Query psy14113
Match_columns 543
No_of_seqs 258 out of 1867
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 19:52:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14113.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14113hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 100.0 2.1E-43 4.6E-48 365.2 13.5 195 312-532 270-465 (468)
2 KOG2272|consensus 99.9 1.4E-29 3E-34 247.5 -3.8 204 312-527 69-310 (332)
3 KOG2272|consensus 99.9 2.6E-25 5.7E-30 217.5 -0.6 201 316-532 12-255 (332)
4 KOG1044|consensus 99.9 3.1E-24 6.6E-29 229.4 5.1 198 316-526 16-247 (670)
5 KOG1703|consensus 99.9 3.1E-24 6.7E-29 234.0 3.0 178 314-526 301-478 (479)
6 KOG4577|consensus 99.7 4.3E-20 9.4E-25 183.8 -3.4 124 401-533 32-157 (383)
7 KOG1701|consensus 99.7 1.7E-18 3.8E-23 180.6 2.1 130 316-465 334-467 (468)
8 KOG1703|consensus 99.7 1.1E-17 2.4E-22 182.8 5.9 175 319-531 246-422 (479)
9 KOG4577|consensus 99.7 8.6E-19 1.9E-23 174.6 -4.7 126 315-465 32-158 (383)
10 KOG1044|consensus 99.7 2E-17 4.4E-22 177.6 1.6 151 268-445 80-236 (670)
11 PF00412 LIM: LIM domain; Int 99.2 2.1E-11 4.5E-16 95.2 4.1 55 319-373 1-55 (58)
12 PF00412 LIM: LIM domain; Int 99.0 1.7E-10 3.7E-15 90.1 3.6 56 405-461 1-58 (58)
13 KOG1700|consensus 99.0 9.9E-11 2.2E-15 114.6 0.1 143 317-461 8-167 (200)
14 KOG1700|consensus 98.9 2.8E-10 6.2E-15 111.5 0.8 121 402-532 7-169 (200)
15 smart00132 LIM Zinc-binding do 98.2 8.7E-07 1.9E-11 63.0 2.7 38 318-355 1-38 (39)
16 smart00132 LIM Zinc-binding do 98.0 3.7E-06 8.1E-11 59.7 2.5 36 404-439 1-38 (39)
17 KOG0490|consensus 97.0 9.2E-05 2E-09 72.8 -1.6 114 321-460 1-119 (235)
18 KOG0490|consensus 96.9 0.00011 2.3E-09 72.4 -1.9 113 408-529 2-119 (235)
19 KOG1702|consensus 96.9 0.0001 2.2E-09 71.8 -1.9 57 317-374 5-61 (264)
20 KOG1702|consensus 96.2 0.00064 1.4E-08 66.4 -1.9 59 403-462 5-64 (264)
21 PF08394 Arc_trans_TRASH: Arch 75.6 1.4 3.1E-05 32.1 1.0 29 319-347 1-29 (37)
22 KOG2462|consensus 69.1 3.5 7.6E-05 42.6 2.5 16 492-507 240-255 (279)
23 KOG2462|consensus 60.2 16 0.00035 37.9 5.3 40 402-441 215-256 (279)
24 KOG0971|consensus 58.3 92 0.002 37.5 11.4 22 132-153 91-112 (1243)
25 KOG4443|consensus 53.0 9.9 0.00021 43.6 2.6 63 425-507 65-127 (694)
26 PF10367 Vps39_2: Vacuolar sor 50.0 12 0.00026 32.1 2.2 31 316-346 78-108 (109)
27 KOG0260|consensus 49.6 3.2E+02 0.007 34.2 14.1 9 144-152 1448-1456(1605)
28 KOG4443|consensus 48.5 7.9 0.00017 44.4 1.0 20 421-440 108-127 (694)
29 COG1645 Uncharacterized Zn-fin 47.7 9.5 0.00021 35.4 1.2 23 497-527 30-52 (131)
30 smart00504 Ubox Modified RING 47.7 27 0.00059 27.0 3.7 38 496-537 2-39 (63)
31 KOG0956|consensus 47.0 13 0.00028 43.0 2.3 16 397-412 112-127 (900)
32 KOG0320|consensus 46.8 11 0.00023 36.9 1.4 49 426-474 129-179 (187)
33 PF14446 Prok-RING_1: Prokaryo 45.4 13 0.00028 29.4 1.5 30 316-345 5-36 (54)
34 PF10367 Vps39_2: Vacuolar sor 43.4 18 0.00038 31.0 2.2 27 403-429 79-107 (109)
35 PF08394 Arc_trans_TRASH: Arch 41.6 11 0.00024 27.6 0.5 24 405-428 1-26 (37)
36 KOG4739|consensus 40.7 17 0.00036 37.0 1.8 41 433-473 8-48 (233)
37 PF05502 Dynactin_p62: Dynacti 40.6 16 0.00034 41.0 1.8 15 426-440 50-64 (483)
38 PF09943 DUF2175: Uncharacteri 39.5 11 0.00024 33.5 0.3 32 317-349 3-35 (101)
39 PF13240 zinc_ribbon_2: zinc-r 38.9 17 0.00036 23.7 1.0 11 319-329 2-12 (23)
40 smart00504 Ubox Modified RING 36.8 34 0.00074 26.5 2.7 44 429-474 2-47 (63)
41 PRK14559 putative protein seri 35.2 26 0.00056 40.7 2.5 10 318-327 3-12 (645)
42 PF14634 zf-RING_5: zinc-RING 35.2 32 0.00069 25.3 2.2 40 431-470 2-44 (44)
43 PF10764 Gin: Inhibitor of sig 34.5 30 0.00065 26.4 1.9 35 497-536 1-35 (46)
44 COG1645 Uncharacterized Zn-fin 32.6 29 0.00063 32.3 1.9 22 346-372 30-51 (131)
45 PF05502 Dynactin_p62: Dynacti 32.5 31 0.00066 38.7 2.5 37 464-508 28-65 (483)
46 PF14835 zf-RING_6: zf-RING of 32.5 43 0.00093 27.5 2.6 46 429-475 8-53 (65)
47 COG2191 Formylmethanofuran deh 30.8 23 0.00049 35.3 1.0 29 345-373 173-201 (206)
48 PF14835 zf-RING_6: zf-RING of 30.3 40 0.00086 27.7 2.1 22 365-390 28-49 (65)
49 PF11781 RRN7: RNA polymerase 29.2 35 0.00075 24.7 1.4 25 345-373 9-33 (36)
50 PRK14559 putative protein seri 29.1 49 0.0011 38.5 3.4 22 452-473 17-38 (645)
51 PF12773 DZR: Double zinc ribb 28.9 40 0.00086 25.3 1.8 9 347-355 15-23 (50)
52 PF13920 zf-C3HC4_3: Zinc fing 28.0 55 0.0012 24.6 2.5 42 430-473 4-48 (50)
53 KOG0956|consensus 28.0 86 0.0019 36.6 4.9 55 459-525 114-177 (900)
54 PF10235 Cript: Microtubule-as 26.5 35 0.00076 29.8 1.3 42 424-474 40-81 (90)
55 PF07754 DUF1610: Domain of un 25.9 46 0.001 22.1 1.4 12 319-330 1-12 (24)
56 PRK00807 50S ribosomal protein 25.5 49 0.0011 25.8 1.8 25 318-342 3-29 (52)
57 PF01258 zf-dskA_traR: Prokary 25.3 15 0.00033 26.1 -1.0 29 498-529 6-34 (36)
58 KOG0320|consensus 25.0 44 0.00095 32.7 1.7 43 494-538 130-172 (187)
59 PF13248 zf-ribbon_3: zinc-rib 24.6 46 0.001 22.0 1.3 12 317-328 3-14 (26)
60 cd00162 RING RING-finger (Real 24.2 52 0.0011 22.7 1.7 40 431-471 2-44 (45)
61 KOG1280|consensus 24.1 44 0.00096 35.8 1.7 15 491-505 75-89 (381)
62 COG0068 HypF Hydrogenase matur 23.8 37 0.00079 39.7 1.1 83 316-438 101-183 (750)
63 PF06677 Auto_anti-p27: Sjogre 22.9 37 0.0008 25.3 0.7 10 516-525 31-40 (41)
64 smart00531 TFIIE Transcription 22.8 72 0.0016 29.8 2.7 57 293-355 78-134 (147)
65 KOG1924|consensus 22.7 2.9E+02 0.0063 33.1 7.9 11 101-111 410-420 (1102)
66 PF14471 DUF4428: Domain of un 22.5 57 0.0012 25.3 1.6 30 497-529 1-30 (51)
67 TIGR00270 conserved hypothetic 22.3 66 0.0014 30.6 2.4 32 430-463 2-35 (154)
68 PF00645 zf-PARP: Poly(ADP-rib 21.9 38 0.00083 28.1 0.6 11 403-413 8-18 (82)
69 COG0068 HypF Hydrogenase matur 21.5 41 0.0009 39.3 1.0 84 402-506 101-184 (750)
70 KOG2593|consensus 21.0 60 0.0013 35.8 2.0 61 292-357 106-166 (436)
71 PF06906 DUF1272: Protein of u 20.6 1.1E+02 0.0023 24.6 2.7 44 430-474 7-53 (57)
72 PF11571 Med27: Mediator compl 20.6 46 0.001 28.6 0.9 16 457-472 49-64 (90)
No 1
>KOG1701|consensus
Probab=100.00 E-value=2.1e-43 Score=365.22 Aligned_cols=195 Identities=55% Similarity=1.230 Sum_probs=182.3
Q ss_pred cCccccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccch
Q psy14113 312 EGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLI 391 (543)
Q Consensus 312 ~~~~~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I 391 (543)
..+++.+|.+|+|.|.+.+..++||++.||..||+|..|++.|.++.||.+|+++|||.||. .
