Query 040725
Match_columns 164
No_of_seqs 174 out of 1351
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 11:07:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701 Focal adhesion adaptor 99.8 9.3E-22 2E-26 155.5 -0.8 115 11-153 275-397 (468)
2 KOG1701 Focal adhesion adaptor 99.8 7.7E-21 1.7E-25 150.3 -0.6 114 9-143 333-451 (468)
3 KOG4577 Transcription factor L 99.8 1.3E-20 2.9E-25 142.4 -3.4 123 9-158 32-171 (383)
4 KOG2272 Focal adhesion protein 99.7 9E-19 1.9E-23 130.4 1.6 118 7-153 134-257 (332)
5 KOG2272 Focal adhesion protein 99.7 3.5E-19 7.6E-24 132.6 -4.4 115 2-143 4-119 (332)
6 KOG1703 Adaptor protein Enigma 99.6 1.7E-16 3.7E-21 131.7 4.9 116 9-151 302-423 (479)
7 KOG1044 Actin-binding LIM Zn-f 99.6 2.3E-16 4.9E-21 129.1 1.9 104 9-140 132-236 (670)
8 KOG1700 Regulatory protein MLP 99.6 6.3E-16 1.4E-20 114.6 3.8 139 4-143 1-155 (200)
9 KOG1703 Adaptor protein Enigma 99.6 3.7E-16 8.1E-21 129.7 2.1 108 9-143 362-470 (479)
10 PF00412 LIM: LIM domain; Int 99.5 4E-14 8.6E-19 84.8 4.9 57 13-69 1-58 (58)
11 KOG1044 Actin-binding LIM Zn-f 99.5 5.3E-14 1.1E-18 115.4 5.0 138 11-150 17-192 (670)
12 PF00412 LIM: LIM domain; Int 99.0 1.9E-10 4.1E-15 68.6 2.6 38 112-149 15-58 (58)
13 smart00132 LIM Zinc-binding do 98.6 4.4E-08 9.5E-13 53.3 2.9 37 12-48 1-38 (39)
14 KOG4577 Transcription factor L 98.4 3.2E-08 7E-13 75.7 -1.2 66 9-74 91-159 (383)
15 smart00132 LIM Zinc-binding do 98.3 3.7E-07 8.1E-12 49.5 1.6 25 110-134 14-38 (39)
16 KOG1700 Regulatory protein MLP 98.0 1.5E-06 3.2E-11 64.6 0.6 69 7-75 105-173 (200)
17 KOG1702 Nebulin repeat protein 97.9 7.4E-07 1.6E-11 65.3 -3.1 60 11-70 5-64 (264)
18 KOG1702 Nebulin repeat protein 96.7 0.00027 5.8E-09 52.1 -0.9 40 104-143 12-51 (264)
19 KOG0490 Transcription factor, 95.9 0.0011 2.5E-08 49.8 -1.5 100 16-143 2-107 (235)
20 PF10367 Vps39_2: Vacuolar sor 77.7 1.6 3.6E-05 28.4 1.8 29 10-38 78-107 (109)
21 PF09943 DUF2175: Uncharacteri 70.1 1.4 3E-05 29.1 -0.1 30 12-41 4-34 (101)
22 COG2888 Predicted Zn-ribbon RN 65.7 5.8 0.00013 23.5 1.9 30 10-48 9-38 (61)
23 COG1645 Uncharacterized Zn-fin 65.6 4.8 0.0001 27.9 1.8 23 39-66 30-52 (131)
24 PF11781 RRN7: RNA polymerase 65.6 4.1 8.9E-05 21.6 1.2 25 38-66 9-33 (36)
25 PF08209 Sgf11: Sgf11 (transcr 64.7 1.4 3.1E-05 22.9 -0.7 17 124-140 5-21 (33)
26 PF14446 Prok-RING_1: Prokaryo 64.0 4.3 9.3E-05 23.6 1.2 30 9-38 4-36 (54)
27 PF00645 zf-PARP: Poly(ADP-rib 63.0 2.3 4.9E-05 26.6 -0.1 17 9-25 6-22 (82)
28 COG2191 Formylmethanofuran deh 58.9 4.5 9.8E-05 30.1 0.8 31 38-68 173-203 (206)
29 PF10367 Vps39_2: Vacuolar sor 57.8 10 0.00022 24.5 2.4 29 38-66 79-108 (109)
30 PF08394 Arc_trans_TRASH: Arch 56.6 4.4 9.4E-05 21.7 0.3 22 13-34 1-23 (37)
31 PF14471 DUF4428: Domain of un 55.8 7.1 0.00015 22.3 1.1 29 39-68 1-30 (51)
32 PF00096 zf-C2H2: Zinc finger, 55.5 5.5 0.00012 18.1 0.6 12 124-135 1-12 (23)
33 PF06677 Auto_anti-p27: Sjogre 54.8 7.4 0.00016 21.2 1.0 22 39-64 19-40 (41)
34 PRK14890 putative Zn-ribbon RN 54.7 8.1 0.00018 22.9 1.3 30 9-47 6-35 (59)
35 PF13240 zinc_ribbon_2: zinc-r 53.9 6.5 0.00014 18.5 0.6 8 13-20 2-9 (23)
36 COG4847 Uncharacterized protei 53.3 5.9 0.00013 25.8 0.6 31 124-154 7-41 (103)
37 PF01258 zf-dskA_traR: Prokary 52.8 2.1 4.5E-05 22.5 -1.3 27 40-66 6-32 (36)
38 KOG2462 C2H2-type Zn-finger pr 52.1 9.1 0.0002 29.9 1.5 32 34-65 127-158 (279)
39 KOG3579 Predicted E3 ubiquitin 51.2 6.2 0.00014 31.0 0.5 30 12-41 270-299 (352)
40 PF05502 Dynactin_p62: Dynacti 51.0 11 0.00023 32.0 2.0 21 113-133 79-99 (483)
41 PF02069 Metallothio_Pro: Prok 49.5 13 0.00029 21.4 1.6 28 39-66 9-37 (52)
42 PF07649 C1_3: C1-like domain; 49.0 9.4 0.0002 19.0 0.8 16 124-139 1-16 (30)
43 PF13834 DUF4193: Domain of un 47.4 6 0.00013 26.0 -0.1 30 35-64 68-98 (99)
44 PF13894 zf-C2H2_4: C2H2-type 45.6 11 0.00024 16.8 0.7 12 124-135 1-12 (24)
45 PRK00420 hypothetical protein; 45.1 16 0.00035 24.6 1.7 25 38-66 24-48 (112)
46 PF12874 zf-met: Zinc-finger o 45.0 10 0.00022 17.6 0.6 13 124-136 1-13 (25)
47 PF14835 zf-RING_6: zf-RING of 41.7 28 0.00061 21.0 2.2 36 38-73 8-43 (65)
48 PF13912 zf-C2H2_6: C2H2-type 41.0 13 0.00028 17.6 0.6 12 124-135 2-13 (27)
49 PF12674 Zn_ribbon_2: Putative 40.0 9.7 0.00021 24.1 0.0 29 39-67 2-35 (81)
50 cd02336 ZZ_RSC8 Zinc finger, Z 39.7 20 0.00044 19.9 1.3 30 39-68 2-33 (45)
51 PHA00689 hypothetical protein 39.4 17 0.00036 20.7 0.9 23 124-146 18-45 (62)
52 PRK00807 50S ribosomal protein 36.6 18 0.0004 20.7 0.9 12 12-23 3-14 (52)
53 cd02249 ZZ Zinc finger, ZZ typ 36.2 18 0.00039 19.9 0.8 15 124-138 1-15 (46)
54 PF10886 DUF2685: Protein of u 35.6 28 0.0006 20.2 1.5 11 40-50 4-14 (54)
55 PF12171 zf-C2H2_jaz: Zinc-fin 34.2 24 0.00052 16.8 0.9 13 124-136 2-14 (27)
56 PF08790 zf-LYAR: LYAR-type C2 34.0 10 0.00022 18.9 -0.5 17 124-140 1-17 (28)
57 cd02341 ZZ_ZZZ3 Zinc finger, Z 33.0 21 0.00046 20.1 0.7 16 124-139 1-17 (48)
58 PF03107 C1_2: C1 domain; Int 32.9 27 0.00058 17.3 1.0 13 124-136 1-13 (30)
59 PF05864 Chordopox_RPO7: Chord 32.3 12 0.00026 22.0 -0.4 17 124-140 5-21 (63)
60 PHA03082 DNA-dependent RNA pol 31.6 12 0.00026 22.0 -0.5 17 124-140 5-21 (63)
61 PF13465 zf-H2C2_2: Zinc-finge 28.4 29 0.00062 16.5 0.6 10 124-133 15-24 (26)
62 PF00569 ZZ: Zinc finger, ZZ t 28.2 44 0.00095 18.4 1.5 30 38-67 5-37 (46)
