Query 010581
Match_columns 507
No_of_seqs 301 out of 1660
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 02:12:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010581.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010581hhsearch_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 1.2E-85 2.7E-90 625.6 20.3 209 295-503 1-212 (212)
2 KOG1703 Adaptor protein Enigma 99.9 8.6E-29 1.9E-33 267.2 6.9 336 141-506 132-479 (479)
3 KOG1701 Focal adhesion adaptor 99.9 3.9E-23 8.5E-28 213.3 -0.2 158 104-275 293-462 (468)
4 KOG4577 Transcription factor L 99.8 1.6E-20 3.4E-25 185.5 -4.2 127 139-277 29-155 (383)
5 KOG2272 Focal adhesion protein 99.7 5.9E-19 1.3E-23 171.9 -2.7 162 97-275 24-193 (332)
6 KOG2272 Focal adhesion protein 99.7 1.8E-18 4E-23 168.5 -0.1 152 109-275 159-312 (332)
7 KOG1703 Adaptor protein Enigma 99.7 6.2E-18 1.3E-22 183.0 0.1 154 105-272 322-478 (479)
8 KOG1701 Focal adhesion adaptor 99.6 5.2E-18 1.1E-22 175.6 -3.3 120 140-275 271-392 (468)
9 KOG1044 Actin-binding LIM Zn-f 99.6 1.3E-15 2.9E-20 162.4 3.0 120 141-275 131-250 (670)
10 PF00412 LIM: LIM domain; Int 99.3 6.6E-12 1.4E-16 97.1 5.0 57 146-202 1-58 (58)
11 KOG1044 Actin-binding LIM Zn-f 99.0 2.7E-10 5.8E-15 122.4 5.0 139 143-311 16-154 (670)
12 KOG4577 Transcription factor L 98.7 1.4E-09 3.1E-14 108.5 -1.8 103 105-207 52-159 (383)
13 KOG1700 Regulatory protein MLP 98.6 1.2E-08 2.7E-13 99.1 0.7 122 142-277 6-168 (200)
14 smart00132 LIM Zinc-binding do 98.2 8.6E-07 1.9E-11 62.4 3.2 37 145-181 1-38 (39)
15 PF00412 LIM: LIM domain; Int 98.2 1.2E-06 2.5E-11 67.7 3.9 57 206-275 1-57 (58)
16 PF13485 Peptidase_MA_2: Pepti 97.4 0.0012 2.6E-08 57.2 9.4 108 379-501 18-127 (128)
17 KOG1702 Nebulin repeat protein 96.9 0.00011 2.4E-09 71.1 -2.4 59 144-202 5-63 (264)
18 KOG0490 Transcription factor, 96.8 0.00017 3.6E-09 70.3 -1.8 115 148-275 1-119 (235)
19 KOG1700 Regulatory protein MLP 96.7 0.00043 9.3E-09 67.5 -0.0 61 142-202 107-167 (200)
20 smart00132 LIM Zinc-binding do 96.4 0.003 6.5E-08 44.1 2.7 37 205-252 1-37 (39)
21 PF10026 DUF2268: Predicted Zn 91.5 0.69 1.5E-05 44.8 7.6 45 384-428 63-113 (195)
22 PF01433 Peptidase_M1: Peptida 86.6 0.49 1.1E-05 49.5 2.8 44 385-428 294-339 (390)
23 PF04450 BSP: Peptidase of pla 82.4 1.3 2.8E-05 43.6 3.4 91 383-492 93-184 (205)
24 PF14891 Peptidase_M91: Effect 80.9 1.1 2.3E-05 42.7 2.3 19 386-404 103-121 (174)
25 PF01431 Peptidase_M13: Peptid 80.9 0.65 1.4E-05 44.7 0.8 17 385-401 35-51 (206)
26 PF13699 DUF4157: Domain of un 80.9 0.96 2.1E-05 37.8 1.7 18 386-403 61-78 (79)
27 TIGR02412 pepN_strep_liv amino 79.7 8.6 0.00019 45.3 9.6 42 386-427 287-330 (831)
28 PF06524 NOA36: NOA36 protein; 79.3 1.8 4E-05 43.9 3.4 110 113-250 40-179 (314)
29 PF10263 SprT-like: SprT-like 79.1 1.5 3.2E-05 40.4 2.5 22 381-402 55-76 (157)
30 PF06114 DUF955: Domain of unk 79.0 2.8 6.1E-05 35.5 4.1 52 373-424 29-86 (122)
31 PRK03001 M48 family peptidase; 75.4 1.2 2.6E-05 45.5 0.9 20 380-399 118-137 (283)
32 PRK01345 heat shock protein Ht 73.8 1.5 3.2E-05 45.9 1.1 19 381-399 119-137 (317)
33 KOG0490 Transcription factor, 72.9 1.2 2.5E-05 43.3 0.1 94 106-200 16-118 (235)
34 PF10460 Peptidase_M30: Peptid 72.3 4.9 0.00011 42.9 4.5 44 384-427 137-186 (366)
35 PRK02391 heat shock protein Ht 71.7 1.6 3.6E-05 45.1 0.8 21 379-399 126-146 (296)
36 KOG1702 Nebulin repeat protein 71.3 0.7 1.5E-05 45.3 -1.8 96 204-318 5-112 (264)
37 PRK14559 putative protein seri 71.2 3.1 6.7E-05 47.6 2.9 50 144-215 2-53 (645)
38 PRK03072 heat shock protein Ht 70.5 1.6 3.4E-05 44.9 0.4 21 378-398 119-139 (288)
39 PRK14015 pepN aminopeptidase N 70.1 15 0.00032 43.7 8.3 40 386-426 296-338 (875)
40 smart00731 SprT SprT homologue 69.5 4 8.7E-05 37.6 2.8 22 382-403 55-76 (146)
41 KOG0320 Predicted E3 ubiquitin 68.2 2.9 6.4E-05 40.3 1.6 48 168-215 129-179 (187)
42 PRK05457 heat shock protein Ht 65.4 2.3 4.9E-05 43.8 0.3 21 378-398 126-146 (284)
43 PRK02870 heat shock protein Ht 65.1 2.5 5.4E-05 44.7 0.6 18 380-397 167-184 (336)
44 PRK03982 heat shock protein Ht 65.0 2.4 5.1E-05 43.5 0.4 20 380-399 119-138 (288)
45 PRK04897 heat shock protein Ht 64.4 2.3 5E-05 44.0 0.2 20 379-398 130-149 (298)
46 COG2856 Predicted Zn peptidase 63.4 15 0.00032 36.5 5.6 55 373-427 59-120 (213)
47 PF09768 Peptidase_M76: Peptid 63.4 5.3 0.00012 38.4 2.4 21 383-403 68-88 (173)
48 PHA02456 zinc metallopeptidase 61.4 5.1 0.00011 35.9 1.7 15 388-402 81-95 (141)
49 PF14835 zf-RING_6: zf-RING of 60.4 8.2 0.00018 31.3 2.6 47 171-217 8-54 (65)
50 PF12773 DZR: Double zinc ribb 58.9 11 0.00024 28.1 3.0 11 205-215 31-41 (50)
51 PRK01265 heat shock protein Ht 58.5 3.9 8.5E-05 43.0 0.6 17 381-397 135-151 (324)
52 PF01447 Peptidase_M4: Thermol 57.8 6.3 0.00014 36.9 1.8 18 382-399 131-148 (150)
53 TIGR02411 leuko_A4_hydro leuko 57.3 9 0.0002 43.5 3.3 40 387-426 280-321 (601)
54 cd04270 ZnMc_TACE_like Zinc-de 55.8 7.2 0.00016 39.1 2.0 18 381-398 162-179 (244)
55 smart00504 Ubox Modified RING 54.6 14 0.00031 28.3 3.1 44 171-215 2-47 (63)
56 PRK04351 hypothetical protein; 54.6 11 0.00024 35.3 2.8 20 384-403 59-78 (149)
57 KOG1813 Predicted E3 ubiquitin 54.2 6.6 0.00014 40.6 1.4 47 169-216 240-288 (313)
58 PRK14890 putative Zn-ribbon RN 54.2 14 0.0003 29.5 2.8 27 143-179 7-34 (59)
59 PF10367 Vps39_2: Vacuolar sor 53.0 8.9 0.00019 32.6 1.9 31 142-172 77-108 (109)
60 smart00726 UIM Ubiquitin-inter 52.8 6.9 0.00015 26.1 0.8 20 85-104 2-21 (26)
61 PF01435 Peptidase_M48: Peptid 52.2 10 0.00022 36.3 2.4 30 374-403 73-106 (226)
62 PF14471 DUF4428: Domain of un 52.1 9 0.00019 29.5 1.5 30 244-275 1-30 (51)
63 PF04298 Zn_peptidase_2: Putat 51.0 14 0.0003 37.0 3.0 29 379-407 82-110 (222)
64 PF02163 Peptidase_M50: Peptid 49.6 15 0.00032 34.8 3.0 20 385-404 6-26 (192)
65 PF01421 Reprolysin: Reprolysi 49.2 18 0.00039 34.6 3.5 24 374-397 119-142 (199)
66 PF02809 UIM: Ubiquitin intera 48.3 8.5 0.00018 23.5 0.7 16 84-99 2-17 (18)
67 PF10083 DUF2321: Uncharacteri 47.5 13 0.00028 35.1 2.1 53 190-255 27-81 (158)
68 PRK11827 hypothetical protein; 47.4 12 0.00027 29.9 1.6 18 295-312 33-50 (60)
69 PRK04860 hypothetical protein; 47.3 21 0.00046 33.9 3.5 28 382-410 59-89 (160)
70 KOG3931 Uncharacterized conser 46.4 11 0.00023 40.0 1.6 22 381-402 100-121 (484)
71 PF11781 RRN7: RNA polymerase 46.3 13 0.00029 26.6 1.5 25 243-273 9-33 (36)
72 smart00235 ZnMc Zinc-dependent 45.3 11 0.00023 33.9 1.2 11 388-398 88-98 (140)
73 cd06158 S2P-M50_like_1 Unchara 45.2 19 0.00041 34.5 2.9 18 385-402 8-25 (181)
74 cd04267 ZnMc_ADAM_like Zinc-de 44.7 13 0.00028 35.2 1.7 24 374-398 122-145 (192)
75 PF10367 Vps39_2: Vacuolar sor 44.3 21 0.00046 30.2 2.9 28 172-199 80-108 (109)
76 TIGR02414 pepN_proteo aminopep 43.7 81 0.0018 37.6 8.3 36 386-426 283-325 (863)
77 PF13920 zf-C3HC4_3: Zinc fing 43.6 30 0.00065 25.7 3.2 42 172-214 4-48 (50)
78 PRK04023 DNA polymerase II lar 43.3 26 0.00056 42.0 4.1 38 171-216 639-676 (1121)
79 PRK14559 putative protein seri 43.1 21 0.00044 41.1 3.3 37 172-215 3-39 (645)
80 PRK14873 primosome assembly pr 43.0 14 0.00031 42.5 2.0 55 346-401 501-558 (665)
81 COG5152 Uncharacterized conser 42.6 9 0.00019 37.6 0.3 47 169-216 195-243 (259)
82 cd04268 ZnMc_MMP_like Zinc-dep 42.5 14 0.0003 33.9 1.5 14 385-398 93-106 (165)
83 PF01863 DUF45: Protein of unk 42.2 16 0.00034 34.9 1.9 25 374-398 152-176 (205)
84 PF10463 Peptidase_U49: Peptid 42.0 34 0.00073 33.9 4.1 50 380-429 95-145 (206)
85 KOG3624 M13 family peptidase [ 41.2 13 0.00028 42.7 1.3 16 384-399 516-531 (687)
86 PF13240 zinc_ribbon_2: zinc-r 41.1 18 0.00039 23.3 1.4 9 146-154 2-10 (23)
87 PF14471 DUF4428: Domain of un 39.3 20 0.00043 27.6 1.7 29 172-201 1-30 (51)
88 KOG3714 Meprin A metalloprotea 39.3 14 0.0003 40.0 1.1 14 388-401 161-174 (411)
89 cd00203 ZnMc Zinc-dependent me 39.2 20 0.00043 32.7 2.0 16 383-398 93-108 (167)
90 PF00413 Peptidase_M10: Matrix 38.5 20 0.00044 32.3 1.9 17 381-397 100-116 (154)
91 PF04228 Zn_peptidase: Putativ 37.5 27 0.00057 36.3 2.8 21 383-403 167-187 (292)
92 PF14634 zf-RING_5: zinc-RING 37.4 32 0.0007 25.0 2.5 39 173-211 2-44 (44)
93 cd06159 S2P-M50_PDZ_Arch Uncha 37.3 27 0.00059 35.7 2.8 27 378-405 111-138 (263)
94 cd06162 S2P-M50_PDZ_SREBP Ster 37.2 24 0.00051 36.5 2.3 18 385-402 134-151 (277)
95 cd00162 RING RING-finger (Real 36.7 28 0.00061 23.9 2.0 40 173-212 2-44 (45)
96 COG5504 Predicted Zn-dependent 36.4 43 0.00094 34.2 4.0 39 387-426 141-186 (280)
97 cd06161 S2P-M50_SpoIVFB SpoIVF 36.1 33 0.00072 33.5 3.1 21 384-404 36-57 (208)
98 PF06689 zf-C4_ClpX: ClpX C4-t 35.9 30 0.00066 25.3 2.1 32 244-275 3-34 (41)
99 cd05709 S2P-M50 Site-2 proteas 35.7 26 0.00057 32.9 2.3 20 385-404 7-27 (180)
100 COG4357 Zinc finger domain con 35.5 5 0.00011 35.0 -2.4 49 146-194 38-86 (105)
101 PF08394 Arc_trans_TRASH: Arch 35.1 19 0.0004 26.1 0.9 29 146-177 1-30 (37)
102 COG2191 Formylmethanofuran deh 34.8 16 0.00034 36.1 0.6 30 172-201 174-203 (206)
103 PHA00527 hypothetical protein 34.7 1.4E+02 0.003 26.7 6.3 47 372-423 64-113 (129)
104 COG1451 Predicted metal-depend 34.7 22 0.00047 35.4 1.6 27 372-398 161-187 (223)
105 PF14247 DUF4344: Domain of un 34.6 62 0.0013 32.3 4.7 38 385-424 91-128 (220)
106 PF13688 Reprolysin_5: Metallo 34.4 25 0.00055 33.2 2.0 20 382-401 138-157 (196)
107 cd06164 S2P-M50_SpoIVFB_CBS Sp 34.0 34 0.00075 34.0 2.9 21 384-404 51-72 (227)
108 cd04281 ZnMc_BMP1_TLD Zinc-dep 33.0 22 0.00048 34.8 1.3 11 388-398 89-99 (200)
109 COG1645 Uncharacterized Zn-fin 32.8 23 0.00049 32.7 1.2 21 173-198 31-51 (131)
110 COG0501 HtpX Zn-dependent prot 32.8 25 0.00054 35.4 1.7 19 380-398 151-169 (302)
111 TIGR02289 M3_not_pepF oligoend 32.7 52 0.0011 36.8 4.4 45 384-428 335-389 (549)
112 PF05299 Peptidase_M61: M61 gl 32.3 15 0.00032 33.4 0.0 41 386-426 4-57 (122)
113 COG0308 PepN Aminopeptidase N 32.3 53 0.0012 39.0 4.5 115 387-506 308-466 (859)
114 PF12674 Zn_ribbon_2: Putative 32.3 21 0.00045 30.1 0.9 29 172-200 2-35 (81)
115 PRK09672 phage exclusion prote 31.5 64 0.0014 33.8 4.3 50 379-428 158-208 (305)
116 COG2888 Predicted Zn-ribbon RN 31.2 44 0.00095 26.8 2.4 29 143-180 9-37 (61)
117 PF13574 Reprolysin_2: Metallo 31.0 29 0.00062 32.9 1.7 18 386-403 111-128 (173)
118 cd06461 M2_ACE Peptidase famil 30.8 52 0.0011 36.5 3.9 32 389-421 250-289 (477)
119 cd04279 ZnMc_MMP_like_1 Zinc-d 30.8 29 0.00063 31.8 1.6 16 383-398 101-116 (156)
120 PF05572 Peptidase_M43: Pregna 30.4 29 0.00063 32.5 1.6 20 382-402 65-84 (154)
121 cd04327 ZnMc_MMP_like_3 Zinc-d 30.3 33 0.00072 33.0 2.0 16 385-400 91-106 (198)
122 PF14446 Prok-RING_1: Prokaryo 30.3 54 0.0012 25.8 2.8 12 143-154 5-16 (54)
123 KOG2199 Signal transducing ada 30.0 22 0.00048 38.4 0.8 24 82-105 162-185 (462)
124 cd04282 ZnMc_meprin Zinc-depen 29.7 27 0.00058 35.1 1.3 11 388-398 122-132 (230)
125 COG4784 Putative Zn-dependent 29.6 56 0.0012 35.0 3.6 107 375-505 108-220 (479)
126 PF10391 DNA_pol_lambd_f: Fing 29.2 56 0.0012 25.2 2.7 27 474-502 6-32 (52)
127 PF01258 zf-dskA_traR: Prokary 29.0 11 0.00023 26.6 -1.2 28 173-200 6-33 (36)
128 cd04269 ZnMc_adamalysin_II_lik 29.0 54 0.0012 31.1 3.2 16 383-398 128-143 (194)
129 PRK14714 DNA polymerase II lar 28.9 58 0.0012 40.2 4.0 51 243-299 693-743 (1337)
130 cd06160 S2P-M50_like_2 Unchara 28.8 53 0.0011 31.7 3.1 22 384-405 39-61 (183)
131 PF00645 zf-PARP: Poly(ADP-rib 28.8 17 0.00036 30.0 -0.3 17 141-157 5-21 (82)
132 COG2738 Predicted Zn-dependent 28.3 33 0.00071 33.9 1.5 28 378-405 84-111 (226)
133 PRK14873 primosome assembly pr 28.3 34 0.00073 39.5 2.0 44 267-318 424-468 (665)
134 cd04283 ZnMc_hatching_enzyme Z 27.7 32 0.00069 33.3 1.4 12 387-398 78-89 (182)
135 KOG3314 Ku70-binding protein [ 27.2 37 0.00079 32.6 1.6 19 384-402 89-107 (194)
136 KOG4739 Uncharacterized protei 27.0 41 0.0009 33.9 2.1 34 182-215 15-49 (233)
137 TIGR00181 pepF oligoendopeptid 27.0 31 0.00068 38.8 1.4 17 383-399 375-391 (591)
138 PRK14714 DNA polymerase II lar 26.9 50 0.0011 40.7 3.0 49 144-215 668-721 (1337)
139 PF01400 Astacin: Astacin (Pep 26.8 37 0.0008 32.7 1.6 13 386-398 79-91 (191)
140 cd04272 ZnMc_salivary_gland_MP 26.8 39 0.00085 33.0 1.9 15 384-398 143-157 (220)
141 PF10235 Cript: Microtubule-as 26.2 43 0.00093 29.0 1.8 37 171-215 45-81 (90)
142 PF13583 Reprolysin_4: Metallo 25.9 35 0.00077 33.3 1.4 15 388-402 139-153 (206)
143 PF14569 zf-UDP: Zinc-binding 25.9 64 0.0014 27.3 2.6 53 138-211 4-59 (80)
144 PF06677 Auto_anti-p27: Sjogre 25.7 41 0.00089 24.8 1.3 22 172-197 19-40 (41)
145 PLN03208 E3 ubiquitin-protein 25.5 58 0.0013 32.0 2.7 30 170-200 18-47 (193)
146 PF09943 DUF2175: Uncharacteri 25.0 18 0.00039 31.9 -0.8 28 145-172 4-32 (101)
147 TIGR03826 YvyF flagellar opero 24.9 36 0.00079 31.5 1.2 36 244-294 5-40 (137)
148 TIGR00595 priA primosomal prot 24.8 47 0.001 36.9 2.2 27 375-401 374-401 (505)
149 KOG3579 Predicted E3 ubiquitin 24.7 34 0.00073 35.5 1.0 30 145-174 270-299 (352)
150 PF08219 TOM13: Outer membrane 24.7 51 0.0011 27.6 1.8 22 383-405 49-70 (77)
151 PF13248 zf-ribbon_3: zinc-rib 24.6 47 0.001 21.8 1.3 9 145-153 4-12 (26)
152 PF13582 Reprolysin_3: Metallo 24.3 38 0.00083 29.4 1.2 12 387-398 108-119 (124)
153 PF07607 DUF1570: Protein of u 24.0 95 0.0021 28.4 3.7 33 388-420 3-39 (128)
154 COG2835 Uncharacterized conser 23.9 56 0.0012 26.2 1.9 16 296-311 34-49 (60)
155 cd06459 M3B_Oligoendopeptidase 23.6 80 0.0017 33.5 3.7 37 384-420 220-259 (427)
156 KOG2462 C2H2-type Zn-finger pr 23.6 42 0.00092 34.6 1.4 11 243-253 216-226 (279)
157 PF01432 Peptidase_M3: Peptida 23.1 1.7E+02 0.0037 31.7 6.1 18 385-402 241-258 (458)
158 cd06163 S2P-M50_PDZ_RseP-like 23.1 59 0.0013 31.3 2.3 21 384-404 7-28 (182)
159 COG1381 RecO Recombinational D 22.4 81 0.0017 31.8 3.2 31 240-272 152-182 (251)
160 KOG2932 E3 ubiquitin ligase in 22.1 41 0.0009 35.3 1.0 42 173-214 93-134 (389)