T Consensus 270 ~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq-----~------------ 332 (468)
T KOG1701|consen 270 VEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQ-----D------------ 332 (468)
T ss_pred hhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHH-----H------------
Confidence 45667799999999999999999999999999999999999999999999999999999994 2
Q ss_pred hhhhcccccccccccccCccceeeeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCC
Q psy14113 392 MEMYSGFQQTAEKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKG 471 (543)
Q Consensus 392 ~~~~s~~~~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~ 471 (543)
++.+|..|++.|++++++|+|+.||+.||+|..|++.|.|..|+++.++++||..||+++|+++|+.|+++
T Consensus 333 ---------tlekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~P 403 (468)
T KOG1701|consen 333 ---------TLEKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNP 403 (468)
T ss_pred ---------HHHHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCC
Confidence 34456788888889999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcceEEEEeCCCcccCCCCccCCCCCcCCC-CCCcceeecCCcccCchhhhhhhhc
Q psy14113 472 ITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTD-EPDKRCYPLQGRLMCRACHLSHLSR 532 (543)
Q Consensus 472 I~~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~-~~~~~~~~~dg~~yC~~C~~~~~~~ 532 (543)
|++.+|.+|+++|+++|+.||.+||+|++|++.|.. +++.+||.+|++|+|+.||.++++.
T Consensus 404 I~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl~~ 465 (468)
T KOG1701|consen 404 ILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRLQA 465 (468)
T ss_pred ccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhhcc
Confidence 999999999999999999999999999999999994 4447999999999999999998864
No 2
>KOG2272|consensus
Probab=99.94 E-value=1.4e-29 Score=247.48 Aligned_cols=204 Identities=27% Similarity=0.612 Sum_probs=174.8
Q ss_pred cCccccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccc----------------
Q psy14113 312 EGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYS---------------- 375 (543)
Q Consensus 312 ~~~~~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~---------------- 375 (543)
...+.+.|++|++-|.| ++|.+++..||+.||+|..|++.|.+..|+...|+.+|..|-...
T Consensus 69 ~~LfaPcC~kC~EFiiG--rVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~ 146 (332)
T KOG2272|consen 69 HVLFAPCCGKCGEFIIG--RVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAH 146 (332)
T ss_pred hhhhchhhcccccchhh--HHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhh
Confidence 34577999999999987 689999999999999999999999999999888999988876420
Q ss_pred -----------cccccchhhhccccchhhhh----------cccc-cccccccccCccceeeeeeccCccccCcCccCCC
Q psy14113 376 -----------GFQQTAEKCAICGHLIMEMY----------SGFQ-QTAEKCAICGHLIMEMILQAMGKSYHPGCFRCCL 433 (543)
Q Consensus 376 -----------~~~~fa~kCa~C~~~I~~~~----------s~~~-~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~ 433 (543)
.+..+..+|.+|++-+.... +.+. .+.++|..|.++|.++++.++|++||.++|+|+.
T Consensus 147 iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~ 226 (332)
T KOG2272|consen 147 IDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAK 226 (332)
T ss_pred cccccccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehh
Confidence 12334556777776654221 2222 5679999999999999999999999999999999
Q ss_pred CCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCCCCCcceEEEEeCCCcccCCCCccCCCCCcCCCCCCcce
Q psy14113 434 CNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRC 513 (543)
Q Consensus 434 C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~ 513 (543)
|.+++-|..- +++.|..||+.||.++|+..|..|.+.|.+. .+.++++.|.++||.|+.|.+.|... .+|
T Consensus 227 CekPFlGHrH-YEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~-------vv~al~KawCv~cf~Cs~Cdkkl~~K--~Kf 296 (332)
T KOG2272|consen 227 CEKPFLGHRH-YEKKGLAYCETHYHQLFGNLCFICNRVIGGD-------VVSALNKAWCVECFSCSTCDKKLTQK--NKF 296 (332)
T ss_pred cCCcccchhh-hhhcCchhHHHHHHHHhhhhheecCCccCcc-------HHHHhhhhhccccccccccccccccc--cce
Confidence 9999988776 4899999999999999999999999999752 26689999999999999999999987 479
Q ss_pred eecCCcccCchhhh
Q psy14113 514 YPLQGRLMCRACHL 527 (543)
Q Consensus 514 ~~~dg~~yC~~C~~ 527 (543)
|++|-++.|++|+.
T Consensus 297 ~E~DmkP~CKkCy~ 310 (332)
T KOG2272|consen 297 YEFDMKPVCKKCYD 310 (332)
T ss_pred eeeccchHHHHHHh
Confidence 99999999999987
No 3
>KOG2272|consensus
Probab=99.90 E-value=2.6e-25 Score=217.54 Aligned_cols=201 Identities=29% Similarity=0.641 Sum_probs=175.2
Q ss_pred ccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccchhhhh
Q psy14113 316 FGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEMY 395 (543)
Q Consensus 316 ~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~~ 395 (543)
...|.+|......+++++...|..||..||.|+.|-.++.+..||+.+|+.||+.||. .+|+|-|+.|++.|++-.
T Consensus 12 ~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~----~LfaPcC~kC~EFiiGrV 87 (332)
T KOG2272|consen 12 NMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFH----VLFAPCCGKCGEFIIGRV 87 (332)
T ss_pred HHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccch----hhhchhhcccccchhhHH
Confidence 3469999999988889999999999999999999999999999999999999999998 789999999999876310
Q ss_pred ------c------------------cc-------------------ccccccccccCccceeeeeeccCccccCcCccCC
Q psy14113 396 ------S------------------GF-------------------QQTAEKCAICGHLIMEMILQAMGKSYHPGCFRCC 432 (543)
Q Consensus 396 ------s------------------~~-------------------~~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs 432 (543)
| +| ..+.-.|..|...|.+..+...+..||+.+|+|.
T Consensus 88 ikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt 167 (332)
T KOG2272|consen 88 IKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCT 167 (332)
T ss_pred HHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecc
Confidence 0 00 0135678888888888889999999999999999
Q ss_pred CCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCCCCCcceEEEEeCCCcccCCCCccCCCCCcCCCCCCcc
Q psy14113 433 LCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKR 512 (543)
Q Consensus 433 ~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~ 512 (543)
.|++.|....- +..|.+||..|+.++--++|..|.++|.. ..|.+++++||.++|+|..|.+++-+. +
T Consensus 168 ~C~keL~sdaR--evk~eLyClrChD~mgipiCgaC~rpIee-------rvi~amgKhWHveHFvCa~CekPFlGH---r 235 (332)
T KOG2272|consen 168 TCGKELTSDAR--EVKGELYCLRCHDKMGIPICGACRRPIEE-------RVIFAMGKHWHVEHFVCAKCEKPFLGH---R 235 (332)
T ss_pred cccccccchhh--hhccceeccccccccCCcccccccCchHH-------HHHHHhccccchhheeehhcCCcccch---h
Confidence 99999987654 35799999999999888999999999963 135689999999999999999999886 5
Q ss_pred eeecCCcccCchhhhhhhhc
Q psy14113 513 CYPLQGRLMCRACHLSHLSR 532 (543)
Q Consensus 513 ~~~~dg~~yC~~C~~~~~~~ 532 (543)
.|+..|..||+..+.+++.+
T Consensus 236 HYEkkGlaYCe~h~~qLfG~ 255 (332)
T KOG2272|consen 236 HYEKKGLAYCETHYHQLFGN 255 (332)
T ss_pred hhhhcCchhHHHHHHHHhhh
Confidence 69999999999999999886
No 4
>KOG1044|consensus
Probab=99.89 E-value=3.1e-24 Score=229.40 Aligned_cols=198 Identities=28% Similarity=0.574 Sum_probs=158.5
Q ss_pred ccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCC-eeeeccccc-cc-------cccccchh---
Q psy14113 316 FGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHG-RVYCEEDYL-YS-------GFQQTAEK--- 383 (543)
Q Consensus 316 ~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG-~~yC~~cY~-~~-------~~~~fa~k--- 383 (543)
...|.+|++...+ .++.+.+++||..||+|..|++.|...+||.+++ ++||...+. +. --+.|.++
T Consensus 16 ~i~c~~c~~kc~g--evlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~ 93 (670)
T KOG1044|consen 16 GIKCDKCRKKCSG--EVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFS 93 (670)
T ss_pred ceehhhhCCcccc--ceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccce
Confidence 4579999999886 4799999999999999999999999999987765 677764332 11 01234455
Q ss_pred hhccccchhhhh-------------------cc--cccccccccccCccce-eeeeeccCccccCcCccCCCCCCCCCCC
Q psy14113 384 CAICGHLIMEMY-------------------SG--FQQTAEKCAICGHLIM-EMILQAMGKSYHPGCFRCCLCNECLDGV 441 (543)
Q Consensus 384 Ca~C~~~I~~~~-------------------s~--~~~~~~~C~~C~k~I~-~~~v~a~gk~wH~~CF~Cs~C~~~L~g~ 441 (543)
|+.|..++..+. .. -..+...|++|++.|. +.++.|+++.||+.||+|..|...|.++
T Consensus 94 cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge 173 (670)
T KOG1044|consen 94 CSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE 173 (670)
T ss_pred ecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce
Confidence 455666653210 00 1124678999998886 6899999999999999999999999876
Q ss_pred ceeeeecCceeccchhhhhccccccccCCCCCCCCCCcceEEEEeCCCcccCCCCccCCCCCcCCCCCCcceeecCCccc
Q psy14113 442 PFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLM 521 (543)
Q Consensus 442 ~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~~~~dg~~y 521 (543)
. +..+|.+||+.||.+.|+.+|..|.+.|.+. .+.++|++||+.|.+|.+|+.+|.+| +..|.....||
T Consensus 174 y--~skdg~pyce~dy~~~fgvkc~~c~~fisgk-------vLqag~kh~HPtCARCsRCgqmF~eG--EEMYlQGs~iW 242 (670)
T KOG1044|consen 174 Y--MSKDGVPYCEKDYQAKFGVKCEECEKFISGK-------VLQAGDKHFHPTCARCSRCGQMFGEG--EEMYLQGSEIW 242 (670)
T ss_pred e--eccCCCcchhhhhhhhcCeehHHhhhhhhhh-------hhhccCcccCcchhhhhhhccccccc--hheeecccccc
Confidence 4 3689999999999999999999999999863 36789999999999999999999998 46677778888
Q ss_pred Cchhh
Q psy14113 522 CRACH 526 (543)
Q Consensus 522 C~~C~ 526 (543)
=..|-
T Consensus 243 HP~C~ 247 (670)
T KOG1044|consen 243 HPDCK 247 (670)
T ss_pred CCccc
Confidence 77774
No 5
>KOG1703|consensus
Probab=99.89 E-value=3.1e-24 Score=234.00 Aligned_cols=178 Identities=25% Similarity=0.593 Sum_probs=158.0
Q ss_pred ccccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccchhh
Q psy14113 314 EYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIME 393 (543)
Q Consensus 314 ~~~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~ 393 (543)
...+.|..|+..|.+. +++.++++.||..+|.|..|+..+....+...+|++||..|+. ..++
T Consensus 301 ~~~p~c~~c~~~i~~~-~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~----~~~~------------ 363 (479)
T KOG1703|consen 301 VTRPLCLSCNQKIRSV-KVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFH----APFR------------ 363 (479)
T ss_pred cccccccccccCcccc-eeEeeccccccccceeeccccccccCCCccccCCCccHHHHHH----HhhC------------
Confidence 4568999999999763 5799999999999999999999999888889999999999997 3444
Q ss_pred hhcccccccccccccCccceeeeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCC
Q psy14113 394 MYSGFQQTAEKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGIT 473 (543)
Q Consensus 394 ~~s~~~~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~ 473 (543)
+.|.+|++.|.++.|.++++.||++||.|..|++.|....|+ ..+|.+||+.||++++..+|..|.++|.
