Query 010559
Match_columns 507
No_of_seqs 338 out of 1757
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 01:57:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010559.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010559hhsearch_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 2.2E-69 4.8E-74 512.5 14.0 194 305-506 1-194 (212)
2 KOG2272 Focal adhesion protein 99.9 6.9E-26 1.5E-30 218.9 -1.6 179 140-355 59-253 (332)
3 KOG1703 Adaptor protein Enigma 99.9 2.8E-24 6.1E-29 232.3 8.8 321 152-506 133-456 (479)
4 KOG1701 Focal adhesion adaptor 99.8 2.2E-22 4.8E-27 207.1 -1.3 166 150-347 271-438 (468)
5 KOG4577 Transcription factor L 99.8 1E-21 2.2E-26 193.0 -4.8 122 152-285 32-153 (383)
6 KOG1701 Focal adhesion adaptor 99.8 7.4E-20 1.6E-24 188.6 0.2 134 140-285 321-462 (468)
7 KOG2272 Focal adhesion protein 99.6 1.5E-17 3.2E-22 161.5 -1.0 134 136-284 177-311 (332)
8 KOG1044 Actin-binding LIM Zn-f 99.6 6.9E-16 1.5E-20 164.1 2.4 118 151-283 131-248 (670)
9 KOG1703 Adaptor protein Enigma 99.5 7.7E-15 1.7E-19 159.1 5.1 131 152-300 302-433 (479)
10 PF00412 LIM: LIM domain; Int 99.2 5.1E-12 1.1E-16 97.7 3.3 57 156-212 1-58 (58)
11 KOG1044 Actin-binding LIM Zn-f 99.1 1.1E-10 2.4E-15 124.9 5.7 158 154-352 17-188 (670)
12 KOG1700 Regulatory protein MLP 98.6 6.5E-09 1.4E-13 100.8 0.3 121 152-286 6-167 (200)
13 PF00412 LIM: LIM domain; Int 98.4 1.8E-07 3.8E-12 72.2 3.6 57 216-285 1-57 (58)
14 smart00132 LIM Zinc-binding do 98.3 6.2E-07 1.3E-11 63.0 2.9 37 155-191 1-38 (39)
15 KOG4577 Transcription factor L 97.6 7.5E-06 1.6E-10 81.9 -1.3 73 140-212 78-154 (383)
16 KOG1702 Nebulin repeat protein 97.4 1.7E-05 3.7E-10 76.1 -1.7 59 154-212 5-63 (264)
17 KOG1700 Regulatory protein MLP 97.2 0.00011 2.5E-09 71.4 0.4 63 150-212 105-167 (200)
18 KOG0490 Transcription factor, 97.0 0.0001 2.2E-09 72.0 -1.6 114 158-284 1-118 (235)
19 smart00132 LIM Zinc-binding do 96.9 0.00085 1.8E-08 46.8 2.6 38 215-263 1-38 (39)
20 PF13485 Peptidase_MA_2: Pepti 93.7 0.077 1.7E-06 45.8 4.0 44 391-434 19-64 (128)
21 smart00726 UIM Ubiquitin-inter 87.9 0.45 9.7E-06 31.4 2.1 21 40-60 1-21 (26)
22 PF02809 UIM: Ubiquitin intera 83.8 0.52 1.1E-05 28.5 0.8 16 40-55 2-17 (18)
23 PF00595 PDZ: PDZ domain (Also 75.6 0.33 7.2E-06 39.5 -2.5 31 361-391 43-73 (81)
24 PF10026 DUF2268: Predicted Zn 74.0 3.1 6.6E-05 40.2 3.3 44 396-439 64-113 (195)
25 PF14835 zf-RING_6: zf-RING of 67.9 5.8 0.00013 31.9 3.0 47 181-227 8-54 (65)
26 PF04450 BSP: Peptidase of pla 67.4 3.6 7.7E-05 40.4 2.1 38 395-433 94-131 (205)
27 PF01433 Peptidase_M1: Peptida 66.9 2.5 5.4E-05 44.2 1.0 44 396-439 294-339 (390)
28 PF06114 DUF955: Domain of unk 65.4 4.2 9.2E-05 34.4 2.0 52 384-435 29-86 (122)
29 PF10460 Peptidase_M30: Peptid 65.3 4.8 0.0001 42.9 2.8 43 396-438 138-186 (366)
30 TIGR02412 pepN_strep_liv amino 64.6 4.2 9E-05 47.9 2.3 40 398-437 288-329 (831)
31 KOG0320 Predicted E3 ubiquitin 60.7 3.4 7.3E-05 39.7 0.5 48 179-226 130-180 (187)
32 PRK14873 primosome assembly pr 59.8 6.3 0.00014 45.3 2.6 37 182-221 394-430 (665)
33 KOG3549 Syntrophins (type gamm 57.1 7 0.00015 41.2 2.1 36 361-396 99-134 (505)
34 KOG2199 Signal transducing ada 57.0 6.6 0.00014 42.0 2.0 26 37-62 161-186 (462)
35 PF05572 Peptidase_M43: Pregna 56.0 6.8 0.00015 36.6 1.7 47 366-413 33-84 (154)
36 PRK14559 putative protein seri 54.5 12 0.00026 42.9 3.7 11 154-164 2-12 (645)
37 TIGR00595 priA primosomal prot 53.7 10 0.00022 42.2 2.8 37 182-221 224-261 (505)
38 COG2856 Predicted Zn peptidase 53.3 23 0.0005 35.0 5.0 55 384-438 59-120 (213)
39 PF10367 Vps39_2: Vacuolar sor 52.3 12 0.00025 31.8 2.5 12 214-225 79-90 (109)
40 PRK14890 putative Zn-ribbon RN 52.2 11 0.00025 29.8 2.1 27 154-189 8-34 (59)
41 KOG0320 Predicted E3 ubiquitin 51.4 5.7 0.00012 38.2 0.4 50 249-299 128-177 (187)
42 PF10263 SprT-like: SprT-like 51.3 8.4 0.00018 35.3 1.5 23 392-414 55-77 (157)
43 PF14891 Peptidase_M91: Effect 51.2 7.7 0.00017 36.7 1.3 21 392-415 101-121 (174)
44 PHA02456 zinc metallopeptidase 50.3 6.6 0.00014 35.0 0.6 36 398-439 80-116 (141)
45 PF13699 DUF4157: Domain of un 50.0 7.4 0.00016 32.4 0.8 16 399-414 63-78 (79)
46 PF10367 Vps39_2: Vacuolar sor 49.4 12 0.00026 31.7 2.1 29 153-181 78-107 (109)
47 PF05299 Peptidase_M61: M61 gl 48.3 8 0.00017 35.0 0.8 40 398-437 5-57 (122)
48 PF01431 Peptidase_M13: Peptid 46.7 6.8 0.00015 37.6 0.1 16 397-412 36-51 (206)
49 KOG3209 WW domain-containing p 44.0 4 8.7E-05 46.5 -2.1 37 357-393 938-974 (984)
50 KOG1702 Nebulin repeat protein 44.0 6.9 0.00015 38.4 -0.3 59 214-286 5-63 (264)
51 cd00136 PDZ PDZ domain, also c 43.4 6.1 0.00013 30.7 -0.6 26 360-385 30-55 (70)
52 COG1645 Uncharacterized Zn-fin 43.4 13 0.00028 34.1 1.4 22 182-208 30-51 (131)
53 PF13240 zinc_ribbon_2: zinc-r 43.3 14 0.00031 23.5 1.2 9 156-164 2-10 (23)
54 PRK12495 hypothetical protein; 42.9 51 0.0011 32.8 5.5 27 154-191 43-69 (226)
55 COG2191 Formylmethanofuran deh 42.6 11 0.00025 36.8 1.0 30 182-211 174-203 (206)
56 PF09943 DUF2175: Uncharacteri 42.6 7.1 0.00015 34.1 -0.4 29 155-183 4-33 (101)
57 TIGR02411 leuko_A4_hydro leuko 42.4 14 0.00029 42.1 1.7 39 399-437 281-321 (601)
58 KOG3605 Beta amyloid precursor 42.0 6.1 0.00013 44.7 -1.1 32 355-386 768-799 (829)
59 KOG1813 Predicted E3 ubiquitin 42.0 14 0.00029 38.3 1.4 44 181-225 242-287 (313)
60 smart00504 Ubox Modified RING 41.8 17 0.00036 27.8 1.6 45 181-226 2-48 (63)
61 PF13920 zf-C3HC4_3: Zinc fing 41.8 13 0.00028 27.6 1.0 43 182-225 4-49 (50)
62 PF11781 RRN7: RNA polymerase 40.9 15 0.00032 26.1 1.1 25 181-209 9-33 (36)
63 COG4357 Zinc finger domain con 40.7 4.8 0.0001 34.8 -1.7 46 155-200 37-82 (105)
64 PF14471 DUF4428: Domain of un 40.6 13 0.00029 28.4 0.9 30 254-285 1-30 (51)
65 PRK04023 DNA polymerase II lar 39.7 29 0.00063 41.5 3.8 55 150-227 623-677 (1121)
66 KOG3552 FERM domain protein FR 38.8 8.4 0.00018 45.3 -0.7 25 359-383 90-114 (1298)
67 PRK05580 primosome assembly pr 37.7 24 0.00052 40.7 2.7 11 399-409 556-566 (679)
68 PF12773 DZR: Double zinc ribb 37.1 32 0.00069 25.4 2.5 10 275-284 29-38 (50)
69 PF07607 DUF1570: Protein of u 36.3 23 0.00049 32.3 1.8 32 399-430 3-38 (128)
70 PRK14714 DNA polymerase II lar 36.1 48 0.001 40.7 4.9 50 254-309 694-743 (1337)
71 COG1645 Uncharacterized Zn-fin 34.5 23 0.00051 32.4 1.6 24 254-284 30-53 (131)
72 cd00992 PDZ_signaling PDZ doma 34.5 6.9 0.00015 31.2 -1.7 24 359-382 42-65 (82)
73 PHA03308 transcriptional regul 34.3 28 0.00062 40.0 2.5 6 85-90 796-801 (1463)
74 PF12674 Zn_ribbon_2: Putative 34.0 19 0.00041 30.2 0.9 31 254-284 2-35 (81)
75 smart00731 SprT SprT homologue 33.2 24 0.00051 32.4 1.5 22 393-414 55-76 (146)
76 COG2191 Formylmethanofuran deh 32.3 21 0.00046 35.0 1.0 31 253-285 173-203 (206)
77 KOG4739 Uncharacterized protei 32.3 29 0.00064 34.8 2.0 32 194-225 18-49 (233)
78 PF14634 zf-RING_5: zinc-RING 31.2 36 0.00078 24.6 1.9 41 255-295 2-42 (44)
79 PF00645 zf-PARP: Poly(ADP-rib 31.1 8.4 0.00018 31.7 -1.7 19 209-227 3-21 (82)
80 PF06677 Auto_anti-p27: Sjogre 30.9 37 0.0008 24.9 1.9 21 255-281 20-40 (41)
81 PF08394 Arc_trans_TRASH: Arch 30.6 30 0.00065 24.9 1.3 25 156-180 1-26 (37)
82 KOG0978 E3 ubiquitin ligase in 30.3 12 0.00027 42.9 -1.1 46 181-227 644-692 (698)
83 KOG2462 C2H2-type Zn-finger pr 30.2 34 0.00075 35.0 2.1 14 179-192 129-142 (279)
84 PF10083 DUF2321: Uncharacteri 30.1 23 0.00051 33.3 0.9 54 200-266 27-82 (158)
85 PF09768 Peptidase_M76: Peptid 29.9 21 0.00046 34.2 0.6 15 398-412 72-86 (173)
86 KOG0478 DNA replication licens 29.3 51 0.0011 38.1 3.5 30 360-403 342-371 (804)
87 PF13834 DUF4193: Domain of un 28.8 19 0.00042 31.4 0.1 30 251-281 69-98 (99)
88 PRK00420 hypothetical protein; 28.7 38 0.00082 30.2 1.9 26 254-285 25-50 (112)
89 KOG2932 E3 ubiquitin ligase in 27.1 28 0.00062 36.3 0.9 43 182-224 92-134 (389)
90 COG1198 PriA Primosomal protei 27.0 52 0.0011 38.4 3.2 39 181-222 445-484 (730)
91 PF01421 Reprolysin: Reprolysi 27.0 40 0.00088 32.1 2.0 25 384-408 118-142 (199)
92 PRK14559 putative protein seri 26.9 57 0.0012 37.5 3.4 38 182-226 3-40 (645)
93 KOG0490 Transcription factor, 26.7 14 0.00031 35.7 -1.3 52 247-299 18-69 (235)
94 TIGR02414 pepN_proteo aminopep 26.6 37 0.0008 40.4 1.9 41 397-437 283-325 (863)
95 TIGR02420 dksA RNA polymerase- 26.5 41 0.0009 29.5 1.8 30 152-187 79-108 (110)
96 cd00162 RING RING-finger (Real 26.5 26 0.00057 24.0 0.4 39 183-221 2-43 (45)
97 PF10083 DUF2321: Uncharacteri 26.3 25 0.00055 33.1 0.4 51 154-224 29-79 (158)
98 PRK14714 DNA polymerase II lar 26.0 52 0.0011 40.4 3.0 11 215-225 711-721 (1337)
99 cd04270 ZnMc_TACE_like Zinc-de 26.0 29 0.00063 34.7 0.8 21 389-409 157-179 (244)
100 PF14446 Prok-RING_1: Prokaryo 25.9 40 0.00087 26.2 1.4 13 153-165 5-17 (54)
101 PRK14015 pepN aminopeptidase N 25.3 46 0.001 39.6 2.4 41 397-437 296-338 (875)
102 PLN03208 E3 ubiquitin-protein 24.6 58 0.0013 31.8 2.5 13 214-226 69-81 (193)
103 PF04502 DUF572: Family of unk 24.5 49 0.0011 34.6 2.2 18 172-192 35-52 (324)
104 cd00989 PDZ_metalloprotease PD 24.4 45 0.00097 26.3 1.5 18 360-377 29-46 (79)
105 PF06750 DiS_P_DiS: Bacterial 24.1 28 0.00062 29.7 0.3 40 153-194 33-72 (92)
106 COG0308 PepN Aminopeptidase N 23.8 42 0.0009 39.9 1.7 43 395-439 305-351 (859)
107 PRK00420 hypothetical protein; 23.7 47 0.001 29.7 1.6 22 182-207 25-46 (112)
108 COG5152 Uncharacterized conser 23.3 22 0.00047 34.9 -0.7 44 181-225 197-242 (259)
109 PF04502 DUF572: Family of unk 23.0 43 0.00094 35.1 1.4 22 150-171 37-58 (324)
110 cd04267 ZnMc_ADAM_like Zinc-de 22.9 40 0.00087 31.8 1.1 24 385-409 122-145 (192)
111 PF07754 DUF1610: Domain of un 22.6 61 0.0013 21.1 1.5 9 156-164 1-9 (24)
112 KOG1280 Uncharacterized conser 22.6 72 0.0016 33.8 2.9 16 246-261 73-88 (381)
113 PHA00527 hypothetical protein 22.4 1.9E+02 0.0041 25.6 5.0 64 366-434 46-113 (129)
114 PF01447 Peptidase_M4: Thermol 22.4 37 0.0008 31.7 0.7 18 393-410 131-148 (150)
115 COG2888 Predicted Zn-ribbon RN 21.7 47 0.001 26.4 1.0 27 253-284 10-36 (61)
116 cd00991 PDZ_archaeal_metallopr 21.7 54 0.0012 26.4 1.5 19 359-377 26-44 (79)
117 PF01435 Peptidase_M48: Peptid 21.7 36 0.00078 32.5 0.5 16 398-413 90-105 (226)
118 cd04269 ZnMc_adamalysin_II_lik 21.6 59 0.0013 30.8 2.0 24 386-409 120-143 (194)
119 PF06827 zf-FPG_IleRS: Zinc fi 21.6 41 0.0009 22.4 0.6 13 213-225 1-13 (30)
120 PRK00398 rpoP DNA-directed RNA 21.6 42 0.00091 24.6 0.7 10 155-164 5-14 (46)
121 PF10235 Cript: Microtubule-as 21.5 57 0.0012 28.1 1.6 37 181-225 45-81 (90)
122 cd00990 PDZ_glycyl_aminopeptid 21.3 53 0.0011 26.0 1.3 18 360-377 29-46 (80)
123 PF05502 Dynactin_p62: Dynacti 21.0 62 0.0014 35.9 2.2 43 150-193 23-65 (483)
124 PF12388 Peptidase_M57: Dual-a 20.9 61 0.0013 32.1 1.9 38 370-417 112-149 (211)
125 KOG0609 Calcium/calmodulin-dep 20.8 20 0.00044 39.8 -1.6 24 357-380 161-184 (542)
126 cd00988 PDZ_CTP_protease PDZ d 20.7 28 0.00061 28.0 -0.4 19 360-378 30-48 (85)
127 PF01258 zf-dskA_traR: Prokary 20.7 11 0.00024 26.4 -2.4 10 155-164 5-14 (36)
128 PF09538 FYDLN_acid: Protein o 20.7 61 0.0013 28.7 1.7 26 253-284 10-35 (108)
129 PF13180 PDZ_2: PDZ domain; PD 20.5 48 0.001 26.8 0.9 17 360-376 31-47 (82)
130 KOG3714 Meprin A metalloprotea 20.3 37 0.0008 36.8 0.3 10 399-408 161-170 (411)
131 cd04268 ZnMc_MMP_like Zinc-dep 20.1 41 0.00088 30.7 0.5 13 397-409 94-106 (165)
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=2.2e-69 Score=512.51 Aligned_cols=194 Identities=78% Similarity=1.208 Sum_probs=183.1
Q ss_pred hcCCccccccceEEEehhhhHHhhccCCCCccccccccCcccCccchhcccccccccCCCCeeeeeccccccccccceee
Q 010559 305 GLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVT 384 (507)
Q Consensus 305 ~l~~~i~~~iPv~LVe~~aLn~a~e~e~~g~~~~~e~rGlclSee~~v~~~~~~~~~~~G~rilei~~~p~~~~~~~eV~ 384 (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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeecCchhhhhhhhhhcchhhHHHHhcCCCCCCCcchhhHHHHHHHHHhhcccccCCCCCccCCCCCCCCCCCCCCCC
