 TEHEFSLS-GKDPYHKSCFKELTHPKCEVCHQYIPTNG----AGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESW- 246 (499)
Q Consensus 173 ~~~~F~~~-dg~~YC~~CY~~~f~pkC~~C~~~I~~~~----~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~- 246 (499)
++..|.+. ++++||..||+++|+|+|++|+++|...+ .-.|....+.| |.+|++|..|+.++++
T Consensus 371 dgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~f----------Hv~CY~CEDCg~~LS~e 440 (468)
T KOG1701|consen 371 DGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDF----------HVNCYKCEDCGLLLSSE 440 (468)
T ss_pred CCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccc----------cccceehhhcCcccccc
Confidence 99988875 88999999999999999999999998863 33455555443 9999999999998873
Q ss_pred --CCceeEecCCccccchhhhhh
Q 010849 247 --NTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 247 --g~~~~~l~dGr~~C~~C~~sa 267 (499)
+...|.++ |.++|+.|+...
T Consensus 441 ~e~qgCyPld-~HllCk~Ch~~R 462 (468)
T KOG1701|consen 441 EEGQGCYPLD-GHLLCKTCHLKR 462 (468)
T ss_pred CCCCcceecc-Cceeechhhhhh
Confidence 23456665 799999998554
No 4
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.74 E-value=4.6e-20 Score=181.65 Aligned_cols=125 Identities=25% Similarity=0.513 Sum_probs=109.8
Q ss_pred CCCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCCCCcce
Q 010849 133 RSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGL 212 (499)
Q Consensus 133 ~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~g~ 212 (499)
.-.++|++|++.|.+.-++.+++++||..|++|+.|+.+|.+ .+|.+++.+||+.+|.++|+.||..|...|++..
T Consensus 31 ~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtq--- 106 (383)
T KOG4577|consen 31 VEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQ--- 106 (383)
T ss_pred cccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHH---
Confidence 356899999999986667889999999999999999999988 5668899999999999999999999999999852
Q ss_pred EEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhhcc
Q 010849 213 IEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIM 269 (499)
Q Consensus 213 I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~ 269 (499)
+.-+++.| .| |..||.|..|+|.+..|++||.+.|++++|+..|+++-.
T Consensus 107 VVRkAqd~---VY-----Hl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~ 155 (383)
T KOG4577|consen 107 VVRKAQDF---VY-----HLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ 155 (383)
T ss_pred HHHHhhcc---ee-----ehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh
Confidence 22233333 34 999999999999999999999999999999999999865
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.69 E-value=1.4e-18 Score=168.81 Aligned_cols=162 Identities=23% Similarity=0.499 Sum_probs=134.2
Q ss_pred chhhhcCcCCCccccc--chHHHHHHhhcccCCCC-CCCCCCCCCCCCCCCCCCCCCCccCCCceEeecCccccCCCccc
Q 010849 89 LAEDLKRPNGQRWRSN--TDEDYAWALQDSQLNPS-FPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRC 165 (499)
Q Consensus 89 L~Ee~kk~~~~~wh~e--~ce~c~r~Lq~~l~~~~-~~pyC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C 165 (499)
++|.-...++..||+. .|.||-+++++.+..+- ++.||+.|+...++|-|+.|++.|. |++|.+++.+|||.||+|
T Consensus 24 ~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFii-GrVikamnnSwHp~CF~C 102 (332)
T KOG2272|consen 24 PAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFII-GRVIKAMNNSWHPACFRC 102 (332)
T ss_pred chhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchh-hHHHHhhccccCcccchh
Confidence 4555566678899988 89999999988765432 4899999999999999999999995 999999999999999999
Q ss_pred CCCCCCCCCCceEeeCCcccchhhhhhhc-----cccccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCC
Q 010849 166 RSCGYPITEHEFSLSGKDPYHKSCFKELT-----HPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSC 240 (499)
Q Consensus 166 ~~C~~~L~~~~F~~~dg~~YC~~CY~~~f-----~pkC~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C 240 (499)
..|++.|.+..|+-..|..+|..|..+.- .-.|..|+..|... .+.++..| | |+..|+|..|
T Consensus 103 d~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~---~l~fr~d~-----y-----H~yHFkCt~C 169 (332)
T KOG2272|consen 103 DLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ---PLTFRGDP-----Y-----HPYHFKCTTC 169 (332)
T ss_pred HHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc---cccccCCC-----C-----Cccceecccc
Confidence 99999999999999999999999987732 23599999998773 57777655 3 7777999999
Q ss_pred CCccccCCceeEecCCccccchhhhhh
Q 010849 241 ERLESWNTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 241 ~r~~~~g~~~~~l~dGr~~C~~C~~sa 267 (499)
++.+..+.+ .++ |.+||+.|++++
T Consensus 170 ~keL~sdaR--evk-~eLyClrChD~m 193 (332)
T KOG2272|consen 170 GKELTSDAR--EVK-GELYCLRCHDKM 193 (332)
T ss_pred cccccchhh--hhc-cceecccccccc
Confidence 997654443 334 699999998765
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.69 E-value=2.7e-18 Score=166.72 Aligned_cols=148 Identities=16% Similarity=0.363 Sum_probs=124.7
Q ss_pred chHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcc
Q 010849 105 TDEDYAWALQDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDP 184 (499)
Q Consensus 105 ~ce~c~r~Lq~~l~~~~~~pyC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~ 184 (499)
.|..|.+.|......-.+..||..|+...+.++|+.|.++|. ++++.++|+.||.+.|+|+.|.+|+-+.+.+.+.|.+
T Consensus 165 kCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGla 243 (332)
T KOG2272|consen 165 KCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLA 243 (332)
T ss_pred ecccccccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCch
Confidence 666666666543322223669999999999999999999995 8999999999999999999999999999999999999
Q ss_pred cchhhhhhhccccccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhh
Q 010849 185 YHKSCFKELTHPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECM 264 (499)
Q Consensus 185 YC~~CY~~~f~pkC~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~ 264 (499)
||+.+|.++|+..|..|+..|.+. ++.+. ++.| -+.||.|+.|.+.+..-++++.++ -.|+|+.||
T Consensus 244 YCe~h~~qLfG~~CF~C~~~i~G~---vv~al-----~Kaw-----Cv~cf~Cs~Cdkkl~~K~Kf~E~D-mkP~CKkCy 309 (332)
T KOG2272|consen 244 YCETHYHQLFGNLCFICNRVIGGD---VVSAL-----NKAW-----CVECFSCSTCDKKLTQKNKFYEFD-MKPVCKKCY 309 (332)
T ss_pred hHHHHHHHHhhhhheecCCccCcc---HHHHh-----hhhh-----ccccccccccccccccccceeeec-cchHHHHHH
Confidence 999999999999999999999984 34443 3344 566799999999998888877766 599999999
Q ss_pred hhh
Q 010849 265 ESA 267 (499)
Q Consensus 265 ~sa 267 (499)
+..
T Consensus 310 ~rf 312 (332)
T KOG2272|consen 310 DRF 312 (332)
T ss_pred hhc
Confidence 755
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.68 E-value=4.1e-18 Score=184.11 Aligned_cols=154 Identities=23% Similarity=0.453 Sum_probs=131.1
Q ss_pred CCCccccc--chHHHHHHhhcccC-CCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCC
Q 010849 97 NGQRWRSN--TDEDYAWALQDSQL-NPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPIT 173 (499)
Q Consensus 97 ~~~~wh~e--~ce~c~r~Lq~~l~-~~~~~pyC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~ 173 (499)
.+..||.+ .|+.|+..+..... ...+.+||..|+.+...+.|.+|+++|. ++.|.+++..||++||+|..|++++.
T Consensus 322 ~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~ 400 (479)
T KOG1703|consen 322 LGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLK 400 (479)
T ss_pred ccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchH-HhHhhhccCeechhceeeecccCCCC
Confidence 45589988 89999988876544 2335889999999999999999999995 89999999999999999999999999
Q ss_pred CCceEeeCCcccchhhhhhhccccccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEe
Q 010849 174 EHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSL 253 (499)
Q Consensus 174 ~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l 253 (499)
...|+..++.+||..||++++.++|..|.++|..-. -.|+....+ ||..||+|..|.+ .+.++.|..
T Consensus 401 ~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~-~~ie~~~~~----------~h~~~F~c~~c~~--~l~~~~~~~ 467 (479)
T KOG1703|consen 401 NSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS-RQIEADGSP----------FHGDCFRCANCMK--KLTKKTFFE 467 (479)
T ss_pred CCcccccCCccchhhhHhhhccccchhccchhHhhh-hHhhccCcc----------ccccceehhhhhc--cccCCceee
Confidence 999999999999999999999999999999987432 234554443 2999999999999 456667777
Q ss_pred cCCccccchhh
Q 010849 254 EDGRSLCLECM 264 (499)
Q Consensus 254 ~dGr~~C~~C~ 264 (499)
..++++|..|.
T Consensus 468 ~~~~p~c~~~~ 478 (479)
T KOG1703|consen 468 TLDKPLCQKHF 478 (479)
T ss_pred cCCccccccCC
Confidence 77899999985
No 8
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.66 E-value=3.7e-18 Score=176.17 Aligned_cols=123 Identities=21% Similarity=0.545 Sum_probs=102.6
Q ss_pred CCCCCCCCCCCCCccC-CCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCCCC
Q 010849 131 YPRSYKVCGGCNCDIG-YGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNG 209 (499)
Q Consensus 131 ~~~~~~~C~~C~k~I~-~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~ 209 (499)
...++.+|.+|+|.|. ++..+.||++.||..||+|..|++.|.+..||..++++||+.||.+ ...||.+|++.|...
T Consensus 270 ~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~-tlekC~~Cg~~I~d~- 347 (468)
T KOG1701|consen 270 VEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQD-TLEKCNKCGEPIMDR- 347 (468)
T ss_pred hhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHH-HHHHHhhhhhHHHHH-
Confidence 3345569999999994 3456899999999999999999999999999999999999999988 788999999999973
Q ss_pred cceEEeeccCccccccCCCCcCCCCcccCCCCCccccCC-ceeEecCCccccchhhhhhcc
Q 010849 210 AGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNT-RYYSLEDGRSLCLECMESAIM 269 (499)
Q Consensus 210 ~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~-~~~~l~dGr~~C~~C~~sav~ 269 (499)
++.+. |+.| |++||+|.+|.+ .+++ .|....++++||..||.....
T Consensus 348 --iLrA~-----Gkay-----Hp~CF~Cv~C~r--~ldgipFtvd~~n~v~Cv~dfh~kfA 394 (468)
T KOG1701|consen 348 --ILRAL-----GKAY-----HPGCFTCVVCAR--CLDGIPFTVDSQNNVYCVPDFHKKFA 394 (468)
T ss_pred --HHHhc-----cccc-----CCCceEEEEecc--ccCCccccccCCCceeeehhhhhhcC
Confidence 44443 4555 999999999999 4455 555556889999999866544
No 9
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.54 E-value=1.9e-15 Score=160.82 Aligned_cols=123 Identities=21% Similarity=0.506 Sum_probs=106.7
Q ss_pred CCCCCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCCCCc
Q 010849 131 YPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGA 210 (499)
Q Consensus 131 ~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~ 210 (499)
...+...|++|++.|..|+.+.++++.||..||+|..|+..|.+ ++..+++.|||..||.+.|+.+|..|.++|.+.
T Consensus 129 ~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgk-- 205 (670)
T KOG1044|consen 129 ESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGK-- 205 (670)
T ss_pred cccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhh--
Confidence 33467889999999999999999999999999999999999987 899999999999999999999999999999984
Q ss_pred ceEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhhc
Q 010849 211 GLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAI 268 (499)
Q Consensus 211 g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav 268 (499)
++++.. .|||+.|-+|..|+.+|..|.+-|. ....++.+.|-....
T Consensus 206 -vLqag~----------kh~HPtCARCsRCgqmF~eGEEMYl-QGs~iWHP~C~qa~~ 251 (670)
T KOG1044|consen 206 -VLQAGD----------KHFHPTCARCSRCGQMFGEGEEMYL-QGSEIWHPDCKQATK 251 (670)
T ss_pred -hhhccC----------cccCcchhhhhhhccccccchheee-ccccccCCccccccc
Confidence 344432 2679999999999999998877664 445899999975543
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.24 E-value=8.7e-12 Score=96.25 Aligned_cols=57 Identities=32% Similarity=0.865 Sum_probs=52.5
Q ss_pred CCCCCCccCCCceE-eecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhc
Q 010849 138 CGGCNCDIGYGNYL-GCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT 194 (499)
Q Consensus 138 C~~C~k~I~~g~~l-~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f 194 (499)
|.+|+++|..+..+ .++|+.||++||+|..|+++|.+..|+..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 88999999766655 7999999999999999999999888999999999999999876
No 11
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.06 E-value=1.1e-10 Score=124.97 Aligned_cols=111 Identities=21% Similarity=0.513 Sum_probs=91.9
Q ss_pred CCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCCCCcceEE
Q 010849 135 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIE 214 (499)
Q Consensus 135 ~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~g~I~ 214 (499)
...|..|.+... |+++.+.++.||..||+|..|+..|....||.+++. +++++ ..|..+|.+. .+.
T Consensus 16 ~i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~ge---vvs 81 (670)
T KOG1044|consen 16 GIKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGE---VVS 81 (670)
T ss_pred ceehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccce---eEe
Confidence 467999999995 999999999999999999999999999999988765 44555 7788888874 354
Q ss_pred eeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhhccC
Q 010849 215 YRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMD 270 (499)
Q Consensus 215 ~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~d 270 (499)
.. |++| |++||.|+.|+.+++.|++ +.+.....+|..|...+-..
T Consensus 82 a~-----gkty-----h~~cf~cs~ck~pf~~g~~-vt~~gk~~~c~~c~~~~~~~ 126 (670)
T KOG1044|consen 82 TL-----GKTY-----HPKCFSCSTCKSPFKSGDK-VTFSGKECLCQTCSQPMPVS 126 (670)
T ss_pred cc-----ccee-----ccccceecccCCCCCCCCe-eeecchhhhhhhhcCcccCC
Confidence 44 5566 9999999999999998887 56666789999997666543
No 12
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.60 E-value=4.1e-09 Score=104.88 Aligned_cols=103 Identities=19% Similarity=0.368 Sum_probs=86.9
Q ss_pred CCCccccc--chHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEe-ecCccccCCCcccCCCCCCCC
Q 010849 97 NGQRWRSN--TDEDYAWALQDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLG-CMGTYFHPNCFRCRSCGYPIT 173 (499)
Q Consensus 97 ~~~~wh~e--~ce~c~r~Lq~~l~~~~~~pyC~~~y~~~~~~~C~~C~k~I~~g~~l~-algk~wHp~CF~C~~C~~~L~ 173 (499)
.++.||.. .|..|.-.|.+.-+...+.-||..+|+..+.-+|..|++.|.+.++|. +.+..||..||.|..|++.|.
T Consensus 52 l~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~ 131 (383)
T KOG4577|consen 52 LDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLA 131 (383)
T ss_pred HhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccc
Confidence 35689988 899999999877666555889999999999999999999998777765 889999999999999999998
Q ss_pred -CCceEe-eCCcccchhhhhhhcccccc
Q 010849 174 -EHEFSL-SGKDPYHKSCFKELTHPKCE 199 (499)
Q Consensus 174 -~~~F~~-~dg~~YC~~CY~~~f~pkC~ 199 (499)
+.+|+. .|.++.|+.+|...-..-|.
T Consensus 132 TGdEFYLmeD~rLvCK~DYE~Ak~k~~~ 159 (383)
T KOG4577|consen 132 TGDEFYLMEDARLVCKDDYETAKQKHCN 159 (383)
T ss_pred cCCeeEEeccceeehhhhHHHHHhcccc
Confidence 557775 48899999999885444443
No 13
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.56 E-value=1.7e-08 Score=97.91 Aligned_cols=121 Identities=22% Similarity=0.461 Sum_probs=91.0
Q ss_pred CCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhcccc-----------------
Q 010849 135 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK----------------- 197 (499)
Q Consensus 135 ~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pk----------------- 197 (499)
...|.+|++.+..-+.+...|..||+.||.|..|.+.|....+..+++.+||+.||..+++|+
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 458999999997666677889999999999999999999888999999999999887766554
Q ss_pred ------------------------ccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEe
Q 010849 198 ------------------------CEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSL 253 (499)
Q Consensus 198 ------------------------C~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l 253 (499)
|..|.+++.+.+. .+ .. +.. ||..||+|..|+..+. ..-+..
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek-~~-~~-----~~~-----~hk~cfrc~~~~~~ls--~~~~~~ 152 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEK-VT-GN-----GLE-----FHKSCFRCTHCGKKLS--PKNYAA 152 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHH-Hh-hh-----hhh-----hhhhheeecccccccC--Ccchhh
Confidence 6666665554321 11 11 111 3999999999999654 444666
Q ss_pred cCCccccchhhhhhcc
Q 010849 254 EDGRSLCLECMESAIM 269 (499)
Q Consensus 254 ~dGr~~C~~C~~sav~ 269 (499)
.+|.++|...+-....
