Query 018053
Match_columns 361
No_of_seqs 305 out of 1725
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 05:44:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018053.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018053hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577 Transcription factor L 99.8 2E-21 4.3E-26 182.2 -3.0 125 156-292 30-154 (383)
2 KOG1701 Focal adhesion adaptor 99.8 4.7E-20 1E-24 181.2 -0.0 135 146-292 321-463 (468)
3 KOG1701 Focal adhesion adaptor 99.7 2.8E-19 6.2E-24 175.7 -2.4 122 157-293 272-394 (468)
4 KOG2272 Focal adhesion protein 99.7 1.9E-17 4E-22 153.3 0.7 131 145-290 180-311 (332)
5 KOG1044 Actin-binding LIM Zn-f 99.6 2.8E-16 6.1E-21 159.2 2.7 119 157-290 131-249 (670)
6 KOG1703 Adaptor protein Enigma 99.6 4.5E-16 9.7E-21 160.3 1.4 129 146-288 349-478 (479)
7 KOG2272 Focal adhesion protein 99.5 5E-16 1.1E-20 143.9 -1.3 152 146-316 59-217 (332)
8 KOG1703 Adaptor protein Enigma 99.5 3E-14 6.4E-19 146.8 6.7 144 158-316 302-446 (479)
9 PF00412 LIM: LIM domain; Int 99.3 1.8E-12 3.9E-17 95.2 5.0 57 162-218 1-58 (58)
10 KOG1044 Actin-binding LIM Zn-f 98.9 1.2E-09 2.6E-14 111.7 6.9 159 159-344 16-180 (670)
11 KOG1700 Regulatory protein MLP 98.8 6.1E-10 1.3E-14 102.5 0.7 123 158-294 6-169 (200)
12 PF00412 LIM: LIM domain; Int 98.5 1.4E-07 3E-12 69.0 3.8 57 222-291 1-57 (58)
13 smart00132 LIM Zinc-binding do 98.4 3.1E-07 6.7E-12 61.3 3.1 37 161-197 1-38 (39)
14 KOG4577 Transcription factor L 97.8 3.2E-06 6.9E-11 80.5 -0.4 77 146-222 78-158 (383)
15 KOG1700 Regulatory protein MLP 97.4 4.4E-05 9.6E-10 70.4 0.3 63 156-218 105-167 (200)
16 KOG1702 Nebulin repeat protein 97.3 1.8E-05 3.9E-10 72.3 -2.6 59 160-218 5-63 (264)
17 KOG0490 Transcription factor, 97.2 4.9E-05 1.1E-09 70.3 -1.2 114 164-290 1-118 (235)
18 smart00132 LIM Zinc-binding do 97.1 0.00041 9E-09 45.9 2.6 37 221-268 1-37 (39)
19 smart00726 UIM Ubiquitin-inter 90.6 0.21 4.6E-06 31.1 2.0 21 40-60 1-21 (26)
20 PF02809 UIM: Ubiquitin intera 88.7 0.19 4.1E-06 28.6 0.7 16 40-55 2-17 (18)
21 PF14835 zf-RING_6: zf-RING of 78.9 1.9 4.1E-05 32.8 2.6 46 187-232 8-53 (65)
22 KOG0320 Predicted E3 ubiquitin 73.5 2 4.2E-05 39.1 1.6 47 185-231 130-179 (187)
23 COG4357 Zinc finger domain con 70.1 0.57 1.2E-05 38.3 -2.3 59 161-223 37-95 (105)
24 PF10367 Vps39_2: Vacuolar sor 69.7 26 0.00056 28.0 7.4 31 158-188 77-108 (109)
25 KOG2199 Signal transducing ada 69.2 2.9 6.3E-05 42.4 1.9 26 37-62 161-186 (462)
26 PF10367 Vps39_2: Vacuolar sor 59.7 6.3 0.00014 31.6 1.9 12 220-231 79-90 (109)
27 PF13920 zf-C3HC4_3: Zinc fing 59.5 13 0.00027 26.1 3.2 42 188-230 4-48 (50)
28 smart00504 Ubox Modified RING 58.9 11 0.00023 27.3 2.8 44 187-231 2-47 (63)
29 PF02318 FYVE_2: FYVE-type zin 55.4 18 0.00038 30.4 4.0 16 95-110 20-35 (118)
30 cd00162 RING RING-finger (Real 54.7 11 0.00024 24.5 2.2 40 189-228 2-44 (45)
31 PF14634 zf-RING_5: zinc-RING 53.5 14 0.00031 25.2 2.6 39 189-227 2-44 (44)
32 PRK12495 hypothetical protein; 52.1 27 0.00059 32.8 4.9 28 159-197 42-69 (226)
33 KOG0978 E3 ubiquitin ligase in 51.0 5.5 0.00012 43.3 0.3 46 187-233 644-692 (698)
34 PF14569 zf-UDP: Zinc-binding 50.5 17 0.00036 28.7 2.8 50 157-227 7-59 (80)
35 PF14446 Prok-RING_1: Prokaryo 50.0 11 0.00023 27.8 1.5 14 159-172 5-18 (54)
36 COG2888 Predicted Zn-ribbon RN 49.9 6.9 0.00015 29.3 0.5 29 259-292 10-38 (61)
37 PRK14873 primosome assembly pr 49.8 12 0.00025 40.9 2.5 38 188-228 394-431 (665)
38 PF09943 DUF2175: Uncharacteri 47.4 5.5 0.00012 32.9 -0.3 29 161-189 4-33 (101)
39 PF10083 DUF2321: Uncharacteri 44.6 18 0.00039 32.2 2.4 56 206-274 27-84 (158)
40 KOG1702 Nebulin repeat protein 44.3 3.5 7.6E-05 38.3 -2.1 57 220-290 5-61 (264)
41 PRK14559 putative protein seri 44.1 20 0.00043 39.0 3.2 11 160-170 2-12 (645)
42 PLN03208 E3 ubiquitin-protein 43.1 22 0.00048 32.8 2.9 45 187-232 19-81 (193)
43 KOG1813 Predicted E3 ubiquitin 43.1 13 0.00028 36.5 1.4 46 186-232 241-288 (313)
44 PF04502 DUF572: Family of unk 41.8 19 0.00041 35.7 2.4 21 258-278 77-102 (324)
45 PF14471 DUF4428: Domain of un 41.4 19 0.00041 25.9 1.7 29 188-217 1-30 (51)
46 TIGR00595 priA primosomal prot 41.1 20 0.00043 37.7 2.5 38 188-228 224-262 (505)
47 PF08394 Arc_trans_TRASH: Arch 40.8 17 0.00037 24.6 1.3 29 162-193 1-30 (37)
48 PF12674 Zn_ribbon_2: Putative 39.9 15 0.00034 29.0 1.2 31 260-290 2-35 (81)
49 KOG4739 Uncharacterized protei 39.3 19 0.00041 34.2 1.9 34 198-231 15-49 (233)
50 PF11781 RRN7: RNA polymerase 38.8 18 0.00038 24.2 1.2 25 187-215 9-33 (36)
51 COG2191 Formylmethanofuran deh 38.4 13 0.00027 34.6 0.5 14 203-216 189-202 (206)
52 PRK14890 putative Zn-ribbon RN 37.9 30 0.00065 25.9 2.3 27 159-195 7-34 (59)
53 PHA03378 EBNA-3B; Provisional 37.1 23 0.00049 38.6 2.2 35 16-53 303-340 (991)
54 PF13240 zinc_ribbon_2: zinc-r 36.8 21 0.00046 21.4 1.2 8 162-169 2-9 (23)
55 KOG0320 Predicted E3 ubiquitin 36.4 17 0.00036 33.2 1.0 50 255-305 128-177 (187)
56 COG1645 Uncharacterized Zn-fin 36.1 19 0.0004 31.2 1.2 22 188-214 30-51 (131)
57 PF06689 zf-C4_ClpX: ClpX C4-t 35.4 32 0.00069 23.5 2.0 32 260-291 3-34 (41)
58 PF09026 CENP-B_dimeris: Centr 35.3 13 0.00027 30.6 0.0 7 88-94 37-43 (101)
59 PF06677 Auto_anti-p27: Sjogre 34.8 25 0.00055 24.2 1.5 21 261-287 20-40 (41)
60 PF13923 zf-C3HC4_2: Zinc fing 34.6 28 0.0006 23.0 1.6 37 189-225 1-39 (39)
61 KOG3002 Zn finger protein [Gen 34.5 29 0.00063 34.2 2.4 44 187-231 49-92 (299)
62 PF00645 zf-PARP: Poly(ADP-rib 34.4 15 0.00033 28.5 0.3 17 157-173 5-21 (82)
63 PF13834 DUF4193: Domain of un 34.3 12 0.00026 30.8 -0.3 29 258-287 70-98 (99)
64 COG1198 PriA Primosomal protei 33.9 40 0.00086 37.3 3.5 39 187-228 445-484 (730)
65 COG5148 RPN10 26S proteasome r 33.7 16 0.00034 33.8 0.3 30 42-71 207-236 (243)
66 KOG3411 40S ribosomal protein 32.1 40 0.00088 29.2 2.6 55 2-57 73-142 (143)
67 COG5152 Uncharacterized conser 31.7 19 0.00041 33.5 0.5 46 186-232 196-243 (259)
68 PF10235 Cript: Microtubule-as 31.3 32 0.00069 27.9 1.7 37 187-231 45-81 (90)
69 PF01258 zf-dskA_traR: Prokary 29.9 11 0.00023 24.9 -1.0 27 189-215 6-32 (36)
70 COG1645 Uncharacterized Zn-fin 29.3 28 0.00061 30.2 1.2 26 260-292 30-55 (131)
71 PF11571 Med27: Mediator compl 29.1 24 0.00053 28.2 0.7 17 213-229 48-64 (90)
72 PRK00420 hypothetical protein; 29.0 33 0.00071 28.9 1.5 30 259-294 24-53 (112)
73 PLN02195 cellulose synthase A 28.6 47 0.001 37.7 3.0 52 158-230 5-59 (977)
74 KOG1818 Membrane trafficking a 28.6 38 0.00082 36.6 2.2 23 37-59 250-272 (634)
75 PF12156 ATPase-cat_bd: Putati 28.4 90 0.0019 24.9 3.9 16 261-276 3-18 (88)
76 PRK04023 DNA polymerase II lar 27.8 58 0.0013 37.2 3.5 54 156-232 623-676 (1121)
77 KOG0957 PHD finger protein [Ge 27.8 70 0.0015 33.8 3.8 69 158-227 118-190 (707)
78 PRK05580 primosome assembly pr 27.5 44 0.00096 36.5 2.6 38 188-228 392-430 (679)
79 COG2191 Formylmethanofuran deh 26.8 26 0.00057 32.5 0.6 30 259-290 173-202 (206)
80 PF09538 FYDLN_acid: Protein o 26.7 38 0.00083 28.3 1.5 27 259-291 10-36 (108)
81 TIGR03826 YvyF flagellar opero 26.4 60 0.0013 28.3 2.7 63 260-337 5-70 (137)
82 PTZ00415 transmission-blocking 26.2 16 0.00035 43.6 -1.0 25 46-70 133-159 (2849)
83 KOG1832 HIV-1 Vpr-binding prot 25.9 27 0.00059 39.3 0.6 23 64-86 1403-1425(1516)
84 PF07191 zinc-ribbons_6: zinc- 25.5 19 0.00042 27.8 -0.5 10 260-269 52-61 (70)
85 PLN02638 cellulose synthase A 25.5 62 0.0014 37.2 3.3 32 157-196 15-46 (1079)
86 PF06750 DiS_P_DiS: Bacterial 25.5 30 0.00066 27.9 0.7 39 159-199 33-71 (92)
87 TIGR00570 cdk7 CDK-activating 24.5 72 0.0015 31.6 3.2 28 205-232 26-56 (309)
88 cd02335 ZZ_ADA2 Zinc finger, Z 24.4 66 0.0014 22.6 2.2 8 283-290 26-33 (49)
89 PF11239 DUF3040: Protein of u 24.1 85 0.0018 24.5 3.0 29 96-134 3-31 (82)
90 PLN02915 cellulose synthase A 23.9 72 0.0016 36.6 3.4 31 158-196 14-44 (1044)
91 cd02249 ZZ Zinc finger, ZZ typ 23.6 69 0.0015 22.1 2.1 8 283-290 25-32 (46)
92 PHA03377 EBNA-3C; Provisional 23.0 37 0.0008 37.2 0.9 82 16-100 309-398 (1000)
93 PF06827 zf-FPG_IleRS: Zinc fi 22.5 44 0.00096 20.9 0.9 13 219-231 1-13 (30)
94 PF05009 EBV-NA3: Epstein-Barr 22.2 29 0.00062 33.2 -0.1 32 17-51 161-195 (255)
95 smart00291 ZnF_ZZ Zinc-binding 22.1 81 0.0018 21.6 2.2 30 260-290 6-36 (44)
96 PF04502 DUF572: Family of unk 22.0 48 0.001 32.9 1.4 20 158-177 39-58 (324)
97 PF10122 Mu-like_Com: Mu-like 21.9 25 0.00053 25.5 -0.5 28 259-289 5-32 (51)
98 PLN02436 cellulose synthase A 21.7 74 0.0016 36.6 2.9 31 158-196 35-65 (1094)
99 PRK14714 DNA polymerase II lar 21.4 94 0.002 36.4 3.7 10 282-291 710-719 (1337)
100 PLN02189 cellulose synthase 20.8 79 0.0017 36.2 2.9 31 158-196 33-63 (1040)
No 1
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.80 E-value=2e-21 Score=182.20 Aligned_cols=125 Identities=24% Similarity=0.503 Sum_probs=112.3
Q ss_pred CCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccCCcc
Q 018053 156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG 235 (361)
Q Consensus 156 ~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~~ 235 (361)
....++|++|++.|.+.-++.++++.||..|++|+.|..+|.+.. +.++|.+||+.+|.++|++||..|...|++.