161 KOG1046 Puromycin-sensitive am 22.0 1.7E+02 0.0036 35.1 6.1 39 383-426 321-366 (882)
162 cd04280 ZnMc_astacin_like Zinc 21.9 45 0.00097 31.8 1.2 10 388-397 76-85 (180)
163 PRK00420 hypothetical protein; 21.9 45 0.00098 29.9 1.1 30 245-280 26-55 (112)
164 PF13203 DUF2201_N: Putative m 21.8 61 0.0013 33.0 2.2 23 379-401 53-75 (292)
165 cd04278 ZnMc_MMP Zinc-dependen 21.2 46 0.00099 30.6 1.0 19 382-401 103-121 (157)
166 PRK00420 hypothetical protein; 20.8 54 0.0012 29.5 1.3 22 172-197 25-46 (112)
167 PRK04439 S-adenosylmethionine 20.7 95 0.0021 33.7 3.4 22 388-410 104-125 (399)
168 PF13923 zf-C3HC4_2: Zinc fing 20.6 70 0.0015 22.5 1.7 37 173-209 1-39 (39)
169 PF09471 Peptidase_M64: IgA Pe 20.4 53 0.0011 33.6 1.4 19 385-403 215-233 (264)
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=1.2e-85 Score=625.63 Aligned_cols=209 Identities=74% Similarity=1.172 Sum_probs=198.0
Q ss_pred hcccccccccccccccHHHHHHHHhccccCCCCCCcccceeecccceeeeeeccccC-CCCeeeeeeccccccccceeEE
Q 010581 295 GMNMKLDQQIPMLLVERQALNEAIVGEKNGYHHMPETRGLCLSEEQTVTSILRRPRI-GGNRLVGMRTQPQKLTRKCEVT 373 (507)
Q Consensus 295 glgm~~~~~~pl~lv~~~~ln~a~~~e~~g~~~~~~trglclse~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~r~~~v~ 373 (507)
+|||||+|+|||+|||++|||+|+++||+|+||+|+||||||||||||+||.|+|++ +++++++|.|+|++++|+|+||
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 010581 374 AILVLYGLPRLLTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPS--TSSASTSSSSSKKG 451 (507)
Q Consensus 374 ~Ilvl~GLPrl~~g~ilAHE~mHawlrl~g~~~l~~~vEEG~Cq~~a~~wl~~~~~~~~~~~~~--~~~~~~~~~~~~~g 451 (507)
+|||||||||++||||||||||||||||+||++|+++||||||||||||||++|++++.++..+ ++++++++++||||
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 23345566778999
Q ss_pred CchHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHhCHHHHHHHHHhhC
Q 010581 452 GKSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKYGLRRTLEHIRLTG 503 (507)
Q Consensus 452 ~~~~~e~~l~~f~~~qi~~d~s~vYGdGfR~~~~a~~~~gl~~~l~~i~~~g 503 (507)
++++||+||++||+||||+|+|||||||||+|++||++|||++||+|||+||
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=8.6e-29 Score=267.17 Aligned_cols=336 Identities=41% Similarity=0.663 Sum_probs=285.4
Q ss_pred CCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhh-hccccccccCCCcCCCCcc
Q 010581 141 RSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKE-LTHPKCEVCHQYIPTNGAG 219 (507)
Q Consensus 141 ~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k-~f~pkC~~C~k~I~~~~~G 219 (507)
....+|.+|+..|..+..+ ||.|..|..++. .+...||.+ ...++|.+|...|.....+
T Consensus 132 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~p~~----------~~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 191 (479)
T KOG1703|consen 132 PLDSICGGCNSAIEHGRSV----------CFQCKRCSEPLS----------GFPKPSYHESGRSKNEDVEEASSPSSRAG 191 (479)
T ss_pred cccccccCCCcccccccch----------hhhhcccccccC----------Ccccccccccccccccccccccccccccc
Confidence 3457899999999776655 999999998882 233445555 3678899999999988888
Q ss_pred eEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHhhcccc
Q 010581 220 LIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYEGMNMK 299 (507)
Q Consensus 220 ~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~glgm~ 299 (507)
.+.++.++||.+.||+.|.++.+..|+.|++.++++..+..+.+++.+|.+|+..+++++.++||++..+..++....|+
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 010581 300 LDQQIPMLLVERQALNEAIVGEKNGYHHMPETRGLCLSEEQTVTSILRRPRIGGNRLVGMRTQPQKLTRKCEVTAILVLY 379 (507)
Q Consensus 300 ~~~~~pl~lv~~~~ln~a~~~e~~g~~~~~~trglclse~~~~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~v~~Ilvl~ 379 (507)
+++..+++++++++++.+.+.++...++. .++++|++++++|+++ ..++++.++..+....|+|.+|++++
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 010581 380 GLPRLLTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMP-STSSA------STSSSSSKKGG 452 (507)
Q Consensus 380 GLPrl~~g~ilAHE~mHawlrl~g~~~l~~~vEEG~Cq~~a~~wl~~~~~~~~~~~~-~~~~~------~~~~~~~~~g~ 452 (507)
|+|+...|.|++||+||+|++.++++.+.+.+||+||++ +.+|++..-.-..-... ..++. .......++..
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 010581 453 --KSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKY--GLRRTLEHIRLTGNFP 506 (507)
Q Consensus 453 --~~~~e~~l~~f~~~qi~~d~s~vYGdGfR~~~~a~~~~--gl~~~l~~i~~~g~~p 506 (507)
+..++++.++|+.++|+.|.+++||+|||.++.+++.. ++..+++++.....|+
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 78889999999999999999999999999999998777 7999998888776654
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.86 E-value=3.9e-23 Score=213.34 Aligned_cols=158 Identities=25% Similarity=0.441 Sum_probs=132.4
Q ss_pred cCCCccccc--chHHhHHHH--hcccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCC
Q 010581 104 PNGQRWRSN--TDEDYAWAL--QDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYP 179 (507)
Q Consensus 104 ~~~~~wh~e--~ce~c~raL--q~~l~~~~~~pYC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~ 179 (507)
+++..+|++ +|.+|++.| |.+++.+. +|||+.||. ....+|..|++.|. ..+|.++|+.||+.||+|..|++.
T Consensus 293 Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~-k~~CE~cyq-~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ 369 (468)
T KOG1701|consen 293 AMDQLFHVQCFTCRTCRRQLAGQSFYQVDG-KPYCEGCYQ-DTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARC 369 (468)
T ss_pred HhhhhhcccceehHhhhhhhccccccccCC-cccchHHHH-HHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccc
Confidence 345579988 999999999 66677776 999999984 35689999999996 689999999999999999999999
Q ss_pred CCCCceEee-CCcccchhhhhhhccccccccCCCcCCCC----cceEEeeecCccccccCCCccCCCCcccCCCCCcccc
Q 010581 180 ITEHEFSLS-GKDPYHKSCFKELTHPKCEVCHQYIPTNG----AGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESW 254 (507)
Q Consensus 180 L~~~~F~~~-dg~pYCk~CY~k~f~pkC~~C~k~I~~~~----~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~ 254 (507)
|.+..|.+. ++++||..||+++|+|+|++|+++|...+ .-.|..+.++| |.+|++|..|+.+|+.
T Consensus 370 ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~f----------Hv~CY~CEDCg~~LS~ 439 (468)
T KOG1701|consen 370 LDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDF----------HVNCYKCEDCGLLLSS 439 (468)
T ss_pred cCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccc----------cccceehhhcCccccc
Confidence 999999885 88999999999999999999999998763 22344544443 9999999999998874
Q ss_pred ---CCceeEecCCccccchhhhhh
Q 010581 255 ---NTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 255 ---g~~~~~l~dGr~~C~~C~~sa 275 (507)
+...|.+ ||.++|+.|+...
T Consensus 440 e~e~qgCyPl-d~HllCk~Ch~~R 462 (468)
T KOG1701|consen 440 EEEGQGCYPL-DGHLLCKTCHLKR 462 (468)
T ss_pred cCCCCcceec-cCceeechhhhhh
Confidence 3344555 5899999998554
No 4
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.76 E-value=1.6e-20 Score=185.54 Aligned_cols=127 Identities=24% Similarity=0.468 Sum_probs=112.0
Q ss_pred CCCCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCCCCc
Q 010581 139 YPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGA 218 (507)
Q Consensus 139 ~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~ 218 (507)
.....++|++|++.|.+..++.+++++||..|++|+.|..+|.+. ++.+++.+||+++|.++|+.||..|.+.|++..
T Consensus 29 ~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtq- 106 (383)
T KOG4577|consen 29 SNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQ- 106 (383)
T ss_pred cccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcchhhcCCCChHH-
Confidence 333578999999999877778999999999999999999999984 557899999999999999999999999999863
Q ss_pred ceEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhhcc
Q 010581 219 GLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIM 277 (507)
Q Consensus 219 G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~ 277 (507)
+.-+++.|. ||..||.|..|+|++..|++||.+.|++++|+..|++|..
T Consensus 107 --VVRkAqd~V--------YHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~ 155 (383)
T KOG4577|consen 107 --VVRKAQDFV--------YHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ 155 (383)
T ss_pred --HHHHhhcce--------eehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh
Confidence 333444443 4999999999999999999999999999999999999865
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.70 E-value=5.9e-19 Score=171.91 Aligned_cols=162 Identities=22% Similarity=0.484 Sum_probs=134.6
Q ss_pred ccccccccCCCccccc--chHHhHHHHhcccCCC-CCCCCCCCCCCCCCCCCCCCCCCccCCCceEEecCccccCCCccc
Q 010581 97 LAEDLKRPNGQRWRSN--TDEDYAWALQDSQLNP-SFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRC 173 (507)
Q Consensus 97 L~Ee~kk~~~~~wh~e--~ce~c~raLq~~l~~~-~~~pYC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C 173 (507)
++|.-...++..||+. .|.||-+++++.++.+ .++.||+.||...++|.|+.|++.|. |++|.+++.+|||.||+|
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 3455555578899988 8999999998775543 24889999999999999999999995 999999999999999999
Q ss_pred CCCCCCCCCCceEeeCCcccchhhhhhhc-----cccccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCC
Q 010581 174 RSCGYPITEHEFSLSGKDPYHKSCFKELT-----HPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSC 248 (507)
Q Consensus 174 ~~C~~~L~~~~F~~~dg~pYCk~CY~k~f-----~pkC~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C 248 (507)
..|++.|.+..|+-..|..+|..|..+.- .-.|..|+..|... .+.++..|| |+..|+|..|
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---PLTFRGDPY----------HPYHFKCTTC 169 (332)
T ss_pred HHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc---cccccCCCC----------Cccceecccc
Confidence 99999999999999999999999987622 34699999999874 577776553 7777999999
Q ss_pred CCccccCCceeEecCCccccchhhhhh
Q 010581 249 ERLESWNTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 249 ~r~l~~g~~~~~l~dGr~~C~~C~~sa 275 (507)
++.+....+ .-.|.+||+.|++++
T Consensus 170 ~keL~sdaR---evk~eLyClrChD~m 193 (332)
T KOG2272|consen 170 GKELTSDAR---EVKGELYCLRCHDKM 193 (332)
T ss_pred cccccchhh---hhccceecccccccc
Confidence 997765444 234799999998875
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.70 E-value=1.8e-18 Score=168.48 Aligned_cols=152 Identities=16% Similarity=0.378 Sum_probs=125.9
Q ss_pred cccc--chHHhHHHHhcccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceE
Q 010581 109 WRSN--TDEDYAWALQDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFS 186 (507)
Q Consensus 109 wh~e--~ce~c~raLq~~l~~~~~~pYC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~ 186 (507)
+|.. .|..|.+.|...--......||..++...+.++|..|.++|. ++++.++|+.||.+.|+|+.|.+|+-+.+.|
T Consensus 159 yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHY 237 (332)
T KOG2272|consen 159 YHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHY 237 (332)
T ss_pred CCccceecccccccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhh
Confidence 4444 666666666322222222559999999999999999999995 8999999999999999999999999999999
Q ss_pred eeCCcccchhhhhhhccccccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCcc
Q 010581 187 LSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRS 266 (507)
Q Consensus 187 ~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~ 266 (507)
++.|.+||+.+|.++|+..|..|+..|.+.. +.+. ++.+| ++||+|+.|.+.+...++|+.++ -.|
T Consensus 238 EkkGlaYCe~h~~qLfG~~CF~C~~~i~G~v---v~al-----~KawC-----v~cf~Cs~Cdkkl~~K~Kf~E~D-mkP 303 (332)
T KOG2272|consen 238 EKKGLAYCETHYHQLFGNLCFICNRVIGGDV---VSAL-----NKAWC-----VECFSCSTCDKKLTQKNKFYEFD-MKP 303 (332)
T ss_pred hhcCchhHHHHHHHHhhhhheecCCccCccH---HHHh-----hhhhc-----cccccccccccccccccceeeec-cch
Confidence 9999999999999999999999999999853 3332 45555 55699999999998888887776 699
Q ss_pred ccchhhhhh
Q 010581 267 LCLECMESA 275 (507)
Q Consensus 267 ~C~~C~~sa 275 (507)
+|+.||+..
T Consensus 304 ~CKkCy~rf 312 (332)
T KOG2272|consen 304 VCKKCYDRF 312 (332)
T ss_pred HHHHHHhhc
Confidence 999999764
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.67 E-value=6.2e-18 Score=183.02 Aligned_cols=154 Identities=23% Similarity=0.449 Sum_probs=130.4
Q ss_pred CCCccccc--chHHhHHHHhcccC-CCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCC
Q 010581 105 NGQRWRSN--TDEDYAWALQDSQL-NPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPIT 181 (507)
Q Consensus 105 ~~~~wh~e--~ce~c~raLq~~l~-~~~~~pYC~~~y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~ 181 (507)
.+..||.+ .|+.|...+..... ...+.+||..++...+.+.|.+|.++|. ++.|.++++.||+.||.|..|++++.
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 99999988865544 3335889999999999999999999996 89999999999999999999999999
Q ss_pred CCceEeeCCcccchhhhhhhccccccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEe
Q 010581 182 EHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSL 261 (507)
Q Consensus 182 ~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l 261 (507)
...|+..++.+||..||++++.++|..|.++|..-. -.|+....+ ||..||+|..|.+. +.++.|..
T Consensus 401 ~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~-~~ie~~~~~----------~h~~~F~c~~c~~~--l~~~~~~~ 467 (479)
T KOG1703|consen 401 NSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS-RQIEADGSP----------FHGDCFRCANCMKK--LTKKTFFE 467 (479)
T ss_pred CCcccccCCccchhhhHhhhccccchhccchhHhhh-hHhhccCcc----------ccccceehhhhhcc--ccCCceee
Confidence 999999999999999999999999999999977321 134554443 39999999999994 45666777
Q ss_pred cCCccccchhh
Q 010581 262 EDGRSLCLECM 272 (507)
Q Consensus 262 ~dGr~~C~~C~ 272 (507)
..++++|..|+
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=99.65 E-value=5.2e-18 Score=175.63 Aligned_cols=120 Identities=22% Similarity=0.561 Sum_probs=101.2
Q ss_pred CCCCCCCCCCCCccC-CCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCCCCc
Q 010581 140 PRSYKVCGGCNCDIG-YGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGA 218 (507)
Q Consensus 140 ~~~~~~C~~C~k~I~-~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~ 218 (507)
..+..+|.+|+|.|. ++..++||++.||..||+|..|++.|.+..||..++++||+.||.. ...||.+|++.|...