63 smart00504 Ubox Modified RING 27.0 63 0.0014 18.4 2.1 32 38-70 2-33 (63)
64 smart00291 ZnF_ZZ Zinc-binding 26.2 36 0.00078 18.5 0.9 15 125-139 6-20 (44)
65 COG4357 Zinc finger domain con 25.3 5.4 0.00012 26.1 -2.9 41 13-53 38-78 (105)
66 PF12677 DUF3797: Domain of un 24.9 38 0.00082 19.2 0.8 35 3-37 6-42 (49)
67 smart00214 VWC von Willebrand 24.3 46 0.00099 19.2 1.1 17 111-127 6-23 (59)
68 smart00355 ZnF_C2H2 zinc finge 23.9 34 0.00074 15.1 0.4 12 124-135 1-12 (26)
69 PF04810 zf-Sec23_Sec24: Sec23 23.8 54 0.0012 17.5 1.3 10 11-20 3-12 (40)
70 PF07754 DUF1610: Domain of un 23.8 58 0.0013 15.6 1.2 6 15-20 3-8 (24)
71 PF08271 TF_Zn_Ribbon: TFIIB z 23.7 59 0.0013 17.5 1.5 24 39-64 2-25 (43)
72 TIGR03829 YokU_near_AblA uncha 22.6 14 0.0003 23.9 -1.4 38 120-157 32-84 (89)
73 PF01286 XPA_N: XPA protein N- 22.2 43 0.00092 17.5 0.6 10 11-20 4-13 (34)
74 PF13923 zf-C3HC4_2: Zinc fing 22.2 68 0.0015 16.6 1.5 31 40-70 1-31 (39)
75 PF02591 DUF164: Putative zinc 21.6 26 0.00056 20.1 -0.3 26 39-64 24-52 (56)
76 PF10080 DUF2318: Predicted me 21.5 89 0.0019 20.6 2.2 34 32-69 30-63 (102)
77 PF11077 DUF2616: Protein of u 21.5 55 0.0012 23.9 1.3 35 35-69 137-171 (173)
78 cd02340 ZZ_NBR1_like Zinc fing 21.5 53 0.0011 17.9 0.9 13 126-138 3-15 (43)
79 smart00531 TFIIE Transcription 21.4 32 0.0007 24.1 0.1 36 11-49 100-135 (147)
80 PF14255 Cys_rich_CPXG: Cystei 21.2 48 0.001 19.0 0.8 30 12-41 2-31 (52)
81 PF09723 Zn-ribbon_8: Zinc rib 21.0 30 0.00065 18.7 -0.1 6 13-18 8-13 (42)
82 PF06689 zf-C4_ClpX: ClpX C4-t 21.0 1.1E+02 0.0024 16.4 2.2 30 39-68 3-34 (41)
83 smart00451 ZnF_U1 U1-like zinc 21.0 60 0.0013 16.1 1.1 13 124-136 4-16 (35)
84 PF06750 DiS_P_DiS: Bacterial 20.2 46 0.00099 21.4 0.6 43 5-49 28-70 (92)
85 PF05502 Dynactin_p62: Dynacti 20.2 59 0.0013 27.7 1.4 40 10-50 26-65 (483)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.82 E-value=9.3e-22 Score=155.46 Aligned_cols=115 Identities=16% Similarity=0.325 Sum_probs=98.9
Q ss_pred cccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccCC
Q 040725 11 QKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKS 89 (164)
Q Consensus 11 ~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~ 89 (164)
..|.+|+|.|...+. +.+|++.||..||+|..|++.|....||..++++||+.||..... +| ..|
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tle-kC------~~C------- 340 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLE-KC------NKC------- 340 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHH-HH------hhh-------
Confidence 389999999965554 799999999999999999999999999999999999999987653 33 245
Q ss_pred CCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC-------Chhhhccccc
Q 040725 90 TPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG-------NYNHLIKFAS 153 (164)
Q Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g-------~y~~l~~~~~ 153 (164)
+.+|.+..+.|+|+.||+.||+|.+|++.|++..|+.... +|+..|..+=
T Consensus 341 --------------g~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrC 397 (468)
T KOG1701|consen 341 --------------GEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRC 397 (468)
T ss_pred --------------hhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcch
Confidence 5666666799999999999999999999999999998655 8888777653
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.79 E-value=7.7e-21 Score=150.29 Aligned_cols=114 Identities=22% Similarity=0.431 Sum_probs=90.9
Q ss_pred CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeee-eCCeeeecchhhhhccCCCCcCCCCCCCccccc
Q 040725 9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFKESGNINKNFQSPARLVE 87 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~-~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~ 87 (164)
...+|..|++.| ...++.++|+.||+.||+|..|.+.|.+..|.+ .++++||..||++.|+|+|. .|.
T Consensus 333 tlekC~~Cg~~I-~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs------~C~---- 401 (468)
T KOG1701|consen 333 TLEKCNKCGEPI-MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCS------VCG---- 401 (468)
T ss_pred HHHHHhhhhhHH-HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchh------hcc----
Confidence 346899999999 566789999999999999999999999999885 78999999999999999996 352
Q ss_pred CCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCC----CCCeeccCC
Q 040725 88 KSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSIS----PSNYVALEG 143 (164)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~----~~~f~~~~g 143 (164)
.+|.....- +. .-+|.+|++.||.+|++|++|+.+|+ +...|..||
T Consensus 402 -~PI~P~~G~------~e---tvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~ 451 (468)
T KOG1701|consen 402 -NPILPRDGK------DE---TVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDG 451 (468)
T ss_pred -CCccCCCCC------cc---eEEEEEccccccccceehhhcCccccccCCCCcceeccC
Confidence 222211100 10 11488999999999999999999996 446777777
No 3
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.76 E-value=1.3e-20 Score=142.35 Aligned_cols=123 Identities=24% Similarity=0.376 Sum_probs=97.2
Q ss_pred CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725 9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK 88 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~ 88 (164)
..+.|+.|.+.|.+..++.++++.||..|++|+.|..+|... .+.++|.+||+.+|.++|+++|+ .|.