T Consensus 30 ~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drC-FsR~~s~yCkedFfKrfGTKCsaC~~GIpPt--- 105 (383)
T KOG4577|consen 30 NVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRC-FSREGSVYCKEDFFKRFGTKCSACQEGIPPT--- 105 (383)
T ss_pred ccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHH-hhcCCceeehHHHHHHhCCcchhhcCCCChH---
Confidence 336789999999997667778999999999999999999998854 4578999999999999999999999999985
Q ss_pred ceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhhc
Q 018053 236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAI 292 (361)
Q Consensus 236 ~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v 292 (361)
.++.++..| +||..||.|..|+|.|..|+.|+.++|++++|+..|+++-
T Consensus 106 qVVRkAqd~--------VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak 154 (383)
T KOG4577|consen 106 QVVRKAQDF--------VYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAK 154 (383)
T ss_pred HHHHHhhcc--------eeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHH
Confidence 466777776 7899999999999999999999999999999999998764
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.76 E-value=4.7e-20 Score=181.15 Aligned_cols=135 Identities=23% Similarity=0.477 Sum_probs=116.6
Q ss_pred CCCccCCCCCCCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceee-cCCcccchhhhhhhcCCcccc
Q 018053 146 SGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSM-SGNRPYHKHCYKEQHHPKCDV 224 (361)
Q Consensus 146 ~gs~~~p~~~~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~-~dg~~YC~~CY~~~f~pkC~~ 224 (361)
.+++||.--+.....+|..|++.|. ..+|.++|+.||+.||+|.+|++.|.+..|.+ .++.+||..||+++|+|+|.+
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 DGKPYCEGCYQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSV 399 (468)
T ss_pred CCcccchHHHHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhh
Confidence 4555666444556678999999994 78899999999999999999999999998887 688999999999999999999
Q ss_pred CCCccccCC----ccceEeeccccccccCCCCcccCCCCccCCCCCcCC---CCCceEEccCCCccChhhhhhhc
Q 018053 225 CQNFIPTNS----AGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP---RDTKYLSLDDGRKLCLECLDSAI 292 (361)
Q Consensus 225 C~~~I~~~~----~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~---~g~~f~~~~dg~~~C~~C~~~~v 292 (361)
|+++|...+ ...|+.+++.| |.+|++|..|+.+|+ .|...+.+ ||+++|+.|+...+
T Consensus 400 C~~PI~P~~G~~etvRvvamdr~f----------Hv~CY~CEDCg~~LS~e~e~qgCyPl-d~HllCk~Ch~~Rl 463 (468)
T KOG1701|consen 400 CGNPILPRDGKDETVRVVAMDRDF----------HVNCYKCEDCGLLLSSEEEGQGCYPL-DGHLLCKTCHLKRL 463 (468)
T ss_pred ccCCccCCCCCcceEEEEEccccc----------cccceehhhcCccccccCCCCcceec-cCceeechhhhhhh
Confidence 999999863 34689999998 999999999999886 36677876 69999999987654
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.72 E-value=2.8e-19 Score=175.68 Aligned_cols=122 Identities=20% Similarity=0.536 Sum_probs=109.6
Q ss_pred CCCCcCccCCCccccC-ceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccCCcc
Q 018053 157 SGYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG 235 (361)
Q Consensus 157 ~~~~~C~~C~~~I~~g-e~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~~ 235 (361)
....+|.+|++.|+.. ..+.||++.||..||+|..|++.|.+..||..++++||+.||... ..||.+|++.|+..
T Consensus 272 ~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~--- 347 (468)
T KOG1701|consen 272 DYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDR--- 347 (468)
T ss_pred hhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHH---
Confidence 3456999999999643 567999999999999999999999999999999999999999875 56999999999964
Q ss_pred ceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhhcc
Q 018053 236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM 293 (361)
Q Consensus 236 ~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~ 293 (361)
++.+.++.| |.+||+|.+|.|.| .|..|.+..++.+||..||...+.
T Consensus 348 iLrA~Gkay----------Hp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfA 394 (468)
T KOG1701|consen 348 ILRALGKAY----------HPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFA 394 (468)
T ss_pred HHHhccccc----------CCCceEEEEecccc-CCccccccCCCceeeehhhhhhcC
Confidence 678888876 99999999999999 899999999999999999988653
No 4
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.65 E-value=1.9e-17 Score=153.29 Aligned_cols=131 Identities=21% Similarity=0.508 Sum_probs=117.4
Q ss_pred CCCCccCCCCC-CCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccc
Q 018053 145 ESGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD 223 (361)
Q Consensus 145 ~~gs~~~p~~~-~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~ 223 (361)
-.|.+|++.-. ..+.++|+.|.++| ..++|.++|+.||.++|+|+.|.+|+-+...+.+.|.+||+.+|.++|+..|.
T Consensus 180 vk~eLyClrChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF 258 (332)
T KOG2272|consen 180 VKGELYCLRCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCF 258 (332)
T ss_pred hccceeccccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhhe
Confidence 35778888655 67899999999999 58889999999999999999999999999999999999999999999999999
Q ss_pred cCCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhh
Q 018053 224 VCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 290 (361)
Q Consensus 224 ~C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~ 290 (361)
.|+..|.|. ++.+.++. | -..||+|+.|.+.|..-.+|+.+ |-.++|..||+.
T Consensus 259 ~C~~~i~G~---vv~al~Ka-w---------Cv~cf~Cs~Cdkkl~~K~Kf~E~-DmkP~CKkCy~r 311 (332)
T KOG2272|consen 259 ICNRVIGGD---VVSALNKA-W---------CVECFSCSTCDKKLTQKNKFYEF-DMKPVCKKCYDR 311 (332)
T ss_pred ecCCccCcc---HHHHhhhh-h---------ccccccccccccccccccceeee-ccchHHHHHHhh
Confidence 999999974 67777776 4 57899999999999888899986 689999999986
No 5
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.60 E-value=2.8e-16 Score=159.25 Aligned_cols=119 Identities=25% Similarity=0.624 Sum_probs=107.3
Q ss_pred CCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccCCccc
Q 018053 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGL 236 (361)
Q Consensus 157 ~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~~~ 236 (361)
.+...|++|++.|..|..+.++++.||..||+|..|...|.+ +|..++|.|||..||.+.|+.+|..|.++|.+. +
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 467889999999999999999999999999999999999876 788899999999999999999999999999984 6
Q ss_pred eEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhh
Q 018053 237 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 290 (361)
Q Consensus 237 i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~ 290 (361)
+.+.++ |||..|-+|..|+.++..|..-++ ....+|...|-..
T Consensus 207 Lqag~k----------h~HPtCARCsRCgqmF~eGEEMYl-QGs~iWHP~C~qa 249 (670)
T KOG1044|consen 207 LQAGDK----------HFHPTCARCSRCGQMFGEGEEMYL-QGSEIWHPDCKQA 249 (670)
T ss_pred hhccCc----------ccCcchhhhhhhccccccchheee-ccccccCCccccc
Confidence 666665 669999999999999999998875 5688999999754
No 6
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.57 E-value=4.5e-16 Score=160.27 Aligned_cols=129 Identities=26% Similarity=0.570 Sum_probs=110.8
Q ss_pred CCCccCCCCC-CCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCcccc
Q 018053 146 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV 224 (361)
Q Consensus 146 ~gs~~~p~~~-~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~ 224 (361)
.|.+++...+ ....+.|.+|+.+| .++.|.++++.||+.||.|..|+++|....|+.+++.+||..||+++++++|..
