Query psy4072
Match_columns 191
No_of_seqs 201 out of 1316
Neff 8.8
Searched_HMMs 46136
Date Sat Aug 17 00:38:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 8.6E-29 1.9E-33 201.9 3.2 155 3-158 273-466 (468)
2 KOG4577|consensus 99.9 1.1E-25 2.3E-30 175.5 -6.2 152 3-185 32-191 (383)
3 KOG1044|consensus 99.9 6.9E-23 1.5E-27 172.7 5.2 151 3-190 132-282 (670)
4 KOG2272|consensus 99.8 8.3E-23 1.8E-27 156.9 -1.0 120 1-153 192-311 (332)
5 KOG2272|consensus 99.8 1.8E-23 4E-28 160.4 -6.2 150 3-158 72-256 (332)
6 KOG1701|consensus 99.8 1.2E-22 2.5E-27 166.2 -2.1 121 34-159 276-397 (468)
7 KOG1703|consensus 99.7 8.2E-19 1.8E-23 151.2 3.0 123 3-158 302-424 (479)
8 KOG1703|consensus 99.7 5.3E-19 1.2E-23 152.4 1.5 117 3-151 362-478 (479)
9 KOG1044|consensus 99.6 2.5E-15 5.4E-20 127.4 4.3 150 4-159 16-195 (670)
10 PF00412 LIM: LIM domain; Int 99.5 4E-15 8.8E-20 92.2 3.4 56 7-63 1-56 (58)
11 PF00412 LIM: LIM domain; Int 99.5 2E-14 4.2E-19 89.1 3.1 58 97-155 1-58 (58)
12 KOG1700|consensus 99.4 9.6E-14 2.1E-18 106.7 0.7 154 4-161 7-173 (200)
13 smart00132 LIM Zinc-binding do 98.8 3.1E-09 6.7E-14 59.9 2.8 38 6-43 1-38 (39)
14 smart00132 LIM Zinc-binding do 98.7 1.1E-08 2.4E-13 57.6 2.6 38 96-133 1-38 (39)
15 KOG4577|consensus 98.6 6.4E-10 1.4E-14 87.7 -6.6 65 94-161 33-97 (383)
16 KOG1702|consensus 98.1 1.3E-07 2.8E-12 71.5 -3.4 89 95-185 5-98 (264)
17 KOG0490|consensus 97.8 1.6E-06 3.5E-11 68.0 -2.1 115 9-153 1-118 (235)
18 KOG1700|consensus 97.6 3E-05 6.5E-10 59.8 1.9 68 95-164 8-75 (200)
19 KOG1702|consensus 97.4 1.3E-05 2.8E-10 60.8 -2.1 61 3-65 3-63 (264)
20 PF14446 Prok-RING_1: Prokaryo 90.6 0.17 3.7E-06 30.4 1.5 39 94-132 5-51 (54)
21 PF08394 Arc_trans_TRASH: Arch 88.2 0.29 6.2E-06 27.1 1.2 26 7-32 1-26 (37)
22 PF08394 Arc_trans_TRASH: Arch 86.1 0.49 1.1E-05 26.1 1.3 29 97-125 1-29 (37)
23 PF14446 Prok-RING_1: Prokaryo 85.8 0.53 1.1E-05 28.3 1.5 30 4-33 5-36 (54)
24 PRK14890 putative Zn-ribbon RN 82.7 0.62 1.3E-05 28.5 0.8 28 4-41 7-34 (59)
25 KOG0490|consensus 81.0 0.56 1.2E-05 36.5 0.3 53 100-153 2-54 (235)
26 PF09943 DUF2175: Uncharacteri 80.5 0.58 1.3E-05 31.9 0.2 30 34-63 4-33 (101)
27 PF10367 Vps39_2: Vacuolar sor 79.2 1.4 3E-05 29.9 1.8 28 96-123 80-107 (109)
28 PF10367 Vps39_2: Vacuolar sor 77.1 2.1 4.5E-05 28.9 2.2 28 34-62 80-108 (109)
29 COG1645 Uncharacterized Zn-fin 76.2 1.7 3.7E-05 31.1 1.6 22 34-61 30-51 (131)
30 PF09943 DUF2175: Uncharacteri 73.6 1.1 2.3E-05 30.6 -0.0 29 96-124 4-32 (101)
31 PF07754 DUF1610: Domain of un 69.5 2.8 6.1E-05 20.8 1.0 12 97-108 1-12 (24)
32 PF13240 zinc_ribbon_2: zinc-r 67.9 2.8 6E-05 20.5 0.8 10 7-16 2-11 (23)
33 smart00504 Ubox Modified RING 67.2 7.5 0.00016 23.4 2.9 45 33-107 2-48 (63)
34 PF14835 zf-RING_6: zf-RING of 64.7 5.6 0.00012 24.8 1.8 30 79-108 25-54 (65)
35 PF06677 Auto_anti-p27: Sjogre 62.7 3 6.4E-05 23.6 0.3 22 34-60 19-40 (41)
36 PF11781 RRN7: RNA polymerase 62.3 5.2 0.00011 21.9 1.2 22 34-60 10-31 (36)
37 PF07191 zinc-ribbons_6: zinc- 61.5 5 0.00011 25.5 1.2 46 80-133 15-61 (70)
38 KOG2462|consensus 60.9 3.5 7.6E-05 33.2 0.6 16 30-45 128-143 (279)
39 PF07503 zf-HYPF: HypF finger; 59.2 4.5 9.8E-05 22.0 0.7 31 7-43 2-32 (35)
40 PF14471 DUF4428: Domain of un 58.2 4.4 9.5E-05 24.0 0.5 30 124-154 1-30 (51)
41 COG2888 Predicted Zn-ribbon RN 56.2 4.5 9.8E-05 24.7 0.4 27 95-131 10-36 (61)
42 PF11571 Med27: Mediator compl 55.7 2.9 6.2E-05 27.9 -0.6 16 89-104 49-64 (90)
43 PF06906 DUF1272: Protein of u 54.5 16 0.00034 22.1 2.5 24 82-105 29-52 (57)
44 PF02069 Metallothio_Pro: Prok 54.0 7.4 0.00016 23.2 1.0 23 35-58 10-32 (52)
45 PF10235 Cript: Microtubule-as 53.9 13 0.00027 24.9 2.2 24 81-106 58-81 (90)
46 COG2191 Formylmethanofuran deh 52.7 7.4 0.00016 30.0 1.1 31 123-154 173-203 (206)
47 COG2191 Formylmethanofuran deh 50.8 6.5 0.00014 30.3 0.5 30 33-63 173-202 (206)
48 KOG1734|consensus 50.6 4 8.7E-05 32.9 -0.6 43 3-45 223-283 (328)
49 PLN03208 E3 ubiquitin-protein 48.8 52 0.0011 25.3 5.1 12 123-134 69-80 (193)
50 PF00645 zf-PARP: Poly(ADP-rib 48.4 5 0.00011 25.9 -0.3 30 95-124 8-47 (82)
51 PF10083 DUF2321: Uncharacteri 47.6 13 0.00027 27.5 1.6 53 81-136 27-82 (158)
52 PF13248 zf-ribbon_3: zinc-rib 47.0 13 0.00028 18.5 1.1 10 35-44 5-14 (26)
53 KOG3579|consensus 46.4 9.5 0.00021 31.0 0.9 13 33-45 269-281 (352)
54 PF00130 C1_1: Phorbol esters/ 44.3 17 0.00037 21.1 1.6 14 3-16 10-23 (53)
55 PF01258 zf-dskA_traR: Prokary 43.4 2.1 4.6E-05 23.2 -2.3 10 35-44 6-15 (36)
56 PF06827 zf-FPG_IleRS: Zinc fi 43.3 7.1 0.00015 20.1 -0.2 11 95-105 2-12 (30)
57 KOG2893|consensus 42.9 8.4 0.00018 30.5 0.1 39 3-45 9-47 (341)
58 KOG0320|consensus 42.4 14 0.00031 27.9 1.3 29 79-107 150-180 (187)
59 cd00162 RING RING-finger (Real 42.4 15 0.00032 19.7 1.1 26 7-33 2-27 (45)
60 PF04570 DUF581: Protein of un 42.2 17 0.00036 22.2 1.3 12 34-45 18-29 (58)
61 COG4847 Uncharacterized protei 39.9 11 0.00024 25.3 0.3 31 96-126 8-38 (103)
62 PRK00420 hypothetical protein; 38.9 16 0.00034 25.5 0.9 25 33-62 24-48 (112)
63 PF13920 zf-C3HC4_3: Zinc fing 38.2 42 0.00092 19.2 2.7 27 79-105 19-48 (50)
64 cd02336 ZZ_RSC8 Zinc finger, Z 37.9 41 0.00089 19.3 2.4 35 124-159 2-38 (45)
65 KOG0978|consensus 37.7 12 0.00025 34.4 0.2 31 79-109 660-693 (698)
66 PF12773 DZR: Double zinc ribb 36.9 22 0.00047 20.4 1.2 8 125-132 32-39 (50)
67 PF03107 C1_2: C1 domain; Int 36.7 35 0.00077 17.5 1.9 12 6-17 2-13 (30)
68 PF13834 DUF4193: Domain of un 34.5 12 0.00025 25.5 -0.3 30 121-150 69-98 (99)
69 PF12674 Zn_ribbon_2: Putative 34.2 16 0.00035 23.8 0.4 30 124-153 2-35 (81)
70 PF05502 Dynactin_p62: Dynacti 33.8 12 0.00027 32.9 -0.3 105 55-181 6-121 (483)
71 PRK00807 50S ribosomal protein 33.6 39 0.00085 20.0 2.0 23 34-56 3-27 (52)
72 PRK12495 hypothetical protein; 33.5 22 0.00047 27.8 1.1 25 32-62 42-66 (226)
73 COG0068 HypF Hydrogenase matur 33.1 14 0.0003 34.0 -0.1 34 3-42 100-133 (750)
74 PF03854 zf-P11: P-11 zinc fin 32.8 8.6 0.00019 22.4 -0.9 23 83-105 22-46 (50)
75 PF04981 NMD3: NMD3 family ; 32.7 24 0.00051 27.8 1.2 23 35-64 1-23 (236)
76 PF13639 zf-RING_2: Ring finge 31.9 18 0.0004 20.1 0.3 29 96-124 2-31 (44)
77 PRK14559 putative protein seri 31.0 22 0.00048 32.5 0.9 25 81-105 14-38 (645)
78 PF07649 C1_3: C1-like domain; 29.6 18 0.00038 18.5 -0.0 11 6-16 2-12 (30)
79 PF01286 XPA_N: XPA protein N- 27.9 21 0.00045 19.3 0.1 17 4-20 3-19 (34)
80 PF09723 Zn-ribbon_8: Zinc rib 27.8 16 0.00035 20.4 -0.4 10 123-132 6-15 (42)
81 COG5152 Uncharacterized conser 26.9 18 0.0004 27.8 -0.3 28 79-106 213-242 (259)
82 cd02249 ZZ Zinc finger, ZZ typ 26.8 43 0.00094 19.0 1.3 9 145-153 24-32 (46)
83 KOG4739|consensus 26.0 36 0.00079 26.9 1.2 27 79-105 22-48 (233)
84 COG4357 Zinc finger domain con 25.9 6.9 0.00015 26.4 -2.4 38 7-45 38-75 (105)
85 PF10886 DUF2685: Protein of u 25.1 60 0.0013 19.4 1.7 15 6-20 3-17 (54)
86 PF06689 zf-C4_ClpX: ClpX C4-t 24.2 45 0.00097 18.6 1.0 29 124-152 3-32 (41)
87 PF06750 DiS_P_DiS: Bacterial 24.2 33 0.00071 22.9 0.5 40 3-45 32-71 (92)
88 smart00659 RPOLCX RNA polymera 24.0 36 0.00079 19.4 0.6 12 33-44 3-14 (44)
89 PF10892 DUF2688: Protein of u 24.0 16 0.00034 22.1 -0.9 20 83-102 27-46 (60)
90 cd02340 ZZ_NBR1_like Zinc fing 23.7 41 0.00088 19.0 0.8 11 6-16 2-12 (43)
91 TIGR00598 rad14 DNA repair pro 23.5 27 0.00059 26.3 0.0 12 180-191 68-79 (172)
92 PF02591 DUF164: Putative zinc 23.2 16 0.00034 21.8 -1.1 12 34-45 24-35 (56)
93 PF10764 Gin: Inhibitor of sig 23.1 59 0.0013 18.7 1.4 31 125-158 2-32 (46)
94 smart00291 ZnF_ZZ Zinc-binding 22.9 91 0.002 17.4 2.2 9 145-153 28-36 (44)
95 PF14634 zf-RING_5: zinc-RING 22.5 29 0.00064 19.4 0.0 21 81-101 21-43 (44)
96 KOG1829|consensus 22.5 23 0.0005 31.9 -0.6 33 31-63 339-375 (580)
97 KOG1813|consensus 22.2 37 0.0008 27.8 0.5 28 79-106 258-287 (313)
98 PF00096 zf-C2H2: Zinc finger, 21.9 32 0.0007 15.9 0.1 13 33-45 1-13 (23)
99 PF12855 Ecl1: Life-span regul 21.3 36 0.00079 19.4 0.2 11 35-45 9-19 (43)
100 PF05181 XPA_C: XPA protein C- 20.7 61 0.0013 19.3 1.1 11 180-190 38-48 (52)
101 KOG3476|consensus 20.6 42 0.00092 22.2 0.5 27 79-107 66-92 (100)
102 PRK11595 DNA utilization prote 20.5 59 0.0013 25.3 1.4 11 34-44 7-17 (227)
No 1
>KOG1701|consensus
Probab=99.95 E-value=8.6e-29 Score=201.88 Aligned_cols=155 Identities=24% Similarity=0.512 Sum_probs=128.9
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhccc-----ccc---------
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSE-----KNQ--------- 68 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~-----~~~--------- 68 (191)
.+.+|++|+|.|.++.....||++.||..||+|..|++.|.+. .||.+||++||+.||.... +.+
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq-~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iLrA 351 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQ-SFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRILRA 351 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccc-cccccCCcccchHHHHHHHHHHhhhhhHHHHHHHHh
Confidence 3568999999999988877899999999999999999999999 9999999999999997532 221
Q ss_pred ---eecccc--------------ceeeeCCeecchhhhhhhhhhhhhhcCCCccCCC-----eEEEecCccccccccccc
Q psy4072 69 ---FLDENC--------------TCFVRDGKTYCKRDYVRLFGTKCEKCNLNFKRED-----FVMRAKNKIYHVQCFCCV 126 (191)
Q Consensus 69 ---~~~~~c--------------~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~-----~~~~~~~~~~H~~Cf~C~ 126 (191)
..+-.| .....++.+||.+||++.||++|+.|+++|++.| ..|+++++.||.+|++|.