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCs------aC~----- 99 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCS------ACQ----- 99 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcch------hhc-----
Confidence 568999999999777778999999999999999999999874 56899999999999999999985 241
Q ss_pred CCCCccCCCCCCCCCcccccccc-ccccCccccccceeecCCCCCC-CCCCeeccCC-------Chh--------hhccc
Q 040725 89 STPELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCFKCSHGGCSI-SPSNYVALEG-------NYN--------HLIKF 151 (164)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF~C~~C~~~l-~~~~f~~~~g-------~y~--------~l~~~ 151 (164)
..|.+... ..|.+..||.+||.|..|+++| +++.||.+++ +|+ +|.++
T Consensus 100 ---------------~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd 164 (383)
T KOG4577|consen 100 ---------------EGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGD 164 (383)
T ss_pred ---------------CCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccc
Confidence 11112222 4588999999999999999999 5667888877 554 44455
Q ss_pred ccccccc
Q 040725 152 ASMKRAA 158 (164)
Q Consensus 152 ~~~~~~~ 158 (164)
.++||-+
T Consensus 165 ~~nKRPR 171 (383)
T KOG4577|consen 165 ASNKRPR 171 (383)
T ss_pred cccCCCc
Confidence 5666643
No 4
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.73 E-value=9e-19 Score=130.39 Aligned_cols=118 Identities=16% Similarity=0.233 Sum_probs=98.7
Q ss_pred CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccc
Q 040725 7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLV 86 (164)
Q Consensus 7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~ 86 (164)
..|.-.|..|+..| +.+.+...+..||+..|+|..|++.|.+. -....|.+||..|+.+.--|.| +.|
T Consensus 134 ~~g~YvC~KCh~~i-D~~~l~fr~d~yH~yHFkCt~C~keL~sd-aRevk~eLyClrChD~mgipiC------gaC---- 201 (332)
T KOG2272|consen 134 GRGRYVCQKCHAHI-DEQPLTFRGDPYHPYHFKCTTCGKELTSD-AREVKGELYCLRCHDKMGIPIC------GAC---- 201 (332)
T ss_pred ccceeehhhhhhhc-ccccccccCCCCCccceecccccccccch-hhhhccceeccccccccCCccc------ccc----
Confidence 34566899999999 55889999999999999999999999764 3466779999999988755544 245
Q ss_pred cCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725 87 EKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS 153 (164)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~ 153 (164)
+.+|....|.+||+.||.++|+|++|.+++-|.+.|++.| ||.+||++.-
T Consensus 202 -----------------~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~C 257 (332)
T KOG2272|consen 202 -----------------RRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLC 257 (332)
T ss_pred -----------------cCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhh
Confidence 5555555588999999999999999999999999999999 9999998753
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.69 E-value=3.5e-19 Score=132.55 Aligned_cols=115 Identities=18% Similarity=0.403 Sum_probs=99.7
Q ss_pred CCccCCCCccccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCC
Q 040725 2 KAKSFIGTQQKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQ 80 (164)
Q Consensus 2 ~~~~~~~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~ 80 (164)
++|+-......|.+|.....+.+. +...+..||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.|.
T Consensus 4 ~~~~~g~~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~------ 77 (332)
T KOG2272|consen 4 KQMASGLANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCG------ 77 (332)
T ss_pred hhhhhHHHHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhc------
Confidence 345544456789999999877776 6778899999999999999999999999999999999999999999884
Q ss_pred CCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725 81 SPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143 (164)
Q Consensus 81 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g 143 (164)
.| +..|-+..|.+|+..||+.||+|..|++.|....|+...|
T Consensus 78 kC---------------------~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqg 119 (332)
T KOG2272|consen 78 KC---------------------GEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQG 119 (332)
T ss_pred cc---------------------ccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcc
Confidence 56 4444555699999999999999999999999999998888
No 6
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.64 E-value=1.7e-16 Score=131.73 Aligned_cols=116 Identities=19% Similarity=0.377 Sum_probs=103.8
Q ss_pred CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725 9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK 88 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~ 88 (164)
..++|..|...|.....+.+++..||+.+|.|..|...+....+...+|++||..|+.+.+.++|. .|
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~------~C------ 369 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCK------RC------ 369 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCcccc------cc------
Confidence 458999999999443789999999999999999999999988888899999999999999999984 56
Q ss_pred CCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccc
Q 040725 89 STPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKF 151 (164)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~ 151 (164)
...|..+.|.++++.||++||+|..|++.|.+..|+..|| ||++++..
T Consensus 370 ---------------~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~ 423 (479)
T KOG1703|consen 370 ---------------LLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTT 423 (479)
T ss_pred ---------------CCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccc
Confidence 4555666789999999999999999999999999999999 99999973
No 7
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.60 E-value=2.3e-16 Score=129.05 Aligned_cols=104 Identities=21% Similarity=0.411 Sum_probs=89.7
Q ss_pred CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725 9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK 88 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~ 88 (164)
+...|.+|++.|..++.+.++++.||..||+|..|+.-|. +.|..++|.+||+.||.+.|+.+|. .|
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fgvkc~------~c------ 198 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFGVKCE------EC------ 198 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcCeehH------Hh------
Confidence 5678999999999999999999999999999999999886 4788999999999999999998874 35
Q ss_pred CCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCC-CCeec
Q 040725 89 STPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISP-SNYVA 140 (164)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~-~~f~~ 140 (164)
..-|.+..+.+.|+.||+.|-+|..|+..|+. +..|.
T Consensus 199 ---------------~~fisgkvLqag~kh~HPtCARCsRCgqmF~eGEEMYl 236 (670)
T KOG1044|consen 199 ---------------EKFISGKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYL 236 (670)
T ss_pred ---------------hhhhhhhhhhccCcccCcchhhhhhhccccccchheee
Confidence 34455566899999999999999999999854 44444
No 8
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.59 E-value=6.3e-16 Score=114.56 Aligned_cols=139 Identities=47% Similarity=0.788 Sum_probs=105.9
Q ss_pred ccCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC-cCCCCCCC
Q 040725 4 KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-INKNFQSP 82 (164)
Q Consensus 4 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~-~~~~~~~c 82 (164)
|++......|.+|++.++..+.+...+..||..||.|..|...|....+...++.+||..++..+++++.. +.++++.
T Consensus 1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~- 79 (200)
T KOG1700|consen 1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQK- 79 (200)
T ss_pred CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccc-
Confidence 45666777999999999999998899999999999999999999998888999999999988888888753 2333222
Q ss_pred cccc--cCCC-CCcc-----------CCCCCCCCC-ccccccccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725 83 ARLV--EKST-PELT-----------RSPSKAASI-KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143 (164)
Q Consensus 83 ~~~~--~~~~-~~~~-----------~~~~~~~~~-~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g 143 (164)
+... ...+ .... ....++..+ +.+++.+.+...+..||..||+|+.|+..|+...+...+|
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g 155 (200)
T KOG1700|consen 80 AGGLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEG 155 (200)
T ss_pred cCCCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCC
Confidence 1110 0000 0000 001111112 7788899999999999999999999999999999999888
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.59 E-value=3.7e-16 Score=129.72 Aligned_cols=108 Identities=21% Similarity=0.472 Sum_probs=91.8
Q ss_pred CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725 9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK 88 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~ 88 (164)
..+.|.+|..+| .++.|.+.+..||++||.|..|+..|....|+..++.+||..||.+++.++|.+ |.
T Consensus 362 ~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~------~~----- 429 (479)
T KOG1703|consen 362 FRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDY------CK----- 429 (479)
T ss_pred hCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchh------cc-----
Confidence 357899999999 677788889999999999999999999999999999999999999999877642 21
Q ss_pred CCCCccCCCCCCCCCccccc-cccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725 89 STPELTRSPSKAASIKTVCP-LEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143 (164)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~-~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g 143 (164)
+.+.. ...|.+++..||..||+|..|.+.|.++.|+...+
T Consensus 430 ---------------~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~ 470 (479)
T KOG1703|consen 430 ---------------KPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLD 470 (479)
T ss_pred ---------------chhHhhhhHhhccCccccccceehhhhhccccCCceeecCC
Confidence 11111 22389999999999999999999999999988776
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.49 E-value=4e-14 Score=84.80 Aligned_cols=57 Identities=30% Similarity=0.662 Sum_probs=52.5
Q ss_pred cccCCceeecccEE-EeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725 13 YKVYEKTVYPVEQL-SDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69 (164)
Q Consensus 13 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~ 69 (164)
|.+|+++|...+.+ .++++.||.+||+|..|+.+|....++..++++||..||.++|
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 78999999877775 7999999999999999999999988889999999999998875
No 11
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.46 E-value=5.3e-14 Score=115.39 Aligned_cols=138 Identities=18% Similarity=0.325 Sum_probs=94.4
Q ss_pred cccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeee-CCeeeecchh------------hhhccCCCCcCC
Q 040725 11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF------------EQLFKESGNINK 77 (164)
Q Consensus 11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~-~g~~~C~~c~------------~~~~~~~c~~~~ 77 (164)
..|..|.+.- .++++.+.+..||..||.|..|+..|..+.|+.+ +.++|+.... .+.+.++|....