Q 010559 385 AILILYGLPRLLTGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHMWLESEIYSGSGSDVASSSSSSASSSSSSPSS 464 (507)
Q Consensus 385 ~Il~l~glP~~L~gsilaHE~~Hawl~~~g~~~L~~~~eEG~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 464 (507)
+|+|||||||+|||||||||+||||||++|||+|+|+||||||||||||||++|++++.+ +++++|++++++
T Consensus 81 ~Ilvl~GLPrll~gsiLAHE~mHa~Lrl~g~~~L~~~vEEGiCqvla~~wL~~~~~~~~~--------~~~~~s~~~s~~ 152 (212)
T PF12315_consen 81 AILVLYGLPRLLTGSILAHELMHAWLRLNGFPNLSPEVEEGICQVLAYLWLESELASGSG--------SSSSSSSSSSSS 152 (212)
T ss_pred EEEEECCCCHHHHhhHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHHHHHhhhhhcccC--------CcccccCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999998765 112345556677
Q ss_pred CCcCCcCCCcchHHHHHHHHHHhhhhcCCCCCCchhhhhhhc
Q 010559 465 SSTSSKKGKRSDFEKDLGKFFKHQIESDTSSAYGDGLGKVVR 506 (507)
Q Consensus 465 ~~~~~~~~~~~~~~~~l~~~~~~qi~~d~s~~yG~Gfr~~~~ 506 (507)
+++++|||++++||+||++||+|||++|+|||||||||+|++
T Consensus 153 ~~~~skkg~~s~~E~kL~~f~~~qIe~D~SpvYGdGFRaa~~ 194 (212)
T PF12315_consen 153 ASSSSKKGAKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANE 194 (212)
T ss_pred cccccccccccHHHHHHHHHHHHHhccCCCcccchHHHHHHH
Confidence 778899999999999999999999999999999999999985
No 2
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.90 E-value=6.9e-26 Score=218.91 Aligned_cols=179 Identities=26% Similarity=0.549 Sum_probs=156.8
Q ss_pred CCCccCCCCC-CCCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCcccccccccc-----ccC
Q 010559 140 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE-----QHH 213 (507)
Q Consensus 140 ~gsv~~p~~~-~~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~-----~f~ 213 (507)
.|..||..++ ...+|.|++|++.| .|++|.+++.+|||.||+|..|++.|.+..|+...|+.+|..|..+ +-.
T Consensus 59 EgRkYCEhDF~~LfaPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~ 137 (332)
T KOG2272|consen 59 EGRKYCEHDFHVLFAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGR 137 (332)
T ss_pred cCcccccccchhhhchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccce
Confidence 3778899888 77889999999999 6999999999999999999999999999999999999999999866 234
Q ss_pred ccccccCCccccCcccceeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCc
Q 010559 214 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQ 293 (507)
Q Consensus 214 pkC~~C~~~I~~~~~g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~ 293 (507)
..|..|...|... .+.|++.|| |+.+|+|..|++.|..+.+-+ .|.+||+.|+++ |..|+|.
T Consensus 138 YvC~KCh~~iD~~---~l~fr~d~y----------H~yHFkCt~C~keL~sdaRev---k~eLyClrChD~--mgipiCg 199 (332)
T KOG2272|consen 138 YVCQKCHAHIDEQ---PLTFRGDPY----------HPYHFKCTTCGKELTSDAREV---KGELYCLRCHDK--MGIPICG 199 (332)
T ss_pred eehhhhhhhcccc---cccccCCCC----------Cccceecccccccccchhhhh---ccceeccccccc--cCCcccc
Confidence 5799999999873 689999986 777799999999998777765 689999999999 8899999
Q ss_pred cccHHHHHHHhhcCCccccccceEEEehhhhHHhh----------ccCCCCccccccccCcccCccchhccc
Q 010559 294 PLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAM----------EGEKNGHHHLPETRGLCLSEEQTVTTV 355 (507)
Q Consensus 294 ~c~~~I~~f~e~l~~~i~~~iPv~LVe~~aLn~a~----------e~e~~g~~~~~e~rGlclSee~~v~~~ 355 (507)
+|.++|. .++ +.||+++| ++++.||.|| |.+|++|+|+||+..+
T Consensus 200 aC~rpIe-----------erv------i~amgKhWHveHFvCa~CekPFlGHrHY-EkkGlaYCe~h~~qLf 253 (332)
T KOG2272|consen 200 ACRRPIE-----------ERV------IFAMGKHWHVEHFVCAKCEKPFLGHRHY-EKKGLAYCETHYHQLF 253 (332)
T ss_pred cccCchH-----------HHH------HHHhccccchhheeehhcCCcccchhhh-hhcCchhHHHHHHHHh
Confidence 9998883 333 67888887 4889999998 9999999999997653
No 3
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.90 E-value=2.8e-24 Score=232.34 Aligned_cols=321 Identities=43% Similarity=0.688 Sum_probs=266.2
Q ss_pred CCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCcccccccccc-ccCccccccCCccccCcccc
Q 010559 152 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE-QHHPKCDVCQNFIPTNSAGL 230 (507)
Q Consensus 152 g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~-~f~pkC~~C~~~I~~~~~g~ 230 (507)
...+|.+|.-.|..+..+ ||.|..|..++. .+...||.. ...+.|.+|...|.....+.
T Consensus 133 ~~~~~~~~~~~~~~~~~~----------~~~~~~~~~p~~----------~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~ 192 (479)
T KOG1703|consen 133 LDSICGGCNSAIEHGRSV----------CFQCKRCSEPLS----------GFPKPSYHESGRSKNEDVEEASSPSSRAGL 192 (479)
T ss_pred ccccccCCCcccccccch----------hhhhcccccccC----------Cccccccccccccccccccccccccccccc
Confidence 456799999999766555 899999988882 223444544 36678999999999877788
Q ss_pred eeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccccHHHHHHHhhcCCcc
Q 010559 231 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKV 310 (507)
Q Consensus 231 i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c~~~I~~f~e~l~~~i 310 (507)
+.++.++||.++||+.|+++.+..|..|.+..+.+.+|..+.+++.+|..|....+|+.+.|++....++.++....|.+
T Consensus 193 ~~~~~~~~~~~~~~~~~e~~~tp~~~~~~r~e~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~p~~~~~~~~~~~~~~~~ 272 (479)
T KOG1703|consen 193 ILSRSHPFWKQKYCPSHENDGTPKCCSCERLEPLDTRYVELADGRALCLECMGSASMDSPECQPLVSAPRPASEGLHMKV 272 (479)
T ss_pred cccccchhhhhcccccccCCCCCCcccccccccccccceecccchhhhhhccCCcccCCCccCcceeccccccccccccc
Confidence 89999999999999999999999999999998778899999899999999998888999999999999999999999999
Q ss_pred ccccceEEEehhhhHHhhccCCCCccccccccCcccCccchhcccccccccCCCCeeeeeccccccccccceeeeeeeec
Q 010559 311 EQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILY 390 (507)
Q Consensus 311 ~~~iPv~LVe~~aLn~a~e~e~~g~~~~~e~rGlclSee~~v~~~~~~~~~~~G~rilei~~~p~~~~~~~eV~~Il~l~ 390 (507)
.+..++.|+++++++.+..+......|. .++++|.++.++++++ ..|..++++.-+....|++.++.+++
T Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~p~c~~c~~~i~~~---------~~i~~~~~~~h~~~~~c~~~~~~~~~ 342 (479)
T KOG1703|consen 273 EKELPLLLVESEALKKLREEEKPAEYHN-VTRPLCLSCNQKIRSV---------KVIVALGKEWHPEHFSCEVCAIVILD 342 (479)
T ss_pred ccccchhhcccccccccccccccccccc-cccccccccccCcccc---------eeEeeccccccccceeeccccccccC
Confidence 9999999999999999887666554443 6789999999887553 34778888999999999999999999
Q ss_pred CchhhhhhhhhhcchhhHHHHhcCCCCCCCcchhhHHHHHHHHHhhcccccCCCCCccCCCCCCCCCCCCCCCCCCcCCc
Q 010559 391 GLPRLLTGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHMWLESEIYSGSGSDVASSSSSSASSSSSSPSSSSTSSK 470 (507)
Q Consensus 391 glP~~L~gsilaHE~~Hawl~~~g~~~L~~~~eEG~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 470 (507)
+.|+..+|.+++|++||+|++.++...+.+.++++||++ +.+|+....+-..-...- ...+.+..+..+......+
T Consensus 343 ~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~-~~~wH~~cf~C~~C~~~~---~~~~~~~~~~~pyce~~~~ 418 (479)
T KOG1703|consen 343 GGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCAL-GRLWHPECFVCADCGKPL---KNSSFFESDGEPYCEDHYK 418 (479)
T ss_pred CCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhc-cCeechhceeeecccCCC---CCCcccccCCccchhhhHh
Confidence 999999999999999999999999999999999999999 999999887664211000 0111112333333344455
Q ss_pred CCC--cchHHHHHHHHHHhhhhcCCCCCCchhhhhhhc
Q 010559 471 KGK--RSDFEKDLGKFFKHQIESDTSSAYGDGLGKVVR 506 (507)
Q Consensus 471 ~~~--~~~~~~~l~~~~~~qi~~d~s~~yG~Gfr~~~~ 506 (507)
+.. +..+++++++|+.++|+.|.+++||+|||.++.
T Consensus 419 ~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c 456 (479)
T KOG1703|consen 419 KLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANC 456 (479)
T ss_pred hhccccchhccchhHhhhhHhhccCccccccceehhhh
Confidence 554 678899999999999999999999999998864
No 4
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.83 E-value=2.2e-22 Score=207.09 Aligned_cols=166 Identities=20% Similarity=0.419 Sum_probs=136.1
Q ss_pred CCCCCcCccCCccccc-CceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCcc
Q 010559 150 FSGYRICAGCNTEIGH-GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSA 228 (507)
Q Consensus 150 ~~g~~~C~~C~k~I~~-g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~~ 228 (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 3456699999999964 356899999999999999999999999999999999999999975 678999999999984
Q ss_pred cceeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccccHHHHHHHhhcCC
Q 010559 229 GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNM 308 (507)
Q Consensus 229 g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c~~~I~~f~e~l~~ 308 (507)
++.+.++.| |++||+|.+|.+.| +|..|....++.+||..||.+ .++++|..|.++| |
T Consensus 348 -iLrA~Gkay----------Hp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~--kfAPrCs~C~~PI--------~ 405 (468)
T KOG1701|consen 348 -ILRALGKAY----------HPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHK--KFAPRCSVCGNPI--------L 405 (468)
T ss_pred -HHHhccccc----------CCCceEEEEecccc-CCccccccCCCceeeehhhhh--hcCcchhhccCCc--------c
Confidence 666667665 99999999999999 599999988999999999999 5799999999999 5
Q ss_pred cccccc-ceEEEehhhhHHhhccCCCCccccccccCcccC
Q 010559 309 KVEQQV-PLLLVERQALNEAMEGEKNGHHHLPETRGLCLS 347 (507)
Q Consensus 309 ~i~~~i-Pv~LVe~~aLn~a~e~e~~g~~~~~e~rGlclS 347 (507)
+-+.+- .|++|.+. +.|.-.-+--|-.|+-||
T Consensus 406 P~~G~~etvRvvamd-------r~fHv~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 406 PRDGKDETVRVVAMD-------RDFHVNCYKCEDCGLLLS 438 (468)
T ss_pred CCCCCcceEEEEEcc-------ccccccceehhhcCcccc
Confidence 555433 37777433 333222112366788888
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.80 E-value=1e-21 Score=193.03 Aligned_cols=122 Identities=26% Similarity=0.569 Sum_probs=110.9
Q ss_pred CCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCcccce
Q 010559 152 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI 231 (507)
Q Consensus 152 g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~~g~i 231 (507)
..++|++|.+-|.+..++.++++.||..|++|+.|..+|.+.+|. ++|.+||+++|.++|+.||..|...|++. .+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFs-R~~s~yCkedFfKrfGTKCsaC~~GIpPt---qV 107 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFS-REGSVYCKEDFFKRFGTKCSACQEGIPPT---QV 107 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhh-cCCceeehHHHHHHhCCcchhhcCCCChH---HH
Confidence 568999999999766778999999999999999999999998887 67999999999999999999999999985 34
Q ss_pred eeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccc
Q 010559 232 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 285 (507)
Q Consensus 232 ~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~ 285 (507)
+.+...| .||.+||.|..|++.|..|++||+++|+|++|+..|+++
T Consensus 108 VRkAqd~--------VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 108 VRKAQDF--------VYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred HHHhhcc--------eeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 5566655 569999999999999999999999999999999999875
No 6
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.76 E-value=7.4e-20 Score=188.62 Aligned_cols=134 Identities=23% Similarity=0.479 Sum_probs=118.3
Q ss_pred CCCccCCCCCCCCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceee-cCCccccccccccccCccccc
Q 010559 140 SGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSM-SGNRPYHKHCYKEQHHPKCDV 218 (507)
Q Consensus 140 ~gsv~~p~~~~~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~-~~gk~yCk~CY~~~f~pkC~~ 218 (507)
++++||+..+.....+|..|++.| ...+|.++|+.||+.||+|..|++.|.+..|.. .++++||-.||+++|+|+|++
T Consensus 321 ~~k~~CE~cyq~tlekC~~Cg~~I-~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~ 399 (468)
T KOG1701|consen 321 DGKPYCEGCYQDTLEKCNKCGEPI-MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSV 399 (468)
T ss_pred CCcccchHHHHHHHHHHhhhhhHH-HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhh
Confidence 577888887777888999999999 489999999999999999999999999999886 678999999999999999999
Q ss_pred cCCccccCcc----cceeeccccccccccCCCccCCCCCccCCCCCcCC---CCCceEEccCCceecccccccc
Q 010559 219 CQNFIPTNSA----GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP---RDTKYLSLDDGRKLCLECLDSA 285 (507)
Q Consensus 219 C~~~I~~~~~----g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~---~g~~y~~l~dGr~~C~~C~~~~ 285 (507)
|+++|...+. ..|+...+.| |.+|++|..|+.+|+ .|...|.+ ||.++|+.|+.+.