T Consensus 352 ~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CE 431 (468)
T KOG1701|consen 352 LGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCE 431 (468)
T ss_pred cccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceehh
Confidence 111111 1236778999999999999999999999998643 346789999999999999
Q ss_pred cCCCCCCC---CCceeeeCCccCCccccccccCCC
Q psy4072 127 VCGKQLVP---GDEFALREDGLFCKDDHEGMDKSS 158 (191)
Q Consensus 127 ~C~~~l~~---~~~~~~~~~~~~C~~c~~~~~~~~ 158 (191)
.|+..|+. +...+-.++.++|+.|+.++.+..
T Consensus 432 DCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl~~~ 466 (468)
T KOG1701|consen 432 DCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRLQAG 466 (468)
T ss_pred hcCccccccCCCCcceeccCceeechhhhhhhccc
Confidence 99999982 445788899999999988776543
No 2
>KOG4577|consensus
Probab=99.89 E-value=1.1e-25 Score=175.53 Aligned_cols=152 Identities=37% Similarity=0.862 Sum_probs=126.7
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCe
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGK 82 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~ 82 (191)
..++|++|++.|.+++++. ++++.||..|++|+.|..+|... +| .++++
T Consensus 32 eip~CagC~q~IlDrFilK-vl~R~wHs~CLkCs~C~~qL~dr--CF----------------------------sR~~s 80 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILK-VLDRHWHSSCLKCSDCHDQLADR--CF----------------------------SREGS 80 (383)
T ss_pred ccccccchHHHHHHHHHHH-HHhhhhhhhhcchhhhhhHHHHH--Hh----------------------------hcCCc
Confidence 5789999999999999986 67999999999999999999986 33 39999
Q ss_pred ecchhhhhhhhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeee-CCccCCccccccccCCC---
Q psy4072 83 TYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALR-EDGLFCKDDHEGMDKSS--- 158 (191)
Q Consensus 83 ~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~~~--- 158 (191)
+||+++|.++|+.+|..|...|.+...+-.|.+..||..||.|..|++.|..|+.|++. +.++.|+..|+.....-
T Consensus 81 ~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~ 160 (383)
T KOG4577|consen 81 VYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNE 160 (383)
T ss_pred eeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccc
Confidence 99999999999999999999999875445678899999999999999999999999877 56699999998655433
Q ss_pred ----CCCCCCCCCCCCCCCccCCCCCCCCcc
Q psy4072 159 ----NGENNNNNTNINNNLHNLNNEGSNSGK 185 (191)
Q Consensus 159 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (191)
+++...+++..+.+...+-..+.||-|
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~SpK 191 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNTSPK 191 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcCCCc
Confidence 344556667777776666555555543
No 3
>KOG1044|consensus
Probab=99.87 E-value=6.9e-23 Score=172.69 Aligned_cols=151 Identities=27% Similarity=0.602 Sum_probs=120.8
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCe
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGK 82 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~ 82 (191)
++..|++|++.|..+..+ +|+++.||..||+|..|...|.+. |+.+||.
T Consensus 132 ~ps~cagc~~~lk~gq~l-lald~qwhv~cfkc~~c~~vL~ge------------------------------y~skdg~ 180 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQAL-LALDKQWHVSCFKCKSCSAVLNGE------------------------------YMSKDGV 180 (670)
T ss_pred CCccccchhhhhhcccee-eeeccceeeeeeehhhhcccccce------------------------------eeccCCC
Confidence 567899999999977766 499999999999999999999885 5569999
Q ss_pred ecchhhhhhhhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCccccccccCCCCCCC
Q psy4072 83 TYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEGMDKSSNGEN 162 (191)
Q Consensus 83 ~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~ 162 (191)
|||+.||...|+.+|..|.+.|. ++++.|.+++||+.|-+|+.|+..+..|+..++.+..+|-..|-. ....+.
T Consensus 181 pyce~dy~~~fgvkc~~c~~fis--gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q----a~~tE~ 254 (670)
T KOG1044|consen 181 PYCEKDYQAKFGVKCEECEKFIS--GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ----ATKTEE 254 (670)
T ss_pred cchhhhhhhhcCeehHHhhhhhh--hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc----ccchhh
Confidence 99999999999999999999999 458999999999999999999999999999999999999888832 222222
Q ss_pred CCCCCCCCCCCccCCCCCCCCcceeeee
Q psy4072 163 NNNNTNINNNLHNLNNEGSNSGKIQLYL 190 (191)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (191)
...++..++.+.+.+..+++.|..|-++
T Consensus 255 i~~~~rtst~Si~~~~~~Ss~Gsp~~ti 282 (670)
T KOG1044|consen 255 ILKPGRTSTESIYSRPGSSTPGSPGHTI 282 (670)
T ss_pred cccCCCCCcccccCCCCCCCCCCCCcEe
Confidence 2333333333344444555555555443
No 4
>KOG2272|consensus
Probab=99.84 E-value=8.3e-23 Score=156.86 Aligned_cols=120 Identities=29% Similarity=0.633 Sum_probs=109.3
Q ss_pred CCCCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeC
Q psy4072 1 KRRLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRD 80 (191)
Q Consensus 1 ~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~ 80 (191)
+.+.++|..|++||.++.+. ++|+.||.++|+|+.|.+|+-+. ..|++.
T Consensus 192 ~mgipiCgaC~rpIeervi~--amgKhWHveHFvCa~CekPFlGH-----------------------------rHYEkk 240 (332)
T KOG2272|consen 192 KMGIPICGACRRPIEERVIF--AMGKHWHVEHFVCAKCEKPFLGH-----------------------------RHYEKK 240 (332)
T ss_pred ccCCcccccccCchHHHHHH--HhccccchhheeehhcCCcccch-----------------------------hhhhhc
Confidence 35789999999999988775 89999999999999999998877 445699
Q ss_pred CeecchhhhhhhhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCcccccc
Q psy4072 81 GKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEG 153 (191)
Q Consensus 81 ~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 153 (191)
|.+||+.+|.++|+..|..|+.+|.++ ++.+.++.|-++||.|+.|.+.|....+|++.|-+|.|+.||.+
T Consensus 241 GlaYCe~h~~qLfG~~CF~C~~~i~G~--vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 241 GLAYCETHYHQLFGNLCFICNRVIGGD--VVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred CchhHHHHHHHHhhhhheecCCccCcc--HHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 999999999999999999999999853 78899999999999999999999877889999999999999974
No 5
>KOG2272|consensus
Probab=99.84 E-value=1.8e-23 Score=160.44 Aligned_cols=150 Identities=23% Similarity=0.503 Sum_probs=126.9
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccc---cceecccc-----
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEK---NQFLDENC----- 74 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~---~~~~~~~c----- 74 (191)
.+|.|+.|++-|.|+.+. +++.+||+.||+|..|++.|.+. .++...|+..|..|-.+... +++...+|
T Consensus 72 faPcC~kC~EFiiGrVik--amnnSwHp~CF~Cd~Cn~~Lad~-gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD 148 (332)
T KOG2272|consen 72 FAPCCGKCGEFIIGRVIK--AMNNSWHPACFRCDLCNKHLADQ-GFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHID 148 (332)
T ss_pred hchhhcccccchhhHHHH--hhccccCcccchhHHHHHHHhhh-hhHhhcchHHhhhhhhhhcccccceeehhhhhhhcc
Confidence 368899999999999776 88999999999999999999998 78888999999988765221 12221111
Q ss_pred ---------------------------ceeeeCCeecchhhhhhhhhhhhhhcCCCccCCCeEEEecCcccccccccccc
Q psy4072 75 ---------------------------TCFVRDGKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVV 127 (191)
Q Consensus 75 ---------------------------~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 127 (191)
.-.+..|..||..|+.++--|+|..|.++|. |+++.++|+.||.+.|+|+.