T Consensus 271 ~~~~~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 271 EDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQD-TLEKCNKCGEPIMDR-- 347 (468)
T ss_pred hhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHH-HHHHHhhhhhHHHHH--
Confidence 345569999999994 3456899999999999999999999999999999999999999988 789999999999874
Q ss_pred ceEEeeecCccccccCCCccCCCCcccCCCCCccccCC-ceeEecCCccccchhhhhh
Q 010581 219 GLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNT-RYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 219 G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~-~~~~l~dGr~~C~~C~~sa 275 (507)
++.+. |+.| |++||+|.+|.| .+++ .|....++++||..||..-
T Consensus 348 -iLrA~-----Gkay-----Hp~CF~Cv~C~r--~ldgipFtvd~~n~v~Cv~dfh~k 392 (468)
T KOG1701|consen 348 -ILRAL-----GKAY-----HPGCFTCVVCAR--CLDGIPFTVDSQNNVYCVPDFHKK 392 (468)
T ss_pred -HHHhc-----cccc-----CCCceEEEEecc--ccCCccccccCCCceeeehhhhhh
Confidence 33332 5666 999999999999 4454 5555668999999998554
No 9
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.55 E-value=1.3e-15 Score=162.41 Aligned_cols=120 Identities=22% Similarity=0.531 Sum_probs=104.3
Q ss_pred CCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCCCCcce
Q 010581 141 RSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGL 220 (507)
Q Consensus 141 ~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~G~ 220 (507)
.+...|++|++.|..|+.+.++++.||..||+|..|+.-|.+ +|..+++.|||..||++.|+-||..|.++|.+. +
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgk---v 206 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGK---V 206 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhh---h
Confidence 456789999999999999999999999999999999999887 889999999999999999999999999999985 2
Q ss_pred EEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhh
Q 010581 221 IEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 221 I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sa 275 (507)
+.+.. .|||+.|-+|..|+.+|..|.+.|. ....++...|-...
T Consensus 207 Lqag~----------kh~HPtCARCsRCgqmF~eGEEMYl-QGs~iWHP~C~qa~ 250 (670)
T KOG1044|consen 207 LQAGD----------KHFHPTCARCSRCGQMFGEGEEMYL-QGSEIWHPDCKQAT 250 (670)
T ss_pred hhccC----------cccCcchhhhhhhccccccchheee-ccccccCCcccccc
Confidence 33321 2679999999999999998887554 45688999997544
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=99.25 E-value=6.6e-12 Score=97.15 Aligned_cols=57 Identities=32% Similarity=0.865 Sum_probs=52.6
Q ss_pred CCCCCCccCCCceE-EecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhc
Q 010581 146 CGGCNCDIGYGNYL-GCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT 202 (507)
Q Consensus 146 C~~C~k~I~~g~~l-~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f 202 (507)
|.+|+++|..+..+ .++++.||+.||+|..|+++|.+..|+..++++||+.||.++|
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 88999999866665 7999999999999999999999988999999999999999876
No 11
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.00 E-value=2.7e-10 Score=122.44 Aligned_cols=139 Identities=19% Similarity=0.445 Sum_probs=101.1
Q ss_pred CCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCCCCcceEE
Q 010581 143 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIE 222 (507)
Q Consensus 143 ~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~G~I~ 222 (507)
...|..|.+.-. |+++.+.+++||..||.|..|+..|....|+.+++. .++++ ..|.++|.+. .+.
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 999999999999999999999999999999998765 44555 7788888875 244
Q ss_pred eeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHhhccccccc
Q 010581 223 YRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYEGMNMKLDQ 302 (507)
Q Consensus 223 ~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~glgm~~~~ 302 (507)
.. |+.| |++||.|+.|+.+++.|++ +.......+|..|...+-....+. .--.-+.|++-.+..
T Consensus 82 a~-----gkty-----h~~cf~cs~ck~pf~~g~~-vt~~gk~~~c~~c~~~~~~~p~~~-----~~ps~cagc~~~lk~ 145 (670)
T KOG1044|consen 82 TL-----GKTY-----HPKCFSCSTCKSPFKSGDK-VTFSGKECLCQTCSQPMPVSPAES-----YGPSTCAGCGEELKN 145 (670)
T ss_pred cc-----ccee-----ccccceecccCCCCCCCCe-eeecchhhhhhhhcCcccCCcccc-----cCCccccchhhhhhc
Confidence 43 5565 9999999999999998887 445556788999975554431111 112233455555555
Q ss_pred ccccccccH
Q 010581 303 QIPMLLVER 311 (507)
Q Consensus 303 ~~pl~lv~~ 311 (507)
+..||+.++
T Consensus 146 gq~llald~ 154 (670)
T KOG1044|consen 146 GQALLALDK 154 (670)
T ss_pred cceeeeecc
Confidence 555554443
No 12
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.70 E-value=1.4e-09 Score=108.46 Aligned_cols=103 Identities=19% Similarity=0.363 Sum_probs=87.4
Q ss_pred CCCccccc--chHHhHHHHhcccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCceEE-ecCccccCCCcccCCCCCCCC
Q 010581 105 NGQRWRSN--TDEDYAWALQDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDIGYGNYLG-CMGTYFHPNCFRCRSCGYPIT 181 (507)
Q Consensus 105 ~~~~wh~e--~ce~c~raLq~~l~~~~~~pYC~~~y~~~~~~~C~~C~k~I~~g~~l~-algk~wHp~CF~C~~C~~~L~ 181 (507)
.+..||.. .|..|.-.|.+.-+......||..+|+..+.-+|..|++.|-+.++|. +.+..||..||.|..|++.|.
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 35689987 899999999766555555899999999999999999999998777764 889999999999999999998
Q ss_pred -CCceEee-CCcccchhhhhhhcccccc
Q 010581 182 -EHEFSLS-GKDPYHKSCFKELTHPKCE 207 (507)
Q Consensus 182 -~~~F~~~-dg~pYCk~CY~k~f~pkC~ 207 (507)
+.+||.. |.++.|+.+|+..-..-|.
T Consensus 132 TGdEFYLmeD~rLvCK~DYE~Ak~k~~~ 159 (383)
T KOG4577|consen 132 TGDEFYLMEDARLVCKDDYETAKQKHCN 159 (383)
T ss_pred cCCeeEEeccceeehhhhHHHHHhcccc
Confidence 5577765 7899999999986555554
No 13
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.58 E-value=1.2e-08 Score=99.08 Aligned_cols=122 Identities=22% Similarity=0.445 Sum_probs=88.9
Q ss_pred CCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhcccc----------------
Q 010581 142 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK---------------- 205 (507)
Q Consensus 142 ~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pk---------------- 205 (507)
....|..|++.+..-+.+...|..||+.||+|..|.+.|....+..+++.+||+.||-.+++|+
T Consensus 6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence 3458999999997666777899999999999999999999999999999999999887777765
Q ss_pred -------------------------ccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeE
Q 010581 206 -------------------------CEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYS 260 (507)
Q Consensus 206 -------------------------C~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~ 260 (507)
|..|++++.+... +... ++ -||..||+|+.|+..++.+ -+.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek--~~~~-----~~-----~~hk~cfrc~~~~~~ls~~--~~~ 151 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEK--VTGN-----GL-----EFHKSCFRCTHCGKKLSPK--NYA 151 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehHH--Hhhh-----hh-----hhhhhheeecccccccCCc--chh
Confidence 4444443332210 0000 01 1599999999999976543 455
Q ss_pred ecCCccccchhhhhhcc
Q 010581 261 LEDGRSLCLECMESAIM 277 (507)
Q Consensus 261 l~dGr~~C~~C~~sav~ 277 (507)
..+|.++|...+-....
T Consensus 152 ~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 152 ALEGVLYCKHHFAQLFK 168 (200)
T ss_pred hcCCccccchhhheeec
Confidence 66678888776544433
No 14
>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=98.24 E-value=8.6e-07 Score=62.42 Aligned_cols=37 Identities=41% Similarity=1.032 Sum_probs=33.4
Q ss_pred CCCCCCCccCCC-ceEEecCccccCCCcccCCCCCCCC
Q 010581 145 VCGGCNCDIGYG-NYLGCMGTYFHPNCFRCRSCGYPIT 181 (507)
Q Consensus 145 ~C~~C~k~I~~g-~~l~algk~wHp~CF~C~~C~~~L~ 181 (507)
+|.+|++.|..+ ..+.++++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999765 6788999999999999999999985
No 15
>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=98.22 E-value=1.2e-06 Score=67.66 Aligned_cols=57 Identities=19% Similarity=0.437 Sum_probs=41.4
Q ss_pred ccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhh
Q 010581 206 CEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 206 C~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sa 275 (507)
|..|+++|.+... .+.+.. +. ||.+||+|..|++.+. +..+...||++||..||...
T Consensus 1 C~~C~~~I~~~~~-~~~~~~-----~~-----~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTEI-VIKAMG-----KF-----WHPECFKCSKCGKPLN--DGDFYEKDGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSSE-EEEETT-----EE-----EETTTSBETTTTCBTT--TSSEEEETTEEEEHHHHHHH
T ss_pred CCCCCCCccCcEE-EEEeCC-----cE-----EEccccccCCCCCccC--CCeeEeECCEEECHHHHhhh
Confidence 7899999997641 222332 22 3999999999999664 33366777899999998753
No 16
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=97.39 E-value=0.0012 Score=57.17 Aligned_cols=108 Identities=24% Similarity=0.262 Sum_probs=67.6
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHhC--CCCCChhhhhhHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCchHH
Q 010581 379 YGLPRLLTGAILAHELMHGWLRLKG--YRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPSTSSASTSSSSSKKGGKSEV 456 (507)
Q Consensus 379 ~GLPrl~~g~ilAHE~mHawlrl~g--~~~l~~~vEEG~Cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 456 (507)
.+-+.-....+|+||+.|+|+.-.. ...++..+.||++++++..+-. .......... ..+....+
T Consensus 18 ~~~~~~~~~~~l~HE~~H~~~~~~~~~~~~~~~W~~EG~A~y~~~~~~~-~~~~~~~~~~------------~~~~~~~~ 84 (128)
T PF13485_consen 18 QGSDEDWLDRVLAHELAHQWFGNYFGGDDNAPRWFNEGLAEYVEGRIED-EFDEDLKQAI------------ESGSLPPL 84 (128)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCccCchHHHHHHHHHHhcCccc-hhHHHHHHHH------------HcCCCCCh
Confidence 3445555559999999999998873 2478999999999999954211 1000000000 00000111
Q ss_pred HHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHhCHHHHHHHHHh
Q 010581 457 EKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKYGLRRTLEHIRL 501 (507)
Q Consensus 457 e~~l~~f~~~qi~~d~s~vYGdGfR~~~~a~~~~gl~~~l~~i~~ 501 (507)
+ .|...+.. ...+.+..|.-|+-.+....+++|...+.+-|+.
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
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=96.88 E-value=0.00011 Score=71.07 Aligned_cols=59 Identities=19% Similarity=0.507 Sum_probs=53.6
Q ss_pred CCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhc
Q 010581 144 KVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT 202 (507)
Q Consensus 144 ~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f 202 (507)
..|..|++.+.+-+-++++++.||..||+|..|+.+|....+-..+.++||..+|.+..
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 46888999998888899999999999999999999999988888899999999998743
No 18
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.81 E-value=0.00017 Score=70.28 Aligned_cols=115 Identities=20% Similarity=0.328 Sum_probs=88.0
Q ss_pred CCCCccCCCceEEecCccccCCCcccCCCCCCCC--CCceEeeCCcccchhhhhh--hccccccccCCCcCCCCcceEEe
Q 010581 148 GCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPIT--EHEFSLSGKDPYHKSCFKE--LTHPKCEVCHQYIPTNGAGLIEY 223 (507)
Q Consensus 148 ~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~--~~~F~~~dg~pYCk~CY~k--~f~pkC~~C~k~I~~~~~G~I~~ 223 (507)
+|+..|.+...+...+..||..|..|..|..++. ...|.. ++..||..+|.. .+..+|..|...|...+ .
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 4777786555677779999999999999999998 556666 999999999998 78999999999985532 1
Q ss_pred eecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhh
Q 010581 224 RCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 224 ~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sa 275 (507)
...-| ++ -|-.||.|..|.+++..++++.+....+..|...+...
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 11111 11 18889999999998777777666666688887776544
No 19
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=96.68 E-value=0.00043 Score=67.54 Aligned_cols=61 Identities=25% Similarity=0.492 Sum_probs=53.6
Q ss_pred CCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhc
Q 010581 142 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT 202 (507)
Q Consensus 142 ~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f 202 (507)
....|..|.+.+++-+.+...+..||..||+|..|+..|+...+....+.+||...+..++
T Consensus 107 ~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 107 EKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred cccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 3568999999998888888999999999999999999999999999999999976655533
No 20
>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=96.36 E-value=0.003 Score=44.10 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=26.0
Q ss_pred cccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCCCCcc
Q 010581 205 KCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLE 252 (507)
Q Consensus 205 kC~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l 252 (507)
+|..|+++|.+.. ..+.+.. . .||..||+|..|++.|
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~-----~-----~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALG-----K-----VWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCc-EEEEeCC-----c-----cccccCCCCcccCCcC
Confidence 5889999998752 1233322 1 2499999999999854
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=91.54 E-value=0.69 Score=44.79 Aligned_cols=45 Identities=20% Similarity=0.179 Sum_probs=34.8
Q ss_pred hHHHHHHHHHHHHHHHHHh------CCCCCChhhhhhHHHHHHHHHhhccc
Q 010581 384 LLTGAILAHELMHGWLRLK------GYRNLNPEVEEGICQVLSYMWLESEV 428 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~------g~~~l~~~vEEG~Cq~~a~~wl~~~~ 428 (507)
--.-+++|||+-|++..-. +..-|+..|=||+-+.++..-.....
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 4567899999999975542 34456999999999999988665554
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=86.58 E-value=0.49 Score=49.46 Aligned_cols=44 Identities=27% Similarity=0.420 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHh-CCCCC-ChhhhhhHHHHHHHHHhhccc
Q 010581 385 LTGAILAHELMHGWLRLK-GYRNL-NPEVEEGICQVLSYMWLESEV 428 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~-g~~~l-~~~vEEG~Cq~~a~~wl~~~~ 428 (507)
....++|||++|-|+--- ....- +..+-|||+++++++|++...
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=82.36 E-value=1.3 Score=43.63 Aligned_cols=91 Identities=20% Similarity=0.265 Sum_probs=54.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCchHHHHHHHH
Q 010581 383 RLLTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPSTSSASTSSSSSKKGGKSEVEKKLGE 462 (507)
Q Consensus 383 rl~~g~ilAHE~mHawlrl~g~~~l~~~vEEG~Cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~e~~l~~ 462 (507)
+--.-.+|-|||||+|++-- ...-|.-+-|||-.++-+. ....+..- .. . .+......-| ...+
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-----P---GGGDSWDDGY--RTTA 156 (205)
T ss_pred HHHHHHHHHHHHHHHhhcCC-CCCCChhheecHHHHHHHH---cCCCCccc--cC-----C---CCCCCccccc--HHHH
Confidence 45667899999999999874 3467999999999998765 11111000 00 0 0000011112 5567
Q ss_pred HHHhhhhcCCCCCchhhH-HHHHHHHHHhCH
Q 010581 463 FFMHQIAHDASPAYGEGF-RIANAAVNKYGL 492 (507)
Q Consensus 463 f~~~qi~~d~s~vYGdGf-R~~~~a~~~~gl 492 (507)
||+.=+|... |+.|| |..++++.+.+.
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=80.95 E-value=1.1 Score=42.67 Aligned_cols=19 Identities=32% Similarity=0.511 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHhCC
Q 010581 386 TGAILAHELMHGWLRLKGY 404 (507)
Q Consensus 386 ~g~ilAHE~mHawlrl~g~ 404 (507)
--.+|||||.|||=.++|-
T Consensus 103 p~v~L~HEL~HA~~~~~Gt 121 (174)
T PF14891_consen 103 PFVVLYHELIHAYDYMNGT 121 (174)
T ss_pred HHHHHHHHHHHHHHHHCCC
Confidence 3589999999999999983
No 25
>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=80.90 E-value=0.65 Score=44.69 Aligned_cols=17 Identities=53% Similarity=0.575 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHH
Q 010581 385 LTGAILAHELMHGWLRL 401 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl 401 (507)
.+|+|||||||||+-..
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 26
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=80.86 E-value=0.96 Score=37.80 Aligned_cols=18 Identities=44% Similarity=0.547 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHhC
Q 010581 386 TGAILAHELMHGWLRLKG 403 (507)
Q Consensus 386 ~g~ilAHE~mHawlrl~g 403 (507)
.-++|||||+|+++.-.|
T Consensus 61 ~~~llaHEl~Hv~Qq~~g 78 (79)
T PF13699_consen 61 GRALLAHELAHVVQQRRG 78 (79)
T ss_pred cchhHhHHHHHHHhhccC
Confidence 457999999999987654
No 27
>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=79.68 E-value=8.6 Score=45.31 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHH-HhCCCC-CChhhhhhHHHHHHHHHhhcc
Q 010581 386 TGAILAHELMHGWLR-LKGYRN-LNPEVEEGICQVLSYMWLESE 427 (507)
Q Consensus 386 ~g~ilAHE~mHawlr-l~g~~~-l~~~vEEG~Cq~~a~~wl~~~ 427 (507)
...++|||+.|-|.- |=.... =+..+-|||..+|+++|++.-
T Consensus 287 ~~~viaHElAHqWFGnlVT~~wW~dlWLnEGFAty~e~~~~~~~ 330 (831)
T TIGR02412 287 RAGVILHEMAHMWFGDLVTMRWWNDLWLNESFAEYMGTLASAEA 330 (831)
T ss_pred HHHHHHHHHHHHHhCCEeccccccchhHHHHHHHHHHHHHHHhc
Confidence 357999999999973 111111 156899999999999999753
No 28
>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=79.31 E-value=1.8 Score=43.87 Aligned_cols=110 Identities=18% Similarity=0.381 Sum_probs=68.1
Q ss_pred chHHhHHHHhcccCCCCCCCCCCCCCCCCCCCCCCCCCCcc---CCCc--------eEEecC---------ccc--cC-C
Q 010581 113 TDEDYAWALQDSQLNPSFPPYDPSHYYPRSYKVCGGCNCDI---GYGN--------YLGCMG---------TYF--HP-N 169 (507)
Q Consensus 113 ~ce~c~raLq~~l~~~~~~pYC~~~y~~~~~~~C~~C~k~I---~~g~--------~l~alg---------k~w--Hp-~ 169 (507)
+|+.|.+.- . ++.||-.|......|+|+.|++.- ..|. +.+-++ ..| |- .