T Consensus 400 C~~PI~P~~G~~etvRvvamdr~f----------Hv~CY~CEDCg~~LS~e~e~qgCyPl-d~HllCk~Ch~~R 462 (468)
T KOG1701|consen 400 CGNPILPRDGKDETVRVVAMDRDF----------HVNCYKCEDCGLLLSSEEEGQGCYPL-DGHLLCKTCHLKR 462 (468)
T ss_pred ccCCccCCCCCcceEEEEEccccc----------cccceehhhcCccccccCCCCcceec-cCceeechhhhhh
Confidence 9999987542 3467777877 999999999999987 36678888 7999999998764
No 7
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.64 E-value=1.5e-17 Score=161.46 Aligned_cols=134 Identities=22% Similarity=0.510 Sum_probs=117.9
Q ss_pred CCCCCCCccCCCCC-CCCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCc
Q 010559 136 PRYESGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 214 (507)
Q Consensus 136 p~~~~gsv~~p~~~-~~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~p 214 (507)
+|.-+|.+|++... ..+-|+|+.|.++| .+++|.+||+.||.++|+|+.|.+|+-+...+.+.|.+||+.+|.++|+.
T Consensus 177 aRevk~eLyClrChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~ 255 (332)
T KOG2272|consen 177 AREVKGELYCLRCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGN 255 (332)
T ss_pred hhhhccceeccccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhh
Confidence 34446788998776 68899999999999 59999999999999999999999999888888899999999999999999
Q ss_pred cccccCCccccCcccceeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceeccccccc
Q 010559 215 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 284 (507)
Q Consensus 215 kC~~C~~~I~~~~~g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~ 284 (507)
.|..|+..|-+. ++.+.+..| | +.||.|+.|.+.|..-.+|+.+ |-+++|..||++
T Consensus 256 ~CF~C~~~i~G~---vv~al~Kaw-----C-----v~cf~Cs~Cdkkl~~K~Kf~E~-DmkP~CKkCy~r 311 (332)
T KOG2272|consen 256 LCFICNRVIGGD---VVSALNKAW-----C-----VECFSCSTCDKKLTQKNKFYEF-DMKPVCKKCYDR 311 (332)
T ss_pred hheecCCccCcc---HHHHhhhhh-----c-----cccccccccccccccccceeee-ccchHHHHHHhh
Confidence 999999999884 455555543 4 4689999999999888899988 789999999997
No 8
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.57 E-value=6.9e-16 Score=164.09 Aligned_cols=118 Identities=25% Similarity=0.619 Sum_probs=104.8
Q ss_pred CCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCcccc
Q 010559 151 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGL 230 (507)
Q Consensus 151 ~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~~g~ 230 (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 466789999999999999999999999999999999999987 566689999999999999999999999999985 5
Q ss_pred eeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccc
Q 010559 231 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLD 283 (507)
Q Consensus 231 i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~ 283 (507)
+.+.++ |||+.|-+|+.|+.+|+.|++-|+. ...+|-..|-.
T Consensus 207 Lqag~k----------h~HPtCARCsRCgqmF~eGEEMYlQ-Gs~iWHP~C~q 248 (670)
T KOG1044|consen 207 LQAGDK----------HFHPTCARCSRCGQMFGEGEEMYLQ-GSEIWHPDCKQ 248 (670)
T ss_pred hhccCc----------ccCcchhhhhhhccccccchheeec-cccccCCcccc
Confidence 555554 6799999999999999999988865 56888888865
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.51 E-value=7.7e-15 Score=159.13 Aligned_cols=131 Identities=19% Similarity=0.424 Sum_probs=113.8
Q ss_pred CCCcCccCCcccccC-ceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCcccc
Q 010559 152 GYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGL 230 (507)
Q Consensus 152 g~~~C~~C~k~I~~g-~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~~g~ 230 (507)
..+.|..|+..|. + .++.++++.||+.+|.|..|+..|....|...+|++||..||.+.+.|+|..|+++|.++ .
T Consensus 302 ~~p~c~~c~~~i~-~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~---~ 377 (479)
T KOG1703|consen 302 TRPLCLSCNQKIR-SVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEE---G 377 (479)
T ss_pred ccccccccccCcc-cceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHh---H
Confidence 4489999999995 6 999999999999999999999999998888889999999999999999999999999986 3
Q ss_pred eeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccccHHHH
Q 010559 231 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQ 300 (507)
Q Consensus 231 i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c~~~I~ 300 (507)
|.+.++ |||+.||.|..|++.+. +..|+. .+|.+||..||... ++..|..|.++|.
T Consensus 378 v~a~~~----------~wH~~cf~C~~C~~~~~-~~~~~~-~~~~pyce~~~~~~--~~~~~~~~~~p~~ 433 (479)
T KOG1703|consen 378 VCALGR----------LWHPECFVCADCGKPLK-NSSFFE-SDGEPYCEDHYKKL--FTTKCDYCKKPVE 433 (479)
T ss_pred hhhccC----------eechhceeeecccCCCC-CCcccc-cCCccchhhhHhhh--ccccchhccchhH
Confidence 444443 56999999999999885 555664 48999999999994 4578988988874
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=99.23 E-value=5.1e-12 Score=97.66 Aligned_cols=57 Identities=39% Similarity=0.996 Sum_probs=52.0
Q ss_pred CccCCcccccCcee-eecCceeccCCcccCCCCCCCCCcceeecCCcccccccccccc
Q 010559 156 CAGCNTEIGHGRYL-SCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 212 (507)
Q Consensus 156 C~~C~k~I~~g~~i-~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f 212 (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 88999999866655 7999999999999999999999988889999999999998765
No 11
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.08 E-value=1.1e-10 Score=124.95 Aligned_cols=158 Identities=16% Similarity=0.330 Sum_probs=116.7
Q ss_pred CcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCcccceee
Q 010559 154 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEY 233 (507)
Q Consensus 154 ~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~~g~i~~ 233 (507)
-.|..|.+.- .|+++.+.++.||..||.|..|+..|....|+.+++. .++++ ..|..+|.+. ++..
T Consensus 17 i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~ge---vvsa 82 (670)
T KOG1044|consen 17 IKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGE---VVST 82 (670)
T ss_pred eehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccce---eEec
Confidence 4699999998 5999999999999999999999999999888876554 34455 6788888874 5667
Q ss_pred ccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccccC------CCCCCccccHHHHHHHhhcC
Q 010559 234 RAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM------DTHECQPLYLEIQEFYEGLN 307 (507)
Q Consensus 234 ~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~------~t~~C~~c~~~I~~f~e~l~ 307 (507)
.+..| |..||.|+.|+.+++.|++.. +.....+|..|-.-+-. +...|++|...|.
T Consensus 83 ~gkty----------h~~cf~cs~ck~pf~~g~~vt-~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk------- 144 (670)
T KOG1044|consen 83 LGKTY----------HPKCFSCSTCKSPFKSGDKVT-FSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELK------- 144 (670)
T ss_pred cccee----------ccccceecccCCCCCCCCeee-ecchhhhhhhhcCcccCCcccccCCccccchhhhhh-------
Confidence 77765 999999999999999988765 33456789999754222 3467999998872
Q ss_pred CccccccceEEEehhhhHHhhcc------C--CCCccccccccCcccCccchh
Q 010559 308 MKVEQQVPLLLVERQALNEAMEG------E--KNGHHHLPETRGLCLSEEQTV 352 (507)
Q Consensus 308 ~~i~~~iPv~LVe~~aLn~a~e~------e--~~g~~~~~e~rGlclSee~~v 352 (507)
.+|. .=||.++|+. . ..-+..++..+|+.||+.+|.
T Consensus 145 ---~gq~------llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~ 188 (670)
T KOG1044|consen 145 ---NGQA------LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQ 188 (670)
T ss_pred ---ccce------eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhh
Confidence 2232 1256666641 1 111234457788888888874
No 12
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.63 E-value=6.5e-09 Score=100.85 Aligned_cols=121 Identities=22% Similarity=0.444 Sum_probs=89.4
Q ss_pred CCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCcc----------------
Q 010559 152 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK---------------- 215 (507)
Q Consensus 152 g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pk---------------- 215 (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 3458999999999888888999999999999999999999988888999999999876655443
Q ss_pred -------------------------ccccCCccccCcccceeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEE
Q 010559 216 -------------------------CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLS 270 (507)
Q Consensus 216 -------------------------C~~C~~~I~~~~~g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~ 270 (507)
|..|++.+.... -+..... -||..||+|+.|+..|. -..|..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E--k~~~~~~----------~~hk~cfrc~~~~~~ls-~~~~~~ 152 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE--KVTGNGL----------EFHKSCFRCTHCGKKLS-PKNYAA 152 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehH--HHhhhhh----------hhhhhheeecccccccC-Ccchhh
Confidence 444443333211 0111122 35889999999999996 345654
Q ss_pred ccCCceeccccccccc
Q 010559 271 LDDGRKLCLECLDSAI 286 (507)
Q Consensus 271 l~dGr~~C~~C~~~~v 286 (507)
. .|.++|...+...+
T Consensus 153 ~-~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 153 L-EGVLYCKHHFAQLF 167 (200)
T ss_pred c-CCccccchhhheee
Confidence 4 67888877766543
No 13
>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=98.43 E-value=1.8e-07 Score=72.16 Aligned_cols=57 Identities=18% Similarity=0.385 Sum_probs=44.3
Q ss_pred ccccCCccccCcccceeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceecccccccc
Q 010559 216 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 285 (507)
Q Consensus 216 C~~C~~~I~~~~~g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~ 285 (507)
|..|+++|.+.. ..+.+.+.. ||..||+|..|++.|..+. |+.. +|++||..||.+.
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~----------~H~~Cf~C~~C~~~l~~~~-~~~~-~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKF----------WHPECFKCSKCGKPLNDGD-FYEK-DGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEE----------EETTTSBETTTTCBTTTSS-EEEE-TTEEEEHHHHHHH
T ss_pred CCCCCCCccCcE-EEEEeCCcE----------EEccccccCCCCCccCCCe-eEeE-CCEEECHHHHhhh
Confidence 889999999764 223466654 3999999999999997554 6655 7899999999763
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=98.26 E-value=6.2e-07 Score=63.03 Aligned_cols=37 Identities=43% Similarity=1.115 Sum_probs=33.6
Q ss_pred cCccCCcccccC-ceeeecCceeccCCcccCCCCCCCC
Q 010559 155 ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPIT 191 (507)
Q Consensus 155 ~C~~C~k~I~~g-~~i~alg~~wHp~CF~Cs~C~~~L~ 191 (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 589999999766 7788999999999999999999985
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.63 E-value=7.5e-06 Score=81.93 Aligned_cols=73 Identities=22% Similarity=0.437 Sum_probs=61.9
Q ss_pred CCCccCCCCC-CCCCCcCccCCcccccCcee-eecCceeccCCcccCCCCCCCCCc-ce-eecCCcccccccccccc
Q 010559 140 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYL-SCMEAFWHPECFRCHSCNLPITDV-EF-SMSGNRPYHKHCYKEQH 212 (507)
Q Consensus 140 ~gsv~~p~~~-~~g~~~C~~C~k~I~~g~~i-~alg~~wHp~CF~Cs~C~~~L~~~-~f-~~~~gk~yCk~CY~~~f 212 (507)
.|++||..++ ..+.-+|..|...|.+.++| .+.+..||..||.|..|+..|... +| .+.++++.|+.+|..--
T Consensus 78 ~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak 154 (383)
T KOG4577|consen 78 EGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAK 154 (383)
T ss_pred CCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHH
Confidence 5899999887 77778999999999888776 478899999999999999999643 44 45889999999998633
No 16
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.44 E-value=1.7e-05 Score=76.15 Aligned_cols=59 Identities=20% Similarity=0.613 Sum_probs=54.1
Q ss_pred CcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCcccccccccccc
Q 010559 154 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 212 (507)
Q Consensus 154 ~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f 212 (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 46889999999889999999999999999999999999988887889999999998754
No 17
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=97.15 E-value=0.00011 Score=71.40 Aligned_cols=63 Identities=19% Similarity=0.408 Sum_probs=55.2
Q ss_pred CCCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCcccccccccccc
Q 010559 150 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 212 (507)
Q Consensus 150 ~~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f 212 (507)
......|..|.+.+++.+.+...+..||..||+|..|+..|+...|....+.+||+.++..+|
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 334578999999999888899999999999999999999999999998899999987765533
No 18
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.00 E-value=0.0001 Score=71.96 Aligned_cols=114 Identities=19% Similarity=0.410 Sum_probs=87.2
Q ss_pred cCCcccccCceeeecCceeccCCcccCCCCCCCC--CcceeecCCcccccccccc--ccCccccccCCccccCcccceee
Q 010559 158 GCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT--DVEFSMSGNRPYHKHCYKE--QHHPKCDVCQNFIPTNSAGLIEY 233 (507)
Q Consensus 158 ~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~--~~~f~~~~gk~yCk~CY~~--~f~pkC~~C~~~I~~~~~g~i~~ 233 (507)
+|+..|.+...+...+..||..|..|..|...+. ...|.. +|..||..+|.. .+..+|..|...|...+ .+
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~--~l-- 75 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD--EL-- 75 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH--HH--
Confidence 4777886556677779999999999999999998 667777 999999999998 88899999998885432 11
Q ss_pred ccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceeccccccc
Q 010559 234 RAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 284 (507)
Q Consensus 234 ~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~ 284 (507)
...| + .-|--||.|..|.+.+..++.+.+.......|...+..