T Consensus 149 ~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe--ervi~amgKhWHveHFvCa~ 226 (332)
T KOG2272|consen 149 EQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE--ERVIFAMGKHWHVEHFVCAK 226 (332)
T ss_pred cccccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH--HHHHHHhccccchhheeehh
Confidence 1125668899999999888899999999998 67889999999999999999
Q ss_pred CCCCCCCCCceeeeCCccCCccccccccCCC
Q psy4072 128 CGKQLVPGDEFALREDGLFCKDDHEGMDKSS 158 (191)
Q Consensus 128 C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~ 158 (191)
|.+|+- |...++..|..||+.+|.++|+--
T Consensus 227 CekPFl-GHrHYEkkGlaYCe~h~~qLfG~~ 256 (332)
T KOG2272|consen 227 CEKPFL-GHRHYEKKGLAYCETHYHQLFGNL 256 (332)
T ss_pred cCCccc-chhhhhhcCchhHHHHHHHHhhhh
Confidence 999998 889999999999999999998765
No 6
>KOG1701|consensus
Probab=99.84 E-value=1.2e-22 Score=166.20 Aligned_cols=121 Identities=26% Similarity=0.535 Sum_probs=113.1
Q ss_pred cccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCeecchhhhhhhhhhhhhhcCCCccCCCeEEEe
Q psy4072 34 RCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRA 113 (191)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~ 113 (191)
.|..|++.|.+...-..+++.+||..||++..+.+.|..+ .||..|+++||+.||.... .+|..|++.|+ |+++.|
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq-~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~--d~iLrA 351 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQ-SFYQVDGKPYCEGCYQDTL-EKCNKCGEPIM--DRILRA 351 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccc-cccccCCcccchHHHHHHH-HHHhhhhhHHH--HHHHHh
Confidence 7899999999997888899999999999999999999988 8999999999999998765 79999999999 789999
Q ss_pred cCccccccccccccCCCCCCCCCceeee-CCccCCccccccccCCCC
Q psy4072 114 KNKIYHVQCFCCVVCGKQLVPGDEFALR-EDGLFCKDDHEGMDKSSN 159 (191)
Q Consensus 114 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~~~~ 159 (191)
.|+.||+.||+|..|.+.|. |..|.+. ++++||..+|.+.|+++.
T Consensus 352 ~GkayHp~CF~Cv~C~r~ld-gipFtvd~~n~v~Cv~dfh~kfAPrC 397 (468)
T KOG1701|consen 352 LGKAYHPGCFTCVVCARCLD-GIPFTVDSQNNVYCVPDFHKKFAPRC 397 (468)
T ss_pred cccccCCCceEEEEeccccC-CccccccCCCceeeehhhhhhcCcch
Confidence 99999999999999999998 8899877 666999999999999995
No 7
>KOG1703|consensus
Probab=99.73 E-value=8.2e-19 Score=151.23 Aligned_cols=123 Identities=25% Similarity=0.574 Sum_probs=109.1
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCe
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGK 82 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~ 82 (191)
..+.|..|.+.|.+..++ +++++.||+.+|.|..|...|... .+...+|.
T Consensus 302 ~~p~c~~c~~~i~~~~~i-~~~~~~~h~~~~~c~~~~~~~~~~-----------------------------~~~~~~g~ 351 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVI-VALGKEWHPEHFSCEVCAIVILDG-----------------------------GPRELDGK 351 (479)
T ss_pred ccccccccccCcccceeE-eeccccccccceeeccccccccCC-----------------------------CccccCCC
Confidence 358999999999994343 389999999999999999999887 33348999
Q ss_pred ecchhhhhhhhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCccccccccCCC
Q psy4072 83 TYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEGMDKSS 158 (191)
Q Consensus 83 ~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~ 158 (191)
+||.+|+...+++.|.+|.++|. +..|.+.+..||++||.|..|++++. ...|+..++.+||..||..++.++
T Consensus 352 ~~c~~~~~~~~~p~C~~C~~~i~--~~~v~a~~~~wH~~cf~C~~C~~~~~-~~~~~~~~~~pyce~~~~~~~~~~ 424 (479)
T KOG1703|consen 352 ILCHECFHAPFRPNCKRCLLPIL--EEGVCALGRLWHPECFVCADCGKPLK-NSSFFESDGEPYCEDHYKKLFTTK 424 (479)
T ss_pred ccHHHHHHHhhCccccccCCchH--HhHhhhccCeechhceeeecccCCCC-CCcccccCCccchhhhHhhhcccc
Confidence 99999999999999999999999 45788889999999999999999998 668999999999999999999754
No 8
>KOG1703|consensus
Probab=99.73 E-value=5.3e-19 Score=152.38 Aligned_cols=117 Identities=29% Similarity=0.608 Sum_probs=106.3
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCe
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGK 82 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~ 82 (191)
..+.|.+|+++|.++.+. |+++.||+.||.|..|+++|.+. . |+..++.
T Consensus 362 ~~p~C~~C~~~i~~~~v~--a~~~~wH~~cf~C~~C~~~~~~~-~----------------------------~~~~~~~ 410 (479)
T KOG1703|consen 362 FRPNCKRCLLPILEEGVC--ALGRLWHPECFVCADCGKPLKNS-S----------------------------FFESDGE 410 (479)
T ss_pred hCccccccCCchHHhHhh--hccCeechhceeeecccCCCCCC-c----------------------------ccccCCc
Confidence 468899999999998886 67999999999999999999998 3 4459999
Q ss_pred ecchhhhhhhhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCcccc
Q psy4072 83 TYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDH 151 (191)
Q Consensus 83 ~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 151 (191)
|||+.||.+++..+|..|.++|...+..+.+.+..||..||+|..|...|. +..|+...+.++|..|+
T Consensus 411 pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~-~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 411 PYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLT-KKTFFETLDKPLCQKHF 478 (479)
T ss_pred cchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhcccc-CCceeecCCccccccCC
Confidence 999999999999999999999886677889999999999999999999998 77899999999999885
No 9
>KOG1044|consensus
Probab=99.55 E-value=2.5e-15 Score=127.42 Aligned_cols=150 Identities=22% Similarity=0.476 Sum_probs=106.9
Q ss_pred CCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEee-C---------------------Ceecccchh
Q psy4072 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVR-D---------------------GKTYCKRDY 61 (191)
Q Consensus 4 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~---------------------g~~yc~~c~ 61 (191)
...|..|.+.-.+..+- +.+..||..||+|..|+..|... .||.. + |+.||+.||
T Consensus 16 ~i~c~~c~~kc~gevlr--v~d~~fhi~cf~c~~cg~~la~~-gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf 92 (670)
T KOG1044|consen 16 GIKCDKCRKKCSGEVLR--VNDNHFHINCFQCKKCGRNLAEG-GFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCF 92 (670)
T ss_pred ceehhhhCCccccceeE--eeccccceeeeeccccCCCcccc-cceecccceeecccchhhhccceeEecccceeccccc
Confidence 34699999999987654 45999999999999999999887 45443 3 334444444
Q ss_pred hcccccceeccccceeeeCCeecchhhhhhh-------hh-hhhhhcCCCccCCCeEEEecCccccccccccccCCCCCC
Q psy4072 62 VSSEKNQFLDENCTCFVRDGKTYCKRDYVRL-------FG-TKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLV 133 (191)
Q Consensus 62 ~~~~~~~~~~~~c~~~~~~~~~~C~~c~~~~-------~~-~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 133 (191)
.+..+...+.-.-..........|+.|.... .. ..|++|++.|..+ .++.|+++.||..||+|..|...|.
T Consensus 93 ~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~g-q~llald~qwhv~cfkc~~c~~vL~ 171 (670)
T KOG1044|consen 93 SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNG-QALLALDKQWHVSCFKCKSCSAVLN 171 (670)
T ss_pred eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhcc-ceeeeeccceeeeeeehhhhccccc
Confidence 4444332221100111222334555554321 12 2799999999876 5777899999999999999999996
Q ss_pred CCCceeeeCCccCCccccccccCCCC
Q psy4072 134 PGDEFALREDGLFCKDDHEGMDKSSN 159 (191)
Q Consensus 134 ~~~~~~~~~~~~~C~~c~~~~~~~~~ 159 (191)
| .+...++.+||..+|...|+.+.
T Consensus 172 -g-ey~skdg~pyce~dy~~~fgvkc 195 (670)
T KOG1044|consen 172 -G-EYMSKDGVPYCEKDYQAKFGVKC 195 (670)
T ss_pred -c-eeeccCCCcchhhhhhhhcCeeh
Confidence 5 68889999999999999999884
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=99.54 E-value=4e-15 Score=92.21 Aligned_cols=56 Identities=34% Similarity=0.804 Sum_probs=45.9
Q ss_pred ccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhc
Q psy4072 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVS 63 (191)
Q Consensus 7 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~ 63 (191)
|++|+++|.+.++++.++|+.||+.||+|..|+++|.+. .++..+|++||..||.+
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDG-DFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTS-SEEEETTEEEEHHHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCC-eeEeECCEEECHHHHhh
Confidence 889999999988875589999999999999999999998 46765555555555543
No 11
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.48 E-value=2e-14 Score=89.10 Aligned_cols=58 Identities=29% Similarity=0.666 Sum_probs=52.4
Q ss_pred hhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCcccccccc
Q psy4072 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEGMD 155 (191)
Q Consensus 97 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 155 (191)
|.+|+++|.+++.++.+.++.||++||+|..|+++|.. ..++..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND-GDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT-SSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC-CeeEeECCEEECHHHHhhhC
Confidence 78999999988877789999999999999999999984 45899999999999998765
No 12
>KOG1700|consensus
Probab=99.37 E-value=9.6e-14 Score=106.67 Aligned_cols=154 Identities=23% Similarity=0.419 Sum_probs=111.0
Q ss_pred CCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhccccccee--ccccc---eee
Q psy4072 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFL--DENCT---CFV 78 (191)
Q Consensus 4 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~--~~~c~---~~~ 78 (191)
...|..|++.|+-.+.+. ..|..||+.||.|..|.+.|... .+..+++.+||..|+.....++.. .+..+ -..
T Consensus 7 ~~kc~~c~k~vy~~e~~~-~~g~~~hk~c~~c~~~~k~l~~~-~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQ-KDGVDFHKECFKCEKCKKTLTLS-GYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLG 84 (200)
T ss_pred cchhhhccCcchHHHHHh-ccCcchhhhHHhccccccccccc-cccccccccccccchHhhhCcccccccccccccCCCC
Confidence 347999999999877764 78999999999999999999998 788899999999987665543211 11000 000
Q ss_pred eCCe---ecc-----hhhhhhhhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCccc
Q psy4072 79 RDGK---TYC-----KRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDD 150 (191)
Q Consensus 79 ~~~~---~~C-----~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c 150 (191)
.++. .+. ...........|.+|.+.+.+.+.+ ...+..||..||+|+.|+..|+ ...+...++.++|..+
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~-~~~~~~~hk~cfrc~~~~~~ls-~~~~~~~~g~l~~~~~ 162 (200)
T KOG1700|consen 85 KDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKV-TGNGLEFHKSCFRCTHCGKKLS-PKNYAALEGVLYCKHH 162 (200)
T ss_pred cccccccccccccchhHHhhhccccccccccceeeehHHH-hhhhhhhhhhheeecccccccC-CcchhhcCCccccchh
Confidence 0110 111 1111112224899999999987754 4589999999999999999998 4578888999999888
Q ss_pred cccccCCCCCC
Q psy4072 151 HEGMDKSSNGE 161 (191)
Q Consensus 151 ~~~~~~~~~~~ 161 (191)
+..++......