T Consensus 364 ---------p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~-~~~~~pyce~~~~~~~~~~~~~~~~p~~ 433 (479)
T KOG1703|consen 364 ---------PNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFF-ESDGEPYCEDHYKKLFTTKCDYCKKPVE 433 (479)
T ss_pred ---------ccccccCCchHHhHhhhccCeechhceeeecccCCCCCCccc-ccCCccchhhhHhhhccccchhccchhH
Confidence 455778888888889999999999999999999999988885 5799999999999999999999999987
Q ss_pred CCCCCcceEEEEeCCCcccCCCCccCCCCCcCCCCCCcceeecCCcccCchhh
Q psy14113 474 PVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRACH 526 (543)
Q Consensus 474 ~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~ 526 (543)
..+ ..+.+++..||..||+|..|.+.|.++ .|+...++++|++|+
T Consensus 434 ~~~-----~~ie~~~~~~h~~~F~c~~c~~~l~~~---~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 434 FGS-----RQIEADGSPFHGDCFRCANCMKKLTKK---TFFETLDKPLCQKHF 478 (479)
T ss_pred hhh-----hHhhccCccccccceehhhhhccccCC---ceeecCCccccccCC
Confidence 543 247789999999999999999999986 789899999999986
No 6
>KOG4577|consensus
Probab=99.75 E-value=4.3e-20 Score=183.81 Aligned_cols=124 Identities=29% Similarity=0.709 Sum_probs=108.3
Q ss_pred ccccccccCcccee-eeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCCCCCc
Q psy14113 401 TAEKCAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTE 479 (543)
Q Consensus 401 ~~~~C~~C~k~I~~-~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~eg~~ 479 (543)
..+.|++|.+.|.+ .++.+++++||..|++|+.|...|....| .++|.+||+++|+++|+.+|..|+.+|.+..
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCF--sR~~s~yCkedFfKrfGTKCsaC~~GIpPtq--- 106 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCF--SREGSVYCKEDFFKRFGTKCSACQEGIPPTQ--- 106 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHh--hcCCceeehHHHHHHhCCcchhhcCCCChHH---
Confidence 46789999999988 57889999999999999999999988877 4899999999999999999999999999864
Q ss_pred ceEEEEeCCCcccCCCCccCCCCCcCCCCCCcceeec-CCcccCchhhhhhhhcc
Q psy14113 480 ETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPL-QGRLMCRACHLSHLSRH 533 (543)
Q Consensus 480 e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~~~~-dg~~yC~~C~~~~~~~~ 533 (543)
+.-.+.|..||.+||.|..|++.|..|+ .||.+ |.+++|+.-+...-++.
T Consensus 107 --VVRkAqd~VYHl~CF~C~iC~R~L~TGd--EFYLmeD~rLvCK~DYE~Ak~k~ 157 (383)
T KOG4577|consen 107 --VVRKAQDFVYHLHCFACFICKRQLATGD--EFYLMEDARLVCKDDYETAKQKH 157 (383)
T ss_pred --HHHHhhcceeehhhhhhHhhhcccccCC--eeEEeccceeehhhhHHHHHhcc
Confidence 2224789999999999999999999984 67765 78999999887665553
No 7
>KOG1701|consensus
Probab=99.71 E-value=1.7e-18 Score=180.57 Aligned_cols=130 Identities=26% Similarity=0.637 Sum_probs=107.8
Q ss_pred ccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCcee-eeCCeeeeccccccccccccchhhhccccchhhh
Q psy14113 316 FGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFY-NVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEM 394 (543)
Q Consensus 316 ~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~-~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~ 394 (543)
+.+|..|++.|.+ +++.|+|+.||+.||+|..|.+.|.+..|. ..++++||..||+ +.|+++|+.|.++|+..
T Consensus 334 lekC~~Cg~~I~d--~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh----~kfAPrCs~C~~PI~P~ 407 (468)
T KOG1701|consen 334 LEKCNKCGEPIMD--RILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFH----KKFAPRCSVCGNPILPR 407 (468)
T ss_pred HHHHhhhhhHHHH--HHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhh----hhcCcchhhccCCccCC
Confidence 4579999999975 789999999999999999999999998886 5788999999999 78999999998888753
Q ss_pred hcccccccccccccCccceeeeeeccCccccCcCccCCCCCCCCCC---CceeeeecCceeccchhhhhccccc
Q psy14113 395 YSGFQQTAEKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDG---VPFTVDVDNKIYCVNDYHRMFAPKC 465 (543)
Q Consensus 395 ~s~~~~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~C~~~L~g---~~f~v~~dGkpYC~~CY~k~f~pkC 465 (543)
.++.+.| .|.+|++.||.+|++|.+|+..|+. ..-.+-.||+++|+.|..++....|
T Consensus 408 -----------~G~~etv---Rvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl~~~~ 467 (468)
T KOG1701|consen 408 -----------DGKDETV---RVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRLQAGS 467 (468)
T ss_pred -----------CCCcceE---EEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhhcccC
Confidence 3443333 4678999999999999999999981 1122356999999999988766544
No 8
>KOG1703|consensus
Probab=99.70 E-value=1.1e-17 Score=182.80 Aligned_cols=175 Identities=20% Similarity=0.359 Sum_probs=153.5
Q ss_pred cccCCceeecCcceeeccCceeccCCcccC-ccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccchhhhhcc
Q psy14113 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICC-SCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEMYSG 397 (543)
Q Consensus 319 C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs-~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~~s~ 397 (543)
|..|..++.+ ..+.+....||...|+|. .|...|....++.+.+...+..+|. ..
T Consensus 246 ~~~~~~p~~~--p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~------------------ 301 (479)
T KOG1703|consen 246 SASMDSPECQ--PLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYH----NV------------------ 301 (479)
T ss_pred CcccCCCccC--cceecccccccccccccccccchhhccccccccccccccccccc----cc------------------
Confidence 6677777754 467889999999999998 7999998889999999999999886 22
Q ss_pred cccccccccccCcccee-eeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCCC
Q psy14113 398 FQQTAEKCAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVE 476 (543)
Q Consensus 398 ~~~~~~~C~~C~k~I~~-~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~e 476 (543)
..++|..|...|.+ .++.++++.||+.+|.|..|...+....| ...+|.+||..||.+.+.+.|.+|+++|...
T Consensus 302 ---~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~-~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~- 376 (479)
T KOG1703|consen 302 ---TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGP-RELDGKILCHECFHAPFRPNCKRCLLPILEE- 376 (479)
T ss_pred ---ccccccccccCcccceeEeeccccccccceeeccccccccCCCc-cccCCCccHHHHHHHhhCccccccCCchHHh-
Confidence 24567888888888 99999999999999999999999987777 5679999999999999999999999999853
Q ss_pred CCcceEEEEeCCCcccCCCCccCCCCCcCCCCCCcceeecCCcccCchhhhhhhh
Q psy14113 477 GTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRACHLSHLS 531 (543)
Q Consensus 477 g~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~~~ 531 (543)
.|.+.++.||++||.|..|++.|... .||..++.+||..|+.++..
T Consensus 377 ------~v~a~~~~wH~~cf~C~~C~~~~~~~---~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 377 ------GVCALGRLWHPECFVCADCGKPLKNS---SFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred ------HhhhccCeechhceeeecccCCCCCC---cccccCCccchhhhHhhhcc
Confidence 36678999999999999999999886 78999999999999999987
No 9
>KOG4577|consensus
Probab=99.68 E-value=8.6e-19 Score=174.62 Aligned_cols=126 Identities=26% Similarity=0.652 Sum_probs=108.5
Q ss_pred cccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccchhhh
Q psy14113 315 YFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEM 394 (543)
Q Consensus 315 ~~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~ 394 (543)
-.++|++|.+.|.+.. ++.+++++||..|++|+.|...|.+ .+|.++|.+||+++|. ++|+.||.+|+.+|.+.