T Consensus 76 -er~f--~-----~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 76 -ERAF--E-----KVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred -HHhh--c-----CCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 1111 0 01557999999999887777776665557778777765
No 19
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=96.86 E-value=0.00085 Score=46.83 Aligned_cols=38 Identities=16% Similarity=0.249 Sum_probs=28.7
Q ss_pred cccccCCccccCcccceeeccccccccccCCCccCCCCCccCCCCCcCC
Q 010559 215 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP 263 (507)
Q Consensus 215 kC~~C~~~I~~~~~g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~ 263 (507)
+|..|+++|.+.. ..+.+.+.. ||..||+|..|++.|.
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~~~----------~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALGKV----------WHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCc-EEEEeCCcc----------ccccCCCCcccCCcCc
Confidence 5899999998752 234455554 4999999999999873
No 20
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=93.74 E-value=0.077 Score=45.80 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=33.4
Q ss_pred CchhhhhhhhhhcchhhHHHHhcCC--CCCCCcchhhHHHHHHHHH
Q 010559 391 GLPRLLTGSILAHEMMHAWLRLKGY--PNLRPDVEEGICQVLAHMW 434 (507)
Q Consensus 391 glP~~L~gsilaHE~~Hawl~~~g~--~~L~~~~eEG~cq~~a~~w 434 (507)
+.+..-...+|+||+.|+|+....- ..++..+.||+++.++..|
T Consensus 19 ~~~~~~~~~~l~HE~~H~~~~~~~~~~~~~~~W~~EG~A~y~~~~~ 64 (128)
T PF13485_consen 19 GSDEDWLDRVLAHELAHQWFGNYFGGDDNAPRWFNEGLAEYVEGRI 64 (128)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCCCccCchHHHHHHHHHHhcCc
Confidence 3444434479999999999877632 4677899999999999653
No 21
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=87.87 E-value=0.45 Score=31.44 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=17.1
Q ss_pred CChhHHHHHHHhhhhhhhccC
Q 010559 40 FDNEEIDRAIALSLVEVDQKG 60 (507)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~ 60 (507)
.|+|+|.+||++||.|.....
T Consensus 1 ~EDe~Lq~Ai~lSl~e~e~~~ 21 (26)
T smart00726 1 DEDEDLQLALELSLQEAEESX 21 (26)
T ss_pred ChHHHHHHHHHHhHHHhhhcc
Confidence 368999999999998776544
No 22
>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=83.79 E-value=0.52 Score=28.47 Aligned_cols=16 Identities=38% Similarity=0.646 Sum_probs=13.6
Q ss_pred CChhHHHHHHHhhhhh
Q 010559 40 FDNEEIDRAIALSLVE 55 (507)
Q Consensus 40 ~~~~~~~~~~~~~~~~ 55 (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 4678999999999865
No 23
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=75.57 E-value=0.33 Score=39.47 Aligned_cols=31 Identities=19% Similarity=0.279 Sum_probs=24.7
Q ss_pred cCCCCeeeeeccccccccccceeeeeeeecC
Q 010559 361 IGAGYRLIDMITEPYRLIRRCEVTAILILYG 391 (507)
Q Consensus 361 ~~~G~rilei~~~p~~~~~~~eV~~Il~l~g 391 (507)
|++||+|++|||++++.....++..+|.-.+
T Consensus 43 l~~GD~Il~INg~~v~~~~~~~~~~~l~~~~ 73 (81)
T PF00595_consen 43 LKVGDRILEINGQSVRGMSHDEVVQLLKSAS 73 (81)
T ss_dssp SSTTEEEEEETTEESTTSBHHHHHHHHHHST
T ss_pred cchhhhhheeCCEeCCCCCHHHHHHHHHCCC
Confidence 8899999999999999887777655554443
No 24
>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=74.00 E-value=3.1 Score=40.24 Aligned_cols=44 Identities=20% Similarity=0.196 Sum_probs=31.9
Q ss_pred hhhhhhhcchhhHHHHh------cCCCCCCCcchhhHHHHHHHHHhhccc
Q 010559 396 LTGSILAHEMMHAWLRL------KGYPNLRPDVEEGICQVLAHMWLESEI 439 (507)
Q Consensus 396 L~gsilaHE~~Hawl~~------~g~~~L~~~~eEG~cq~~a~~wl~~~~ 439 (507)
-.-++||||+-|++-.- .+...|...|-||+.+.++..-.....
T Consensus 64 ~l~~~iaHE~hH~~r~~~~~~~~~~~TLld~~I~EGlAe~f~~~~~g~~~ 113 (195)
T PF10026_consen 64 ELPALIAHEYHHNCRYEQIGWDPEDTTLLDSLIMEGLAEYFAEELYGEEY 113 (195)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCCCCCHHHHHHHhhHHHHHHHHHcCCCC
Confidence 34579999999985322 134466789999999999887765544
No 25
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=67.92 E-value=5.8 Score=31.94 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=24.0
Q ss_pred cccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNS 227 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~ 227 (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 57888877765532223446799999999999999999998876544
No 26
>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=67.43 E-value=3.6 Score=40.42 Aligned_cols=38 Identities=26% Similarity=0.300 Sum_probs=30.6
Q ss_pred hhhhhhhhcchhhHHHHhcCCCCCCCcchhhHHHHHHHH
Q 010559 395 LLTGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHM 433 (507)
Q Consensus 395 ~L~gsilaHE~~Hawl~~~g~~~L~~~~eEG~cq~~a~~ 433 (507)
.-...+|-||+||+|+-- |...-|..+-|||..++-+.
T Consensus 94 ~Ei~Gvl~HE~~H~~Q~~-~~~~~P~~liEGIADyVRl~ 131 (205)
T PF04450_consen 94 DEIIGVLYHEMVHCWQWD-GRGTAPGGLIEGIADYVRLK 131 (205)
T ss_pred HHHHHHHHHHHHHHhhcC-CCCCCChhheecHHHHHHHH
Confidence 333558999999999977 55577889999999988765
No 27
>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=66.94 E-value=2.5 Score=44.25 Aligned_cols=44 Identities=25% Similarity=0.305 Sum_probs=32.4
Q ss_pred hhhhhhhcchhhHHHHhc-CCCCC-CCcchhhHHHHHHHHHhhccc
Q 010559 396 LTGSILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLESEI 439 (507)
Q Consensus 396 L~gsilaHE~~Hawl~~~-g~~~L-~~~~eEG~cq~~a~~wl~~~~ 439 (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 345789999999997521 12222 237999999999999999755
No 28
>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=65.37 E-value=4.2 Score=34.43 Aligned_cols=52 Identities=23% Similarity=0.150 Sum_probs=34.2
Q ss_pred eeeeeecCchhhhhhhhhhcchhhHHHHhcCC------CCCCCcchhhHHHHHHHHHh
Q 010559 384 TAILILYGLPRLLTGSILAHEMMHAWLRLKGY------PNLRPDVEEGICQVLAHMWL 435 (507)
Q Consensus 384 ~~Il~l~glP~~L~gsilaHE~~Hawl~~~g~------~~L~~~~eEG~cq~~a~~wl 435 (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 45566667777777889999999999988642 23455566666666666554
No 29
>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=65.33 E-value=4.8 Score=42.87 Aligned_cols=43 Identities=23% Similarity=0.264 Sum_probs=31.1
Q ss_pred hhhhhhhcchhhH---HHH--hcCC-CCCCCcchhhHHHHHHHHHhhcc
Q 010559 396 LTGSILAHEMMHA---WLR--LKGY-PNLRPDVEEGICQVLAHMWLESE 438 (507)
Q Consensus 396 L~gsilaHE~~Ha---wl~--~~g~-~~L~~~~eEG~cq~~a~~wl~~~ 438 (507)
.+-+|||||++|. +.+ +.|- ...+..++||+-+++.++.-...
T Consensus 138 ~~~sTlAHEfQHmInfy~~~v~~g~~~~~dtWLnE~lS~~aEdl~s~~~ 186 (366)
T PF10460_consen 138 TVYSTLAHEFQHMINFYQRGVLHGKQYAMDTWLNEMLSMSAEDLYSSKI 186 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHhcCC
Confidence 3468999999996 333 2232 35788999999999999764433
No 30
>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=64.59 E-value=4.2 Score=47.86 Aligned_cols=40 Identities=18% Similarity=0.305 Sum_probs=30.4
Q ss_pred hhhhhcchhhHHHH-hcCCCCC-CCcchhhHHHHHHHHHhhc
Q 010559 398 GSILAHEMMHAWLR-LKGYPNL-RPDVEEGICQVLAHMWLES 437 (507)
Q Consensus 398 gsilaHE~~Hawl~-~~g~~~L-~~~~eEG~cq~~a~~wl~~ 437 (507)
..+||||+.|-|.. +-...-- ...+-|||..+|+++|++.
T Consensus 288 ~~viaHElAHqWFGnlVT~~wW~dlWLnEGFAty~e~~~~~~ 329 (831)
T TIGR02412 288 AGVILHEMAHMWFGDLVTMRWWNDLWLNESFAEYMGTLASAE 329 (831)
T ss_pred HHHHHHHHHHHHhCCEeccccccchhHHHHHHHHHHHHHHHh
Confidence 46999999999975 2122211 3488999999999999975
No 31
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.67 E-value=3.4 Score=39.66 Aligned_cols=48 Identities=19% Similarity=0.510 Sum_probs=37.0
Q ss_pred CCcccCCCCCCCCCcc-eeecCCccccccccccc--cCccccccCCccccC
Q 010559 179 ECFRCHSCNLPITDVE-FSMSGNRPYHKHCYKEQ--HHPKCDVCQNFIPTN 226 (507)
Q Consensus 179 ~CF~Cs~C~~~L~~~~-f~~~~gk~yCk~CY~~~--f~pkC~~C~~~I~~~ 226 (507)
.||.|..|=.+..... +..+-|.+||+.|.+.. .+-+|..|++.|+..
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 5688888877666544 55677999999998764 567999999988763
No 32
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.75 E-value=6.3 Score=45.27 Aligned_cols=37 Identities=24% Similarity=0.685 Sum_probs=21.2
Q ss_pred ccCCCCCCCCCcceeecCCccccccccccccCccccccCC
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQN 221 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~ 221 (507)
+|..|+.+|. |....+.+.|.-|-......+|..|+.
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs 430 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGS 430 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcC
Confidence 6778887775 223345566666644434445666654
No 33
>KOG3549 consensus Syntrophins (type gamma) [Extracellular structures]
Probab=57.06 E-value=7 Score=41.19 Aligned_cols=36 Identities=19% Similarity=0.024 Sum_probs=30.9
Q ss_pred cCCCCeeeeeccccccccccceeeeeeeecCchhhh
Q 010559 361 IGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLL 396 (507)
Q Consensus 361 ~~~G~rilei~~~p~~~~~~~eV~~Il~l~glP~~L 396 (507)
+=+||.||.|||+-|+.-+++||-.||..-|=-..|
T Consensus 99 LFvGDAilqvNGi~v~~c~HeevV~iLRNAGdeVtl 134 (505)
T KOG3549|consen 99 LFVGDAILQVNGIYVTACPHEEVVNILRNAGDEVTL 134 (505)
T ss_pred eEeeeeeEEeccEEeecCChHHHHHHHHhcCCEEEE
Confidence 347999999999999999999998888777776666
No 34
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=57.05 E-value=6.6 Score=42.05 Aligned_cols=26 Identities=42% Similarity=0.510 Sum_probs=22.5
Q ss_pred CCCCChhHHHHHHHhhhhhhhccCCc
Q 010559 37 SSGFDNEEIDRAIALSLVEVDQKGKK 62 (507)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (507)
.+..|.|||..||+|||.|..+.+|.
T Consensus 161 ~~k~EeEdiaKAi~lSL~E~~~Q~k~ 186 (462)
T KOG2199|consen 161 SSKQEEEDIAKAIELSLKEQEKQKKL 186 (462)
T ss_pred cccccHHHHHHHHHhhHHHHhhchhh
Confidence 44689999999999999999887766
No 35
>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=56.04 E-value=6.8 Score=36.59 Aligned_cols=47 Identities=26% Similarity=0.445 Sum_probs=24.2
Q ss_pred eeeeeccccccccccceeeeeeeecC-c----hhhhhhhhhhcchhhHHHHhc
Q 010559 366 RLIDMITEPYRLIRRCEVTAILILYG-L----PRLLTGSILAHEMMHAWLRLK 413 (507)
Q Consensus 366 rilei~~~p~~~~~~~eV~~Il~l~g-l----P~~L~gsilaHE~~Hawl~~~ 413 (507)
.++.+...|........+..|++.+. + +..-.|.||+||++| ||.|.
T Consensus 33 ~~~G~A~~P~~~~~~~~~~~vv~~~~~l~~~~~~~~~g~TltHEvGH-~LGL~ 84 (154)
T PF05572_consen 33 SILGYAYFPWSGMSDNGTDGVVINYRYLGGNNSQYNFGKTLTHEVGH-WLGLY 84 (154)
T ss_dssp EESEEE--TTS-GGG-SEEEEGGGSSSSTT--TTS-SSHHHHHHHHH-HTT--
T ss_pred CCCeEEeCCCCCCCCCCCCEEEEcCcccCCCCCccccccchhhhhhh-hhccc
Confidence 34555555655334445555555431 2 233448899999999 77764
No 36
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=54.50 E-value=12 Score=42.90 Aligned_cols=11 Identities=36% Similarity=0.661 Sum_probs=7.8
Q ss_pred CcCccCCcccc
Q 010559 154 RICAGCNTEIG 164 (507)
Q Consensus 154 ~~C~~C~k~I~ 164 (507)
.+|..|+..+.
T Consensus 2 ~~Cp~Cg~~n~ 12 (645)
T PRK14559 2 LICPQCQFENP 12 (645)
T ss_pred CcCCCCCCcCC
Confidence 36888887764
No 37
>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=53.68 E-value=10 Score=42.18 Aligned_cols=37 Identities=16% Similarity=0.478 Sum_probs=20.7
Q ss_pred ccCCCCCCCCCcceeecCCcccccccccc-ccCccccccCC
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHCYKE-QHHPKCDVCQN 221 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~-~f~pkC~~C~~ 221 (507)
+|..|+.+|. |....+.+.|.-|-.. .+...|..|+.
T Consensus 224 ~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 224 CCPNCDVSLT---YHKKEGKLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCceE---EecCCCeEEcCCCcCcCCCCCCCCCCCC
Confidence 5777777764 3334566666666433 23445666654
No 38
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=53.26 E-value=23 Score=35.03 Aligned_cols=55 Identities=27% Similarity=0.164 Sum_probs=36.8
Q ss_pred eeeeeecCchhhhhhhhhhcchhhHHHHhcC------CCCC-CCcchhhHHHHHHHHHhhcc
Q 010559 384 TAILILYGLPRLLTGSILAHEMMHAWLRLKG------YPNL-RPDVEEGICQVLAHMWLESE 438 (507)
Q Consensus 384 ~~Il~l~glP~~L~gsilaHE~~Hawl~~~g------~~~L-~~~~eEG~cq~~a~~wl~~~ 438 (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 3455555445444446999999999997764 1232 23566788999998887644
No 39
>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=52.28 E-value=12 Score=31.81 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=7.2
Q ss_pred ccccccCCcccc
Q 010559 214 PKCDVCQNFIPT 225 (507)
Q Consensus 214 pkC~~C~~~I~~ 225 (507)
..|.+|+++|..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 456666666654
No 40
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=52.21 E-value=11 Score=29.76 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=14.7
Q ss_pred CcCccCCcccccCceeeecCceeccCCcccCCCCCC
Q 010559 154 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLP 189 (507)
Q Consensus 154 ~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~ 189 (507)
++|..|+..|....... -|.|-.|+..