T Consensus 163 ~~~~~~~~~~~ 173 (200)
T KOG1700|consen 163 FAQLFKGKGNY 173 (200)
T ss_pred hheeecCCCcc
Confidence 77766555433
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=98.82 E-value=3.1e-09 Score=59.90 Aligned_cols=38 Identities=32% Similarity=0.815 Sum_probs=32.6
Q ss_pred cccccccccccceeEeecCCCcccccCccccccccccC
Q psy4072 6 LCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLD 43 (191)
Q Consensus 6 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 43 (191)
.|.+|+++|.+.+....+.++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58999999999733335789999999999999999986
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.70 E-value=1.1e-08 Score=57.59 Aligned_cols=38 Identities=39% Similarity=0.906 Sum_probs=34.0
Q ss_pred hhhhcCCCccCCCeEEEecCccccccccccccCCCCCC
Q psy4072 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLV 133 (191)
Q Consensus 96 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 133 (191)
+|.+|+++|.+.+..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 48899999997656788899999999999999999985
No 15
>KOG4577|consensus
Probab=98.58 E-value=6.4e-10 Score=87.66 Aligned_cols=65 Identities=23% Similarity=0.529 Sum_probs=58.2
Q ss_pred hhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCccccccccCCCCCC
Q psy4072 94 GTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEGMDKSSNGE 161 (191)
Q Consensus 94 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~ 161 (191)
-++|++|.+.|.+. .++.++++.||..|++|+.|..+|. +..+.+++.+||+++|.++|+++..+
T Consensus 33 ip~CagC~q~IlDr-FilKvl~R~wHs~CLkCs~C~~qL~--drCFsR~~s~yCkedFfKrfGTKCsa 97 (383)
T KOG4577|consen 33 IPICAGCDQHILDR-FILKVLDRHWHSSCLKCSDCHDQLA--DRCFSREGSVYCKEDFFKRFGTKCSA 97 (383)
T ss_pred cccccchHHHHHHH-HHHHHHhhhhhhhhcchhhhhhHHH--HHHhhcCCceeehHHHHHHhCCcchh
Confidence 37999999999954 5678899999999999999999995 68889999999999999999999654
No 16
>KOG1702|consensus
Probab=98.11 E-value=1.3e-07 Score=71.49 Aligned_cols=89 Identities=19% Similarity=0.345 Sum_probs=69.4
Q ss_pred hhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCccccccccCCCCCCCCCC-----CCCC
Q psy4072 95 TKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEGMDKSSNGENNNN-----NTNI 169 (191)
Q Consensus 95 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~-----~~~~ 169 (191)
+.|..|++.+.+.|. +..+++.||..||.|..|+.+|. ...+...+.++||..+|.+..++....++.. .+.-
T Consensus 5 ~n~~~cgk~vYPvE~-v~cldk~whk~cfkce~c~mtln-mKnyKgy~kkpycn~hYpkq~at~~adTPEm~Rik~n~en 82 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEE-VKCLDKVWHKQCFKCEVCGMTLN-MKNYKGYDKKPYCNPHYPKQVATVMADTPEMRRIKENTEN 82 (264)
T ss_pred chhhhhccccccHHH-HhhHHHHHHHHhheeeeccCChh-hhhccccccCCCcCcccccceeeeecCCHHHHHHHhhhcc
Confidence 367889998888764 56789999999999999999997 6677778889999999998887765444322 2445
Q ss_pred CCCCccCCCCCCCCcc
Q psy4072 170 NNNLHNLNNEGSNSGK 185 (191)
Q Consensus 170 ~~~~~~~~~~~~~~~~ 185 (191)
.++++.+++.++++|+
T Consensus 83 qS~vkY~~e~ekmKG~ 98 (264)
T KOG1702|consen 83 QSNVKYHAEYEKMKGT 98 (264)
T ss_pred chhhhhHHHHHHhcCC
Confidence 5667777888888876
No 17
>KOG0490|consensus
Probab=97.83 E-value=1.6e-06 Score=68.03 Aligned_cols=115 Identities=43% Similarity=0.878 Sum_probs=91.4
Q ss_pred ccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCeecchhh
Q psy4072 9 GCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGKTYCKRD 88 (191)
Q Consensus 9 ~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~~~C~~c 88 (191)
.|+..|.+...+. ..+..||..|..|..|...|......+. ++|..||..+
T Consensus 1 ~~~~~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------~~g~~~~~~d 51 (235)
T KOG0490|consen 1 GCGRQILDRYLLR-VLDRYWHASCLKCAECDNPLGVGDTCFS----------------------------KDGSIYCKRD 51 (235)
T ss_pred CCCccccchHHhh-cccHHHHHHHHhhhhhcchhccCCCccc----------------------------CCCccccccc
Confidence 4788888888775 5599999999999999999972212332 4888888888
Q ss_pred hhh--hhhhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCC-ccCCcccccc
Q psy4072 89 YVR--LFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALRED-GLFCKDDHEG 153 (191)
Q Consensus 89 ~~~--~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~-~~~C~~c~~~ 153 (191)
|.. .+..+|.+|...|...|.+..+..+. |..||.|..|...+..+..+.+..+ +..|...+..
T Consensus 52 ~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 52 YQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred chhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 887 66679999999987666666667777 9999999999988877888888877 6888877643
No 18
>KOG1700|consensus
Probab=97.60 E-value=3e-05 Score=59.79 Aligned_cols=68 Identities=24% Similarity=0.425 Sum_probs=56.0
Q ss_pred hhhhhcCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCccccccccCCCCCCCCC
Q psy4072 95 TKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEGMDKSSNGENNN 164 (191)
Q Consensus 95 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~ 164 (191)
.+|.+|++.+...+++. ..+..||+.||+|..|.+.|. ...+...++.+||..++...+++.......
T Consensus 8 ~kc~~c~k~vy~~e~~~-~~g~~~hk~c~~c~~~~k~l~-~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~ 75 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQ-KDGVDFHKECFKCEKCKKTLT-LSGYSEHEGVPYCKNCHVAQFGPKGGGFGK 75 (200)
T ss_pred chhhhccCcchHHHHHh-ccCcchhhhHHhccccccccc-cccccccccccccccchHhhhCcccccccc
Confidence 58999999998766544 689999999999999999998 456777899999999888888887654443
No 19
>KOG1702|consensus
Probab=97.42 E-value=1.3e-05 Score=60.80 Aligned_cols=61 Identities=23% Similarity=0.477 Sum_probs=52.0
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCCceEEeeCCeecccchhhccc
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSE 65 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~ 65 (191)
....|..|++.+++.+.+. .+++.||..||+|..|+.+|... .+-.++.++||..+|-...
T Consensus 3 ~k~n~~~cgk~vYPvE~v~-cldk~whk~cfkce~c~mtlnmK-nyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 3 KKCNREDCGKTVYPVEEVK-CLDKVWHKQCFKCEVCGMTLNMK-NYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred ccchhhhhccccccHHHHh-hHHHHHHHHhheeeeccCChhhh-hccccccCCCcCcccccce
Confidence 3456889999999877764 78999999999999999999887 6667999999999996543
No 20
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.60 E-value=0.17 Score=30.40 Aligned_cols=39 Identities=33% Similarity=0.796 Sum_probs=27.2
Q ss_pred hhhhhhcCCCccCCCeEEE--ecCcccccccc----cccc--CCCCC
Q psy4072 94 GTKCEKCNLNFKREDFVMR--AKNKIYHVQCF----CCVV--CGKQL 132 (191)
Q Consensus 94 ~~~C~~C~~~I~~~~~~~~--~~~~~~H~~Cf----~C~~--C~~~l 132 (191)
+.+|..|+++|.++|.++. .-+..||++|+ .|.. |+..+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 4589999999975554554 34788999998 4654 55444
No 21
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=88.20 E-value=0.29 Score=27.05 Aligned_cols=26 Identities=27% Similarity=0.551 Sum_probs=17.7
Q ss_pred ccccccccccceeEeecCCCcccccC
Q psy4072 7 CVGCGGQIHDQYILRVAPDLEWHAAC 32 (191)
Q Consensus 7 C~~C~~~I~~~~~~~~~~~~~~H~~C 32 (191)
|..|+++|.+..++.-..|+.||.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 67788888876665445677776444
No 22
>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=86.10 E-value=0.49 Score=26.12 Aligned_cols=29 Identities=31% Similarity=0.717 Sum_probs=20.7
Q ss_pred hhhcCCCccCCCeEEEecCcccccccccc
Q psy4072 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCC 125 (191)
Q Consensus 97 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C 125 (191)
|+-|+..|.+...++...++.|+.-|-.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence 66788888876556677788887655444
No 23
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=85.82 E-value=0.53 Score=28.30 Aligned_cols=30 Identities=20% Similarity=0.459 Sum_probs=20.4
Q ss_pred CCcccccccccc--cceeEeecCCCcccccCc
Q psy4072 4 LSLCVGCGGQIH--DQYILRVAPDLEWHAACL 33 (191)
Q Consensus 4 ~~~C~~C~~~I~--~~~~~~~~~~~~~H~~Cf 33 (191)
...|..|+++|. ++-++-..-+..||.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 457889999995 333433456778888886
No 24
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=82.66 E-value=0.62 Score=28.47 Aligned_cols=28 Identities=21% Similarity=0.515 Sum_probs=16.5
Q ss_pred CCcccccccccccceeEeecCCCcccccCccccccccc
Q psy4072 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQF 41 (191)
Q Consensus 4 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 41 (191)
.+.|..|+.+|.+.+... . |.|-.|++.
T Consensus 7 ~~~CtSCg~~i~~~~~~~-~---------F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAV-K---------FLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccC-E---------eeCCCCCCe
Confidence 456777777776655321 2 666666655
No 25
>KOG0490|consensus
Probab=80.96 E-value=0.56 Score=36.45 Aligned_cols=53 Identities=23% Similarity=0.663 Sum_probs=40.4
Q ss_pred cCCCccCCCeEEEecCccccccccccccCCCCCCCCCceeeeCCccCCcccccc
Q psy4072 100 CNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHEG 153 (191)
Q Consensus 100 C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 153 (191)
|+..|.+. ..+.+.+..||..|..|..|...+..+...+..++..||...+.+
T Consensus 2 ~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~ 54 (235)
T KOG0490|consen 2 CGRQILDR-YLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQR 54 (235)
T ss_pred CCccccch-HHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchh
Confidence 56667643 345566999999999999999999633445544888999999887
No 26
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=80.54 E-value=0.58 Score=31.88 Aligned_cols=30 Identities=10% Similarity=0.099 Sum_probs=14.5
Q ss_pred cccccccccCCCceEEeeCCeecccchhhc
Q psy4072 34 RCAECHQFLDENCTCFVRDGKTYCKRDYVS 63 (191)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~ 63 (191)
+|..|+.++.....|....+.+-|-.||..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 455555555444334333445555555544
No 27
>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=79.20 E-value=1.4 Score=29.87 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=16.7
Q ss_pred hhhhcCCCccCCCeEEEecCcccccccc
Q psy4072 96 KCEKCNLNFKREDFVMRAKNKIYHVQCF 123 (191)
Q Consensus 96 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf 123 (191)
.|+.|+++|.....++-..+..+|..|+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccc
Confidence 5777777776543333334566676664
No 28
>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=77.06 E-value=2.1 Score=28.94 Aligned_cols=28 Identities=18% Similarity=0.271 Sum_probs=19.8
Q ss_pred cccccccccCCCceEEe-eCCeecccchhh
Q psy4072 34 RCAECHQFLDENCTCFV-RDGKTYCKRDYV 62 (191)
Q Consensus 34 ~C~~C~~~l~~~~~~~~-~~g~~yc~~c~~ 62 (191)
.|..|+++|... .|.. .+|.++|..|+.