T Consensus 349 ~g~~~c~~~~~~~~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~ 427 (479)
T KOG1703|consen 349 DGKILCHECFHAPFRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDY 427 (479)
T ss_pred CCCccHHHHHHHhhCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchh
Confidence 4556655444 56789999999999 589999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhh
Q 018053 225 CQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECL 288 (361)
Q Consensus 225 C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~ 288 (361)
|..+|... ...|...+.+| |..||+|..|.+.+ .+..|+. ..++++|..|+
T Consensus 428 ~~~p~~~~-~~~ie~~~~~~----------h~~~F~c~~c~~~l-~~~~~~~-~~~~p~c~~~~ 478 (479)
T KOG1703|consen 428 CKKPVEFG-SRQIEADGSPF----------HGDCFRCANCMKKL-TKKTFFE-TLDKPLCQKHF 478 (479)
T ss_pred ccchhHhh-hhHhhccCccc----------cccceehhhhhccc-cCCceee-cCCccccccCC
Confidence 99988743 13678888885 99999999999988 5555654 56899999885
No 7
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.54 E-value=5e-16 Score=143.89 Aligned_cols=152 Identities=25% Similarity=0.565 Sum_probs=127.2
Q ss_pred CCCccCCCCC-CCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhc-----C
Q 018053 146 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH-----H 219 (361)
Q Consensus 146 ~gs~~~p~~~-~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f-----~ 219 (361)
.|..|+..++ ...+|.|+.|++-| .|++|.+++.+|||.||+|..|++.|.+..|+...|+.+|..|..+.- .
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 3667888888 88899999999998 599999999999999999999999999999999999999999976521 2
Q ss_pred CccccCCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhhccCCCCCc
Q 018053 220 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQ 299 (361)
Q Consensus 220 pkC~~C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~d~~~cq 299 (361)
-.|..|+..|... .+.|++.|| |.-.|+|..|++.|....+-+ .|.+||+.|+++ |..++|.
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 2699999999863 789999997 777799999999997666644 478999999997 7888998
Q ss_pred hhhHHHHH-HHHhcCccc
Q 018053 300 PLYLEIQE-FYEGLNMKV 316 (361)
Q Consensus 300 ~~~~~i~~-f~egl~mk~ 316 (361)
.+.+.|.+ ...+||-..
T Consensus 200 aC~rpIeervi~amgKhW 217 (332)
T KOG2272|consen 200 ACRRPIEERVIFAMGKHW 217 (332)
T ss_pred cccCchHHHHHHHhcccc
Confidence 88887753 234566533
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.49 E-value=3e-14 Score=146.82 Aligned_cols=144 Identities=18% Similarity=0.391 Sum_probs=115.6
Q ss_pred CCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccCCccce
Q 018053 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI 237 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~~~i 237 (361)
..+.|..|++.|.....+.++++.||+.+|.|..|...|....+...+|.+||..||...+.|+|.+|+++|.++ .|
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~---~v 378 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEE---GV 378 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHh---Hh
Confidence 448999999999533999999999999999999999999988888899999999999999999999999999986 46
Q ss_pred EeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhhccC-CCCCchhhHHHHHHHHhcCccc
Q 018053 238 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMD-THECQPLYLEIQEFYEGLNMKV 316 (361)
Q Consensus 238 ~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~d-~~~cq~~~~~i~~f~egl~mk~ 316 (361)
.+.++. | |..||.|..|++.+ .+..|+. .+|.+||..||..+++. +..|..+......+.++++-+.
T Consensus 379 ~a~~~~-w---------H~~cf~C~~C~~~~-~~~~~~~-~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~ 446 (479)
T KOG1703|consen 379 CALGRL-W---------HPECFVCADCGKPL-KNSSFFE-SDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPF 446 (479)
T ss_pred hhccCe-e---------chhceeeecccCCC-CCCcccc-cCCccchhhhHhhhccccchhccchhHhhhhHhhccCccc
Confidence 666553 4 99999999998888 4455553 68999999999998762 2334343333334555555433
No 9
>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=99.32 E-value=1.8e-12 Score=95.25 Aligned_cols=57 Identities=39% Similarity=0.996 Sum_probs=52.5
Q ss_pred CccCCCccccCceE-EeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhc
Q 018053 162 CAGCNTEIGHGRYL-SCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 218 (361)
Q Consensus 162 C~~C~~~I~~ge~l-~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f 218 (361)
|++|+++|.....+ .++|+.||+.||+|..|+++|....|+..+|++||..||.++|
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 88999999876665 6999999999999999999999988999999999999999876
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=98.94 E-value=1.2e-09 Score=111.69 Aligned_cols=159 Identities=15% Similarity=0.341 Sum_probs=122.4
Q ss_pred CCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccCCccceE
Q 018053 159 YRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIE 238 (361)
Q Consensus 159 ~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~~~~~i~ 238 (361)
.-.|..|.+.- .|+++.+.++.||..||.|..|+..|....|+..++. +++++ ..|..+|.+. ++.
T Consensus 16 ~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~ge---vvs 81 (670)
T KOG1044|consen 16 GIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGE---VVS 81 (670)
T ss_pred ceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccce---eEe
Confidence 45799999988 5999999999999999999999999999888886553 44455 6788888874 688
Q ss_pred eeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhhcc------CCCCCchhhHHHHHHHHhc
Q 018053 239 YRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM------DTHECQPLYLEIQEFYEGL 312 (361)
Q Consensus 239 ~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~------d~~~cq~~~~~i~~f~egl 312 (361)
..++.| |..||.|+.|..+++.|++-. +.....+|..|-...-. +...|..+-.+|.. .+.
T Consensus 82 a~gkty----------h~~cf~cs~ck~pf~~g~~vt-~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~--gq~ 148 (670)
T KOG1044|consen 82 TLGKTY----------HPKCFSCSTCKSPFKSGDKVT-FSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKN--GQA 148 (670)
T ss_pred ccccee----------ccccceecccCCCCCCCCeee-ecchhhhhhhhcCcccCCcccccCCccccchhhhhhc--cce
Confidence 889887 999999999999999999855 45566889999754322 34567777666532 112
Q ss_pred CccccccccccccchHHHHHHhcCCCCCCCCC
Q 018053 313 NMKVEQQVPLLLVERQALNEAMEGEKNGHHHL 344 (361)
Q Consensus 313 ~mk~~~~~P~llv~~~aln~a~~~e~~~~~~~ 344 (361)
-+.+..++-++.+...+..+++-||-+..+.+
T Consensus 149 llald~qwhv~cfkc~~c~~vL~gey~skdg~ 180 (670)
T KOG1044|consen 149 LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGV 180 (670)
T ss_pred eeeeccceeeeeeehhhhcccccceeeccCCC
Confidence 23557788888888888888888886655443
No 11
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.85 E-value=6.1e-10 Score=102.54 Aligned_cols=123 Identities=21% Similarity=0.409 Sum_probs=92.9
Q ss_pred CCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCc----------------
Q 018053 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK---------------- 221 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pk---------------- 221 (361)
....|..|++.|+..+.+...|..||+.||+|..|...|....+..+++.+||+.||-..++|+
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 4568999999999888888999999999999999999999988999999999999887766654
Q ss_pred -------------------------cccCCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEE
Q 018053 222 -------------------------CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLS 276 (361)
Q Consensus 222 -------------------------C~~C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~ 276 (361)
|..|.+++.... .+...+.. ||..||+|+.|+..|.. ..|..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E--k~~~~~~~----------~hk~cfrc~~~~~~ls~-~~~~~ 152 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE--KVTGNGLE----------FHKSCFRCTHCGKKLSP-KNYAA 152 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehH--HHhhhhhh----------hhhhheeecccccccCC-cchhh
Confidence 444444443321 12222333 49999999999999844 45554
Q ss_pred ccCCCccChhhhhhhccC
Q 018053 277 LDDGRKLCLECLDSAIMD 294 (361)
Q Consensus 277 ~~dg~~~C~~C~~~~v~d 294 (361)
..|.++|...+...++.
T Consensus 153 -~~g~l~~~~~~~~~~~~ 169 (200)
T KOG1700|consen 153 -LEGVLYCKHHFAQLFKG 169 (200)
T ss_pred -cCCccccchhhheeecC
Confidence 45888888777665443
No 12
>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=98.47 E-value=1.4e-07 Score=69.02 Aligned_cols=57 Identities=19% Similarity=0.508 Sum_probs=44.8
Q ss_pred cccCCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhh
Q 018053 222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 291 (361)
Q Consensus 222 C~~C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~ 291 (361)
|..|+++|.+.. ..+.+.++. | |..||+|..|++.|..+. |+. .+|++||..||...
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~-~---------H~~Cf~C~~C~~~l~~~~-~~~-~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKF-W---------HPECFKCSKCGKPLNDGD-FYE-KDGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEE-E---------ETTTSBETTTTCBTTTSS-EEE-ETTEEEEHHHHHHH
T ss_pred CCCCCCCccCcE-EEEEeCCcE-E---------EccccccCCCCCccCCCe-eEe-ECCEEECHHHHhhh
Confidence 789999999763 223466665 4 999999999999996555 665 57899999999764
No 13
>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=98.36 E-value=3.1e-07 Score=61.31 Aligned_cols=37 Identities=43% Similarity=1.115 Sum_probs=33.5
Q ss_pred cCccCCCccccC-ceEEeCCceecCCCcccCCCCCCCC
Q 018053 161 ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPIT 197 (361)
Q Consensus 161 ~C~~C~~~I~~g-e~l~a~gk~wH~~CF~C~~C~~~L~ 197 (361)
+|.+|+++|... ..+.++++.||+.||+|..|+.+|.
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 7788999999999999999999885
No 14
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.83 E-value=3.2e-06 Score=80.51 Aligned_cols=77 Identities=22% Similarity=0.470 Sum_probs=64.7
Q ss_pred CCCccCCCCC-CCCCCcCccCCCccccCceE-EeCCceecCCCcccCCCCCCCCCc-cee-ecCCcccchhhhhhhcCCc
Q 018053 146 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYL-SCMEAFWHPECFRCHSCNLPITDV-EFS-MSGNRPYHKHCYKEQHHPK 221 (361)
Q Consensus 146 ~gs~~~p~~~-~~~~~~C~~C~~~I~~ge~l-~a~gk~wH~~CF~C~~C~~~L~~~-~f~-~~dg~~YC~~CY~~~f~pk 221 (361)
.|++||..++ ..+.-.|..|...|.+..+| .+.+..||..||.|..|++.|..+ +|+ +.++++.|+.+|..--..-
T Consensus 78 ~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~ 157 (383)
T KOG4577|consen 78 EGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKH 157 (383)
T ss_pred CCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcc
Confidence 6899999888 66778999999999777776 589999999999999999999544 565 5789999999998764444
Q ss_pred c
Q 018053 222 C 222 (361)
Q Consensus 222 C 222 (361)
|
T Consensus 158 ~ 158 (383)
T KOG4577|consen 158 C 158 (383)
T ss_pred c
Confidence 5
No 15
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=97.37 E-value=4.4e-05 Score=70.43 Aligned_cols=63 Identities=19% Similarity=0.408 Sum_probs=56.3
Q ss_pred CCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhc
Q 018053 156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 218 (361)
Q Consensus 156 ~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f 218 (361)
......|..|.+.+++.+.+...+..||..||+|+.|+..|+...+....+.+||..++..+|
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 445678999999999889999999999999999999999999999999999999988776644
No 16
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.34 E-value=1.8e-05 Score=72.29 Aligned_cols=59 Identities=20% Similarity=0.613 Sum_probs=53.4
Q ss_pred CcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhc
Q 018053 160 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 218 (361)
Q Consensus 160 ~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f 218 (361)
..|..|++.+++-+.+.++++.||..||+|..|+.+|....+-..+.++||..+|.+..