T Consensus 153 ~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 153 LEGVLYCKHHFAQLFK 168 (200)
T ss_pred cCCccccchhhheeec
Confidence 6778888777655544
No 14
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=98.33 E-value=5.3e-07 Score=69.42 Aligned_cols=57 Identities=19% Similarity=0.415 Sum_probs=41.8
Q ss_pred ccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhh
Q 010849 198 CEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 198 C~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sa 267 (499)
|..|+++|.+.. ..+.+.. +. ||+.||+|..|++.+. +..+...||++||..||...
T Consensus 1 C~~C~~~I~~~~-~~~~~~~-----~~-----~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMG-----KF-----WHPECFKCSKCGKPLN--DGDFYEKDGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSS-EEEEETT-----EE-----EETTTSBETTTTCBTT--TSSEEEETTEEEEHHHHHHH
T ss_pred CCCCCCCccCcE-EEEEeCC-----cE-----EEccccccCCCCCccC--CCeeEeECCEEECHHHHhhh
Confidence 789999999764 1223432 22 3999999999999654 44366777899999999754
No 15
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.20 E-value=1.2e-06 Score=61.51 Aligned_cols=37 Identities=41% Similarity=1.032 Sum_probs=33.4
Q ss_pred CCCCCCCccCCC-ceEeecCccccCCCcccCCCCCCCC
Q 010849 137 VCGGCNCDIGYG-NYLGCMGTYFHPNCFRCRSCGYPIT 173 (499)
Q Consensus 137 ~C~~C~k~I~~g-~~l~algk~wHp~CF~C~~C~~~L~ 173 (499)
.|.+|+++|..+ ..+.+.++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999765 6788999999999999999999985
No 16
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=97.32 E-value=0.00049 Score=59.53 Aligned_cols=108 Identities=24% Similarity=0.258 Sum_probs=67.5
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHhC--CCCCChhhhhhHHHHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCCCCchHH
Q 010849 371 YGLPRLLTGAILAHELMHGWLRLKG--YRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPSTSSASTSSSSSKKGGKSEV 448 (499)
Q Consensus 371 ~gLPrl~~g~ilAHE~mHa~l~l~g--~~~l~~~veEG~Cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 448 (499)
.+-+.-.+..+|+||+.|+|+.-.. ...++..+.||++++++..+-. ........... .+....+
T Consensus 18 ~~~~~~~~~~~l~HE~~H~~~~~~~~~~~~~~~W~~EG~A~y~~~~~~~-~~~~~~~~~~~------------~~~~~~~ 84 (128)
T PF13485_consen 18 QGSDEDWLDRVLAHELAHQWFGNYFGGDDNAPRWFNEGLAEYVEGRIED-EFDEDLKQAIE------------SGSLPPL 84 (128)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCccCchHHHHHHHHHHhcCccc-hhHHHHHHHHH------------cCCCCCh
Confidence 3455555559999999999998873 2478999999999999954211 00000000000 0000111
Q ss_pred HHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHhCHHHHHHHHHh
Q 010849 449 EKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKYGLRRTLEHIRL 493 (499)
Q Consensus 449 e~~l~~~~~~qi~~d~s~vYGdGfR~~~~a~~~~gl~~~l~~i~~ 493 (499)
+ .|...+.. ...+.+..|.-|+-.+....+++|...+.+-|+.
T Consensus 85 ~-~l~~~~~~-~~~~~~~~Y~~~~~~~~~L~~~~G~~~~~~~l~~ 127 (128)
T PF13485_consen 85 E-PLNSSFDF-SWEDDSLAYYQGYLFVRFLEEKYGREKFKAFLRE 127 (128)
T ss_pred H-HHhccccc-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 22222211 5667777999999999999999998777776664
No 17
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.82 E-value=0.00017 Score=70.14 Aligned_cols=115 Identities=20% Similarity=0.328 Sum_probs=88.8
Q ss_pred CCCCccCCCceEeecCccccCCCcccCCCCCCCC--CCceEeeCCcccchhhhhh--hccccccccCCccCCCCcceEEe
Q 010849 140 GCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPIT--EHEFSLSGKDPYHKSCFKE--LTHPKCEVCHQYIPTNGAGLIEY 215 (499)
Q Consensus 140 ~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~--~~~F~~~dg~~YC~~CY~~--~f~pkC~~C~~~I~~~~~g~I~~ 215 (499)
+|+..|.+...+...+..||..|..|..|..++. ...|.. ++..||..+|.. .+..+|..|...|...+ .
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~-----~ 74 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD-----E 74 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH-----H
Confidence 4777886555677779999999999999999998 545656 999999999998 88999999999986532 1
Q ss_pred eccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhh
Q 010849 216 RCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 216 ~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sa 267 (499)
+...| ++ -|.-||.|..|.+....++++.+-...+..|...+...
T Consensus 75 ler~f--~~-----~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 75 LERAF--EK-----VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred HHHhh--cC-----CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 11122 11 18899999999998777777666666688888877554
No 18
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=96.59 E-value=0.00055 Score=66.58 Aligned_cols=62 Identities=24% Similarity=0.487 Sum_probs=54.5
Q ss_pred CCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhcc
Q 010849 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTH 195 (499)
Q Consensus 134 ~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~ 195 (499)
....|.+|.+.+.+-+-+...+..||..||+|..|+..|+...+....+.+||...+.+++.
T Consensus 107 ~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 107 EKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFK 168 (200)
T ss_pred cccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeec
Confidence 45689999999988888889999999999999999999999999999999999877666443
No 19
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=96.52 E-value=0.0022 Score=44.69 Aligned_cols=37 Identities=19% Similarity=0.318 Sum_probs=26.1
Q ss_pred cccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCCCCcc
Q 010849 197 KCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLE 244 (499)
Q Consensus 197 kC~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~ 244 (499)
+|..|+++|.+.. ..+.+... .||..||+|..|++.+
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~~----------~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALGK----------VWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCc-EEEEeCCc----------cccccCCCCcccCCcC
Confidence 5889999998852 23333221 2499999999999854
No 20
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=96.41 E-value=0.00037 Score=67.26 Aligned_cols=59 Identities=19% Similarity=0.507 Sum_probs=53.1
Q ss_pred CCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhc
Q 010849 136 KVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT 194 (499)
Q Consensus 136 ~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f 194 (499)
..|..|++.+.+-+-+.++++.||..||.|..|+-+|....+-..+.++||..+|.+..
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 45888999998888899999999999999999999999888888899999999998754
No 21
>PF10026 DUF2268: Predicted Zn-dependent protease (DUF2268); InterPro: IPR018728 This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Probab=91.65 E-value=0.66 Score=44.77 Aligned_cols=45 Identities=20% Similarity=0.179 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHHHHHHHHh------CCCCCChhhhhhHHHHHHHHHhhccc
Q 010849 376 LLTGAILAHELMHGWLRLK------GYRNLNPEVEEGICQVLSYMWLESEV 420 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~------g~~~l~~~veEG~Cq~~a~~wl~~~~ 420 (499)
-..-+++|||+-|++..-. +..-|+..|=||+-+.++..-.....
T Consensus 63 ~~l~~~iaHE~hH~~r~~~~~~~~~~~TLld~~I~EGlAe~f~~~~~g~~~ 113 (195)
T PF10026_consen 63 EELPALIAHEYHHNCRYEQIGWDPEDTTLLDSLIMEGLAEYFAEELYGEEY 113 (195)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCCCCHHHHHHHhhHHHHHHHHHcCCCC
Confidence 4667999999999975542 34456899999999999988666554
No 22
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=86.50 E-value=0.5 Score=49.35 Aligned_cols=44 Identities=27% Similarity=0.420 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHh-CCCCC-ChhhhhhHHHHHHHHHhhccc
Q 010849 377 LTGAILAHELMHGWLRLK-GYRNL-NPEVEEGICQVLSYMWLESEV 420 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~-g~~~l-~~~veEG~Cq~~a~~wl~~~~ 420 (499)
....++|||++|-|+--- ....- +..+-|||+++++++|++...
T Consensus 294 ~~~~~iahElahqWfGn~vt~~~w~d~WL~Eg~a~y~~~~~~~~~~ 339 (390)
T PF01433_consen 294 EIASLIAHELAHQWFGNLVTPKWWSDLWLNEGFATYLEYLILEKLF 339 (390)
T ss_dssp HHHHHHHHHHHTTTBTTTEEESSGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHhccCCccccchhhhHHHHHHHHHHHHhHhhcc
Confidence 456889999999996421 11111 467999999999999999865
No 23
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=82.25 E-value=1.5 Score=42.93 Aligned_cols=91 Identities=20% Similarity=0.266 Sum_probs=55.2
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCCCCchHHHHHHHH
Q 010849 375 RLLTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPSTSSASTSSSSSKKGGKSEVEKKLGE 454 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~l~l~g~~~l~~~veEG~Cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~e~~l~~ 454 (499)
+--...+|-|||||+|++-- ...-|.-+-|||-.++-+. ....+..- .. ..+......-| ...+
T Consensus 93 ~~Ei~Gvl~HE~~H~~Q~~~-~~~~P~~liEGIADyVRl~---aG~~~~~w--~~--------p~~~~~wd~gY--~~TA 156 (205)
T PF04450_consen 93 RDEIIGVLYHEMVHCWQWDG-RGTAPGGLIEGIADYVRLK---AGYAPPHW--KR--------PGGGDSWDDGY--RTTA 156 (205)
T ss_pred HHHHHHHHHHHHHHHhhcCC-CCCCChhheecHHHHHHHH---cCCCCccc--cC--------CCCCCCccccc--HHHH
Confidence 45667899999999999874 3467999999999999766 11111000 00 00000011112 5567
Q ss_pred HHHhhhhcCCCCCchhhH-HHHHHHHHHhCH
Q 010849 455 FFMHQIAHDASPAYGEGF-RIANAAVNKYGL 484 (499)
Q Consensus 455 ~~~~qi~~d~s~vYGdGf-R~~~~a~~~~gl 484 (499)
||+.=+|... ||.|| |..++++.+.+.
T Consensus 157 ~FL~wle~~~---~~~gfV~~LN~~m~~~~y 184 (205)
T PF04450_consen 157 RFLDWLEDNR---YGKGFVRRLNEAMRRDKY 184 (205)
T ss_pred HHHHHHHhcc---cCccHHHHHHHHHhhCCC
Confidence 7777777622 56666 778888766443
No 24
>PF14891 Peptidase_M91: Effector protein
Probab=81.36 E-value=1 Score=42.69 Aligned_cols=20 Identities=30% Similarity=0.448 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHhCC
Q 010849 377 LTGAILAHELMHGWLRLKGY 396 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~g~ 396 (499)
.-..+|||||.|||=.++|-
T Consensus 102 ~p~v~L~HEL~HA~~~~~Gt 121 (174)
T PF14891_consen 102 PPFVVLYHELIHAYDYMNGT 121 (174)
T ss_pred HHHHHHHHHHHHHHHHHCCC
Confidence 33589999999999999983
No 25
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=81.03 E-value=0.94 Score=37.71 Aligned_cols=18 Identities=44% Similarity=0.547 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHhC
Q 010849 378 TGAILAHELMHGWLRLKG 395 (499)
Q Consensus 378 ~g~ilAHE~mHa~l~l~g 395 (499)
.-++|||||+|+++.-.|
T Consensus 61 ~~~llaHEl~Hv~Qq~~g 78 (79)
T PF13699_consen 61 GRALLAHELAHVVQQRRG 78 (79)
T ss_pred cchhHhHHHHHHHhhccC
Confidence 457999999999987654
No 26
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=80.87 E-value=2.3 Score=36.02 Aligned_cols=52 Identities=23% Similarity=0.128 Sum_probs=35.1
Q ss_pred EEEEEEcCCchhHHHHHHHHHHHHHHHHHhCC------CCCChhhhhhHHHHHHHHHh
Q 010849 365 TAILVLYGLPRLLTGAILAHELMHGWLRLKGY------RNLNPEVEEGICQVLSYMWL 416 (499)
Q Consensus 365 ~~Ilvl~gLPrl~~g~ilAHE~mHa~l~l~g~------~~l~~~veEG~Cq~~a~~wl 416 (499)
.-|+|=..++..-.-.+||||++|.++.-.+. ........|=-++.+|...|
T Consensus 29 ~~I~in~~~~~~~~~f~laHELgH~~~~~~~~~~~~~~~~~~~~~~E~~An~fA~~lL 86 (122)
T PF06114_consen 29 PIIFINSNLSPERQRFTLAHELGHILLHHGDETFNYYLNYFFNERQEREANAFAAALL 86 (122)
T ss_dssp TEEEEESSS-HHHHHHHHHHHHHHHHHHH-HHHHHHHHHH--THHHHHHHHHHHHHHH
T ss_pred CEEEECCCCCHHHHHHHHHHHHHHHHhhhccccchhhccccchhhHHHHHHHHHHHHh
Confidence 36888888999999999999999999998752 23344444555555555544
No 27
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M13 (neprilysin family, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=80.70 E-value=0.67 Score=44.51 Aligned_cols=17 Identities=53% Similarity=0.575 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHH
Q 010849 377 LTGAILAHELMHGWLRL 393 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l 393 (499)
.+|+|||||||||+-..
T Consensus 35 ~lG~ilahel~hafd~~ 51 (206)
T PF01431_consen 35 GLGFILAHELMHAFDPE 51 (206)
T ss_dssp THHHHHHHHHHHCTSTT
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 47999999999998663
No 28
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=80.17 E-value=1.3 Score=40.62 Aligned_cols=22 Identities=23% Similarity=0.087 Sum_probs=20.1
Q ss_pred CchhHHHHHHHHHHHHHHHHHh
Q 010849 373 LPRLLTGAILAHELMHGWLRLK 394 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa~l~l~ 394 (499)
.|.-.+-.+|+|||.|||+.+.
T Consensus 55 ~~~~~~~~tL~HEm~H~~~~~~ 76 (157)
T PF10263_consen 55 NPEEELIDTLLHEMAHAAAYVF 76 (157)
T ss_pred hHHHHHHHHHHHHHHHHHhhhc
Confidence 6777889999999999999998
No 29
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=80.14 E-value=8.3 Score=45.30 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHH-HhCCCC-CChhhhhhHHHHHHHHHhhcc
Q 010849 378 TGAILAHELMHGWLR-LKGYRN-LNPEVEEGICQVLSYMWLESE 419 (499)
Q Consensus 378 ~g~ilAHE~mHa~l~-l~g~~~-l~~~veEG~Cq~~a~~wl~~~ 419 (499)
...++|||+.|-|.- |=.... =+..+-|||..+++++|++..
T Consensus 287 ~~~viaHElAHqWFGnlVT~~wW~dlWLnEGFAty~e~~~~~~~ 330 (831)
T TIGR02412 287 RAGVILHEMAHMWFGDLVTMRWWNDLWLNESFAEYMGTLASAEA 330 (831)
T ss_pred HHHHHHHHHHHHHhCCEeccccccchhHHHHHHHHHHHHHHHhc
Confidence 357999999999973 111111 256899999999999999853
No 30
>PRK03001 M48 family peptidase; Provisional
Probab=77.90 E-value=0.96 Score=46.14 Aligned_cols=20 Identities=30% Similarity=0.234 Sum_probs=16.1
Q ss_pred CCchhHHHHHHHHHHHHHHH
Q 010849 372 GLPRLLTGAILAHELMHGWL 391 (499)
Q Consensus 372 gLPrl~~g~ilAHE~mHa~l 391 (499)
.|...-..+|||||+.|.--
T Consensus 118 ~l~~~El~aVlAHElgHi~~ 137 (283)
T PRK03001 118 VLSEREIRGVMAHELAHVKH 137 (283)
T ss_pred hCCHHHHHHHHHHHHHHHhC
Confidence 45677788999999999753
No 31
>PRK01345 heat shock protein HtpX; Provisional
Probab=76.49 E-value=1.2 Score=46.48 Aligned_cols=19 Identities=32% Similarity=0.288 Sum_probs=15.7
Q ss_pred CchhHHHHHHHHHHHHHHH
Q 010849 373 LPRLLTGAILAHELMHGWL 391 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa~l 391 (499)
|...-..+|||||+.|.-.