T Consensus 80 ~C~vC~k~l~~~-~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNS-VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCc-eEEEeCCCeEEeccccc
Confidence 588999999886 4443 367777777753
No 29
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=76.22 E-value=1.7 Score=31.07 Aligned_cols=22 Identities=32% Similarity=0.771 Sum_probs=17.0
Q ss_pred cccccccccCCCceEEeeCCeecccchh
Q psy4072 34 RCAECHQFLDENCTCFVRDGKTYCKRDY 61 (191)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~g~~yc~~c~ 61 (191)
.|..|+.|| |..+|++||+-|-
T Consensus 30 hCp~Cg~PL------F~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL------FRKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc------eeeCCeEECCCCC
Confidence 478888877 3478888888886
No 30
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=73.65 E-value=1.1 Score=30.61 Aligned_cols=29 Identities=24% Similarity=0.451 Sum_probs=14.0
Q ss_pred hhhhcCCCccCCCeEEEecCccccccccc
Q psy4072 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFC 124 (191)
Q Consensus 96 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~ 124 (191)
+|..|+++|..++..--..+..-|-.||+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHH
Confidence 45556666655432222233445555554
No 31
>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=69.52 E-value=2.8 Score=20.76 Aligned_cols=12 Identities=17% Similarity=0.642 Sum_probs=6.6
Q ss_pred hhhcCCCccCCC
Q psy4072 97 CEKCNLNFKRED 108 (191)
Q Consensus 97 C~~C~~~I~~~~ 108 (191)
|.+|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 455666665443
No 32
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.90 E-value=2.8 Score=20.46 Aligned_cols=10 Identities=50% Similarity=1.315 Sum_probs=5.6
Q ss_pred cccccccccc
Q psy4072 7 CVGCGGQIHD 16 (191)
Q Consensus 7 C~~C~~~I~~ 16 (191)
|..|+.+|.+
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 5556665544
No 33
>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=67.21 E-value=7.5 Score=23.37 Aligned_cols=45 Identities=13% Similarity=0.248 Sum_probs=28.2
Q ss_pred ccccccccccCCCceEEeeCCeecccchhhcccccceeccccceeeeCCeecchhhhhhhhh--hhhhhcCCCccCC
Q psy4072 33 LRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEKNQFLDENCTCFVRDGKTYCKRDYVRLFG--TKCEKCNLNFKRE 107 (191)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~~~~~~~~~~c~~~~~~~~~~C~~c~~~~~~--~~C~~C~~~I~~~ 107 (191)
|.|..|+..+... +.. ..|..||+.+..+.+. ..|+.|++++...
T Consensus 2 ~~Cpi~~~~~~~P--v~~----------------------------~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKDP--VIL----------------------------PSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCCC--EEC----------------------------CCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 5678888887775 333 4456666666554432 3687888777543
No 34
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=64.67 E-value=5.6 Score=24.81 Aligned_cols=30 Identities=17% Similarity=0.358 Sum_probs=16.6
Q ss_pred eCCeecchhhhhhhhhhhhhhcCCCccCCC
Q psy4072 79 RDGKTYCKRDYVRLFGTKCEKCNLNFKRED 108 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~ 108 (191)
.=...||..|..+.++..|+.|..|....|
T Consensus 25 ~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 25 GCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 335678888888888888999998876554
No 35
>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=62.72 E-value=3 Score=23.58 Aligned_cols=22 Identities=36% Similarity=0.845 Sum_probs=12.3
Q ss_pred cccccccccCCCceEEeeCCeecccch
Q psy4072 34 RCAECHQFLDENCTCFVRDGKTYCKRD 60 (191)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~g~~yc~~c 60 (191)
.|..|+.||-.. ++|+.||..|
T Consensus 19 ~Cp~C~~PL~~~-----k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMRD-----KDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEEe-----cCCCEECCCC
Confidence 456777776543 4555555443
No 36
>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=62.28 E-value=5.2 Score=21.86 Aligned_cols=22 Identities=32% Similarity=0.652 Sum_probs=11.8
Q ss_pred cccccccccCCCceEEeeCCeecccch
Q psy4072 34 RCAECHQFLDENCTCFVRDGKTYCKRD 60 (191)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~g~~yc~~c 60 (191)
.|..|+.. .+...+|..||..|
T Consensus 10 ~C~~C~~~-----~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 10 PCPVCGSR-----WFYSDDGFYYCDRC 31 (36)
T ss_pred cCCCCCCe-----EeEccCCEEEhhhC
Confidence 46777554 24445555555444
No 37
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=61.48 E-value=5 Score=25.48 Aligned_cols=46 Identities=17% Similarity=0.399 Sum_probs=20.3
Q ss_pred CCeecchhhhhhhh-hhhhhhcCCCccCCCeEEEecCccccccccccccCCCCCC
Q psy4072 80 DGKTYCKRDYVRLF-GTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLV 133 (191)
Q Consensus 80 ~~~~~C~~c~~~~~-~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 133 (191)
++..+|..|-.... ...|+.|++++. ++.|-|.. =|.|..|+..++
T Consensus 15 ~~~~~C~~C~~~~~~~a~CPdC~~~Le----~LkACGAv----dYFC~~c~gLiS 61 (70)
T PF07191_consen 15 GGHYHCEACQKDYKKEAFCPDCGQPLE----VLKACGAV----DYFCNHCHGLIS 61 (70)
T ss_dssp TTEEEETTT--EEEEEEE-TTT-SB-E----EEEETTEE----EEE-TTTT-EE-
T ss_pred CCEEECccccccceecccCCCcccHHH----HHHHhccc----ceeeccCCceee
Confidence 34555555533211 147888888774 45554431 155777777665
No 38
>KOG2462|consensus
Probab=60.86 E-value=3.5 Score=33.22 Aligned_cols=16 Identities=19% Similarity=0.532 Sum_probs=12.3
Q ss_pred ccCccccccccccCCC
Q psy4072 30 AACLRCAECHQFLDEN 45 (191)
Q Consensus 30 ~~Cf~C~~C~~~l~~~ 45 (191)
...++|..|++.+...
T Consensus 128 ~~r~~c~eCgk~ysT~ 143 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTS 143 (279)
T ss_pred CCceeccccccccccc
Confidence 3467899999988765
No 39
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=59.17 E-value=4.5 Score=21.97 Aligned_cols=31 Identities=19% Similarity=0.545 Sum_probs=18.7
Q ss_pred ccccccccccceeEeecCCCcccccCccccccccccC
Q psy4072 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLD 43 (191)
Q Consensus 7 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 43 (191)
|..|.+++.+ ..++.||..=..|..|+-.+.
T Consensus 2 C~~C~~Ey~~------p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFD------PSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCS------TTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHcC------CCCCcccCcCccCCCCCCCEE
Confidence 5566554433 458999999999999987664
No 40
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=58.24 E-value=4.4 Score=24.01 Aligned_cols=30 Identities=27% Similarity=0.675 Sum_probs=21.8
Q ss_pred ccccCCCCCCCCCceeeeCCccCCccccccc
Q psy4072 124 CCVVCGKQLVPGDEFALREDGLFCKDDHEGM 154 (191)
Q Consensus 124 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 154 (191)
.|..|+..++.-..+-+.|| ..|..|+.++
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 37788888864334556677 6899999877
No 41
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=56.22 E-value=4.5 Score=24.73 Aligned_cols=27 Identities=22% Similarity=0.661 Sum_probs=18.4
Q ss_pred hhhhhcCCCccCCCeEEEecCccccccccccccCCCC
Q psy4072 95 TKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQ 131 (191)
Q Consensus 95 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 131 (191)
+.|.+|+..|.+++..+. |.|-.|+..
T Consensus 10 ~~CtSCg~~i~p~e~~v~----------F~CPnCGe~ 36 (61)
T COG2888 10 PVCTSCGREIAPGETAVK----------FPCPNCGEV 36 (61)
T ss_pred ceeccCCCEeccCCceeE----------eeCCCCCce
Confidence 589999998876665544 556666633
No 42
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=55.71 E-value=2.9 Score=27.87 Aligned_cols=16 Identities=44% Similarity=0.918 Sum_probs=13.3
Q ss_pred hhhhhhhhhhhcCCCc
Q psy4072 89 YVRLFGTKCEKCNLNF 104 (191)
Q Consensus 89 ~~~~~~~~C~~C~~~I 104 (191)
|...|...|..|++.+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 5667778999999987
No 43
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=54.52 E-value=16 Score=22.13 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=19.6
Q ss_pred eecchhhhhhhhhhhhhhcCCCcc
Q psy4072 82 KTYCKRDYVRLFGTKCEKCNLNFK 105 (191)
Q Consensus 82 ~~~C~~c~~~~~~~~C~~C~~~I~ 105 (191)
-.||.+|....+...|+.|+..+.
T Consensus 29 CTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 29 CTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CcccHHHHHHHhcCcCcCCCCccc
Confidence 467899988888889999987665
No 44
>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=53.99 E-value=7.4 Score=23.19 Aligned_cols=23 Identities=35% Similarity=0.904 Sum_probs=10.1
Q ss_pred ccccccccCCCceEEeeCCeeccc
Q psy4072 35 CAECHQFLDENCTCFVRDGKTYCK 58 (191)
Q Consensus 35 C~~C~~~l~~~~~~~~~~g~~yc~ 58 (191)
|..|.-.++.. .-+..||+.||-
T Consensus 10 C~~C~C~V~~~-~Ai~~dGk~YCS 32 (52)
T PF02069_consen 10 CPSCSCVVSEE-EAIQKDGKYYCS 32 (52)
T ss_dssp STT----B-TT-TSEESSS-EESS
T ss_pred CCCCEeEECch-HhHHhCCEeeec
Confidence 56777777755 455656666663
No 45
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=53.93 E-value=13 Score=24.90 Aligned_cols=24 Identities=21% Similarity=0.516 Sum_probs=16.7
Q ss_pred CeecchhhhhhhhhhhhhhcCCCccC
Q psy4072 81 GKTYCKRDYVRLFGTKCEKCNLNFKR 106 (191)
Q Consensus 81 ~~~~C~~c~~~~~~~~C~~C~~~I~~ 106 (191)
|.-||..|-.+. ..|+-|++.|.+
T Consensus 58 g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 58 GAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred CCccChhhhccc--CcccccCCeecc
Confidence 556788884333 389999988863
No 46
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=52.66 E-value=7.4 Score=30.01 Aligned_cols=31 Identities=19% Similarity=0.357 Sum_probs=25.4
Q ss_pred cccccCCCCCCCCCceeeeCCccCCccccccc
Q psy4072 123 FCCVVCGKQLVPGDEFALREDGLFCKDDHEGM 154 (191)
Q Consensus 123 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 154 (191)
-+|+.|+..+. .......+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~-e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFM-EPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccc-cchhhhcCCceecccccccc
Confidence 58999999987 45667779999999998754
No 47
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=50.77 E-value=6.5 Score=30.31 Aligned_cols=30 Identities=30% Similarity=0.611 Sum_probs=21.1
Q ss_pred ccccccccccCCCceEEeeCCeecccchhhc
Q psy4072 33 LRCAECHQFLDENCTCFVRDGKTYCKRDYVS 63 (191)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~g~~yc~~c~~~ 63 (191)
-+|..|+..+... .....+|++.|..|+..