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 46888999999889999999999999999999999998877777789999999998764
No 17
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.22 E-value=4.9e-05 Score=70.35 Aligned_cols=114 Identities=19% Similarity=0.369 Sum_probs=88.0
Q ss_pred cCCCccccCceEEeCCceecCCCcccCCCCCCCC--CcceeecCCcccchhhhhh--hcCCccccCCCccccCCccceEe
Q 018053 164 GCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT--DVEFSMSGNRPYHKHCYKE--QHHPKCDVCQNFIPTNSAGLIEY 239 (361)
Q Consensus 164 ~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~--~~~f~~~dg~~YC~~CY~~--~f~pkC~~C~~~I~~~~~~~i~~ 239 (361)
+|+..|.+...+...+..||..|..|..|...+. ...|.. +|..||...|.. .+..+|..|...|...+ .+...
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~-~ler~ 78 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD-ELERA 78 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH-HHHHh
Confidence 4777886556677779999999999999999997 545666 999999999998 78889999999996542 11112
Q ss_pred eccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhh
Q 018053 240 RAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 290 (361)
Q Consensus 240 ~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~ 290 (361)
.... |.-||.|..|.+.+..++.+.+.......|...+..
T Consensus 79 f~~~-----------h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 79 FEKV-----------HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred hcCC-----------CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 1221 678999999999887888877655557788877754
No 18
>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=97.09 E-value=0.00041 Score=45.88 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=29.5
Q ss_pred ccccCCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcC
Q 018053 221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME 268 (361)
Q Consensus 221 kC~~C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l 268 (361)
+|..|+++|.+. ...+.+.+.. | |..||+|..|++.|
T Consensus 1 ~C~~C~~~i~~~-~~~~~~~~~~-~---------H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRALGKV-W---------HPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCC-cEEEEeCCcc-c---------cccCCCCcccCCcC
Confidence 589999999875 2355666665 3 99999999999977
No 19
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=90.61 E-value=0.21 Score=31.10 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=16.9
Q ss_pred CChhHHHHHHHhhhhhhhhcC
Q 018053 40 FDNEEIDRAIALSLVEVDQKG 60 (361)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~ 60 (361)
.|+++|.+||++||.|.....
T Consensus 1 ~EDe~Lq~Ai~lSl~e~e~~~ 21 (26)
T smart00726 1 DEDEDLQLALELSLQEAEESX 21 (26)
T ss_pred ChHHHHHHHHHHhHHHhhhcc
Confidence 368999999999998775543
No 20
>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=88.75 E-value=0.19 Score=28.61 Aligned_cols=16 Identities=38% Similarity=0.646 Sum_probs=13.5
Q ss_pred CChhHHHHHHHhhhhh
Q 018053 40 FDNEEIDRAIALSLVE 55 (361)
Q Consensus 40 ~~~~~~~~~~~~~~~~ 55 (361)
.|+++|.+||++|+.|
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 21
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=78.90 E-value=1.9 Score=32.76 Aligned_cols=46 Identities=15% Similarity=0.322 Sum_probs=23.5
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccC
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTN 232 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~ 232 (361)
.+|+.|...|..-.....=.+.||..|-...++..|.+|+.+-...
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q 53 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ 53 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence 5778887776553333345578999999999999999999887654
No 22
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.46 E-value=2 Score=39.06 Aligned_cols=47 Identities=19% Similarity=0.516 Sum_probs=36.8
Q ss_pred CCcccCCCCCCCCCcc-eeecCCcccchhhhhhh--cCCccccCCCcccc
Q 018053 185 ECFRCHSCNLPITDVE-FSMSGNRPYHKHCYKEQ--HHPKCDVCQNFIPT 231 (361)
Q Consensus 185 ~CF~C~~C~~~L~~~~-f~~~dg~~YC~~CY~~~--f~pkC~~C~~~I~~ 231 (361)
.||.|..|-.+..... +...=|++||+.|-+.. .+.+|..|++.|..
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 4688888877776554 55678999999998864 44599999998875
No 23
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=70.07 E-value=0.57 Score=38.25 Aligned_cols=59 Identities=24% Similarity=0.583 Sum_probs=38.4
Q ss_pred cCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccc
Q 018053 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD 223 (361)
Q Consensus 161 ~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~ 223 (361)
.|..|+..+..-.+....-..+++.+.-|.+|...|+-.+|.....-|||. ..|.|.|.
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~----spFNp~Ck 95 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ----SPFNPGCK 95 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC----CCCCcccc
Confidence 477777777555666666677888888888888888776665544434442 23555553
No 24
>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=69.70 E-value=26 Score=27.97 Aligned_cols=31 Identities=16% Similarity=0.465 Sum_probs=22.6
Q ss_pred CCCcCccCCCccccCceEEe-CCceecCCCcc
Q 018053 158 GYRICAGCNTEIGHGRYLSC-MEAFWHPECFR 188 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a-~gk~wH~~CF~ 188 (361)
....|..|+++|....++.. .|..+|..|++
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 34679999999977655543 56778888863
No 25
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=69.24 E-value=2.9 Score=42.40 Aligned_cols=26 Identities=42% Similarity=0.510 Sum_probs=22.2
Q ss_pred CCCCChhHHHHHHHhhhhhhhhcCCc
Q 018053 37 SSGFDNEEIDRAIALSLVEVDQKGKK 62 (361)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (361)
.+..|.|||..||+|||+|..+..|+
T Consensus 161 ~~k~EeEdiaKAi~lSL~E~~~Q~k~ 186 (462)
T KOG2199|consen 161 SSKQEEEDIAKAIELSLKEQEKQKKL 186 (462)
T ss_pred cccccHHHHHHHHHhhHHHHhhchhh
Confidence 35689999999999999998877665
No 26
>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=59.67 E-value=6.3 Score=31.60 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=7.7
Q ss_pred CccccCCCcccc
Q 018053 220 PKCDVCQNFIPT 231 (361)
Q Consensus 220 pkC~~C~~~I~~ 231 (361)
.+|.+|+++|..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 467777766654
No 27
>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=59.48 E-value=13 Score=26.08 Aligned_cols=42 Identities=19% Similarity=0.457 Sum_probs=29.0
Q ss_pred ccCCCCCCCCCcceeecCCcc-cchhhhhhh--cCCccccCCCccc
Q 018053 188 RCHSCNLPITDVEFSMSGNRP-YHKHCYKEQ--HHPKCDVCQNFIP 230 (361)
Q Consensus 188 ~C~~C~~~L~~~~f~~~dg~~-YC~~CY~~~--f~pkC~~C~~~I~ 230 (361)
.|..|...... ..+..=|+. +|..|+.+. ...+|..|..+|.
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 56677666544 333456677 999999876 4579999999986
No 28
>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=58.86 E-value=11 Score=27.34 Aligned_cols=44 Identities=14% Similarity=0.212 Sum_probs=32.8
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhhc--CCccccCCCcccc
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPT 231 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~~ 231 (361)
|.|..|+..+.. ......|+.||+.|..+.+ ...|..|++.+..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 578888888776 3445678999999877543 4579999888854
No 29
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=55.43 E-value=18 Score=30.40 Aligned_cols=16 Identities=38% Similarity=0.453 Sum_probs=10.7
Q ss_pred HhhhHHHHHHHHHHHH
Q 018053 95 IAQQEEDERRAKAQQE 110 (361)
Q Consensus 95 ~~~~~E~~~l~~~q~e 110 (361)
.+.+.|++++.+|+++
T Consensus 20 ~l~~~E~~Ri~kLk~~ 35 (118)
T PF02318_consen 20 ELRKKEEERIRKLKQE 35 (118)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4556677777777764
No 30
>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=54.71 E-value=11 Score=24.49 Aligned_cols=40 Identities=13% Similarity=0.404 Sum_probs=22.7
Q ss_pred cCCCCCCCCCcceeecCCcccchhhhhhhc---CCccccCCCc
Q 018053 189 CHSCNLPITDVEFSMSGNRPYHKHCYKEQH---HPKCDVCQNF 228 (361)
Q Consensus 189 C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f---~pkC~~C~~~ 228 (361)
|..|...+........=|..||..|....+ ..+|..|+..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 555655553222223356778888876543 3467777654
No 31
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=53.50 E-value=14 Score=25.19 Aligned_cols=39 Identities=21% Similarity=0.505 Sum_probs=26.2
Q ss_pred cCCCCCCCCC--cceeecCCcccchhhhhhhc--CCccccCCC
Q 018053 189 CHSCNLPITD--VEFSMSGNRPYHKHCYKEQH--HPKCDVCQN 227 (361)
Q Consensus 189 C~~C~~~L~~--~~f~~~dg~~YC~~CY~~~f--~pkC~~C~~ 227 (361)
|..|...+.. ..+...=|..+|..|..... ..+|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 5666666622 22444568899999988876 557877763
No 32
>PRK12495 hypothetical protein; Provisional
Probab=52.15 E-value=27 Score=32.82 Aligned_cols=28 Identities=29% Similarity=0.542 Sum_probs=20.3
Q ss_pred CCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCC
Q 018053 159 YRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT 197 (361)
Q Consensus 159 ~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~ 197 (361)
...|..|+.+|. =++.+-+|..|+....
T Consensus 42 a~hC~~CG~PIp-----------a~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 42 NAHCDECGDPIF-----------RHDGQEFCPTCQQPVT 69 (226)
T ss_pred hhhcccccCccc-----------CCCCeeECCCCCCccc
Confidence 357999999995 1266778888876653
No 33
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=50.97 E-value=5.5 Score=43.33 Aligned_cols=46 Identities=20% Similarity=0.503 Sum_probs=29.9
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhhcCC---ccccCCCccccCC
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP---KCDVCQNFIPTNS 233 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~p---kC~~C~~~I~~~~ 233 (361)
.+|+.|+...-+ .....-++.||..|-..++.. +|..|+.++.+++
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 456666644433 122244567888887766554 7999999888764
No 34
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=50.45 E-value=17 Score=28.71 Aligned_cols=50 Identities=26% Similarity=0.743 Sum_probs=18.8
Q ss_pred CCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhh---hcCCccccCCC
Q 018053 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE---QHHPKCDVCQN 227 (361)
Q Consensus 157 ~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~---~f~pkC~~C~~ 227 (361)
....+|.-|+..|. +...|..| ..|..|+- |.|+.||.- .-...|..|+.