T Consensus 119 L~~dEL~aVlAHElgHi~~ 137 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVKN 137 (317)
T ss_pred CCHHHHHHHHHHHHHHHHc
Confidence 5667788999999999764
No 32
>PRK02391 heat shock protein HtpX; Provisional
Probab=74.66 E-value=1.3 Score=45.76 Aligned_cols=21 Identities=38% Similarity=0.177 Sum_probs=16.7
Q ss_pred cCCchhHHHHHHHHHHHHHHH
Q 010849 371 YGLPRLLTGAILAHELMHGWL 391 (499)
Q Consensus 371 ~gLPrl~~g~ilAHE~mHa~l 391 (499)
..|...-..+|||||+.|.--
T Consensus 126 ~~L~~~El~aVlaHElgHi~~ 146 (296)
T PRK02391 126 RRLDPDELEAVLAHELSHVKN 146 (296)
T ss_pred hhCCHHHHHHHHHHHHHHHHc
Confidence 456677788999999999643
No 33
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=74.43 E-value=0.57 Score=45.74 Aligned_cols=97 Identities=15% Similarity=0.277 Sum_probs=57.7
Q ss_pred cccccccCCccCCCCcceEEeeccCccccccCCCCcCCCCcccCCCCCccccCCceeEecCCccccchhhhhhccCCCCC
Q 010849 195 HPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDC 274 (499)
Q Consensus 195 ~pkC~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt~e~ 274 (499)
.+.|..|++.+.+.+ .+. ....|| |..||+|..|+. ++.-+.+.-.|.++||-.+|..-+..+---
T Consensus 4 k~n~~~cgk~vYPvE--~v~-cldk~w---------hk~cfkce~c~m--tlnmKnyKgy~kkpycn~hYpkq~at~~ad 69 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVE--EVK-CLDKVW---------HKQCFKCEVCGM--TLNMKNYKGYDKKPYCNPHYPKQVATVMAD 69 (264)
T ss_pred cchhhhhccccccHH--HHh-hHHHHH---------HHHhheeeeccC--ChhhhhccccccCCCcCcccccceeeeecC
Confidence 345677877766532 111 123456 999999999997 555555665678999999996554433222
Q ss_pred CchhhhHHH------------HHhhcccccccccccccccHHHHHHHH
Q 010849 275 QPLYHAIRD------------YYEGMNMKLDQQIPMLLVERQALNEAI 310 (499)
Q Consensus 275 qpl~~~i~~------------f~~g~~m~~~~~~p~~lv~~~~ln~a~ 310 (499)
.|-...|.+ -|+.+ .+-|.++.|-++|.+.-
T Consensus 70 TPEm~Rik~n~enqS~vkY~~e~ekm-----KG~~s~iaDtPem~r~K 112 (264)
T KOG1702|consen 70 TPEMRRIKENTENQSNVKYHAEYEKM-----KGTKSEIADTPEMERLK 112 (264)
T ss_pred CHHHHHHHhhhccchhhhhHHHHHHh-----cCCcceecCCHHHHHHH
Confidence 233333321 22221 23466777888887653
No 34
>PRK03072 heat shock protein HtpX; Provisional
Probab=73.20 E-value=1.3 Score=45.50 Aligned_cols=21 Identities=33% Similarity=0.336 Sum_probs=16.8
Q ss_pred EcCCchhHHHHHHHHHHHHHH
Q 010849 370 LYGLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 370 l~gLPrl~~g~ilAHE~mHa~ 390 (499)
|.-|++.-..+|||||+.|.-
T Consensus 119 l~~l~~~El~aVlAHElgHi~ 139 (288)
T PRK03072 119 LQILNERELRGVLGHELSHVY 139 (288)
T ss_pred HHhCCHHHHHHHHHHHHHHHh
Confidence 355677778899999999954
No 35
>PF10460 Peptidase_M30: Peptidase M30; InterPro: IPR019501 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family contains metallopeptidases belonging to MEROPS peptidase family M30 (hyicolysin family, clan MA). Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue.
Probab=72.56 E-value=4.8 Score=42.88 Aligned_cols=44 Identities=18% Similarity=0.151 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHH---HHHH--hCC-CCCChhhhhhHHHHHHHHHhhcc
Q 010849 376 LLTGAILAHELMHG---WLRL--KGY-RNLNPEVEEGICQVLSYMWLESE 419 (499)
Q Consensus 376 l~~g~ilAHE~mHa---~l~l--~g~-~~l~~~veEG~Cq~~a~~wl~~~ 419 (499)
-.+-++||||++|. |.+. .|- ...+..++||+-+++.++.-...
T Consensus 137 ~~~~sTlAHEfQHmInfy~~~v~~g~~~~~dtWLnE~lS~~aEdl~s~~~ 186 (366)
T PF10460_consen 137 DTVYSTLAHEFQHMINFYQRGVLHGKQYAMDTWLNEMLSMSAEDLYSSKI 186 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHhcCC
Confidence 34679999999986 4432 332 35799999999999999765443
No 36
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=70.77 E-value=3.6 Score=37.79 Aligned_cols=22 Identities=41% Similarity=0.333 Sum_probs=18.2
Q ss_pred chhHHHHHHHHHHHHHHHHHhC
Q 010849 374 PRLLTGAILAHELMHGWLRLKG 395 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l~l~g 395 (499)
|...+-.||+|||.|++..+.|
T Consensus 55 ~~~~l~~~l~HEm~H~~~~~~g 76 (146)
T smart00731 55 GRDRLRETLLHELCHAALYLFG 76 (146)
T ss_pred cHHHHHhhHHHHHHHHHHHHhC
Confidence 4456677999999999999865
No 37
>PRK14015 pepN aminopeptidase N; Provisional
Probab=70.52 E-value=15 Score=43.67 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHhCC--CCC-ChhhhhhHHHHHHHHHhhcc
Q 010849 378 TGAILAHELMHGWLRLKGY--RNL-NPEVEEGICQVLSYMWLESE 419 (499)
Q Consensus 378 ~g~ilAHE~mHa~l~l~g~--~~l-~~~veEG~Cq~~a~~wl~~~ 419 (499)
..+|+|||+.|-|.- |-. ..- +..+-||+.-++.++|.+..
T Consensus 296 i~~vIaHElaHqWFG-NlVT~~~W~dLWLnEGFAty~e~~~~~~~ 339 (875)
T PRK14015 296 IESVIAHEYFHNWTG-NRVTCRDWFQLSLKEGLTVFRDQEFSADL 339 (875)
T ss_pred HHHHHHHHHHHHHHh-CcceecchhhhhhhhHHHHHHHHHHHHHh
Confidence 568999999999941 111 111 35679999999988887653
No 38
>PRK02870 heat shock protein HtpX; Provisional
Probab=68.55 E-value=1.9 Score=45.31 Aligned_cols=18 Identities=44% Similarity=0.412 Sum_probs=15.2
Q ss_pred CCchhHHHHHHHHHHHHH
Q 010849 372 GLPRLLTGAILAHELMHG 389 (499)
Q Consensus 372 gLPrl~~g~ilAHE~mHa 389 (499)
-|++.-..+|||||+.|.
T Consensus 167 ~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 167 KLDRDELQAVMAHELSHI 184 (336)
T ss_pred hCCHHHHHHHHHHHHHHH
Confidence 456677889999999997
No 39
>PRK03982 heat shock protein HtpX; Provisional
Probab=68.31 E-value=1.9 Score=44.13 Aligned_cols=20 Identities=30% Similarity=0.119 Sum_probs=16.3
Q ss_pred CCchhHHHHHHHHHHHHHHH
Q 010849 372 GLPRLLTGAILAHELMHGWL 391 (499)
Q Consensus 372 gLPrl~~g~ilAHE~mHa~l 391 (499)
.|...-..+|||||+.|.--
T Consensus 119 ~l~~~El~AVlAHElgHi~~ 138 (288)
T PRK03982 119 LLNEDELEGVIAHELTHIKN 138 (288)
T ss_pred hCCHHHHHHHHHHHHHHHHc
Confidence 45777789999999999753
No 40
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=68.07 E-value=11 Score=37.36 Aligned_cols=55 Identities=20% Similarity=0.056 Sum_probs=42.0
Q ss_pred EEEEEEcCCchhHHHHHHHHHHHHHHHHHhC------CCC-CChhhhhhHHHHHHHHHhhcc
Q 010849 365 TAILVLYGLPRLLTGAILAHELMHGWLRLKG------YRN-LNPEVEEGICQVLSYMWLESE 419 (499)
Q Consensus 365 ~~Ilvl~gLPrl~~g~ilAHE~mHa~l~l~g------~~~-l~~~veEG~Cq~~a~~wl~~~ 419 (499)
.-|++---++-..---+|||||.||+|--.+ .++ -....-|=.|+.+|-..|-..
T Consensus 59 ~~I~iN~n~~~~r~rFtlAHELGH~llH~~~~~~~~~~~~~~~~~~~E~~AN~FAa~lLmP~ 120 (213)
T COG2856 59 PVIYINANNSLERKRFTLAHELGHALLHTDLNTRFDAEPTLQQDRKIEAEANAFAAELLMPE 120 (213)
T ss_pred ceEEEeCCCCHHHHHHHHHHHHhHHHhccccchhhhcccccchhHHHHHHHHHHHHHHhCCh
Confidence 4677777778888889999999999997765 122 244556778999999888765
No 41
>PRK04897 heat shock protein HtpX; Provisional
Probab=67.52 E-value=1.9 Score=44.52 Aligned_cols=20 Identities=20% Similarity=0.169 Sum_probs=16.6
Q ss_pred cCCchhHHHHHHHHHHHHHH
Q 010849 371 YGLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 371 ~gLPrl~~g~ilAHE~mHa~ 390 (499)
..|++.-..+|||||+.|.-
T Consensus 130 ~~l~~~El~aVlAHElgHi~ 149 (298)
T PRK04897 130 AIMNREELEGVIGHEISHIR 149 (298)
T ss_pred hhCCHHHHHHHHHHHHHHHh
Confidence 45677888999999999954
No 42
>PRK05457 heat shock protein HtpX; Provisional
Probab=66.97 E-value=2.3 Score=43.59 Aligned_cols=21 Identities=38% Similarity=0.379 Sum_probs=17.5
Q ss_pred EcCCchhHHHHHHHHHHHHHH
Q 010849 370 LYGLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 370 l~gLPrl~~g~ilAHE~mHa~ 390 (499)
|.-|++--..+|||||+.|.-
T Consensus 126 l~~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 126 LQNMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred hhhCCHHHHHHHHHHHHHHHH
Confidence 345788899999999999963
No 43
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=66.47 E-value=2 Score=41.58 Aligned_cols=94 Identities=20% Similarity=0.312 Sum_probs=66.1
Q ss_pred CCccccc--chHHHHHHhh--cccCCCCCCCCCCCCCCC--CCCCCCCCCCCccCCCc-eEeecCccccCCCcccCCCCC
Q 010849 98 GQRWRSN--TDEDYAWALQ--DSQLNPSFPPYDPSHYYP--RSYKVCGGCNCDIGYGN-YLGCMGTYFHPNCFRCRSCGY 170 (499)
Q Consensus 98 ~~~wh~e--~ce~c~r~Lq--~~l~~~~~~pyC~~~y~~--~~~~~C~~C~k~I~~g~-~l~algk~wHp~CF~C~~C~~ 170 (499)
...||.. .|..|...+. .......+..||..+|.. .....|.+|...+..-+ +..+..++ |-.||.|..|..
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la 94 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLA 94 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHh
Confidence 4467755 5666666664 222222347899999977 67889999999985433 34566677 999999999998
Q ss_pred CCC-CCceEeeCC-cccchhhhhh
Q 010849 171 PIT-EHEFSLSGK-DPYHKSCFKE 192 (499)
Q Consensus 171 ~L~-~~~F~~~dg-~~YC~~CY~~ 192 (499)
.+. ..++.+... +.+|..++.+
T Consensus 95 ~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 95 LLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred hcCCCCeeeeehhhhhhcHhhhhh
Confidence 665 446777655 8888877765
No 44
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.80 E-value=3.5 Score=39.57 Aligned_cols=48 Identities=21% Similarity=0.504 Sum_probs=38.6
Q ss_pred CCCcccCCCCCCCCCCc-eEeeCCcccchhhhhhhc--cccccccCCccCC
Q 010849 160 PNCFRCRSCGYPITEHE-FSLSGKDPYHKSCFKELT--HPKCEVCHQYIPT 207 (499)
Q Consensus 160 p~CF~C~~C~~~L~~~~-F~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~~ 207 (499)
..||.|..|=.+..... +..+-|.+||+.|.+... +-+|..|++.|..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 35788888887777654 667889999999998754 6789999998875
No 45
>PF09768 Peptidase_M76: Peptidase M76 family; InterPro: IPR019165 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. Mitochondrial inner membrane protease ATP23 has two roles in the assembly of mitochondrial ATPase. Firstly, it acts as a protease that removes the N-terminal 10 residues of mitochondrial ATPase CF(0) subunit 6 (ATP6) at the intermembrane space side. Secondly, it is involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of ATP6 with the subunit 9 ring [, ].; GO: 0004222 metalloendopeptidase activity
Probab=65.43 E-value=4.6 Score=38.65 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=18.2
Q ss_pred chhHHHHHHHHHHHHHHHHHhC
Q 010849 374 PRLLTGAILAHELMHGWLRLKG 395 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l~l~g 395 (499)
-+.....+|+|||.|||=.+..
T Consensus 67 ~~~~l~~~l~HELIHayD~cr~ 88 (173)
T PF09768_consen 67 SQGHLEDTLTHELIHAYDHCRA 88 (173)
T ss_pred CHHHHHHHHHHHHHHHHHHHhc
Confidence 3456678999999999988874
No 46
>PRK01265 heat shock protein HtpX; Provisional
Probab=65.23 E-value=2.5 Score=44.29 Aligned_cols=17 Identities=41% Similarity=0.311 Sum_probs=14.4
Q ss_pred CchhHHHHHHHHHHHHH
Q 010849 373 LPRLLTGAILAHELMHG 389 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa 389 (499)
|.+.-..+|||||+.|.
T Consensus 135 l~~~El~aVlAHElgHi 151 (324)
T PRK01265 135 LNRDEIKAVAGHELGHL 151 (324)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 56677889999999994
No 47
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=62.37 E-value=4.8 Score=35.91 Aligned_cols=15 Identities=47% Similarity=0.683 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHh
Q 010849 380 AILAHELMHGWLRLK 394 (499)
Q Consensus 380 ~ilAHE~mHa~l~l~ 394 (499)
-.||||+.|||+.-.
T Consensus 81 ~TL~HEL~H~WQ~Rs 95 (141)
T PHA02456 81 DTLAHELNHAWQFRT 95 (141)
T ss_pred HHHHHHHHHHHhhhc
Confidence 679999999999765
No 48
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=61.08 E-value=8 Score=31.25 Aligned_cols=46 Identities=22% Similarity=0.406 Sum_probs=22.4
Q ss_pred cccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCCC
Q 010849 163 FRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTN 208 (499)
Q Consensus 163 F~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~ 208 (499)
.+|+.|..-+...-....=...||..|....++..|.+|+.|-...
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q 53 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ 53 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence 4677777666542223345688999999998899999999886543
No 49
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.21 E-value=7.3 Score=44.56 Aligned_cols=49 Identities=22% Similarity=0.497 Sum_probs=25.5
Q ss_pred CCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCccC
Q 010849 136 KVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIP 206 (499)
Q Consensus 136 ~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~ 206 (499)
.+|..|+..+..+. -.|..|+.+|.. ..|..|-...- ...|..|+....
T Consensus 2 ~~Cp~Cg~~n~~~a-------------kFC~~CG~~l~~---------~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 2 LICPQCQFENPNNN-------------RFCQKCGTSLTH---------KPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCcCCCCC-------------ccccccCCCCCC---------CcCCCCCCCCCcccccccccCCccc
Confidence 46888888774321 235666666632 13555544421 334666665543
No 50
>PF01447 Peptidase_M4: Thermolysin metallopeptidase, catalytic domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR013856 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft []. This entry represents a domain found in peptidase M4 family members.; GO: 0004222 metalloendopeptidase activity; PDB: 3NQX_A 3NQZ_B 3NQY_B 1BQB_A 1U4G_A 1EZM_A 3DBK_A 1ESP_A 1NPC_A 1LND_E ....
Probab=58.35 E-value=6.1 Score=36.84 Aligned_cols=18 Identities=39% Similarity=0.499 Sum_probs=12.5
Q ss_pred chhHHHHHHHHHHHHHHH
Q 010849 374 PRLLTGAILAHELMHGWL 391 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l 391 (499)
|-.-..=|+||||+|+..
T Consensus 131 ~~~~~lDVvaHEltHGVt 148 (150)
T PF01447_consen 131 PFASSLDVVAHELTHGVT 148 (150)
T ss_dssp -GGG-HHHHHHHHHHHHH
T ss_pred cCccccceeeeccccccc
Confidence 333346799999999864
No 51
>TIGR02411 leuko_A4_hydro leukotriene A-4 hydrolase/aminopeptidase. Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (pfam01433). The majority of the members of pfam01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known.
Probab=57.53 E-value=8.8 Score=43.49 Aligned_cols=40 Identities=23% Similarity=0.221 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHh-CCCCC-ChhhhhhHHHHHHHHHhhc
Q 010849 379 GAILAHELMHGWLRLK-GYRNL-NPEVEEGICQVLSYMWLES 418 (499)
Q Consensus 379 g~ilAHE~mHa~l~l~-g~~~l-~~~veEG~Cq~~a~~wl~~ 418 (499)
..++|||++|-|.--- ....= +..+-||+.-++.+.+++.