T Consensus 40 eCdkC~r~Q------K-nRAFCYFC~s~qrlp~Ca~Cgk~KCm~k~gdCvvkH~g~~~tGl~mvGaiCDfCEawvCHgrk 112 (314)
T PF06524_consen 40 ECDKCQRKQ------K-NRAFCYFCQSVQRLPMCAHCGKTKCMLKTGDCVVKHPGVFTTGLGMVGAICDFCEAWVCHGRK 112 (314)
T ss_pred cchhhhhhc------c-ccceeehhhhhhcCchhhhcCCeeeeccCCCeEEecCceeecccchhhhhhccchhheecccc
Confidence 888888632 1 255666666666789999999852 2233 222221 123 44 5
Q ss_pred CcccCCCCCCCCCCce-------EeeCCcccchhhhhhhccccccccCCCcCCCCcceEEeeecCccccccCCCccCCCC
Q 010581 170 CFRCRSCGYPITEHEF-------SLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHT 242 (507)
Q Consensus 170 CF~C~~C~~~L~~~~F-------~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~C 242 (507)
|+.-+.|..||.+... +.++|++ -+|..|..++-..+ .|-+|.-|..- -...
T Consensus 113 Cl~~HaC~Cpl~da~C~EC~R~vw~hGGri-----------f~CsfC~~flCEDD---------QFEHQAsCQvL-e~E~ 171 (314)
T PF06524_consen 113 CLSTHACTCPLQDAVCIECERGVWDHGGRI-----------FKCSFCDNFLCEDD---------QFEHQASCQVL-ESET 171 (314)
T ss_pred ccccccccCcCCCcEeeeeecccccCCCeE-----------EEeecCCCeeeccc---------hhhhhhhhhhh-hccc
Confidence 8888899999987533 2233333 35888888886643 13344444443 4677
Q ss_pred cccCCCCC
Q 010581 243 SRCCSCER 250 (507)
Q Consensus 243 F~C~~C~r 250 (507)
|+|.+|+|
T Consensus 172 ~KC~SCNr 179 (314)
T PF06524_consen 172 FKCQSCNR 179 (314)
T ss_pred cccccccc
Confidence 99999998
No 29
>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=79.13 E-value=1.5 Score=40.38 Aligned_cols=22 Identities=23% Similarity=0.087 Sum_probs=20.1
Q ss_pred CchhHHHHHHHHHHHHHHHHHh
Q 010581 381 LPRLLTGAILAHELMHGWLRLK 402 (507)
Q Consensus 381 LPrl~~g~ilAHE~mHawlrl~ 402 (507)
.|.-.+-.+|+|||.|||+.+.
T Consensus 55 ~~~~~~~~tL~HEm~H~~~~~~ 76 (157)
T PF10263_consen 55 NPEEELIDTLLHEMAHAAAYVF 76 (157)
T ss_pred hHHHHHHHHHHHHHHHHHhhhc
Confidence 5777888999999999999998
No 30
>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=78.99 E-value=2.8 Score=35.52 Aligned_cols=52 Identities=23% Similarity=0.128 Sum_probs=34.6
Q ss_pred EEEEEEcCCchhHHHHHHHHHHHHHHHHHhCC------CCCChhhhhhHHHHHHHHHh
Q 010581 373 TAILVLYGLPRLLTGAILAHELMHGWLRLKGY------RNLNPEVEEGICQVLSYMWL 424 (507)
Q Consensus 373 ~~Ilvl~GLPrl~~g~ilAHE~mHawlrl~g~------~~l~~~vEEG~Cq~~a~~wl 424 (507)
.-|+|=..++..---.+||||++|.++.-.+. ........|=-++.+|...|
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 23344444555555554443
No 31
>PRK03001 M48 family peptidase; Provisional
Probab=75.45 E-value=1.2 Score=45.51 Aligned_cols=20 Identities=30% Similarity=0.234 Sum_probs=15.9
Q ss_pred CCchhHHHHHHHHHHHHHHH
Q 010581 380 GLPRLLTGAILAHELMHGWL 399 (507)
Q Consensus 380 GLPrl~~g~ilAHE~mHawl 399 (507)
.|...-..+|||||+.|.--
T Consensus 118 ~l~~~El~aVlAHElgHi~~ 137 (283)
T PRK03001 118 VLSEREIRGVMAHELAHVKH 137 (283)
T ss_pred hCCHHHHHHHHHHHHHHHhC
Confidence 45667778999999999753
No 32
>PRK01345 heat shock protein HtpX; Provisional
Probab=73.77 E-value=1.5 Score=45.88 Aligned_cols=19 Identities=32% Similarity=0.288 Sum_probs=15.5
Q ss_pred CchhHHHHHHHHHHHHHHH
Q 010581 381 LPRLLTGAILAHELMHGWL 399 (507)
Q Consensus 381 LPrl~~g~ilAHE~mHawl 399 (507)
|...-..+|||||+.|.-.
T Consensus 119 L~~dEL~aVlAHElgHi~~ 137 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVKN 137 (317)
T ss_pred CCHHHHHHHHHHHHHHHHc
Confidence 4666778999999999763
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=72.88 E-value=1.2 Score=43.29 Aligned_cols=94 Identities=20% Similarity=0.312 Sum_probs=67.5
Q ss_pred CCccccc--chHHhHHHHh--cccCCCCCCCCCCCCCCC--CCCCCCCCCCCccCCCc-eEEecCccccCCCcccCCCCC
Q 010581 106 GQRWRSN--TDEDYAWALQ--DSQLNPSFPPYDPSHYYP--RSYKVCGGCNCDIGYGN-YLGCMGTYFHPNCFRCRSCGY 178 (507)
Q Consensus 106 ~~~wh~e--~ce~c~raLq--~~l~~~~~~pYC~~~y~~--~~~~~C~~C~k~I~~g~-~l~algk~wHp~CF~C~~C~~ 178 (507)
...||.. .|..|...+. .......+..||..+|.. .....|.+|...+..-+ +..+..+. |-.||.|..|..
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 4567755 5666666664 333333457899999977 77889999999985333 34466777 999999999988
Q ss_pred CCC-CCceEeeCC-cccchhhhhh
Q 010581 179 PIT-EHEFSLSGK-DPYHKSCFKE 200 (507)
Q Consensus 179 ~L~-~~~F~~~dg-~pYCk~CY~k 200 (507)
.+. ..++.+... +.+|...+.+
T Consensus 95 ~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 95 LLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred hcCCCCeeeeehhhhhhcHhhhhh
Confidence 665 456777655 8888877765
No 34
>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=72.27 E-value=4.9 Score=42.95 Aligned_cols=44 Identities=18% Similarity=0.151 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHHHH---HHHH--hCC-CCCChhhhhhHHHHHHHHHhhcc
Q 010581 384 LLTGAILAHELMHG---WLRL--KGY-RNLNPEVEEGICQVLSYMWLESE 427 (507)
Q Consensus 384 l~~g~ilAHE~mHa---wlrl--~g~-~~l~~~vEEG~Cq~~a~~wl~~~ 427 (507)
-.+-++||||++|. |.+. .|- ...+..+|||+-+++.++.-...
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 35
>PRK02391 heat shock protein HtpX; Provisional
Probab=71.72 E-value=1.6 Score=45.09 Aligned_cols=21 Identities=38% Similarity=0.177 Sum_probs=16.5
Q ss_pred cCCchhHHHHHHHHHHHHHHH
Q 010581 379 YGLPRLLTGAILAHELMHGWL 399 (507)
Q Consensus 379 ~GLPrl~~g~ilAHE~mHawl 399 (507)
..|...-.-+|||||+.|.--
T Consensus 126 ~~L~~~El~aVlaHElgHi~~ 146 (296)
T PRK02391 126 RRLDPDELEAVLAHELSHVKN 146 (296)
T ss_pred hhCCHHHHHHHHHHHHHHHHc
Confidence 456667788999999999643
No 36
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=71.25 E-value=0.7 Score=45.33 Aligned_cols=96 Identities=16% Similarity=0.267 Sum_probs=56.7
Q ss_pred ccccccCCCcCCCCcceEEeeecCccccccCCCccCCCCcccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCC
Q 010581 204 PKCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQ 283 (507)
Q Consensus 204 pkC~~C~k~I~~~~~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~dt~e~q 283 (507)
+.|..|++.+.+-+ .+ -....|| |..||+|..|+- ++.-+.+.-.|.++||-..|..-+..+---.
T Consensus 5 ~n~~~cgk~vYPvE--~v-~cldk~w---------hk~cfkce~c~m--tlnmKnyKgy~kkpycn~hYpkq~at~~adT 70 (264)
T KOG1702|consen 5 CNREDCGKTVYPVE--EV-KCLDKVW---------HKQCFKCEVCGM--TLNMKNYKGYDKKPYCNPHYPKQVATVMADT 70 (264)
T ss_pred chhhhhccccccHH--HH-hhHHHHH---------HHHhheeeeccC--ChhhhhccccccCCCcCcccccceeeeecCC
Confidence 45667777765532 01 1123455 999999999996 5566666656789999999865543332223
Q ss_pred chhhhHHH------------HHhhcccccccccccccccHHHHHHHH
Q 010581 284 PLYHAIRD------------YYEGMNMKLDQQIPMLLVERQALNEAI 318 (507)
Q Consensus 284 pl~~~i~~------------f~~glgm~~~~~~pl~lv~~~~ln~a~ 318 (507)
|....|.+ -|+.| .+-|.++.|-++|.+.-
T Consensus 71 PEm~Rik~n~enqS~vkY~~e~ekm-----KG~~s~iaDtPem~r~K 112 (264)
T KOG1702|consen 71 PEMRRIKENTENQSNVKYHAEYEKM-----KGTKSEIADTPEMERLK 112 (264)
T ss_pred HHHHHHHhhhccchhhhhHHHHHHh-----cCCcceecCCHHHHHHH
Confidence 33333321 22221 23366677888886653
No 37
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=71.16 E-value=3.1 Score=47.62 Aligned_cols=50 Identities=24% Similarity=0.503 Sum_probs=26.6
Q ss_pred CCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhh--ccccccccCCCcCC
Q 010581 144 KVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKEL--THPKCEVCHQYIPT 215 (507)
Q Consensus 144 ~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~--f~pkC~~C~k~I~~ 215 (507)
.+|+.|+..+..+. -.|..|+.+|.. ..|..|-.+. -...|..|+.....
T Consensus 2 ~~Cp~Cg~~n~~~a-------------kFC~~CG~~l~~---------~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 2 LICPQCQFENPNNN-------------RFCQKCGTSLTH---------KPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CcCCCCCCcCCCCC-------------ccccccCCCCCC---------CcCCCCCCCCCcccccccccCCcccc
Confidence 46888888774321 135666666632 1355555442 23456666665443
No 38
>PRK03072 heat shock protein HtpX; Provisional
Probab=70.46 E-value=1.6 Score=44.93 Aligned_cols=21 Identities=33% Similarity=0.336 Sum_probs=16.6
Q ss_pred EcCCchhHHHHHHHHHHHHHH
Q 010581 378 LYGLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 378 l~GLPrl~~g~ilAHE~mHaw 398 (507)
|.-|.+--..+|||||+.|.-
T Consensus 119 l~~l~~~El~aVlAHElgHi~ 139 (288)
T PRK03072 119 LQILNERELRGVLGHELSHVY 139 (288)
T ss_pred HHhCCHHHHHHHHHHHHHHHh
Confidence 345677778899999999953
No 39
>PRK14015 pepN aminopeptidase N; Provisional
Probab=70.09 E-value=15 Score=43.73 Aligned_cols=40 Identities=20% Similarity=0.432 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHhCC--CCC-ChhhhhhHHHHHHHHHhhc
Q 010581 386 TGAILAHELMHGWLRLKGY--RNL-NPEVEEGICQVLSYMWLES 426 (507)
Q Consensus 386 ~g~ilAHE~mHawlrl~g~--~~l-~~~vEEG~Cq~~a~~wl~~ 426 (507)
..+|+|||+.|-|.- |-. ..- +..+-||+.-++.++|.+.
T Consensus 296 i~~vIaHElaHqWFG-NlVT~~~W~dLWLnEGFAty~e~~~~~~ 338 (875)
T PRK14015 296 IESVIAHEYFHNWTG-NRVTCRDWFQLSLKEGLTVFRDQEFSAD 338 (875)
T ss_pred HHHHHHHHHHHHHHh-CcceecchhhhhhhhHHHHHHHHHHHHH
Confidence 568999999999941 111 111 3567999999998888765
No 40
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=69.47 E-value=4 Score=37.61 Aligned_cols=22 Identities=41% Similarity=0.333 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHHHHHhC
Q 010581 382 PRLLTGAILAHELMHGWLRLKG 403 (507)
Q Consensus 382 Prl~~g~ilAHE~mHawlrl~g 403 (507)
|...+-.||+|||.|++..+.|
T Consensus 55 ~~~~l~~~l~HEm~H~~~~~~g 76 (146)
T smart00731 55 GRDRLRETLLHELCHAALYLFG 76 (146)
T ss_pred cHHHHHhhHHHHHHHHHHHHhC
Confidence 4455667999999999999865
No 41
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.23 E-value=2.9 Score=40.27 Aligned_cols=48 Identities=21% Similarity=0.517 Sum_probs=39.1
Q ss_pred CCCcccCCCCCCCCCCc-eEeeCCcccchhhhhhh--ccccccccCCCcCC
Q 010581 168 PNCFRCRSCGYPITEHE-FSLSGKDPYHKSCFKEL--THPKCEVCHQYIPT 215 (507)
Q Consensus 168 p~CF~C~~C~~~L~~~~-F~~~dg~pYCk~CY~k~--f~pkC~~C~k~I~~ 215 (507)
..||+|..|=.+..... +.-+-|.+||+.|-+.. ..-+|..|++.|..
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 45788999977777654 66788999999999875 47889999998875
No 42
>PRK05457 heat shock protein HtpX; Provisional
Probab=65.37 E-value=2.3 Score=43.76 Aligned_cols=21 Identities=38% Similarity=0.379 Sum_probs=17.4
Q ss_pred EcCCchhHHHHHHHHHHHHHH
Q 010581 378 LYGLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 378 l~GLPrl~~g~ilAHE~mHaw 398 (507)
|.-|++--..+|||||+.|.-
T Consensus 126 l~~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 126 LQNMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred hhhCCHHHHHHHHHHHHHHHH
Confidence 345788889999999999963
No 43
>PRK02870 heat shock protein HtpX; Provisional
Probab=65.15 E-value=2.5 Score=44.67 Aligned_cols=18 Identities=44% Similarity=0.412 Sum_probs=15.0
Q ss_pred CCchhHHHHHHHHHHHHH
Q 010581 380 GLPRLLTGAILAHELMHG 397 (507)
Q Consensus 380 GLPrl~~g~ilAHE~mHa 397 (507)
-|++--..+|||||+.|.
T Consensus 167 ~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 167 KLDRDELQAVMAHELSHI 184 (336)
T ss_pred hCCHHHHHHHHHHHHHHH
Confidence 356667889999999997
No 44
>PRK03982 heat shock protein HtpX; Provisional
Probab=65.04 E-value=2.4 Score=43.50 Aligned_cols=20 Identities=30% Similarity=0.119 Sum_probs=16.2
Q ss_pred CCchhHHHHHHHHHHHHHHH
Q 010581 380 GLPRLLTGAILAHELMHGWL 399 (507)
Q Consensus 380 GLPrl~~g~ilAHE~mHawl 399 (507)
.|...-.-+|||||+.|.--
T Consensus 119 ~l~~~El~AVlAHElgHi~~ 138 (288)
T PRK03982 119 LLNEDELEGVIAHELTHIKN 138 (288)
T ss_pred hCCHHHHHHHHHHHHHHHHc
Confidence 45677788999999999753
No 45
>PRK04897 heat shock protein HtpX; Provisional
Probab=64.44 E-value=2.3 Score=43.95 Aligned_cols=20 Identities=20% Similarity=0.169 Sum_probs=16.4
Q ss_pred cCCchhHHHHHHHHHHHHHH
Q 010581 379 YGLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 379 ~GLPrl~~g~ilAHE~mHaw 398 (507)
..|++.-..+|||||+.|.-
T Consensus 130 ~~l~~~El~aVlAHElgHi~ 149 (298)
T PRK04897 130 AIMNREELEGVIGHEISHIR 149 (298)
T ss_pred hhCCHHHHHHHHHHHHHHHh
Confidence 35677888999999999954
No 46
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=63.42 E-value=15 Score=36.52 Aligned_cols=55 Identities=20% Similarity=0.056 Sum_probs=41.4
Q ss_pred EEEEEEcCCchhHHHHHHHHHHHHHHHHHhC------CCC-CChhhhhhHHHHHHHHHhhcc
Q 010581 373 TAILVLYGLPRLLTGAILAHELMHGWLRLKG------YRN-LNPEVEEGICQVLSYMWLESE 427 (507)
Q Consensus 373 ~~Ilvl~GLPrl~~g~ilAHE~mHawlrl~g------~~~-l~~~vEEG~Cq~~a~~wl~~~ 427 (507)
.-|++---++-..---+|||||.|++|--.+ .++ -....-|=.|+.+|--.|-..
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 4677777778888888999999999997765 122 244556778999998888664
No 47
>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=63.36 E-value=5.3 Score=38.37 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=17.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhC
Q 010581 383 RLLTGAILAHELMHGWLRLKG 403 (507)
Q Consensus 383 rl~~g~ilAHE~mHawlrl~g 403 (507)
+...-.+|+|||.|||=.+..