T Consensus 8 ~~CtSCg~~i~~~~~~~---------~F~CPnCG~~ 34 (59)
T PRK14890 8 PKCTSCGIEIAPREKAV---------KFLCPNCGEV 34 (59)
T ss_pred ccccCCCCcccCCCccC---------EeeCCCCCCe
Confidence 46777777775333111 1566666654
No 41
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.45 E-value=5.7 Score=38.16 Aligned_cols=50 Identities=24% Similarity=0.551 Sum_probs=37.6
Q ss_pred CCCCCccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccccHHH
Q 010559 249 RDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI 299 (507)
Q Consensus 249 H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c~~~I 299 (507)
...||.|-.|-.....-.. +.-+=|.+||..|...++..+..|--|.++|
T Consensus 128 ~~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkI 177 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKI 177 (187)
T ss_pred cccccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCCCCCccccc
Confidence 3467888888664422111 3345699999999999999999999999888
No 42
>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=51.28 E-value=8.4 Score=35.27 Aligned_cols=23 Identities=35% Similarity=0.239 Sum_probs=19.2
Q ss_pred chhhhhhhhhhcchhhHHHHhcC
Q 010559 392 LPRLLTGSILAHEMMHAWLRLKG 414 (507)
Q Consensus 392 lP~~L~gsilaHE~~Hawl~~~g 414 (507)
.|...+-.||.|||.|+|+.+.+
T Consensus 55 ~~~~~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 55 NPEEELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred hHHHHHHHHHHHHHHHHHhhhcc
Confidence 46666778999999999998874
No 43
>PF14891 Peptidase_M91: Effector protein
Probab=51.25 E-value=7.7 Score=36.74 Aligned_cols=21 Identities=33% Similarity=0.684 Sum_probs=17.4
Q ss_pred chhhhhhhhhhcchhhHHHHhcCC
Q 010559 392 LPRLLTGSILAHEMMHAWLRLKGY 415 (507)
Q Consensus 392 lP~~L~gsilaHE~~Hawl~~~g~ 415 (507)
.|-.+ +|+|||.|||=.++|-
T Consensus 101 ~~p~v---~L~HEL~HA~~~~~Gt 121 (174)
T PF14891_consen 101 RPPFV---VLYHELIHAYDYMNGT 121 (174)
T ss_pred HHHHH---HHHHHHHHHHHHHCCC
Confidence 34455 9999999999999984
No 44
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=50.35 E-value=6.6 Score=34.97 Aligned_cols=36 Identities=31% Similarity=0.490 Sum_probs=21.5
Q ss_pred hhhhhcchhhHHHHhc-CCCCCCCcchhhHHHHHHHHHhhccc
Q 010559 398 GSILAHEMMHAWLRLK-GYPNLRPDVEEGICQVLAHMWLESEI 439 (507)
Q Consensus 398 gsilaHE~~Hawl~~~-g~~~L~~~~eEG~cq~~a~~wl~~~~ 439 (507)
.-|||||+.|+|..-. |+ .-|. -.-.|+-.|=-.+.
T Consensus 80 ~~TL~HEL~H~WQ~RsYG~--i~PI----TY~F~~~~WE~~~P 116 (141)
T PHA02456 80 RDTLAHELNHAWQFRTYGL--VQPI----TYAFSAKVWEPEVP 116 (141)
T ss_pred HHHHHHHHHHHHhhhccce--eeee----ehhhhHhhcCCCCC
Confidence 4599999999997654 53 2221 12356667733333
No 45
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=49.95 E-value=7.4 Score=32.36 Aligned_cols=16 Identities=38% Similarity=0.677 Sum_probs=12.8
Q ss_pred hhhhcchhhHHHHhcC
Q 010559 399 SILAHEMMHAWLRLKG 414 (507)
Q Consensus 399 silaHE~~Hawl~~~g 414 (507)
.+||||++|++..-.|
T Consensus 63 ~llaHEl~Hv~Qq~~g 78 (79)
T PF13699_consen 63 ALLAHELAHVVQQRRG 78 (79)
T ss_pred hhHhHHHHHHHhhccC
Confidence 5899999999876543
No 46
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=49.35 E-value=12 Score=31.69 Aligned_cols=29 Identities=17% Similarity=0.476 Sum_probs=20.3
Q ss_pred CCcCccCCcccccCceeee-cCceeccCCc
Q 010559 153 YRICAGCNTEIGHGRYLSC-MEAFWHPECF 181 (507)
Q Consensus 153 ~~~C~~C~k~I~~g~~i~a-lg~~wHp~CF 181 (507)
...|..|+++|..+.++.. .|..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 4579999999976555443 3566787775
No 47
>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=48.34 E-value=8 Score=34.95 Aligned_cols=40 Identities=30% Similarity=0.505 Sum_probs=28.6
Q ss_pred hhhhhcchhhHHH--HhcCC---------CCCC--CcchhhHHHHHHHHHhhc
Q 010559 398 GSILAHEMMHAWL--RLKGY---------PNLR--PDVEEGICQVLAHMWLES 437 (507)
Q Consensus 398 gsilaHE~~Hawl--~~~g~---------~~L~--~~~eEG~cq~~a~~wl~~ 437 (507)
-.++|||+-|+|- |+... |+.. ..|-||+-+.++.+-|-+
T Consensus 5 l~l~sHEffH~WnvkrirP~~l~p~dy~~~~~t~~LWv~EG~T~Y~~~l~l~R 57 (122)
T PF05299_consen 5 LGLLSHEFFHSWNVKRIRPAELGPFDYEKPNYTELLWVYEGFTSYYGDLLLVR 57 (122)
T ss_pred hhhhhhhccccccceEeccccccCCCCCCCCCCCCEeeeeCcHHHHHHHHHHH
Confidence 4689999999996 33321 1221 278899999999988653
No 48
>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=46.73 E-value=6.8 Score=37.59 Aligned_cols=16 Identities=56% Similarity=0.706 Sum_probs=13.3
Q ss_pred hhhhhhcchhhHHHHh
Q 010559 397 TGSILAHEMMHAWLRL 412 (507)
Q Consensus 397 ~gsilaHE~~Hawl~~ 412 (507)
+|+|||||+||+.-..
T Consensus 36 lG~ilahel~hafd~~ 51 (206)
T PF01431_consen 36 LGFILAHELMHAFDPE 51 (206)
T ss_dssp HHHHHHHHHHHCTSTT
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4999999999987543
No 49
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=44.05 E-value=4 Score=46.52 Aligned_cols=37 Identities=14% Similarity=0.176 Sum_probs=28.9
Q ss_pred cccccCCCCeeeeeccccccccccceeeeeeeecCch
Q 010559 357 RRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLP 393 (507)
Q Consensus 357 ~~~~~~~G~rilei~~~p~~~~~~~eV~~Il~l~glP 393 (507)
+..+|++||.|+||||++-+...+..-..||...|.-
T Consensus 938 rdGrm~VGDqi~eINGesTkgmtH~rAIelIk~gg~~ 974 (984)
T KOG3209|consen 938 RDGRMRVGDQITEINGESTKGMTHDRAIELIKQGGRR 974 (984)
T ss_pred ccCceeecceEEEecCcccCCCcHHHHHHHHHhCCeE
Confidence 6789999999999999999988876655555554443
No 50
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=44.00 E-value=6.9 Score=38.39 Aligned_cols=59 Identities=10% Similarity=0.120 Sum_probs=37.0
Q ss_pred ccccccCCccccCcccceeeccccccccccCCCccCCCCCccCCCCCcCCCCCceEEccCCceeccccccccc
Q 010559 214 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAI 286 (507)
Q Consensus 214 pkC~~C~~~I~~~~~g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v 286 (507)
+.|..|++.+.+-. -+ .....| ||..||+|..|+..+.. .+|-. .+.++||-.+|.+.+
T Consensus 5 ~n~~~cgk~vYPvE--~v-~cldk~---------whk~cfkce~c~mtlnm-KnyKg-y~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVE--EV-KCLDKV---------WHKQCFKCEVCGMTLNM-KNYKG-YDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHH--HH-hhHHHH---------HHHHhheeeeccCChhh-hhccc-cccCCCcCcccccce
Confidence 45677877665411 11 112233 48899999999987642 22322 278999999997543
No 51
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=43.37 E-value=6.1 Score=30.66 Aligned_cols=26 Identities=12% Similarity=0.129 Sum_probs=19.6
Q ss_pred ccCCCCeeeeeccccccccccceeee
Q 010559 360 RIGAGYRLIDMITEPYRLIRRCEVTA 385 (507)
Q Consensus 360 ~~~~G~rilei~~~p~~~~~~~eV~~ 385 (507)
.|.+||.|+.||++++......++..
T Consensus 30 gl~~GD~I~~Ing~~v~~~~~~~~~~ 55 (70)
T cd00136 30 GLQAGDVILAVNGTDVKNLTLEDVAE 55 (70)
T ss_pred CCCCCCEEEEECCEECCCCCHHHHHH
Confidence 57899999999999987664444433
No 52
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=43.37 E-value=13 Score=34.06 Aligned_cols=22 Identities=18% Similarity=0.548 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCcceeecCCcccccccc
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHCY 208 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~CY 208 (507)
.|..|+.||- .++|.+||.-|-
T Consensus 30 hCp~Cg~PLF-----~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPLF-----RKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcce-----eeCCeEECCCCC
Confidence 4777888773 378999987764
No 53
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.29 E-value=14 Score=23.54 Aligned_cols=9 Identities=44% Similarity=1.165 Sum_probs=4.8
Q ss_pred CccCCcccc
Q 010559 156 CAGCNTEIG 164 (507)
Q Consensus 156 C~~C~k~I~ 164 (507)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555555553
No 54
>PRK12495 hypothetical protein; Provisional
Probab=42.86 E-value=51 Score=32.82 Aligned_cols=27 Identities=30% Similarity=0.580 Sum_probs=18.3
Q ss_pred CcCccCCcccccCceeeecCceeccCCcccCCCCCCCC
Q 010559 154 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT 191 (507)
Q Consensus 154 ~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~ 191 (507)
..|..|+.+|. -++.|-+|..|+....
T Consensus 43 ~hC~~CG~PIp-----------a~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 43 AHCDECGDPIF-----------RHDGQEFCPTCQQPVT 69 (226)
T ss_pred hhcccccCccc-----------CCCCeeECCCCCCccc
Confidence 57888998884 1366677777765443
No 55
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=42.60 E-value=11 Score=36.81 Aligned_cols=30 Identities=20% Similarity=0.499 Sum_probs=17.3
Q ss_pred ccCCCCCCCCCcceeecCCccccccccccc
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 211 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~ 211 (507)
+|+.|+.......-...+|++.|+.||.+.
T Consensus 174 ~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 174 RCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eccccCcccccchhhhcCCceecccccccc
Confidence 344444443333333467888999988653
No 56
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=42.59 E-value=7.1 Score=34.15 Aligned_cols=29 Identities=31% Similarity=0.538 Sum_probs=18.2
Q ss_pred cCccCCcccccCceeeecC-ceeccCCccc
Q 010559 155 ICAGCNTEIGHGRYLSCME-AFWHPECFRC 183 (507)
Q Consensus 155 ~C~~C~k~I~~g~~i~alg-~~wHp~CF~C 183 (507)
.|..|+++|+.|+.+++.. ..-|-.||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 5777777777776666533 4556666643
No 57
>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=42.43 E-value=14 Score=42.08 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=29.0
Q ss_pred hhhhcchhhHHHHhc-CCCCC-CCcchhhHHHHHHHHHhhc
Q 010559 399 SILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLES 437 (507)
Q Consensus 399 silaHE~~Hawl~~~-g~~~L-~~~~eEG~cq~~a~~wl~~ 437 (507)
.+||||++|-|..-- ....= ...+-|||+-+|.+.+++.
T Consensus 281 ~viaHElAHqWfGNlVT~~~W~d~WLnEGfaty~e~~~~~~ 321 (601)
T TIGR02411 281 DVIAHELAHSWSGNLVTNCSWEHFWLNEGWTVYLERRIVGR 321 (601)
T ss_pred hhHHHHHHhhccCceeecCCchHHHHHhhHHHHHHHHHHHH
Confidence 599999999998621 22222 3478999999999987763
No 58
>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]
Probab=42.04 E-value=6.1 Score=44.69 Aligned_cols=32 Identities=13% Similarity=0.258 Sum_probs=25.8
Q ss_pred cccccccCCCCeeeeeccccccccccceeeee
Q 010559 355 VLRRPRIGAGYRLIDMITEPYRLIRRCEVTAI 386 (507)
Q Consensus 355 ~~~~~~~~~G~rilei~~~p~~~~~~~eV~~I 386 (507)
|.-|.-+++|+||+||||+.|-.++++.|-.+
T Consensus 768 IAERGGVRVGHRIIEINgQSVVA~pHekIV~l 799 (829)
T KOG3605|consen 768 IAERGGVRVGHRIIEINGQSVVATPHEKIVQL 799 (829)
T ss_pred chhccCceeeeeEEEECCceEEeccHHHHHHH
Confidence 34566778999999999999998888876443
No 59
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.97 E-value=14 Score=38.28 Aligned_cols=44 Identities=18% Similarity=0.356 Sum_probs=32.2
Q ss_pred cccCCCCCCCCCcceeecCCcccccccccccc--CccccccCCcccc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPT 225 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f--~pkC~~C~~~I~~ 225 (507)
|.|..|....... ....-+..||+.|....| +++|.+|++.+.+
T Consensus 242 f~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccccccccccccc-hhhcCCceeehhhhccccccCCcceeccccccc
Confidence 7777787765542 223457789999987755 5799999999876
No 60
>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=41.81 E-value=17 Score=27.85 Aligned_cols=45 Identities=13% Similarity=0.204 Sum_probs=32.0
Q ss_pred cccCCCCCCCCCcceeecCCcccccccccccc--CccccccCCccccC
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPTN 226 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f--~pkC~~C~~~I~~~ 226 (507)
|.|..|+..+.+. .....|..||+.|..+.+ ...|..|++.+...
T Consensus 2 ~~Cpi~~~~~~~P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKDP-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCCC-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 6788888888764 444668999998876432 45788888877543
No 61
>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=41.75 E-value=13 Score=27.59 Aligned_cols=43 Identities=21% Similarity=0.477 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCcceeecCCcc-ccccccccc--cCccccccCCcccc
Q 010559 182 RCHSCNLPITDVEFSMSGNRP-YHKHCYKEQ--HHPKCDVCQNFIPT 225 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~-yCk~CY~~~--f~pkC~~C~~~I~~ 225 (507)
.|..|........+. .=|.. +|..|+.+. ...+|..|.++|..