T Consensus 32 eip~CagC~q~IlDrF-ilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFf----KrfGTKCsaC~~GIpPt 105 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRF-ILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFF----KRFGTKCSACQEGIPPT 105 (383)
T ss_pred ccccccchHHHHHHHH-HHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHH----HHhCCcchhhcCCCChH
Confidence 3578999999998764 6789999999999999999999985 4667899999999995 89999998888887541
Q ss_pred hcccccccccccccCccceeeeeeccCccccCcCccCCCCCCCCC-CCceeeeecCceeccchhhhhccccc
Q psy14113 395 YSGFQQTAEKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYCVNDYHRMFAPKC 465 (543)
Q Consensus 395 ~s~~~~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~C~~~L~-g~~f~v~~dGkpYC~~CY~k~f~pkC 465 (543)
..+.+|.+..||..||.|..|++.|. |.+|++..|+++.|+.+|++.....|
T Consensus 106 -------------------qVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 106 -------------------QVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred -------------------HHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 23456888999999999999999997 88898888999999999998766666
No 10
>KOG1044|consensus
Probab=99.65 E-value=2e-17 Score=177.57 Aligned_cols=151 Identities=29% Similarity=0.565 Sum_probs=111.6
Q ss_pred CCCCCCCCCCCccCCCCCCCcchHHHHHHHHHHH-----HHHHHhhhhccCccccccccCCceeecCcceeeccCceecc
Q psy14113 268 VTPYGKNLLPYNVTPPRPMGPTEAERKIEELTRQ-----LEEEMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHT 342 (543)
Q Consensus 268 ~t~~g~~~~P~~~t~p~p~~ps~~e~~l~~lt~~-----l~~~m~~~~~~~~~~~~C~~C~k~I~g~~~~v~a~gk~wH~ 342 (543)
+.+.|+.+||..+.+.....|.....+.....+. ....|...+.+.-+...|++|++.|. .++++.|+++.||.
T Consensus 80 vsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk-~gq~llald~qwhv 158 (670)
T KOG1044|consen 80 VSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELK-NGQALLALDKQWHV 158 (670)
T ss_pred EecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhh-ccceeeeeccceee
Confidence 5577888888888776665554433332211111 11112222223335568999999997 45789999999999
Q ss_pred CCcccCccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccchhhhhcccccccccccccCccceeeeeeccCc
Q psy14113 343 NCFICCSCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEMYSGFQQTAEKCAICGHLIMEMILQAMGK 422 (543)
Q Consensus 343 ~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~~s~~~~~~~~C~~C~k~I~~~~v~a~gk 422 (543)
.||+|..|+..|. .+|+.+||.+||+.||. ..|+.|| ..|.+.|.+.++.+.++
T Consensus 159 ~cfkc~~c~~vL~-gey~skdg~pyce~dy~----~~fgvkc---------------------~~c~~fisgkvLqag~k 212 (670)
T KOG1044|consen 159 SCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQ----AKFGVKC---------------------EECEKFISGKVLQAGDK 212 (670)
T ss_pred eeeehhhhccccc-ceeeccCCCcchhhhhh----hhcCeeh---------------------HHhhhhhhhhhhhccCc
Confidence 9999999999887 47999999999999998 5677766 55666677889999999
Q ss_pred cccCcCccCCCCCCCCC-CCceee
Q psy14113 423 SYHPGCFRCCLCNECLD-GVPFTV 445 (543)
Q Consensus 423 ~wH~~CF~Cs~C~~~L~-g~~f~v 445 (543)
+||+.|-+|..|+..+. |++.++
T Consensus 213 h~HPtCARCsRCgqmF~eGEEMYl 236 (670)
T KOG1044|consen 213 HFHPTCARCSRCGQMFGEGEEMYL 236 (670)
T ss_pred ccCcchhhhhhhccccccchheee
Confidence 99999999999999987 555543
No 11
>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=99.17 E-value=2.1e-11 Score=95.24 Aligned_cols=55 Identities=36% Similarity=0.986 Sum_probs=51.2
Q ss_pred cccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccc
Q psy14113 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYL 373 (543)
Q Consensus 319 C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~ 373 (543)
|.+|++.|.+.+.++.++|+.||.+||+|..|++.|.+..|+..+|++||+.||.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 55 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQ 55 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHh
Confidence 8899999998776667999999999999999999999888999999999999996
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=99.03 E-value=1.7e-10 Score=90.05 Aligned_cols=56 Identities=41% Similarity=0.955 Sum_probs=48.7
Q ss_pred ccccCcccee--eeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhc
Q psy14113 405 CAICGHLIME--MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMF 461 (543)
Q Consensus 405 C~~C~k~I~~--~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f 461 (543)
|.+|++.|.+ .++.++++.||++||+|..|++.|.+..| +..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~-~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDF-YEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSE-EEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCee-EeECCEEECHHHHhhhC
Confidence 6788888885 34469999999999999999999998876 46899999999999876
No 13
>KOG1700|consensus
Probab=98.97 E-value=9.9e-11 Score=114.65 Aligned_cols=143 Identities=24% Similarity=0.557 Sum_probs=104.9
Q ss_pred cccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccc------cccc----cchhhhc
Q psy14113 317 GICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYS------GFQQ----TAEKCAI 386 (543)
Q Consensus 317 ~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~------~~~~----fa~kCa~ 386 (543)
..|..|++.|+-.++ +...|..||..||+|..|.+.|....+...++.+||+.||..+ +|.. +..+=..
T Consensus 8 ~kc~~c~k~vy~~e~-~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEK-VQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred chhhhccCcchHHHH-HhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 479999999987665 5588999999999999999999988898999999999975421 1111 1110000
Q ss_pred cccchh------hhhcccccccccccccCcccee-eeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhh
Q psy14113 387 CGHLIM------EMYSGFQQTAEKCAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHR 459 (543)
Q Consensus 387 C~~~I~------~~~s~~~~~~~~C~~C~k~I~~-~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k 459 (543)
...... .++.-+......|..|.+.+.. +-+...+..||..||+|+.|+..|....+. ..+|.+||..++..
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~-~~~g~l~~~~~~~~ 165 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYA-ALEGVLYCKHHFAQ 165 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchh-hcCCccccchhhhe
Confidence 000000 0112233457899999999986 567778899999999999999999988874 56899999887766
Q ss_pred hc
Q psy14113 460 MF 461 (543)
Q Consensus 460 ~f 461 (543)
++
T Consensus 166 ~~ 167 (200)
T KOG1700|consen 166 LF 167 (200)
T ss_pred ee
Confidence 54
No 14
>KOG1700|consensus
Probab=98.91 E-value=2.8e-10 Score=111.45 Aligned_cols=121 Identities=30% Similarity=0.686 Sum_probs=97.3
Q ss_pred cccccccCcccee-eeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccc-----------------
Q psy14113 402 AEKCAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAP----------------- 463 (543)
Q Consensus 402 ~~~C~~C~k~I~~-~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~p----------------- 463 (543)
...|..|++.++- ..+...+..||..||+|..|.+.|....+. ..++.+||..||...+++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~-~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYS-EHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhcccccccccccccc-ccccccccccchHhhhCcccccccccccccCCCCc
Confidence 4467888888873 344588999999999999999999977775 479999999976554422
Q ss_pred ------------------------cccccCCCCCCCCCCcceEEEEeCCCcccCCCCccCCCCCcCCCCCCcceeecCCc
Q psy14113 464 ------------------------KCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGR 519 (543)
Q Consensus 464 ------------------------kC~~C~k~I~~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~~~~dg~ 519 (543)
.|..|++.+-+.+ .+...+..||..||+|+.|+..|... .+-...+.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E------k~~~~~~~~hk~cfrc~~~~~~ls~~---~~~~~~g~ 156 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE------KVTGNGLEFHKSCFRCTHCGKKLSPK---NYAALEGV 156 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehH------HHhhhhhhhhhhheeecccccccCCc---chhhcCCc
Confidence 3999999998765 36678899999999999999999996 56667899
Q ss_pred ccCchhhhhhhhc
Q psy14113 520 LMCRACHLSHLSR 532 (543)
Q Consensus 520 ~yC~~C~~~~~~~ 532 (543)
+||...+..++.-
T Consensus 157 l~~~~~~~~~~~~ 169 (200)
T KOG1700|consen 157 LYCKHHFAQLFKG 169 (200)
T ss_pred cccchhhheeecC
Confidence 9999876665444
No 15
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.21 E-value=8.7e-07 Score=62.99 Aligned_cols=38 Identities=34% Similarity=0.978 Sum_probs=34.1
Q ss_pred ccccCCceeecCcceeeccCceeccCCcccCccCCCCC
Q psy14113 318 ICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR 355 (543)
Q Consensus 318 ~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~ 355 (543)
+|.+|++.|.+.+..+.++++.||..||+|..|+..|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 48999999987656788999999999999999999885
No 16
>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=98.00 E-value=3.7e-06 Score=59.68 Aligned_cols=36 Identities=47% Similarity=1.088 Sum_probs=31.6
Q ss_pred cccccCcccee--eeeeccCccccCcCccCCCCCCCCC
Q psy14113 404 KCAICGHLIME--MILQAMGKSYHPGCFRCCLCNECLD 439 (543)
Q Consensus 404 ~C~~C~k~I~~--~~v~a~gk~wH~~CF~Cs~C~~~L~ 439 (543)
+|.+|++.|.+ ..+.+.++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 47888888876 6788899999999999999999885
No 17
>KOG0490|consensus
Probab=97.02 E-value=9.2e-05 Score=72.79 Aligned_cols=114 Identities=26% Similarity=0.551 Sum_probs=83.8
Q ss_pred cCCceeecCcceeeccCceeccCCcccCccCCCCC--CCceeeeCCeeeeccccccccccccchhhhccccchhhhhccc
Q psy14113 321 TCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR--GKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEMYSGF 398 (543)
Q Consensus 321 ~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~--~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~~s~~ 398 (543)
.|+..|.+.. .+.+.+..||..|.+|..|...|. ...|.. +|..||..+|... ..+.
T Consensus 1 ~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~--~~~~----------------- 59 (235)
T KOG0490|consen 1 GCGRQILDRY-LLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQRE--FKFS----------------- 59 (235)
T ss_pred CCCccccchH-HhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhh--hhcc-----------------
Confidence 3677776654 466679999999999999999997 445555 9999999998620 0222
Q ss_pred ccccccccccCccce--eeeeeccCccccCcCccCCCCCCCCC-CCceeeeecCceeccchhhhh
Q psy14113 399 QQTAEKCAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYCVNDYHRM 460 (543)
Q Consensus 399 ~~~~~~C~~C~k~I~--~~~v~a~gk~wH~~CF~Cs~C~~~L~-g~~f~v~~dGkpYC~~CY~k~ 460 (543)
.+|.+|...|. +++..+..+. |..||.|..|...+. +.++.+..+.+..|..++.+.