T Consensus 280 ~~viaHElAHqWfGNlVT~~~W~d~WLnEGfaty~e~~~~~~ 321 (601)
T TIGR02411 280 VDVIAHELAHSWSGNLVTNCSWEHFWLNEGWTVYLERRIVGR 321 (601)
T ss_pred hhhHHHHHHhhccCceeecCCchHHHHHhhHHHHHHHHHHHH
Confidence 4799999999997421 11111 5678999999999877654
No 52
>cd04270 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
Probab=57.29 E-value=6.6 Score=39.28 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=15.4
Q ss_pred CchhHHHHHHHHHHHHHH
Q 010849 373 LPRLLTGAILAHELMHGW 390 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa~ 390 (499)
+|...+..++||||.|.|
T Consensus 162 ~~~~~~a~t~AHElGHnl 179 (244)
T cd04270 162 VPTKESDLVTAHELGHNF 179 (244)
T ss_pred cchhHHHHHHHHHHHHhc
Confidence 466778899999999986
No 53
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=56.71 E-value=7.5 Score=36.59 Aligned_cols=54 Identities=19% Similarity=0.506 Sum_probs=36.3
Q ss_pred CcccchhhhhhhccccccccCCccCCCC--cceEEeeccCccccccCCCCcCCCCcccCCCCCccccCC
Q 010849 182 KDPYHKSCFKELTHPKCEVCHQYIPTNG--AGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNT 248 (499)
Q Consensus 182 g~~YC~~CY~~~f~pkC~~C~~~I~~~~--~g~I~~~~~pfWgq~YCp~H~H~~CF~C~~C~r~~~~g~ 248 (499)
.+-||.+|-.+ .-..|..|+.+|.|.. .|.+.+. ..| +.-- -|..|+++.|...
T Consensus 27 ~~~fC~kCG~~-tI~~Cp~C~~~IrG~y~v~gv~~~g------~~~-----~~Ps-YC~~CGkpyPWt~ 82 (158)
T PF10083_consen 27 REKFCSKCGAK-TITSCPNCSTPIRGDYHVEGVFGLG------GHY-----EAPS-YCHNCGKPYPWTE 82 (158)
T ss_pred HHHHHHHhhHH-HHHHCcCCCCCCCCceecCCeeeeC------CCC-----CCCh-hHHhCCCCCchHH
Confidence 46789999776 5678999999999973 4555442 122 2111 2889999877643
No 54
>PRK04351 hypothetical protein; Provisional
Probab=56.53 E-value=9.7 Score=35.53 Aligned_cols=20 Identities=40% Similarity=0.431 Sum_probs=16.8
Q ss_pred hHHHHHHHHHHHHHHHHHhC
Q 010849 376 LLTGAILAHELMHGWLRLKG 395 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~g 395 (499)
..+..||+|||.|+.+.+.|
T Consensus 59 ~~l~~vv~HElcH~~~~~~g 78 (149)
T PRK04351 59 EELIGIIKHELCHYHLHLEG 78 (149)
T ss_pred HHHHhhHHHHHHHHHHHHHC
Confidence 34568999999999999875
No 55
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=55.70 E-value=9.8 Score=38.68 Aligned_cols=110 Identities=18% Similarity=0.417 Sum_probs=65.2
Q ss_pred chHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCcc---CCCc--------eEeecC---c------cc--cC-C
Q 010849 105 TDEDYAWALQDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDI---GYGN--------YLGCMG---T------YF--HP-N 161 (499)
Q Consensus 105 ~ce~c~r~Lq~~l~~~~~~pyC~~~y~~~~~~~C~~C~k~I---~~g~--------~l~alg---k------~w--Hp-~ 161 (499)
+|+.|.+.-. ++.||-.|....-.|+|+.|++.- ..|. +.+-++ . .| |- .
T Consensus 40 eCdkC~r~QK-------nRAFCYFC~s~qrlp~Ca~Cgk~KCm~k~gdCvvkH~g~~~tGl~mvGaiCDfCEawvCHgrk 112 (314)
T PF06524_consen 40 ECDKCQRKQK-------NRAFCYFCQSVQRLPMCAHCGKTKCMLKTGDCVVKHPGVFTTGLGMVGAICDFCEAWVCHGRK 112 (314)
T ss_pred cchhhhhhcc-------ccceeehhhhhhcCchhhhcCCeeeeccCCCeEEecCceeecccchhhhhhccchhheecccc
Confidence 7888876421 256666666666789999999862 2232 222221 1 23 43 5
Q ss_pred CcccCCCCCCCCCCce-------EeeCCcccchhhhhhhccccccccCCccCCCCcceEEeeccCccccccCCCCcCCCC
Q 010849 162 CFRCRSCGYPITEHEF-------SLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHT 234 (499)
Q Consensus 162 CF~C~~C~~~L~~~~F-------~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~g~I~~~~~pfWgq~YCp~H~H~~C 234 (499)
|+.-+.|..||.+... +.++|++| +|.-|..++-..+ .|-.|.-|..- -...
T Consensus 113 Cl~~HaC~Cpl~da~C~EC~R~vw~hGGrif-----------~CsfC~~flCEDD---------QFEHQAsCQvL-e~E~ 171 (314)
T PF06524_consen 113 CLSTHACTCPLQDAVCIECERGVWDHGGRIF-----------KCSFCDNFLCEDD---------QFEHQASCQVL-ESET 171 (314)
T ss_pred ccccccccCcCCCcEeeeeecccccCCCeEE-----------EeecCCCeeeccc---------hhhhhhhhhhh-hccc
Confidence 8888889999986532 23344433 5888888776542 12222223222 4567
Q ss_pred cccCCCCC
Q 010849 235 SRCCSCER 242 (499)
Q Consensus 235 F~C~~C~r 242 (499)
|+|.+|+|
T Consensus 172 ~KC~SCNr 179 (314)
T PF06524_consen 172 FKCQSCNR 179 (314)
T ss_pred cccccccc
Confidence 99999998
No 56
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=54.55 E-value=9 Score=36.61 Aligned_cols=23 Identities=39% Similarity=0.170 Sum_probs=18.5
Q ss_pred CchhHHHHHHHHHHHHHHHHHhC
Q 010849 373 LPRLLTGAILAHELMHGWLRLKG 395 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa~l~l~g 395 (499)
++..-..+|||||+.|...+-.-
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~ 106 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHIL 106 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcc
Confidence 45666779999999999977653
No 57
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=54.25 E-value=7 Score=25.91 Aligned_cols=20 Identities=40% Similarity=0.521 Sum_probs=16.7
Q ss_pred hhhhHHHHHHhcchhhhcCc
Q 010849 77 EKEELDHAIALSLAEDLKRP 96 (499)
Q Consensus 77 e~edid~ai~~sL~Ee~kk~ 96 (499)
|+|+|.+||.+|+.|.+...
T Consensus 2 EDe~Lq~Ai~lSl~e~e~~~ 21 (26)
T smart00726 2 EDEDLQLALELSLQEAEESX 21 (26)
T ss_pred hHHHHHHHHHHhHHHhhhcc
Confidence 68999999999998876543
No 58
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=54.09 E-value=15 Score=28.11 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=33.2
Q ss_pred cccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCccCC
Q 010849 163 FRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIPT 207 (499)
Q Consensus 163 F~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~~ 207 (499)
|.|..|+..+.+ ......|..||+.|..+.+ ..+|..|++++..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 568888888776 4555678999999987643 5678888888754
No 59
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=53.57 E-value=7.1 Score=23.67 Aligned_cols=16 Identities=44% Similarity=0.696 Sum_probs=13.7
Q ss_pred hhhhhHHHHHHhcchh
Q 010849 76 REKEELDHAIALSLAE 91 (499)
Q Consensus 76 ~e~edid~ai~~sL~E 91 (499)
.|++++.+||.+|+.|
T Consensus 2 ~Ed~~L~~Al~~S~~e 17 (18)
T PF02809_consen 2 DEDEDLQRALEMSLEE 17 (18)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHhhhcc
Confidence 4788999999999865
No 60
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=53.05 E-value=12 Score=37.20 Aligned_cols=29 Identities=31% Similarity=0.424 Sum_probs=23.2
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHhCCCCC
Q 010849 371 YGLPRLLTGAILAHELMHGWLRLKGYRNL 399 (499)
Q Consensus 371 ~gLPrl~~g~ilAHE~mHa~l~l~g~~~l 399 (499)
|+=.-+..-+|-|||..||-+.-+||.-|
T Consensus 82 y~~~SiaAvaVAAHEvGHAiQ~a~~Y~pl 110 (222)
T PF04298_consen 82 YNGRSIAAVAVAAHEVGHAIQHAEGYAPL 110 (222)
T ss_pred CCCCCHHHHHHHHHHHhHHHhccccCcHH
Confidence 44455677799999999999999998543
No 61
>PRK11827 hypothetical protein; Provisional
Probab=52.36 E-value=9.5 Score=30.36 Aligned_cols=18 Identities=28% Similarity=0.499 Sum_probs=14.2
Q ss_pred hcccccccccccccccHH
Q 010849 287 GMNMKLDQQIPMLLVERQ 304 (499)
Q Consensus 287 g~~m~~~~~~p~~lv~~~ 304 (499)
++.-+|..+||++|++..
T Consensus 33 ~laYPI~dgIPVlL~deA 50 (60)
T PRK11827 33 NLAFPLRDGIPVLLETEA 50 (60)
T ss_pred CeeccccCCccccCHHHh
Confidence 456678999999999643
No 62
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=52.31 E-value=8.5 Score=29.47 Aligned_cols=30 Identities=23% Similarity=0.787 Sum_probs=22.4
Q ss_pred ccCCCCCccccCCceeEecCCccccchhhhhh
Q 010849 236 RCCSCERLESWNTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 236 ~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sa 267 (499)
.|..|+.-..+-.+ +.+.|| .+|..|+..+
T Consensus 1 ~C~iCg~kigl~~~-~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR-FKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc-eeccCc-cchHHHHHHh
Confidence 47888885444333 678898 7999999887
No 63
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=51.62 E-value=9.8 Score=27.08 Aligned_cols=25 Identities=28% Similarity=0.697 Sum_probs=19.8
Q ss_pred cccCCCCCccccCCceeEecCCccccchhhh
Q 010849 235 SRCCSCERLESWNTRYYSLEDGRSLCLECME 265 (499)
Q Consensus 235 F~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~ 265 (499)
+.|..|+. .+|...||..||..|..
T Consensus 9 ~~C~~C~~------~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGS------RWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCC------eEeEccCCEEEhhhCce
Confidence 45888875 26889999999999853
No 64
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.24 E-value=8 Score=39.93 Aligned_cols=46 Identities=20% Similarity=0.302 Sum_probs=36.4
Q ss_pred CcccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCccCCC
Q 010849 162 CFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIPTN 208 (499)
Q Consensus 162 CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~~~ 208 (499)
=|.|..|.+++.. .....-+..+|..|..+.+ +++|.+|++.+.+.
T Consensus 241 Pf~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 241 PFKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred Ccccccccccccc-chhhcCCceeehhhhccccccCCcceecccccccc
Confidence 4778888888765 4455578899999998876 57999999998874
No 65
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=49.94 E-value=15 Score=34.73 Aligned_cols=20 Identities=35% Similarity=0.293 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHh-CC
Q 010849 377 LTGAILAHELMHGWLRLK-GY 396 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~-g~ 396 (499)
+..+++.||++|++.... |.
T Consensus 6 ~~i~i~~HE~gH~~~a~~~G~ 26 (192)
T PF02163_consen 6 LLISIVLHELGHALAARLYGD 26 (192)
T ss_dssp HHHHHHHHHHHHHHHHHTTT-
T ss_pred ccccccccccccccccccccc
Confidence 457899999999999875 53
No 66
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=49.61 E-value=17 Score=34.59 Aligned_cols=24 Identities=33% Similarity=0.304 Sum_probs=19.0
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHH
Q 010849 366 AILVLYGLPRLLTGAILAHELMHG 389 (499)
Q Consensus 366 ~Ilvl~gLPrl~~g~ilAHE~mHa 389 (499)
+|....+..-+.++.++|||++|.
T Consensus 119 ~i~~~~~~~~~~~a~~~AHelGH~ 142 (199)
T PF01421_consen 119 GIVEDHSRSGLSFAVIIAHELGHN 142 (199)
T ss_dssp EEEE-SSSSHHHHHHHHHHHHHHH
T ss_pred cEeeeccchhHHHHHHHHHHHHHh
Confidence 566666677788999999999995
No 67
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=49.34 E-value=11 Score=31.93 Aligned_cols=30 Identities=20% Similarity=0.466 Sum_probs=21.0
Q ss_pred CCCCCCCCCCccCCCceEeec-CccccCCCc
Q 010849 134 SYKVCGGCNCDIGYGNYLGCM-GTYFHPNCF 163 (499)
Q Consensus 134 ~~~~C~~C~k~I~~g~~l~al-gk~wHp~CF 163 (499)
....|..|+++|..+.++... |..+|..|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 356799999999766655544 455777775
No 68
>KOG3931 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.83 E-value=9.5 Score=40.28 Aligned_cols=22 Identities=32% Similarity=0.452 Sum_probs=19.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHh
Q 010849 373 LPRLLTGAILAHELMHGWLRLK 394 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa~l~l~ 394 (499)
-||--.--.|-|||.||||+..
T Consensus 100 RPRkDLVETLLHEMIHAYlFV~ 121 (484)
T KOG3931|consen 100 RPRKDLVETLLHEMIHAYLFVT 121 (484)
T ss_pred CchHHHHHHHHHHHHHHheeEe
Confidence 3888888999999999999984
No 69
>PRK04860 hypothetical protein; Provisional
Probab=48.77 E-value=19 Score=34.00 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=21.5
Q ss_pred chhHHHHHHHHHHHHHHHHHh-C--CCCCChh
Q 010849 374 PRLLTGAILAHELMHGWLRLK-G--YRNLNPE 402 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l~l~-g--~~~l~~~ 402 (499)
+...+-.|++|||.|.++.+. | ++. +.+
T Consensus 59 ~~~~l~~~v~HEl~H~~~~~~~g~~~~H-g~e 89 (160)
T PRK04860 59 QQAFIDEVVPHELAHLLVYQLFGRVAPH-GKE 89 (160)
T ss_pred cHHHHHhHHHHHHHHHHHHHHcCCCCCC-CHH
Confidence 456668999999999999987 4 455 553
No 70
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=48.21 E-value=22 Score=26.34 Aligned_cols=42 Identities=24% Similarity=0.474 Sum_probs=29.3
Q ss_pred ccCCCCCCCCCCceEeeCCcc-cchhhhhhh--ccccccccCCccC
Q 010849 164 RCRSCGYPITEHEFSLSGKDP-YHKSCFKEL--THPKCEVCHQYIP 206 (499)
Q Consensus 164 ~C~~C~~~L~~~~F~~~dg~~-YC~~CY~~~--f~pkC~~C~~~I~ 206 (499)
.|..|...... -.+..=+.. +|..|..+. ...+|..|.++|.
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 46666666544 344556777 999999887 4788999999886
No 71
>PF12773 DZR: Double zinc ribbon
Probab=47.44 E-value=22 Score=26.32 Aligned_cols=11 Identities=27% Similarity=0.570 Sum_probs=6.3
Q ss_pred cccccCCccCC
Q 010849 197 KCEVCHQYIPT 207 (499)
Q Consensus 197 kC~~C~~~I~~ 207 (499)
.|..|+..+..
T Consensus 31 ~C~~Cg~~~~~ 41 (50)
T PF12773_consen 31 ICPNCGAENPP 41 (50)
T ss_pred CCcCCcCCCcC
Confidence 46666665543
No 72
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=46.14 E-value=18 Score=34.58 Aligned_cols=18 Identities=28% Similarity=0.471 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010849 377 LTGAILAHELMHGWLRLK 394 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~ 394 (499)
+.-++..||++|||....
T Consensus 8 ~~~~i~~HE~aHa~~A~~ 25 (181)
T cd06158 8 VLLAITLHEFAHAYVAYR 25 (181)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455899999999999886
No 73
>smart00235 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.
Probab=45.84 E-value=10 Score=33.90 Aligned_cols=11 Identities=45% Similarity=0.628 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q 010849 380 AILAHELMHGW 390 (499)
Q Consensus 380 ~ilAHE~mHa~ 390 (499)
.+++||+|||-
T Consensus 88 ~~~~HEigHaL 98 (140)
T smart00235 88 GVAAHELGHAL 98 (140)
T ss_pred ccHHHHHHHHh
Confidence 39999999993
No 74
>PF10463 Peptidase_U49: Peptidase U49; InterPro: IPR019504 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This entry contains peptidases belonging to MEROPS peptidase family U49 (Lit peptidase, clan U-). The Lit peptidase from Escherichia coli functions in bacterial cell death in response to infection by Enterobacteria phage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Probab=45.83 E-value=27 Score=34.37 Aligned_cols=50 Identities=26% Similarity=0.112 Sum_probs=38.8
Q ss_pred CCchhHHHHHHHHHHHHHHHHHhCC-CCCChhhhhhHHHHHHHHHhhcccC
Q 010849 372 GLPRLLTGAILAHELMHGWLRLKGY-RNLNPEVEEGICQVLSYMWLESEVL 421 (499)
Q Consensus 372 gLPrl~~g~ilAHE~mHa~l~l~g~-~~l~~~veEG~Cq~~a~~wl~~~~~ 421 (499)
.|=-..++-||+||+.|+.+.--+. ..-...-||==|-..|-.||-+...