T Consensus 4 ~C~iC~~~~~~~~~~-pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 4 ECPICFENPRDVVLL-PCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp B-TTTSSSBSSEEEE-TTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred CCccCCccCCceEEe-CCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 566676666554444 34566 999998775 46899999998863
No 62
>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=40.89 E-value=15 Score=26.09 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=17.7
Q ss_pred cccCCCCCCCCCcceeecCCccccccccc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYK 209 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~ 209 (507)
+.|..|+.. .|...+|..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 457788765 4556789999977743
No 63
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=40.70 E-value=4.8 Score=34.84 Aligned_cols=46 Identities=22% Similarity=0.509 Sum_probs=30.5
Q ss_pred cCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCC
Q 010559 155 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN 200 (507)
Q Consensus 155 ~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~g 200 (507)
.|..|...+..-.+....-..+++.+..|.+|...|+-.+|...+.
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~ 82 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGS 82 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCC
Confidence 3666666665445555555677888888888888887666654444
No 64
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=40.60 E-value=13 Score=28.38 Aligned_cols=30 Identities=23% Similarity=0.679 Sum_probs=21.9
Q ss_pred ccCCCCCcCCCCCceEEccCCceecccccccc
Q 010559 254 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 285 (507)
Q Consensus 254 ~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~ 285 (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 48889987764444 446688 6899999874
No 65
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.70 E-value=29 Score=41.48 Aligned_cols=55 Identities=24% Similarity=0.373 Sum_probs=37.7
Q ss_pred CCCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccCc
Q 010559 150 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNS 227 (507)
Q Consensus 150 ~~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~~ 227 (507)
+.+.+.|..|+... .=|+|..|+.. .....+|..|-...-...|..|+..+....
T Consensus 623 EVg~RfCpsCG~~t---------------~~frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 623 EIGRRKCPSCGKET---------------FYRRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTPYS 677 (1121)
T ss_pred cccCccCCCCCCcC---------------CcccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCccc
Confidence 44556788887763 11788888876 123457888866666678999998777643
No 66
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=38.84 E-value=8.4 Score=45.27 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=20.7
Q ss_pred cccCCCCeeeeecccccccccccee
Q 010559 359 PRIGAGYRLIDMITEPYRLIRRCEV 383 (507)
Q Consensus 359 ~~~~~G~rilei~~~p~~~~~~~eV 383 (507)
.++.|||.|+-||++||+..+++.|
T Consensus 90 GKL~PGDQIl~vN~Epv~daprerv 114 (1298)
T KOG3552|consen 90 GKLQPGDQILAVNGEPVKDAPRERV 114 (1298)
T ss_pred ccccCCCeEEEecCcccccccHHHH
Confidence 4678999999999999997666554
No 67
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.67 E-value=24 Score=40.70 Aligned_cols=11 Identities=18% Similarity=0.132 Sum_probs=8.2
Q ss_pred hhhhcchhhHH
Q 010559 399 SILAHEMMHAW 409 (507)
Q Consensus 399 silaHE~~Haw 409 (507)
+++.|++.-.|
T Consensus 556 ~~~~~d~~~f~ 566 (679)
T PRK05580 556 ALLAQDYDAFA 566 (679)
T ss_pred HHHhCCHHHHH
Confidence 57888887666
No 68
>PF12773 DZR: Double zinc ribbon
Probab=37.14 E-value=32 Score=25.41 Aligned_cols=10 Identities=30% Similarity=0.860 Sum_probs=4.7
Q ss_pred ceeccccccc
Q 010559 275 RKLCLECLDS 284 (507)
Q Consensus 275 r~~C~~C~~~ 284 (507)
..+|..|-..
T Consensus 29 ~~~C~~Cg~~ 38 (50)
T PF12773_consen 29 KKICPNCGAE 38 (50)
T ss_pred CCCCcCCcCC
Confidence 3445555443
No 69
>PF07607 DUF1570: Protein of unknown function (DUF1570); InterPro: IPR011464 This entry represents hypothetical proteins confined to bacteria.
Probab=36.29 E-value=23 Score=32.31 Aligned_cols=32 Identities=31% Similarity=0.408 Sum_probs=23.2
Q ss_pred hhhhcchhhHHHHhcC-CCCC---CCcchhhHHHHH
Q 010559 399 SILAHEMMHAWLRLKG-YPNL---RPDVEEGICQVL 430 (507)
Q Consensus 399 silaHE~~Hawl~~~g-~~~L---~~~~eEG~cq~~ 430 (507)
+||+||..|=-+.--| .+++ |..|-|||...+
T Consensus 3 ~T~~HEa~HQl~~N~Gl~~r~~~~P~Wv~EGlA~yF 38 (128)
T PF07607_consen 3 ATIAHEATHQLAFNTGLHPRLADWPRWVSEGLATYF 38 (128)
T ss_pred hHHHHHHHHHHHHHccccccCCCCchHHHHhHHHHc
Confidence 6999999997655556 3455 348889988754
No 70
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.09 E-value=48 Score=40.68 Aligned_cols=50 Identities=20% Similarity=0.288 Sum_probs=21.8
Q ss_pred ccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccccHHHHHHHhhcCCc
Q 010559 254 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMK 309 (507)
Q Consensus 254 ~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c~~~I~~f~e~l~~~ 309 (507)
.|..|+..++.+. .+...|..|-..++.....=-.+.....+-++.+|..
T Consensus 694 ~CPsCGaev~~de------s~a~~CP~CGtplv~~~~~~i~~~~~~~~A~~~~g~~ 743 (1337)
T PRK14714 694 VCPDCGAEVPPDE------SGRVECPRCDVELTPYQRRTINVKEEYRSALENVGER 743 (1337)
T ss_pred eCccCCCccCCCc------cccccCCCCCCcccccceEEecHHHHHHHHHHHhCcc
Confidence 4556666554221 1234566665544333322223333333444455544
No 71
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=34.54 E-value=23 Score=32.40 Aligned_cols=24 Identities=25% Similarity=0.557 Sum_probs=18.6
Q ss_pred ccCCCCCcCCCCCceEEccCCceeccccccc
Q 010559 254 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS 284 (507)
Q Consensus 254 ~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~ 284 (507)
.|..|+.+| |. .||..||+.|-.+
T Consensus 30 hCp~Cg~PL------F~-KdG~v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPL------FR-KDGEVFCPVCGYR 53 (131)
T ss_pred hCcccCCcc------ee-eCCeEECCCCCce
Confidence 478888877 33 6999999999744
No 72
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=34.46 E-value=6.9 Score=31.17 Aligned_cols=24 Identities=13% Similarity=0.155 Sum_probs=18.3
Q ss_pred cccCCCCeeeeeccccccccccce
Q 010559 359 PRIGAGYRLIDMITEPYRLIRRCE 382 (507)
Q Consensus 359 ~~~~~G~rilei~~~p~~~~~~~e 382 (507)
..|++||.|+.||+.++......+
T Consensus 42 ~gl~~GD~I~~ing~~i~~~~~~~ 65 (82)
T cd00992 42 GGLRVGDRILEVNGVSVEGLTHEE 65 (82)
T ss_pred CCCCCCCEEEEECCEEcCccCHHH
Confidence 468899999999999887433333
No 73
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=34.27 E-value=28 Score=40.01 Aligned_cols=6 Identities=0% Similarity=0.174 Sum_probs=2.2
Q ss_pred HHHHhh
Q 010559 85 EIRAIA 90 (507)
Q Consensus 85 ~~~~~~ 90 (507)
+-+||.
T Consensus 796 gl~rks 801 (1463)
T PHA03308 796 GLKRKS 801 (1463)
T ss_pred hhhccc
Confidence 333333
No 74
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=33.99 E-value=19 Score=30.21 Aligned_cols=31 Identities=26% Similarity=0.553 Sum_probs=21.1
Q ss_pred ccCCCCCcCCCCCceEEccCC---ceeccccccc
Q 010559 254 RCCSCERMEPRDTKYLSLDDG---RKLCLECLDS 284 (507)
Q Consensus 254 ~C~~C~~~l~~g~~y~~l~dG---r~~C~~C~~~ 284 (507)
.|.+|+.++.....+-...|| .-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 488899988654434344444 4699999976
No 75
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=33.24 E-value=24 Score=32.43 Aligned_cols=22 Identities=41% Similarity=0.347 Sum_probs=16.7
Q ss_pred hhhhhhhhhhcchhhHHHHhcC
Q 010559 393 PRLLTGSILAHEMMHAWLRLKG 414 (507)
Q Consensus 393 P~~L~gsilaHE~~Hawl~~~g 414 (507)
|...+-.||.|||.|+++.+.|
T Consensus 55 ~~~~l~~~l~HEm~H~~~~~~g 76 (146)
T smart00731 55 GRDRLRETLLHELCHAALYLFG 76 (146)
T ss_pred cHHHHHhhHHHHHHHHHHHHhC
Confidence 3334457999999999988754
No 76
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=32.30 E-value=21 Score=35.03 Aligned_cols=31 Identities=19% Similarity=0.534 Sum_probs=23.5
Q ss_pred CccCCCCCcCCCCCceEEccCCceecccccccc
Q 010559 253 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 285 (507)
Q Consensus 253 F~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~ 285 (507)
-+|..|+-++. .....+.+|+++|..|+...
T Consensus 173 v~C~kCGE~~~--e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFM--EPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccc--cchhhhcCCceecccccccc
Confidence 58999998874 23344558999999999863
No 77
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=32.30 E-value=29 Score=34.78 Aligned_cols=32 Identities=19% Similarity=0.416 Sum_probs=25.7
Q ss_pred ceeecCCccccccccccccCccccccCCcccc
Q 010559 194 EFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPT 225 (507)
Q Consensus 194 ~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~ 225 (507)
-|...-..+||..|...-+.+.|.-|++.|..
T Consensus 18 f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 18 FFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred eeeeechhhhhhhhcccCCccccccccceeee
Confidence 34445678999999988888899999998764
No 78
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=31.17 E-value=36 Score=24.63 Aligned_cols=41 Identities=17% Similarity=0.335 Sum_probs=27.1
Q ss_pred cCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccc
Q 010559 255 CCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPL 295 (507)
Q Consensus 255 C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c 295 (507)
|..|...+.....++++.=|..+|..|..........|.-|
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C 42 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPIC 42 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCC
Confidence 66677766445567778789999999988754223344433
No 79
>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=31.06 E-value=8.4 Score=31.70 Aligned_cols=19 Identities=21% Similarity=0.490 Sum_probs=12.6
Q ss_pred ccccCccccccCCccccCc
Q 010559 209 KEQHHPKCDVCQNFIPTNS 227 (507)
Q Consensus 209 ~~~f~pkC~~C~~~I~~~~ 227 (507)
.+.-..+|.+|++.|..+.
T Consensus 3 Aks~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 3 AKSGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp -SSSTEBETTTSCBE-TTS
T ss_pred CCCCCccCcccCCcCCCCC
Confidence 3344568999999998764
No 80
>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=30.92 E-value=37 Score=24.87 Aligned_cols=21 Identities=29% Similarity=0.796 Sum_probs=13.6
Q ss_pred cCCCCCcCCCCCceEEccCCceecccc
Q 010559 255 CCSCERMEPRDTKYLSLDDGRKLCLEC 281 (507)
Q Consensus 255 C~~C~~~l~~g~~y~~l~dGr~~C~~C 281 (507)
|..|+.++ +...+|+.||..|
T Consensus 20 Cp~C~~PL------~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPL------MRDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCee------EEecCCCEECCCC
Confidence 44566655 2345788888877
No 81
>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=30.59 E-value=30 Score=24.87 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=16.5
Q ss_pred CccCCcccccC-ceeeecCceeccCC
Q 010559 156 CAGCNTEIGHG-RYLSCMEAFWHPEC 180 (507)
Q Consensus 156 C~~C~k~I~~g-~~i~alg~~wHp~C 180 (507)
|.-|+++|... ..+...++.||.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 67788888533 34567778888433
No 82
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=30.32 E-value=12 Score=42.89 Aligned_cols=46 Identities=20% Similarity=0.482 Sum_probs=28.3
Q ss_pred cccCCCCCCCCCcceeecCCccccccccccccC---ccccccCCccccCc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH---PKCDVCQNFIPTNS 227 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~---pkC~~C~~~I~~~~ 227 (507)
.+|+.|+...-+.- ...-+.+||..|...++. -+|..|+...-.++
T Consensus 644 LkCs~Cn~R~Kd~v-I~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAV-ITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchhhHH-HHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 46677765443321 123456788888776654 47888887776654
No 83
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=30.17 E-value=34 Score=35.04 Aligned_cols=14 Identities=14% Similarity=0.636 Sum_probs=7.7
Q ss_pred CCcccCCCCCCCCC
Q 010559 179 ECFRCHSCNLPITD 192 (507)
Q Consensus 179 ~CF~Cs~C~~~L~~ 192 (507)
..++|..|++.++.
T Consensus 129 ~r~~c~eCgk~ysT 142 (279)
T KOG2462|consen 129 PRYKCPECGKSYST 142 (279)
T ss_pred Cceecccccccccc
Confidence 34566666665543
No 84
>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=30.11 E-value=23 Score=33.31 Aligned_cols=54 Identities=17% Similarity=0.405 Sum_probs=35.1
Q ss_pred CccccccccccccCccccccCCccccCcc--cceeeccccccccccCCCccCCCCCccCCCCCcCCCCC
Q 010559 200 NRPYHKHCYKEQHHPKCDVCQNFIPTNSA--GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDT 266 (507)
Q Consensus 200 gk~yCk~CY~~~f~pkC~~C~~~I~~~~~--g~i~~~~hpfw~~~yCp~h~H~~CF~C~~C~~~l~~g~ 266 (507)
..-||.+|-.+ ....|..|+.+|.+... |++.+..+ |+ -=-.|..|++++|...