T Consensus 60 ----~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 ----KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ----ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 35566776664 4566666676 999999999988655 667777666788998887653
No 18
>KOG0490|consensus
Probab=96.95 E-value=0.00011 Score=72.39 Aligned_cols=113 Identities=25% Similarity=0.589 Sum_probs=86.0
Q ss_pred cCcccee-eeeeccCccccCcCccCCCCCCCCC--CCceeeeecCceeccchhhh--hccccccccCCCCCCCCCCcceE
Q psy14113 408 CGHLIME-MILQAMGKSYHPGCFRCCLCNECLD--GVPFTVDVDNKIYCVNDYHR--MFAPKCAACGKGITPVEGTEETV 482 (543)
Q Consensus 408 C~k~I~~-~~v~a~gk~wH~~CF~Cs~C~~~L~--g~~f~v~~dGkpYC~~CY~k--~f~pkC~~C~k~I~~~eg~~e~~ 482 (543)
|+..|.+ ..+.+.+..||..|..|..|...|. ...| .. +|..||..+|.. .+..+|.+|...|...+..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~l---- 75 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCF-SK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDEL---- 75 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcc-cC-CCcccccccchhhhhccccccCCCCCcCHHHHH----
Confidence 5566665 3455668999999999999999997 4444 34 999999999998 7889999999999655421
Q ss_pred EEEeCCCcccCCCCccCCCCCcCCCCCCcceeecCCcccCchhhhhh
Q psy14113 483 RVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRACHLSH 529 (543)
Q Consensus 483 ~v~a~dk~yH~~CF~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~ 529 (543)
..+.++. |.-||.|..|.+.+..... .-+..+....|.+...+.
T Consensus 76 -er~f~~~-h~Pd~~~r~~la~~~~~~e-~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 76 -ERAFEKV-HLPCFACRECLALLLTGDE-FRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred -HHhhcCC-CcCccchHHHHhhcCCCCe-eeeehhhhhhcHhhhhhh
Confidence 2245555 9999999999998888642 234456689999876554
No 19
>KOG1702|consensus
Probab=96.95 E-value=0.0001 Score=71.84 Aligned_cols=57 Identities=25% Similarity=0.601 Sum_probs=50.8
Q ss_pred cccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeecccccc
Q psy14113 317 GICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLY 374 (543)
Q Consensus 317 ~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~ 374 (543)
..|..|++.++..++ +..+++.||..||+|..|+..|.-..+-..+.++||..+|..
T Consensus 5 ~n~~~cgk~vYPvE~-v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpk 61 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEE-VKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPK 61 (264)
T ss_pred chhhhhccccccHHH-HhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccc
Confidence 468899999987765 889999999999999999999988888778999999999974
No 20
>KOG1702|consensus
Probab=96.22 E-value=0.00064 Score=66.44 Aligned_cols=59 Identities=25% Similarity=0.583 Sum_probs=49.3
Q ss_pred ccccccCcccee-eeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhcc
Q psy14113 403 EKCAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFA 462 (543)
Q Consensus 403 ~~C~~C~k~I~~-~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~ 462 (543)
..|..|++.++. +-+..+++.||..||+|..|+.+|.-..+. ..+.++||..+|.+..+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyK-gy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYK-GYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhcc-ccccCCCcCccccccee
Confidence 356888888876 567788999999999999999999877764 35889999999987653
No 21
>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=75.64 E-value=1.4 Score=32.15 Aligned_cols=29 Identities=28% Similarity=0.663 Sum_probs=22.4
Q ss_pred cccCCceeecCcceeeccCceeccCCccc
Q psy14113 319 CHTCGEKVTGAGQACQAMGNLYHTNCFIC 347 (543)
Q Consensus 319 C~~C~k~I~g~~~~v~a~gk~wH~~CF~C 347 (543)
|..|+++|.++..++...++.||.-|-.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence 77899999888777788888887655443
No 22
>KOG2462|consensus
Probab=69.13 E-value=3.5 Score=42.60 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=10.1
Q ss_pred cCCCCccCCCCCcCCC
Q psy14113 492 HVDCYMCEDCGLQLTD 507 (543)
Q Consensus 492 H~~CF~C~~C~k~L~~ 507 (543)
+.+=|.|..|+|.|..
T Consensus 240 ~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 240 DVKKHQCPRCGKSFAL 255 (279)
T ss_pred CCccccCcchhhHHHH
Confidence 3445777777776654
No 23
>KOG2462|consensus
Probab=60.17 E-value=16 Score=37.86 Aligned_cols=40 Identities=20% Similarity=0.363 Sum_probs=21.9
Q ss_pred cccccccCccceeee-eec-cCccccCcCccCCCCCCCCCCC
Q psy14113 402 AEKCAICGHLIMEMI-LQA-MGKSYHPGCFRCCLCNECLDGV 441 (543)
Q Consensus 402 ~~~C~~C~k~I~~~~-v~a-~gk~wH~~CF~Cs~C~~~L~g~ 441 (543)
...|..|++.+.|+. ++| +..+=+.+-|.|..|++.+...
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence 355677777766631 222 2333445567777776665443
No 24
>KOG0971|consensus
Probab=58.30 E-value=92 Score=37.49 Aligned_cols=22 Identities=36% Similarity=0.409 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCCCCCCCceecc
Q psy14113 132 SHSSVGSQDSKHSSPRGSYVSN 153 (543)
Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~ 153 (543)
.+.+.|+--++||||++|.-+.
T Consensus 91 tp~sa~sk~~~~ss~~tSla~S 112 (1243)
T KOG0971|consen 91 TPRSAGSKASPGSSPGTSLAAS 112 (1243)
T ss_pred CCCccccCCCCCCCCCCChhhh
Confidence 3457788899999999998764
No 25
>KOG4443|consensus
Probab=53.00 E-value=9.9 Score=43.60 Aligned_cols=63 Identities=22% Similarity=0.428 Sum_probs=39.6
Q ss_pred cCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCCCCCcceEEEEeCCCcccCCCCccCCCCCc
Q psy14113 425 HPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQ 504 (543)
Q Consensus 425 H~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~eg~~e~~~v~a~dk~yH~~CF~C~~C~k~ 504 (543)
.+.|-.|..|++.- +...-++|..|-... .| .|.++-.. .+..+..+.++|+.|..|+..
T Consensus 65 C~~crvCe~c~~~g-------D~~kf~~Ck~cDvsy---h~-yc~~P~~~---------~v~sg~~~ckk~~~c~qc~~~ 124 (694)
T KOG4443|consen 65 CPSCRVCEACGTTG-------DPKKFLLCKRCDVSY---HC-YCQKPPND---------KVPSGPWLCKKCTRCRQCDST 124 (694)
T ss_pred cCCceeeeeccccC-------Ccccccccccccccc---cc-cccCCccc---------cccCcccccHHHHhhhhcccc
Confidence 46777788887321 123345777763321 22 26666542 244566789999999999998
Q ss_pred CCC
Q psy14113 505 LTD 507 (543)
Q Consensus 505 L~~ 507 (543)
|..
T Consensus 125 lpg 127 (694)
T KOG4443|consen 125 LPG 127 (694)
T ss_pred ccc
Confidence 877
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=50.02 E-value=12 Score=32.12 Aligned_cols=31 Identities=19% Similarity=0.443 Sum_probs=18.9
Q ss_pred ccccccCCceeecCcceeeccCceeccCCcc
Q psy14113 316 FGICHTCGEKVTGAGQACQAMGNLYHTNCFI 346 (543)
Q Consensus 316 ~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~ 346 (543)
...|..|++.|....-++.-.|..+|..|++
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 3568888888864322233345667777753
No 27
>KOG0260|consensus
Probab=49.63 E-value=3.2e+02 Score=34.24 Aligned_cols=9 Identities=56% Similarity=0.309 Sum_probs=4.4
Q ss_pred CCCCCceec
Q psy14113 144 SSPRGSYVS 152 (543)
Q Consensus 144 ~~~~~~~~~ 152 (543)
|||--|.-|
T Consensus 1448 ssp~~s~ts 1456 (1605)
T KOG0260|consen 1448 SSPGYSPTS 1456 (1605)
T ss_pred CCCCCCCCC
Confidence 555544444
No 28
>KOG4443|consensus
Probab=48.51 E-value=7.9 Score=44.38 Aligned_cols=20 Identities=35% Similarity=0.745 Sum_probs=16.0
Q ss_pred CccccCcCccCCCCCCCCCC
Q psy14113 421 GKSYHPGCFRCCLCNECLDG 440 (543)
Q Consensus 421 gk~wH~~CF~Cs~C~~~L~g 440 (543)
+..+.++||+|..|+..+.+
T Consensus 108 g~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 108 GPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cccccHHHHhhhhccccccc
Confidence 56677888889999888776
No 29
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=47.72 E-value=9.5 Score=35.41 Aligned_cols=23 Identities=30% Similarity=0.941 Sum_probs=18.5
Q ss_pred ccCCCCCcCCCCCCcceeecCCcccCchhhh
Q psy14113 497 MCEDCGLQLTDEPDKRCYPLQGRLMCRACHL 527 (543)
Q Consensus 497 ~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~ 527 (543)
.|..|+.+| |..+|.+||..|-.