T Consensus 17 i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs 95 (670)
T KOG1044|consen 17 IKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS 95 (670)
T ss_pred eehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence 4799999998 7899999999999999999999999999998875 4467775322 122334443211
Q ss_pred CCC----------------CCccccc--CCCCCccCCCCCCCCCccc-cccccccccCccccccceeecCCCCCCCCCCe
Q 040725 78 NFQ----------------SPARLVE--KSTPELTRSPSKAASIKTV-CPLEKVAVESQAYHKTCFKCSHGGCSISPSNY 138 (164)
Q Consensus 78 ~~~----------------~c~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f 138 (164)
.+. .|..++. ...+.....++.++.++.. +.++.+.++++.||+.||+|..|+..|.++ |
T Consensus 96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge-y 174 (670)
T KOG1044|consen 96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE-Y 174 (670)
T ss_pred ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce-e
Confidence 110 0111110 0111112345566666444 444558899999999999999999999887 7
Q ss_pred eccCC------Chhhhcc
Q 040725 139 VALEG------NYNHLIK 150 (164)
Q Consensus 139 ~~~~g------~y~~l~~ 150 (164)
+..|| +|.+.|+
T Consensus 175 ~skdg~pyce~dy~~~fg 192 (670)
T KOG1044|consen 175 MSKDGVPYCEKDYQAKFG 192 (670)
T ss_pred eccCCCcchhhhhhhhcC
Confidence 78888 7777665
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=99.01 E-value=1.9e-10 Score=68.63 Aligned_cols=38 Identities=24% Similarity=0.622 Sum_probs=34.2
Q ss_pred ccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhc
Q 040725 112 VAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLI 149 (164)
Q Consensus 112 v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~ 149 (164)
+.++|+.||++||+|..|+++|.+..|+..|| ||.++|
T Consensus 15 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 15 IKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp EEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred EEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 35999999999999999999999999999999 777664
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=98.59 E-value=4.4e-08 Score=53.27 Aligned_cols=37 Identities=35% Similarity=0.531 Sum_probs=32.8
Q ss_pred ccccCCceeecc-cEEEeCCcccCCCCcccCCCCCcCc
Q 040725 12 KYKVYEKTVYPV-EQLSDDGVVYHKSCFKCSHCKGTLK 48 (164)
Q Consensus 12 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~ 48 (164)
+|..|++.|... ..+.+.+..||..||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 588999999766 5578899999999999999999885
No 14
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.40 E-value=3.2e-08 Score=75.65 Aligned_cols=66 Identities=24% Similarity=0.481 Sum_probs=55.7
Q ss_pred CccccccCCceeecccEE-EeCCcccCCCCcccCCCCCcCcCC-Cee-eeCCeeeecchhhhhccCCCC
Q 040725 9 TQQKYKVYEKTVYPVEQL-SDDGVVYHKSCFKCSHCKGTLKLS-NYS-SMEGVLYCKPHFEQLFKESGN 74 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~~C~~c~~~~~~~~c~ 74 (164)
...+|..|.+.|.+..++ .+.+..||..||.|..|+.+|..+ .|+ ..++++.|+.+|.+.....|+
T Consensus 91 fGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~ 159 (383)
T KOG4577|consen 91 FGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCN 159 (383)
T ss_pred hCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcccc
Confidence 346899999999777765 788999999999999999999887 566 478999999999987666554
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=98.28 E-value=3.7e-07 Score=49.49 Aligned_cols=25 Identities=28% Similarity=0.624 Sum_probs=22.3
Q ss_pred ccccccCccccccceeecCCCCCCC
Q 040725 110 EKVAVESQAYHKTCFKCSHGGCSIS 134 (164)
Q Consensus 110 ~~v~~~~~~~H~~CF~C~~C~~~l~ 134 (164)
..+.++++.||++||+|..|+++|.
T Consensus 14 ~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 14 LVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred EEEEeCCccccccCCCCcccCCcCc
Confidence 3477899999999999999999985
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.01 E-value=1.5e-06 Score=64.63 Aligned_cols=69 Identities=51% Similarity=1.044 Sum_probs=60.0
Q ss_pred CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCc
Q 040725 7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNI 75 (164)
Q Consensus 7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~ 75 (164)
.+....|..|.+.+++.+.+...+..||..||+|+.|+..|....+....+.+||...+.+++-...++
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~ 173 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNY 173 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcc
Confidence 345678999999999999999999999999999999999999999888899999988888776555443
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.87 E-value=7.4e-07 Score=65.29 Aligned_cols=60 Identities=38% Similarity=0.737 Sum_probs=54.3
Q ss_pred cccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725 11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 70 (164)
Q Consensus 11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~ 70 (164)
..|..|++.+++.|.+.-+++.||..||.|..|+..|.-..+.+.+.++||..+|.++.+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 457889999999999999999999999999999999988888889999999999987653
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=96.71 E-value=0.00027 Score=52.10 Aligned_cols=40 Identities=38% Similarity=0.737 Sum_probs=34.3
Q ss_pred ccccccccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143 (164)
Q Consensus 104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g 143 (164)
+.+++.|.|..+++.||..||+|..|+..|.-.+|-..|-
T Consensus 12 k~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~k 51 (264)
T KOG1702|consen 12 KTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDK 51 (264)
T ss_pred cccccHHHHhhHHHHHHHHhheeeeccCChhhhhcccccc
Confidence 6778889999999999999999999999997776664443
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.88 E-value=0.0011 Score=49.85 Aligned_cols=100 Identities=20% Similarity=0.415 Sum_probs=67.6
Q ss_pred CCceeecccEEEeCCcccCCCCcccCCCCCcCc--CCCeeeeCCeeeecchhhh--hccCCCCcCCCCCCCcccccCCCC
Q 040725 16 YEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYCKPHFEQ--LFKESGNINKNFQSPARLVEKSTP 91 (164)
Q Consensus 16 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~~C~~c~~~--~~~~~c~~~~~~~~c~~~~~~~~~ 91 (164)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|.. .+..+|. .|.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~------rt~-------- 66 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA------RCK-------- 66 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc------CCC--------
Confidence 566675555567779999999999999999997 444445 999999999987 4443332 221
Q ss_pred CccCCCCCCCCCcccccccc-ccccCccccccceeecCCCCCC-CCCCeeccCC
Q 040725 92 ELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCFKCSHGGCSI-SPSNYVALEG 143 (164)
Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF~C~~C~~~l-~~~~f~~~~g 143 (164)
..+...+. ..+..+. |..||.|..|...+ .+..+...+.
T Consensus 67 ------------~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvw 107 (235)
T KOG0490|consen 67 ------------FTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVW 107 (235)
T ss_pred ------------CCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehh
Confidence 11111222 3355666 99999999998864 4555555554
No 20
>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=77.72 E-value=1.6 Score=28.42 Aligned_cols=29 Identities=28% Similarity=0.236 Sum_probs=14.3
Q ss_pred ccccccCCceeecccE-EEeCCcccCCCCc
Q 040725 10 QQKYKVYEKTVYPVEQ-LSDDGVVYHKSCF 38 (164)
Q Consensus 10 ~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf 38 (164)
...|..|++.|..... +...|..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 3456666666643332 2333445555554
No 21
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=70.13 E-value=1.4 Score=29.08 Aligned_cols=30 Identities=20% Similarity=0.301 Sum_probs=19.1
Q ss_pred ccccCCceeecccEEEeC-CcccCCCCcccC
Q 040725 12 KYKVYEKTVYPVEQLSDD-GVVYHKSCFKCS 41 (164)
Q Consensus 12 ~C~~C~~~i~~~~~~~~~-~~~~H~~Cf~C~ 41 (164)
+|..|++.|+.++.+.+. +..-|-.||.-.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 577788887777765442 345677776543
No 22
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=65.73 E-value=5.8 Score=23.51 Aligned_cols=30 Identities=17% Similarity=0.288 Sum_probs=19.9
Q ss_pred ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCc
Q 040725 10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLK 48 (164)
Q Consensus 10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 48 (164)
.+.|..|+..|..++.. .-|.|..|+..+.