T Consensus 173 v~C~kCGE~~~e~-~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEP-RAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccc-hhhhcCCceeccccccc
Confidence 5799999998877 45555666666666653
No 48
>KOG1734|consensus
Probab=50.59 E-value=4 Score=32.87 Aligned_cols=43 Identities=26% Similarity=0.576 Sum_probs=28.3
Q ss_pred CCCcccccccccccce--------eEeecCCCcccccCc----------cccccccccCCC
Q psy4072 3 RLSLCVGCGGQIHDQY--------ILRVAPDLEWHAACL----------RCAECHQFLDEN 45 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~--------~~~~~~~~~~H~~Cf----------~C~~C~~~l~~~ 45 (191)
...+|+.|++.|.... ...+.-+..+|+.|. .|..|++.++.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~ 283 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK 283 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence 3467999999987543 122356889999886 366666555544
No 49
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=48.76 E-value=52 Score=25.26 Aligned_cols=12 Identities=25% Similarity=0.506 Sum_probs=7.7
Q ss_pred cccccCCCCCCC
Q psy4072 123 FCCVVCGKQLVP 134 (191)
Q Consensus 123 f~C~~C~~~l~~ 134 (191)
..|-.|...+..
T Consensus 69 ~~CPvCR~~Is~ 80 (193)
T PLN03208 69 PKCPVCKSDVSE 80 (193)
T ss_pred CcCCCCCCcCCh
Confidence 466777777753
No 50
>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=48.39 E-value=5 Score=25.94 Aligned_cols=30 Identities=27% Similarity=0.728 Sum_probs=17.9
Q ss_pred hhhhhcCCCccCCCeEEEe-----cC-----ccccccccc
Q psy4072 95 TKCEKCNLNFKREDFVMRA-----KN-----KIYHVQCFC 124 (191)
Q Consensus 95 ~~C~~C~~~I~~~~~~~~~-----~~-----~~~H~~Cf~ 124 (191)
..|..|++.|..++..+.. .+ ..||..||.
T Consensus 8 a~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 8 AKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp EBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred ccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 3788999999876533321 11 345777765
No 51
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=47.63 E-value=13 Score=27.50 Aligned_cols=53 Identities=19% Similarity=0.436 Sum_probs=35.7
Q ss_pred CeecchhhhhhhhhhhhhhcCCCccCCCe---EEEecCccccccccccccCCCCCCCCC
Q psy4072 81 GKTYCKRDYVRLFGTKCEKCNLNFKREDF---VMRAKNKIYHVQCFCCVVCGKQLVPGD 136 (191)
Q Consensus 81 ~~~~C~~c~~~~~~~~C~~C~~~I~~~~~---~~~~~~~~~H~~Cf~C~~C~~~l~~~~ 136 (191)
..-||..|-.+.. ..|+.|+.+|.+... ++. .+..|+.- --|..|+++..+..
T Consensus 27 ~~~fC~kCG~~tI-~~Cp~C~~~IrG~y~v~gv~~-~g~~~~~P-sYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 27 REKFCSKCGAKTI-TSCPNCSTPIRGDYHVEGVFG-LGGHYEAP-SYCHNCGKPYPWTE 82 (158)
T ss_pred HHHHHHHhhHHHH-HHCcCCCCCCCCceecCCeee-eCCCCCCC-hhHHhCCCCCchHH
Confidence 3568888876655 689999999986421 222 34555533 34889999988643
No 52
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.97 E-value=13 Score=18.50 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=4.8
Q ss_pred ccccccccCC
Q psy4072 35 CAECHQFLDE 44 (191)
Q Consensus 35 C~~C~~~l~~ 44 (191)
|..|++.+..
T Consensus 5 Cp~Cg~~~~~ 14 (26)
T PF13248_consen 5 CPNCGAEIDP 14 (26)
T ss_pred CcccCCcCCc
Confidence 4555554433
No 53
>KOG3579|consensus
Probab=46.36 E-value=9.5 Score=31.00 Aligned_cols=13 Identities=38% Similarity=0.948 Sum_probs=7.4
Q ss_pred ccccccccccCCC
Q psy4072 33 LRCAECHQFLDEN 45 (191)
Q Consensus 33 f~C~~C~~~l~~~ 45 (191)
++|..|...|.+.
T Consensus 269 LcCTLC~ERLEDT 281 (352)
T KOG3579|consen 269 LCCTLCHERLEDT 281 (352)
T ss_pred eeehhhhhhhccC
Confidence 5555566666554
No 54
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=44.35 E-value=17 Score=21.09 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=9.1
Q ss_pred CCCccccccccccc
Q psy4072 3 RLSLCVGCGGQIHD 16 (191)
Q Consensus 3 ~~~~C~~C~~~I~~ 16 (191)
.+..|..|++.|.+
T Consensus 10 ~~~~C~~C~~~i~g 23 (53)
T PF00130_consen 10 KPTYCDVCGKFIWG 23 (53)
T ss_dssp STEB-TTSSSBECS
T ss_pred CCCCCcccCcccCC
Confidence 45678888888843
No 55
>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=43.42 E-value=2.1 Score=23.19 Aligned_cols=10 Identities=30% Similarity=0.929 Sum_probs=4.0
Q ss_pred ccccccccCC
Q psy4072 35 CAECHQFLDE 44 (191)
Q Consensus 35 C~~C~~~l~~ 44 (191)
|..|+.+|..
T Consensus 6 C~~CGe~I~~ 15 (36)
T PF01258_consen 6 CEDCGEPIPE 15 (36)
T ss_dssp -TTTSSBEEH
T ss_pred ccccCChHHH
Confidence 4444444443
No 56
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=43.27 E-value=7.1 Score=20.06 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=5.6
Q ss_pred hhhhhcCCCcc
Q psy4072 95 TKCEKCNLNFK 105 (191)
Q Consensus 95 ~~C~~C~~~I~ 105 (191)
.+|.+|+..|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 36888888775
No 57
>KOG2893|consensus
Probab=42.91 E-value=8.4 Score=30.52 Aligned_cols=39 Identities=26% Similarity=0.457 Sum_probs=29.2
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCC
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDEN 45 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 45 (191)
..+-|..|++.+.+..+++ - .--..+|+|..|.+.|-+.
T Consensus 9 ~kpwcwycnrefddekili-q---hqkakhfkchichkkl~sg 47 (341)
T KOG2893|consen 9 DKPWCWYCNREFDDEKILI-Q---HQKAKHFKCHICHKKLFSG 47 (341)
T ss_pred CCceeeecccccchhhhhh-h---hhhhccceeeeehhhhccC
Confidence 4566999999999887763 2 2335679999999888655
No 58
>KOG0320|consensus
Probab=42.45 E-value=14 Score=27.88 Aligned_cols=29 Identities=17% Similarity=0.540 Sum_probs=20.7
Q ss_pred eCCeecchhhhhhhhh--hhhhhcCCCccCC
Q psy4072 79 RDGKTYCKRDYVRLFG--TKCEKCNLNFKRE 107 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~--~~C~~C~~~I~~~ 107 (191)
+=|.+||..|-..... .+|+.|++.|...
T Consensus 150 kCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 150 KCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 5577778777665443 5899999988743
No 59
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=42.40 E-value=15 Score=19.72 Aligned_cols=26 Identities=15% Similarity=0.459 Sum_probs=14.1
Q ss_pred ccccccccccceeEeecCCCcccccCc
Q psy4072 7 CVGCGGQIHDQYILRVAPDLEWHAACL 33 (191)
Q Consensus 7 C~~C~~~I~~~~~~~~~~~~~~H~~Cf 33 (191)
|..|...+.....+ ..-|..||..|+
T Consensus 2 C~iC~~~~~~~~~~-~~C~H~~c~~C~ 27 (45)
T cd00162 2 CPICLEEFREPVVL-LPCGHVFCRSCI 27 (45)
T ss_pred CCcCchhhhCceEe-cCCCChhcHHHH
Confidence 66677666332222 235666666665
No 60
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=42.16 E-value=17 Score=22.20 Aligned_cols=12 Identities=33% Similarity=0.617 Sum_probs=9.6
Q ss_pred cccccccccCCC
Q psy4072 34 RCAECHQFLDEN 45 (191)
Q Consensus 34 ~C~~C~~~l~~~ 45 (191)
.|..|++.|...
T Consensus 18 ~C~~C~k~L~~~ 29 (58)
T PF04570_consen 18 FCYLCKKKLDPG 29 (58)
T ss_pred HHHccCCCCCCC
Confidence 578899999854
No 61
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.92 E-value=11 Score=25.33 Aligned_cols=31 Identities=19% Similarity=0.301 Sum_probs=15.0
Q ss_pred hhhhcCCCccCCCeEEEecCccccccccccc
Q psy4072 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCV 126 (191)
Q Consensus 96 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~ 126 (191)
+|..|+.+|..++..--....+.|-+||.=+
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s 38 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAES 38 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHH
Confidence 4566666665544322223444555555443
No 62
>PRK00420 hypothetical protein; Validated
Probab=38.88 E-value=16 Score=25.51 Aligned_cols=25 Identities=28% Similarity=0.413 Sum_probs=15.9
Q ss_pred ccccccccccCCCceEEeeCCeecccchhh
Q psy4072 33 LRCAECHQFLDENCTCFVRDGKTYCKRDYV 62 (191)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~g~~yc~~c~~ 62 (191)
-.|..|+.+|... .+|+.||+.|-.
T Consensus 24 ~~CP~Cg~pLf~l-----k~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFEL-----KDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceec-----CCCceECCCCCC
Confidence 3577888777542 566666666654
No 63
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=38.22 E-value=42 Score=19.17 Aligned_cols=27 Identities=26% Similarity=0.568 Sum_probs=18.7
Q ss_pred eCCee-cchhhhhhhhh--hhhhhcCCCcc
Q psy4072 79 RDGKT-YCKRDYVRLFG--TKCEKCNLNFK 105 (191)
Q Consensus 79 ~~~~~-~C~~c~~~~~~--~~C~~C~~~I~ 105 (191)
.=|.. +|..|..+... ..|+.|+.+|.
T Consensus 19 pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 19 PCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 34555 88888777643 58999998885
No 64
>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=37.88 E-value=41 Score=19.28 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=19.9
Q ss_pred ccccCCCCCCCCCceeee-C-CccCCccccccccCCCC
Q psy4072 124 CCVVCGKQLVPGDEFALR-E-DGLFCKDDHEGMDKSSN 159 (191)
Q Consensus 124 ~C~~C~~~l~~~~~~~~~-~-~~~~C~~c~~~~~~~~~ 159 (191)
.|..|+..+. ...+.-. . +..+|..||.+-..+..
T Consensus 2 ~C~~Cg~D~t-~vryh~~~~~~~dLC~~CF~~G~f~~~ 38 (45)
T cd02336 2 HCFTCGNDCT-RVRYHNLKAKKYDLCPSCYQEGRFPSN 38 (45)
T ss_pred cccCCCCccC-ceEEEecCCCccccChHHHhCcCCCCC
Confidence 4666777775 3334322 2 23689999865544443
No 65
>KOG0978|consensus
Probab=37.73 E-value=12 Score=34.41 Aligned_cols=31 Identities=32% Similarity=0.706 Sum_probs=25.1
Q ss_pred eCCeecchhhhhhhhhh---hhhhcCCCccCCCe
Q psy4072 79 RDGKTYCKRDYVRLFGT---KCEKCNLNFKREDF 109 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~~---~C~~C~~~I~~~~~ 109 (191)
+=+..||..|...++.. +|+.|+.+..+.|.