T Consensus 30 hCp~Cg~PL--------F~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL--------FRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc--------eeeCCeEECCCCCc
Confidence 588888886 44799999999973
No 30
>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=47.68 E-value=27 Score=26.99 Aligned_cols=38 Identities=18% Similarity=0.225 Sum_probs=27.4
Q ss_pred CccCCCCCcCCCCCCcceeecCCcccCchhhhhhhhccCCCC
Q psy14113 496 YMCEDCGLQLTDEPDKRCYPLQGRLMCRACHLSHLSRHHQSP 537 (543)
Q Consensus 496 F~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~~~~~~~~~ 537 (543)
|.|..|+..+.+. .....|++||+.|..+.+..+..++
T Consensus 2 ~~Cpi~~~~~~~P----v~~~~G~v~~~~~i~~~~~~~~~cP 39 (63)
T smart00504 2 FLCPISLEVMKDP----VILPSGQTYERRAIEKWLLSHGTDP 39 (63)
T ss_pred cCCcCCCCcCCCC----EECCCCCEEeHHHHHHHHHHCCCCC
Confidence 5788888888774 3445789999999888887644433
No 31
>KOG0956|consensus
Probab=46.96 E-value=13 Score=42.98 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=10.2
Q ss_pred ccccccccccccCccc
Q psy14113 397 GFQQTAEKCAICGHLI 412 (543)
Q Consensus 397 ~~~~~~~~C~~C~k~I 412 (543)
+...+...|..|.+.-
T Consensus 112 P~dRfnKtCYIC~E~G 127 (900)
T KOG0956|consen 112 PHDRFNKTCYICNEEG 127 (900)
T ss_pred chhhhcceeeeecccC
Confidence 3455667777777653
No 32
>KOG0320|consensus
Probab=46.76 E-value=11 Score=36.88 Aligned_cols=49 Identities=20% Similarity=0.480 Sum_probs=34.9
Q ss_pred CcCccCCCCCCCCCCCceeeeecCceeccchhhhh--ccccccccCCCCCC
Q psy14113 426 PGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRM--FAPKCAACGKGITP 474 (543)
Q Consensus 426 ~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~--f~pkC~~C~k~I~~ 474 (543)
..||+|-.|-.......-.-..=|++||..|.... .+.+|..|++.|+.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 45678888866655433111346999999998864 46899999999974
No 33
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=45.44 E-value=13 Score=29.41 Aligned_cols=30 Identities=27% Similarity=0.640 Sum_probs=19.8
Q ss_pred ccccccCCceeecCcceeec--cCceeccCCc
Q psy14113 316 FGICHTCGEKVTGAGQACQA--MGNLYHTNCF 345 (543)
Q Consensus 316 ~~~C~~C~k~I~g~~~~v~a--~gk~wH~~CF 345 (543)
..+|..|++.|...+.+|.- =+..||.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 35799999999654444442 3556777765
No 34
>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=43.41 E-value=18 Score=31.02 Aligned_cols=27 Identities=26% Similarity=0.736 Sum_probs=12.2
Q ss_pred ccccccCcccee--eeeeccCccccCcCc
Q psy14113 403 EKCAICGHLIME--MILQAMGKSYHPGCF 429 (543)
Q Consensus 403 ~~C~~C~k~I~~--~~v~a~gk~wH~~CF 429 (543)
..|..|++.|.. .++-..|..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 346666655543 122223344555443
No 35
>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=41.60 E-value=11 Score=27.57 Aligned_cols=24 Identities=29% Similarity=0.632 Sum_probs=13.8
Q ss_pred ccccCcccee--eeeeccCccccCcC
Q psy14113 405 CAICGHLIME--MILQAMGKSYHPGC 428 (543)
Q Consensus 405 C~~C~k~I~~--~~v~a~gk~wH~~C 428 (543)
|.-|++.|.+ .++...++.||.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 4556666653 45556666666444
No 36
>KOG4739|consensus
Probab=40.66 E-value=17 Score=37.01 Aligned_cols=41 Identities=20% Similarity=0.391 Sum_probs=32.4
Q ss_pred CCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCC
Q psy14113 433 LCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGIT 473 (543)
Q Consensus 433 ~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~ 473 (543)
.|...-++..|++..=++++|+.|...-.+..|.-|++.|.
T Consensus 8 ~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 8 KCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred cccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 34444446778776678999999998888889999999985
No 37
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=40.59 E-value=16 Score=40.99 Aligned_cols=15 Identities=33% Similarity=0.791 Sum_probs=12.3
Q ss_pred CcCccCCCCCCCCCC
Q psy14113 426 PGCFRCCLCNECLDG 440 (543)
Q Consensus 426 ~~CF~Cs~C~~~L~g 440 (543)
.+||.|-.|...|..
T Consensus 50 r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 50 RNCFDCPICFSPLSV 64 (483)
T ss_pred cccccCCCCCCccee
Confidence 489999999888863
No 38
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=39.51 E-value=11 Score=33.53 Aligned_cols=32 Identities=19% Similarity=0.291 Sum_probs=22.8
Q ss_pred cccccCCceeecCcceeec-cCceeccCCcccCc
Q psy14113 317 GICHTCGEKVTGAGQACQA-MGNLYHTNCFICCS 349 (543)
Q Consensus 317 ~~C~~C~k~I~g~~~~v~a-~gk~wH~~CF~Cs~ 349 (543)
..|..|++.|+... .+++ .+..-|-.||+=..
T Consensus 3 WkC~iCg~~I~~gq-lFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQ-LFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecc-eEEEecCCcEeHHHHHHHH
Confidence 57999999998654 4544 45677888886543
No 39
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.85 E-value=17 Score=23.67 Aligned_cols=11 Identities=27% Similarity=0.999 Sum_probs=6.9
Q ss_pred cccCCceeecC
Q psy14113 319 CHTCGEKVTGA 329 (543)
Q Consensus 319 C~~C~k~I~g~ 329 (543)
|..|+..|...
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 66677766543
No 40
>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=36.76 E-value=34 Score=26.45 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=31.8
Q ss_pred ccCCCCCCCCCCCceeeeecCceeccchhhhhc--cccccccCCCCCC
Q psy14113 429 FRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMF--APKCAACGKGITP 474 (543)
Q Consensus 429 F~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f--~pkC~~C~k~I~~ 474 (543)
|.|..|+..+.. .. +...|+.||+.|..+.+ ...|..|++.+..
T Consensus 2 ~~Cpi~~~~~~~-Pv-~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-PV-ILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-CE-ECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 578888887764 33 34679999999987644 3568888888753
No 41
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.24 E-value=26 Score=40.74 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=5.9
Q ss_pred ccccCCceee
Q psy14113 318 ICHTCGEKVT 327 (543)
Q Consensus 318 ~C~~C~k~I~ 327 (543)
+|..|+..+.
T Consensus 3 ~Cp~Cg~~n~ 12 (645)
T PRK14559 3 ICPQCQFENP 12 (645)
T ss_pred cCCCCCCcCC
Confidence 5666666553
No 42
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=35.18 E-value=32 Score=25.31 Aligned_cols=40 Identities=23% Similarity=0.496 Sum_probs=27.0
Q ss_pred CCCCCCCCC-CCceeeeecCceeccchhhhhc--cccccccCC
Q psy14113 431 CCLCNECLD-GVPFTVDVDNKIYCVNDYHRMF--APKCAACGK 470 (543)
Q Consensus 431 Cs~C~~~L~-g~~f~v~~dGkpYC~~CY~k~f--~pkC~~C~k 470 (543)
|..|...+. ...+++..=|..+|..|..+.. ...|..|++
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 556666663 3345455568899999988877 567777764
No 43
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=34.54 E-value=30 Score=26.40 Aligned_cols=35 Identities=17% Similarity=0.543 Sum_probs=25.7
Q ss_pred ccCCCCCcCCCCCCcceeecCCcccCchhhhhhhhccCCC
Q psy14113 497 MCEDCGLQLTDEPDKRCYPLQGRLMCRACHLSHLSRHHQS 536 (543)
Q Consensus 497 ~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~~~~~~~~ 536 (543)
+|..|++....| ..+.|..+|..|-.+.++.+..+
T Consensus 1 ~CiiC~~~~~~G-----I~I~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKEEG-----IHIYGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCCCC-----EEEECeEehHHHHHHhccCCCCC
Confidence 477788877765 44788899999988887765443
No 44
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=32.61 E-value=29 Score=32.31 Aligned_cols=22 Identities=32% Similarity=0.757 Sum_probs=16.0
Q ss_pred ccCccCCCCCCCceeeeCCeeeecccc
Q psy14113 346 ICCSCGRALRGKAFYNVHGRVYCEEDY 372 (543)
Q Consensus 346 ~Cs~C~~~L~~~~f~~~dG~~yC~~cY 372 (543)
.|-.||.+| |.++|.+||..|-
T Consensus 30 hCp~Cg~PL-----F~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc-----eeeCCeEECCCCC
Confidence 367777766 3378888888776
No 45
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=32.54 E-value=31 Score=38.71 Aligned_cols=37 Identities=22% Similarity=0.449 Sum_probs=22.5
Q ss_pred cccccCCCCCCCCCCcceEEEEeCCCcccC-CCCccCCCCCcCCCC
Q psy14113 464 KCAACGKGITPVEGTEETVRVVSMDKDFHV-DCYMCEDCGLQLTDE 508 (543)
Q Consensus 464 kC~~C~k~I~~~eg~~e~~~v~a~dk~yH~-~CF~C~~C~k~L~~~ 508 (543)
.|..|-..+...+ +...+..+. .||.|..|...|...
T Consensus 28 yCp~CL~~~p~~e--------~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 28 YCPNCLFEVPSSE--------ARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred ECccccccCChhh--------heeccceeccccccCCCCCCcceeE
Confidence 4556665555432 123344454 899999998888764
No 46
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=32.46 E-value=43 Score=27.53 Aligned_cols=46 Identities=20% Similarity=0.509 Sum_probs=21.8
Q ss_pred ccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCC
Q psy14113 429 FRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPV 475 (543)
Q Consensus 429 F~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~ 475 (543)
++|..|...|.. ...+..=.+.||..|-...++..|..|..+-...