T Consensus 68 ~~~l~~~l~HELIHayD~cr~ 88 (173)
T PF09768_consen 68 QGHLEDTLTHELIHAYDHCRA 88 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 456678999999999988874
No 48
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=61.43 E-value=5.1 Score=35.92 Aligned_cols=15 Identities=47% Similarity=0.683 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHh
Q 010581 388 AILAHELMHGWLRLK 402 (507)
Q Consensus 388 ~ilAHE~mHawlrl~ 402 (507)
-.|||||.|+|+.-.
T Consensus 81 ~TL~HEL~H~WQ~Rs 95 (141)
T PHA02456 81 DTLAHELNHAWQFRT 95 (141)
T ss_pred HHHHHHHHHHHhhhc
Confidence 679999999998765
No 49
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=60.37 E-value=8.2 Score=31.34 Aligned_cols=47 Identities=21% Similarity=0.398 Sum_probs=22.8
Q ss_pred cccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCCCC
Q 010581 171 FRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNG 217 (507)
Q Consensus 171 F~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~~ 217 (507)
.+|+.|..-|...-....=...||..|-...++..|.+|+.|....+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 46777766655432233456789999998888899999999876543
No 50
>PF12773 DZR: Double zinc ribbon
Probab=58.85 E-value=11 Score=28.08 Aligned_cols=11 Identities=27% Similarity=0.570 Sum_probs=6.5
Q ss_pred cccccCCCcCC
Q 010581 205 KCEVCHQYIPT 215 (507)
Q Consensus 205 kC~~C~k~I~~ 215 (507)
.|..|+..+..
T Consensus 31 ~C~~Cg~~~~~ 41 (50)
T PF12773_consen 31 ICPNCGAENPP 41 (50)
T ss_pred CCcCCcCCCcC
Confidence 46666666544
No 51
>PRK01265 heat shock protein HtpX; Provisional
Probab=58.53 E-value=3.9 Score=42.97 Aligned_cols=17 Identities=41% Similarity=0.311 Sum_probs=14.2
Q ss_pred CchhHHHHHHHHHHHHH
Q 010581 381 LPRLLTGAILAHELMHG 397 (507)
Q Consensus 381 LPrl~~g~ilAHE~mHa 397 (507)
|.+.-..+|||||+.|.
T Consensus 135 l~~~El~aVlAHElgHi 151 (324)
T PRK01265 135 LNRDEIKAVAGHELGHL 151 (324)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 46667789999999994
No 52
>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=57.85 E-value=6.3 Score=36.88 Aligned_cols=18 Identities=39% Similarity=0.499 Sum_probs=12.5
Q ss_pred chhHHHHHHHHHHHHHHH
Q 010581 382 PRLLTGAILAHELMHGWL 399 (507)
Q Consensus 382 Prl~~g~ilAHE~mHawl 399 (507)
|-.-..=|+||||+|+..
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 53
>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=57.32 E-value=9 Score=43.52 Aligned_cols=40 Identities=23% Similarity=0.221 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHh-CCCCC-ChhhhhhHHHHHHHHHhhc
Q 010581 387 GAILAHELMHGWLRLK-GYRNL-NPEVEEGICQVLSYMWLES 426 (507)
Q Consensus 387 g~ilAHE~mHawlrl~-g~~~l-~~~vEEG~Cq~~a~~wl~~ 426 (507)
..++|||++|-|.--- ....= +..+-||+.-++.+++++.
T Consensus 280 ~~viaHElAHqWfGNlVT~~~W~d~WLnEGfaty~e~~~~~~ 321 (601)
T TIGR02411 280 VDVIAHELAHSWSGNLVTNCSWEHFWLNEGWTVYLERRIVGR 321 (601)
T ss_pred hhhHHHHHHhhccCceeecCCchHHHHHhhHHHHHHHHHHHH
Confidence 3799999999997421 11111 5678999999998877653
No 54
>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=55.77 E-value=7.2 Score=39.11 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=15.3
Q ss_pred CchhHHHHHHHHHHHHHH
Q 010581 381 LPRLLTGAILAHELMHGW 398 (507)
Q Consensus 381 LPrl~~g~ilAHE~mHaw 398 (507)
+|...+..++||||.|.|
T Consensus 162 ~~~~~~a~t~AHElGHnl 179 (244)
T cd04270 162 VPTKESDLVTAHELGHNF 179 (244)
T ss_pred cchhHHHHHHHHHHHHhc
Confidence 466778899999999986
No 55
>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=54.64 E-value=14 Score=28.32 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=33.3
Q ss_pred cccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCCcCC
Q 010581 171 FRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIPT 215 (507)
Q Consensus 171 F~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f--~pkC~~C~k~I~~ 215 (507)
|.|..|+..+.+ ......|..||+.|..+.. ..+|..|++++..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 578888888776 3455678999999987643 5678888888754
No 56
>PRK04351 hypothetical protein; Provisional
Probab=54.57 E-value=11 Score=35.33 Aligned_cols=20 Identities=40% Similarity=0.431 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHHhC
Q 010581 384 LLTGAILAHELMHGWLRLKG 403 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~g 403 (507)
..+..||+|||.|+.+.+.|
T Consensus 59 ~~l~~vv~HElcH~~~~~~g 78 (149)
T PRK04351 59 EELIGIIKHELCHYHLHLEG 78 (149)
T ss_pred HHHHhhHHHHHHHHHHHHHC
Confidence 34568999999999999875
No 57
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.23 E-value=6.6 Score=40.64 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=36.5
Q ss_pred CCcccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCCcCCC
Q 010581 169 NCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIPTN 216 (507)
Q Consensus 169 ~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f--~pkC~~C~k~I~~~ 216 (507)
-=|.|..|++++.. .....-+..+|..|..+.+ +++|.+|++.+.+.
T Consensus 240 ~Pf~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 240 LPFKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred CCcccccccccccc-chhhcCCceeehhhhccccccCCcceecccccccc
Confidence 35788888887765 3344567889999998766 58999999998873
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.23 E-value=14 Score=29.54 Aligned_cols=27 Identities=26% Similarity=0.600 Sum_probs=15.9
Q ss_pred CCCCCCCCCccCCCc-eEEecCccccCCCcccCCCCCC
Q 010581 143 YKVCGGCNCDIGYGN-YLGCMGTYFHPNCFRCRSCGYP 179 (507)
Q Consensus 143 ~~~C~~C~k~I~~g~-~l~algk~wHp~CF~C~~C~~~ 179 (507)
.++|..|+..|...+ .+. |.|..|+..
T Consensus 7 ~~~CtSCg~~i~~~~~~~~----------F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVK----------FLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccCE----------eeCCCCCCe
Confidence 456777777775333 222 666777664
No 59
>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=53.00 E-value=8.9 Score=32.56 Aligned_cols=31 Identities=19% Similarity=0.480 Sum_probs=21.6
Q ss_pred CCCCCCCCCCccCCCceEEec-CccccCCCcc
Q 010581 142 SYKVCGGCNCDIGYGNYLGCM-GTYFHPNCFR 172 (507)
Q Consensus 142 ~~~~C~~C~k~I~~g~~l~al-gk~wHp~CF~ 172 (507)
....|+.|++.|..+.++..- |..+|..|++
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 356799999999765555543 5667877753
No 60
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=52.76 E-value=6.9 Score=26.08 Aligned_cols=20 Identities=40% Similarity=0.521 Sum_probs=16.6
Q ss_pred hhhhHHHHHHhccccccccc
Q 010581 85 EKEELDHAIALSLAEDLKRP 104 (507)
Q Consensus 85 e~edid~aia~sL~Ee~kk~ 104 (507)
|+|+|.+||++|+.|.+...
T Consensus 2 EDe~Lq~Ai~lSl~e~e~~~ 21 (26)
T smart00726 2 EDEDLQLALELSLQEAEESX 21 (26)
T ss_pred hHHHHHHHHHHhHHHhhhcc
Confidence 68999999999998776543
No 61
>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=52.23 E-value=10 Score=36.28 Aligned_cols=30 Identities=40% Similarity=0.264 Sum_probs=21.5
Q ss_pred EEEEEcC----CchhHHHHHHHHHHHHHHHHHhC
Q 010581 374 AILVLYG----LPRLLTGAILAHELMHGWLRLKG 403 (507)
Q Consensus 374 ~Ilvl~G----LPrl~~g~ilAHE~mHawlrl~g 403 (507)
.|+|-.| ++..-..+|||||+.|...+-.-
T Consensus 73 ~I~v~~~ll~~~~~~el~aVlaHElgH~~~~h~~ 106 (226)
T PF01435_consen 73 RIVVTSGLLESLSEDELAAVLAHELGHIKHRHIL 106 (226)
T ss_dssp EEEEEHHHHHHSSHHHHHHHHHHHHHHHHTTHCC
T ss_pred EEEEeChhhhcccHHHHHHHHHHHHHHHHcCCcc
Confidence 3444444 45566779999999999977653
No 62
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=52.11 E-value=9 Score=29.48 Aligned_cols=30 Identities=23% Similarity=0.787 Sum_probs=22.2
Q ss_pred ccCCCCCccccCCceeEecCCccccchhhhhh
Q 010581 244 RCCSCERLESWNTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 244 ~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sa 275 (507)
.|..|+.-+.+-.+ +.+.|| .+|..|+..+
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 47888885544333 668888 7999999887
No 63
>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=51.03 E-value=14 Score=36.99 Aligned_cols=29 Identities=31% Similarity=0.424 Sum_probs=23.1
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHhCCCCC
Q 010581 379 YGLPRLLTGAILAHELMHGWLRLKGYRNL 407 (507)
Q Consensus 379 ~GLPrl~~g~ilAHE~mHawlrl~g~~~l 407 (507)
|+=.-+..-+|-|||..||-+.-+||.-|
T Consensus 82 y~~~SiaAvaVAAHEvGHAiQ~a~~Y~pl 110 (222)
T PF04298_consen 82 YNGRSIAAVAVAAHEVGHAIQHAEGYAPL 110 (222)
T ss_pred CCCCCHHHHHHHHHHHhHHHhccccCcHH
Confidence 44455667799999999999999998543
No 64
>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=49.64 E-value=15 Score=34.77 Aligned_cols=20 Identities=35% Similarity=0.293 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHh-CC
Q 010581 385 LTGAILAHELMHGWLRLK-GY 404 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~-g~ 404 (507)
+..+++.||++|++.... |.
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 567899999999999875 53
No 65
>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=49.19 E-value=18 Score=34.61 Aligned_cols=24 Identities=33% Similarity=0.304 Sum_probs=19.0
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHH
Q 010581 374 AILVLYGLPRLLTGAILAHELMHG 397 (507)
Q Consensus 374 ~Ilvl~GLPrl~~g~ilAHE~mHa 397 (507)
+|....+..-+.++.++|||++|.
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 66
>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=48.28 E-value=8.5 Score=23.48 Aligned_cols=16 Identities=44% Similarity=0.696 Sum_probs=13.5
Q ss_pred hhhhhHHHHHHhcccc
Q 010581 84 REKEELDHAIALSLAE 99 (507)
Q Consensus 84 ~e~edid~aia~sL~E 99 (507)
.|+++|.+||++|+.|
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 67
>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=47.51 E-value=13 Score=35.15 Aligned_cols=53 Identities=19% Similarity=0.438 Sum_probs=35.9
Q ss_pred CcccchhhhhhhccccccccCCCcCCCC--cceEEeeecCccccccCCCccCCCCcccCCCCCccccC
Q 010581 190 KDPYHKSCFKELTHPKCEVCHQYIPTNG--AGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWN 255 (507)
Q Consensus 190 g~pYCk~CY~k~f~pkC~~C~k~I~~~~--~G~I~~~~~~fWgqkyCp~h~H~~CF~C~~C~r~l~~g 255 (507)
.+-||..|-.+ ...+|..|+.+|.+.. .|.+.+.. + ++.- .-|..|++.+|+-
T Consensus 27 ~~~fC~kCG~~-tI~~Cp~C~~~IrG~y~v~gv~~~g~-~----------~~~P-sYC~~CGkpyPWt 81 (158)
T PF10083_consen 27 REKFCSKCGAK-TITSCPNCSTPIRGDYHVEGVFGLGG-H----------YEAP-SYCHNCGKPYPWT 81 (158)
T ss_pred HHHHHHHhhHH-HHHHCcCCCCCCCCceecCCeeeeCC-C----------CCCC-hhHHhCCCCCchH
Confidence 46789999776 6778999999999973 35554422 1 1211 1288999988764
No 68
>PRK11827 hypothetical protein; Provisional
Probab=47.37 E-value=12 Score=29.89 Aligned_cols=18 Identities=28% Similarity=0.499 Sum_probs=14.2
Q ss_pred hcccccccccccccccHH
Q 010581 295 GMNMKLDQQIPMLLVERQ 312 (507)
Q Consensus 295 glgm~~~~~~pl~lv~~~ 312 (507)
++.-+|..+||++|++..
T Consensus 33 ~laYPI~dgIPVlL~deA 50 (60)
T PRK11827 33 NLAFPLRDGIPVLLETEA 50 (60)
T ss_pred CeeccccCCccccCHHHh
Confidence 456678999999999643
No 69
>PRK04860 hypothetical protein; Provisional
Probab=47.25 E-value=21 Score=33.86 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=21.5
Q ss_pred chhHHHHHHHHHHHHHHHHHh-C--CCCCChh
Q 010581 382 PRLLTGAILAHELMHGWLRLK-G--YRNLNPE 410 (507)
Q Consensus 382 Prl~~g~ilAHE~mHawlrl~-g--~~~l~~~ 410 (507)
+...+-.|++|||.|.++.+. | ++. +.+
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 455668999999999999987 4 455 553
No 70
>KOG3931 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.44 E-value=11 Score=40.01 Aligned_cols=22 Identities=32% Similarity=0.452 Sum_probs=19.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHh
Q 010581 381 LPRLLTGAILAHELMHGWLRLK 402 (507)
Q Consensus 381 LPrl~~g~ilAHE~mHawlrl~ 402 (507)
-||--.--.|-|||.||||+..
T Consensus 100 RPRkDLVETLLHEMIHAYlFV~ 121 (484)
T KOG3931|consen 100 RPRKDLVETLLHEMIHAYLFVT 121 (484)
T ss_pred CchHHHHHHHHHHHHHHheeEe
Confidence 3888888999999999999884
No 71
>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=46.28 E-value=13 Score=26.56 Aligned_cols=25 Identities=28% Similarity=0.697 Sum_probs=19.6
Q ss_pred cccCCCCCccccCCceeEecCCccccchhhh
Q 010581 243 SRCCSCERLESWNTRYYSLEDGRSLCLECME 273 (507)
Q Consensus 243 F~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~ 273 (507)
+.|..|+. .++...||..||..|..
T Consensus 9 ~~C~~C~~------~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGS------RWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCC------eEeEccCCEEEhhhCce
Confidence 45888874 26888999999999853
No 72
>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=45.34 E-value=11 Score=33.91 Aligned_cols=11 Identities=45% Similarity=0.628 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q 010581 388 AILAHELMHGW 398 (507)
Q Consensus 388 ~ilAHE~mHaw 398 (507)
.+++||+|||-
T Consensus 88 ~~~~HEigHaL 98 (140)
T smart00235 88 GVAAHELGHAL 98 (140)
T ss_pred ccHHHHHHHHh
Confidence 39999999993
No 73
>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=45.16 E-value=19 Score=34.53 Aligned_cols=18 Identities=28% Similarity=0.471 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010581 385 LTGAILAHELMHGWLRLK 402 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~ 402 (507)
+.-++..||++|||....
T Consensus 8 ~~~~i~~HE~aHa~~A~~ 25 (181)
T cd06158 8 VLLAITLHEFAHAYVAYR 25 (181)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 445899999999999886
No 74
>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=44.70 E-value=13 Score=35.23 Aligned_cols=24 Identities=38% Similarity=0.423 Sum_probs=17.2
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHHH
Q 010581 374 AILVLYGLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 374 ~Ilvl~GLPrl~~g~ilAHE~mHaw 398 (507)
+|....+ +.+..+.++|||++|.+
T Consensus 122 ~v~~~~~-~~~~~~~~~aHElGH~l 145 (192)
T cd04267 122 GVVEDTG-FTLLTALTMAHELGHNL 145 (192)
T ss_pred EEEecCC-cceeehhhhhhhHHhhc
Confidence 4444444 35678899999999975
No 75
>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=44.27 E-value=21 Score=30.18 Aligned_cols=28 Identities=32% Similarity=0.694 Sum_probs=23.0
Q ss_pred ccCCCCCCCCCCceEee-CCcccchhhhh
Q 010581 172 RCRSCGYPITEHEFSLS-GKDPYHKSCFK 199 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~-dg~pYCk~CY~ 199 (507)
.|..|+++|....|.+. +|..+|..|..
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 58999999998777765 67888888864
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=43.65 E-value=81 Score=37.65 Aligned_cols=36 Identities=25% Similarity=0.519 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHHhCCCCC-------ChhhhhhHHHHHHHHHhhc
Q 010581 386 TGAILAHELMHGWLRLKGYRNL-------NPEVEEGICQVLSYMWLES 426 (507)
Q Consensus 386 ~g~ilAHE~mHawlrl~g~~~l-------~~~vEEG~Cq~~a~~wl~~ 426 (507)
..+|+|||+.|-|. | || +..+-||+.-++..+|.+.
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
>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=43.63 E-value=30 Score=25.72 Aligned_cols=42 Identities=24% Similarity=0.474 Sum_probs=29.0
Q ss_pred ccCCCCCCCCCCceEeeCCcc-cchhhhhhh--ccccccccCCCcC
Q 010581 172 RCRSCGYPITEHEFSLSGKDP-YHKSCFKEL--THPKCEVCHQYIP 214 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~dg~p-YCk~CY~k~--f~pkC~~C~k~I~ 214 (507)
.|..|...... -.+..=|.. +|..|..+. ...+|..|.++|.
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 46666665544 334456777 999999886 4788999999886
No 78
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.30 E-value=26 Score=42.00 Aligned_cols=38 Identities=24% Similarity=0.383 Sum_probs=23.5
Q ss_pred cccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCCC
Q 010581 171 FRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTN 216 (507)
Q Consensus 171 F~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~~ 216 (507)
|+|..|+.. .....+|..|-.......|..|+..+.+.