T Consensus 27 ~~~fC~kCG~~-tI~~Cp~C~~~IrG~y~v~gv~~~g~~-----------~~-~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 27 REKFCSKCGAK-TITSCPNCSTPIRGDYHVEGVFGLGGH-----------YE-APSYCHNCGKPYPWTE 82 (158)
T ss_pred HHHHHHHhhHH-HHHHCcCCCCCCCCceecCCeeeeCCC-----------CC-CChhHHhCCCCCchHH
Confidence 45789999654 55689999999998632 33333221 12 1123899999988544
No 85
>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=29.87 E-value=21 Score=34.19 Aligned_cols=15 Identities=33% Similarity=0.583 Sum_probs=12.4
Q ss_pred hhhhhcchhhHHHHh
Q 010559 398 GSILAHEMMHAWLRL 412 (507)
Q Consensus 398 gsilaHE~~Hawl~~ 412 (507)
.-||+|||.|||=.+
T Consensus 72 ~~~l~HELIHayD~c 86 (173)
T PF09768_consen 72 EDTLTHELIHAYDHC 86 (173)
T ss_pred HHHHHHHHHHHHHHH
Confidence 569999999998544
No 86
>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]
Probab=29.29 E-value=51 Score=38.09 Aligned_cols=30 Identities=23% Similarity=0.221 Sum_probs=19.1
Q ss_pred ccCCCCeeeeeccccccccccceeeeeeeecCchhhhhhhhhhc
Q 010559 360 RIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAH 403 (507)
Q Consensus 360 ~~~~G~rilei~~~p~~~~~~~eV~~Il~l~glP~~L~gsilaH 403 (507)
+..||||| +||+|+....++.--+-..+.-
T Consensus 342 ~v~pGDrv--------------~VTGi~ra~p~r~np~~r~vkS 371 (804)
T KOG0478|consen 342 KVRPGDRV--------------EVTGILRATPVRVNPRMRMVKS 371 (804)
T ss_pred ccCCCCeE--------------EEEEEEEeEEeccCcchhhHHH
Confidence 45699999 5788887776655433333333
No 87
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=28.78 E-value=19 Score=31.37 Aligned_cols=30 Identities=23% Similarity=0.596 Sum_probs=20.5
Q ss_pred CCCccCCCCCcCCCCCceEEccCCceecccc
Q 010559 251 GTPRCCSCERMEPRDTKYLSLDDGRKLCLEC 281 (507)
Q Consensus 251 ~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C 281 (507)
.=|+|++|--.-- ..+-....+|.++|..|
T Consensus 69 DEFTCssCFLV~H-RSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHH-RSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEec-hhhhccccCCCEecccc
Confidence 3489999976542 23334455799999988
No 88
>PRK00420 hypothetical protein; Validated
Probab=28.75 E-value=38 Score=30.24 Aligned_cols=26 Identities=23% Similarity=0.369 Sum_probs=18.4
Q ss_pred ccCCCCCcCCCCCceEEccCCceecccccccc
Q 010559 254 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 285 (507)
Q Consensus 254 ~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~ 285 (507)
.|..|+.++ +.+.+|..+|+.|-...
T Consensus 25 ~CP~Cg~pL------f~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 25 HCPVCGLPL------FELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCcc------eecCCCceECCCCCCee
Confidence 466677655 44568999999997643
No 89
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.06 E-value=28 Score=36.25 Aligned_cols=43 Identities=16% Similarity=0.514 Sum_probs=28.5
Q ss_pred ccCCCCCCCCCcceeecCCccccccccccccCccccccCCccc
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIP 224 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~ 224 (507)
.|..|+.+|.-..-..--...||-+|...---..|..|...|.
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQ 134 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHH
Confidence 4777777776543333345678888866544557888987764
No 90
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.05 E-value=52 Score=38.37 Aligned_cols=39 Identities=18% Similarity=0.421 Sum_probs=22.8
Q ss_pred cccCCCCCCCCCcceeecCCcccccccccc-ccCccccccCCc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKE-QHHPKCDVCQNF 222 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~-~f~pkC~~C~~~ 222 (507)
++|..|+.+|+ |....+.+.|.-|-.. ..-..|..|+..
T Consensus 445 ~~Cp~Cd~~lt---~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT---LHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE---EecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 46777877765 3334466777666544 233356666644
No 91
>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=26.99 E-value=40 Score=32.11 Aligned_cols=25 Identities=28% Similarity=0.235 Sum_probs=17.9
Q ss_pred eeeeeecCchhhhhhhhhhcchhhH
Q 010559 384 TAILILYGLPRLLTGSILAHEMMHA 408 (507)
Q Consensus 384 ~~Il~l~glP~~L~gsilaHE~~Ha 408 (507)
-+|....+.....++.|||||++|.
T Consensus 118 ~~i~~~~~~~~~~~a~~~AHelGH~ 142 (199)
T PF01421_consen 118 CGIVEDHSRSGLSFAVIIAHELGHN 142 (199)
T ss_dssp EEEEE-SSSSHHHHHHHHHHHHHHH
T ss_pred CcEeeeccchhHHHHHHHHHHHHHh
Confidence 3444555566777899999999994
No 92
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.90 E-value=57 Score=37.54 Aligned_cols=38 Identities=21% Similarity=0.606 Sum_probs=30.3
Q ss_pred ccCCCCCCCCCcceeecCCccccccccccccCccccccCCccccC
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTN 226 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~~ 226 (507)
+|..|+... .++..||..|-...-...|..|+..++.+
T Consensus 3 ~Cp~Cg~~n-------~~~akFC~~CG~~l~~~~Cp~CG~~~~~~ 40 (645)
T PRK14559 3 ICPQCQFEN-------PNNNRFCQKCGTSLTHKPCPQCGTEVPVD 40 (645)
T ss_pred cCCCCCCcC-------CCCCccccccCCCCCCCcCCCCCCCCCcc
Confidence 688887764 46999999998776667899999887763
No 93
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=26.69 E-value=14 Score=35.71 Aligned_cols=52 Identities=15% Similarity=0.261 Sum_probs=40.8
Q ss_pred ccCCCCCccCCCCCcCCCCCceEEccCCceecccccccccCCCCCCccccHHH
Q 010559 247 HERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI 299 (507)
Q Consensus 247 h~H~~CF~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~~v~~t~~C~~c~~~I 299 (507)
+||..|..|..|...+..+...+.. +|..||...|.........|..|.+.|
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 18 YWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred HHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 3588899999999988645666667 899999999987334467888888766
No 94
>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=26.59 E-value=37 Score=40.38 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=27.6
Q ss_pred hhhhhhcchhhHHHHhc-CCCCC-CCcchhhHHHHHHHHHhhc
Q 010559 397 TGSILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLES 437 (507)
Q Consensus 397 ~gsilaHE~~Hawl~~~-g~~~L-~~~~eEG~cq~~a~~wl~~ 437 (507)
..+|||||+.|-|..=. -+..- ...+-|||+-++.++|.+.
T Consensus 283 i~~VIaHElaHqWfGNlVT~~~W~~LWLnEGfAty~e~~~~~~ 325 (863)
T TIGR02414 283 IESVIAHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSAD 325 (863)
T ss_pred HHHHHHHHHHHHHhcceeeecchhhhhhhhhHHHHHHHHHHHH
Confidence 35799999999995210 01111 2357999999988877553
No 95
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=26.47 E-value=41 Score=29.47 Aligned_cols=30 Identities=37% Similarity=0.794 Sum_probs=19.9
Q ss_pred CCCcCccCCcccccCceeeecCceeccCCcccCCCC
Q 010559 152 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCN 187 (507)
Q Consensus 152 g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~ 187 (507)
...+|..|+++|. -..+.+ .|++..|..|.
T Consensus 79 ~yG~C~~Cge~I~-~~RL~a-----~P~a~~Cv~Cq 108 (110)
T TIGR02420 79 EYGYCEECGEEIG-LRRLEA-----RPTATLCIDCK 108 (110)
T ss_pred CCCchhccCCccc-HHHHhh-----CCCccccHHhH
Confidence 3469999999994 333433 46666666664
No 96
>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=26.45 E-value=26 Score=23.98 Aligned_cols=39 Identities=13% Similarity=0.446 Sum_probs=17.1
Q ss_pred cCCCCCCCCCcceeecCCcccccccccccc---CccccccCC
Q 010559 183 CHSCNLPITDVEFSMSGNRPYHKHCYKEQH---HPKCDVCQN 221 (507)
Q Consensus 183 Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f---~pkC~~C~~ 221 (507)
|..|...+........=|..||..|....+ ..+|..|+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 444544442222222234556666654322 335666654
No 97
>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=26.31 E-value=25 Score=33.08 Aligned_cols=51 Identities=20% Similarity=0.408 Sum_probs=33.6
Q ss_pred CcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcceeecCCccccccccccccCccccccCCccc
Q 010559 154 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIP 224 (507)
Q Consensus 154 ~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~ 224 (507)
.-|.+||.... -.|..|+.+|.+.++. +|.++-..+|. --..|+.|+++-+
T Consensus 29 ~fC~kCG~~tI----------------~~Cp~C~~~IrG~y~v--~gv~~~g~~~~--~PsYC~~CGkpyP 79 (158)
T PF10083_consen 29 KFCSKCGAKTI----------------TSCPNCSTPIRGDYHV--EGVFGLGGHYE--APSYCHNCGKPYP 79 (158)
T ss_pred HHHHHhhHHHH----------------HHCcCCCCCCCCceec--CCeeeeCCCCC--CChhHHhCCCCCc
Confidence 45888887653 4788999999876443 44444444443 2336999998765
No 98
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.05 E-value=52 Score=40.39 Aligned_cols=11 Identities=18% Similarity=0.585 Sum_probs=6.3
Q ss_pred cccccCCcccc
Q 010559 215 KCDVCQNFIPT 225 (507)
Q Consensus 215 kC~~C~~~I~~ 225 (507)
.|..|+.++..
T Consensus 711 ~CP~CGtplv~ 721 (1337)
T PRK14714 711 ECPRCDVELTP 721 (1337)
T ss_pred cCCCCCCcccc
Confidence 56666655443
No 99
>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=25.99 E-value=29 Score=34.70 Aligned_cols=21 Identities=33% Similarity=0.536 Sum_probs=15.1
Q ss_pred ecCc--hhhhhhhhhhcchhhHH
Q 010559 389 LYGL--PRLLTGSILAHEMMHAW 409 (507)
Q Consensus 389 l~gl--P~~L~gsilaHE~~Haw 409 (507)
.+|. |...+..|+|||++|.+
T Consensus 157 ~~~~~~~~~~~a~t~AHElGHnl 179 (244)
T cd04270 157 NYGKRVPTKESDLVTAHELGHNF 179 (244)
T ss_pred ccCCccchhHHHHHHHHHHHHhc
Confidence 4554 44456779999999976
No 100
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.88 E-value=40 Score=26.25 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=9.4
Q ss_pred CCcCccCCccccc
Q 010559 153 YRICAGCNTEIGH 165 (507)
Q Consensus 153 ~~~C~~C~k~I~~ 165 (507)
..+|..|++.|..
T Consensus 5 ~~~C~~Cg~~~~~ 17 (54)
T PF14446_consen 5 GCKCPVCGKKFKD 17 (54)
T ss_pred CccChhhCCcccC
Confidence 3578888888853
No 101
>PRK14015 pepN aminopeptidase N; Provisional
Probab=25.26 E-value=46 Score=39.62 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=28.5
Q ss_pred hhhhhhcchhhHHHHhc-CCCCC-CCcchhhHHHHHHHHHhhc
Q 010559 397 TGSILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLES 437 (507)
Q Consensus 397 ~gsilaHE~~Hawl~~~-g~~~L-~~~~eEG~cq~~a~~wl~~ 437 (507)
..++||||+.|-|..=. -+..- ...+-|||.-++.++|.+.
T Consensus 296 i~~vIaHElaHqWFGNlVT~~~W~dLWLnEGFAty~e~~~~~~ 338 (875)
T PRK14015 296 IESVIAHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSAD 338 (875)
T ss_pred HHHHHHHHHHHHHHhCcceecchhhhhhhhHHHHHHHHHHHHH
Confidence 45799999999995210 01111 2357999999998888764
No 102
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=24.56 E-value=58 Score=31.81 Aligned_cols=13 Identities=38% Similarity=0.961 Sum_probs=8.7
Q ss_pred ccccccCCccccC
Q 010559 214 PKCDVCQNFIPTN 226 (507)
Q Consensus 214 pkC~~C~~~I~~~ 226 (507)
++|..|+..|...
T Consensus 69 ~~CPvCR~~Is~~ 81 (193)
T PLN03208 69 PKCPVCKSDVSEA 81 (193)
T ss_pred CcCCCCCCcCChh
Confidence 5677777777654
No 103
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=24.46 E-value=49 Score=34.63 Aligned_cols=18 Identities=17% Similarity=0.294 Sum_probs=8.8
Q ss_pred cCceeccCCcccCCCCCCCCC
Q 010559 172 MEAFWHPECFRCHSCNLPITD 192 (507)
Q Consensus 172 lg~~wHp~CF~Cs~C~~~L~~ 192 (507)
+-..|+.+ |..|+..|..
T Consensus 35 f~~Pf~i~---C~~C~~~I~k 52 (324)
T PF04502_consen 35 FMMPFNIW---CNTCGEYIYK 52 (324)
T ss_pred EcCCccCc---CCCCcccccc
Confidence 34445543 4555566543
No 104
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=24.38 E-value=45 Score=26.26 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=15.6
Q ss_pred ccCCCCeeeeeccccccc
Q 010559 360 RIGAGYRLIDMITEPYRL 377 (507)
Q Consensus 360 ~~~~G~rilei~~~p~~~ 377 (507)
.|++||.|+.|||.++..
T Consensus 29 gl~~GD~I~~ing~~i~~ 46 (79)
T cd00989 29 GLKAGDRILAINGQKIKS 46 (79)
T ss_pred CCCCCCEEEEECCEECCC
Confidence 478999999999998863
No 105
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=24.11 E-value=28 Score=29.73 Aligned_cols=40 Identities=18% Similarity=0.364 Sum_probs=25.7
Q ss_pred CCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCcc
Q 010559 153 YRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVE 194 (507)
Q Consensus 153 ~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~~ 194 (507)
...|..|++++..-+.+...+-.+.. -+|..|+++|.-.+
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~~y 72 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPPRY 72 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCChHH
Confidence 35788888888655656555444443 36777777776544
No 106
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=23.81 E-value=42 Score=39.86 Aligned_cols=43 Identities=21% Similarity=0.391 Sum_probs=32.2
Q ss_pred hhhhhhhhcchhhHHHHhcCCCCCC----CcchhhHHHHHHHHHhhccc
Q 010559 395 LLTGSILAHEMMHAWLRLKGYPNLR----PDVEEGICQVLAHMWLESEI 439 (507)
Q Consensus 395 ~L~gsilaHE~~Hawl~~~g~~~L~----~~~eEG~cq~~a~~wl~~~~ 439 (507)
+-+.+++|||+.|.|-.= ...+. ..+-|||.-+|.+.|.++..
T Consensus 305 ~~~~~viaHElaHqWfGn--lVT~~~W~~lWLnEgfat~~e~~~~~~~~ 351 (859)
T COG0308 305 ENVEEVIAHELAHQWFGN--LVTMKWWDDLWLNEGFATFREVLWSEDLG 351 (859)
T ss_pred HHHHHHHHHHHhhhcccc--eeeccCHHHHHHhhhhHHHHHHHHHHHhc
Confidence 444559999999999531 11222 58999999999999998665
No 107
>PRK00420 hypothetical protein; Validated
Probab=23.71 E-value=47 Score=29.69 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=11.9
Q ss_pred ccCCCCCCCCCcceeecCCccccccc
Q 010559 182 RCHSCNLPITDVEFSMSGNRPYHKHC 207 (507)
Q Consensus 182 ~Cs~C~~~L~~~~f~~~~gk~yCk~C 207 (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 45566665532 24666665554
No 108
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=23.33 E-value=22 Score=34.85 Aligned_cols=44 Identities=16% Similarity=0.358 Sum_probs=0.0
Q ss_pred cccCCCCCCCCCcceeecCCcccccccccccc--CccccccCCcccc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPT 225 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f--~pkC~~C~~~I~~ 225 (507)
|.|..|.+-... .....-|..||..|+...+ ++.|.+|++...+
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhcc
No 109
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=23.00 E-value=43 Score=35.06 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=17.2
Q ss_pred CCCCCcCccCCcccccCceeee
Q 010559 150 FSGYRICAGCNTEIGHGRYLSC 171 (507)
Q Consensus 150 ~~g~~~C~~C~k~I~~g~~i~a 171 (507)
.++.-.|.+|+..|+.|...++
T Consensus 37 ~Pf~i~C~~C~~~I~kG~rFNA 58 (324)
T PF04502_consen 37 MPFNIWCNTCGEYIYKGVRFNA 58 (324)
T ss_pred CCccCcCCCCccccccceeeee
Confidence 3445689999999988877665
No 110
>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=22.86 E-value=40 Score=31.85 Aligned_cols=24 Identities=33% Similarity=0.454 Sum_probs=16.3
Q ss_pred eeeeecCchhhhhhhhhhcchhhHH
Q 010559 385 AILILYGLPRLLTGSILAHEMMHAW 409 (507)
Q Consensus 385 ~Il~l~glP~~L~gsilaHE~~Haw 409 (507)
+|....+. ....+.|+|||++|..