T Consensus 8 LrCs~C~~~l~~-pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q 53 (65)
T PF14835_consen 8 LRCSICFDILKE-PVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ 53 (65)
T ss_dssp TS-SSS-S--SS--B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred cCCcHHHHHhcC-CceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence 467777666542 2223334678899998888888899999887543
No 47
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=30.82 E-value=23 Score=35.30 Aligned_cols=29 Identities=17% Similarity=0.378 Sum_probs=24.7
Q ss_pred cccCccCCCCCCCceeeeCCeeeeccccc
Q psy14113 345 FICCSCGRALRGKAFYNVHGRVYCEEDYL 373 (543)
Q Consensus 345 F~Cs~C~~~L~~~~f~~~dG~~yC~~cY~ 373 (543)
-+|..||..+....-...+|+++|..||.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~ 201 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAE 201 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccc
Confidence 68899998887777778899999999986
No 48
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=30.30 E-value=40 Score=27.74 Aligned_cols=22 Identities=14% Similarity=0.558 Sum_probs=6.9
Q ss_pred eeeeccccccccccccchhhhccccc
Q psy14113 365 RVYCEEDYLYSGFQQTAEKCAICGHL 390 (543)
Q Consensus 365 ~~yC~~cY~~~~~~~fa~kCa~C~~~ 390 (543)
..||..|-. +.++..|+.|+.+
T Consensus 28 H~fCs~Ci~----~~~~~~CPvC~~P 49 (65)
T PF14835_consen 28 HIFCSSCIR----DCIGSECPVCHTP 49 (65)
T ss_dssp --B-TTTGG----GGTTTB-SSS--B
T ss_pred cHHHHHHhH----HhcCCCCCCcCCh
Confidence 345555543 2233345444443
No 49
>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=29.21 E-value=35 Score=24.66 Aligned_cols=25 Identities=32% Similarity=0.579 Sum_probs=17.0
Q ss_pred cccCccCCCCCCCceeeeCCeeeeccccc
Q psy14113 345 FICCSCGRALRGKAFYNVHGRVYCEEDYL 373 (543)
Q Consensus 345 F~Cs~C~~~L~~~~f~~~dG~~yC~~cY~ 373 (543)
+.|..|+.. .|...+|..||..|-+
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 447777753 4667788888876653
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.10 E-value=49 Score=38.51 Aligned_cols=22 Identities=18% Similarity=0.591 Sum_probs=10.1
Q ss_pred eccchhhhhccccccccCCCCC
Q psy14113 452 YCVNDYHRMFAPKCAACGKGIT 473 (543)
Q Consensus 452 YC~~CY~k~f~pkC~~C~k~I~ 473 (543)
||..|-..+-...|..|+..+.
T Consensus 17 FC~~CG~~l~~~~Cp~CG~~~~ 38 (645)
T PRK14559 17 FCQKCGTSLTHKPCPQCGTEVP 38 (645)
T ss_pred cccccCCCCCCCcCCCCCCCCC
Confidence 4444433322234555555554
No 51
>PF12773 DZR: Double zinc ribbon
Probab=28.95 E-value=40 Score=25.28 Aligned_cols=9 Identities=44% Similarity=1.091 Sum_probs=4.3
Q ss_pred cCccCCCCC
Q psy14113 347 CCSCGRALR 355 (543)
Q Consensus 347 Cs~C~~~L~ 355 (543)
|..|+..|.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 444555444
No 52
>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=28.02 E-value=55 Score=24.56 Aligned_cols=42 Identities=21% Similarity=0.464 Sum_probs=28.4
Q ss_pred cCCCCCCCCCCCceeeeecCce-eccchhhhh--ccccccccCCCCC
Q psy14113 430 RCCLCNECLDGVPFTVDVDNKI-YCVNDYHRM--FAPKCAACGKGIT 473 (543)
Q Consensus 430 ~Cs~C~~~L~g~~f~v~~dGkp-YC~~CY~k~--f~pkC~~C~k~I~ 473 (543)
.|..|...... ..+..=|+. +|..|+.+. ...+|..|+++|.
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 46666665433 333356777 999999886 4578999999985
No 53
>KOG0956|consensus
Probab=27.98 E-value=86 Score=36.62 Aligned_cols=55 Identities=24% Similarity=0.510 Sum_probs=29.2
Q ss_pred hhccccccccCCCCCCCCCCcceEEEEeC----CCcccCCCCc-----cCCCCCcCCCCCCcceeecCCcccCchh
Q psy14113 459 RMFAPKCAACGKGITPVEGTEETVRVVSM----DKDFHVDCYM-----CEDCGLQLTDEPDKRCYPLQGRLMCRAC 525 (543)
Q Consensus 459 k~f~pkC~~C~k~I~~~eg~~e~~~v~a~----dk~yH~~CF~-----C~~C~k~L~~~~~~~~~~~dg~~yC~~C 525 (543)
.+|...|.-|.+.-.+.+-. ....|... .+.||..|.. |+.=+ -..|+..||.-|
T Consensus 114 dRfnKtCYIC~E~GrpnkA~-~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~g-----------n~~dNVKYCGYC 177 (900)
T KOG0956|consen 114 DRFNKTCYICNEEGRPNKAA-KGACMTCNKSGCKQAFHVTCAQRAGLLCEEEG-----------NISDNVKYCGYC 177 (900)
T ss_pred hhhcceeeeecccCCccccc-cccceecccccchhhhhhhHhhhhccceeccc-----------cccccceechhH
Confidence 45677788887765554311 11223321 3457877743 43311 225666777766
No 54
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=26.50 E-value=35 Score=29.79 Aligned_cols=42 Identities=29% Similarity=0.581 Sum_probs=27.7
Q ss_pred ccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCC
Q psy14113 424 YHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITP 474 (543)
Q Consensus 424 wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~ 474 (543)
|-..--.|..|...+ ...|.-||..|-.++ -+|+-|++.|..
T Consensus 40 y~~~~~~C~~CK~~v-------~q~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 40 YAPYSSKCKICKTKV-------HQPGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred ccccCcccccccccc-------ccCCCccChhhhccc--CcccccCCeecc
Confidence 333334577787644 234667899996654 489999999864
No 55
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=25.85 E-value=46 Score=22.12 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=7.4
Q ss_pred cccCCceeecCc
Q psy14113 319 CHTCGEKVTGAG 330 (543)
Q Consensus 319 C~~C~k~I~g~~ 330 (543)
|..|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 566777776544
No 56
>PRK00807 50S ribosomal protein L24e; Validated
Probab=25.47 E-value=49 Score=25.82 Aligned_cols=25 Identities=24% Similarity=0.670 Sum_probs=16.7
Q ss_pred ccccCCceee-cCcce-eeccCceecc
Q psy14113 318 ICHTCGEKVT-GAGQA-CQAMGNLYHT 342 (543)
Q Consensus 318 ~C~~C~k~I~-g~~~~-v~a~gk~wH~ 342 (543)
.|..|+..|. +.+.. +..+|+.|+.
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~F 29 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILYF 29 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEEE
Confidence 5888888886 44443 4566777643
No 57
>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=25.33 E-value=15 Score=26.09 Aligned_cols=29 Identities=34% Similarity=0.866 Sum_probs=19.5
Q ss_pred cCCCCCcCCCCCCcceeecCCcccCchhhhhh
Q psy14113 498 CEDCGLQLTDEPDKRCYPLQGRLMCRACHLSH 529 (543)
Q Consensus 498 C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~ 529 (543)
|..|+..+... +...+.+..+|..|....
T Consensus 6 C~~CGe~I~~~---Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 6 CEDCGEPIPEE---RLVAVPGATLCVECQERR 34 (36)
T ss_dssp -TTTSSBEEHH---HHHHCTTECS-HHHHHHH
T ss_pred ccccCChHHHH---HHHhCCCcEECHHHhCcc
Confidence 77888877764 445567889999987654
No 58
>KOG0320|consensus
Probab=24.97 E-value=44 Score=32.75 Aligned_cols=43 Identities=21% Similarity=0.468 Sum_probs=27.4
Q ss_pred CCCccCCCCCcCCCCCCcceeecCCcccCchhhhhhhhccCCCCC
Q psy14113 494 DCYMCEDCGLQLTDEPDKRCYPLQGRLMCRACHLSHLSRHHQSPT 538 (543)
Q Consensus 494 ~CF~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~~~~~~~~~~ 538 (543)
.||+|..|-....... -+-..-|+++|+.|....+...+.+++
T Consensus 130 ~~~~CPiCl~~~sek~--~vsTkCGHvFC~~Cik~alk~~~~CP~ 172 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKV--PVSTKCGHVFCSQCIKDALKNTNKCPT 172 (187)
T ss_pred cccCCCceecchhhcc--ccccccchhHHHHHHHHHHHhCCCCCC
Confidence 4677777766554431 122356888888888887777666654
No 59
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.65 E-value=46 Score=22.03 Aligned_cols=12 Identities=25% Similarity=0.811 Sum_probs=7.5
Q ss_pred cccccCCceeec
Q psy14113 317 GICHTCGEKVTG 328 (543)
Q Consensus 317 ~~C~~C~k~I~g 328 (543)
..|..|+..|..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 357777776543
No 60
>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=24.21 E-value=52 Score=22.72 Aligned_cols=40 Identities=18% Similarity=0.491 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeeeecCceeccchhhhhc---cccccccCCC
Q psy14113 431 CCLCNECLDGVPFTVDVDNKIYCVNDYHRMF---APKCAACGKG 471 (543)
Q Consensus 431 Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f---~pkC~~C~k~ 471 (543)
|..|...+. ..+.+..=|..||..|..+.+ ..+|..|+..
T Consensus 2 C~iC~~~~~-~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFR-EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhh-CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 445555442 222222246667777765433 2356666654
No 61
>KOG1280|consensus
Probab=24.12 E-value=44 Score=35.82 Aligned_cols=15 Identities=20% Similarity=0.731 Sum_probs=11.8
Q ss_pred ccCCCCccCCCCCcC
Q psy14113 491 FHVDCYMCEDCGLQL 505 (543)
Q Consensus 491 yH~~CF~C~~C~k~L 505 (543)
|-+.||+|.-|++.=
T Consensus 75 y~~qSftCPyC~~~G 89 (381)
T KOG1280|consen 75 YDPQSFTCPYCGIMG 89 (381)
T ss_pred cccccccCCcccccc
Confidence 456799999999863
No 62
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.78 E-value=37 Score=39.71 Aligned_cols=83 Identities=19% Similarity=0.424 Sum_probs=52.9
Q ss_pred ccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCCceeeeCCeeeeccccccccccccchhhhccccchhhhh
Q psy14113 316 FGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYLYSGFQQTAEKCAICGHLIMEMY 395 (543)
Q Consensus 316 ~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~~f~~~dG~~yC~~cY~~~~~~~fa~kCa~C~~~I~~~~ 395 (543)
..+|..|-+.|.+. .++.||=--..|+.||- .|.....-||=...-. ..