T Consensus 95 ~l~~~A~~fil~HE~~Hv~~~h~~~~~~~~~~~eE~~AD~~A~~~il~~~~ 145 (206)
T PF10463_consen 95 DLFCCAIAFILLHELAHVVLGHEGDSSPSQSIQEEKEADSYATEMILSDVG 145 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCccccccchhHHHHHhhhHHHHHHHHHHHH
Confidence 3445678899999999988888776 4455666777899999999866543
No 75
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=45.16 E-value=13 Score=35.21 Aligned_cols=24 Identities=38% Similarity=0.423 Sum_probs=17.2
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHHH
Q 010849 366 AILVLYGLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 366 ~Ilvl~gLPrl~~g~ilAHE~mHa~ 390 (499)
+|....+ +.+..+.++|||++|.+
T Consensus 122 ~v~~~~~-~~~~~~~~~aHElGH~l 145 (192)
T cd04267 122 GVVEDTG-FTLLTALTMAHELGHNL 145 (192)
T ss_pred EEEecCC-cceeehhhhhhhHHhhc
Confidence 4444444 35678899999999975
No 76
>TIGR02414 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile. This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc.
Probab=44.54 E-value=79 Score=37.64 Aligned_cols=36 Identities=25% Similarity=0.519 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHhCCCCC-------ChhhhhhHHHHHHHHHhhc
Q 010849 378 TGAILAHELMHGWLRLKGYRNL-------NPEVEEGICQVLSYMWLES 418 (499)
Q Consensus 378 ~g~ilAHE~mHa~l~l~g~~~l-------~~~veEG~Cq~~a~~wl~~ 418 (499)
..+|+|||+.|-|. | || +..+-||+.-++..+|.+.
T Consensus 283 i~~VIaHElaHqWf---G--NlVT~~~W~~LWLnEGfAty~e~~~~~~ 325 (863)
T TIGR02414 283 IESVIAHEYFHNWT---G--NRVTCRDWFQLSLKEGLTVFRDQEFSAD 325 (863)
T ss_pred HHHHHHHHHHHHHh---c--ceeeecchhhhhhhhhHHHHHHHHHHHH
Confidence 45899999999994 3 22 3457999999888777554
No 77
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=43.56 E-value=15 Score=35.02 Aligned_cols=25 Identities=24% Similarity=0.165 Sum_probs=20.6
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHHH
Q 010849 366 AILVLYGLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 366 ~Ilvl~gLPrl~~g~ilAHE~mHa~ 390 (499)
==+-|.-+|.-+.-+|++|||.|..
T Consensus 152 ln~~L~~~P~~~idYVvvHEL~Hl~ 176 (205)
T PF01863_consen 152 LNWRLVMAPPEVIDYVVVHELCHLR 176 (205)
T ss_pred eecccccCCccHHHHHHHHHHHHhc
Confidence 3345667999999999999999974
No 78
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=43.51 E-value=25 Score=27.96 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=16.2
Q ss_pred CCCCCCCCCccCCCceEeecCccccCCCcccCCCCCC
Q 010849 135 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYP 171 (499)
Q Consensus 135 ~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~ 171 (499)
.+.|..|+..|...+. ---|.|..|+..
T Consensus 7 ~~~CtSCg~~i~~~~~---------~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREK---------AVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCc---------cCEeeCCCCCCe
Confidence 4567788877753321 112667777665
No 79
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=43.02 E-value=13 Score=33.86 Aligned_cols=14 Identities=29% Similarity=0.223 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 010849 377 LTGAILAHELMHGW 390 (499)
Q Consensus 377 ~~g~ilAHE~mHa~ 390 (499)
..-.+++||++||-
T Consensus 93 ~~~~~~~HEiGHaL 106 (165)
T cd04268 93 RLRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHHh
Confidence 46799999999994
No 80
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=42.05 E-value=9.2 Score=37.41 Aligned_cols=45 Identities=16% Similarity=0.266 Sum_probs=35.3
Q ss_pred CcccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCccCC
Q 010849 162 CFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIPT 207 (499)
Q Consensus 162 CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~~ 207 (499)
=|.|..|.+.... .....-|..||..|+.+.+ ++.|.+|++.-.+
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 5788999887654 3444568899999998876 7899999987665
No 81
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=41.96 E-value=24 Score=29.81 Aligned_cols=28 Identities=32% Similarity=0.694 Sum_probs=22.8
Q ss_pred ccCCCCCCCCCCceEee-CCcccchhhhh
Q 010849 164 RCRSCGYPITEHEFSLS-GKDPYHKSCFK 191 (499)
Q Consensus 164 ~C~~C~~~L~~~~F~~~-dg~~YC~~CY~ 191 (499)
.|..|+++|....|... +|..+|..|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 59999999998777654 77888888865
No 82
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=41.51 E-value=6.9 Score=32.22 Aligned_cols=18 Identities=28% Similarity=0.604 Sum_probs=13.1
Q ss_pred CCCCCCCCCCCCccCCCc
Q 010849 132 PRSYKVCGGCNCDIGYGN 149 (499)
Q Consensus 132 ~~~~~~C~~C~k~I~~g~ 149 (499)
..+...|.+|++.|..|.
T Consensus 4 ks~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 4 KSGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp SSSTEBETTTSCBE-TTS
T ss_pred CCCCccCcccCCcCCCCC
Confidence 345678999999997664
No 83
>KOG3624 consensus M13 family peptidase [Amino acid transport and metabolism]
Probab=40.52 E-value=13 Score=42.47 Aligned_cols=15 Identities=40% Similarity=0.687 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHH
Q 010849 377 LTGAILAHELMHGWL 391 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l 391 (499)
..|.|||||++|++=
T Consensus 517 ~iG~vigHEl~H~FD 531 (687)
T KOG3624|consen 517 GIGFVIGHELTHGFD 531 (687)
T ss_pred HHHHHHHHHHhhccc
Confidence 579999999999873
No 84
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=40.23 E-value=4.2 Score=35.29 Aligned_cols=49 Identities=22% Similarity=0.478 Sum_probs=27.4
Q ss_pred CCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccc
Q 010849 138 CGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYH 186 (499)
Q Consensus 138 C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC 186 (499)
|..|...+.+-.+....-..+++.+..|..|.+.|+-.++.....=|||
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 5555555543344444445667777777777777765555544443333
No 85
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=40.00 E-value=19 Score=32.79 Aligned_cols=16 Identities=31% Similarity=0.306 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHHHHHH
Q 010849 375 RLLTGAILAHELMHGW 390 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~ 390 (499)
...+..++|||++|+.
T Consensus 93 ~~~~~~~~~HElGH~L 108 (167)
T cd00203 93 TKEGAQTIAHELGHAL 108 (167)
T ss_pred cccchhhHHHHHHHHh
Confidence 3467899999999985
No 86
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=39.82 E-value=19 Score=32.42 Aligned_cols=17 Identities=18% Similarity=0.075 Sum_probs=13.4
Q ss_pred CchhHHHHHHHHHHHHH
Q 010849 373 LPRLLTGAILAHELMHG 389 (499)
Q Consensus 373 LPrl~~g~ilAHE~mHa 389 (499)
.+......|++||+.||
T Consensus 100 ~~~~~~~~v~~HEiGHa 116 (154)
T PF00413_consen 100 DSGNDLQSVAIHEIGHA 116 (154)
T ss_dssp SSSEEHHHHHHHHHHHH
T ss_pred hhhhhhhhhhhhccccc
Confidence 34445678999999999
No 87
>PF04228 Zn_peptidase: Putative neutral zinc metallopeptidase; InterPro: IPR007343 Members of this family of bacterial proteins are described as hypothetical proteins or zinc metallopeptidases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=39.76 E-value=23 Score=36.64 Aligned_cols=21 Identities=33% Similarity=0.376 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHHHHHHhC
Q 010849 375 RLLTGAILAHELMHGWLRLKG 395 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~l~l~g 395 (499)
.+...+|||||+.|.-+.|.|
T Consensus 167 ~~a~ayVlAHEyGHHVQ~l~G 187 (292)
T PF04228_consen 167 DFAQAYVLAHEYGHHVQNLLG 187 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 456678999999999999987
No 88
>KOG3714 consensus Meprin A metalloprotease [Posttranslational modification, protein turnover, chaperones]
Probab=39.66 E-value=14 Score=40.00 Aligned_cols=14 Identities=36% Similarity=0.434 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHH
Q 010849 380 AILAHELMHGWLRL 393 (499)
Q Consensus 380 ~ilAHE~mHa~l~l 393 (499)
.|.+||||||==..
T Consensus 161 G~i~HEl~HaLGf~ 174 (411)
T KOG3714|consen 161 GTIVHELMHALGFW 174 (411)
T ss_pred chhHHHHHHHhhhh
Confidence 57899999995443
No 89
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.60 E-value=18 Score=41.53 Aligned_cols=55 Identities=13% Similarity=0.063 Sum_probs=26.5
Q ss_pred eccccC-CCCeeeeeecccccccccee-EEEEEEEcCCch-hHHHHHHHHHHHHHHHHH
Q 010849 338 LRRPRI-GGNRLVGMRTQPQKLTRKCE-VTAILVLYGLPR-LLTGAILAHELMHGWLRL 393 (499)
Q Consensus 338 ~~~~~~-~~~~~~~~~~~~~~~~r~~~-v~~Ilvl~gLPr-l~~g~ilAHE~mHa~l~l 393 (499)
+..|.+ .+-+.+...++...+.++.+ -=.|+|.+ -|. -+..+++.|.+-..|-+.
T Consensus 501 L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq~-~p~~~~~~~l~~~d~~~F~~~E 558 (665)
T PRK14873 501 LGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVA-ESSLPTVQALIRWDPVGHAERE 558 (665)
T ss_pred hcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEEe-CCCCHHHHHHHhCCHHHHHHHH
Confidence 344544 22244444444443333211 11234444 776 455667778777666443
No 90
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=38.84 E-value=30 Score=25.11 Aligned_cols=39 Identities=26% Similarity=0.546 Sum_probs=25.6
Q ss_pred cCCCCCCCCC--CceEeeCCcccchhhhhhhc--cccccccCC
Q 010849 165 CRSCGYPITE--HEFSLSGKDPYHKSCFKELT--HPKCEVCHQ 203 (499)
Q Consensus 165 C~~C~~~L~~--~~F~~~dg~~YC~~CY~~~f--~pkC~~C~~ 203 (499)
|..|...... ..+...=+..+|..|..+.. ..+|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 5666666632 23444568899999998876 556666653
No 91
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=38.66 E-value=25 Score=24.08 Aligned_cols=40 Identities=20% Similarity=0.455 Sum_probs=22.2
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhhhc---cccccccCCc
Q 010849 165 CRSCGYPITEHEFSLSGKDPYHKSCFKELT---HPKCEVCHQY 204 (499)
Q Consensus 165 C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f---~pkC~~C~~~ 204 (499)
|..|...+........=+..||..|..+.+ ..+|..|+..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 555655553222222356778888876543 3457666654
No 92
>COG5504 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=39 Score=34.39 Aligned_cols=39 Identities=31% Similarity=0.462 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHh------C-CCCCChhhhhhHHHHHHHHHhhc
Q 010849 379 GAILAHELMHGWLRLK------G-YRNLNPEVEEGICQVLSYMWLES 418 (499)
Q Consensus 379 g~ilAHE~mHa~l~l~------g-~~~l~~~veEG~Cq~~a~~wl~~ 418 (499)
-|++|||+=|. -|+. | ...|+.-|-||+.|-.++.=..+
T Consensus 141 ~aliaHE~HH~-~R~~~i~~~eg~vtLle~lV~EGLAE~av~E~~Gr 186 (280)
T COG5504 141 PALIAHEYHHN-CRLRYIDYGEGSVTLLEALVMEGLAEHAVFELFGR 186 (280)
T ss_pred HHHHHHHHHhh-heecccccCCCceeHHHHHHHHHHHHHHHHHHhCc
Confidence 37899999996 2333 1 23468899999999876654433
No 93
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=38.25 E-value=51 Score=32.80 Aligned_cols=39 Identities=26% Similarity=0.137 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhh
Q 010849 377 LTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLE 417 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~g~~~l~~~veEG~Cq~~a~~wl~ 417 (499)
-+-.||-||+.||.+-+.+.|.|= -||----.+|-+.|-
T Consensus 91 ~~~~~l~HE~GHAlI~~~~lPv~G--rEEDaaD~lAa~~ll 129 (220)
T PF14247_consen 91 NVLFTLYHELGHALIDDLDLPVLG--REEDAADQLAALLLL 129 (220)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccc--chhhHHHHHHHHHHh
Confidence 456899999999999999877764 355555555544443
No 94
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=38.08 E-value=26 Score=35.69 Aligned_cols=27 Identities=37% Similarity=0.598 Sum_probs=19.9
Q ss_pred EcCCchhHHHHHHHHHHHHHHHHHh-CCC
Q 010849 370 LYGLPRLLTGAILAHELMHGWLRLK-GYR 397 (499)
Q Consensus 370 l~gLPrl~~g~ilAHE~mHa~l~l~-g~~ 397 (499)
++++. .++-+++.||++||+.... |.+
T Consensus 111 ~~~~i-aL~isv~iHElgHa~~Ar~~G~~ 138 (263)
T cd06159 111 PYGII-ALVVGVVVHELSHGILARVEGIK 138 (263)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHcCCE
Confidence 34443 3677899999999999886 543
No 95
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=37.53 E-value=23 Score=36.42 Aligned_cols=18 Identities=28% Similarity=0.340 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010849 377 LTGAILAHELMHGWLRLK 394 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~ 394 (499)
++.+++.||++||+....
T Consensus 134 l~isvvvHElgHal~A~~ 151 (277)
T cd06162 134 LLISGVVHEMGHGVAAVR 151 (277)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 577999999999999885
No 96
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=36.95 E-value=32 Score=33.52 Aligned_cols=21 Identities=38% Similarity=0.507 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHHHHHHHh-CC
Q 010849 376 LLTGAILAHELMHGWLRLK-GY 396 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~-g~ 396 (499)
.++.+++.||+.|++.... |.
T Consensus 36 ~l~~~v~iHElgH~~~A~~~G~ 57 (208)
T cd06161 36 LLFLSVLLHELGHALVARRYGI 57 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5788999999999998776 64
No 97
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=36.34 E-value=23 Score=30.43 Aligned_cols=36 Identities=19% Similarity=0.583 Sum_probs=24.0
Q ss_pred ccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCC
Q 010849 164 RCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPT 207 (499)
Q Consensus 164 ~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~ 207 (499)
.|..|...+.. .+.-||..|..+ .-.|+.|++.|..
T Consensus 46 ~C~~CK~~v~q------~g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 46 KCKICKTKVHQ------PGAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred ccccccccccc------CCCccChhhhcc--cCcccccCCeecc
Confidence 45555554432 356788888665 3589999999865
No 98
>PHA00527 hypothetical protein
Probab=36.24 E-value=1.3e+02 Score=26.69 Aligned_cols=47 Identities=26% Similarity=0.364 Sum_probs=31.9
Q ss_pred EEEEEEEcCCchhHHHHHHHHHHHHHHHHH-h--CCCCCChhhhhhHHHHHHHHH
Q 010849 364 VTAILVLYGLPRLLTGAILAHELMHGWLRL-K--GYRNLNPEVEEGICQVLSYMW 415 (499)
Q Consensus 364 v~~Ilvl~gLPrl~~g~ilAHE~mHa~l~l-~--g~~~l~~~veEG~Cq~~a~~w 415 (499)
+.-|-|..|- .+.||||+.|.=... . |...=|-+.-|-.|-+|+-|.
T Consensus 64 L~~~GVFNGK-----~~T~~HECAH~AF~vC~~VGV~~E~G~ANETYCY~~~R~~ 113 (129)
T PHA00527 64 LYLLGVFNGK-----AATLVHECAHVAFYVCRDVGVTTEPGDANETYCYMLDRMF 113 (129)
T ss_pred EEEEEEeccH-----HHHHHHHHHHHHHHHHHhcCcccCCCccchhHHHHHHHHH
Confidence 3455566663 488999999965444 3 555556677788888887663
No 99
>PRK09672 phage exclusion protein Lit; Provisional
Probab=35.89 E-value=50 Score=34.42 Aligned_cols=50 Identities=22% Similarity=0.161 Sum_probs=39.0
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHhCCCCC-ChhhhhhHHHHHHHHHhhccc
Q 010849 371 YGLPRLLTGAILAHELMHGWLRLKGYRNL-NPEVEEGICQVLSYMWLESEV 420 (499)
Q Consensus 371 ~gLPrl~~g~ilAHE~mHa~l~l~g~~~l-~~~veEG~Cq~~a~~wl~~~~ 420 (499)
.-|=-..++-|+.||+.|+.+-..++... +-.-||==|...|.-||-...
T Consensus 158 ndLfl~A~a~i~~HEiaHv~~~h~~~~~~e~s~~eE~eaDs~At~~il~~~ 208 (305)
T PRK09672 158 NDLFLCALAWILLHEIAHVEFQHSSLESNEDSIQEEKEADSYATNWLLSKS 208 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccccCchHHHHHHHHHHHHHHHHHHhcc
Confidence 34445788999999999999999886444 334567779999999997744
No 100
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.86 E-value=40 Score=40.37 Aligned_cols=52 Identities=21% Similarity=0.379 Sum_probs=32.3
Q ss_pred CCCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCCC
Q 010849 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTN 208 (499)
Q Consensus 134 ~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~ 208 (499)
+.+.|..|+.... =|+|..|+.. .....+|..|-.......|..|+..+.+.