T Consensus 9 ~~~CtSCg~~i~p~e~~---------v~F~CPnCGe~~I 38 (61)
T COG2888 9 PPVCTSCGREIAPGETA---------VKFPCPNCGEVEI 38 (61)
T ss_pred CceeccCCCEeccCCce---------eEeeCCCCCceee
Confidence 57899999888555432 2367777775443
No 23
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=65.63 E-value=4.8 Score=27.89 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=18.0
Q ss_pred ccCCCCCcCcCCCeeeeCCeeeecchhh
Q 040725 39 KCSHCKGTLKLSNYSSMEGVLYCKPHFE 66 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~ 66 (164)
.|..|+.+| +.++|.+||..|-.
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 378888877 33999999999963
No 24
>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=65.61 E-value=4.1 Score=21.55 Aligned_cols=25 Identities=24% Similarity=0.494 Sum_probs=17.3
Q ss_pred cccCCCCCcCcCCCeeeeCCeeeecchhh
Q 040725 38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFE 66 (164)
Q Consensus 38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~ 66 (164)
+.|..|+.. .+...+|..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 347777663 4567899999977643
No 25
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=64.65 E-value=1.4 Score=22.90 Aligned_cols=17 Identities=18% Similarity=0.583 Sum_probs=14.3
Q ss_pred eeecCCCCCCCCCCeec
Q 040725 124 FKCSHGGCSISPSNYVA 140 (164)
Q Consensus 124 F~C~~C~~~l~~~~f~~ 140 (164)
|.|..|++++...+|+.
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 78999999999988876
No 26
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.03 E-value=4.3 Score=23.62 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=20.2
Q ss_pred CccccccCCceeeccc-EE--EeCCcccCCCCc
Q 040725 9 TQQKYKVYEKTVYPVE-QL--SDDGVVYHKSCF 38 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~-~~--~~~~~~~H~~Cf 38 (164)
...+|..|++.|.+++ .+ ..=+..||++|.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 3467999999995343 32 334667888887
No 27
>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=63.00 E-value=2.3 Score=26.64 Aligned_cols=17 Identities=24% Similarity=0.116 Sum_probs=12.5
Q ss_pred CccccccCCceeecccE
Q 040725 9 TQQKYKVYEKTVYPVEQ 25 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~ 25 (164)
+...|..|++.|..+++
T Consensus 6 ~Ra~Ck~C~~~I~kg~l 22 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGEL 22 (82)
T ss_dssp STEBETTTSCBE-TTSE
T ss_pred CCccCcccCCcCCCCCE
Confidence 45689999999966664
No 28
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=58.86 E-value=4.5 Score=30.13 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=25.6
Q ss_pred cccCCCCCcCcCCCeeeeCCeeeecchhhhh
Q 040725 38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 68 (164)
Q Consensus 38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~ 68 (164)
-+|+.|+-......-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5799999988776666789999999998754
No 29
>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=57.81 E-value=10 Score=24.54 Aligned_cols=29 Identities=24% Similarity=0.265 Sum_probs=22.1
Q ss_pred cccCCCCCcCcCCCeee-eCCeeeecchhh
Q 040725 38 FKCSHCKGTLKLSNYSS-MEGVLYCKPHFE 66 (164)
Q Consensus 38 f~C~~C~~~L~~~~~~~-~~g~~~C~~c~~ 66 (164)
-.|..|+++|....|.. .+|.++...|..
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 35999999999877765 577887777753
No 30
>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=56.58 E-value=4.4 Score=21.67 Aligned_cols=22 Identities=9% Similarity=-0.034 Sum_probs=9.7
Q ss_pred cccCCceeecccE-EEeCCcccC
Q 040725 13 YKVYEKTVYPVEQ-LSDDGVVYH 34 (164)
Q Consensus 13 C~~C~~~i~~~~~-~~~~~~~~H 34 (164)
|.-|+..|..... +...++.|+
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~ 23 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY 23 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE
Confidence 3445555522222 344555555
No 31
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=55.78 E-value=7.1 Score=22.34 Aligned_cols=29 Identities=28% Similarity=0.675 Sum_probs=21.3
Q ss_pred ccCCCCCcCcCCC-eeeeCCeeeecchhhhh
Q 040725 39 KCSHCKGTLKLSN-YSSMEGVLYCKPHFEQL 68 (164)
Q Consensus 39 ~C~~C~~~L~~~~-~~~~~g~~~C~~c~~~~ 68 (164)
.|..|+..++-.. +...|| ..|..|+.+.
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 4778888776543 446677 6899999886
No 32
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=55.54 E-value=5.5 Score=18.10 Aligned_cols=12 Identities=42% Similarity=0.711 Sum_probs=9.7
Q ss_pred eeecCCCCCCCC
Q 040725 124 FKCSHGGCSISP 135 (164)
Q Consensus 124 F~C~~C~~~l~~ 135 (164)
|+|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 789999988754
No 33
>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=54.81 E-value=7.4 Score=21.25 Aligned_cols=22 Identities=27% Similarity=0.741 Sum_probs=13.9
Q ss_pred ccCCCCCcCcCCCeeeeCCeeeecch
Q 040725 39 KCSHCKGTLKLSNYSSMEGVLYCKPH 64 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~~~g~~~C~~c 64 (164)
.|..|+.+|-. .++|+.||..|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEECCCC
Confidence 35566666632 46778888665
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.72 E-value=8.1 Score=22.87 Aligned_cols=30 Identities=20% Similarity=0.397 Sum_probs=18.8
Q ss_pred CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcC
Q 040725 9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTL 47 (164)
Q Consensus 9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L 47 (164)
....|..|+..|.+.+. ..-|.|..|+..+
T Consensus 6 ~~~~CtSCg~~i~~~~~---------~~~F~CPnCG~~~ 35 (59)
T PRK14890 6 EPPKCTSCGIEIAPREK---------AVKFLCPNCGEVI 35 (59)
T ss_pred cCccccCCCCcccCCCc---------cCEeeCCCCCCee
Confidence 34578888888854431 2236777777753
No 35
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=53.90 E-value=6.5 Score=18.52 Aligned_cols=8 Identities=0% Similarity=-0.081 Sum_probs=3.6
Q ss_pred cccCCcee
Q 040725 13 YKVYEKTV 20 (164)
Q Consensus 13 C~~C~~~i 20 (164)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44444444
No 36
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.26 E-value=5.9 Score=25.78 Aligned_cols=31 Identities=23% Similarity=0.427 Sum_probs=20.7
Q ss_pred eeecCCCCCC-CCCCeecc-CC--Chhhhcccccc
Q 040725 124 FKCSHGGCSI-SPSNYVAL-EG--NYNHLIKFASM 154 (164)
Q Consensus 124 F~C~~C~~~l-~~~~f~~~-~g--~y~~l~~~~~~ 154 (164)
|+|.+|+.++ .|+.|+.. .| ||+=+..+.+.
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~ 41 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRK 41 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhc
Confidence 6899999885 67755433 55 88766655443
No 37
>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=52.82 E-value=2.1 Score=22.46 Aligned_cols=27 Identities=19% Similarity=0.461 Sum_probs=12.7
Q ss_pred cCCCCCcCcCCCeeeeCCeeeecchhh
Q 040725 40 CSHCKGTLKLSNYSSMEGVLYCKPHFE 66 (164)
Q Consensus 40 C~~C~~~L~~~~~~~~~g~~~C~~c~~ 66 (164)
|..|+.++.........+..+|..|..