T Consensus 7 ~~~qiCqiCGD~VG----l~~~Ge~F----VAC~eC~f-------------PvCr~CyEYErkeg~q~CpqCkt 59 (80)
T PF14569_consen 7 LNGQICQICGDDVG----LTENGEVF----VACHECAF-------------PVCRPCYEYERKEGNQVCPQCKT 59 (80)
T ss_dssp -SS-B-SSS--B------B-SSSSB------S-SSS------------------HHHHHHHHHTS-SB-TTT--
T ss_pred cCCcccccccCccc----cCCCCCEE----EEEcccCC-------------ccchhHHHHHhhcCcccccccCC
Confidence 35678999988875 33445544 24555543 568888852 23346788874
No 35
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.99 E-value=11 Score=27.75 Aligned_cols=14 Identities=21% Similarity=0.484 Sum_probs=9.7
Q ss_pred CCcCccCCCccccC
Q 018053 159 YRICAGCNTEIGHG 172 (361)
Q Consensus 159 ~~~C~~C~~~I~~g 172 (361)
..+|..|+++|..+
T Consensus 5 ~~~C~~Cg~~~~~~ 18 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG 18 (54)
T ss_pred CccChhhCCcccCC
Confidence 45788888888543
No 36
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=49.91 E-value=6.9 Score=29.28 Aligned_cols=29 Identities=28% Similarity=0.529 Sum_probs=14.3
Q ss_pred CccCCCCCcCCCCCceEEccCCCccChhhhhhhc
Q 018053 259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAI 292 (361)
Q Consensus 259 f~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v 292 (361)
..|.+|+..|..+..++. ..|..|-+..|
T Consensus 10 ~~CtSCg~~i~p~e~~v~-----F~CPnCGe~~I 38 (61)
T COG2888 10 PVCTSCGREIAPGETAVK-----FPCPNCGEVEI 38 (61)
T ss_pred ceeccCCCEeccCCceeE-----eeCCCCCceee
Confidence 355555555544554442 34555554433
No 37
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.77 E-value=12 Score=40.93 Aligned_cols=38 Identities=24% Similarity=0.628 Sum_probs=27.5
Q ss_pred ccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCc
Q 018053 188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNF 228 (361)
Q Consensus 188 ~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~ 228 (361)
+|..|+.+|+ |....+.+.|.-|-......+|..|+..
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 5777777775 3334567889999666555699999985
No 38
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=47.43 E-value=5.5 Score=32.92 Aligned_cols=29 Identities=31% Similarity=0.529 Sum_probs=15.5
Q ss_pred cCccCCCccccCceEEe-CCceecCCCccc
Q 018053 161 ICAGCNTEIGHGRYLSC-MEAFWHPECFRC 189 (361)
Q Consensus 161 ~C~~C~~~I~~ge~l~a-~gk~wH~~CF~C 189 (361)
.|..|+++|+.|+.+.+ .+..-|-.||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 46666666666655443 234455555543
No 39
>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=44.64 E-value=18 Score=32.22 Aligned_cols=56 Identities=14% Similarity=0.331 Sum_probs=36.6
Q ss_pred CcccchhhhhhhcCCccccCCCccccCC--ccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCce
Q 018053 206 NRPYHKHCYKEQHHPKCDVCQNFIPTNS--AGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKY 274 (361)
Q Consensus 206 g~~YC~~CY~~~f~pkC~~C~~~I~~~~--~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f 274 (361)
..-||..|-.+. -..|..|+.+|.|.. .|++.+. .+ |+. =--|..|++..|+....
T Consensus 27 ~~~fC~kCG~~t-I~~Cp~C~~~IrG~y~v~gv~~~g-~~----------~~~-PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 27 REKFCSKCGAKT-ITSCPNCSTPIRGDYHVEGVFGLG-GH----------YEA-PSYCHNCGKPYPWTENA 84 (158)
T ss_pred HHHHHHHhhHHH-HHHCcCCCCCCCCceecCCeeeeC-CC----------CCC-ChhHHhCCCCCchHHHH
Confidence 456899996665 458999999999962 2344442 22 121 12388999988775544
No 40
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=44.29 E-value=3.5 Score=38.33 Aligned_cols=57 Identities=12% Similarity=0.150 Sum_probs=37.4
Q ss_pred CccccCCCccccCCccceEeeccccccccCCCCcccCCCCccCCCCCcCCCCCceEEccCCCccChhhhhh
Q 018053 220 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 290 (361)
Q Consensus 220 pkC~~C~~~I~~~~~~~i~~~~~pfW~~~yCp~h~H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~ 290 (361)
+.|..|++.+.+-+ . +.....|| |..||+|..|+..+. -.+|- -.+.++||-.+|..
T Consensus 5 ~n~~~cgk~vYPvE--~-v~cldk~w---------hk~cfkce~c~mtln-mKnyK-gy~kkpycn~hYpk 61 (264)
T KOG1702|consen 5 CNREDCGKTVYPVE--E-VKCLDKVW---------HKQCFKCEVCGMTLN-MKNYK-GYDKKPYCNPHYPK 61 (264)
T ss_pred chhhhhccccccHH--H-HhhHHHHH---------HHHhheeeeccCChh-hhhcc-ccccCCCcCccccc
Confidence 45667777666532 2 22234567 999999999997652 22332 23689999999964
No 41
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=44.08 E-value=20 Score=39.00 Aligned_cols=11 Identities=36% Similarity=0.661 Sum_probs=6.8
Q ss_pred CcCccCCCccc
Q 018053 160 RICAGCNTEIG 170 (361)
Q Consensus 160 ~~C~~C~~~I~ 170 (361)
.+|+.|+..+.
T Consensus 2 ~~Cp~Cg~~n~ 12 (645)
T PRK14559 2 LICPQCQFENP 12 (645)
T ss_pred CcCCCCCCcCC
Confidence 35777776653
No 42
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=43.12 E-value=22 Score=32.76 Aligned_cols=45 Identities=22% Similarity=0.495 Sum_probs=25.5
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhh------------------cCCccccCCCccccC
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ------------------HHPKCDVCQNFIPTN 232 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~------------------f~pkC~~C~~~I~~~ 232 (361)
|.|..|...+.+. ....=|+.||..|-.+- -.++|..|+..|...
T Consensus 19 ~~CpICld~~~dP-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 19 FDCNICLDQVRDP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred cCCccCCCcCCCc-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 4555555444332 22334556666665431 235899999998764
No 43
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.12 E-value=13 Score=36.46 Aligned_cols=46 Identities=17% Similarity=0.343 Sum_probs=34.0
Q ss_pred CcccCCCCCCCCCcceeecCCcccchhhhhhhcC--CccccCCCccccC
Q 018053 186 CFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH--PKCDVCQNFIPTN 232 (361)
Q Consensus 186 CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~--pkC~~C~~~I~~~ 232 (361)
=|.|..|+.++... ....-+..+|..|....|. ++|.+|++.+.+.
T Consensus 241 Pf~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 241 PFKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred Cccccccccccccc-hhhcCCceeehhhhccccccCCcceecccccccc
Confidence 57888888877542 3334567889999876554 6999999998873
No 44
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=41.75 E-value=19 Score=35.72 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=10.1
Q ss_pred CCccCCCCCcC-----CCCCceEEcc
Q 018053 258 TPRCCSCERME-----PRDTKYLSLD 278 (361)
Q Consensus 258 Cf~C~~C~r~l-----~~g~~f~~~~ 278 (361)
.++|..|.-.| |.+..|++..
T Consensus 77 ~~kC~~C~~~i~~kTDPkn~dY~~~~ 102 (324)
T PF04502_consen 77 YIKCPRCSNEIEFKTDPKNTDYVVES 102 (324)
T ss_pred EEEcCCCCCEEeeecCCCCCCeeeec
Confidence 34555555543 2344555543
No 45
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=41.39 E-value=19 Score=25.94 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=21.7
Q ss_pred ccCCCCCCCCCcc-eeecCCcccchhhhhhh
Q 018053 188 RCHSCNLPITDVE-FSMSGNRPYHKHCYKEQ 217 (361)
Q Consensus 188 ~C~~C~~~L~~~~-f~~~dg~~YC~~CY~~~ 217 (361)
.|..|+..++-.. +-..|| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 4788888876544 556788 6899998875
No 46
>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=41.10 E-value=20 Score=37.73 Aligned_cols=38 Identities=16% Similarity=0.448 Sum_probs=25.3
Q ss_pred ccCCCCCCCCCcceeecCCcccchhhhhhh-cCCccccCCCc
Q 018053 188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQ-HHPKCDVCQNF 228 (361)
Q Consensus 188 ~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~-f~pkC~~C~~~ 228 (361)
+|..|+.+|+ |....+.+.|..|-... +...|..|+..
T Consensus 224 ~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLT---YHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceE---EecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4556666553 34457788899885543 45589999874
No 47
>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=40.75 E-value=17 Score=24.58 Aligned_cols=29 Identities=24% Similarity=0.504 Sum_probs=18.0
Q ss_pred CccCCCccccC-ceEEeCCceecCCCcccCCCC
Q 018053 162 CAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCN 193 (361)
Q Consensus 162 C~~C~~~I~~g-e~l~a~gk~wH~~CF~C~~C~ 193 (361)
|.-|+.+|... ..+...++.|| |.|..|.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~ 30 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCL 30 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHH
Confidence 66788888533 34567788886 4444443
No 48
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=39.93 E-value=15 Score=28.99 Aligned_cols=31 Identities=29% Similarity=0.576 Sum_probs=21.7
Q ss_pred ccCCCCCcCCCCCceEEccCCCc---cChhhhhh
Q 018053 260 RCCSCERMEPRDTKYLSLDDGRK---LCLECLDS 290 (361)
Q Consensus 260 ~C~~C~r~l~~g~~f~~~~dg~~---~C~~C~~~ 290 (361)
.|.+|+.++.....|.+..||.. ||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 47888888765554555555554 99999975
No 49
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=39.32 E-value=19 Score=34.15 Aligned_cols=34 Identities=18% Similarity=0.431 Sum_probs=27.4
Q ss_pred Ccceee-cCCcccchhhhhhhcCCccccCCCcccc
Q 018053 198 DVEFSM-SGNRPYHKHCYKEQHHPKCDVCQNFIPT 231 (361)
Q Consensus 198 ~~~f~~-~dg~~YC~~CY~~~f~pkC~~C~~~I~~ 231 (361)
...|++ .=.+++|..|...-+.+.|..|++.|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 445554 5678999999888888899999999875
No 50
>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=38.77 E-value=18 Score=24.19 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=16.9
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhh
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYK 215 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~ 215 (361)
+.|..|+.. .|...+|..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 347777653 4566789999977743
No 51
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=38.37 E-value=13 Score=34.60 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=9.8
Q ss_pred ecCCcccchhhhhh
Q 018053 203 MSGNRPYHKHCYKE 216 (361)
Q Consensus 203 ~~dg~~YC~~CY~~ 216 (361)
..+|++.|+.||..
T Consensus 189 ~~ng~~vC~~C~~~ 202 (206)
T COG2191 189 VLNGKPVCKPCAEK 202 (206)
T ss_pred hcCCceeccccccc
Confidence 45777778887764
No 52
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=37.86 E-value=30 Score=25.85 Aligned_cols=27 Identities=26% Similarity=0.548 Sum_probs=16.4
Q ss_pred CCcCccCCCccccCc-eEEeCCceecCCCcccCCCCCC
Q 018053 159 YRICAGCNTEIGHGR-YLSCMEAFWHPECFRCHSCNLP 195 (361)
Q Consensus 159 ~~~C~~C~~~I~~ge-~l~a~gk~wH~~CF~C~~C~~~ 195 (361)
.+.|..|+..|...+ .+ -|.|..|+..