T Consensus 122 ~v~~~~~~-~~~~~~~~aHElGH~l 145 (192)
T cd04267 122 GVVEDTGF-TLLTALTMAHELGHNL 145 (192)
T ss_pred EEEecCCc-ceeehhhhhhhHHhhc
Confidence 44444443 4556889999999954
No 111
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=22.62 E-value=61 Score=21.12 Aligned_cols=9 Identities=33% Similarity=1.043 Sum_probs=4.4
Q ss_pred CccCCcccc
Q 010559 156 CAGCNTEIG 164 (507)
Q Consensus 156 C~~C~k~I~ 164 (507)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 444555553
No 112
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=22.59 E-value=72 Score=33.84 Aligned_cols=16 Identities=31% Similarity=0.420 Sum_probs=13.1
Q ss_pred CccCCCCCccCCCCCc
Q 010559 246 SHERDGTPRCCSCERM 261 (507)
Q Consensus 246 ~h~H~~CF~C~~C~~~ 261 (507)
+||-+.||+|--|++.
T Consensus 73 ~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 73 SHYDPQSFTCPYCGIM 88 (381)
T ss_pred cccccccccCCccccc
Confidence 4677779999999975
No 113
>PHA00527 hypothetical protein
Probab=22.39 E-value=1.9e+02 Score=25.64 Aligned_cols=64 Identities=23% Similarity=0.311 Sum_probs=39.6
Q ss_pred eeeeecccccccccccee-eeeeeecCchhhhhhhhhhcchhhHHH---HhcCCCCCCCcchhhHHHHHHHHH
Q 010559 366 RLIDMITEPYRLIRRCEV-TAILILYGLPRLLTGSILAHEMMHAWL---RLKGYPNLRPDVEEGICQVLAHMW 434 (507)
Q Consensus 366 rilei~~~p~~~~~~~eV-~~Il~l~glP~~L~gsilaHE~~Hawl---~~~g~~~L~~~~eEG~cq~~a~~w 434 (507)
-.|--||.+.-.+...++ -.|=|..|.. +||+||.+|.=. +--|...-|-+.-|-.|-+|.-|.
T Consensus 46 ~mla~~~~S~~~s~~~~~L~~~GVFNGK~-----~T~~HECAH~AF~vC~~VGV~~E~G~ANETYCY~~~R~~ 113 (129)
T PHA00527 46 EMLAGATQSYCNTETGENLYLLGVFNGKA-----ATLVHECAHVAFYVCRDVGVTTEPGDANETYCYMLDRMF 113 (129)
T ss_pred hhhhccccccccccCCCeEEEEEEeccHH-----HHHHHHHHHHHHHHHHhcCcccCCCccchhHHHHHHHHH
Confidence 344455555555554443 3333455653 599999999632 222555555588899999998876
No 114
>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=22.38 E-value=37 Score=31.68 Aligned_cols=18 Identities=28% Similarity=0.379 Sum_probs=11.7
Q ss_pred hhhhhhhhhhcchhhHHH
Q 010559 393 PRLLTGSILAHEMMHAWL 410 (507)
Q Consensus 393 P~~L~gsilaHE~~Hawl 410 (507)
|+.-.--|+|||++|+..
T Consensus 131 ~~~~~lDVvaHEltHGVt 148 (150)
T PF01447_consen 131 PFASSLDVVAHELTHGVT 148 (150)
T ss_dssp -GGG-HHHHHHHHHHHHH
T ss_pred cCccccceeeeccccccc
Confidence 333333599999999854
No 115
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=21.72 E-value=47 Score=26.44 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=15.2
Q ss_pred CccCCCCCcCCCCCceEEccCCceeccccccc
Q 010559 253 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 284 (507)
Q Consensus 253 F~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~ 284 (507)
.+|.+|+..|..+..++ ...|..|-+.
T Consensus 10 ~~CtSCg~~i~p~e~~v-----~F~CPnCGe~ 36 (61)
T COG2888 10 PVCTSCGREIAPGETAV-----KFPCPNCGEV 36 (61)
T ss_pred ceeccCCCEeccCCcee-----EeeCCCCCce
Confidence 45666666665455554 3446666544
No 116
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=21.71 E-value=54 Score=26.43 Aligned_cols=19 Identities=11% Similarity=0.153 Sum_probs=16.2
Q ss_pred cccCCCCeeeeeccccccc
Q 010559 359 PRIGAGYRLIDMITEPYRL 377 (507)
Q Consensus 359 ~~~~~G~rilei~~~p~~~ 377 (507)
..|++||.|+.||+.+++.
T Consensus 26 aGL~~GDiI~~Ing~~v~~ 44 (79)
T cd00991 26 AVLHTGDVIYSINGTPITT 44 (79)
T ss_pred cCCCCCCEEEEECCEEcCC
Confidence 3578999999999999873
No 117
>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=21.65 E-value=36 Score=32.51 Aligned_cols=16 Identities=38% Similarity=0.428 Sum_probs=13.4
Q ss_pred hhhhhcchhhHHHHhc
Q 010559 398 GSILAHEMMHAWLRLK 413 (507)
Q Consensus 398 gsilaHE~~Hawl~~~ 413 (507)
.++||||+.|...+..
T Consensus 90 ~aVlaHElgH~~~~h~ 105 (226)
T PF01435_consen 90 AAVLAHELGHIKHRHI 105 (226)
T ss_dssp HHHHHHHHHHHHTTHC
T ss_pred HHHHHHHHHHHHcCCc
Confidence 6799999999877663
No 118
>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=21.63 E-value=59 Score=30.78 Aligned_cols=24 Identities=25% Similarity=0.220 Sum_probs=15.9
Q ss_pred eeeecCchhhhhhhhhhcchhhHH
Q 010559 386 ILILYGLPRLLTGSILAHEMMHAW 409 (507)
Q Consensus 386 Il~l~glP~~L~gsilaHE~~Haw 409 (507)
|....+-....+..|+|||++|.+
T Consensus 120 v~~~~~~~~~~~a~~~AHElGH~l 143 (194)
T cd04269 120 VVQDHSRNLLLFAVTMAHELGHNL 143 (194)
T ss_pred EEEeCCcchHHHHHHHHHHHHhhc
Confidence 333444334566789999999965
No 119
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.60 E-value=41 Score=22.36 Aligned_cols=13 Identities=38% Similarity=0.802 Sum_probs=7.5
Q ss_pred CccccccCCcccc
Q 010559 213 HPKCDVCQNFIPT 225 (507)
Q Consensus 213 ~pkC~~C~~~I~~ 225 (507)
+.+|..|...|..
T Consensus 1 G~~C~rC~~~~~~ 13 (30)
T PF06827_consen 1 GEKCPRCWNYIED 13 (30)
T ss_dssp TSB-TTT--BBEE
T ss_pred CCcCccCCCcceE
Confidence 4578889888875
No 120
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.57 E-value=42 Score=24.63 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=5.9
Q ss_pred cCccCCcccc
Q 010559 155 ICAGCNTEIG 164 (507)
Q Consensus 155 ~C~~C~k~I~ 164 (507)
+|..|+..+.
T Consensus 5 ~C~~CG~~~~ 14 (46)
T PRK00398 5 KCARCGREVE 14 (46)
T ss_pred ECCCCCCEEE
Confidence 4666666553
No 121
>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=21.52 E-value=57 Score=28.06 Aligned_cols=37 Identities=19% Similarity=0.518 Sum_probs=24.3
Q ss_pred cccCCCCCCCCCcceeecCCccccccccccccCccccccCCcccc
Q 010559 181 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPT 225 (507)
Q Consensus 181 F~Cs~C~~~L~~~~f~~~~gk~yCk~CY~~~f~pkC~~C~~~I~~ 225 (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 356666665532 366788888543 3479999888865
No 122
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=21.33 E-value=53 Score=26.03 Aligned_cols=18 Identities=17% Similarity=0.036 Sum_probs=15.6
Q ss_pred ccCCCCeeeeeccccccc
Q 010559 360 RIGAGYRLIDMITEPYRL 377 (507)
Q Consensus 360 ~~~~G~rilei~~~p~~~ 377 (507)
.|.+||.|+.||+.+++.
T Consensus 29 Gl~~GD~I~~Ing~~v~~ 46 (80)
T cd00990 29 GLVAGDELVAVNGWRVDA 46 (80)
T ss_pred CCCCCCEEEEECCEEhHH
Confidence 478999999999998864
No 123
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.99 E-value=62 Score=35.88 Aligned_cols=43 Identities=19% Similarity=0.345 Sum_probs=30.0
Q ss_pred CCCCCcCccCCcccccCceeeecCceeccCCcccCCCCCCCCCc
Q 010559 150 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDV 193 (507)
Q Consensus 150 ~~g~~~C~~C~k~I~~g~~i~alg~~wHp~CF~Cs~C~~~L~~~ 193 (507)
......|..|-..+. ..-+...+..-...||.|-.|..+|...
T Consensus 23 Ei~~~yCp~CL~~~p-~~e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 23 EIDSYYCPNCLFEVP-SSEARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred ccceeECccccccCC-hhhheeccceeccccccCCCCCCcceeE
Confidence 344566888888773 3334444555566999999999999754
No 124
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=20.95 E-value=61 Score=32.09 Aligned_cols=38 Identities=21% Similarity=0.389 Sum_probs=23.6
Q ss_pred eccccccccccceeeeeeeecCchhhhhhhhhhcchhhHHHHhcCCCC
Q 010559 370 MITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGYPN 417 (507)
Q Consensus 370 i~~~p~~~~~~~eV~~Il~l~glP~~L~gsilaHE~~Hawl~~~g~~~ 417 (507)
.+|.|.+.+.. .-+......+...||+||+.|+- |||+
T Consensus 112 s~G~P~~~I~I------~~~~~~~~~~~~hvi~HEiGH~I----GfRH 149 (211)
T PF12388_consen 112 SNGNPYKFIQI------YGLSNYSVNVIEHVITHEIGHCI----GFRH 149 (211)
T ss_pred CCCCCCceEEE------EecCCCchhHHHHHHHHHhhhhc----cccc
Confidence 45555544442 33344455566789999999975 5555
No 125
>KOG0609 consensus Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]
Probab=20.75 E-value=20 Score=39.84 Aligned_cols=24 Identities=8% Similarity=0.056 Sum_probs=20.1
Q ss_pred cccccCCCCeeeeecccccccccc
Q 010559 357 RRPRIGAGYRLIDMITEPYRLIRR 380 (507)
Q Consensus 357 ~~~~~~~G~rilei~~~p~~~~~~ 380 (507)
|.+.+|.||.|+||||..|.....
T Consensus 161 r~glL~~GD~i~EvNGi~v~~~~~ 184 (542)
T KOG0609|consen 161 RQGLLHVGDEILEVNGISVANKSP 184 (542)
T ss_pred hccceeeccchheecCeecccCCH
Confidence 667899999999999999886533
No 126
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=20.73 E-value=28 Score=27.97 Aligned_cols=19 Identities=26% Similarity=0.302 Sum_probs=16.3
Q ss_pred ccCCCCeeeeecccccccc
Q 010559 360 RIGAGYRLIDMITEPYRLI 378 (507)
Q Consensus 360 ~~~~G~rilei~~~p~~~~ 378 (507)
.|.+||.|+.||+.++...
T Consensus 30 gl~~GD~I~~vng~~i~~~ 48 (85)
T cd00988 30 GIKAGDIIVAIDGEPVDGL 48 (85)
T ss_pred CCCCCCEEEEECCEEcCCC
Confidence 5789999999999988764
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=20.70 E-value=11 Score=26.36 Aligned_cols=10 Identities=40% Similarity=0.976 Sum_probs=4.7
Q ss_pred cCccCCcccc
Q 010559 155 ICAGCNTEIG 164 (507)
Q Consensus 155 ~C~~C~k~I~ 164 (507)
+|..|+++|.
T Consensus 5 ~C~~CGe~I~ 14 (36)
T PF01258_consen 5 ICEDCGEPIP 14 (36)
T ss_dssp B-TTTSSBEE
T ss_pred CccccCChHH
Confidence 3555555553
No 128
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.67 E-value=61 Score=28.68 Aligned_cols=26 Identities=27% Similarity=0.663 Sum_probs=17.3
Q ss_pred CccCCCCCcCCCCCceEEccCCceeccccccc
Q 010559 253 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 284 (507)
Q Consensus 253 F~C~~C~~~l~~g~~y~~l~dGr~~C~~C~~~ 284 (507)
..|.+|++ +||-|...-+.|+.|-..
T Consensus 10 R~Cp~CG~------kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPSCGA------KFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred ccCCCCcc------hhccCCCCCccCCCCCCc
Confidence 46777765 678776655668888554
No 129
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=20.51 E-value=48 Score=26.81 Aligned_cols=17 Identities=12% Similarity=0.284 Sum_probs=14.4
Q ss_pred ccCCCCeeeeecccccc
Q 010559 360 RIGAGYRLIDMITEPYR 376 (507)
Q Consensus 360 ~~~~G~rilei~~~p~~ 376 (507)
-|.+||.|+.||+.++.
T Consensus 31 Gl~~GD~I~~ing~~v~ 47 (82)
T PF13180_consen 31 GLQPGDIILAINGKPVN 47 (82)
T ss_dssp TS-TTEEEEEETTEESS
T ss_pred CCCCCcEEEEECCEEcC
Confidence 47899999999999985
No 130
>KOG3714 consensus Meprin A metalloprotease [Posttranslational modification, protein turnover, chaperones]
Probab=20.31 E-value=37 Score=36.76 Aligned_cols=10 Identities=50% Similarity=0.926 Sum_probs=9.0
Q ss_pred hhhhcchhhH
Q 010559 399 SILAHEMMHA 408 (507)
Q Consensus 399 silaHE~~Ha 408 (507)
.|++||+|||
T Consensus 161 G~i~HEl~Ha 170 (411)
T KOG3714|consen 161 GTIVHELMHA 170 (411)
T ss_pred chhHHHHHHH
Confidence 3899999998
No 131
>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=20.06 E-value=41 Score=30.69 Aligned_cols=13 Identities=31% Similarity=0.345 Sum_probs=10.8
Q ss_pred hhhhhhcchhhHH
Q 010559 397 TGSILAHEMMHAW 409 (507)
Q Consensus 397 ~gsilaHE~~Haw 409 (507)
+-.|++||++||-
T Consensus 94 ~~~~~~HEiGHaL 106 (165)
T cd04268 94 LRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHh
Confidence 3469999999994
Done!