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 555555554444334455555655543
No 38
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=52.13 E-value=9.1 Score=29.89 Aligned_cols=32 Identities=16% Similarity=0.181 Sum_probs=19.1
Q ss_pred CCCCcccCCCCCcCcCCCeeeeCCeeeecchh
Q 040725 34 HKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65 (164)
Q Consensus 34 H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~ 65 (164)
-...+.|..|++.+....-..+..+..|..+-
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s 158 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDS 158 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccc
Confidence 34567788888887665433445555554443
No 39
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.21 E-value=6.2 Score=30.99 Aligned_cols=30 Identities=23% Similarity=0.356 Sum_probs=16.4
Q ss_pred ccccCCceeecccEEEeCCcccCCCCcccC
Q 040725 12 KYKVYEKTVYPVEQLSDDGVVYHKSCFKCS 41 (164)
Q Consensus 12 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~ 41 (164)
.|.-|++.+.+..++.--.-.-|+-||-|+
T Consensus 270 cCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 270 CCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred eehhhhhhhccCceeecCCCcccceecccC
Confidence 455566655444445544455555566555
No 40
>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=51.03 E-value=11 Score=32.03 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=12.1
Q ss_pred cccCccccccceeecCCCCCC
Q 040725 113 AVESQAYHKTCFKCSHGGCSI 133 (164)
Q Consensus 113 ~~~~~~~H~~CF~C~~C~~~l 133 (164)
...++.|...|.-|.==.+.+
T Consensus 79 ~~~~~~~~l~C~~C~Wss~~i 99 (483)
T PF05502_consen 79 DSGGKPYYLSCSYCRWSSRDI 99 (483)
T ss_pred cCCCCCEEEECCCceeecccc
Confidence 345677777776665433333
No 41
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=49.45 E-value=13 Score=21.39 Aligned_cols=28 Identities=18% Similarity=0.483 Sum_probs=15.3
Q ss_pred ccCCCCCcCcCCCeeeeCCeeeec-chhh
Q 040725 39 KCSHCKGTLKLSNYSSMEGVLYCK-PHFE 66 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~~~g~~~C~-~c~~ 66 (164)
-|..|...+....-+.++|+.||. .|..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 367777777766667899999984 5544
No 42
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=49.03 E-value=9.4 Score=18.97 Aligned_cols=16 Identities=25% Similarity=0.559 Sum_probs=5.1
Q ss_pred eeecCCCCCCCCCCee
Q 040725 124 FKCSHGGCSISPSNYV 139 (164)
Q Consensus 124 F~C~~C~~~l~~~~f~ 139 (164)
|+|..|++++.+..+|
T Consensus 1 ~~C~~C~~~~~~~~~Y 16 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFY 16 (30)
T ss_dssp ---TTTS----S--EE
T ss_pred CcCCcCCCcCCCCceE
Confidence 6788898888774343
No 43
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=47.44 E-value=6 Score=26.00 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=18.4
Q ss_pred CCCcccCCCCCcCcCCCee-eeCCeeeecch
Q 040725 35 KSCFKCSHCKGTLKLSNYS-SMEGVLYCKPH 64 (164)
Q Consensus 35 ~~Cf~C~~C~~~L~~~~~~-~~~g~~~C~~c 64 (164)
..=|+|+.|..--..+... ..+|.++|..|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhccccCCCEecccc
Confidence 4458888886543322222 46788888776
No 44
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=45.64 E-value=11 Score=16.76 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=7.5
Q ss_pred eeecCCCCCCCC
Q 040725 124 FKCSHGGCSISP 135 (164)
Q Consensus 124 F~C~~C~~~l~~ 135 (164)
|.|..|+..+..
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 689999887644
No 45
>PRK00420 hypothetical protein; Validated
Probab=45.08 E-value=16 Score=24.59 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=16.7
Q ss_pred cccCCCCCcCcCCCeeeeCCeeeecchhh
Q 040725 38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFE 66 (164)
Q Consensus 38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~ 66 (164)
-.|..|+.+|- ..++|..||..|-.
T Consensus 24 ~~CP~Cg~pLf----~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLF----ELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcce----ecCCCceECCCCCC
Confidence 35677776652 23788888888854
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=44.96 E-value=10 Score=17.57 Aligned_cols=13 Identities=31% Similarity=0.419 Sum_probs=10.2
Q ss_pred eeecCCCCCCCCC
Q 040725 124 FKCSHGGCSISPS 136 (164)
Q Consensus 124 F~C~~C~~~l~~~ 136 (164)
|.|..|++.+.+.
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 6899999887654
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=41.72 E-value=28 Score=21.03 Aligned_cols=36 Identities=17% Similarity=0.304 Sum_probs=16.7
Q ss_pred cccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCC
Q 040725 38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG 73 (164)
Q Consensus 38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c 73 (164)
++|+.|..-|..--..+.=+.+||..|..+.++..|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~C 43 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSEC 43 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCC
Confidence 567888777754323355667899999877665544
No 48
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=40.95 E-value=13 Score=17.60 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=9.5
Q ss_pred eeecCCCCCCCC
Q 040725 124 FKCSHGGCSISP 135 (164)
Q Consensus 124 F~C~~C~~~l~~ 135 (164)
|.|..|++.+..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 689999987754
No 49
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=39.99 E-value=9.7 Score=24.06 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=19.9
Q ss_pred ccCCCCCcCcCCCeee-----eCCeeeecchhhh
Q 040725 39 KCSHCKGTLKLSNYSS-----MEGVLYCKPHFEQ 67 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~-----~~g~~~C~~c~~~ 67 (164)
.|..|+.||.....++ ....-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4888999997765332 2335689999864
No 50
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=39.71 E-value=20 Score=19.89 Aligned_cols=30 Identities=13% Similarity=0.361 Sum_probs=19.0
Q ss_pred ccCCCCCcCcCCCeee--eCCeeeecchhhhh
Q 040725 39 KCSHCKGTLKLSNYSS--MEGVLYCKPHFEQL 68 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~--~~g~~~C~~c~~~~ 68 (164)
.|..|+..+....|.. ..+..+|.+||.+-
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhCc
Confidence 4677777776544432 23467799998763
No 51
>PHA00689 hypothetical protein
Probab=39.43 E-value=17 Score=20.69 Aligned_cols=23 Identities=26% Similarity=0.693 Sum_probs=13.2
Q ss_pred eeecCCCCC-C----CCCCeeccCCChh
Q 040725 124 FKCSHGGCS-I----SPSNYVALEGNYN 146 (164)
Q Consensus 124 F~C~~C~~~-l----~~~~f~~~~g~y~ 146 (164)
.+|..|++. | +++.+..++|||+
T Consensus 18 vtckrcgktglrweddggewvlmeghyk 45 (62)
T PHA00689 18 VTCKRCGKTGLRWEDDGGEWVLMEGHYK 45 (62)
T ss_pred eehhhccccCceeecCCCcEEEEeccee
Confidence 457777765 2 3445555566664
No 52
>PRK00807 50S ribosomal protein L24e; Validated
Probab=36.58 E-value=18 Score=20.71 Aligned_cols=12 Identities=17% Similarity=0.177 Sum_probs=5.7
Q ss_pred ccccCCceeecc
Q 040725 12 KYKVYEKTVYPV 23 (164)
Q Consensus 12 ~C~~C~~~i~~~ 23 (164)
.|..|+..|+++
T Consensus 3 ~C~fcG~~I~pg 14 (52)
T PRK00807 3 TCSFCGKEIEPG 14 (52)
T ss_pred ccCCCCCeEcCC
Confidence 355555555433
No 53
>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=36.24 E-value=18 Score=19.89 Aligned_cols=15 Identities=20% Similarity=0.346 Sum_probs=9.5
Q ss_pred eeecCCCCCCCCCCe
Q 040725 124 FKCSHGGCSISPSNY 138 (164)
Q Consensus 124 F~C~~C~~~l~~~~f 138 (164)
|.|..|+++|.+.+|
T Consensus 1 ~~C~~C~~~i~g~r~ 15 (46)
T cd02249 1 YSCDGCLKPIVGVRY 15 (46)
T ss_pred CCCcCCCCCCcCCEE
Confidence 457777777766433
No 54
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=35.64 E-value=28 Score=20.22 Aligned_cols=11 Identities=27% Similarity=0.688 Sum_probs=5.5
Q ss_pred cCCCCCcCcCC
Q 040725 40 CSHCKGTLKLS 50 (164)
Q Consensus 40 C~~C~~~L~~~ 50 (164)
|..|++++...