T Consensus 7 ~~~CtSCg~~i~~~~~~~----------~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAV----------KFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccC----------EeeCCCCCCe
Confidence 356888887775443 22 2667777654
No 53
>PHA03378 EBNA-3B; Provisional
Probab=37.05 E-value=23 Score=38.56 Aligned_cols=35 Identities=26% Similarity=0.296 Sum_probs=18.5
Q ss_pred cccccCCCCCcc-cccc--cccCCCCCCChhHHHHHHHhhh
Q 018053 16 YHARYGDDRTWD-ERRY--SAADDSSGFDNEEIDRAIALSL 53 (361)
Q Consensus 16 ~~~~~~~~~~~~-~~~~--~~~~~~~~~~~~~~~~~~~~~~ 53 (361)
-.|++.-..-|. .++. .++ .....+||+-|.|..+
T Consensus 303 ~iGt~kpt~PWl~a~P~e~pYh---rpLtsedi~~AfarGq 340 (991)
T PHA03378 303 CTGRPRPTKPWLRAHPVAVPYD---DPLTSEEIDLAYARGL 340 (991)
T ss_pred hcCCCCCCCcccCCCCcccccc---ccchHHHHHHHHHHHH
Confidence 356666556676 3332 232 2345678876665444
No 54
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=36.75 E-value=21 Score=21.38 Aligned_cols=8 Identities=50% Similarity=1.344 Sum_probs=3.7
Q ss_pred CccCCCcc
Q 018053 162 CAGCNTEI 169 (361)
Q Consensus 162 C~~C~~~I 169 (361)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44444444
No 55
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.36 E-value=17 Score=33.16 Aligned_cols=50 Identities=22% Similarity=0.503 Sum_probs=36.9
Q ss_pred cCCCCccCCCCCcCCCCCceEEccCCCccChhhhhhhccCCCCCchhhHHH
Q 018053 255 RDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI 305 (361)
Q Consensus 255 H~~Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~d~~~cq~~~~~i 305 (361)
..+||.|-.|--....-..+. -+=|+++|..|.+.++..+..|.-+...|
T Consensus 128 ~~~~~~CPiCl~~~sek~~vs-TkCGHvFC~~Cik~alk~~~~CP~C~kkI 177 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVS-TKCGHVFCSQCIKDALKNTNKCPTCRKKI 177 (187)
T ss_pred cccccCCCceecchhhccccc-cccchhHHHHHHHHHHHhCCCCCCccccc
Confidence 347788888876543333333 35699999999999999888998887655
No 56
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.12 E-value=19 Score=31.24 Aligned_cols=22 Identities=18% Similarity=0.548 Sum_probs=14.8
Q ss_pred ccCCCCCCCCCcceeecCCcccchhhh
Q 018053 188 RCHSCNLPITDVEFSMSGNRPYHKHCY 214 (361)
Q Consensus 188 ~C~~C~~~L~~~~f~~~dg~~YC~~CY 214 (361)
.|..|+.||- .++|.+||..|-
T Consensus 30 hCp~Cg~PLF-----~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPLF-----RKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcce-----eeCCeEECCCCC
Confidence 4667777763 278888887663
No 57
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=35.44 E-value=32 Score=23.50 Aligned_cols=32 Identities=34% Similarity=0.709 Sum_probs=20.7
Q ss_pred ccCCCCCcCCCCCceEEccCCCccChhhhhhh
Q 018053 260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 291 (361)
Q Consensus 260 ~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~ 291 (361)
+|+-|+|......+.+.-.++..+|..|....
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 68999998766666665454788999997653
No 58
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=35.33 E-value=13 Score=30.59 Aligned_cols=7 Identities=43% Similarity=0.805 Sum_probs=0.0
Q ss_pred chHHHHH
Q 018053 88 DEDEIRA 94 (361)
Q Consensus 88 ~~~~~~~ 94 (361)
++++.+.
T Consensus 37 e~de~p~ 43 (101)
T PF09026_consen 37 EEDEVPV 43 (101)
T ss_dssp -------
T ss_pred ccccccc
Confidence 3333333
No 59
>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=34.83 E-value=25 Score=24.23 Aligned_cols=21 Identities=29% Similarity=0.796 Sum_probs=12.7
Q ss_pred cCCCCCcCCCCCceEEccCCCccChhh
Q 018053 261 CCSCERMEPRDTKYLSLDDGRKLCLEC 287 (361)
Q Consensus 261 C~~C~r~l~~g~~f~~~~dg~~~C~~C 287 (361)
|..|+.+| +...+|+.+|..|
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 44566554 2235677888776
No 60
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=34.63 E-value=28 Score=23.00 Aligned_cols=37 Identities=27% Similarity=0.624 Sum_probs=21.9
Q ss_pred cCCCCCCCCCcceeecCCcccchhhhhhhc--CCccccC
Q 018053 189 CHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVC 225 (361)
Q Consensus 189 C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f--~pkC~~C 225 (361)
|..|...+........=|+.||..|..+.+ .++|..|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 456666665533456678899999976543 3455544
No 61
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=34.47 E-value=29 Score=34.16 Aligned_cols=44 Identities=20% Similarity=0.429 Sum_probs=33.7
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCcccc
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPT 231 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~ 231 (361)
+-|.+|..+|..-.|.-.+|++.|..|-.+ ...+|..|..+|..
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~-~~~~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTK-VSNKCPTCRLPIGN 92 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhh-hcccCCcccccccc
Confidence 566777777777677778888899888543 46789999998873
No 62
>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=34.40 E-value=15 Score=28.46 Aligned_cols=17 Identities=41% Similarity=0.935 Sum_probs=12.6
Q ss_pred CCCCcCccCCCccccCc
Q 018053 157 SGYRICAGCNTEIGHGR 173 (361)
Q Consensus 157 ~~~~~C~~C~~~I~~ge 173 (361)
++...|.+|+..|..+.
T Consensus 5 s~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp SSTEBETTTSCBE-TTS
T ss_pred CCCccCcccCCcCCCCC
Confidence 35678999999997663
No 63
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=34.30 E-value=12 Score=30.81 Aligned_cols=29 Identities=28% Similarity=0.661 Sum_probs=19.3
Q ss_pred CCccCCCCCcCCCCCceEEccCCCccChhh
Q 018053 258 TPRCCSCERMEPRDTKYLSLDDGRKLCLEC 287 (361)
Q Consensus 258 Cf~C~~C~r~l~~g~~f~~~~dg~~~C~~C 287 (361)
=|+|++|--+-.+. +...-.+|.++|..|
T Consensus 70 EFTCssCFLV~HRS-qLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRS-QLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechh-hhccccCCCEecccc
Confidence 38899997654332 233345789999988
No 64
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.86 E-value=40 Score=37.26 Aligned_cols=39 Identities=21% Similarity=0.503 Sum_probs=26.9
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhhcCC-ccccCCCc
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP-KCDVCQNF 228 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~p-kC~~C~~~ 228 (361)
++|..|..+|+ |....+.+.|+-|-.+.-.| .|..|+..
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 46777777764 33345788898886663333 79999886
No 65
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=33.74 E-value=16 Score=33.80 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=20.5
Q ss_pred hhHHHHHHHhhhhhhhhcCCccccCccCCc
Q 018053 42 NEEIDRAIALSLVEVDQKGKKVIENEYDSE 71 (361)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 (361)
+-||.-||.||+.|+.++.+-+....||++
T Consensus 207 DpELA~AlrLSmeEek~rQe~~~qk~~ee~ 236 (243)
T COG5148 207 DPELAEALRLSMEEEKKRQEVAAQKSSEET 236 (243)
T ss_pred CHHHHHHHHhhHHHHHHHHHHHHHhhhhcc
Confidence 557888999999888776665554444433
No 66
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=32.14 E-value=40 Score=29.23 Aligned_cols=55 Identities=29% Similarity=0.352 Sum_probs=35.8
Q ss_pred cchhhhhcCCCCcc-----cccccC----------CCCCcccccccccCCCCCCChhHHHHHHHhhhhhhh
Q 018053 2 GWLTKILKGSSRRH-----YHARYG----------DDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVD 57 (361)
Q Consensus 2 ~~~~~~~~~~~~~~-----~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (361)
|-|+|+.-|+.+|+ |-+.++ +.+.|-+.+.---..++.+-.-|||| ||-++.|+.
T Consensus 73 g~~~KiYGg~krrGvrPsh~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~Gqrdldr-Ia~~i~~~~ 142 (143)
T KOG3411|consen 73 GALTKIYGGSKRRGVRPSHFCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDR-IAGQIREEQ 142 (143)
T ss_pred hHHHHHhcccccCCCCChhhhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHH-HHHHHHhcc
Confidence 45889998888775 333333 66777766532211378888889998 556666553
No 67
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=31.74 E-value=19 Score=33.46 Aligned_cols=46 Identities=15% Similarity=0.322 Sum_probs=33.9
Q ss_pred CcccCCCCCCCCCcceeecCCcccchhhhhhhc--CCccccCCCccccC
Q 018053 186 CFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPTN 232 (361)
Q Consensus 186 CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f--~pkC~~C~~~I~~~ 232 (361)
=|.|..|.+-... ..+..-|+-||..|+.+.+ ++.|.+|++...+.
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 5889999876644 2333567889999988764 57999999877663
No 68
>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=31.27 E-value=32 Score=27.90 Aligned_cols=37 Identities=19% Similarity=0.511 Sum_probs=25.8
Q ss_pred cccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCcccc
Q 018053 187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPT 231 (361)
Q Consensus 187 F~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~ 231 (361)
-.|..|...+. ..|.-||..|-.+ .-.|+.|++.|..
T Consensus 45 ~~C~~CK~~v~------q~g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 45 SKCKICKTKVH------QPGAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred ccccccccccc------cCCCccChhhhcc--cCcccccCCeecc
Confidence 36777776553 2367899999544 2489999999864
No 69
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=29.87 E-value=11 Score=24.87 Aligned_cols=27 Identities=19% Similarity=0.500 Sum_probs=11.9
Q ss_pred cCCCCCCCCCcceeecCCcccchhhhh
Q 018053 189 CHSCNLPITDVEFSMSGNRPYHKHCYK 215 (361)
Q Consensus 189 C~~C~~~L~~~~f~~~dg~~YC~~CY~ 215 (361)
|..|+.+|.........+..+|..|+.