T Consensus 639 frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 639 RRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTPY 676 (1121)
T ss_pred ccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCcc
Confidence 667777665 12234577776655556677777766654
No 79
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=43.12 E-value=21 Score=41.13 Aligned_cols=37 Identities=24% Similarity=0.670 Sum_probs=29.8
Q ss_pred ccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCC
Q 010581 172 RCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPT 215 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~ 215 (507)
+|..|+.. ..++..||..|-..+-..+|..|+..++.
T Consensus 3 ~Cp~Cg~~-------n~~~akFC~~CG~~l~~~~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFE-------NPNNNRFCQKCGTSLTHKPCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCc-------CCCCCccccccCCCCCCCcCCCCCCCCCc
Confidence 57788665 34689999999888777889999998876
No 80
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.95 E-value=14 Score=42.49 Aligned_cols=55 Identities=13% Similarity=0.063 Sum_probs=26.5
Q ss_pred eccccC-CCCeeeeeecccccccccee-EEEEEEEcCCch-hHHHHHHHHHHHHHHHHH
Q 010581 346 LRRPRI-GGNRLVGMRTQPQKLTRKCE-VTAILVLYGLPR-LLTGAILAHELMHGWLRL 401 (507)
Q Consensus 346 ~~~~~~-~g~~~~~~~~~~~~~~r~~~-v~~Ilvl~GLPr-l~~g~ilAHE~mHawlrl 401 (507)
+..|.+ .+-+.+...++...+.++.+ -=.|+|.+ -|. -+.-+++.|.+-..|-+.
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 81
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=42.57 E-value=9 Score=37.64 Aligned_cols=47 Identities=15% Similarity=0.237 Sum_probs=35.8
Q ss_pred CCcccCCCCCCCCCCceEeeCCcccchhhhhhhc--cccccccCCCcCCC
Q 010581 169 NCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVCHQYIPTN 216 (507)
Q Consensus 169 ~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f--~pkC~~C~k~I~~~ 216 (507)
-=|.|..|++.... .....-|..||..|+.+.+ ++.|.+|++...+.
T Consensus 195 IPF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 195 IPFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred Cceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 35889999887654 3334467889999998866 78999999987663
No 82
>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=42.50 E-value=14 Score=33.86 Aligned_cols=14 Identities=29% Similarity=0.223 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHH
Q 010581 385 LTGAILAHELMHGW 398 (507)
Q Consensus 385 ~~g~ilAHE~mHaw 398 (507)
..-.+++||++||-
T Consensus 93 ~~~~~~~HEiGHaL 106 (165)
T cd04268 93 RLRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHHh
Confidence 46799999999994
No 83
>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=42.24 E-value=16 Score=34.88 Aligned_cols=25 Identities=24% Similarity=0.165 Sum_probs=20.6
Q ss_pred EEEEEcCCchhHHHHHHHHHHHHHH
Q 010581 374 AILVLYGLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 374 ~Ilvl~GLPrl~~g~ilAHE~mHaw 398 (507)
==+-|.-+|.-+.-+|++|||.|..
T Consensus 152 ln~~L~~~P~~~idYVvvHEL~Hl~ 176 (205)
T PF01863_consen 152 LNWRLVMAPPEVIDYVVVHELCHLR 176 (205)
T ss_pred eecccccCCccHHHHHHHHHHHHhc
Confidence 3345666999999999999999974
No 84
>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=41.97 E-value=34 Score=33.88 Aligned_cols=50 Identities=26% Similarity=0.112 Sum_probs=38.4
Q ss_pred CCchhHHHHHHHHHHHHHHHHHhCC-CCCChhhhhhHHHHHHHHHhhcccc
Q 010581 380 GLPRLLTGAILAHELMHGWLRLKGY-RNLNPEVEEGICQVLSYMWLESEVL 429 (507)
Q Consensus 380 GLPrl~~g~ilAHE~mHawlrl~g~-~~l~~~vEEG~Cq~~a~~wl~~~~~ 429 (507)
.|=-..++-||+||+.|+.+.--+. ..-...-||==|-..|--||-+...
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 4445666777899999999866543
No 85
>KOG3624 consensus M13 family peptidase [Amino acid transport and metabolism]
Probab=41.16 E-value=13 Score=42.70 Aligned_cols=16 Identities=38% Similarity=0.553 Sum_probs=13.5
Q ss_pred hHHHHHHHHHHHHHHH
Q 010581 384 LLTGAILAHELMHGWL 399 (507)
Q Consensus 384 l~~g~ilAHE~mHawl 399 (507)
-..|.|||||++|++=
T Consensus 516 g~iG~vigHEl~H~FD 531 (687)
T KOG3624|consen 516 GGIGFVIGHELTHGFD 531 (687)
T ss_pred HHHHHHHHHHHhhccc
Confidence 3589999999999873
No 86
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.08 E-value=18 Score=23.31 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=4.8
Q ss_pred CCCCCCccC
Q 010581 146 CGGCNCDIG 154 (507)
Q Consensus 146 C~~C~k~I~ 154 (507)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555555553
No 87
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=39.28 E-value=20 Score=27.57 Aligned_cols=29 Identities=31% Similarity=0.657 Sum_probs=21.8
Q ss_pred ccCCCCCCCCCC-ceEeeCCcccchhhhhhh
Q 010581 172 RCRSCGYPITEH-EFSLSGKDPYHKSCFKEL 201 (507)
Q Consensus 172 ~C~~C~~~L~~~-~F~~~dg~pYCk~CY~k~ 201 (507)
.|..|+..++-. .+-..|| ..|.+|+.+.
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 477888887743 3667777 7899999884
No 88
>KOG3714 consensus Meprin A metalloprotease [Posttranslational modification, protein turnover, chaperones]
Probab=39.27 E-value=14 Score=40.04 Aligned_cols=14 Identities=36% Similarity=0.434 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHH
Q 010581 388 AILAHELMHGWLRL 401 (507)
Q Consensus 388 ~ilAHE~mHawlrl 401 (507)
.|.+||||||==..
T Consensus 161 G~i~HEl~HaLGf~ 174 (411)
T KOG3714|consen 161 GTIVHELMHALGFW 174 (411)
T ss_pred chhHHHHHHHhhhh
Confidence 57899999995443
No 89
>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=39.16 E-value=20 Score=32.73 Aligned_cols=16 Identities=31% Similarity=0.306 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHHHHHH
Q 010581 383 RLLTGAILAHELMHGW 398 (507)
Q Consensus 383 rl~~g~ilAHE~mHaw 398 (507)
...+..++|||++|+.
T Consensus 93 ~~~~~~~~~HElGH~L 108 (167)
T cd00203 93 TKEGAQTIAHELGHAL 108 (167)
T ss_pred cccchhhHHHHHHHHh
Confidence 3467899999999985
No 90
>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=38.54 E-value=20 Score=32.29 Aligned_cols=17 Identities=18% Similarity=0.075 Sum_probs=13.3
Q ss_pred CchhHHHHHHHHHHHHH
Q 010581 381 LPRLLTGAILAHELMHG 397 (507)
Q Consensus 381 LPrl~~g~ilAHE~mHa 397 (507)
.+..-...|+.||+.||
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 91
>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=37.46 E-value=27 Score=36.35 Aligned_cols=21 Identities=33% Similarity=0.376 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHHHHHHhC
Q 010581 383 RLLTGAILAHELMHGWLRLKG 403 (507)
Q Consensus 383 rl~~g~ilAHE~mHawlrl~g 403 (507)
.+...+|||||+.|.-+.|.|
T Consensus 167 ~~a~ayVlAHEyGHHVQ~l~G 187 (292)
T PF04228_consen 167 DFAQAYVLAHEYGHHVQNLLG 187 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 456678999999999999987
No 92
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=37.39 E-value=32 Score=25.02 Aligned_cols=39 Identities=26% Similarity=0.546 Sum_probs=25.2
Q ss_pred cCCCCCCCCC--CceEeeCCcccchhhhhhhc--cccccccCC
Q 010581 173 CRSCGYPITE--HEFSLSGKDPYHKSCFKELT--HPKCEVCHQ 211 (507)
Q Consensus 173 C~~C~~~L~~--~~F~~~dg~pYCk~CY~k~f--~pkC~~C~k 211 (507)
|..|...+.. ..+...=+..+|..|..+.. ..+|..|++
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 23444568889999988866 556666653
No 93
>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=37.35 E-value=27 Score=35.68 Aligned_cols=27 Identities=37% Similarity=0.598 Sum_probs=19.9
Q ss_pred EcCCchhHHHHHHHHHHHHHHHHHh-CCC
Q 010581 378 LYGLPRLLTGAILAHELMHGWLRLK-GYR 405 (507)
Q Consensus 378 l~GLPrl~~g~ilAHE~mHawlrl~-g~~ 405 (507)
++++. .++-+++.||++||+.... |.+
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 94
>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=37.20 E-value=24 Score=36.49 Aligned_cols=18 Identities=28% Similarity=0.340 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010581 385 LTGAILAHELMHGWLRLK 402 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~ 402 (507)
++.+++.||++||+....
T Consensus 134 l~isvvvHElgHal~A~~ 151 (277)
T cd06162 134 LLISGVVHEMGHGVAAVR 151 (277)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 577999999999999885
No 95
>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=36.65 E-value=28 Score=23.91 Aligned_cols=40 Identities=20% Similarity=0.455 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhhhc---cccccccCCC
Q 010581 173 CRSCGYPITEHEFSLSGKDPYHKSCFKELT---HPKCEVCHQY 212 (507)
Q Consensus 173 C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f---~pkC~~C~k~ 212 (507)
|..|...+........-+..||..|..+.+ ..+|..|+..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 455555553222222256677888776543 3456666554
No 96
>COG5504 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=36.44 E-value=43 Score=34.23 Aligned_cols=39 Identities=31% Similarity=0.462 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHh------C-CCCCChhhhhhHHHHHHHHHhhc
Q 010581 387 GAILAHELMHGWLRLK------G-YRNLNPEVEEGICQVLSYMWLES 426 (507)
Q Consensus 387 g~ilAHE~mHawlrl~------g-~~~l~~~vEEG~Cq~~a~~wl~~ 426 (507)
-|++|||+=|. -|+. | ...|+.-|-||+.|-.++-=..+
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 23468899999999876653333
No 97
>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=36.10 E-value=33 Score=33.48 Aligned_cols=21 Identities=38% Similarity=0.507 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHHHHHHHh-CC
Q 010581 384 LLTGAILAHELMHGWLRLK-GY 404 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~-g~ 404 (507)
.++.+++.||+.|++.... |.
T Consensus 36 ~l~~~v~iHElgH~~~A~~~G~ 57 (208)
T cd06161 36 LLFLSVLLHELGHALVARRYGI 57 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5788999999999998776 64
No 98
>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=35.86 E-value=30 Score=25.27 Aligned_cols=32 Identities=44% Similarity=0.684 Sum_probs=20.9
Q ss_pred ccCCCCCccccCCceeEecCCccccchhhhhh
Q 010581 244 RCCSCERLESWNTRYYSLEDGRSLCLECMESA 275 (507)
Q Consensus 244 ~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sa 275 (507)
+|+.|+|.....++.+.-.++-..|..|.+.+
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 58999997766666665555789999997665
No 99
>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=35.71 E-value=26 Score=32.86 Aligned_cols=20 Identities=30% Similarity=0.406 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHh-CC
Q 010581 385 LTGAILAHELMHGWLRLK-GY 404 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~-g~ 404 (507)
++.++..||++|++.... |.
T Consensus 7 ~~i~i~iHE~gH~~~A~~~G~ 27 (180)
T cd05709 7 LLISVTVHELGHALVARRLGV 27 (180)
T ss_pred HHHHHHHHHHHHHHHHHHcCC
Confidence 466899999999996654 65
No 100
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=35.47 E-value=5 Score=34.98 Aligned_cols=49 Identities=22% Similarity=0.478 Sum_probs=26.9
Q ss_pred CCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccc
Q 010581 146 CGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYH 194 (507)
Q Consensus 146 C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYC 194 (507)
|..|...+.+-.+....-..+++.+..|..|.+.|+-.+|.+.+.-|||
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 4455555543334444445666677777777776665555544443333
No 101
>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=35.13 E-value=19 Score=26.14 Aligned_cols=29 Identities=21% Similarity=0.415 Sum_probs=17.4
Q ss_pred CCCCCCccCC-CceEEecCccccCCCcccCCCC
Q 010581 146 CGGCNCDIGY-GNYLGCMGTYFHPNCFRCRSCG 177 (507)
Q Consensus 146 C~~C~k~I~~-g~~l~algk~wHp~CF~C~~C~ 177 (507)
|.-|+.+|.. ...+...++.|| |.|..|.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~ 30 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCL 30 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHH
Confidence 6678888742 234567777777 4444443
No 102
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=34.80 E-value=16 Score=36.07 Aligned_cols=30 Identities=27% Similarity=0.523 Sum_probs=18.9
Q ss_pred ccCCCCCCCCCCceEeeCCcccchhhhhhh
Q 010581 172 RCRSCGYPITEHEFSLSGKDPYHKSCFKEL 201 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~ 201 (507)
+|..|+..+....-...+|++.|+.||.+.
T Consensus 174 ~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 174 RCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eccccCcccccchhhhcCCceecccccccc
Confidence 344444444444445668899999998753
No 103
>PHA00527 hypothetical protein
Probab=34.69 E-value=1.4e+02 Score=26.65 Aligned_cols=47 Identities=26% Similarity=0.364 Sum_probs=31.8
Q ss_pred EEEEEEEcCCchhHHHHHHHHHHHHHHHHH-h--CCCCCChhhhhhHHHHHHHHH
Q 010581 372 VTAILVLYGLPRLLTGAILAHELMHGWLRL-K--GYRNLNPEVEEGICQVLSYMW 423 (507)
Q Consensus 372 v~~Ilvl~GLPrl~~g~ilAHE~mHawlrl-~--g~~~l~~~vEEG~Cq~~a~~w 423 (507)
+.-|-|..|- .+.||||+.|.=... . |...=|-+..|-.|-+|+-|.
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 478999999965444 3 555556677788888887663
No 104
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=34.67 E-value=22 Score=35.44 Aligned_cols=27 Identities=22% Similarity=0.170 Sum_probs=22.0
Q ss_pred EEEEEEEcCCchhHHHHHHHHHHHHHH
Q 010581 372 VTAILVLYGLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 372 v~~Ilvl~GLPrl~~g~ilAHE~mHaw 398 (507)
++==+.|-.+|.-+..+|++|||.|--
T Consensus 161 i~~~~~l~~~p~~~i~YVvvHELaHLk 187 (223)
T COG1451 161 IRFNWRLVMAPEEVIDYVVVHELAHLK 187 (223)
T ss_pred EEeehhhhcCCHHHHHHHHHHHHHHHh
Confidence 334456778999999999999999953
No 105
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=34.57 E-value=62 Score=32.32 Aligned_cols=38 Identities=26% Similarity=0.165 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHh
Q 010581 385 LTGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWL 424 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~g~~~l~~~vEEG~Cq~~a~~wl 424 (507)
-+-.||-||+.||.+-+.+.|.|= -||----.+|-+.|
T Consensus 91 ~~~~~l~HE~GHAlI~~~~lPv~G--rEEDaaD~lAa~~l 128 (220)
T PF14247_consen 91 NVLFTLYHELGHALIDDLDLPVLG--REEDAADQLAALLL 128 (220)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccc--chhhHHHHHHHHHH
Confidence 455889999999999999877764 35555544444433
No 106
>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=34.40 E-value=25 Score=33.24 Aligned_cols=20 Identities=25% Similarity=0.237 Sum_probs=14.5
Q ss_pred chhHHHHHHHHHHHHHHHHH
Q 010581 382 PRLLTGAILAHELMHGWLRL 401 (507)
Q Consensus 382 Prl~~g~ilAHE~mHawlrl 401 (507)
|-.....++|||+.|.+=-.
T Consensus 138 ~~~~~~~~~AHEiGH~lGa~ 157 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNLGAP 157 (196)
T ss_dssp -HHHHHHHHHHHHHHHTT--
T ss_pred CCCceehhhHHhHHHhcCCC
Confidence 45777899999999987433
No 107
>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=34.05 E-value=34 Score=33.99 Aligned_cols=21 Identities=38% Similarity=0.583 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHHHh-CC
Q 010581 384 LLTGAILAHELMHGWLRLK-GY 404 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~-g~ 404 (507)
.++.+++.||+.|++.... |+
T Consensus 51 ~l~~~v~iHElgH~~~A~~~G~ 72 (227)
T cd06164 51 LLFASVLLHELGHSLVARRYGI 72 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5789999999999998775 54
No 108
>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=32.97 E-value=22 Score=34.81 Aligned_cols=11 Identities=45% Similarity=0.528 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q 010581 388 AILAHELMHGW 398 (507)
Q Consensus 388 ~ilAHE~mHaw 398 (507)
.+++||||||-
T Consensus 89 Gti~HEl~HaL 99 (200)
T cd04281 89 GIVVHELGHVI 99 (200)
T ss_pred chHHHHHHHHh
Confidence 48999999995
No 109
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=32.84 E-value=23 Score=32.67 Aligned_cols=21 Identities=24% Similarity=0.648 Sum_probs=15.3
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhh
Q 010581 173 CRSCGYPITEHEFSLSGKDPYHKSCF 198 (507)
Q Consensus 173 C~~C~~~L~~~~F~~~dg~pYCk~CY 198 (507)
|..|+.|| |.++|.+||.-|-
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 67777777 3388888887664
No 110
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=32.81 E-value=25 Score=35.40 Aligned_cols=19 Identities=42% Similarity=0.169 Sum_probs=15.6
Q ss_pred CCchhHHHHHHHHHHHHHH
Q 010581 380 GLPRLLTGAILAHELMHGW 398 (507)
Q Consensus 380 GLPrl~~g~ilAHE~mHaw 398 (507)
-|.+.-.-+|||||+.|.-
T Consensus 151 ~l~~dEl~aVlaHElgHi~ 169 (302)
T COG0501 151 LLNDDELEAVLAHELGHIK 169 (302)
T ss_pred hCCHHHHHHHHHHHHHHHh
Confidence 4666777899999999974
No 111
>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=32.73 E-value=52 Score=36.82 Aligned_cols=45 Identities=24% Similarity=0.236 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHHHHHHH--h-C----CCCCChhhhh---hHHHHHHHHHhhccc
Q 010581 384 LLTGAILAHELMHGWLRL--K-G----YRNLNPEVEE---GICQVLSYMWLESEV 428 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl--~-g----~~~l~~~vEE---G~Cq~~a~~wl~~~~ 428 (507)
.---.+||||++||+--. + + +...+.++-| =+++.+.+-||....