T Consensus 660 kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 660 KCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred hcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 44678999999888875 79999998887763
No 66
>PF12773 DZR: Double zinc ribbon
Probab=36.93 E-value=22 Score=20.42 Aligned_cols=8 Identities=38% Similarity=0.995 Sum_probs=3.6
Q ss_pred cccCCCCC
Q psy4072 125 CVVCGKQL 132 (191)
Q Consensus 125 C~~C~~~l 132 (191)
|..|+..+
T Consensus 32 C~~Cg~~~ 39 (50)
T PF12773_consen 32 CPNCGAEN 39 (50)
T ss_pred CcCCcCCC
Confidence 44444443
No 67
>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=36.73 E-value=35 Score=17.45 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=8.1
Q ss_pred cccccccccccc
Q psy4072 6 LCVGCGGQIHDQ 17 (191)
Q Consensus 6 ~C~~C~~~I~~~ 17 (191)
.|..|++.+.+.
T Consensus 2 ~C~~C~~~~~~~ 13 (30)
T PF03107_consen 2 WCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCcCCC
Confidence 466777777666
No 68
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=34.53 E-value=12 Score=25.49 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=17.7
Q ss_pred cccccccCCCCCCCCCceeeeCCccCCccc
Q psy4072 121 QCFCCVVCGKQLVPGDEFALREDGLFCKDD 150 (191)
Q Consensus 121 ~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c 150 (191)
.=|.|+.|-..--...-....+|.++|..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 347788775443322223345678899887
No 69
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=34.24 E-value=16 Score=23.84 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=17.7
Q ss_pred ccccCCCCCCCCCcee-eeCCc---cCCcccccc
Q psy4072 124 CCVVCGKQLVPGDEFA-LREDG---LFCKDDHEG 153 (191)
Q Consensus 124 ~C~~C~~~l~~~~~~~-~~~~~---~~C~~c~~~ 153 (191)
.|..|+.||.....+. ..+|. -||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 3778888887433122 22333 588888753
No 70
>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=33.78 E-value=12 Score=32.87 Aligned_cols=105 Identities=17% Similarity=0.269 Sum_probs=0.0
Q ss_pred ecccchhhcccccceeccccceeeeCCeecchhhhhhhhhh-hhhhcCCCccCCCeEEEecCccccccccccccCCCCCC
Q psy4072 55 TYCKRDYVSSEKNQFLDENCTCFVRDGKTYCKRDYVRLFGT-KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLV 133 (191)
Q Consensus 55 ~yc~~c~~~~~~~~~~~~~c~~~~~~~~~~C~~c~~~~~~~-~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 133 (191)
.||+.|. ++-|..|.....-. -|+.|-..+...+ +.+.+..-..+||.|-.|..+|.
T Consensus 6 ~fC~~C~--------------------~irc~~c~~~Ei~~~yCp~CL~~~p~~e--~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 6 YFCEHCH--------------------KIRCPRCVSEEIDSYYCPNCLFEVPSSE--ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred eeccccc--------------------ccCChhhcccccceeECccccccCChhh--heeccceeccccccCCCCCCcce
Q ss_pred CCCcee---------eeCCccCCccccccccCCCCCCCC-CCCCCCCCCCccCCCCCC
Q psy4072 134 PGDEFA---------LREDGLFCKDDHEGMDKSSNGENN-NNNTNINNNLHNLNNEGS 181 (191)
Q Consensus 134 ~~~~~~---------~~~~~~~C~~c~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 181 (191)
....-. ...+.+|=..|..=++.++..... ..|+++..+.+.+.+...
T Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~~igi~Fdkpt~l~~QL~kl~~~~~ 121 (483)
T PF05502_consen 64 VRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSRDIGIKFDKPTGLRAQLSKLTNGGD 121 (483)
T ss_pred eEecccccccccccccCCCCCEEEECCCceeeccccCccccCchhHHHHHHhhccccc
No 71
>PRK00807 50S ribosomal protein L24e; Validated
Probab=33.64 E-value=39 Score=20.00 Aligned_cols=23 Identities=17% Similarity=0.430 Sum_probs=12.0
Q ss_pred cccccccccCCC--ceEEeeCCeec
Q psy4072 34 RCAECHQFLDEN--CTCFVRDGKTY 56 (191)
Q Consensus 34 ~C~~C~~~l~~~--~~~~~~~g~~y 56 (191)
.|+.|+..|.+. ..++..||++|
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~ 27 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTIL 27 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEE
Confidence 366777776522 12334455554
No 72
>PRK12495 hypothetical protein; Provisional
Probab=33.47 E-value=22 Score=27.83 Aligned_cols=25 Identities=24% Similarity=0.515 Sum_probs=15.7
Q ss_pred CccccccccccCCCceEEeeCCeecccchhh
Q psy4072 32 CLRCAECHQFLDENCTCFVRDGKTYCKRDYV 62 (191)
Q Consensus 32 Cf~C~~C~~~l~~~~~~~~~~g~~yc~~c~~ 62 (191)
=+.|..|+.+|. .+.|..+|..|-.
T Consensus 42 a~hC~~CG~PIp------a~pG~~~Cp~CQ~ 66 (226)
T PRK12495 42 NAHCDECGDPIF------RHDGQEFCPTCQQ 66 (226)
T ss_pred hhhcccccCccc------CCCCeeECCCCCC
Confidence 366788888886 2355555555543
No 73
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.14 E-value=14 Score=33.96 Aligned_cols=34 Identities=18% Similarity=0.457 Sum_probs=23.1
Q ss_pred CCCcccccccccccceeEeecCCCcccccCcccccccccc
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFL 42 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 42 (191)
...+|..|-++|.+. .++.||=.=-.|+.|+-.+
T Consensus 100 D~a~C~~Cl~Ei~dp------~~rrY~YPF~~CT~CGPRf 133 (750)
T COG0068 100 DAATCEDCLEEIFDP------NSRRYLYPFINCTNCGPRF 133 (750)
T ss_pred chhhhHHHHHHhcCC------CCcceeccccccCCCCcce
Confidence 456788888777653 3566666666788887654
No 74
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=32.82 E-value=8.6 Score=22.44 Aligned_cols=23 Identities=13% Similarity=0.428 Sum_probs=10.5
Q ss_pred ecchhhhhhhhh--hhhhhcCCCcc
Q psy4072 83 TYCKRDYVRLFG--TKCEKCNLNFK 105 (191)
Q Consensus 83 ~~C~~c~~~~~~--~~C~~C~~~I~ 105 (191)
.+|..|...+.+ +.|..|++++.
T Consensus 22 YLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 22 YLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred hHHHHHHHHHhccccCCCcccCcCc
Confidence 344444444433 46777766553
No 75
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=32.69 E-value=24 Score=27.83 Aligned_cols=23 Identities=22% Similarity=0.580 Sum_probs=13.9
Q ss_pred ccccccccCCCceEEeeCCeecccchhhcc
Q psy4072 35 CAECHQFLDENCTCFVRDGKTYCKRDYVSS 64 (191)
Q Consensus 35 C~~C~~~l~~~~~~~~~~g~~yc~~c~~~~ 64 (191)
|..||.+.... .+ -.|.+||...
T Consensus 1 C~~CG~~~~~~-----~~--~lC~~C~~~~ 23 (236)
T PF04981_consen 1 CPRCGREIEPL-----ID--GLCPDCYLKR 23 (236)
T ss_pred CCCCCCCCCCc-----cc--ccChHHhccc
Confidence 67788866554 11 2677777653
No 76
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=31.85 E-value=18 Score=20.08 Aligned_cols=29 Identities=21% Similarity=0.575 Sum_probs=16.8
Q ss_pred hhhhcCCCccCCCeEEEe-cCccccccccc
Q psy4072 96 KCEKCNLNFKREDFVMRA-KNKIYHVQCFC 124 (191)
Q Consensus 96 ~C~~C~~~I~~~~~~~~~-~~~~~H~~Cf~ 124 (191)
.|+.|...+.+++.++.. =+..||..|+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHH
Confidence 366677767544444332 36777777753
No 77
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.04 E-value=22 Score=32.49 Aligned_cols=25 Identities=16% Similarity=0.505 Sum_probs=12.7
Q ss_pred CeecchhhhhhhhhhhhhhcCCCcc
Q psy4072 81 GKTYCKRDYVRLFGTKCEKCNLNFK 105 (191)
Q Consensus 81 ~~~~C~~c~~~~~~~~C~~C~~~I~ 105 (191)
+.-||..|-...-...|..|+..+.
T Consensus 14 ~akFC~~CG~~l~~~~Cp~CG~~~~ 38 (645)
T PRK14559 14 NNRFCQKCGTSLTHKPCPQCGTEVP 38 (645)
T ss_pred CCccccccCCCCCCCcCCCCCCCCC
Confidence 3345555543332245666666554
No 78
>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=29.56 E-value=18 Score=18.54 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=3.6
Q ss_pred ccccccccccc
Q psy4072 6 LCVGCGGQIHD 16 (191)
Q Consensus 6 ~C~~C~~~I~~ 16 (191)
.|..|++++.+
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF07649_consen 2 RCDACGKPIDG 12 (30)
T ss_dssp --TTTS----S
T ss_pred cCCcCCCcCCC
Confidence 46777777766
No 79
>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=27.95 E-value=21 Score=19.26 Aligned_cols=17 Identities=35% Similarity=0.825 Sum_probs=9.7
Q ss_pred CCcccccccccccceeE
Q psy4072 4 LSLCVGCGGQIHDQYIL 20 (191)
Q Consensus 4 ~~~C~~C~~~I~~~~~~ 20 (191)
.+.|..|++++.+.++.
T Consensus 3 ~~~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLL 19 (34)
T ss_dssp -EE-TTT--EES-SSCC
T ss_pred CchHhHhCCHHHHHHHH
Confidence 56788999988888775
No 80
>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=27.85 E-value=16 Score=20.43 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=4.7
Q ss_pred cccccCCCCC
Q psy4072 123 FCCVVCGKQL 132 (191)
Q Consensus 123 f~C~~C~~~l 132 (191)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 3455555444
No 81
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=26.91 E-value=18 Score=27.82 Aligned_cols=28 Identities=18% Similarity=0.468 Sum_probs=19.3
Q ss_pred eCCeecchhhhhhhhh--hhhhhcCCCccC
Q psy4072 79 RDGKTYCKRDYVRLFG--TKCEKCNLNFKR 106 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~--~~C~~C~~~I~~ 106 (191)
.=|..+|..|+.+.+. +.|..|++...+
T Consensus 213 ~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 213 ECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred hcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 3456677777776663 688888886663
No 82
>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=26.84 E-value=43 Score=18.97 Aligned_cols=9 Identities=11% Similarity=0.135 Sum_probs=5.6
Q ss_pred cCCcccccc
Q psy4072 145 LFCKDDHEG 153 (191)
Q Consensus 145 ~~C~~c~~~ 153 (191)
-+|..||..
T Consensus 24 dLC~~Cf~~ 32 (46)
T cd02249 24 DLCSSCYAK 32 (46)
T ss_pred cCHHHHHCc
Confidence 467777653
No 83
>KOG4739|consensus
Probab=25.97 E-value=36 Score=26.90 Aligned_cols=27 Identities=11% Similarity=0.282 Sum_probs=19.9
Q ss_pred eCCeecchhhhhhhhhhhhhhcCCCcc
Q psy4072 79 RDGKTYCKRDYVRLFGTKCEKCNLNFK 105 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~~~C~~C~~~I~ 105 (191)
.=..++|..|.....++.|.-|++.|.