T Consensus 4 CvVCKqpi~~a 14 (54)
T PF10886_consen 4 CVVCKQPIDDA 14 (54)
T ss_pred eeeeCCccCcc
Confidence 44555555443
No 55
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=34.21 E-value=24 Score=16.81 Aligned_cols=13 Identities=23% Similarity=0.342 Sum_probs=10.6
Q ss_pred eeecCCCCCCCCC
Q 040725 124 FKCSHGGCSISPS 136 (164)
Q Consensus 124 F~C~~C~~~l~~~ 136 (164)
|.|..|++.+.++
T Consensus 2 ~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 2 FYCDACDKYFSSE 14 (27)
T ss_dssp CBBTTTTBBBSSH
T ss_pred CCcccCCCCcCCH
Confidence 6799999988665
No 56
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=33.99 E-value=10 Score=18.94 Aligned_cols=17 Identities=18% Similarity=0.429 Sum_probs=12.5
Q ss_pred eeecCCCCCCCCCCeec
Q 040725 124 FKCSHGGCSISPSNYVA 140 (164)
Q Consensus 124 F~C~~C~~~l~~~~f~~ 140 (164)
|.|-.|++.|.+..|..
T Consensus 1 ~sCiDC~~~F~~~~y~~ 17 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSYKS 17 (28)
T ss_dssp EEETTTTEEEEGGGTTT
T ss_pred CeeecCCCCcCcCCcCC
Confidence 67899998887665543
No 57
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.02 E-value=21 Score=20.10 Aligned_cols=16 Identities=38% Similarity=0.756 Sum_probs=9.0
Q ss_pred eeecCCCC-CCCCCCee
Q 040725 124 FKCSHGGC-SISPSNYV 139 (164)
Q Consensus 124 F~C~~C~~-~l~~~~f~ 139 (164)
|+|..|++ +|.+.+|.
T Consensus 1 y~Cd~C~~~pI~G~R~~ 17 (48)
T cd02341 1 FKCDSCGIEPIPGTRYH 17 (48)
T ss_pred CCCCCCCCCccccceEE
Confidence 45666666 56555443
No 58
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=32.91 E-value=27 Score=17.34 Aligned_cols=13 Identities=23% Similarity=0.220 Sum_probs=9.8
Q ss_pred eeecCCCCCCCCC
Q 040725 124 FKCSHGGCSISPS 136 (164)
Q Consensus 124 F~C~~C~~~l~~~ 136 (164)
|.|..|.+.+++.
T Consensus 1 ~~C~~C~~~~~~~ 13 (30)
T PF03107_consen 1 FWCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCCcCCC
Confidence 5688888887765
No 59
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=32.28 E-value=12 Score=21.99 Aligned_cols=17 Identities=29% Similarity=0.514 Sum_probs=13.7
Q ss_pred eeecCCCCCCCCCCeec
Q 040725 124 FKCSHGGCSISPSNYVA 140 (164)
Q Consensus 124 F~C~~C~~~l~~~~f~~ 140 (164)
..|+.||+-|+.++|..
T Consensus 5 lvCSTCGrDlSeeRy~L 21 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRL 21 (63)
T ss_pred eeecccCCcchHHHHHH
Confidence 36999999998887654
No 60
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=31.56 E-value=12 Score=22.00 Aligned_cols=17 Identities=29% Similarity=0.514 Sum_probs=13.4
Q ss_pred eeecCCCCCCCCCCeec
Q 040725 124 FKCSHGGCSISPSNYVA 140 (164)
Q Consensus 124 F~C~~C~~~l~~~~f~~ 140 (164)
..|+.|++-|+.++|..
T Consensus 5 lVCsTCGrDlSeeRy~L 21 (63)
T PHA03082 5 LVCSTCGRDLSEERYRL 21 (63)
T ss_pred eeecccCcchhHHHHHH
Confidence 36999999998876654
No 61
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=28.38 E-value=29 Score=16.50 Aligned_cols=10 Identities=40% Similarity=0.767 Sum_probs=8.1
Q ss_pred eeecCCCCCC
Q 040725 124 FKCSHGGCSI 133 (164)
Q Consensus 124 F~C~~C~~~l 133 (164)
|.|..|++.+
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 7899998765
No 62
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=28.17 E-value=44 Score=18.38 Aligned_cols=30 Identities=17% Similarity=0.450 Sum_probs=14.1
Q ss_pred cccCCCCC-cCcCCCee--eeCCeeeecchhhh
Q 040725 38 FKCSHCKG-TLKLSNYS--SMEGVLYCKPHFEQ 67 (164)
Q Consensus 38 f~C~~C~~-~L~~~~~~--~~~g~~~C~~c~~~ 67 (164)
+.|..|+. ++.+..|. .=.+--+|..||.+
T Consensus 5 ~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 5 YTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp CE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred eECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 34555555 33333332 11335678888876
No 63
>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=27.01 E-value=63 Score=18.43 Aligned_cols=32 Identities=19% Similarity=0.216 Sum_probs=23.9
Q ss_pred cccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725 38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 70 (164)
Q Consensus 38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~ 70 (164)
|.|..|+..+.. ......|..||..+..+.+.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 567888887765 44557789999999887653
No 64
>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=26.21 E-value=36 Score=18.51 Aligned_cols=15 Identities=27% Similarity=0.457 Sum_probs=10.2
Q ss_pred eecCCCCCCCCCCee
Q 040725 125 KCSHGGCSISPSNYV 139 (164)
Q Consensus 125 ~C~~C~~~l~~~~f~ 139 (164)
.|..|+++|.+.+|.
T Consensus 6 ~C~~C~~~i~g~ry~ 20 (44)
T smart00291 6 SCDTCGKPIVGVRYH 20 (44)
T ss_pred CCCCCCCCCcCCEEE
Confidence 477777777776664
No 65
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=25.33 E-value=5.4 Score=26.06 Aligned_cols=41 Identities=10% Similarity=0.105 Sum_probs=21.9
Q ss_pred cccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCee
Q 040725 13 YKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYS 53 (164)
Q Consensus 13 C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~ 53 (164)
|..|...+..-......-..++..+..|-.|...|....|.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~ 78 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYG 78 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHh
Confidence 44444444333333444455666677777777766544443
No 66
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=24.88 E-value=38 Score=19.22 Aligned_cols=35 Identities=11% Similarity=0.074 Sum_probs=20.9
Q ss_pred CccCCCCccccccCCcee-ecccE-EEeCCcccCCCC
Q 040725 3 AKSFIGTQQKYKVYEKTV-YPVEQ-LSDDGVVYHKSC 37 (164)
Q Consensus 3 ~~~~~~~~~~C~~C~~~i-~~~~~-~~~~~~~~H~~C 37 (164)
+++....-..|..|+-.. ..++. +.+.+..|++.|
T Consensus 6 ~~~L~~kY~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 6 TLKLSNKYCKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred hcchhhhhccCcccCCcEeecCcceEEEeccceeeee
Confidence 344444456788887654 23333 667777777766
No 67
>smart00214 VWC von Willebrand factor (vWF) type C domain.
Probab=24.33 E-value=46 Score=19.21 Aligned_cols=17 Identities=18% Similarity=0.579 Sum_probs=12.8
Q ss_pred cccccCcccccc-ceeec
Q 040725 111 KVAVESQAYHKT-CFKCS 127 (164)
Q Consensus 111 ~v~~~~~~~H~~-CF~C~ 127 (164)
.+...|..|+++ |..|.
T Consensus 6 ~~y~~G~~W~~~~C~~C~ 23 (59)
T smart00214 6 EVYNDGETWKPDPCQICT 23 (59)
T ss_pred EEeCCCCEECCCCCeECC
Confidence 356678999998 77764
No 68
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.95 E-value=34 Score=15.12 Aligned_cols=12 Identities=17% Similarity=0.623 Sum_probs=8.5
Q ss_pred eeecCCCCCCCC
Q 040725 124 FKCSHGGCSISP 135 (164)
Q Consensus 124 F~C~~C~~~l~~ 135 (164)
|.|..|++.+..