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 567777888877654
No 112
>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=32.34 E-value=15 Score=33.35 Aligned_cols=41 Identities=27% Similarity=0.380 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHH--HHhC--C-------CCC--ChhhhhhHHHHHHHHHhhc
Q 010581 386 TGAILAHELMHGWL--RLKG--Y-------RNL--NPEVEEGICQVLSYMWLES 426 (507)
Q Consensus 386 ~g~ilAHE~mHawl--rl~g--~-------~~l--~~~vEEG~Cq~~a~~wl~~ 426 (507)
+-.++|||+-|+|- |++. . ++. -+.|-||+=+.++.+-|-+
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 2478899999999886544
No 113
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=32.33 E-value=53 Score=39.02 Aligned_cols=115 Identities=22% Similarity=0.297 Sum_probs=66.0
Q ss_pred HHHHHHHHHHHHHHHhCCCCC----ChhhhhhHHHHHHHHHhhcccc------CC---CCCC-C----CCCCC------C
Q 010581 387 GAILAHELMHGWLRLKGYRNL----NPEVEEGICQVLSYMWLESEVL------PD---YRNM-P----STSSA------S 442 (507)
Q Consensus 387 g~ilAHE~mHawlrl~g~~~l----~~~vEEG~Cq~~a~~wl~~~~~------~~---~~~~-~----~~~~~------~ 442 (507)
.++.||||.|.|.-= ...+ +..+-||+--++.+.|.+..-. .. .++. + +..++ .
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 349999999999411 0111 3778899999999999887542 00 0000 0 00000 0
Q ss_pred ---------CCCCCCCCCC-----------chHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHHHHHhCHHHHHHHHHhh
Q 010581 443 ---------TSSSSSKKGG-----------KSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAAVNKYGLRRTLEHIRLT 502 (507)
Q Consensus 443 ---------~~~~~~~~g~-----------~~~~e~~l~~f~~~qi~~d~s~vYGdGfR~~~~a~~~~gl~~~l~~i~~~ 502 (507)
.+.++=.||. ...|-+-|..||.. .+-..+.++=|..+.+.+...-|..+++.-...
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 44566777777776 455556677777777777777777666666665
Q ss_pred CCCC
Q 010581 503 GNFP 506 (507)
Q Consensus 503 g~~p 506 (507)
.-+|
T Consensus 463 ~G~P 466 (859)
T COG0308 463 AGYP 466 (859)
T ss_pred CCCC
Confidence 5555
No 114
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=32.25 E-value=21 Score=30.10 Aligned_cols=29 Identities=28% Similarity=0.707 Sum_probs=20.4
Q ss_pred ccCCCCCCCCCCceEee-----CCcccchhhhhh
Q 010581 172 RCRSCGYPITEHEFSLS-----GKDPYHKSCFKE 200 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~-----dg~pYCk~CY~k 200 (507)
.|..|+.||.....+.. .+.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 48889999886552222 346799999886
No 115
>PRK09672 phage exclusion protein Lit; Provisional
Probab=31.45 E-value=64 Score=33.76 Aligned_cols=50 Identities=22% Similarity=0.161 Sum_probs=38.8
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHhCCCCC-ChhhhhhHHHHHHHHHhhccc
Q 010581 379 YGLPRLLTGAILAHELMHGWLRLKGYRNL-NPEVEEGICQVLSYMWLESEV 428 (507)
Q Consensus 379 ~GLPrl~~g~ilAHE~mHawlrl~g~~~l-~~~vEEG~Cq~~a~~wl~~~~ 428 (507)
.-|=-..++-|+.||+.|+.+-..++... +-.-||==|...|--||=+..
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 334567779999999997643
No 116
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=31.21 E-value=44 Score=26.80 Aligned_cols=29 Identities=31% Similarity=0.588 Sum_probs=17.0
Q ss_pred CCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCC
Q 010581 143 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPI 180 (507)
Q Consensus 143 ~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L 180 (507)
.++|..|+..|..++.... |.|..|+..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~ 37 (61)
T COG2888 9 PPVCTSCGREIAPGETAVK---------FPCPNCGEVE 37 (61)
T ss_pred CceeccCCCEeccCCceeE---------eeCCCCCcee
Confidence 4678888887744432211 6677776433
No 117
>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=31.01 E-value=29 Score=32.87 Aligned_cols=18 Identities=28% Similarity=0.108 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHhC
Q 010581 386 TGAILAHELMHGWLRLKG 403 (507)
Q Consensus 386 ~g~ilAHE~mHawlrl~g 403 (507)
...++|||+.|.+=.-+.
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 118
>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=30.82 E-value=52 Score=36.52 Aligned_cols=32 Identities=22% Similarity=0.412 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHhCCCCCC--------hhhhhhHHHHHHH
Q 010581 389 ILAHELMHGWLRLKGYRNLN--------PEVEEGICQVLSY 421 (507)
Q Consensus 389 ilAHE~mHawlrl~g~~~l~--------~~vEEG~Cq~~a~ 421 (507)
++-|||.||+..+. |+++| |-..|-+|+++|.
T Consensus 250 t~~HE~GH~~yy~~-y~~~p~~~r~~anp~fheav~e~~sm 289 (477)
T cd06461 250 TVHHEMGHIQYYLQ-YKDQPVLFREGANPGFHEAVGDAIAL 289 (477)
T ss_pred HHHHHHHHHHHHHH-hccCCHHHhCCCCCChHHHHHHHHHH
Confidence 46699999987766 55554 4445578988864
No 119
>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=30.82 E-value=29 Score=31.85 Aligned_cols=16 Identities=38% Similarity=0.235 Sum_probs=13.1
Q ss_pred hhHHHHHHHHHHHHHH
Q 010581 383 RLLTGAILAHELMHGW 398 (507)
Q Consensus 383 rl~~g~ilAHE~mHaw 398 (507)
..-+-+|+.||++||-
T Consensus 101 ~~~~~~~~~HEiGHaL 116 (156)
T cd04279 101 AENLQAIALHELGHAL 116 (156)
T ss_pred chHHHHHHHHHhhhhh
Confidence 4566799999999983
No 120
>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=30.39 E-value=29 Score=32.46 Aligned_cols=20 Identities=40% Similarity=0.665 Sum_probs=13.6
Q ss_pred chhHHHHHHHHHHHHHHHHHh
Q 010581 382 PRLLTGAILAHELMHGWLRLK 402 (507)
Q Consensus 382 Prl~~g~ilAHE~mHawlrl~ 402 (507)
+..-.|.+|+||++| ||-|.
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 355668999999999 55553
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=30.32 E-value=33 Score=33.03 Aligned_cols=16 Identities=19% Similarity=0.102 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 010581 385 LTGAILAHELMHGWLR 400 (507)
Q Consensus 385 ~~g~ilAHE~mHawlr 400 (507)
.+..++.||+|||-=.
T Consensus 91 ~~~~~i~HElgHaLG~ 106 (198)
T cd04327 91 EFSRVVLHEFGHALGF 106 (198)
T ss_pred hHHHHHHHHHHHHhcC
Confidence 4456999999999633
No 122
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.29 E-value=54 Score=25.76 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=8.7
Q ss_pred CCCCCCCCCccC
Q 010581 143 YKVCGGCNCDIG 154 (507)
Q Consensus 143 ~~~C~~C~k~I~ 154 (507)
..+|..|++.|.
T Consensus 5 ~~~C~~Cg~~~~ 16 (54)
T PF14446_consen 5 GCKCPVCGKKFK 16 (54)
T ss_pred CccChhhCCccc
Confidence 457888888874
No 123
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=29.97 E-value=22 Score=38.37 Aligned_cols=24 Identities=38% Similarity=0.558 Sum_probs=21.4
Q ss_pred hhhhhhhHHHHHHhcccccccccC
Q 010581 82 ADREKEELDHAIALSLAEDLKRPN 105 (507)
Q Consensus 82 ~~~e~edid~aia~sL~Ee~kk~~ 105 (507)
+..|.|||..||++||.|.++.++
T Consensus 162 ~k~EeEdiaKAi~lSL~E~~~Q~k 185 (462)
T KOG2199|consen 162 SKQEEEDIAKAIELSLKEQEKQKK 185 (462)
T ss_pred ccccHHHHHHHHHhhHHHHhhchh
Confidence 568999999999999999988765
No 124
>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=29.68 E-value=27 Score=35.08 Aligned_cols=11 Identities=36% Similarity=0.721 Sum_probs=9.7
Q ss_pred HHHHHHHHHHH
Q 010581 388 AILAHELMHGW 398 (507)
Q Consensus 388 ~ilAHE~mHaw 398 (507)
.+++||||||-
T Consensus 122 Gti~HEl~Hal 132 (230)
T cd04282 122 ATVEHEFLHAL 132 (230)
T ss_pred chHHHHHHHHh
Confidence 68999999995
No 125
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=29.60 E-value=56 Score=34.95 Aligned_cols=107 Identities=23% Similarity=0.287 Sum_probs=59.9
Q ss_pred EEEEcCCchhH-----HHHHHHHHHHHHHHHHhCCCCCChhhhhhHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCC
Q 010581 375 ILVLYGLPRLL-----TGAILAHELMHGWLRLKGYRNLNPEVEEGICQVLSYMWLESEVLPDYRNMPSTSSASTSSSSSK 449 (507)
Q Consensus 375 Ilvl~GLPrl~-----~g~ilAHE~mHawlrl~g~~~l~~~vEEG~Cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~ 449 (507)
|+|-.||=.++ ..++|||||.|+=-+- |...-..+-+|+|---+...-|.+...... ..-
T Consensus 108 lYitRGLlAland~sEvAAVl~HEmgHVtAnH-gi~rQ~~e~a~~ia~rvva~vl~~~~agk~--------------A~~ 172 (479)
T COG4784 108 LYITRGLLALANDSSEVAAVLAHEMGHVTANH-GIQRQQREAAEVIASRVVAEVLGSDAAGKQ--------------ALI 172 (479)
T ss_pred EEEehhHHHHcCCHHHHHHHHHhhhhheecch-hHHHHHHHHHHHHHHHHHHHHhCCcchhhH--------------HHh
Confidence 56667776554 5789999999975432 344445677777654333333332221000 001
Q ss_pred CCCchHHHHHHHHHHHhhhhcCCCCCchhhHHHHHHH-HHHhCHHHHHHHHHhhCCC
Q 010581 450 KGGKSEVEKKLGEFFMHQIAHDASPAYGEGFRIANAA-VNKYGLRRTLEHIRLTGNF 505 (507)
Q Consensus 450 ~g~~~~~e~~l~~f~~~qi~~d~s~vYGdGfR~~~~a-~~~~gl~~~l~~i~~~g~~ 505 (507)
.|+ .+|+.|=++ +|--.| +-|-|..-+| |+-|-..++|+.+..+-+|
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 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=29.24 E-value=56 Score=25.20 Aligned_cols=27 Identities=33% Similarity=0.470 Sum_probs=18.4
Q ss_pred CCchhhHHHHHHHHHHhCHHHHHHHHHhh
Q 010581 474 PAYGEGFRIANAAVNKYGLRRTLEHIRLT 502 (507)
Q Consensus 474 ~vYGdGfR~~~~a~~~~gl~~~l~~i~~~ 502 (507)
.|||-|-..|.+-++ .|++ +|+.|+..
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
>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=29.00 E-value=11 Score=26.58 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=16.9
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhh
Q 010581 173 CRSCGYPITEHEFSLSGKDPYHKSCFKE 200 (507)
Q Consensus 173 C~~C~~~L~~~~F~~~dg~pYCk~CY~k 200 (507)
|..|+.++.........+..+|..|..+
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 6666666665555555677778877654
No 128
>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=28.98 E-value=54 Score=31.07 Aligned_cols=16 Identities=44% Similarity=0.513 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHHHHH
Q 010581 383 RLLTGAILAHELMHGW 398 (507)
Q Consensus 383 rl~~g~ilAHE~mHaw 398 (507)
-+.+..++|||++|.+
T Consensus 128 ~~~~a~~~AHElGH~l 143 (194)
T cd04269 128 LLLFAVTMAHELGHNL 143 (194)
T ss_pred hHHHHHHHHHHHHhhc
Confidence 3677899999999976
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.90 E-value=58 Score=40.15 Aligned_cols=51 Identities=16% Similarity=0.197 Sum_probs=26.9
Q ss_pred cccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHhhcccc
Q 010581 243 SRCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYEGMNMK 299 (507)
Q Consensus 243 F~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~glgm~ 299 (507)
+.|..|+...+.+. .+...|..|-..++..+..--++-..+.+=.+.+|+.
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 45777776443221 1245688887666655543334444444444555555
No 130
>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=28.85 E-value=53 Score=31.69 Aligned_cols=22 Identities=23% Similarity=0.243 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHHHHHHHh-CCC
Q 010581 384 LLTGAILAHELMHGWLRLK-GYR 405 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~-g~~ 405 (507)
.++.+++.||+.|+|.... |.+
T Consensus 39 ~l~~~l~iHElgH~~~A~~~G~~ 61 (183)
T cd06160 39 ALLAILGIHEMGHYLAARRHGVK 61 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCC
Confidence 3567889999999999876 654
No 131
>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=28.80 E-value=17 Score=30.01 Aligned_cols=17 Identities=29% Similarity=0.651 Sum_probs=12.4
Q ss_pred CCCCCCCCCCCccCCCc
Q 010581 141 RSYKVCGGCNCDIGYGN 157 (507)
Q Consensus 141 ~~~~~C~~C~k~I~~g~ 157 (507)
.+-..|.+|++.|..|.
T Consensus 5 s~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp SSTEBETTTSCBE-TTS
T ss_pred CCCccCcccCCcCCCCC
Confidence 45568999999997554
No 132
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=28.33 E-value=33 Score=33.87 Aligned_cols=28 Identities=29% Similarity=0.309 Sum_probs=23.3
Q ss_pred EcCCchhHHHHHHHHHHHHHHHHHhCCC
Q 010581 378 LYGLPRLLTGAILAHELMHGWLRLKGYR 405 (507)
Q Consensus 378 l~GLPrl~~g~ilAHE~mHawlrl~g~~ 405 (507)
-|+=|.+..-++.|||..||.+-..+|+
T Consensus 84 ~y~g~Sia~~aVAAHEVGHAiQd~~~Y~ 111 (226)
T COG2738 84 NYYGPSIAAIAVAAHEVGHAIQDQEDYA 111 (226)
T ss_pred ccCCccHHHHHHHHHHhhHHHhhhcccH
Confidence 3677889999999999999987777653
No 133
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.31 E-value=34 Score=39.53 Aligned_cols=44 Identities=7% Similarity=0.234 Sum_probs=23.4
Q ss_pred ccchhhhhhccC-CCCCCchhhhHHHHHhhcccccccccccccccHHHHHHHH
Q 010581 267 LCLECMESAIMD-TGDCQPLYHAIRDYYEGMNMKLDQQIPMLLVERQALNEAI 318 (507)
Q Consensus 267 ~C~~C~~sav~d-t~e~qpl~~~i~~f~~glgm~~~~~~pl~lv~~~~ln~a~ 318 (507)
.|..|....+.. ..-.+.+..++.+.|- +.|++.++++.+-+..
T Consensus 424 ~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP--------~~~V~r~d~d~~l~~~ 468 (665)
T PRK14873 424 RCPRCGSDRLRAVVVGARRTAEELGRAFP--------GVPVVTSGGDQVVDTV 468 (665)
T ss_pred cCCCCcCCcceeeeccHHHHHHHHHHHCC--------CCCEEEEChHHHHHhh
Confidence 577776543322 2234555555555552 3566777777643333
No 134
>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=27.71 E-value=32 Score=33.25 Aligned_cols=12 Identities=42% Similarity=0.783 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 010581 387 GAILAHELMHGW 398 (507)
Q Consensus 387 g~ilAHE~mHaw 398 (507)
-.+++||+|||-
T Consensus 78 ~G~i~HEl~HaL 89 (182)
T cd04283 78 KGIIQHELLHAL 89 (182)
T ss_pred cchHHHHHHHHh
Confidence 358999999994
No 135
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=27.17 E-value=37 Score=32.63 Aligned_cols=19 Identities=21% Similarity=0.378 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHHHHHHHh
Q 010581 384 LLTGAILAHELMHGWLRLK 402 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~ 402 (507)
...--+++|||.|||=-++
T Consensus 89 ~h~n~vv~HElIH~fDd~r 107 (194)
T KOG3314|consen 89 DHVNQVVIHELIHAFDDCR 107 (194)
T ss_pred HHHHHHHHHHHHHHHHhhh
Confidence 4566789999999997765
No 136
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=26.99 E-value=41 Score=33.88 Aligned_cols=34 Identities=21% Similarity=0.546 Sum_probs=27.7
Q ss_pred CCceEee-CCcccchhhhhhhccccccccCCCcCC
Q 010581 182 EHEFSLS-GKDPYHKSCFKELTHPKCEVCHQYIPT 215 (507)
Q Consensus 182 ~~~F~~~-dg~pYCk~CY~k~f~pkC~~C~k~I~~ 215 (507)
...|++. -..++|..|...-+++.|..|++.|..
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 4466654 678999999888788899999999765
No 137
>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=26.97 E-value=31 Score=38.76 Aligned_cols=17 Identities=41% Similarity=0.317 Sum_probs=13.3
Q ss_pred hhHHHHHHHHHHHHHHH
Q 010581 383 RLLTGAILAHELMHGWL 399 (507)
Q Consensus 383 rl~~g~ilAHE~mHawl 399 (507)
.+---.+|||||+||+-
T Consensus 375 ~~~dv~TLaHElGHa~H 391 (591)
T TIGR00181 375 TLNSVFTLAHELGHSMH 391 (591)
T ss_pred CcchHHHHHHHhhhHHH
Confidence 44556899999999983
No 138
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.90 E-value=50 Score=40.66 Aligned_cols=49 Identities=20% Similarity=0.453 Sum_probs=27.3
Q ss_pred CCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhhccc-----cccccCCCcCC
Q 010581 144 KVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHP-----KCEVCHQYIPT 215 (507)
Q Consensus 144 ~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~p-----kC~~C~k~I~~ 215 (507)
.+|..|+..+.. +.|..|+.++.. ...|..|-.+.-.. .|..|+.+...