T Consensus 22 aC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred echhhhhhhhcccCCccccccccceee
Confidence 335677888877666668999998875
No 84
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=25.92 E-value=6.9 Score=26.40 Aligned_cols=38 Identities=18% Similarity=0.461 Sum_probs=27.7
Q ss_pred ccccccccccceeEeecCCCcccccCccccccccccCCC
Q psy4072 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDEN 45 (191)
Q Consensus 7 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 45 (191)
|..|+.++..-..+. ..-..+++.+..|..|++.|+-.
T Consensus 38 Cy~CHdel~~Hpf~p-~~~~~~~~~~iiCGvC~~~LT~~ 75 (105)
T COG4357 38 CYHCHDELEDHPFEP-WGLQEFNPKAIICGVCRKLLTRA 75 (105)
T ss_pred HHHHHhHHhcCCCcc-CChhhcCCccEEhhhhhhhhhHH
Confidence 667777777655543 23467888999999999988765
No 85
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=25.12 E-value=60 Score=19.45 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=8.9
Q ss_pred cccccccccccceeE
Q psy4072 6 LCVGCGGQIHDQYIL 20 (191)
Q Consensus 6 ~C~~C~~~I~~~~~~ 20 (191)
+|..|++||.....+
T Consensus 3 ~CvVCKqpi~~a~~v 17 (54)
T PF10886_consen 3 ICVVCKQPIDDALVV 17 (54)
T ss_pred eeeeeCCccCcceEE
Confidence 466666666665443
No 86
>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=24.24 E-value=45 Score=18.57 Aligned_cols=29 Identities=17% Similarity=0.394 Sum_probs=13.7
Q ss_pred ccccCCCCCCCCCceeeeC-CccCCccccc
Q psy4072 124 CCVVCGKQLVPGDEFALRE-DGLFCKDDHE 152 (191)
Q Consensus 124 ~C~~C~~~l~~~~~~~~~~-~~~~C~~c~~ 152 (191)
+|+.|+++.........-. +...|..|..
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 4777777776433333323 4455776643
No 87
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=24.16 E-value=33 Score=22.89 Aligned_cols=40 Identities=18% Similarity=0.292 Sum_probs=26.8
Q ss_pred CCCcccccccccccceeEeecCCCcccccCccccccccccCCC
Q psy4072 3 RLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDEN 45 (191)
Q Consensus 3 ~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 45 (191)
....|..|++++..-+.+-+. .|=..=-+|..|+++|+..
T Consensus 32 ~rS~C~~C~~~L~~~~lIPi~---S~l~lrGrCr~C~~~I~~~ 71 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIPIL---SYLLLRGRCRYCGAPIPPR 71 (92)
T ss_pred CCCcCcCCCCcCcccccchHH---HHHHhCCCCcccCCCCChH
Confidence 346799999999877765322 2322334788899888764
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.04 E-value=36 Score=19.37 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=7.4
Q ss_pred ccccccccccCC
Q psy4072 33 LRCAECHQFLDE 44 (191)
Q Consensus 33 f~C~~C~~~l~~ 44 (191)
+.|..|+..+..
T Consensus 3 Y~C~~Cg~~~~~ 14 (44)
T smart00659 3 YICGECGRENEI 14 (44)
T ss_pred EECCCCCCEeec
Confidence 467777765543
No 89
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=23.98 E-value=16 Score=22.07 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=13.7
Q ss_pred ecchhhhhhhhhhhhhhcCC
Q psy4072 83 TYCKRDYVRLFGTKCEKCNL 102 (191)
Q Consensus 83 ~~C~~c~~~~~~~~C~~C~~ 102 (191)
.|=.++....++..|..|-.
T Consensus 27 L~Gad~lr~klG~IC~~Cit 46 (60)
T PF10892_consen 27 LIGADDLRVKLGGICGDCIT 46 (60)
T ss_pred hhChHHHHHHHcchhhccCC
Confidence 34455667788888888843
No 90
>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=23.65 E-value=41 Score=18.97 Aligned_cols=11 Identities=45% Similarity=1.120 Sum_probs=7.3
Q ss_pred ccccccccccc
Q psy4072 6 LCVGCGGQIHD 16 (191)
Q Consensus 6 ~C~~C~~~I~~ 16 (191)
.|.+|+++|.|
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 47777776655
No 91
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.49 E-value=27 Score=26.26 Aligned_cols=12 Identities=33% Similarity=0.628 Sum_probs=9.4
Q ss_pred CCCCcceeeeeC
Q psy4072 180 GSNSGKIQLYLL 191 (191)
Q Consensus 180 ~~~~~~~~~~~~ 191 (191)
.++.+.||+||.
T Consensus 68 ~~~~~~MkLYlr 79 (172)
T TIGR00598 68 NPRWGDMKLYLK 79 (172)
T ss_pred CCCcccceeehH
Confidence 357799999983
No 92
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=23.17 E-value=16 Score=21.82 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=6.5
Q ss_pred cccccccccCCC
Q psy4072 34 RCAECHQFLDEN 45 (191)
Q Consensus 34 ~C~~C~~~l~~~ 45 (191)
+|..|+..|+..
T Consensus 24 ~C~gC~~~l~~~ 35 (56)
T PF02591_consen 24 TCSGCHMELPPQ 35 (56)
T ss_pred ccCCCCEEcCHH
Confidence 455555555544
No 93
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=23.12 E-value=59 Score=18.73 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=15.4
Q ss_pred cccCCCCCCCCCceeeeCCccCCccccccccCCC
Q psy4072 125 CVVCGKQLVPGDEFALREDGLFCKDDHEGMDKSS 158 (191)
Q Consensus 125 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~ 158 (191)
|..|+++... .....+...|..|-.++..+.
T Consensus 2 CiiC~~~~~~---GI~I~~~fIC~~CE~~iv~~~ 32 (46)
T PF10764_consen 2 CIICGKEKEE---GIHIYGKFICSDCEKEIVNTE 32 (46)
T ss_pred eEeCCCcCCC---CEEEECeEehHHHHHHhccCC
Confidence 4555555542 222245566666655554443
No 94
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=22.94 E-value=91 Score=17.44 Aligned_cols=9 Identities=11% Similarity=0.264 Sum_probs=5.8
Q ss_pred cCCcccccc
Q psy4072 145 LFCKDDHEG 153 (191)
Q Consensus 145 ~~C~~c~~~ 153 (191)
-+|..||..
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 467777753
No 95
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=22.50 E-value=29 Score=19.35 Aligned_cols=21 Identities=29% Similarity=0.792 Sum_probs=11.0
Q ss_pred Ceecchhhhhhhh--hhhhhhcC
Q psy4072 81 GKTYCKRDYVRLF--GTKCEKCN 101 (191)
Q Consensus 81 ~~~~C~~c~~~~~--~~~C~~C~ 101 (191)
|..+|..|..+.. ...|+.|+
T Consensus 21 gH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 21 GHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CCHHHHHHHHhhcCCCCCCcCCC
Confidence 4555666655544 23555554
No 96
>KOG1829|consensus
Probab=22.45 E-value=23 Score=31.86 Aligned_cols=33 Identities=21% Similarity=0.354 Sum_probs=24.8
Q ss_pred cCccccccccccCCC----ceEEeeCCeecccchhhc
Q psy4072 31 ACLRCAECHQFLDEN----CTCFVRDGKTYCKRDYVS 63 (191)
Q Consensus 31 ~Cf~C~~C~~~l~~~----~~~~~~~g~~yc~~c~~~ 63 (191)
.-|+|+.|+.+|... ..+-.+.|+.||..|...
T Consensus 339 Q~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~ 375 (580)
T KOG1829|consen 339 QNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQN 375 (580)
T ss_pred cCceecccCCCcccccccchhHhhhhhhhhCchhccc
Confidence 458899999999843 233457899999999864
No 97
>KOG1813|consensus
Probab=22.23 E-value=37 Score=27.84 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=17.5
Q ss_pred eCCeecchhhhhhhhh--hhhhhcCCCccC
Q psy4072 79 RDGKTYCKRDYVRLFG--TKCEKCNLNFKR 106 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~--~~C~~C~~~I~~ 106 (191)
.-+..+|+.|..+.+. ++|..|++.+.+
T Consensus 258 ~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 258 KCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cCCceeehhhhccccccCCcceeccccccc
Confidence 3445566666555443 578888887763
No 98
>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=21.87 E-value=32 Score=15.88 Aligned_cols=13 Identities=15% Similarity=0.618 Sum_probs=8.1
Q ss_pred ccccccccccCCC
Q psy4072 33 LRCAECHQFLDEN 45 (191)
Q Consensus 33 f~C~~C~~~l~~~ 45 (191)
|+|..|++.....
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 4677777666543
No 99
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=21.27 E-value=36 Score=19.36 Aligned_cols=11 Identities=27% Similarity=0.779 Sum_probs=6.1
Q ss_pred ccccccccCCC
Q psy4072 35 CAECHQFLDEN 45 (191)
Q Consensus 35 C~~C~~~l~~~ 45 (191)
|..|.+.+...
T Consensus 9 C~~Cdk~~~~~ 19 (43)
T PF12855_consen 9 CIVCDKQIDPP 19 (43)
T ss_pred HHHhhccccCC
Confidence 35566666543
No 100
>PF05181 XPA_C: XPA protein C-terminus; InterPro: IPR022656 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 describes the uncharacterised C-terminal in the XPA protein; PDB: 1D4U_A 1XPA_A.
Probab=20.70 E-value=61 Score=19.29 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=6.6
Q ss_pred CCCCcceeeee
Q psy4072 180 GSNSGKIQLYL 190 (191)
Q Consensus 180 ~~~~~~~~~~~ 190 (191)
.++.|.||+||
T Consensus 38 ~~~w~~MkLyL 48 (52)
T PF05181_consen 38 NSTWGDMKLYL 48 (52)
T ss_dssp SS-TTS-EEE-
T ss_pred CCCccCeeEEE
Confidence 45789999997
No 101
>KOG3476|consensus
Probab=20.55 E-value=42 Score=22.19 Aligned_cols=27 Identities=19% Similarity=0.476 Sum_probs=20.5
Q ss_pred eCCeecchhhhhhhhhhhhhhcCCCccCC
Q psy4072 79 RDGKTYCKRDYVRLFGTKCEKCNLNFKRE 107 (191)
Q Consensus 79 ~~~~~~C~~c~~~~~~~~C~~C~~~I~~~ 107 (191)
.+|..||..|-.+. ..|+-|++.|...
T Consensus 66 Q~GshYC~tCAY~K--giCAMCGKki~nT 92 (100)
T KOG3476|consen 66 QPGSHYCQTCAYKK--GICAMCGKKILNT 92 (100)
T ss_pred CCcchhHhHhhhhh--hHHHHhhhHhhcc
Confidence 56778999995443 3899999999843
No 102
>PRK11595 DNA utilization protein GntX; Provisional
Probab=20.54 E-value=59 Score=25.33 Aligned_cols=11 Identities=27% Similarity=0.338 Sum_probs=6.6
Q ss_pred cccccccccCC
Q psy4072 34 RCAECHQFLDE 44 (191)
Q Consensus 34 ~C~~C~~~l~~ 44 (191)
.|..|++++..
T Consensus 7 ~C~~C~~~~~~ 17 (227)
T PRK11595 7 LCWLCRMPLAL 17 (227)
T ss_pred cCccCCCccCC
Confidence 35667776643
Done!