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhC
Confidence 444444444333333445556666654
No 70
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=29.32 E-value=28 Score=30.16 Aligned_cols=26 Identities=23% Similarity=0.554 Sum_probs=19.3
Q ss_pred ccCCCCCcCCCCCceEEccCCCccChhhhhhhc
Q 018053 260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSAI 292 (361)
Q Consensus 260 ~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v 292 (361)
.|..|+.+| +. ++|.+||+.|-...+
T Consensus 30 hCp~Cg~PL------F~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 30 HCPKCGTPL------FR-KDGEVFCPVCGYREV 55 (131)
T ss_pred hCcccCCcc------ee-eCCeEECCCCCceEE
Confidence 477888877 33 689999999984433
No 71
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=29.09 E-value=24 Score=28.22 Aligned_cols=17 Identities=18% Similarity=0.696 Sum_probs=15.0
Q ss_pred hhhhhcCCccccCCCcc
Q 018053 213 CYKEQHHPKCDVCQNFI 229 (361)
Q Consensus 213 CY~~~f~pkC~~C~~~I 229 (361)
-|..+|..+|.+|++.+
T Consensus 48 sY~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 48 SYRNLFSTPCKKCGKLL 64 (90)
T ss_pred HHhhhccchhhHHHhHh
Confidence 46788999999999988
No 72
>PRK00420 hypothetical protein; Validated
Probab=28.96 E-value=33 Score=28.93 Aligned_cols=30 Identities=23% Similarity=0.381 Sum_probs=20.7
Q ss_pred CccCCCCCcCCCCCceEEccCCCccChhhhhhhccC
Q 018053 259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMD 294 (361)
Q Consensus 259 f~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~d 294 (361)
-.|..|+.++ +.+.+|..+|+.|....+..
T Consensus 24 ~~CP~Cg~pL------f~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPL------FELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcc------eecCCCceECCCCCCeeeec
Confidence 3566677655 33468999999998865443
No 73
>PLN02195 cellulose synthase A
Probab=28.63 E-value=47 Score=37.72 Aligned_cols=52 Identities=29% Similarity=0.667 Sum_probs=34.7
Q ss_pred CCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhh--hh-cCCccccCCCccc
Q 018053 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK--EQ-HHPKCDVCQNFIP 230 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~--~~-f~pkC~~C~~~I~ 230 (361)
+..+|.-|+..|. +...|..| -.|..|+- |.|++||. +. -...|..|+..-.
T Consensus 5 ~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~-------------pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVG----VDSNGEAF----VACHECSY-------------PLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCccceecccccC----cCCCCCeE----EEeccCCC-------------ccccchhhhhhhcCCccCCccCCccc
Confidence 5678999998885 33556655 45666654 55888874 22 3347888888776
No 74
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=28.61 E-value=38 Score=36.62 Aligned_cols=23 Identities=30% Similarity=0.338 Sum_probs=20.3
Q ss_pred CCCCChhHHHHHHHhhhhhhhhc
Q 018053 37 SSGFDNEEIDRAIALSLVEVDQK 59 (361)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~ 59 (361)
...++.|||+.||+||++|+.++
T Consensus 250 ~~~keeed~~lAi~lSq~E~~~~ 272 (634)
T KOG1818|consen 250 LEEKEEEDLSLAIALSQSEAEAA 272 (634)
T ss_pred ccchhhHHHHHHHHHhHHHHHHh
Confidence 56678889999999999999877
No 75
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=28.36 E-value=90 Score=24.87 Aligned_cols=16 Identities=25% Similarity=0.499 Sum_probs=8.3
Q ss_pred cCCCCCcCCCCCceEE
Q 018053 261 CCSCERMEPRDTKYLS 276 (361)
Q Consensus 261 C~~C~r~l~~g~~f~~ 276 (361)
|..|+..++.+..+..
T Consensus 3 C~HCg~~~p~~~~~~~ 18 (88)
T PF12156_consen 3 CYHCGLPVPEGAKITV 18 (88)
T ss_pred CCCCCCCCCCCCCeee
Confidence 5556655554444443
No 76
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.84 E-value=58 Score=37.18 Aligned_cols=54 Identities=22% Similarity=0.366 Sum_probs=34.7
Q ss_pred CCCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCCccccC
Q 018053 156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTN 232 (361)
Q Consensus 156 ~~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~~I~~~ 232 (361)
..+.+.|..|+... .=|+|..|+.. .....+|..|-.......|..|+..+.+.
T Consensus 623 EVg~RfCpsCG~~t---------------~~frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 623 EIGRRKCPSCGKET---------------FYRRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTPY 676 (1121)
T ss_pred cccCccCCCCCCcC---------------CcccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCcc
Confidence 44667788887653 12677888765 12234677775555556788888877764
No 77
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=27.80 E-value=70 Score=33.77 Aligned_cols=69 Identities=23% Similarity=0.429 Sum_probs=37.4
Q ss_pred CCCcCccCCCc-cc-cCceEEe--CCceecCCCcccCCCCCCCCCcceeecCCcccchhhhhhhcCCccccCCC
Q 018053 158 GYRICAGCNTE-IG-HGRYLSC--MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQN 227 (361)
Q Consensus 158 ~~~~C~~C~~~-I~-~ge~l~a--~gk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~f~pkC~~C~~ 227 (361)
...+|..|-.. +. .+++|.+ -|-..|..|+-=. =+..|.+..---...--||..|-....-|-|.-|-.
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~-dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElCPn 190 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVL-DNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELCPN 190 (707)
T ss_pred cceEEEEeecCccccccceeeccccCceecccccccc-cccccCCCCccCCCCchhhhhHhcCCCCCccccCCC
Confidence 44588888432 22 2366644 3555677776433 112222211111113468999977766689998865
No 78
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.46 E-value=44 Score=36.45 Aligned_cols=38 Identities=21% Similarity=0.474 Sum_probs=23.7
Q ss_pred ccCCCCCCCCCcceeecCCcccchhhhhhh-cCCccccCCCc
Q 018053 188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQ-HHPKCDVCQNF 228 (361)
Q Consensus 188 ~C~~C~~~L~~~~f~~~dg~~YC~~CY~~~-f~pkC~~C~~~ 228 (361)
+|..|+.+|. |....+.+.|..|-... ...+|..|+..
T Consensus 392 ~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLT---LHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCcee---EECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 4455555553 33346778888886543 44589999775
No 79
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=26.83 E-value=26 Score=32.55 Aligned_cols=30 Identities=20% Similarity=0.562 Sum_probs=22.8
Q ss_pred CccCCCCCcCCCCCceEEccCCCccChhhhhh
Q 018053 259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 290 (361)
Q Consensus 259 f~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~ 290 (361)
-+|..|+.++.. ....+.+|+++|..|+..
T Consensus 173 v~C~kCGE~~~e--~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFME--PRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCccccc--chhhhcCCceeccccccc
Confidence 589999997632 234456899999999875
No 80
>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=26.68 E-value=38 Score=28.28 Aligned_cols=27 Identities=26% Similarity=0.610 Sum_probs=18.8
Q ss_pred CccCCCCCcCCCCCceEEccCCCccChhhhhhh
Q 018053 259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 291 (361)
Q Consensus 259 f~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~ 291 (361)
..|.+|++ +||-|+..-+.|+.|....
T Consensus 10 R~Cp~CG~------kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGA------KFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcc------hhccCCCCCccCCCCCCcc
Confidence 45677764 6787776666799997653
No 81
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=26.37 E-value=60 Score=28.31 Aligned_cols=63 Identities=19% Similarity=0.378 Sum_probs=36.9
Q ss_pred ccCCCCCcCCCCCceEEccCCCccChhhhhhhccCCCCCchhhHHHHHHHHh-cC--ccccccccccccchHHHHHHhcC
Q 018053 260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEG-LN--MKVEQQVPLLLVERQALNEAMEG 336 (361)
Q Consensus 260 ~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~~~v~d~~~cq~~~~~i~~f~eg-l~--mk~~~~~P~llv~~~aln~a~~~ 336 (361)
.|..|++++ + ..++.+|..|+.... ..|..|++|... -+ .-+..=+-.+.|+..-++.-+.+
T Consensus 5 nC~~CgklF------~--~~~~~iCp~C~~~~e-------~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ire 69 (137)
T TIGR03826 5 NCPKCGRLF------V--KTGRDVCPSCYEEEE-------REFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIRE 69 (137)
T ss_pred cccccchhh------h--hcCCccCHHHhHHHH-------HHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHc
Confidence 578888866 2 136789999997642 357788888653 12 12222223345666666665444
Q ss_pred C
Q 018053 337 E 337 (361)
Q Consensus 337 e 337 (361)
.
T Consensus 70 G 70 (137)
T TIGR03826 70 G 70 (137)
T ss_pred C
Confidence 3
No 82
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=26.23 E-value=16 Score=43.58 Aligned_cols=25 Identities=28% Similarity=0.385 Sum_probs=17.4
Q ss_pred HHHHHhhhhhhhhcCCc--cccCccCC
Q 018053 46 DRAIALSLVEVDQKGKK--VIENEYDS 70 (361)
Q Consensus 46 ~~~~~~~~~~~~~~~~~--~~~~~~~~ 70 (361)
-|-.|.-|+|||..+.. ||+.|.++
T Consensus 133 ~~~~~r~l~eed~~~~~~~~~d~~~~~ 159 (2849)
T PTZ00415 133 KRRRARHLAEEDMSPRDNFVIDDDDED 159 (2849)
T ss_pred ehHHhhccchhhcCcccccccCCcccc
Confidence 46678899999976655 66655433
No 83
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=25.95 E-value=27 Score=39.28 Aligned_cols=23 Identities=26% Similarity=0.549 Sum_probs=13.6
Q ss_pred ccCccCCchhhhcccCCCCcccc
Q 018053 64 IENEYDSEDDLQCIKSDDSDEDE 86 (361)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~ 86 (361)
.++|+++|||++-+.+|++|+.|
T Consensus 1403 ~~dd~DeeeD~e~Ed~dEddd~e 1425 (1516)
T KOG1832|consen 1403 TDDDSDEEEDDETEDEDEDDDEE 1425 (1516)
T ss_pred CccccCccccchhhccccccccc
Confidence 45666666666666555554443
No 84
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=25.50 E-value=19 Score=27.82 Aligned_cols=10 Identities=20% Similarity=0.590 Sum_probs=3.6
Q ss_pred ccCCCCCcCC
Q 018053 260 RCCSCERMEP 269 (361)
Q Consensus 260 ~C~~C~r~l~ 269 (361)
.|..|+.+++
T Consensus 52 FC~~c~gLiS 61 (70)
T PF07191_consen 52 FCNHCHGLIS 61 (70)
T ss_dssp E-TTTT-EE-
T ss_pred eeccCCceee
Confidence 4555555543
No 85
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.48 E-value=62 Score=37.17 Aligned_cols=32 Identities=22% Similarity=0.694 Sum_probs=21.6
Q ss_pred CCCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCC
Q 018053 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPI 196 (361)
Q Consensus 157 ~~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L 196 (361)
....+|.-|+..|. +...|..| -.|..|+-|+
T Consensus 15 ~~~qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPV 46 (1079)
T PLN02638 15 GGGQVCQICGDNVG----KTVDGEPF----VACDVCAFPV 46 (1079)
T ss_pred cCCceeeecccccC----cCCCCCEE----EEeccCCCcc
Confidence 35569999998885 44566666 4567776544
No 86
>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=25.48 E-value=30 Score=27.89 Aligned_cols=39 Identities=18% Similarity=0.396 Sum_probs=24.5
Q ss_pred CCcCccCCCccccCceEEeCCceecCCCcccCCCCCCCCCc
Q 018053 159 YRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDV 199 (361)
Q Consensus 159 ~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L~~~ 199 (361)
...|..|++++..-+.+...+-.+.. -+|..|+.+|+..