T Consensus 668 rkCPkCG~~t~~---------------~fCP~CGs~te~--------vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 668 RRCPSCGTETYE---------------NRCPDCGTHTEP--------VYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EECCCCCCcccc---------------ccCcccCCcCCC--------ceeCccCCCccCCCccccccCCCCCCcccc
Confidence 567777776531 156666665522 12466665543322 68888766544
No 139
>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=26.81 E-value=37 Score=32.71 Aligned_cols=13 Identities=31% Similarity=0.401 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHH
Q 010581 386 TGAILAHELMHGW 398 (507)
Q Consensus 386 ~g~ilAHE~mHaw 398 (507)
...+++||+|||-
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 140
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=26.78 E-value=39 Score=32.98 Aligned_cols=15 Identities=27% Similarity=0.224 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHHHHH
Q 010581 384 LLTGAILAHELMHGW 398 (507)
Q Consensus 384 l~~g~ilAHE~mHaw 398 (507)
.....++|||++|..
T Consensus 143 ~~~~~~~AHElGH~l 157 (220)
T cd04272 143 YYGVYTMTHELAHLL 157 (220)
T ss_pred cccHHHHHHHHHHHh
Confidence 455799999999975
No 141
>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=26.24 E-value=43 Score=28.95 Aligned_cols=37 Identities=19% Similarity=0.542 Sum_probs=24.2
Q ss_pred cccCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcCC
Q 010581 171 FRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPT 215 (507)
Q Consensus 171 F~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~~ 215 (507)
-.|..|+..+.. .+.-||..|-.+ .-.|+-|++.|..
T Consensus 45 ~~C~~CK~~v~q------~g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 45 SKCKICKTKVHQ------PGAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred cccccccccccc------CCCccChhhhcc--cCcccccCCeecc
Confidence 356666665433 256788888554 3478889888865
No 142
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=25.92 E-value=35 Score=33.27 Aligned_cols=15 Identities=27% Similarity=0.224 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHh
Q 010581 388 AILAHELMHGWLRLK 402 (507)
Q Consensus 388 ~ilAHE~mHawlrl~ 402 (507)
.++|||++|++=--+
T Consensus 139 ~~~aHEiGH~lGl~H 153 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRH 153 (206)
T ss_pred hHHHHHHHHHhcCCC
Confidence 679999999975444
No 143
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=25.88 E-value=64 Score=27.26 Aligned_cols=53 Identities=25% Similarity=0.599 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCCCCccCCCceEEecCccccCCCcccCCCCCCCCCCceEeeCCcccchhhhhhh---ccccccccCC
Q 010581 138 YYPRSYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKEL---THPKCEVCHQ 211 (507)
Q Consensus 138 y~~~~~~~C~~C~k~I~~g~~l~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k~---f~pkC~~C~k 211 (507)
.......+|.-|+..|. ++..|..| -.|..|+ -|.|+.||.-. -...|..|+.
T Consensus 4 ~k~~~~qiCqiCGD~VG----l~~~Ge~F----VAC~eC~-------------fPvCr~CyEYErkeg~q~CpqCkt 59 (80)
T PF14569_consen 4 LKNLNGQICQICGDDVG----LTENGEVF----VACHECA-------------FPVCRPCYEYERKEGNQVCPQCKT 59 (80)
T ss_dssp -S--SS-B-SSS--B------B-SSSSB------S-SSS------------------HHHHHHHHHTS-SB-TTT--
T ss_pred hhhcCCcccccccCccc----cCCCCCEE----EEEcccC-------------CccchhHHHHHhhcCcccccccCC
Confidence 34456788999998884 22333333 2344443 46799998642 2455777764
No 144
>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=25.71 E-value=41 Score=24.84 Aligned_cols=22 Identities=32% Similarity=0.751 Sum_probs=13.0
Q ss_pred ccCCCCCCCCCCceEeeCCcccchhh
Q 010581 172 RCRSCGYPITEHEFSLSGKDPYHKSC 197 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~dg~pYCk~C 197 (507)
.|..|+.||-. .++++.||..|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEECCCC
Confidence 35566666632 45677777655
No 145
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=25.49 E-value=58 Score=31.96 Aligned_cols=30 Identities=13% Similarity=0.317 Sum_probs=17.8
Q ss_pred CcccCCCCCCCCCCceEeeCCcccchhhhhh
Q 010581 170 CFRCRSCGYPITEHEFSLSGKDPYHKSCFKE 200 (507)
Q Consensus 170 CF~C~~C~~~L~~~~F~~~dg~pYCk~CY~k 200 (507)
.|.|..|...+.+ .....-+..||..|..+
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~ 47 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHK 47 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHH
Confidence 4666666665544 23344667777777654
No 146
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=24.99 E-value=18 Score=31.91 Aligned_cols=28 Identities=29% Similarity=0.428 Sum_probs=0.0
Q ss_pred CCCCCCCccCCCceEEecCcc-ccCCCcc
Q 010581 145 VCGGCNCDIGYGNYLGCMGTY-FHPNCFR 172 (507)
Q Consensus 145 ~C~~C~k~I~~g~~l~algk~-wHp~CF~ 172 (507)
+|..|+++|..|+.+++..+. -|-.||+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHH
No 147
>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=24.92 E-value=36 Score=31.54 Aligned_cols=36 Identities=25% Similarity=0.646 Sum_probs=26.7
Q ss_pred ccCCCCCccccCCceeEecCCccccchhhhhhccCCCCCCchhhhHHHHHh
Q 010581 244 RCCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTGDCQPLYHAIRDYYE 294 (507)
Q Consensus 244 ~C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~dt~e~qpl~~~i~~f~~ 294 (507)
.|..|+++|. - .++.+|..|++.. ...|..|.+|.+
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 1 2788999998766 456788888885
No 148
>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=24.75 E-value=47 Score=36.94 Aligned_cols=27 Identities=11% Similarity=0.012 Sum_probs=15.7
Q ss_pred EEEEcCCch-hHHHHHHHHHHHHHHHHH
Q 010581 375 ILVLYGLPR-LLTGAILAHELMHGWLRL 401 (507)
Q Consensus 375 Ilvl~GLPr-l~~g~ilAHE~mHawlrl 401 (507)
++|...-|. .+.-+.+.|.+-..|-+.
T Consensus 374 viiqt~~p~~~~~~~~~~~d~~~f~~~e 401 (505)
T TIGR00595 374 VIIQTYNPNHPAIQAALTGDYEAFYEQE 401 (505)
T ss_pred EEEEeCCCCCHHHHHHHhCCHHHHHHHH
Confidence 344555564 345566677777777443
No 149
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.73 E-value=34 Score=35.49 Aligned_cols=30 Identities=23% Similarity=0.616 Sum_probs=16.8
Q ss_pred CCCCCCCccCCCceEEecCccccCCCcccC
Q 010581 145 VCGGCNCDIGYGNYLGCMGTYFHPNCFRCR 174 (507)
Q Consensus 145 ~C~~C~k~I~~g~~l~algk~wHp~CF~C~ 174 (507)
.|.-|++.+.+..+|.+-.-.-|+.||-|+
T Consensus 270 cCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 270 CCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred eehhhhhhhccCceeecCCCcccceecccC
Confidence 455555555555555555555555555554
No 150
>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=24.70 E-value=51 Score=27.65 Aligned_cols=22 Identities=27% Similarity=0.318 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCC
Q 010581 383 RLLTGAILAHELMHGWLRLKGYR 405 (507)
Q Consensus 383 rl~~g~ilAHE~mHawlrl~g~~ 405 (507)
.|=||-|+|||+.+-|=| .|++
T Consensus 49 MLGFGEl~AhE~~fr~gW-~g~k 70 (77)
T PF08219_consen 49 MLGFGELFAHEIAFRLGW-SGTK 70 (77)
T ss_pred hHhHHHHHHHHHHHHhcc-Ccce
Confidence 577999999999887744 4554
No 151
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.57 E-value=47 Score=21.77 Aligned_cols=9 Identities=33% Similarity=1.091 Sum_probs=4.7
Q ss_pred CCCCCCCcc
Q 010581 145 VCGGCNCDI 153 (507)
Q Consensus 145 ~C~~C~k~I 153 (507)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455555544
No 152
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=24.26 E-value=38 Score=29.43 Aligned_cols=12 Identities=33% Similarity=0.412 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHH
Q 010581 387 GAILAHELMHGW 398 (507)
Q Consensus 387 g~ilAHE~mHaw 398 (507)
..++|||+.|.+
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 153
>PF07607 DUF1570: Protein of unknown function (DUF1570); InterPro: IPR011464 This entry represents hypothetical proteins confined to bacteria.
Probab=24.02 E-value=95 Score=28.40 Aligned_cols=33 Identities=27% Similarity=0.297 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHhCC-CC---CChhhhhhHHHHHH
Q 010581 388 AILAHELMHGWLRLKGY-RN---LNPEVEEGICQVLS 420 (507)
Q Consensus 388 ~ilAHE~mHawlrl~g~-~~---l~~~vEEG~Cq~~a 420 (507)
+.++||..|-=+.-.|. ++ -|..|-|||-..+.
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 47889999877653
No 154
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=23.94 E-value=56 Score=26.21 Aligned_cols=16 Identities=25% Similarity=0.555 Sum_probs=12.4
Q ss_pred cccccccccccccccH
Q 010581 296 MNMKLDQQIPMLLVER 311 (507)
Q Consensus 296 lgm~~~~~~pl~lv~~ 311 (507)
+.-+|..+||++|.+.
T Consensus 34 ~aYpI~dGIPvlL~~e 49 (60)
T COG2835 34 LAYPIRDGIPVLLPDE 49 (60)
T ss_pred ceeecccCccccCchh
Confidence 4457899999999853
No 155
>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=23.63 E-value=80 Score=33.46 Aligned_cols=37 Identities=24% Similarity=0.163 Sum_probs=20.4
Q ss_pred hHHHHHHHHHHHHHHHHHh---CCCCCChhhhhhHHHHHH
Q 010581 384 LLTGAILAHELMHGWLRLK---GYRNLNPEVEEGICQVLS 420 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~---g~~~l~~~vEEG~Cq~~a 420 (507)
.---..|+||++||+--+. ..+.+...+.-.+.++.|
T Consensus 220 ~~~v~tl~HE~GHa~h~~~~~~~~~~~~~~~~~~~~E~~S 259 (427)
T cd06459 220 LDDVFTLAHELGHAFHSYLSRDNQPYLYSDYPIFLAEIAS 259 (427)
T ss_pred hhhHHHHHHHhhHHHHHHHHccCCCcccCCCCchhhHHHH
Confidence 3445789999999864442 223243334444554443
No 156
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=23.59 E-value=42 Score=34.57 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=7.5
Q ss_pred cccCCCCCccc
Q 010581 243 SRCCSCERLES 253 (507)
Q Consensus 243 F~C~~C~r~l~ 253 (507)
|.|..|+|.|.
T Consensus 216 F~C~hC~kAFA 226 (279)
T KOG2462|consen 216 FSCPHCGKAFA 226 (279)
T ss_pred ccCCcccchhc
Confidence 67777777554
No 157
>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=23.13 E-value=1.7e+02 Score=31.68 Aligned_cols=18 Identities=28% Similarity=0.135 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010581 385 LTGAILAHELMHGWLRLK 402 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~ 402 (507)
--..+|+||++||+--+-
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 158
>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=23.09 E-value=59 Score=31.31 Aligned_cols=21 Identities=33% Similarity=0.284 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHHh-CC
Q 010581 384 LLTGAILAHELMHGWLRLK-GY 404 (507)
Q Consensus 384 l~~g~ilAHE~mHawlrl~-g~ 404 (507)
.+..+|+-||+.|+|.... |.
T Consensus 7 ~l~~~v~iHElGH~~~Ar~~Gv 28 (182)
T cd06163 7 VLGILIFVHELGHFLVAKLFGV 28 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 3567899999999998765 54
No 159
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=22.36 E-value=81 Score=31.80 Aligned_cols=31 Identities=26% Similarity=0.684 Sum_probs=24.6
Q ss_pred CCCcccCCCCCccccCCceeEecCCccccchhh
Q 010581 240 DHTSRCCSCERLESWNTRYYSLEDGRSLCLECM 272 (507)
Q Consensus 240 ~~CF~C~~C~r~l~~g~~~~~l~dGr~~C~~C~ 272 (507)
++=..|+.|++ +....++....|..+|..|.
T Consensus 152 ~~l~~Ca~cg~--~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGT--PVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCC--cCCCcceeeccCcccchhcc
Confidence 34467999999 54556788888999999998
No 160
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=22.08 E-value=41 Score=35.28 Aligned_cols=42 Identities=19% Similarity=0.544 Sum_probs=22.8
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhhhccccccccCCCcC
Q 010581 173 CRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIP 214 (507)
Q Consensus 173 C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f~pkC~~C~k~I~ 214 (507)
|..|+.+|.-..-.+--+..||.+|-..---+.|..|...|.
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 455555554333233344556666654434457888887654
No 161
>KOG1046 consensus Puromycin-sensitive aminopeptidase and related aminopeptidases [Amino acid transport and metabolism; Posttranslational modification, protein turnover, chaperones]
Probab=22.00 E-value=1.7e+02 Score=35.09 Aligned_cols=39 Identities=28% Similarity=0.606 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCC-------ChhhhhhHHHHHHHHHhhc
Q 010581 383 RLLTGAILAHELMHGWLRLKGYRNL-------NPEVEEGICQVLSYMWLES 426 (507)
Q Consensus 383 rl~~g~ilAHE~mHawlrl~g~~~l-------~~~vEEG~Cq~~a~~wl~~ 426 (507)
+.-...++|||+.|-|. .|| +..+-|||-.+|+++=++.
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 162
>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=21.93 E-value=45 Score=31.80 Aligned_cols=10 Identities=50% Similarity=0.906 Sum_probs=9.3
Q ss_pred HHHHHHHHHH
Q 010581 388 AILAHELMHG 397 (507)
Q Consensus 388 ~ilAHE~mHa 397 (507)
.++.||+|||
T Consensus 76 g~v~HE~~Ha 85 (180)
T cd04280 76 GTIVHELMHA 85 (180)
T ss_pred chhHHHHHHH
Confidence 6889999999
No 163
>PRK00420 hypothetical protein; Validated
Probab=21.92 E-value=45 Score=29.94 Aligned_cols=30 Identities=23% Similarity=0.528 Sum_probs=21.6
Q ss_pred cCCCCCccccCCceeEecCCccccchhhhhhccCCC
Q 010581 245 CCSCERLESWNTRYYSLEDGRSLCLECMESAIMDTG 280 (507)
Q Consensus 245 C~~C~r~l~~g~~~~~l~dGr~~C~~C~~sav~dt~ 280 (507)
|..|+. | .|.+.+|+.+|+.|-...+....
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 556665 2 46678999999999886665443
No 164
>PF13203 DUF2201_N: Putative metallopeptidase domain
Probab=21.80 E-value=61 Score=32.97 Aligned_cols=23 Identities=30% Similarity=0.328 Sum_probs=18.5
Q ss_pred cCCchhHHHHHHHHHHHHHHHHH
Q 010581 379 YGLPRLLTGAILAHELMHGWLRL 401 (507)
Q Consensus 379 ~GLPrl~~g~ilAHE~mHawlrl 401 (507)
.+|+.--...+|+||+||.-++-
T Consensus 53 ~~l~~~~~~~~l~HevlH~~~~H 75 (292)
T PF13203_consen 53 ESLSPEERVGLLLHEVLHCLLRH 75 (292)
T ss_pred hcCCHHHHHHHHHHHHHHHHccc
Confidence 56677777789999999987765
No 165
>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=21.15 E-value=46 Score=30.62 Aligned_cols=19 Identities=32% Similarity=0.237 Sum_probs=14.5
Q ss_pred chhHHHHHHHHHHHHHHHHH
Q 010581 382 PRLLTGAILAHELMHGWLRL 401 (507)
Q Consensus 382 Prl~~g~ilAHE~mHawlrl 401 (507)
+..-+-+|+.||+.|| |-|
T Consensus 103 ~~~~~~~~~~HEiGHa-LGL 121 (157)
T cd04278 103 GGTDLFSVAAHEIGHA-LGL 121 (157)
T ss_pred ccchHHHHHHHHhccc-ccc
Confidence 3455778999999999 444
No 166
>PRK00420 hypothetical protein; Validated
Probab=20.75 E-value=54 Score=29.45 Aligned_cols=22 Identities=27% Similarity=0.588 Sum_probs=10.9
Q ss_pred ccCCCCCCCCCCceEeeCCcccchhh
Q 010581 172 RCRSCGYPITEHEFSLSGKDPYHKSC 197 (507)
Q Consensus 172 ~C~~C~~~L~~~~F~~~dg~pYCk~C 197 (507)
.|..|+.||-. .++|+.||..|
T Consensus 25 ~CP~Cg~pLf~----lk~g~~~Cp~C 46 (112)
T PRK00420 25 HCPVCGLPLFE----LKDGEVVCPVH 46 (112)
T ss_pred CCCCCCCccee----cCCCceECCCC
Confidence 35555555522 24555555444
No 167
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=20.69 E-value=95 Score=33.70 Aligned_cols=22 Identities=41% Similarity=0.591 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHhCCCCCChh
Q 010581 388 AILAHELMHGWLRLKGYRNLNPE 410 (507)
Q Consensus 388 ~ilAHE~mHawlrl~g~~~l~~~ 410 (507)
.-+|-|....||+-+ .|+|+++
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 168
>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=20.63 E-value=70 Score=22.48 Aligned_cols=37 Identities=24% Similarity=0.627 Sum_probs=21.2
Q ss_pred cCCCCCCCCCCceEeeCCcccchhhhhhhc--ccccccc
Q 010581 173 CRSCGYPITEHEFSLSGKDPYHKSCFKELT--HPKCEVC 209 (507)
Q Consensus 173 C~~C~~~L~~~~F~~~dg~pYCk~CY~k~f--~pkC~~C 209 (507)
|..|...+.+.-....=|..||..|..+.. .++|..|
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 455666555533455678889999876632 3445443
No 169
>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=20.43 E-value=53 Score=33.63 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHhC
Q 010581 385 LTGAILAHELMHGWLRLKG 403 (507)
Q Consensus 385 ~~g~ilAHE~mHawlrl~g 403 (507)
.+..|+.||+.|.+..|..
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
Done!