T Consensus 625 g~RfCpsCG~~t~---------------~frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 625 GRRKCPSCGKETF---------------YRRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTPY 676 (1121)
T ss_pred cCccCCCCCCcCC---------------cccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCcc
Confidence 3456777776531 1677777766 12234577776665566788888776654
No 101
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=35.86 E-value=26 Score=32.79 Aligned_cols=20 Identities=30% Similarity=0.406 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHh-CC
Q 010849 377 LTGAILAHELMHGWLRLK-GY 396 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~-g~ 396 (499)
++.++..||++|++.... |.
T Consensus 7 ~~i~i~iHE~gH~~~A~~~G~ 27 (180)
T cd05709 7 LLISVTVHELGHALVARRLGV 27 (180)
T ss_pred HHHHHHHHHHHHHHHHHHcCC
Confidence 456899999999996654 65
No 102
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=35.77 E-value=21 Score=35.52 Aligned_cols=27 Identities=22% Similarity=0.170 Sum_probs=22.0
Q ss_pred EEEEEEEcCCchhHHHHHHHHHHHHHH
Q 010849 364 VTAILVLYGLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 364 v~~Ilvl~gLPrl~~g~ilAHE~mHa~ 390 (499)
++==+.|-.+|.-+..+|++|||.|--
T Consensus 161 i~~~~~l~~~p~~~i~YVvvHELaHLk 187 (223)
T COG1451 161 IRFNWRLVMAPEEVIDYVVVHELAHLK 187 (223)
T ss_pred EEeehhhhcCCHHHHHHHHHHHHHHHh
Confidence 334456778999999999999999953
No 103
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=35.27 E-value=22 Score=35.79 Aligned_cols=19 Identities=42% Similarity=0.169 Sum_probs=15.8
Q ss_pred CCchhHHHHHHHHHHHHHH
Q 010849 372 GLPRLLTGAILAHELMHGW 390 (499)
Q Consensus 372 gLPrl~~g~ilAHE~mHa~ 390 (499)
-|.+.-..+|||||+.|.-
T Consensus 151 ~l~~dEl~aVlaHElgHi~ 169 (302)
T COG0501 151 LLNDDELEAVLAHELGHIK 169 (302)
T ss_pred hCCHHHHHHHHHHHHHHHh
Confidence 5677778899999999974
No 104
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=35.21 E-value=46 Score=37.17 Aligned_cols=45 Identities=24% Similarity=0.236 Sum_probs=29.2
Q ss_pred hHHHHHHHHHHHHHHHHH--h-C----CCCCChhhhh---hHHHHHHHHHhhccc
Q 010849 376 LLTGAILAHELMHGWLRL--K-G----YRNLNPEVEE---GICQVLSYMWLESEV 420 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l--~-g----~~~l~~~veE---G~Cq~~a~~wl~~~~ 420 (499)
.---.+||||++||+--. + + +...+.++-| =+++.+.+-||....
T Consensus 335 ~~dv~TL~HElGHa~H~~~s~~~~~~~~~~~~~~~aE~aS~~~E~l~~~~l~~~~ 389 (549)
T TIGR02289 335 SGDIDVLTHEAGHAFHVYESRKDLLPEYRWPTYEAAELASMSMELLSMPWWDLFY 389 (549)
T ss_pred hhHHHHHHHHhhHHHHHHHhcCCcccccccCcchhhhhhHHHHHHHHHHHHHHHc
Confidence 344578999999997432 2 2 2223455555 577888888877654
No 105
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=34.92 E-value=25 Score=33.24 Aligned_cols=20 Identities=25% Similarity=0.237 Sum_probs=14.5
Q ss_pred chhHHHHHHHHHHHHHHHHH
Q 010849 374 PRLLTGAILAHELMHGWLRL 393 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l~l 393 (499)
|-.....++|||+.|.+=-.
T Consensus 138 ~~~~~~~~~AHEiGH~lGa~ 157 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNLGAP 157 (196)
T ss_dssp -HHHHHHHHHHHHHHHTT--
T ss_pred CCCceehhhHHhHHHhcCCC
Confidence 46777899999999987433
No 106
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=34.69 E-value=33 Score=34.00 Aligned_cols=21 Identities=38% Similarity=0.583 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHHHh-CC
Q 010849 376 LLTGAILAHELMHGWLRLK-GY 396 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~-g~ 396 (499)
.++.+++.||+.|++.... |+
T Consensus 51 ~l~~~v~iHElgH~~~A~~~G~ 72 (227)
T cd06164 51 LLFASVLLHELGHSLVARRYGI 72 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5789999999999998775 54
No 107
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.26 E-value=25 Score=22.51 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=4.7
Q ss_pred CCCCCCccC
Q 010849 138 CGGCNCDIG 146 (499)
Q Consensus 138 C~~C~k~I~ 146 (499)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 455555553
No 108
>PF05299 Peptidase_M61: M61 glycyl aminopeptidase; InterPro: IPR007963 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M61 (glycyl aminopeptidase family, clan MA(E)).The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example is glycyl aminopeptidase from Sphingomonas capsulata.
Probab=33.57 E-value=14 Score=33.43 Aligned_cols=41 Identities=27% Similarity=0.380 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHH--HHhC--C-------CCC--ChhhhhhHHHHHHHHHhhc
Q 010849 378 TGAILAHELMHGWL--RLKG--Y-------RNL--NPEVEEGICQVLSYMWLES 418 (499)
Q Consensus 378 ~g~ilAHE~mHa~l--~l~g--~-------~~l--~~~veEG~Cq~~a~~wl~~ 418 (499)
+-.++|||+-|+|- |++. . |+. -+.|-||+=+.++.+-|-+
T Consensus 4 ~l~l~sHEffH~WnvkrirP~~l~p~dy~~~~~t~~LWv~EG~T~Y~~~l~l~R 57 (122)
T PF05299_consen 4 FLGLLSHEFFHSWNVKRIRPAELGPFDYEKPNYTELLWVYEGFTSYYGDLLLVR 57 (122)
T ss_pred hhhhhhhhccccccceEeccccccCCCCCCCCCCCCEeeeeCcHHHHHHHHHHH
Confidence 45789999999997 3332 1 111 2478899999999886655
No 109
>cd04281 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
Probab=33.54 E-value=22 Score=34.80 Aligned_cols=11 Identities=45% Similarity=0.528 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q 010849 380 AILAHELMHGW 390 (499)
Q Consensus 380 ~ilAHE~mHa~ 390 (499)
.+++||||||-
T Consensus 89 Gti~HEl~HaL 99 (200)
T cd04281 89 GIVVHELGHVI 99 (200)
T ss_pred chHHHHHHHHh
Confidence 48999999995
No 110
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=32.66 E-value=29 Score=26.54 Aligned_cols=29 Identities=31% Similarity=0.657 Sum_probs=21.0
Q ss_pred ccCCCCCCCCCC-ceEeeCCcccchhhhhhh
Q 010849 164 RCRSCGYPITEH-EFSLSGKDPYHKSCFKEL 193 (499)
Q Consensus 164 ~C~~C~~~L~~~-~F~~~dg~~YC~~CY~~~ 193 (499)
.|..|+..++-- .+-..|| ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 377788777643 3666777 6899999885
No 111
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=32.45 E-value=24 Score=32.37 Aligned_cols=28 Identities=21% Similarity=0.558 Sum_probs=20.4
Q ss_pred cCCCCCccccCCceeEecCCccccchhhhhhccCC
Q 010849 237 CCSCERLESWNTRYYSLEDGRSLCLECMESAIMDT 271 (499)
Q Consensus 237 C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt 271 (499)
|..|+.++ |. +||..||+.|-...+..+
T Consensus 31 Cp~Cg~PL------F~-KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 31 CPKCGTPL------FR-KDGEVFCPVCGYREVVVE 58 (131)
T ss_pred CcccCCcc------ee-eCCeEECCCCCceEEEee
Confidence 77888843 55 899999999975544433
No 112
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=32.37 E-value=26 Score=32.03 Aligned_cols=16 Identities=38% Similarity=0.235 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHHHHHH
Q 010849 375 RLLTGAILAHELMHGW 390 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~ 390 (499)
..-+-+|+.||++||-
T Consensus 101 ~~~~~~~~~HEiGHaL 116 (156)
T cd04279 101 AENLQAIALHELGHAL 116 (156)
T ss_pred chHHHHHHHHHhhhhh
Confidence 4567899999999983
No 113
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=32.27 E-value=22 Score=38.32 Aligned_cols=25 Identities=36% Similarity=0.533 Sum_probs=21.7
Q ss_pred chhhhhhhHHHHHHhcchhhhcCcC
Q 010849 73 RADREKEELDHAIALSLAEDLKRPN 97 (499)
Q Consensus 73 ~~~~e~edid~ai~~sL~Ee~kk~~ 97 (499)
.+.+|.|||..||++||.|.++.++
T Consensus 161 ~~k~EeEdiaKAi~lSL~E~~~Q~k 185 (462)
T KOG2199|consen 161 SSKQEEEDIAKAIELSLKEQEKQKK 185 (462)
T ss_pred cccccHHHHHHHHHhhHHHHhhchh
Confidence 3568999999999999999988755
No 114
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=32.13 E-value=55 Score=38.81 Aligned_cols=115 Identities=22% Similarity=0.297 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHHHHHhCCCCC----ChhhhhhHHHHHHHHHhhcccC------CC---CCCC-C----CCCCC------C
Q 010849 379 GAILAHELMHGWLRLKGYRNL----NPEVEEGICQVLSYMWLESEVL------PD---YRNM-P----STSSA------S 434 (499)
Q Consensus 379 g~ilAHE~mHa~l~l~g~~~l----~~~veEG~Cq~~a~~wl~~~~~------~~---~~~~-~----~~~~~------~ 434 (499)
.++.||||.|.|.-= ...+ +..+-||+--++.+.|.+.... .. .++. + +..++ .
T Consensus 308 ~~viaHElaHqWfGn--lVT~~~W~~lWLnEgfat~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~~~~hPi~~~~ 385 (859)
T COG0308 308 EEVIAHELAHQWFGN--LVTMKWWDDLWLNEGFATFREVLWSEDLGGRAWKRWEDFRTLRTSIALAEDSLPSSHPIRVDV 385 (859)
T ss_pred HHHHHHHHhhhcccc--eeeccCHHHHHHhhhhHHHHHHHHHHHhcchHHHHHHHHHHHhhhHHHhhccccccCCcccCC
Confidence 449999999999421 0111 3778899999999999887542 00 0000 0 00000 0
Q ss_pred ---------CCCCCCCCCC-----------chHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHhCHHHHHHHHHhh
Q 010849 435 ---------TSSSSSKKGG-----------KSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKYGLRRTLEHIRLT 494 (499)
Q Consensus 435 ---------~~~~~~~~g~-----------~~~~e~~l~~~~~~qi~~d~s~vYGdGfR~~~~a~~~~gl~~~l~~i~~~ 494 (499)
.+.++=.||. ...|-+-|..||.. .+-..+.++=|..+.+.+...-|..+++.-...
T Consensus 386 ~~~~ei~~~fD~i~Y~KGs~vlrml~~~lG~e~F~kgl~~yf~~---h~~~~~~~~Dl~~a~~~~sg~dl~~~~~~w~~q 462 (859)
T COG0308 386 YDPKEINDFFDAIVYEKGASVLRMLETLLGEEAFRKGLSLYFKR---HAGGNATTMDLWKALEDASGKDLSAFFESWLSQ 462 (859)
T ss_pred CCccchhhhcchhhcchhHHHHHHHHHHHCHHHHHHHHHHHHHh---cCCCCCCHHHHHHHHHHHhCCcHHHHHHHHHhC
Confidence 0000112222 44566677777766 445556677777777777766677666666555
Q ss_pred CCCC
Q 010849 495 GNFP 498 (499)
Q Consensus 495 g~~p 498 (499)
.-+|
T Consensus 463 ~G~P 466 (859)
T COG0308 463 AGYP 466 (859)
T ss_pred CCCC
Confidence 5555
No 115
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=31.67 E-value=27 Score=32.58 Aligned_cols=20 Identities=40% Similarity=0.665 Sum_probs=13.6
Q ss_pred chhHHHHHHHHHHHHHHHHHh
Q 010849 374 PRLLTGAILAHELMHGWLRLK 394 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l~l~ 394 (499)
+..-.|.+|+||++| ||-|.
T Consensus 65 ~~~~~g~TltHEvGH-~LGL~ 84 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGH-WLGLY 84 (154)
T ss_dssp TTS-SSHHHHHHHHH-HTT--
T ss_pred Cccccccchhhhhhh-hhccc
Confidence 356668999999999 55553
No 116
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=31.65 E-value=33 Score=36.32 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=12.8
Q ss_pred CCcCCCCcccCCCCCc
Q 010849 228 SHEHDHTSRCCSCERL 243 (499)
Q Consensus 228 ~H~H~~CF~C~~C~r~ 243 (499)
+|+-+.||+|--|+++
T Consensus 73 ~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 73 SHYDPQSFTCPYCGIM 88 (381)
T ss_pred cccccccccCCccccc
Confidence 3556779999999985
No 117
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=31.64 E-value=38 Score=24.64 Aligned_cols=32 Identities=44% Similarity=0.684 Sum_probs=21.2
Q ss_pred ccCCCCCccccCCceeEecCCccccchhhhhh
Q 010849 236 RCCSCERLESWNTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 236 ~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sa 267 (499)
+|+-|++.....+..+.-.++-.+|..|.+.+
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 58899997766666665555789999998665
No 118
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.56 E-value=40 Score=38.68 Aligned_cols=37 Identities=24% Similarity=0.671 Sum_probs=30.4
Q ss_pred ccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccCC
Q 010849 164 RCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPT 207 (499)
Q Consensus 164 ~C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~ 207 (499)
.|..|+... .++..||..|-..+-...|..|+..++.
T Consensus 3 ~Cp~Cg~~n-------~~~akFC~~CG~~l~~~~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFEN-------PNNNRFCQKCGTSLTHKPCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCcC-------CCCCccccccCCCCCCCcCCCCCCCCCc
Confidence 577887664 4699999999888877889999998876
No 119
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=31.55 E-value=28 Score=32.87 Aligned_cols=18 Identities=28% Similarity=0.108 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHhC
Q 010849 378 TGAILAHELMHGWLRLKG 395 (499)
Q Consensus 378 ~g~ilAHE~mHa~l~l~g 395 (499)
...++|||+.|.+=.-+.
T Consensus 111 ~~~~~aHElGH~lGa~Hd 128 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHD 128 (173)
T ss_dssp HHHHHHHHHHHHHT---S
T ss_pred eeeeehhhhHhhcCCCCC
Confidence 567899999999855553
No 120
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=31.52 E-value=50 Score=36.56 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHhCCCCCC--------hhhhhhHHHHHHHH
Q 010849 381 ILAHELMHGWLRLKGYRNLN--------PEVEEGICQVLSYM 414 (499)
Q Consensus 381 ilAHE~mHa~l~l~g~~~l~--------~~veEG~Cq~~a~~ 414 (499)
++-|||.||+..+. |+++| |-..|-+|+++|..
T Consensus 250 t~~HE~GH~~yy~~-y~~~p~~~r~~anp~fheav~e~~smS 290 (477)
T cd06461 250 TVHHEMGHIQYYLQ-YKDQPVLFREGANPGFHEAVGDAIALS 290 (477)
T ss_pred HHHHHHHHHHHHHH-hccCCHHHhCCCCCChHHHHHHHHHHh
Confidence 46699999987766 55554 44455789888653
No 121
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=31.39 E-value=31 Score=33.13 Aligned_cols=16 Identities=19% Similarity=0.102 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 010849 377 LTGAILAHELMHGWLR 392 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~ 392 (499)
.+..++.||+|||-=.