T Consensus 101 ~a~C~~Cl~Ei~dp------~~rrY~YPF~~CT~CGP-----RfTIi~alPYDR~nTs----M~---------------- 149 (750)
T COG0068 101 AATCEDCLEEIFDP------NSRRYLYPFINCTNCGP-----RFTIIEALPYDRENTS----MA---------------- 149 (750)
T ss_pred hhhhHHHHHHhcCC------CCcceeccccccCCCCc-----ceeeeccCCCCcccCc----cc----------------
Confidence 35788998777543 46788888889999984 4444455554221111 00
Q ss_pred cccccccccccccCccceeeeeeccCccccCcCccCCCCCCCC
Q psy14113 396 SGFQQTAEKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECL 438 (543)
Q Consensus 396 s~~~~~~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~C~~~L 438 (543)
.-+.|..|.+. +-...++.||..=..|..|+-.+
T Consensus 150 -----~F~lC~~C~~E----Y~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 150 -----DFPLCPFCDKE----YKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred -----cCcCCHHHHHH----hcCccccccccccccCcccCCCe
Confidence 11356666553 33456899999999999998655
No 63
>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=22.94 E-value=37 Score=25.32 Aligned_cols=10 Identities=30% Similarity=1.092 Sum_probs=5.7
Q ss_pred cCCcccCchh
Q psy14113 516 LQGRLMCRAC 525 (543)
Q Consensus 516 ~dg~~yC~~C 525 (543)
.++++||..|
T Consensus 31 k~g~~~Cv~C 40 (41)
T PF06677_consen 31 KDGKIYCVSC 40 (41)
T ss_pred cCCCEECCCC
Confidence 3556666655
No 64
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.77 E-value=72 Score=29.76 Aligned_cols=57 Identities=26% Similarity=0.540 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHhhhhccCccccccccCCceeecCcceeeccCceeccCCcccCccCCCCC
Q psy14113 293 RKIEELTRQLEEEMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR 355 (543)
Q Consensus 293 ~~l~~lt~~l~~~m~~~~~~~~~~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~ 355 (543)
.++..+...+++.+.... ....-+|..|+..+...+ ++...+. ..-|.|..||..|.
T Consensus 78 ~r~~~~~~~L~~~l~~e~--~~~~Y~Cp~C~~~y~~~e-a~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 78 YKLDKMRKRLEDKLEDET--NNAYYKCPNCQSKYTFLE-ANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred HHHHHHHHHHHHHHhccc--CCcEEECcCCCCEeeHHH-HHHhcCC---CCcEECCCCCCEEE
Confidence 344555555555544322 223457999998875332 2322231 33499999998875
No 65
>KOG1924|consensus
Probab=22.70 E-value=2.9e+02 Score=33.10 Aligned_cols=11 Identities=36% Similarity=0.437 Sum_probs=6.6
Q ss_pred CCccccccccC
Q psy14113 101 SPLYENVDYYN 111 (543)
Q Consensus 101 ~~~~~~~~~~~ 111 (543)
-=||-|-|||-
T Consensus 410 hlllirnDy~~ 420 (1102)
T KOG1924|consen 410 HLLLIRNDYYI 420 (1102)
T ss_pred HHHHHhhhhhh
Confidence 34566667775
No 66
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=22.54 E-value=57 Score=25.33 Aligned_cols=30 Identities=27% Similarity=0.528 Sum_probs=20.2
Q ss_pred ccCCCCCcCCCCCCcceeecCCcccCchhhhhh
Q psy14113 497 MCEDCGLQLTDEPDKRCYPLQGRLMCRACHLSH 529 (543)
Q Consensus 497 ~C~~C~k~L~~~~~~~~~~~dg~~yC~~C~~~~ 529 (543)
.|..|+..++-- .++-..|| .+|..|+.+.
T Consensus 1 ~C~iCg~kigl~--~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLF--KRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccc--cceeccCc-cchHHHHHHh
Confidence 477888877663 23323355 7999999887
No 67
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.33 E-value=66 Score=30.59 Aligned_cols=32 Identities=19% Similarity=0.491 Sum_probs=24.9
Q ss_pred cCCCCCCCCCCCceeeeecCce--eccchhhhhccc
Q psy14113 430 RCCLCNECLDGVPFTVDVDNKI--YCVNDYHRMFAP 463 (543)
Q Consensus 430 ~Cs~C~~~L~g~~f~v~~dGkp--YC~~CY~k~f~p 463 (543)
.|..|++.+.+..+.+..+|-. .|..|+ +|+.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGK 35 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHH--hcCC
Confidence 3899999999887888788854 499998 4543
No 68
>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=21.90 E-value=38 Score=28.11 Aligned_cols=11 Identities=36% Similarity=0.667 Sum_probs=6.6
Q ss_pred ccccccCccce
Q psy14113 403 EKCAICGHLIM 413 (543)
Q Consensus 403 ~~C~~C~k~I~ 413 (543)
-.|.+|++.|.
T Consensus 8 a~Ck~C~~~I~ 18 (82)
T PF00645_consen 8 AKCKGCKKKIA 18 (82)
T ss_dssp EBETTTSCBE-
T ss_pred ccCcccCCcCC
Confidence 45667777774
No 69
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.51 E-value=41 Score=39.28 Aligned_cols=84 Identities=23% Similarity=0.473 Sum_probs=55.4
Q ss_pred cccccccCccceeeeeeccCccccCcCccCCCCCCCCCCCceeeeecCceeccchhhhhccccccccCCCCCCCCCCcce
Q psy14113 402 AEKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTEET 481 (543)
Q Consensus 402 ~~~C~~C~k~I~~~~v~a~gk~wH~~CF~Cs~C~~~L~g~~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~~eg~~e~ 481 (543)
...|..|.+.|.+ -.++.||=---.|+.|+-.+ .+ .+..||=+..-.-.--+.|..|.+.-.
T Consensus 101 ~a~C~~Cl~Ei~d----p~~rrY~YPF~~CT~CGPRf-----TI-i~alPYDR~nTsM~~F~lC~~C~~EY~-------- 162 (750)
T COG0068 101 AATCEDCLEEIFD----PNSRRYLYPFINCTNCGPRF-----TI-IEALPYDRENTSMADFPLCPFCDKEYK-------- 162 (750)
T ss_pred hhhhHHHHHHhcC----CCCcceeccccccCCCCcce-----ee-eccCCCCcccCccccCcCCHHHHHHhc--------
Confidence 3456677666654 34677887777899997544 33 355666444333333467888877432
Q ss_pred EEEEeCCCcccCCCCccCCCCCcCC
Q psy14113 482 VRVVSMDKDFHVDCYMCEDCGLQLT 506 (543)
Q Consensus 482 ~~v~a~dk~yH~~CF~C~~C~k~L~ 506 (543)
-..|+.||-.=..|..|+=.+.
T Consensus 163 ---dP~nRRfHAQp~aCp~CGP~~~ 184 (750)
T COG0068 163 ---DPLNRRFHAQPIACPKCGPHLF 184 (750)
T ss_pred ---CccccccccccccCcccCCCeE
Confidence 3678999999999999997653
No 70
>KOG2593|consensus
Probab=21.04 E-value=60 Score=35.80 Aligned_cols=61 Identities=28% Similarity=0.586 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHhhhhccCccccccccCCceeecCcceeeccCceeccCCcccCccCCCCCCC
Q psy14113 292 ERKIEELTRQLEEEMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGK 357 (543)
Q Consensus 292 e~~l~~lt~~l~~~m~~~~~~~~~~~~C~~C~k~I~g~~~~v~a~gk~wH~~CF~Cs~C~~~L~~~ 357 (543)
.=+|..|.+.++..+........+ .|..|++....-+ ++..++. -..-|.|..|+..|...
T Consensus 106 KyKlh~m~krled~~~d~t~~~~Y--~Cp~C~kkyt~Le-a~~L~~~--~~~~F~C~~C~gelveD 166 (436)
T KOG2593|consen 106 KYKLHQMRKRLEDRLRDDTNVAGY--VCPNCQKKYTSLE-ALQLLDN--ETGEFHCENCGGELVED 166 (436)
T ss_pred HHHHHHHHHHHHHHhhhccccccc--cCCccccchhhhH-HHHhhcc--cCceEEEecCCCchhcc
Confidence 446788888998887765544444 6999999864322 1222211 11248899999988644
No 71
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=20.59 E-value=1.1e+02 Score=24.65 Aligned_cols=44 Identities=18% Similarity=0.460 Sum_probs=29.5
Q ss_pred cCCCCCCCCCCC---ceeeeecCceeccchhhhhccccccccCCCCCC
Q psy14113 430 RCCLCNECLDGV---PFTVDVDNKIYCVNDYHRMFAPKCAACGKGITP 474 (543)
Q Consensus 430 ~Cs~C~~~L~g~---~f~v~~dGkpYC~~CY~k~f~pkC~~C~k~I~~ 474 (543)
.|..|++.|... .++- .-.=-||..|-..++...|..|+..+..
T Consensus 7 nCE~C~~dLp~~s~~A~IC-SfECTFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYIC-SFECTFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEE-eEeCcccHHHHHHHhcCcCcCCCCcccc
Confidence 356677776532 2322 2334578888888888899999887754
No 72
>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=20.57 E-value=46 Score=28.64 Aligned_cols=16 Identities=38% Similarity=1.030 Sum_probs=13.6
Q ss_pred hhhhccccccccCCCC
Q psy14113 457 YHRMFAPKCAACGKGI 472 (543)
Q Consensus 457 Y~k~f~pkC~~C~k~I 472 (543)
|..+|...|.+|++-+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 5677888999999888
Done!