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 468888877654
No 69
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=23.80 E-value=54 Score=17.46 Aligned_cols=10 Identities=0% Similarity=0.029 Sum_probs=3.1
Q ss_pred cccccCCcee
Q 040725 11 QKYKVYEKTV 20 (164)
Q Consensus 11 ~~C~~C~~~i 20 (164)
.+|..|+.-|
T Consensus 3 ~rC~~C~ayl 12 (40)
T PF04810_consen 3 VRCRRCRAYL 12 (40)
T ss_dssp -B-TTT--BS
T ss_pred cccCCCCCEE
Confidence 3455555544
No 70
>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=23.79 E-value=58 Score=15.56 Aligned_cols=6 Identities=0% Similarity=0.202 Sum_probs=2.3
Q ss_pred cCCcee
Q 040725 15 VYEKTV 20 (164)
Q Consensus 15 ~C~~~i 20 (164)
.|+..|
T Consensus 3 sC~~~i 8 (24)
T PF07754_consen 3 SCGRPI 8 (24)
T ss_pred cCCCcc
Confidence 343333
No 71
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=23.75 E-value=59 Score=17.45 Aligned_cols=24 Identities=25% Similarity=0.571 Sum_probs=11.6
Q ss_pred ccCCCCCcCcCCCeeeeCCeeeecch
Q 040725 39 KCSHCKGTLKLSNYSSMEGVLYCKPH 64 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~~~g~~~C~~c 64 (164)
+|..|+... ..+-...|.+.|..|
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~C 25 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNC 25 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCC
Confidence 456665532 111124566667665
No 72
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=22.56 E-value=14 Score=23.85 Aligned_cols=38 Identities=18% Similarity=0.468 Sum_probs=24.3
Q ss_pred cccceeecCCCCCCCCC--------CeeccCC-------Chhhhccccccccc
Q 040725 120 HKTCFKCSHGGCSISPS--------NYVALEG-------NYNHLIKFASMKRA 157 (164)
Q Consensus 120 H~~CF~C~~C~~~l~~~--------~f~~~~g-------~y~~l~~~~~~~~~ 157 (164)
+.-|..|+.||...-.. .+...|- .|++|++..++=+|
T Consensus 32 nVPa~~C~~CGe~y~~dev~~eIE~~l~l~~~~~~p~~~~y~~lm~~~~~lk~ 84 (89)
T TIGR03829 32 ETPSISCSHCGMEYQDDTTVKEIEDQLLLVDTKKLPDETTYEELMKMPRLLKR 84 (89)
T ss_pred cCCcccccCCCcEeecHHHHHHHHhhhEEeecccCCccccHHHHhhcHHHHhh
Confidence 46789999998764221 2222232 89999887765444
No 73
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=22.19 E-value=43 Score=17.48 Aligned_cols=10 Identities=20% Similarity=0.109 Sum_probs=4.2
Q ss_pred cccccCCcee
Q 040725 11 QKYKVYEKTV 20 (164)
Q Consensus 11 ~~C~~C~~~i 20 (164)
+.|..|++..
T Consensus 4 ~~C~eC~~~f 13 (34)
T PF01286_consen 4 PKCDECGKPF 13 (34)
T ss_dssp EE-TTT--EE
T ss_pred chHhHhCCHH
Confidence 4566666665
No 74
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=22.16 E-value=68 Score=16.61 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=19.0
Q ss_pred cCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725 40 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 70 (164)
Q Consensus 40 C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~ 70 (164)
|..|...+........=|..||..|..+.+.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 3445555544223456889999999877653
No 75
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.59 E-value=26 Score=20.12 Aligned_cols=26 Identities=19% Similarity=0.530 Sum_probs=14.0
Q ss_pred ccCCCCCcCcCCCeee---eCCeeeecch
Q 040725 39 KCSHCKGTLKLSNYSS---MEGVLYCKPH 64 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~~---~~g~~~C~~c 64 (164)
+|..|...|..+.+.. .++.++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 5666666665554331 2345666555
No 76
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=21.55 E-value=89 Score=20.63 Aligned_cols=34 Identities=21% Similarity=0.294 Sum_probs=23.7
Q ss_pred ccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725 32 VYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69 (164)
Q Consensus 32 ~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~ 69 (164)
.+...==.|..| ....|+..++.+.|..|-.+..
T Consensus 30 ~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 30 SYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred CEEEEEEecccc----CCCceEEECCEEEEecCCCEEe
Confidence 344333347777 4567889999999999976544
No 77
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=21.49 E-value=55 Score=23.86 Aligned_cols=35 Identities=23% Similarity=0.475 Sum_probs=21.9
Q ss_pred CCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725 35 KSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69 (164)
Q Consensus 35 ~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~ 69 (164)
..|+.|..-....+...+.-.+-+++|..|+..+|
T Consensus 137 ~kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF 171 (173)
T PF11077_consen 137 DKCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLF 171 (173)
T ss_pred cccCcCCCCcccccceeEEecChhhcccccCcccc
Confidence 34555554433333323556788999999987766
No 78
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=21.45 E-value=53 Score=17.87 Aligned_cols=13 Identities=23% Similarity=0.373 Sum_probs=6.7
Q ss_pred ecCCCCCCCCCCe
Q 040725 126 CSHGGCSISPSNY 138 (164)
Q Consensus 126 C~~C~~~l~~~~f 138 (164)
|..|+++|.+.+|
T Consensus 3 Cd~C~~~i~G~ry 15 (43)
T cd02340 3 CDGCQGPIVGVRY 15 (43)
T ss_pred CCCCCCcCcCCeE
Confidence 5555555555443
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.44 E-value=32 Score=24.08 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=21.7
Q ss_pred cccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC
Q 040725 11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL 49 (164)
Q Consensus 11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~ 49 (164)
-.|..|+......+.+...+. ..-|.|..|+..|..
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELEE 135 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEEE
Confidence 468888877754443332221 223888888887743
No 80
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=21.17 E-value=48 Score=19.03 Aligned_cols=30 Identities=13% Similarity=0.220 Sum_probs=19.3
Q ss_pred ccccCCceeecccEEEeCCcccCCCCcccC
Q 040725 12 KYKVYEKTVYPVEQLSDDGVVYHKSCFKCS 41 (164)
Q Consensus 12 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~ 41 (164)
.|..|++.+...--.+..++.|-..|-.|-
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 588899988332224556777887775543
No 81
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.03 E-value=30 Score=18.69 Aligned_cols=6 Identities=0% Similarity=-0.103 Sum_probs=2.5
Q ss_pred cccCCc
Q 040725 13 YKVYEK 18 (164)
Q Consensus 13 C~~C~~ 18 (164)
|..|+.
T Consensus 8 C~~Cg~ 13 (42)
T PF09723_consen 8 CEECGH 13 (42)
T ss_pred eCCCCC
Confidence 444443
No 82
>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=21.02 E-value=1.1e+02 Score=16.35 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=17.1
Q ss_pred ccCCCCCcCcCCCee--eeCCeeeecchhhhh
Q 040725 39 KCSHCKGTLKLSNYS--SMEGVLYCKPHFEQL 68 (164)
Q Consensus 39 ~C~~C~~~L~~~~~~--~~~g~~~C~~c~~~~ 68 (164)
+|+.|+++....... ..++...|..|....
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 588899887665432 344677798887543
No 83
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=20.97 E-value=60 Score=16.11 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=10.3
Q ss_pred eeecCCCCCCCCC
Q 040725 124 FKCSHGGCSISPS 136 (164)
Q Consensus 124 F~C~~C~~~l~~~ 136 (164)
|.|..|++.+.+.
T Consensus 4 ~~C~~C~~~~~~~ 16 (35)
T smart00451 4 FYCKLCNVTFTDE 16 (35)
T ss_pred eEccccCCccCCH
Confidence 6799999988643
No 84
>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=20.22 E-value=46 Score=21.44 Aligned_cols=43 Identities=12% Similarity=0.056 Sum_probs=26.4
Q ss_pred cCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC
Q 040725 5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL 49 (164)
Q Consensus 5 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~ 49 (164)
++......|..|++.+...+.+-..+ |-..--+|..|+.++..
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S--~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILS--YLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHH--HHHhCCCCcccCCCCCh
Confidence 44455678888988886555544333 22333567777777754
No 85
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.20 E-value=59 Score=27.66 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=27.4
Q ss_pred ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCC
Q 040725 10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLS 50 (164)
Q Consensus 10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~ 50 (164)
...|..|-..+. ...+...+....++||.|-.|...|...
T Consensus 26 ~~yCp~CL~~~p-~~e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 26 SYYCPNCLFEVP-SSEARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred eeECccccccCC-hhhheeccceeccccccCCCCCCcceeE
Confidence 345777766662 2224455556678999999999998654
Done!