T Consensus 91 ~~~~~i~HElgHaLG~ 106 (198)
T cd04327 91 EFSRVVLHEFGHALGF 106 (198)
T ss_pred hHHHHHHHHHHHHhcC
Confidence 4456999999999633
No 122
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=31.37 E-value=23 Score=25.55 Aligned_cols=22 Identities=14% Similarity=0.184 Sum_probs=12.7
Q ss_pred CCCCCCccCC-CceEeecCcccc
Q 010849 138 CGGCNCDIGY-GNYLGCMGTYFH 159 (499)
Q Consensus 138 C~~C~k~I~~-g~~l~algk~wH 159 (499)
|.-|+.+|.. ..++...++.||
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~ 23 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY 23 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE
Confidence 5567777742 234556666666
No 123
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=31.19 E-value=66 Score=34.30 Aligned_cols=107 Identities=23% Similarity=0.288 Sum_probs=61.0
Q ss_pred EEEEcCCchhH-----HHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCC
Q 010849 367 ILVLYGLPRLL-----TGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPSTSSASTSSSSSK 441 (499)
Q Consensus 367 Ilvl~gLPrl~-----~g~ilAHE~mHa~l~l~g~~~l~~~veEG~Cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~ 441 (499)
|+|-.||=.++ ..++|||||.|+=-+- |...-..+-+|+|---+....|.+.... .. ..-
T Consensus 108 lYitRGLlAland~sEvAAVl~HEmgHVtAnH-gi~rQ~~e~a~~ia~rvva~vl~~~~ag-k~-------------A~~ 172 (479)
T COG4784 108 LYITRGLLALANDSSEVAAVLAHEMGHVTANH-GIQRQQREAAEVIASRVVAEVLGSDAAG-KQ-------------ALI 172 (479)
T ss_pred EEEehhHHHHcCCHHHHHHHHHhhhhheecch-hHHHHHHHHHHHHHHHHHHHHhCCcchh-hH-------------HHh
Confidence 56666776554 5789999999975432 3444566777777544444434333211 00 000
Q ss_pred CCCchHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHH-HHHhCHHHHHHHHHhhCCC
Q 010849 442 KGGKSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAA-VNKYGLRRTLEHIRLTGNF 497 (499)
Q Consensus 442 ~g~~~~~e~~l~~~~~~qi~~d~s~vYGdGfR~~~~a-~~~~gl~~~l~~i~~~g~~ 497 (499)
.|+ .+|+.|=++ +|--.| +-|-|..-+| |+-|-..++|+.+..+-.|
T Consensus 173 rGk-----lrla~fsRn-qELqAD---~iG~~~lgeAGYDP~A~~rfl~sm~ay~~F 220 (479)
T COG4784 173 RGK-----LRLAQFSRN-QELQAD---AIGIKMLGEAGYDPYAAARFLQSMAAYTDF 220 (479)
T ss_pred hhh-----HHHhhhccc-hhhhhh---hhhHHHHHhcCCChHHHHHHHHHHHhhhhh
Confidence 121 255555444 343333 4566665554 7777788888888777666
No 124
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=30.77 E-value=28 Score=34.18 Aligned_cols=28 Identities=29% Similarity=0.309 Sum_probs=23.4
Q ss_pred EcCCchhHHHHHHHHHHHHHHHHHhCCC
Q 010849 370 LYGLPRLLTGAILAHELMHGWLRLKGYR 397 (499)
Q Consensus 370 l~gLPrl~~g~ilAHE~mHa~l~l~g~~ 397 (499)
-|+=|.+...++.|||..||.+-..+|+
T Consensus 84 ~y~g~Sia~~aVAAHEVGHAiQd~~~Y~ 111 (226)
T COG2738 84 NYYGPSIAAIAVAAHEVGHAIQDQEDYA 111 (226)
T ss_pred ccCCccHHHHHHHHHHhhHHHhhhcccH
Confidence 3677889999999999999987777653
No 125
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=30.32 E-value=48 Score=32.37 Aligned_cols=30 Identities=13% Similarity=0.317 Sum_probs=19.2
Q ss_pred CcccCCCCCCCCCCceEeeCCcccchhhhhh
Q 010849 162 CFRCRSCGYPITEHEFSLSGKDPYHKSCFKE 192 (499)
Q Consensus 162 CF~C~~C~~~L~~~~F~~~dg~~YC~~CY~~ 192 (499)
.|.|..|...+.+ .....-+..||..|..+
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~ 47 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHK 47 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHH
Confidence 4667777666544 34445677888888754
No 126
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=30.26 E-value=53 Score=25.23 Aligned_cols=27 Identities=33% Similarity=0.470 Sum_probs=18.4
Q ss_pred CCchhhHHHHHHHHHHhCHHHHHHHHHhh
Q 010849 466 PAYGEGFRIANAAVNKYGLRRTLEHIRLT 494 (499)
Q Consensus 466 ~vYGdGfR~~~~a~~~~gl~~~l~~i~~~ 494 (499)
.|||-|-..|.+-++ .|++ +|+.|+..
T Consensus 6 ~I~GVG~~tA~~w~~-~G~r-tl~Dl~~~ 32 (52)
T PF10391_consen 6 GIWGVGPKTARKWYA-KGIR-TLEDLRKS 32 (52)
T ss_dssp TSTT--HHHHHHHHH-TT---SHHHHHHG
T ss_pred hcccccHHHHHHHHH-hCCC-CHHHHhhh
Confidence 499999999999998 7875 56666653
No 127
>cd04282 ZnMc_meprin Zinc-dependent metalloprotease, meprin_like subfamily. Meprins are membrane-bound or secreted extracellular proteases, which cleave a variety of targets, including peptides such as parathyroid hormone, gastrin, and cholecystokinin, cytokines such as osteopontin, and proteins such as collagen IV, fibronectin, casein and gelatin. Meprins may also be able to release proteins from the cell surface. Closely related meprin alpha- and beta-subunits form homo- and hetero-oligomers; these complexes are found on epithelial cells of the intestine, for example, and are also expressed in certain cancer cells.
Probab=30.24 E-value=26 Score=35.06 Aligned_cols=12 Identities=33% Similarity=0.631 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 010849 379 GAILAHELMHGW 390 (499)
Q Consensus 379 g~ilAHE~mHa~ 390 (499)
-.+++||||||-
T Consensus 121 ~Gti~HEl~Hal 132 (230)
T cd04282 121 KATVEHEFLHAL 132 (230)
T ss_pred CchHHHHHHHHh
Confidence 368999999995
No 128
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=29.87 E-value=26 Score=32.39 Aligned_cols=36 Identities=25% Similarity=0.646 Sum_probs=27.2
Q ss_pred ccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHh
Q 010849 236 RCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYE 286 (499)
Q Consensus 236 ~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~ 286 (499)
.|..|+++|. . .++.+|+.|++.. ...|..|.+|.+
T Consensus 5 nC~~CgklF~-------~-~~~~iCp~C~~~~-------e~~f~kV~~yLr 40 (137)
T TIGR03826 5 NCPKCGRLFV-------K-TGRDVCPSCYEEE-------EREFEKVYKFLR 40 (137)
T ss_pred cccccchhhh-------h-cCCccCHHHhHHH-------HHHHHHHHHHHH
Confidence 4888888653 2 2688999999776 456888889875
No 129
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=29.84 E-value=21 Score=35.00 Aligned_cols=18 Identities=17% Similarity=0.278 Sum_probs=12.9
Q ss_pred ceEeeCCcccchhhhhhh
Q 010849 176 EFSLSGKDPYHKSCFKEL 193 (499)
Q Consensus 176 ~F~~~dg~~YC~~CY~~~ 193 (499)
.-...+|++.|+.||.+.
T Consensus 186 ~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 186 RAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred hhhhcCCceecccccccc
Confidence 334567888999998753
No 130
>cd04269 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=29.75 E-value=52 Score=31.13 Aligned_cols=16 Identities=44% Similarity=0.513 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHHHHH
Q 010849 375 RLLTGAILAHELMHGW 390 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~ 390 (499)
-+.+..++|||++|.+
T Consensus 128 ~~~~a~~~AHElGH~l 143 (194)
T cd04269 128 LLLFAVTMAHELGHNL 143 (194)
T ss_pred hHHHHHHHHHHHHhhc
Confidence 3677899999999976
No 131
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=29.73 E-value=50 Score=31.74 Aligned_cols=22 Identities=23% Similarity=0.243 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHHHHHHHh-CCC
Q 010849 376 LLTGAILAHELMHGWLRLK-GYR 397 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~-g~~ 397 (499)
.++.+++.||++|+|.... |.+
T Consensus 39 ~l~~~l~iHElgH~~~A~~~G~~ 61 (183)
T cd06160 39 ALLAILGIHEMGHYLAARRHGVK 61 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCC
Confidence 3567889999999999876 654
No 132
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=29.68 E-value=10 Score=26.55 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=15.9
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhh
Q 010849 165 CRSCGYPITEHEFSLSGKDPYHKSCFKE 192 (499)
Q Consensus 165 C~~C~~~L~~~~F~~~dg~~YC~~CY~~ 192 (499)
|..|+.+|.........+..+|..|..+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 5566666655444455667777777654
No 133
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=29.42 E-value=40 Score=26.91 Aligned_cols=16 Identities=25% Similarity=0.555 Sum_probs=12.4
Q ss_pred cccccccccccccccH
Q 010849 288 MNMKLDQQIPMLLVER 303 (499)
Q Consensus 288 ~~m~~~~~~p~~lv~~ 303 (499)
+.-+|..+||++|.+.
T Consensus 34 ~aYpI~dGIPvlL~~e 49 (60)
T COG2835 34 LAYPIRDGIPVLLPDE 49 (60)
T ss_pred ceeecccCccccCchh
Confidence 3457889999999853
No 134
>PRK00420 hypothetical protein; Validated
Probab=29.29 E-value=28 Score=31.14 Aligned_cols=30 Identities=23% Similarity=0.528 Sum_probs=22.2
Q ss_pred cCCCCCccccCCceeEecCCccccchhhhhhccCCC
Q 010849 237 CCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTG 272 (499)
Q Consensus 237 C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt~ 272 (499)
|..|+. | .|.+.+|+.+|+.|-...+....
T Consensus 26 CP~Cg~--p----Lf~lk~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 26 CPVCGL--P----LFELKDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred CCCCCC--c----ceecCCCceECCCCCCeeeeccH
Confidence 666776 3 36678999999999887665443
No 135
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.84 E-value=29 Score=31.85 Aligned_cols=21 Identities=24% Similarity=0.648 Sum_probs=14.6
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhh
Q 010849 165 CRSCGYPITEHEFSLSGKDPYHKSCF 190 (499)
Q Consensus 165 C~~C~~~L~~~~F~~~dg~~YC~~CY 190 (499)
|..|+.|| |.++|.+||.-|-
T Consensus 31 Cp~Cg~PL-----F~KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL-----FRKDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc-----eeeCCeEECCCCC
Confidence 66777776 3388888886653
No 136
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=28.69 E-value=18 Score=31.60 Aligned_cols=30 Identities=23% Similarity=0.618 Sum_probs=21.1
Q ss_pred CcccCCCCCccccCCceeEecCCccccchhh
Q 010849 234 TSRCCSCERLESWNTRYYSLEDGRSLCLECM 264 (499)
Q Consensus 234 CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~ 264 (499)
=|+|.+|--+- ...+.....+|+++|..|.
T Consensus 70 EFTCssCFLV~-HRSqLa~~~~g~~iC~DCa 99 (99)
T PF13834_consen 70 EFTCSSCFLVH-HRSQLAREKDGQPICRDCA 99 (99)
T ss_pred ceeeeeeeeEe-chhhhccccCCCEeccccC
Confidence 38999997543 2334445678999999993
No 137
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=28.68 E-value=51 Score=26.33 Aligned_cols=29 Identities=31% Similarity=0.588 Sum_probs=17.1
Q ss_pred CCCCCCCCCccCCCceEeecCccccCCCcccCCCCCCC
Q 010849 135 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPI 172 (499)
Q Consensus 135 ~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L 172 (499)
.+.|..|+..|..++-.. -|.|..|+..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v---------~F~CPnCGe~~ 37 (61)
T COG2888 9 PPVCTSCGREIAPGETAV---------KFPCPNCGEVE 37 (61)
T ss_pred CceeccCCCEeccCCcee---------EeeCCCCCcee
Confidence 467888888884443211 26677776443
No 138
>cd04283 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.
Probab=28.27 E-value=31 Score=33.24 Aligned_cols=12 Identities=42% Similarity=0.783 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 010849 379 GAILAHELMHGW 390 (499)
Q Consensus 379 g~ilAHE~mHa~ 390 (499)
-.+++||+|||-
T Consensus 78 ~G~i~HEl~HaL 89 (182)
T cd04283 78 KGIIQHELLHAL 89 (182)
T ss_pred cchHHHHHHHHh
Confidence 368999999994
No 139
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=27.98 E-value=35 Score=32.63 Aligned_cols=20 Identities=20% Similarity=0.385 Sum_probs=16.1
Q ss_pred hhHHHHHHHHHHHHHHHHHh
Q 010849 375 RLLTGAILAHELMHGWLRLK 394 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~l~l~ 394 (499)
......+++|||.|||=-++
T Consensus 88 q~h~n~vv~HElIH~fDd~r 107 (194)
T KOG3314|consen 88 QDHVNQVVIHELIHAFDDCR 107 (194)
T ss_pred HHHHHHHHHHHHHHHHHhhh
Confidence 34567899999999997765
No 140
>TIGR00181 pepF oligoendopeptidase F. This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PubMed:8757883), with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis.
Probab=27.64 E-value=30 Score=38.82 Aligned_cols=17 Identities=41% Similarity=0.317 Sum_probs=13.4
Q ss_pred hhHHHHHHHHHHHHHHH
Q 010849 375 RLLTGAILAHELMHGWL 391 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~l 391 (499)
.+---.+|||||+||+-
T Consensus 375 ~~~dv~TLaHElGHa~H 391 (591)
T TIGR00181 375 TLNSVFTLAHELGHSMH 391 (591)
T ss_pred CcchHHHHHHHhhhHHH
Confidence 44556899999999983
No 141
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=27.60 E-value=37 Score=33.05 Aligned_cols=15 Identities=27% Similarity=0.224 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHHHHH
Q 010849 376 LLTGAILAHELMHGW 390 (499)
Q Consensus 376 l~~g~ilAHE~mHa~ 390 (499)
.....++|||++|..
T Consensus 143 ~~~~~~~AHElGH~l 157 (220)
T cd04272 143 YYGVYTMTHELAHLL 157 (220)
T ss_pred cccHHHHHHHHHHHh
Confidence 455799999999975
No 142
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=27.32 E-value=36 Score=32.70 Aligned_cols=13 Identities=31% Similarity=0.401 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHH
Q 010849 378 TGAILAHELMHGW 390 (499)
Q Consensus 378 ~g~ilAHE~mHa~ 390 (499)
...+++||+|||-
T Consensus 79 ~~~~i~HEl~HaL 91 (191)
T PF01400_consen 79 SVGTILHELGHAL 91 (191)
T ss_dssp SHHHHHHHHHHHH
T ss_pred CccchHHHHHHHH
Confidence 4568999999995
No 143
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=27.02 E-value=36 Score=37.48 Aligned_cols=18 Identities=28% Similarity=0.230 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 010849 376 LLTGAILAHELMHGWLRL 393 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l 393 (499)
--..+|||||..|.=.|-
T Consensus 128 sElagViAHEigHv~qrH 145 (484)
T COG4783 128 SELAGVIAHEIGHVAQRH 145 (484)
T ss_pred HHHHHHHHHHHHHHhhhh
Confidence 445699999999986654
No 144
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.74 E-value=38 Score=39.04 Aligned_cols=58 Identities=14% Similarity=0.308 Sum_probs=31.2
Q ss_pred CcccCCCCCccccCCceeEecCCccccchhhhhhccCC-CCCCchhhhHHHHHhhcccccccccccccccHHHHHHHH
Q 010849 234 TSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDT-GDCQPLYHAIRDYYEGMNMKLDQQIPMLLVERQALNEAI 310 (499)
Q Consensus 234 CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt-~e~qpl~~~i~~f~~g~~m~~~~~~p~~lv~~~~ln~a~ 310 (499)
-.+|..|+... ....|+.|-...+... ...+.+..++.+.|- +.|++.++++.+-+..
T Consensus 410 ~l~Ch~CG~~~-----------~p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP--------~~~V~r~d~d~~l~~~ 468 (665)
T PRK14873 410 TPRCRWCGRAA-----------PDWRCPRCGSDRLRAVVVGARRTAEELGRAFP--------GVPVVTSGGDQVVDTV 468 (665)
T ss_pred eeECCCCcCCC-----------cCccCCCCcCCcceeeeccHHHHHHHHHHHCC--------CCCEEEEChHHHHHhh
Confidence 46677777521 1235777766543322 234555555555542 4566777777643333
No 145
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=26.48 E-value=34 Score=33.28 Aligned_cols=15 Identities=27% Similarity=0.224 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHh
Q 010849 380 AILAHELMHGWLRLK 394 (499)
Q Consensus 380 ~ilAHE~mHa~l~l~ 394 (499)
.++|||++|++=--+
T Consensus 139 ~~~aHEiGH~lGl~H 153 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRH 153 (206)
T ss_pred hHHHHHHHHHhcCCC
Confidence 679999999975444
No 146
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=26.47 E-value=43 Score=33.67 Aligned_cols=34 Identities=21% Similarity=0.546 Sum_probs=27.8
Q ss_pred CCceEee-CCcccchhhhhhhccccccccCCccCC
Q 010849 174 EHEFSLS-GKDPYHKSCFKELTHPKCEVCHQYIPT 207 (499)
Q Consensus 174 ~~~F~~~-dg~~YC~~CY~~~f~pkC~~C~~~I~~ 207 (499)
...|+.. -..++|..|...-+++.|..|++.|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 4456654 679999999988888899999999775
No 147
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=26.32 E-value=44 Score=24.57 Aligned_cols=21 Identities=29% Similarity=0.766 Sum_probs=14.1
Q ss_pred cCCCCCccccCCceeEecCCccccchh
Q 010849 237 CCSCERLESWNTRYYSLEDGRSLCLEC 263 (499)
Q Consensus 237 C~~C~r~~~~g~~~~~l~dGr~~C~~C 263 (499)
|..|+.++ +...+|+.+|..|
T Consensus 20 Cp~C~~PL------~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPL------MRDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCee------EEecCCCEECCCC
Confidence 45566632 4457888999887
No 148
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.96 E-value=70 Score=25.01 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=8.4
Q ss_pred CCCCCCCCCccC
Q 010849 135 YKVCGGCNCDIG 146 (499)
Q Consensus 135 ~~~C~~C~k~I~ 146 (499)
..+|..|+++|.