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~~ 71 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPPR 71 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCChH
Confidence 46788999888655555544433322 3677777777653
No 87
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.54 E-value=72 Score=31.61 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=19.4
Q ss_pred CCcccchhhhhhhcC---CccccCCCccccC
Q 018053 205 GNRPYHKHCYKEQHH---PKCDVCQNFIPTN 232 (361)
Q Consensus 205 dg~~YC~~CY~~~f~---pkC~~C~~~I~~~ 232 (361)
=|+.||..|....|. ..|..|+..+..+
T Consensus 26 CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 26 CGHTLCESCVDLLFVRGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCcccHHHHHHHhcCCCCCCCCCCCccchh
Confidence 456778888776552 3688888877753
No 88
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.44 E-value=66 Score=22.63 Aligned_cols=8 Identities=63% Similarity=1.589 Sum_probs=4.8
Q ss_pred cChhhhhh
Q 018053 283 LCLECLDS 290 (361)
Q Consensus 283 ~C~~C~~~ 290 (361)
+|..||..
T Consensus 26 LC~~Cf~~ 33 (49)
T cd02335 26 LCLECFSA 33 (49)
T ss_pred hhHHhhhC
Confidence 56666654
No 89
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=24.10 E-value=85 Score=24.51 Aligned_cols=29 Identities=14% Similarity=0.315 Sum_probs=21.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHhh
Q 018053 96 AQQEEDERRAKAQQEEDERRARARAQLEEDEQLAKAIQD 134 (361)
Q Consensus 96 ~~~~E~~~l~~~q~ee~~~l~ra~~~~~ede~laraiq~ 134 (361)
+|..|.+.|.+++++.. .+|+.+++.+..
T Consensus 3 LSe~E~r~L~eiEr~L~----------~~DP~fa~~l~~ 31 (82)
T PF11239_consen 3 LSEHEQRRLEEIERQLR----------ADDPRFAARLRS 31 (82)
T ss_pred CCHHHHHHHHHHHHHHH----------hcCcHHHHHhcc
Confidence 56778888999988532 378888888776
No 90
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=23.94 E-value=72 Score=36.57 Aligned_cols=31 Identities=26% Similarity=0.732 Sum_probs=21.6
Q ss_pred CCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCC
Q 018053 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPI 196 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L 196 (361)
...+|.-|+..|. +.+.|..| -.|..|+-|+
T Consensus 14 ~~~~c~iCGd~vg----~~~~Ge~F----VAC~eC~fpv 44 (1044)
T PLN02915 14 DAKTCRVCGDEVG----VKEDGQPF----VACHVCGFPV 44 (1044)
T ss_pred CcchhhccccccC----cCCCCCEE----EEeccCCCcc
Confidence 5678999998885 34566666 4567776554
No 91
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=23.62 E-value=69 Score=22.12 Aligned_cols=8 Identities=38% Similarity=1.036 Sum_probs=4.9
Q ss_pred cChhhhhh
Q 018053 283 LCLECLDS 290 (361)
Q Consensus 283 ~C~~C~~~ 290 (361)
+|..||..
T Consensus 25 LC~~Cf~~ 32 (46)
T cd02249 25 LCSSCYAK 32 (46)
T ss_pred CHHHHHCc
Confidence 56666654
No 92
>PHA03377 EBNA-3C; Provisional
Probab=23.05 E-value=37 Score=37.21 Aligned_cols=82 Identities=16% Similarity=0.211 Sum_probs=36.3
Q ss_pred cccccCCCCCccccccccc-CCCCCCChhHHHHHHHh------hhhhh-hhcCCccccCccCCchhhhcccCCCCccccc
Q 018053 16 YHARYGDDRTWDERRYSAA-DDSSGFDNEEIDRAIAL------SLVEV-DQKGKKVIENEYDSEDDLQCIKSDDSDEDEL 87 (361)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~------~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (361)
-.|++.--.-|..+++... ++.-....++|+-|.+. +|.+- ..-...+|-++++++| + ..++.|.|.|.
T Consensus 309 ~iGt~kp~~PWl~~P~E~Pyh~~rglt~~~i~~Af~rGqa~GLslL~t~~eP~ddat~ETssEeE-~--~~~~sD~E~Es 385 (1000)
T PHA03377 309 TIGNFKPYYPWNAPPNENPYHARRGIKEDVIQTAFRKAQRQGLSMLATGGEPRGDATSETSSDED-T--GRQGSDVELES 385 (1000)
T ss_pred hcCCCCCCCCCCCCCccCcccccccchHHHHHHHHHHHHHhhhhhhccccCCCCCccccccchhh-c--ccccccccccc
Confidence 3466655666876553211 12223556777655443 44222 2233344544443222 1 22223333333
Q ss_pred chHHHHHHhhhHH
Q 018053 88 DEDEIRAIAQQEE 100 (361)
Q Consensus 88 ~~~~~~~~~~~~E 100 (361)
+++++...+.-.|
T Consensus 386 SD~ELP~IvP~~e 398 (1000)
T PHA03377 386 SDDELPYIDPNME 398 (1000)
T ss_pred CcccCceecCCCC
Confidence 4444555555443
No 93
>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=22.52 E-value=44 Score=20.88 Aligned_cols=13 Identities=38% Similarity=0.802 Sum_probs=7.5
Q ss_pred CCccccCCCcccc
Q 018053 219 HPKCDVCQNFIPT 231 (361)
Q Consensus 219 ~pkC~~C~~~I~~ 231 (361)
+.+|..|...|..
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 3579999998875
No 94
>PF05009 EBV-NA3: Epstein-Barr virus nuclear antigen 3 (EBNA-3); InterPro: IPR007706 This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4)-induced B-cell immortalisation and the immune response to EBVG infection. ; GO: 0016032 viral reproduction, 0042025 host cell nucleus; PDB: 3SJV_H 3DXA_M.
Probab=22.16 E-value=29 Score=33.17 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=0.0
Q ss_pred ccccCCCCCcc-ccc--ccccCCCCCCChhHHHHHHHh
Q 018053 17 HARYGDDRTWD-ERR--YSAADDSSGFDNEEIDRAIAL 51 (361)
Q Consensus 17 ~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~ 51 (361)
.|++.-..-|. .++ .+.. ...-.++|+-|.|.
T Consensus 161 ~Gt~k~~~PW~~~~P~~~py~---~~l~~~~~~~a~~r 195 (255)
T PF05009_consen 161 IGTTKPQTPWLSAHPNEVPYH---RGLTSEDITAAFAR 195 (255)
T ss_dssp --------------------------------------
T ss_pred cCCCCCCCCCCCCCCcccccc---cchhHHHHHHHHHH
Confidence 34444445566 333 2221 23345666655543
No 95
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=22.07 E-value=81 Score=21.60 Aligned_cols=30 Identities=23% Similarity=0.570 Sum_probs=13.6
Q ss_pred ccCCCCCcCCCCCceEEcc-CCCccChhhhhh
Q 018053 260 RCCSCERMEPRDTKYLSLD-DGRKLCLECLDS 290 (361)
Q Consensus 260 ~C~~C~r~l~~g~~f~~~~-dg~~~C~~C~~~ 290 (361)
.|..|++.+ .|.+|--+. ..--+|..||..
T Consensus 6 ~C~~C~~~i-~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 6 SCDTCGKPI-VGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred CCCCCCCCC-cCCEEECCCCCCccchHHHHhC
Confidence 455555533 344442111 123367777765
No 96
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=22.00 E-value=48 Score=32.86 Aligned_cols=20 Identities=20% Similarity=0.255 Sum_probs=11.3
Q ss_pred CCCcCccCCCccccCceEEe
Q 018053 158 GYRICAGCNTEIGHGRYLSC 177 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a 177 (361)
+.-.|..|+..|+.|..+++
T Consensus 39 f~i~C~~C~~~I~kG~rFNA 58 (324)
T PF04502_consen 39 FNIWCNTCGEYIYKGVRFNA 58 (324)
T ss_pred ccCcCCCCccccccceeeee
Confidence 44566666666665544443
No 97
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=21.85 E-value=25 Score=25.54 Aligned_cols=28 Identities=18% Similarity=0.501 Sum_probs=18.7
Q ss_pred CccCCCCCcCCCCCceEEccCCCccChhhhh
Q 018053 259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLD 289 (361)
Q Consensus 259 f~C~~C~r~l~~g~~f~~~~dg~~~C~~C~~ 289 (361)
++|..|+++|.....|.. ..+-|..|-.
T Consensus 5 iRC~~CnklLa~~g~~~~---leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIE---LEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccE---EEEECCCCCc
Confidence 688888888866444443 3467777754
No 98
>PLN02436 cellulose synthase A
Probab=21.65 E-value=74 Score=36.58 Aligned_cols=31 Identities=26% Similarity=0.652 Sum_probs=20.9
Q ss_pred CCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCC
Q 018053 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPI 196 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L 196 (361)
...+|.-|+..|. +...|..| -.|..|+-|+
T Consensus 35 ~~~iCqICGD~Vg----~t~dGe~F----VACn~C~fpv 65 (1094)
T PLN02436 35 SGQTCQICGDEIE----LTVDGEPF----VACNECAFPV 65 (1094)
T ss_pred CCccccccccccC----cCCCCCEE----EeeccCCCcc
Confidence 4568999998885 33556666 4567776554
No 99
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.43 E-value=94 Score=36.41 Aligned_cols=10 Identities=20% Similarity=0.291 Sum_probs=5.0
Q ss_pred ccChhhhhhh
Q 018053 282 KLCLECLDSA 291 (361)
Q Consensus 282 ~~C~~C~~~~ 291 (361)
..|..|-..+
T Consensus 710 ~~CP~CGtpl 719 (1337)
T PRK14714 710 VECPRCDVEL 719 (1337)
T ss_pred ccCCCCCCcc
Confidence 3455555443
No 100
>PLN02189 cellulose synthase
Probab=20.81 E-value=79 Score=36.23 Aligned_cols=31 Identities=29% Similarity=0.836 Sum_probs=20.4
Q ss_pred CCCcCccCCCccccCceEEeCCceecCCCcccCCCCCCC
Q 018053 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPI 196 (361)
Q Consensus 158 ~~~~C~~C~~~I~~ge~l~a~gk~wH~~CF~C~~C~~~L 196 (361)
...+|.-|+..|. +...|..| -.|..|+-|+
T Consensus 33 ~~~~C~iCgd~vg----~~~~g~~f----vaC~~C~fpv 63 (1040)
T PLN02189 33 DGQVCEICGDEIG----LTVDGDLF----VACNECGFPV 63 (1040)
T ss_pred cCccccccccccC----cCCCCCEE----EeeccCCCcc
Confidence 4568999998885 23456655 4566676544
Done!