T Consensus 5 ~~~C~~Cg~~~~ 16 (54)
T PF14446_consen 5 GCKCPVCGKKFK 16 (54)
T ss_pred CccChhhCCccc
Confidence 356777777774
No 149
>PF08219 TOM13: Outer membrane protein TOM13; InterPro: IPR013262 The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins [].; GO: 0005741 mitochondrial outer membrane
Probab=25.93 E-value=47 Score=27.72 Aligned_cols=23 Identities=26% Similarity=0.264 Sum_probs=17.4
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCC
Q 010849 375 RLLTGAILAHELMHGWLRLKGYRN 398 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~l~l~g~~~ 398 (499)
.|=||-|+|||+.+-|=| .|++-
T Consensus 49 MLGFGEl~AhE~~fr~gW-~g~ki 71 (77)
T PF08219_consen 49 MLGFGELFAHEIAFRLGW-SGTKI 71 (77)
T ss_pred hHhHHHHHHHHHHHHhcc-Cccee
Confidence 577999999999887754 45543
No 150
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=25.91 E-value=64 Score=32.45 Aligned_cols=31 Identities=26% Similarity=0.684 Sum_probs=24.8
Q ss_pred CCCcccCCCCCccccCCceeEecCCccccchhh
Q 010849 232 DHTSRCCSCERLESWNTRYYSLEDGRSLCLECM 264 (499)
Q Consensus 232 ~~CF~C~~C~r~~~~g~~~~~l~dGr~~C~~C~ 264 (499)
++=..|+.|++ +.+..+|....|..+|..|.
T Consensus 152 ~~l~~Ca~cg~--~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGT--PVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCC--cCCCcceeeccCcccchhcc
Confidence 33456999999 55556788888999999998
No 151
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=25.11 E-value=74 Score=33.67 Aligned_cols=38 Identities=24% Similarity=0.142 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHHHHHHHh---CCCCCChhhhhhHHHHHHH
Q 010849 376 LLTGAILAHELMHGWLRLK---GYRNLNPEVEEGICQVLSY 413 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~---g~~~l~~~veEG~Cq~~a~ 413 (499)
.---..|+||++||+--+. ..+.+...+.-.+.++.|-
T Consensus 220 ~~~v~tl~HE~GHa~h~~~~~~~~~~~~~~~~~~~~E~~S~ 260 (427)
T cd06459 220 LDDVFTLAHELGHAFHSYLSRDNQPYLYSDYPIFLAEIAST 260 (427)
T ss_pred hhhHHHHHHHhhHHHHHHHHccCCCcccCCCCchhhHHHHH
Confidence 4445789999999864442 2232433344445554443
No 152
>PF07607 DUF1570: Protein of unknown function (DUF1570); InterPro: IPR011464 This entry represents hypothetical proteins confined to bacteria.
Probab=24.97 E-value=80 Score=28.78 Aligned_cols=33 Identities=27% Similarity=0.297 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHhCC-CC---CChhhhhhHHHHHH
Q 010849 380 AILAHELMHGWLRLKGY-RN---LNPEVEEGICQVLS 412 (499)
Q Consensus 380 ~ilAHE~mHa~l~l~g~-~~---l~~~veEG~Cq~~a 412 (499)
+.++||..|-=+.-.|. ++ -|..|-|||-..+.
T Consensus 3 ~T~~HEa~HQl~~N~Gl~~r~~~~P~Wv~EGlA~yFE 39 (128)
T PF07607_consen 3 ATIAHEATHQLAFNTGLHPRLADWPRWVSEGLATYFE 39 (128)
T ss_pred hHHHHHHHHHHHHHccccccCCCCchHHHHhHHHHcC
Confidence 68999999998887784 33 47889999876653
No 153
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.86 E-value=34 Score=28.69 Aligned_cols=29 Identities=28% Similarity=0.707 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCCceEee-----CCcccchhhhhh
Q 010849 164 RCRSCGYPITEHEFSLS-----GKDPYHKSCFKE 192 (499)
Q Consensus 164 ~C~~C~~~L~~~~F~~~-----dg~~YC~~CY~~ 192 (499)
.|..|+-||.....+.. .+.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 47788888875542222 236789999876
No 154
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=24.76 E-value=37 Score=29.44 Aligned_cols=12 Identities=33% Similarity=0.412 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHH
Q 010849 379 GAILAHELMHGW 390 (499)
Q Consensus 379 g~ilAHE~mHa~ 390 (499)
..++|||+.|.+
T Consensus 108 ~~~~~HEiGH~l 119 (124)
T PF13582_consen 108 VDTFAHEIGHNL 119 (124)
T ss_dssp TTHHHHHHHHHT
T ss_pred ceEeeehhhHhc
Confidence 389999999974
No 155
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=24.66 E-value=1.5e+02 Score=31.96 Aligned_cols=18 Identities=28% Similarity=0.135 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010849 377 LTGAILAHELMHGWLRLK 394 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~ 394 (499)
---.+|+||++||+--+-
T Consensus 241 ~~v~tLfHE~GHa~H~~l 258 (458)
T PF01432_consen 241 DDVETLFHEFGHAMHSLL 258 (458)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHhHHHHHHH
Confidence 356899999999998774
No 156
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=23.30 E-value=59 Score=31.25 Aligned_cols=21 Identities=33% Similarity=0.284 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHHh-CC
Q 010849 376 LLTGAILAHELMHGWLRLK-GY 396 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~-g~ 396 (499)
.+..+|+-||+.|+|.... |.
T Consensus 7 ~l~~~v~iHElGH~~~Ar~~Gv 28 (182)
T cd06163 7 VLGILIFVHELGHFLVAKLFGV 28 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 3567899999999998765 54
No 157
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=23.18 E-value=39 Score=35.35 Aligned_cols=42 Identities=19% Similarity=0.544 Sum_probs=24.1
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCccC
Q 010849 165 CRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIP 206 (499)
Q Consensus 165 C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f~pkC~~C~~~I~ 206 (499)
|..|+.+|.-..-..--+..||.+|...---+.|..|...|.
T Consensus 93 Cd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 93 CDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQ 134 (389)
T ss_pred ecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHH
Confidence 455555554332233345666777765544557888887764
No 158
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.06 E-value=90 Score=38.45 Aligned_cols=51 Identities=16% Similarity=0.197 Sum_probs=27.9
Q ss_pred cccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHhhcccc
Q 010849 235 SRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYEGMNMK 291 (499)
Q Consensus 235 F~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~g~~m~ 291 (499)
+.|..|+...+.+. .+...|+.|-..++..+..--++-....+=.+.+|+.
T Consensus 693 y~CPsCGaev~~de------s~a~~CP~CGtplv~~~~~~i~~~~~~~~A~~~~g~~ 743 (1337)
T PRK14714 693 YVCPDCGAEVPPDE------SGRVECPRCDVELTPYQRRTINVKEEYRSALENVGER 743 (1337)
T ss_pred eeCccCCCccCCCc------cccccCCCCCCcccccceEEecHHHHHHHHHHHhCcc
Confidence 45777777433221 1245688887777665544444444444445555555
No 159
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=22.79 E-value=40 Score=30.89 Aligned_cols=19 Identities=32% Similarity=0.237 Sum_probs=14.6
Q ss_pred chhHHHHHHHHHHHHHHHHH
Q 010849 374 PRLLTGAILAHELMHGWLRL 393 (499)
Q Consensus 374 Prl~~g~ilAHE~mHa~l~l 393 (499)
+..-+-+|+.||+.|| |-|
T Consensus 103 ~~~~~~~~~~HEiGHa-LGL 121 (157)
T cd04278 103 GGTDLFSVAAHEIGHA-LGL 121 (157)
T ss_pred ccchHHHHHHHHhccc-ccc
Confidence 4456778999999999 444
No 160
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=22.70 E-value=69 Score=23.54 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=6.9
Q ss_pred Ccccchhhhhh
Q 010849 182 KDPYHKSCFKE 192 (499)
Q Consensus 182 g~~YC~~CY~~ 192 (499)
+--+|..||..
T Consensus 22 d~dLC~~Cf~~ 32 (46)
T cd02249 22 DFDLCSSCYAK 32 (46)
T ss_pred CCcCHHHHHCc
Confidence 34567777765
No 161
>PF13203 DUF2201_N: Putative metallopeptidase domain
Probab=22.65 E-value=57 Score=33.08 Aligned_cols=23 Identities=30% Similarity=0.328 Sum_probs=18.6
Q ss_pred cCCchhHHHHHHHHHHHHHHHHH
Q 010849 371 YGLPRLLTGAILAHELMHGWLRL 393 (499)
Q Consensus 371 ~gLPrl~~g~ilAHE~mHa~l~l 393 (499)
.+|+.--...+|+||+||.-++-
T Consensus 53 ~~l~~~~~~~~l~HevlH~~~~H 75 (292)
T PF13203_consen 53 ESLSPEERVGLLLHEVLHCLLRH 75 (292)
T ss_pred hcCCHHHHHHHHHHHHHHHHccc
Confidence 56677777889999999987765
No 162
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.58 E-value=53 Score=21.39 Aligned_cols=9 Identities=33% Similarity=1.091 Sum_probs=4.9
Q ss_pred CCCCCCCcc
Q 010849 137 VCGGCNCDI 145 (499)
Q Consensus 137 ~C~~C~k~I 145 (499)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455555554
No 163
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=22.51 E-value=36 Score=33.51 Aligned_cols=31 Identities=26% Similarity=0.591 Sum_probs=23.3
Q ss_pred cccCCCCCccccCCceeEecCCccccchhhhhh
Q 010849 235 SRCCSCERLESWNTRYYSLEDGRSLCLECMESA 267 (499)
Q Consensus 235 F~C~~C~r~~~~g~~~~~l~dGr~~C~~C~~sa 267 (499)
-+|..|+-++. .....+.+|+++|..|+...
T Consensus 173 v~C~kCGE~~~--e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFM--EPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccc--cchhhhcCCceecccccccc
Confidence 57999998553 33456778999999998743
No 164
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=22.51 E-value=60 Score=22.73 Aligned_cols=37 Identities=24% Similarity=0.627 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhhhc--ccccccc
Q 010849 165 CRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVC 201 (499)
Q Consensus 165 C~~C~~~L~~~~F~~~dg~~YC~~CY~~~f--~pkC~~C 201 (499)
|..|...+.+.-....=|..||..|..+.. .++|..|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 455666665532455678899999987643 3444443
No 165
>cd04280 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.
Probab=22.36 E-value=43 Score=31.79 Aligned_cols=10 Identities=50% Similarity=0.906 Sum_probs=9.3
Q ss_pred HHHHHHHHHH
Q 010849 380 AILAHELMHG 389 (499)
Q Consensus 380 ~ilAHE~mHa 389 (499)
.++.||+|||
T Consensus 76 g~v~HE~~Ha 85 (180)
T cd04280 76 GTIVHELMHA 85 (180)
T ss_pred chhHHHHHHH
Confidence 6889999999
No 166
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.07 E-value=61 Score=35.96 Aligned_cols=27 Identities=11% Similarity=0.012 Sum_probs=15.9
Q ss_pred EEEEcCCch-hHHHHHHHHHHHHHHHHH
Q 010849 367 ILVLYGLPR-LLTGAILAHELMHGWLRL 393 (499)
Q Consensus 367 Ilvl~gLPr-l~~g~ilAHE~mHa~l~l 393 (499)
++|...-|. .+.-+.+.|.+-..|-+.
T Consensus 374 viiqt~~p~~~~~~~~~~~d~~~f~~~e 401 (505)
T TIGR00595 374 VIIQTYNPNHPAIQAALTGDYEAFYEQE 401 (505)
T ss_pred EEEEeCCCCCHHHHHHHhCCHHHHHHHH
Confidence 344555565 345566677777777443
No 167
>KOG1046 consensus Puromycin-sensitive aminopeptidase and related aminopeptidases [Amino acid transport and metabolism; Posttranslational modification, protein turnover, chaperones]
Probab=21.79 E-value=1.7e+02 Score=34.89 Aligned_cols=39 Identities=28% Similarity=0.606 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCC-------ChhhhhhHHHHHHHHHhhc
Q 010849 375 RLLTGAILAHELMHGWLRLKGYRNL-------NPEVEEGICQVLSYMWLES 418 (499)
Q Consensus 375 rl~~g~ilAHE~mHa~l~l~g~~~l-------~~~veEG~Cq~~a~~wl~~ 418 (499)
+.....++|||+.|-|. .|| +..+-|||-.+|++.=++.
T Consensus 321 k~~va~vIaHElAHQWF-----GNLVTm~wW~dLWLnEGfAt~~~~~~v~~ 366 (882)
T KOG1046|consen 321 KQRVAEVIAHELAHQWF-----GNLVTMKWWNDLWLNEGFATYVEYLAVDH 366 (882)
T ss_pred HHHHHHHHHHHHHHHHh-----cCcccHhhhhhhhhcccHHHHHHHHhhcc
Confidence 45677899999999995 344 3567899999999987773
No 168
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=21.27 E-value=50 Score=33.72 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHhC
Q 010849 377 LTGAILAHELMHGWLRLKG 395 (499)
Q Consensus 377 ~~g~ilAHE~mHa~l~l~g 395 (499)
.+..|+.||+.|.+..|..
T Consensus 215 ~~~~v~vHE~GHsf~~LaD 233 (264)
T PF09471_consen 215 SFKQVVVHEFGHSFGGLAD 233 (264)
T ss_dssp THHHHHHHHHHHHTT----
T ss_pred cccceeeeecccccccccc
Confidence 6899999999999999974
No 169
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=21.21 E-value=1.5e+02 Score=30.78 Aligned_cols=37 Identities=22% Similarity=0.093 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHHHHHHHHh---CCCC-----CChhhhhhHHHHHH
Q 010849 376 LLTGAILAHELMHGWLRLK---GYRN-----LNPEVEEGICQVLS 412 (499)
Q Consensus 376 l~~g~ilAHE~mHa~l~l~---g~~~-----l~~~veEG~Cq~~a 412 (499)
.---.+|+||++||.--+. .++. .+.++-|-.-+++-
T Consensus 152 ~~~v~tl~HE~GHa~h~~l~~~~~~~~~g~~~~~~~~E~~S~~~E 196 (365)
T cd06258 152 HDDINTLFHEFGHAVHFLLIQQRYPFQERTPTSTDFAEAQSMFLE 196 (365)
T ss_pred HHHHHHHHHHHhHHHHHHHhcCCCCcCCCCCCCccHHhccHHHHH
Confidence 3344679999999995553 2332 35555555545443
No 170
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=20.96 E-value=86 Score=33.90 Aligned_cols=22 Identities=41% Similarity=0.591 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHhCCCCCChh
Q 010849 380 AILAHELMHGWLRLKGYRNLNPE 402 (499)
Q Consensus 380 ~ilAHE~mHa~l~l~g~~~l~~~ 402 (499)
.-+|-|....||+-+ .|+|+++
T Consensus 104 ~~Ia~~Aak~~L~~~-l~~lD~e 125 (399)
T PRK04439 104 GEIAIEAAKEYLREN-LRNLDPE 125 (399)
T ss_pred HHHHHHHHHHHHHHh-CccCCcc
Confidence 667899999999998 7888764
No 171
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=20.85 E-value=25 Score=30.89 Aligned_cols=28 Identities=29% Similarity=0.428 Sum_probs=0.0
Q ss_pred CCCCCCCccCCCceEeecCcc-ccCCCcc
Q 010849 137 VCGGCNCDIGYGNYLGCMGTY-FHPNCFR 164 (499)
Q Consensus 137 ~C~~C~k~I~~g~~l~algk~-wHp~CF~ 164 (499)
.|.-|+++|..|+..++..+. -|-.||+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHH
No 172
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.69 E-value=46 Score=34.41 Aligned_cols=29 Identities=24% Similarity=0.637 Sum_probs=13.9
Q ss_pred CCCCCCccCCCceEeecCccccCCCcccC
Q 010849 138 CGGCNCDIGYGNYLGCMGTYFHPNCFRCR 166 (499)
Q Consensus 138 C~~C~k~I~~g~~l~algk~wHp~CF~C~ 166 (499)
|.-|++.+.+..+|.+-.-.-|+-||-|+
T Consensus 271 CTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 271 CTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred ehhhhhhhccCceeecCCCcccceecccC
Confidence 44455554444444444444444444443
No 173
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=20.45 E-value=86 Score=22.87 Aligned_cols=11 Identities=27% Similarity=0.567 Sum_probs=7.2
Q ss_pred Ccccchhhhhh
Q 010849 182 KDPYHKSCFKE 192 (499)
Q Consensus 182 g~~YC~~CY~~ 192 (499)
+.-+|..||.+
T Consensus 26 d~dlC~~Cf~~ 36 (44)
T smart00291 26 DYDLCQSCFAK 36 (44)
T ss_pred CccchHHHHhC
Confidence 34568888765
No 174
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=20.32 E-value=38 Score=39.13 Aligned_cols=27 Identities=19% Similarity=0.491 Sum_probs=17.7
Q ss_pred cccchhhhhhhc---cccccccCCccCCCC
Q 010849 183 DPYHKSCFKELT---HPKCEVCHQYIPTNG 209 (499)
Q Consensus 183 ~~YC~~CY~~~f---~pkC~~C~~~I~~~~ 209 (499)
+.||..|...++ .-+|..|+.+..+++
T Consensus 663 H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 663 HVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred hHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 455666666555 456888888776654
Done!